Executing: uname -s stdout: Linux ================================================================================ ================================================================================ Starting configure run at Mon, 26 Apr 2021 14:49:30 -0400 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --prefix=/home2/barretk3/ff-petsc/r MAKEFLAGS= --with-debugging=0 COPTFLAGS="-O3 -mtune=native" CXXOPTFLAGS="-O3 -mtune=native" FOPTFLAGS="-O3 -mtune=native" --with-cxx-dialect=C++11 --with-ssl=0 --with-x=0 --with-fortran-bindings=0 --with-cudac=0 --with-cc=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc --with-cxx=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx --with-fc=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --with-scalar-type=real --download-f2cblaslapack --download-metis --download-ptscotch --download-hypre --download-parmetis --download-mmg --download-parmmg --download-superlu --download-suitesparse --download-tetgen --download-slepc --download-hpddm --download-scalapack --download-mumps --download-slepc-configure-arguments=--download-arpack=https://github.com/prj-/arpack-ng/archive/b64dccb.tar.gz PETSC_ARCH=fr Working directory: /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 Machine platform: ('Linux', 'vegaln1', '3.10.0-693.11.6.el7.x86_64', '#1 SMP Thu Jan 4 01:06:37 UTC 2018', 'x86_64', 'x86_64') Python version: 2.7.5 (default, Nov 16 2020, 22:23:17) [GCC 4.8.5 20150623 (Red Hat 4.8.5-44)] ================================================================================ Environmental variables HDF5LIB=hdf5 MODULE_VERSION=3.2.10 VT_ADD_LIBS=-ldwarf -lelf -lvtunwind -lnsl -lm -ldl -lpthread INTEL_LICENSE_FILE=/cm/shared/licenses/intel HDF5_ROOT=/cm/shared/apps/hdf5/1.10.0 VT_LIB_DIR=/cm/shared/apps/intel/itac/2019.5.075/intel64/lib ENABLE_LMOD=0 LESSOPEN=||/usr/bin/lesspipe.sh %s SSH_CLIENT=155.31.114.10 41362 22 CPATH=/cm/shared/apps/openblas/0.2.18/include:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include CRAYPE_NETWORK_TARGET=infiniband VT_MPI=impi4 HOME=/home2/barretk3 PATH=/cm/local/apps/cmake/3.9.6/bin:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin:/cm/shared/apps/intel/itac/2019.5.075/intel64/bin:/cm/shared/apps/hdf5/1.10.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:.:/home2/barretk3/.local/bin:/home2/barretk3/bin BLASDIR=/cm/shared/apps/openblas/0.2.18/lib LD_LIBRARY_PATH=/cm/shared/apps/lapack/gcc/64/3.7.0:/cm/shared/apps/openblas/0.2.18/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib:/cm/shared/apps/hdf5/1.10.0/lib MAKEFLAGS= LOADEDMODULES=craype-network-infiniband:craype-broadwell:hdf5/1.10.0:intel/itac/2019/5.075:intel/mpi/64/2019/5.075:cmake/3.9.6:openblas/dynamic/0.2.18:lapack/gcc/64/3.7.0 LANG=en_US.UTF-8 TERM=xterm-256color SHELL=/bin/bash LIBRARY_PATH=/cm/shared/apps/lapack/gcc/64/3.7.0:/cm/shared/apps/openblas/0.2.18/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib:/cm/shared/apps/hdf5/1.10.0/lib BASH_FUNC_module()=() { eval `/cm/local/apps/environment-modules/3.2.10/Modules/$MODULE_VERSION/bin/modulecmd bash $*` } SHLVL=2 LD_RUN_PATH=/cm/shared/apps/openblas/0.2.18/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib:/cm/shared/apps/hdf5/1.10.0/lib HDF5INCLUDE=/cm/shared/apps/hdf5/1.10.0/include HISTSIZE=1000 LAPACK_DIR=/cm/shared/apps/lapack/gcc/64/3.7.0 CRAY_CPU_TARGET=broadwell MANPATH=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/man:/cm/shared/apps/intel/itac/2019.5.075/man:/usr/local/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man:/opt/ibutils/share/man:/cm/local/apps/environment-modules/current/share/man _LMFILES_=/opt/cray/craype/default/modulefiles/craype-network-infiniband:/opt/cray/craype/default/modulefiles/craype-broadwell:/cm/shared/modulefiles/hdf5/1.10.0:/cm/shared/modulefiles/intel/itac/2019/5.075:/cm/shared/modulefiles/intel/mpi/64/2019/5.075:/cm/shared/modulefiles/cmake/3.9.6:/cm/shared/modulefiles/openblas/dynamic/0.2.18:/cm/shared/modulefiles/lapack/gcc/64/3.7.0 SSH_CONNECTION=155.31.114.10 41362 155.31.18.51 22 VT_SLIB_DIR=/cm/shared/apps/intel/itac/2019.5.075/intel64/slib HDF5DIR=/cm/shared/apps/hdf5/1.10.0/lib MFLAGS= MODULESHOME=/cm/local/apps/environment-modules/3.2.10/Modules/3.2.10 VT_ROOT=/cm/shared/apps/intel/itac/2019.5.075 MODULE_VERSION_STACK=3.2.10 XDG_RUNTIME_DIR=/run/user/23069 LOGNAME=barretk3 CLASSPATH=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/mpi.jar MPIRUN=mpiexec I_MPI_TMPDIR=/tmp I_MPI_ROOT=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi VT_ARCH=intel64 PE_PRODUCT_LIST=CRAYPE_BROADWELL QT_GRAPHICSSYSTEM_CHECKED=1 XDG_SESSION_ID=124879 MPI_RUN=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpirun MODULEPATH=/opt/cray/craype/default/modulefiles:/opt/cray/modulefiles:/cm/local/modulefiles:/opt/modulefiles:/cm/shared/modulefiles I_MPI_HYDRA_CLEANUP=enable SSH_TTY=/dev/pts/9 HOSTNAME=vegaln1 CPLUS_INCLUDE_PATH=/cm/shared/apps/openblas/0.2.18/include HISTCONTROL=ignoredups MAKELEVEL=1 PWD=/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 BLASLIB=openblas FI_PROVIDER_PATH=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib/prov SCRATCH=/scratch/barretk3 MAIL=/var/spool/mail/barretk3 LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: C_INCLUDE_PATH=/cm/shared/apps/openblas/0.2.18/include USER=barretk3 Files in path provided by default path /cm/local/apps/cmake/3.9.6/bin: ccmake cmake cpack ctest /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin: fi_info /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin: IMB-MPI1 IMB-MT IMB-NBC IMB-P2P IMB-RMA cpuinfo hydra_bstrap_proxy hydra_nameserver hydra_pmi_proxy impi_info legacy mpiexec mpiexec.hydra mpirun mpitune mpivars.csh mpivars.sh tune mpicc mpicxx mpif77 mpif90 mpifc mpigcc mpigxx mpiicc mpiicpc mpiifort mpicleanup /cm/shared/apps/intel/itac/2019.5.075/intel64/bin: convert-stats.pl expandvtlog.pl itacvars.csh itacvars.sh stftool xstftool VTserver otf2-to-stf itcconfig platforms rtlib traceanalyzer traceanalyzer.bin traceidealizer traceidealizer.bin /cm/shared/apps/hdf5/1.10.0/bin: gif2h5 h52gif h5c++ h5cc h5clear h5copy h5debug h5diff h5dump h5fc h5format_convert h5import h5jam h5ls h5mkgrp h5perf_serial h5redeploy h5repack h5repart h5stat h5unjam h5watch /usr/local/bin: ccache-swig swig qnodes chk_tree hostn nqs2pbs pbs_track pbsdsh pbsnodes printjob printserverdb printtracking qalter qchkpt qdel qdisable qenable qgpumode qgpureset qhold qmgr qmove qmsg qorder qrerun qrls qrun qselect qsig qstart qstat qstop qsub qterm tracejob pbs-config apt apt-get dpkg pan_manage_routes pan_atime pan_attr pan_collect_logs pan_df pan_du pan_iorouter pan_iperf pan_netperf pan_nettest pan_sitesync pan_sitesync_worker pan_quota /usr/bin: Mail X apropos atq atrm awk bashbug bunzip2 bzcat bzcmp bzless cancel captoinfo cc circo csh desktop-file-edit dnsdomainname domainname dot2gxl emacs etags ex f95 fdp flex++ geqn ghostscript gmake gneqn gnroff gpg gpgv gpic gsoelim gtar gtbl gtroff gv2gxl gxl2dot i386 infotocap ipmicmd ipmish iptables-xml java keytool ksh lastb ld ldapadd lex linux32 linux64 lp lpq lpr lprm lpstat mail mailq mailq.postfix makeinfo mst mysql_config nail nc neato newaliases newaliases.postfix nisdomainname open orbd osage pack200 patchwork pax ping6 psfaddtable psfgettable psfstriptable pstack pstree.x11 python python-config python2 python2-config reset rksh rmail rmid rmiregistry rnano rpmquery rpmverify rvi rview rvim servertool setup setup-nsssysinit sfdp sg sh slogin cryptest sudoedit systemd-coredumpctl systemd-loginctl tclsh tnameserv traceroute6 twopi unpack200 unxz view vimdiff wish x86_64 xzcat xzcmp xzegrep xzfgrep ypdomainname zsoelim addr2line GET alias HEAD arch POST ar Xorg as [ bzip2recover a2p aclocal abs2rel acyclic aclocal-1.13 bashbug-64 asadmin batch cal ascii-xfr bc cat aserver bzmore at c++filt attr bcomps aulast bdftopcf aulastlog bdftruncate ausyscall bg cd autoconf bison cgget autoexpect bond2team autoheader bootctl autom4te build-classpath automake-1.13 build-jar-repository automake autoreconf bundle_image autoscan busctl autoupdate bzdiff auvirt bzgrep base64 bzip2 cgset basename ca-legacy bash c99 c89 chacl build-classpath-directory dbus-cleanup-sockets cairo-sphinx dbus-send cancel.cups dbus-monitor catchsegv dbus-uuidgen catman db_stat expr cciss_vol_status dc false ccomps db_tuner fc centrino-decode dd fg certutil deallocvt cfadmin desktop-file-install cgclassify debuginfo-install cgcreate desktop-file-validate cgdelete dgawk fgrep cgexec df file cgsnapshot eject chage diff find chardetect diff-jars chattr elbadmin chcon db_upgrade flex check-binary-files diff3 flint checksctp elfedit chfn emacsclient chgrp eps2eps chmod env chown envsubst chrt erb chsh eqn chvt diffimg cifsiostat eu-addr2line cksum db_verify flock clean-binary-files etags.emacs clear dig fmt cluster eu-elflint cmp dijkstra cmsutil dimax_init cmtime eu-ar col dir fold colcrt eu-elfcmp colrm dircolors column eu-ranlib comm dirname command dislocate compile_et dmesg free consolehelper dot gawk coredumpctl dotlockfile coverage dotty gc coverage-2.7 dracut coverage2 eu-nm cp eu-objdump cpio eu-readelf cpp dtest gcore cpupower eu-size cq dbus-binding-tool create-jar-links dtestcm crlutil dtestsrq crontab dtestx csplit dtrace csslint-0.6 du gcov cupstestdsc dump2psl.pl cupstestppd eu-stack curl eu-strings cut eu-strip cvt dump2slvl.pl cwutil dumpkeys dapltest eu-unstrip date dvipdf db_archive dwp gdb db_checkpoint dwz gdbus db_deadlock dynamodb_dump db_dump dynamodb_load db_dump185 easy_install db_hotbackup echo gem db_load easy_install-2.7 db_log_verify ebrowse db_printlog emacs-24.3-nox db_recover ed gpg2 db_replicate egrep gpgv2 dbus-daemon gprof gpgsplit iconv eu-elfcompress gr2fonttest id eu-findtextrel graphml2gv idn eu-make-debug-archive grub2-file expand grub2-fstest expect grub2-glue-efi facter grub2-kbdcomp factor grub2-menulst2cfg fallocate grub2-mkfont fc-cache grub2-mkimage fc-cat grub2-mklayout fc-list grub2-mknetdir fc-match grub2-mkpasswd-pbkdf2 fc-pattern grub2-mkrelpath fc-query grub2-mkrescue fc-scan grub2-mkstandalone fc-validate grub2-render-label fdupes grub2-script-check fetch_file grub2-syslinux2cfg fgconsole gs igawk find-jar grep ib_write_lat find-repos-of-install gsbj info find2perl gsdj ipcmk findmnt gsdj500 fipscheck gsettings fipshmac gslj ipcrm firewall-cmd grep-changelog firewall-offline-cmd gslp ipcs flint_ext gsnd irb font2c gss-client fonttosfnt gstack ftp-rfc gtf jobs funzip gtk-update-icon-cache fwtrace gunzip gapplication gv2gml gcc-ar gvcolor gcc-nm gvgen join gcc-ranlib groff ibcongest gconf-merge-tree gvmap jwt gconftool-2 gvmap.sh gctags gvpack gdb-add-index ibtopodiff ibsim gdk-pixbuf-query-loaders-64 gvpr kill gencat gxl2gv gendiff gzexe kmod geoiplookup gzip ksh93 geoiplookup6 h2ph last geoipupdate h2xs lchfn get_module hca_self_test.ofed getconf hdsploader getent head lchsh getfacl hexdump getfattr hiera ldd getkeycodes host lefty getopt hostid getopts hostname gettext hostnamectl gettext.sh i2c less gfortran grops ibdev2netdev gio-querymodules-64 ib_acme glacier grotty lfs glib-compile-schemas ib_atomic_bw gml2gv ib_atomic_lat gpasswd ib_read_bw gpg-agent groups link gpg-connect-agent ib_read_lat gpg-error ib_send_bw gpg-zip ib_send_lat gpgconf ib_write_bw gpgparsemail grub2-editenv ln gsettings-data-convert gtk-query-immodules-2.0-64 ibdiagm.sh ibdiagnet ibdiagnet_csv2xml.py ibdiagpath ibdmchk ibdmtr ibdump ibgenperm ibnetsplit ibnlparse libtoolize mesg ibv_asyncwatch libtool mib2c ibv_cc_pingpong localedef ibv_dcini locate ibv_dctgt logger ibv_devices login mic ibv_devinfo loginctl ibv_intf list_instances ibv_polldcinfo linux-boot-prober ibv_rc_pingpong logname ibv_shared_mr llobdstat minit ibv_srq_pingpong llstat mkdir ibv_task_pingpong loadkeys mknod ibv_uc_pingpong lneato mm2gv ibv_ud_pingpong look more ibv_umr loadunimap mount ibv_xsrq_pingpong lp.cups iceauth lpoptions ifnames lppasswd infocmp lpq.cups infokey lpr.cups install msgexec msgen instance_events lprm.cups instmodsh lprsetup.sh ionice lpstat.cups iostat lpunlock ipcalc ls mstop ipmi_ui lsattr ipmilan lsb_release isosize lsblk mturk itrace lscgroup journalctl lscpu munge jvmjar lsinitrd kbd_mode lsipc mv kbdinfo lslocks kbdrate lslogins kdumpctl locale mwm kernel-install lsns namei keyctl lss3 nano keyring lsscsi kibitz lssubsys kill_instance lsusb ncat killall lsusb.py koi8rxterm lua neqn krb5-config luac nice lastlog localectl nl launch_instance lwp-download ld.bfd lwp-dump ld.gold lwp-mirror ldapcompare lwp-request ldapdelete lynx nm ldapexop m4 sem ldapmodify machinectl ldapmodrdn mailx pchrt ldappasswd make nohup ldapsearch makedb ldapurl man nop ldapwhoami mandb nproc lessecho manpath lesskey mapscrn lesspipe.sh mckey nroff lexgrog mcookie lfs_migrate mcra od libnetcfg md5sum mdevices_info memhog mft_uninstall.sh mget_temp mget_temp_ext mib2c-update migratepages migspeed minicom mixartloader mkfifo mkfontdir mkfontscale mkinitrd mkpasswd mktemp mlnx_dump_parser mlnx_get_vfs.pl mlnx_interface_mgr.sh mlnx_perf mlnx_qcn mlnx_qos mlx_fpga mlx_fpga_ext mlx_lossy mlxburn mlxcables mlxcables_ext mlxconfig mlxdump mlxdump_ext mlxfwmanager mlxfwmanager_pci mlxfwreset mlxi2c mlxmcg mlxmdio mlxphyburn mlxreg mlxreg_ext mlxtrace mlxtrace_ext mlxuptime modutil mokutil mountpoint mpi-selector mpi-selector-menu mpstat mremote msgattrib msgcat msgcmp msgcomm msgconv package-cleanup msgfilter gst-inspect-1.0 msgfmt pango-view msggrep papi_avail msghack papi_clockres msginit papi_command_line msgmerge papi_component_avail msgunfmt papi_cost msguniq openssl pgawk mst_ib_add.tcl papi_decode mstconfig papi_error_codes mstdump papi_event_chooser mstflint papi_mem_info mstmcra papi_multiplex_cost mstmread papi_native_avail mstmtserver papi_version mstmwrite papi_xml_event_info mstregdump passmass mstvpd passwd mtserver paste pgrep ndptool openipmish pic needs-restarting patch ping net-snmp-cert pathchk netstat pckt_drop nettle-hash openvt pinky nettle-lfib-stream pcre-config newgrp pkttyagent pkill nfsiostat-sysstat pdf2dsc ngettext pdf2ps genl-ctrl-list os-prober pl2pm edac-util perlivp pstruct mlx_fs_dump pdfdetach nsenter pdffonts nslookup pdfimages nsupdate pdfinfo ntpstat pdfseparate numactl pdftocairo numademo pdftohtml numastat pdftoppm numfmt pdftops objcopy pdftotext objdump pdfunite ofed_info peekfd ofed_rpm_info perl5.16.3 oldfind perl pldd omshell perldoc openipmicmd p11-kit pmap perlsh perlthanks perlbug pf2afm pfbtopfa piconv pidstat pinentry pinentry-curses pk12util pkaction pkcheck pkcs1-conv pkexec pkg-config quotasync sadf pkla-admin-identities rpmkeys rpmdb pkla-check-authorization rdoc sar plot-llstat mlxlink plymouth idiag-socket-details pod2html mlxlink_ext pod2man read scp pod2texi readelf pod2text readlink pod2usage realpath post-grohtml ranlib sdiff powernow-k8-decode rpmbuild ppdc recode-sr-latin ppdhtml rpmgraph ppdi red secon ppdmerge rpmspec ppdpo rstream pphs ruby pr redhat_lsb_init pre-grohtml remunge preconv rename printafm renice printenv repo-graph printf repo-rss prlimit rsync prove repoclosure prtstat runcon prune run-parts ps repodiff ps2ascii repomanage ps2epsi repoquery ps2pdf reposync ps2pdf12 repotrack ps2pdf13 resize ps2pdf14 resizecons ps2pdfwr runscript ps2ps rev sed ps2ps2 rftp seq psfxtable ri sftp pstree riostream net-snmp-config rx c2ph ptx rz pwd psed pwdx rlogin-cwd pwmake rm shred pwscore raw rb pyami_sendmail s2p pydoc rmail.postfix pyrsa-decrypt raw_ethernet_bw pyrsa-decrypt-2 raw_ethernet_lat pyrsa-decrypt-bigfile python2.7-config shuf pyrsa-decrypt-bigfile-2 rmcp_ping pyrsa-encrypt rcopy sccmap pyrsa-encrypt-2 rdate s3put pyrsa-encrypt-bigfile qperf rmdir size pyrsa-encrypt-bigfile-2 rngtest pyrsa-keygen rdma_client skill pyrsa-keygen-2 rdma_server sleep pyrsa-priv2pub rdma_xclient snice pyrsa-priv2pub-2 route53 pyrsa-sign rpcgen pyrsa-sign-2 rping sort pyrsa-verify rdma_xserver spax pyrsa-verify-2 rpm split python2.7 quota rpm2cpio rebuild-jar-repository sum tracepath rsyslog-recover-qi.pl sudoreplay tset run_perftest_loopback sync tracepath6 sas_disk_blink systemd-cgtop hunspell systemd-delta screen systemd-detect-virt script systemd-escape scriptreplay systemd-firstboot scsi_ch_swp systemd-hwdb sctp_darn systemd-inhibit sctp_status systemd-notify sctp_test systemd-nspawn sdbadmin systemd-run sdparm systemd-path mlxvpd systemd-sysv-convert sessreg systemd-stdio-bridge setarch systemd-tmpfiles setfacl sz tsort setfattr systool setfont sx tty setkeycodes tabs ul setleds sb umask setmetamode t2a uname setpriv tac uniq setserial tail users setsid tailf uuid setterm systemctl vdir setup-nsssysinit.sh tapestat setvtrgb tar vi setxkbmap taskadmin sexp-conv taskset sha1sum tbl vim sha224sum tc_wrap.py sha256sum tclsh8.5 sha384sum tcptraceroute sha512sum tcsh vlock shcomp systemd-analyze show-changed-rco systemd-ask-password show-installed systemd-cat w showconsolefont teamd wait showkey teamdctl showrgb teamnl signtool tee wall signver telnet sim_client test watch slabtop systemd-machine-id-setup snmp-bridge-mib testgdbm soapcpp2 testrb soelim texi2any solterm tftp wc sotruss tic wdctl splain traceroute sprof time wget sqlite3 traptoemail ssh timed-read ssh-add timed-run ssh-agent timedatectl ssh-copy-id timeout ssh-keygen tload which ssh-keyscan tmon who sshpass toe write ssltap top g++ startx tred stat touch c++ stdbuf update-ca-trust strace systemd-cgls gcc strace-log-merge tput xargs strings troff strip true stty truncate su trust sudo tr xauth hwloc-distrib xterm git systemd-tty-ask-password-agent ttmkfdir turbostat tzselect ucmatose ucs2any udaddy udevadm udpong umount unalias unbuffer unexpand unflatten unicode_start unicode_stop unix-lpr.sh unlink unmunge unshare unzipsfx xmvn-builddep hwloc-info update-desktop-database xset hwloc-patch update-gtk-immodules xsetmode svn update-mime-database xsubpp updatedb xz qdbus uptime xxd qdoc3 urlgrabber xzdec rcc usb-devices xzdiff usbhid-dump xzgrep usleep xzless usx2yloader xzmore utmpdump yes uic3 uuclient yum Xvfb uuidgen yum-builddep uxterm yum-debug-dump verifytree yum-config-manager vimdot yum-debug-restore vimtutor yum-groups-manager vmstat zcat tmux vpi_tcpdump yumdownloader vxloader zcmp 7z watchgnupg zdiff 7za weather zegrep wftopfa zfgrep whatis zforce whereis zgrep pdcp whiptail zip pdsh whoami zipcloak wish8.5 zipdetails withsctp zipgrep wqdump zipinfo wqdump_ext unzip rpdcp wsdl2h xorg-x11-fonts-update-dirs x86_64-redhat-linux-g++ xrandr hwloc-ps x86_64-redhat-linux-c++ x86_64-redhat-linux-gcc xrdb zipsplit x86_energy_perf_policy xsetpointer xpdf xdg-desktop-icon xsetroot gio xdg-desktop-menu zipnote xdg-email xsltproc gcc44 xdg-icon-resource zless pigz xdg-mime zmore unlz4 xdg-open xstdcmap tidy xdg-screensaver znew pxz xdg-settings hwloc-assembler xgamma applydeltarpm xgettext makedeltarpm xhost mergerepo xinit combinedeltarpm xinput createrepo xkbcomp hwloc-annotate xkibitz modifyrepo xkill hwloc-calc xmbind hwloc-bind xminicom hwloc-distances xml2-config hwloc-ls xmlcatalog hwloc-compress-dir xmllint rpmdumpheader xmlwf hwloc-diff xmodmap xrefresh git-shell nf-ct-list nl-neigh-add hwloc-assembler-remote pdftopng Xvnc hwloc-gather-topology perltidy lz4 lstopo-no-graphics net-snmp-config-x86_64 nf-exp-add lz4c pip grn git-upload-archive gdbus-codegen cjpeg git-upload-pack nf-monitor svnadmin glib-compile-resources svndumpfilter nf-queue svnlook nl-addr-add svnrdump nl-addr-delete svnserve nl-addr-list svnsync nl-class-add svnversion nl-qdisc-delete nl-qdisc-add svn-populate-node-origins-index paperconf nl-neigh-list svn-rep-sharing-stats glib-genmarshal svnauthz-validate nl-class-delete svnmucc glib-gettextize svnraisetreeconflict glib-mkenums djpeg freetype-config patchelf gst-feedback htop rhash gst-inspect git-receive-pack gst-launch pip2 lkbib gst-typefind gobject-query pekwm gst-xmlinspect gresource xprop gst-xmllaunch gtester xev gst-feedback-0.10 gtester-report gst-inspect-0.10 gcov44 cpan gst-launch-0.10 gdk-pixbuf-thumbnailer gst-typefind-0.10 gio-querymodules-32 gst-xmlinspect-0.10 gdk-pixbuf-query-loaders-32 gst-xmllaunch-0.10 lz4cat lzf ncurses5-config gst-launch-1.0 ncursesw5-config gst-stats-1.0 unlzf orc-bugreport addftinfo qmlviewer pip2.7 designer-qt4 sasl2-sample-client lconvert nl-class-list linguist-qt4 nl-classid-lookup lrelease-qt4 parallel lupdate-qt4 nl-cls-add moc-qt4 nl-cls-delete pixeltool gst-typefind-1.0 qcollectiongenerator niceload qdbuscpp2xml nl-cls-list qdbusxml2cpp enchant refer qhelpconverter enchant-lsmod lftp qhelpgenerator sql urxvt qmake-qt4 secret-tool qmlplugindump nl-fib-lookup qt3to4 nf-exp-delete qttracereplay nl-link-enslave uic-qt4 nl-link-ifindex2name xmlpatterns unpigz xmlpatternsvalidator nl-link-list gnuplot-wx nl-link-name2ifindex xvfb-run nl-link-release glewinfo nl-link-set visualinfo nl-link-stats icu-config nf-exp-list icu-config-64 nl-list-caches icuinfo gnuplot nl-list-sockets dshbak nl-monitor nf-ct-add nf-log nl-neigh-delete nl-neightbl-list nl-pktloc-lookup urxvt256cc nl-qdisc-list urxvt256cd nl-route-add pfbtops nl-route-delete nl-route-get nl-route-list nl-rule-list pic2graph nl-tctree-list nl-util-addr pflags ping;5a57e618 ptaskset indxbib raw_ethernet_burst_lat tfmtodit raw_ethernet_fs_rate lookbib run_perftest_multi_devices rxe_cfg dbiproxy flamegraph.pl nytprofcsv nytprofmerge cpanel_json_xs gindxbib grefer pdfroff event_rpcgen.py sasl2-sample-server dbus-run-session cvtsudoers dbus-test-tool grolbp dbus-update-activation-environment dialog vncconfig vncpasswd jpegtran rdjpgcom wrjpgcom pygtk-demo fslint-gui ed2k-link gost-hash has160-hash magnet-link sfv-hash tiger-hash tth-hash urxvtc whirlpool-hash db4_archive db4_checkpoint db4_deadlock db4_dump db4_dump185 urxvtd db4_hotbackup db4_load db4_printlog db4_recover db4_sql db4_stat db4_upgrade db4_verify xlsfonts grolj4 dbilogstrip dbiprof pwhich nytprofpf lftpget sslscan grap2graph hpftodit vncserver edid-decode xdpyinfo xlsatoms xlsclients xvinfo xwininfo shasum nytprofcalls nytprofcg nytprofhtml eqn2graph gdiffmk glookbib grodvi urxvt256c /usr/local/sbin: trqauthd sendmail mlxup lustre_tune.sh rmmod-acpi_pad.sh momctl lastboot pan_filecount pan_snap_delta pan_snap_replicator pan_snap_replicator_slave pan_tcp_capture_client check_panfs config_panfs kcollect pan_sm_vol_attrs panfs_stat panfs_trace panfs_trace_manage sign_check trpost /usr/sbin: accept adduser authconfig authconfig-tui btrfsck cache_check cache_dump cache_metadata_size cache_repair cache_restore clock ctstat cupsdisable cupsenable cupsreject depmod dmraid.static dmstats dosfsck dosfslabel dracut era_check era_dump era_invalidate era_restore fsck.msdos fsck.vfat genhomedircon halt ibsrpdm in.tftpd init insmod ip6tables ip6tables-restore ip6tables-save iptables iptables-restore iptables-save lpc lsmod lvchange lvconvert lvcreate lvdisplay lvextend nl-class-add lvmconfig lvmdiskscan lvmsadc lvmsar lvreduce lvremove lvrename lvresize lvs lvscan mkdict mkdosfs mkfs.msdos mkfs.vfat modinfo modprobe mount.nfs4 named-compilezone packer pidof ping6 poweroff pvchange pvck pvcreate pvdisplay pvmove pvremove pvresize pvs pvscan quotaoff reboot reject restorecon rmmod rtstat run_srp_daemon runlevel sendmail shutdown systemctl telinit thin_check thin_delta thin_dump thin_ls thin_metadata_size thin_repair thin_restore thin_rmap thin_trim tracepath tracepath6 udevadm umount.nfs umount.nfs4 update-alternatives vgcfgbackup vgcfgrestore vgchange vgck vgconvert vgcreate vgdisplay vgexport vgextend vgimport vgimportclone vgmerge vgmknodes vgreduce vgremove vgrename vgs vgscan vgsplit vigr aureport cbq cache_writeback autrace accessdb avahi-autoipd addgnupghome avahi-daemon addpart avcstat agetty badblocks alternatives biosdecode anacron ausearch chat applygnupgdefaults bridge arp biosdevname arpaname btrfs arpd blkdeactivate arping btrfs-convert atd blkdiscard atftpd btrfs-image atrun blkid chcpu audispd blkmapd auditctl blockdev auditd brctl crond augenrules cfdisk capsh btrfs-debug-tree btrfs-find-root btrfs-map-logical btrfs-select-super genl-ctrl-list btrfs-zero-log btrfstune build-locale-archive cacertdir_rehash fsck.ext3 cgclear efibootmgr ifcfg cgconfigparser fsck.ext2 cgrulesengd nl-class-list ifup check_lft_balance.pl e2fsck chkconfig fsck.fat chpasswd fsck.minix chroot fsck.xfs clockdiff fsfreeze cma_roce_mode edquota hwclock common_irq_affinity.sh ether-wake ip compat_gid_gen ethtool kdump connectx_port_config fstrim consoletype genhostid convertquota exportfs kexec cracklib-check faillock lctl cracklib-format fatlabel ldev cracklib-packer fdformat lid cracklib-unpacker fdisk ib2ib_setup create-cracklib-dict fxload ctrlaltdel genl lsof cups-browsed getcap cupsaccept nl-class-delete cupsaddsmb genrandom cupsctl ibacm cupsd getenforce cupsfilter getpcaps ddns-confgen getsebool debugfs groupadd delpart groupdel dhclient filefrag lspci dhclient-script ibaddr dhcpd groupmems dhcrelay groupmod dmevent_tool grpck lst dm_dso_reg_tool dmeventd grpconv dmidecode grpunconv dmraid grub2-mkconfig dmsetup grub2-bios-setup dnsmasq findfs lvm dnssec-checkds firewalld mdadm dnssec-coverage fixfiles mdmon dnssec-dsfromkey fsadm ibcacheedit dnssec-importkey fsck ibccconfig dnssec-keyfromlabel grub2-install dnssec-keygen grub2-macbless dnssec-revoke fsck.btrfs mkfs dnssec-settime fsck.cramfs named dnssec-signzone grub2-ofpathname dnssec-verify grub2-reboot dump_fts grub2-probe dump_lfts.sh grub2-set-default dump_mfts.sh grub2-rpm-sort dumpe2fs grub2-setpassword e2freefrag grub2-sparc64-setup e2image gss-server e2undo grubby e4defrag gssproxy eapol_test hardlink ebtables fsck.ext4 nscd ebtables-restore ibcheckportstate ebtables-save ibccquery fuser ibcheckerrors ntp-keygen nslcd glibc_post_upgrade.i686 lgroupmod nl-cls-list glibc_post_upgrade.x86_64 lhsmtool_posix nstat grub2-get-kernel-settings ibcheckerrs ibchecknet ibchecknode ibcheckport llverfs ntpd ibcheckportwidth luseradd ibcheckstate luserdel ibcheckwidth lnewusers ntpdc ibclearcounters lusermod ibclearerrors lnstat ntpq ibdatacounters lustre_rmmod ibdatacounts lustre_routes_config ibdiscover.pl load_policy partx ibfindnodesusing.pl lustre_rsync ibhosts lockdev pppd ibidsverify.pl lvmconf iblinkinfo lvmdump iblinkinfo.pl lvmetad ibmirror lvmpolld ibnetdiscover makedumpfile ibnodes matchpathcon ibping mcelog ibportstate mii-diag ibprintca.pl mii-tool ibprintrt.pl logrotate pwck ibprintswitch.pl mkdumprd ibqueryerrors logsave quot ibqueryerrors.pl mkfs.btrfs ibroute mkfs.cramfs ibrouters mkfs.ext4 ibstat mkfs.ext3 ibstatus mkfs.ext2 ibswitches losetup rdisc ibswportwatch.pl mke2fs ibsysstat mkfs.fat ibtracert lpadmin rndc iconvconfig.i686 lpasswd rngd iconvconfig.x86_64 nl-link-list iconvconfig mkfs.minix ifconfig mkfs.xfs ifdown mkhomedir_helper ifenslave mklost+found ifstat mkswap install-info mlnx_affinity installkernel lpc.cups route intel-microcode2ucode mlnx_tune ipmaddr nl-classid-lookup nl-cls-add nl-cls-delete iprconfig mount.lustre iprdbg mount.nfs iprdump mountstats iprinit munged iprsos lwresd iprupdate named-checkconf iptunnel named-checkzone irqbalance lpinfo rtmon isc-hmac-fixup lpmove rtpr key.dns_resolver named-journalprint killall5 nl-qdisc-add setup ko2iblnd-probe nameif kpartx netreport l_getidentity new-kernel-pkg lchage newusers ldattach nfsdcltrack ldconfig nfsidmap lgroupadd nfsiostat lgroupdel nfsstat lustre_routes_conversion nl-pktloc-lookup nl-qdisc-delete nl-qdisc-list thin_show_duplicates dmfilemapd cma_roce_tos edac-ctl devlink sasl2-shared-mechlist nologin nsec3hash saquery ntpdate sasldblistusers2 ntptime saslpasswd2 ntsysv rsyslogd tcpd ofed_uninstall.sh sefcontext_compile opensm selabel_digest openvpn selabel_lookup osd_login selabel_partial_match osmtest selinux_restorecon ownership rtacct tcsd pam_console_apply selinuxconlist pam_tally2 rtcwake tuned pam_timestamp_check selinuxdefcon parted selinuxenabled partprobe selinuxexeccon pdata_tools semodule perfquery sendmail.postfix pethtool service pifconfig sestatus pivot_root set_irq_affinity.sh plipconfig tcpdmatch tc plymouth-set-default-theme set_nodedesc.sh plymouthd setcap postalias setenforce postcat setfiles postconf setpci postdrop setquota postfix setsebool postkick sfdisk postlock sgpio vipw postlog show_gids postmap show_irq_affinity.sh postmulti showmount postqueue sim_server postsuper skdump ppp-watch sktest pppdump runuser yumdb pppoe-discovery slattach pppstats sldd.sh pwconv safe_finger zdump pwhistory_helper sln zic pwunconv sm-notify quotacheck smartctl quotaon smartd quotastats sminfo raid-check smparquery readprofile rpcdebug switch_root redhat_lsb_trigger.x86_64 smpdump repquota smpquery request-key smtp-sink resize2fs smtp-source resizepart srp_daemon rndc-confgen srp_daemon.sh routef ss iotop routel ipset routerstat sshd rpc.gssd sshd-keygen rpc.idmapd start-statd rpc.mountd sulogin rpc.nfsd sushell rpc.rquotad swaplabel rpc.statd swapoff ko2iblnd-probe.orig swapon rpcbind rpcinfo sys-unconfig selabel_lookup_best_match set_irq_affinity_bynode.sh set_irq_affinity_cpulist.sh show_irq_affinity_hints.sh sysctl sysctl_perf_tuning sysinfo-snapshot.py tcpdump tcpslice tickadj try-from tune2fs e2label tuned-adm unix_chkpwd unix_update update-pciids update-smart-drivedb useradd userdel userhelper usermod usernetctl uuserver vendor_post_uninstall.sh vendor_pre_uninstall.sh vendstat virt-what visudo vmcore-dmesg vpddecode weak-modules wipefs testsaslauthd wpa_cli wpa_passphrase wpa_supplicant xfs_admin xfs_bmap xfs_copy xfs_db xfs_estimate xfs_freeze xfs_fsr xfs_growfs xfs_info xfs_io xfs_logprint xfs_mdrestore xfs_metadump xfs_mkfile xfs_ncheck xfs_quota xfs_repair xfs_rtcp xqmstats xtables-multi yum-complete-transaction lustre-probe lustre-probe.do hwloc-dump-hwdata paperconfig zramctl iptraf-ng rvnamed-ng l_idmap ldlm_debug_upcall lgss_keyring lgss_sk ll_decode_linkea lsvcgssd setup_mr_cache.sh mount.panfs pluginviewer saslauthd /opt/ibutils/bin: IBMgtSim RunSimTest dump2psl.pl dump2slvl.pl ibdiagnet ibdiagpath ibdiagui ibdmchk ibdmsh ibdmtr ibis ibmsquit ibmssh ibnlparse ibtopodiff mkSimNodeDir /sbin: accept adduser authconfig authconfig-tui btrfsck cache_check cache_dump cache_metadata_size cache_repair cache_restore clock ctstat cupsdisable cupsenable cupsreject depmod dmraid.static dmstats dosfsck dosfslabel dracut era_check era_dump era_invalidate era_restore fsck.msdos fsck.vfat genhomedircon halt ibsrpdm in.tftpd init insmod ip6tables ip6tables-restore ip6tables-save iptables iptables-restore iptables-save lpc lsmod lvchange lvconvert lvcreate lvdisplay lvextend nl-class-add lvmconfig lvmdiskscan lvmsadc lvmsar lvreduce lvremove lvrename lvresize lvs lvscan mkdict mkdosfs mkfs.msdos mkfs.vfat modinfo modprobe mount.nfs4 named-compilezone packer pidof ping6 poweroff pvchange pvck pvcreate pvdisplay pvmove pvremove pvresize pvs pvscan quotaoff reboot reject restorecon rmmod rtstat run_srp_daemon runlevel sendmail shutdown systemctl telinit thin_check thin_delta thin_dump thin_ls thin_metadata_size thin_repair thin_restore thin_rmap thin_trim tracepath tracepath6 udevadm umount.nfs umount.nfs4 update-alternatives vgcfgbackup vgcfgrestore vgchange vgck vgconvert vgcreate vgdisplay vgexport vgextend vgimport vgimportclone vgmerge vgmknodes vgreduce vgremove vgrename vgs vgscan vgsplit vigr aureport cbq cache_writeback autrace accessdb avahi-autoipd addgnupghome avahi-daemon addpart avcstat agetty badblocks alternatives biosdecode anacron ausearch chat applygnupgdefaults bridge arp biosdevname arpaname btrfs arpd blkdeactivate arping btrfs-convert atd blkdiscard atftpd btrfs-image atrun blkid chcpu audispd blkmapd auditctl blockdev auditd brctl crond augenrules cfdisk capsh btrfs-debug-tree btrfs-find-root btrfs-map-logical btrfs-select-super genl-ctrl-list btrfs-zero-log btrfstune build-locale-archive cacertdir_rehash fsck.ext3 cgclear efibootmgr ifcfg cgconfigparser fsck.ext2 cgrulesengd nl-class-list ifup check_lft_balance.pl e2fsck chkconfig fsck.fat chpasswd fsck.minix chroot fsck.xfs clockdiff fsfreeze cma_roce_mode edquota hwclock common_irq_affinity.sh ether-wake ip compat_gid_gen ethtool kdump connectx_port_config fstrim consoletype genhostid convertquota exportfs kexec cracklib-check faillock lctl cracklib-format fatlabel ldev cracklib-packer fdformat lid cracklib-unpacker fdisk ib2ib_setup create-cracklib-dict fxload ctrlaltdel genl lsof cups-browsed getcap cupsaccept nl-class-delete cupsaddsmb genrandom cupsctl ibacm cupsd getenforce cupsfilter getpcaps ddns-confgen getsebool debugfs groupadd delpart groupdel dhclient filefrag lspci dhclient-script ibaddr dhcpd groupmems dhcrelay groupmod dmevent_tool grpck lst dm_dso_reg_tool dmeventd grpconv dmidecode grpunconv dmraid grub2-mkconfig dmsetup grub2-bios-setup dnsmasq findfs lvm dnssec-checkds firewalld mdadm dnssec-coverage fixfiles mdmon dnssec-dsfromkey fsadm ibcacheedit dnssec-importkey fsck ibccconfig dnssec-keyfromlabel grub2-install dnssec-keygen grub2-macbless dnssec-revoke fsck.btrfs mkfs dnssec-settime fsck.cramfs named dnssec-signzone grub2-ofpathname dnssec-verify grub2-reboot dump_fts grub2-probe dump_lfts.sh grub2-set-default dump_mfts.sh grub2-rpm-sort dumpe2fs grub2-setpassword e2freefrag grub2-sparc64-setup e2image gss-server e2undo grubby e4defrag gssproxy eapol_test hardlink ebtables fsck.ext4 nscd ebtables-restore ibcheckportstate ebtables-save ibccquery fuser ibcheckerrors ntp-keygen nslcd glibc_post_upgrade.i686 lgroupmod nl-cls-list glibc_post_upgrade.x86_64 lhsmtool_posix nstat grub2-get-kernel-settings ibcheckerrs ibchecknet ibchecknode ibcheckport llverfs ntpd ibcheckportwidth luseradd ibcheckstate luserdel ibcheckwidth lnewusers ntpdc ibclearcounters lusermod ibclearerrors lnstat ntpq ibdatacounters lustre_rmmod ibdatacounts lustre_routes_config ibdiscover.pl load_policy partx ibfindnodesusing.pl lustre_rsync ibhosts lockdev pppd ibidsverify.pl lvmconf iblinkinfo lvmdump iblinkinfo.pl lvmetad ibmirror lvmpolld ibnetdiscover makedumpfile ibnodes matchpathcon ibping mcelog ibportstate mii-diag ibprintca.pl mii-tool ibprintrt.pl logrotate pwck ibprintswitch.pl mkdumprd ibqueryerrors logsave quot ibqueryerrors.pl mkfs.btrfs ibroute mkfs.cramfs ibrouters mkfs.ext4 ibstat mkfs.ext3 ibstatus mkfs.ext2 ibswitches losetup rdisc ibswportwatch.pl mke2fs ibsysstat mkfs.fat ibtracert lpadmin rndc iconvconfig.i686 lpasswd rngd iconvconfig.x86_64 nl-link-list iconvconfig mkfs.minix ifconfig mkfs.xfs ifdown mkhomedir_helper ifenslave mklost+found ifstat mkswap install-info mlnx_affinity installkernel lpc.cups route intel-microcode2ucode mlnx_tune ipmaddr nl-classid-lookup nl-cls-add nl-cls-delete iprconfig mount.lustre iprdbg mount.nfs iprdump mountstats iprinit munged iprsos lwresd iprupdate named-checkconf iptunnel named-checkzone irqbalance lpinfo rtmon isc-hmac-fixup lpmove rtpr key.dns_resolver named-journalprint killall5 nl-qdisc-add setup ko2iblnd-probe nameif kpartx netreport l_getidentity new-kernel-pkg lchage newusers ldattach nfsdcltrack ldconfig nfsidmap lgroupadd nfsiostat lgroupdel nfsstat lustre_routes_conversion nl-pktloc-lookup nl-qdisc-delete nl-qdisc-list thin_show_duplicates dmfilemapd cma_roce_tos edac-ctl devlink sasl2-shared-mechlist nologin nsec3hash saquery ntpdate sasldblistusers2 ntptime saslpasswd2 ntsysv rsyslogd tcpd ofed_uninstall.sh sefcontext_compile opensm selabel_digest openvpn selabel_lookup osd_login selabel_partial_match osmtest selinux_restorecon ownership rtacct tcsd pam_console_apply selinuxconlist pam_tally2 rtcwake tuned pam_timestamp_check selinuxdefcon parted selinuxenabled partprobe selinuxexeccon pdata_tools semodule perfquery sendmail.postfix pethtool service pifconfig sestatus pivot_root set_irq_affinity.sh plipconfig tcpdmatch tc plymouth-set-default-theme set_nodedesc.sh plymouthd setcap postalias setenforce postcat setfiles postconf setpci postdrop setquota postfix setsebool postkick sfdisk postlock sgpio vipw postlog show_gids postmap show_irq_affinity.sh postmulti showmount postqueue sim_server postsuper skdump ppp-watch sktest pppdump runuser yumdb pppoe-discovery slattach pppstats sldd.sh pwconv safe_finger zdump pwhistory_helper sln zic pwunconv sm-notify quotacheck smartctl quotaon smartd quotastats sminfo raid-check smparquery readprofile rpcdebug switch_root redhat_lsb_trigger.x86_64 smpdump repquota smpquery request-key smtp-sink resize2fs smtp-source resizepart srp_daemon rndc-confgen srp_daemon.sh routef ss iotop routel ipset routerstat sshd rpc.gssd sshd-keygen rpc.idmapd start-statd rpc.mountd sulogin rpc.nfsd sushell rpc.rquotad swaplabel rpc.statd swapoff ko2iblnd-probe.orig swapon rpcbind rpcinfo sys-unconfig selabel_lookup_best_match set_irq_affinity_bynode.sh set_irq_affinity_cpulist.sh show_irq_affinity_hints.sh sysctl sysctl_perf_tuning sysinfo-snapshot.py tcpdump tcpslice tickadj try-from tune2fs e2label tuned-adm unix_chkpwd unix_update update-pciids update-smart-drivedb useradd userdel userhelper usermod usernetctl uuserver vendor_post_uninstall.sh vendor_pre_uninstall.sh vendstat virt-what visudo vmcore-dmesg vpddecode weak-modules wipefs testsaslauthd wpa_cli wpa_passphrase wpa_supplicant xfs_admin xfs_bmap xfs_copy xfs_db xfs_estimate xfs_freeze xfs_fsr xfs_growfs xfs_info xfs_io xfs_logprint xfs_mdrestore xfs_metadump xfs_mkfile xfs_ncheck xfs_quota xfs_repair xfs_rtcp xqmstats xtables-multi yum-complete-transaction lustre-probe lustre-probe.do hwloc-dump-hwdata paperconfig zramctl iptraf-ng rvnamed-ng l_idmap ldlm_debug_upcall lgss_keyring lgss_sk ll_decode_linkea lsvcgssd setup_mr_cache.sh mount.panfs pluginviewer saslauthd /usr/sbin: accept adduser authconfig authconfig-tui btrfsck cache_check cache_dump cache_metadata_size cache_repair cache_restore clock ctstat cupsdisable cupsenable cupsreject depmod dmraid.static dmstats dosfsck dosfslabel dracut era_check era_dump era_invalidate era_restore fsck.msdos fsck.vfat genhomedircon halt ibsrpdm in.tftpd init insmod ip6tables ip6tables-restore ip6tables-save iptables iptables-restore iptables-save lpc lsmod lvchange lvconvert lvcreate lvdisplay lvextend nl-class-add lvmconfig lvmdiskscan lvmsadc lvmsar lvreduce lvremove lvrename lvresize lvs lvscan mkdict mkdosfs mkfs.msdos mkfs.vfat modinfo modprobe mount.nfs4 named-compilezone packer pidof ping6 poweroff pvchange pvck pvcreate pvdisplay pvmove pvremove pvresize pvs pvscan quotaoff reboot reject restorecon rmmod rtstat run_srp_daemon runlevel sendmail shutdown systemctl telinit thin_check thin_delta thin_dump thin_ls thin_metadata_size thin_repair thin_restore thin_rmap thin_trim tracepath tracepath6 udevadm umount.nfs umount.nfs4 update-alternatives vgcfgbackup vgcfgrestore vgchange vgck vgconvert vgcreate vgdisplay vgexport vgextend vgimport vgimportclone vgmerge vgmknodes vgreduce vgremove vgrename vgs vgscan vgsplit vigr aureport cbq cache_writeback autrace accessdb avahi-autoipd addgnupghome avahi-daemon addpart avcstat agetty badblocks alternatives biosdecode anacron ausearch chat applygnupgdefaults bridge arp biosdevname arpaname btrfs arpd blkdeactivate arping btrfs-convert atd blkdiscard atftpd btrfs-image atrun blkid chcpu audispd blkmapd auditctl blockdev auditd brctl crond augenrules cfdisk capsh btrfs-debug-tree btrfs-find-root btrfs-map-logical btrfs-select-super genl-ctrl-list btrfs-zero-log btrfstune build-locale-archive cacertdir_rehash fsck.ext3 cgclear efibootmgr ifcfg cgconfigparser fsck.ext2 cgrulesengd nl-class-list ifup check_lft_balance.pl e2fsck chkconfig fsck.fat chpasswd fsck.minix chroot fsck.xfs clockdiff fsfreeze cma_roce_mode edquota hwclock common_irq_affinity.sh ether-wake ip compat_gid_gen ethtool kdump connectx_port_config fstrim consoletype genhostid convertquota exportfs kexec cracklib-check faillock lctl cracklib-format fatlabel ldev cracklib-packer fdformat lid cracklib-unpacker fdisk ib2ib_setup create-cracklib-dict fxload ctrlaltdel genl lsof cups-browsed getcap cupsaccept nl-class-delete cupsaddsmb genrandom cupsctl ibacm cupsd getenforce cupsfilter getpcaps ddns-confgen getsebool debugfs groupadd delpart groupdel dhclient filefrag lspci dhclient-script ibaddr dhcpd groupmems dhcrelay groupmod dmevent_tool grpck lst dm_dso_reg_tool dmeventd grpconv dmidecode grpunconv dmraid grub2-mkconfig dmsetup grub2-bios-setup dnsmasq findfs lvm dnssec-checkds firewalld mdadm dnssec-coverage fixfiles mdmon dnssec-dsfromkey fsadm ibcacheedit dnssec-importkey fsck ibccconfig dnssec-keyfromlabel grub2-install dnssec-keygen grub2-macbless dnssec-revoke fsck.btrfs mkfs dnssec-settime fsck.cramfs named dnssec-signzone grub2-ofpathname dnssec-verify grub2-reboot dump_fts grub2-probe dump_lfts.sh grub2-set-default dump_mfts.sh grub2-rpm-sort dumpe2fs grub2-setpassword e2freefrag grub2-sparc64-setup e2image gss-server e2undo grubby e4defrag gssproxy eapol_test hardlink ebtables fsck.ext4 nscd ebtables-restore ibcheckportstate ebtables-save ibccquery fuser ibcheckerrors ntp-keygen nslcd glibc_post_upgrade.i686 lgroupmod nl-cls-list glibc_post_upgrade.x86_64 lhsmtool_posix nstat grub2-get-kernel-settings ibcheckerrs ibchecknet ibchecknode ibcheckport llverfs ntpd ibcheckportwidth luseradd ibcheckstate luserdel ibcheckwidth lnewusers ntpdc ibclearcounters lusermod ibclearerrors lnstat ntpq ibdatacounters lustre_rmmod ibdatacounts lustre_routes_config ibdiscover.pl load_policy partx ibfindnodesusing.pl lustre_rsync ibhosts lockdev pppd ibidsverify.pl lvmconf iblinkinfo lvmdump iblinkinfo.pl lvmetad ibmirror lvmpolld ibnetdiscover makedumpfile ibnodes matchpathcon ibping mcelog ibportstate mii-diag ibprintca.pl mii-tool ibprintrt.pl logrotate pwck ibprintswitch.pl mkdumprd ibqueryerrors logsave quot ibqueryerrors.pl mkfs.btrfs ibroute mkfs.cramfs ibrouters mkfs.ext4 ibstat mkfs.ext3 ibstatus mkfs.ext2 ibswitches losetup rdisc ibswportwatch.pl mke2fs ibsysstat mkfs.fat ibtracert lpadmin rndc iconvconfig.i686 lpasswd rngd iconvconfig.x86_64 nl-link-list iconvconfig mkfs.minix ifconfig mkfs.xfs ifdown mkhomedir_helper ifenslave mklost+found ifstat mkswap install-info mlnx_affinity installkernel lpc.cups route intel-microcode2ucode mlnx_tune ipmaddr nl-classid-lookup nl-cls-add nl-cls-delete iprconfig mount.lustre iprdbg mount.nfs iprdump mountstats iprinit munged iprsos lwresd iprupdate named-checkconf iptunnel named-checkzone irqbalance lpinfo rtmon isc-hmac-fixup lpmove rtpr key.dns_resolver named-journalprint killall5 nl-qdisc-add setup ko2iblnd-probe nameif kpartx netreport l_getidentity new-kernel-pkg lchage newusers ldattach nfsdcltrack ldconfig nfsidmap lgroupadd nfsiostat lgroupdel nfsstat lustre_routes_conversion nl-pktloc-lookup nl-qdisc-delete nl-qdisc-list thin_show_duplicates dmfilemapd cma_roce_tos edac-ctl devlink sasl2-shared-mechlist nologin nsec3hash saquery ntpdate sasldblistusers2 ntptime saslpasswd2 ntsysv rsyslogd tcpd ofed_uninstall.sh sefcontext_compile opensm selabel_digest openvpn selabel_lookup osd_login selabel_partial_match osmtest selinux_restorecon ownership rtacct tcsd pam_console_apply selinuxconlist pam_tally2 rtcwake tuned pam_timestamp_check selinuxdefcon parted selinuxenabled partprobe selinuxexeccon pdata_tools semodule perfquery sendmail.postfix pethtool service pifconfig sestatus pivot_root set_irq_affinity.sh plipconfig tcpdmatch tc plymouth-set-default-theme set_nodedesc.sh plymouthd setcap postalias setenforce postcat setfiles postconf setpci postdrop setquota postfix setsebool postkick sfdisk postlock sgpio vipw postlog show_gids postmap show_irq_affinity.sh postmulti showmount postqueue sim_server postsuper skdump ppp-watch sktest pppdump runuser yumdb pppoe-discovery slattach pppstats sldd.sh pwconv safe_finger zdump pwhistory_helper sln zic pwunconv sm-notify quotacheck smartctl quotaon smartd quotastats sminfo raid-check smparquery readprofile rpcdebug switch_root redhat_lsb_trigger.x86_64 smpdump repquota smpquery request-key smtp-sink resize2fs smtp-source resizepart srp_daemon rndc-confgen srp_daemon.sh routef ss iotop routel ipset routerstat sshd rpc.gssd sshd-keygen rpc.idmapd start-statd rpc.mountd sulogin rpc.nfsd sushell rpc.rquotad swaplabel rpc.statd swapoff ko2iblnd-probe.orig swapon rpcbind rpcinfo sys-unconfig selabel_lookup_best_match set_irq_affinity_bynode.sh set_irq_affinity_cpulist.sh show_irq_affinity_hints.sh sysctl sysctl_perf_tuning sysinfo-snapshot.py tcpdump tcpslice tickadj try-from tune2fs e2label tuned-adm unix_chkpwd unix_update update-pciids update-smart-drivedb useradd userdel userhelper usermod usernetctl uuserver vendor_post_uninstall.sh vendor_pre_uninstall.sh vendstat virt-what visudo vmcore-dmesg vpddecode weak-modules wipefs testsaslauthd wpa_cli wpa_passphrase wpa_supplicant xfs_admin xfs_bmap xfs_copy xfs_db xfs_estimate xfs_freeze xfs_fsr xfs_growfs xfs_info xfs_io xfs_logprint xfs_mdrestore xfs_metadump xfs_mkfile xfs_ncheck xfs_quota xfs_repair xfs_rtcp xqmstats xtables-multi yum-complete-transaction lustre-probe lustre-probe.do hwloc-dump-hwdata paperconfig zramctl iptraf-ng rvnamed-ng l_idmap ldlm_debug_upcall lgss_keyring lgss_sk ll_decode_linkea lsvcgssd setup_mr_cache.sh mount.panfs pluginviewer saslauthd /cm/local/apps/environment-modules/3.2.10/bin: add.modules mkroot modulecmd .: PKG-INFO TAGS CTAGS makefile CODE_OF_CONDUCT.md GNUmakefile share systems petscdir.mk config interfaces include src setup.py configure LICENSE .dir-locals.el lib gmakefile .gitlab-alcf-ci.yml CONTRIBUTING gmakefile.test tag-tar RDict.log fr configure.log.bkp configure.log Warning accessing /home2/barretk3/.local/bin gives errors: [Errno 2] No such file or directory: '/home2/barretk3/.local/bin' Warning accessing /home2/barretk3/bin gives errors: [Errno 2] No such file or directory: '/home2/barretk3/bin' ============================================================================================= TESTING: configureExternalPackagesDir from config.framework(config/BuildSystem/config/framework.py:967) child config.utilities.macosFirewall 0.000006 ============================================================================================= TESTING: configureDebuggers from config.utilities.debuggers(config/BuildSystem/config/utilities/debuggers.py:21) Find a default debugger and determine its arguments Executing: uname -s stdout: Linux Checking for program /cm/local/apps/cmake/3.9.6/bin/gdb...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/gdb...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/gdb...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/gdb...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/gdb...not found Checking for program /usr/local/bin/gdb...not found Checking for program /usr/bin/gdb...found Defined make macro "GDB" to "/usr/bin/gdb" Defined "USE_DEBUGGER" to ""gdb"" Executing: uname -s stdout: Linux Defined make macro "DSYMUTIL" to "true" Executing: uname -s stdout: Linux child config.utilities.debuggers 0.031989 ============================================================================================= TESTING: configureDirectories from PETSc.options.petscdir(config/PETSc/options/petscdir.py:23) Checks PETSC_DIR and sets if not set Version Information: #define PETSC_VERSION_RELEASE 1 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 15 #define PETSC_VERSION_SUBMINOR 0 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "Mar 30, 2021" #define PETSC_VERSION_GIT "v3.15" #define PETSC_VERSION_DATE_GIT "2021-03-30 16:22:19 -0500" #define PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_ PETSC_VERSION_EQ #define PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ child PETSc.options.petscdir 0.004902 ============================================================================================= TESTING: getDatafilespath from PETSc.options.dataFilesPath(config/PETSc/options/dataFilesPath.py:29) Checks what DATAFILESPATH should be child PETSc.options.dataFilesPath 0.000887 ============================================================================================= TESTING: configureGit from config.sourceControl(config/BuildSystem/config/sourceControl.py:24) Find the Git executable Checking for program /cm/local/apps/cmake/3.9.6/bin/git...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/git...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/git...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/git...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/git...not found Checking for program /usr/local/bin/git...not found Checking for program /usr/bin/git...found Defined make macro "GIT" to "git" Executing: git --version stdout: git version 1.8.3.1 ============================================================================================= TESTING: configureMercurial from config.sourceControl(config/BuildSystem/config/sourceControl.py:35) Find the Mercurial executable Checking for program /cm/local/apps/cmake/3.9.6/bin/hg...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/hg...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/hg...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/hg...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/hg...not found Checking for program /usr/local/bin/hg...not found Checking for program /usr/bin/hg...not found Checking for program /usr/local/sbin/hg...not found Checking for program /usr/sbin/hg...not found Checking for program /opt/ibutils/bin/hg...not found Checking for program /sbin/hg...not found Checking for program /usr/sbin/hg...not found Checking for program /cm/local/apps/environment-modules/3.2.10/bin/hg...not found Checking for program ./hg...not found Checking for program /home2/barretk3/.local/bin/hg...not found Checking for program /home2/barretk3/bin/hg...not found Checking for program /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/lib/petsc/bin/win32fe/hg...not found child config.sourceControl 0.026530 ============================================================================================= TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:20) This is a tarball installation child PETSc.options.petscclone 0.001183 ============================================================================================= TESTING: setNativeArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:31) ============================================================================================= TESTING: configureArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:43) Checks PETSC_ARCH and sets if not set No previous hashfile found Setting hashfile: fr/lib/petsc/conf/configure-hash Deleting configure hash file: fr/lib/petsc/conf/configure-hash Unable to delete configure hash file: fr/lib/petsc/conf/configure-hash child PETSc.options.arch 0.062620 ============================================================================================= TESTING: setInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:39) setup installDir to either prefix or if that is not set to PETSC_DIR/PETSC_ARCH Defined make macro "PREFIXDIR" to "/home2/barretk3/ff-petsc/r" ============================================================================================= TESTING: saveReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:85) ============================================================================================= TESTING: cleanConfDir from PETSc.options.installDir(config/PETSc/options/installDir.py:78) ============================================================================================= TESTING: configureInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:62) Makes installDir subdirectories if it does not exist for both prefix install location and PETSc work install location Changed persistence directory to /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/lib/petsc/conf ============================================================================================= TESTING: restoreReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:98) child PETSc.options.installDir 0.007209 ============================================================================================= TESTING: setExternalPackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:15) ============================================================================================= TESTING: cleanExternalpackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:22) child PETSc.options.externalpackagesdir 0.001128 ============================================================================================= TESTING: configureCLanguage from PETSc.options.languages(config/PETSc/options/languages.py:27) Choose whether to compile the PETSc library using a C or C++ compiler C language is C Defined "CLANGUAGE_C" to "1" Defined make macro "CLANGUAGE" to "C" child PETSc.options.languages 0.001546 ============================================================================================= TESTING: resetEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1946) MAKEFLAGS (set to ) found in environment variables - ignoring since also set on command line ============================================================================================= TESTING: checkEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1976) ============================================================================================= TESTING: checkMPICompilerOverride from config.setCompilers(config/BuildSystem/config/setCompilers.py:1916) Check if --with-mpi-dir is used along with CC CXX or FC compiler options. This usually prevents mpi compilers from being used - so issue a warning ============================================================================================= TESTING: requireMpiLdPath from config.setCompilers(config/BuildSystem/config/setCompilers.py:1937) OpenMPI wrappers require LD_LIBRARY_PATH set ============================================================================================= TESTING: checkInitialFlags from config.setCompilers(config/BuildSystem/config/setCompilers.py:526) Initialize the compiler and linker flags Initialized CFLAGS to Initialized CFLAGS to Initialized LDFLAGS to Initialized CUDAFLAGS to Initialized CUDAFLAGS to Initialized LDFLAGS to Initialized HIPFLAGS to Initialized HIPFLAGS to Initialized LDFLAGS to Initialized SYCLCXXFLAGS to Initialized SYCLCXXFLAGS to Initialized LDFLAGS to Initialized CXXFLAGS to Initialized CXX_CXXFLAGS to Initialized LDFLAGS to Initialized FFLAGS to Initialized FFLAGS to Initialized LDFLAGS to Initialized CPPFLAGS to Initialized FPPFLAGS to Initialized CUDAPPFLAGS to -Wno-deprecated-gpu-targets Initialized CXXPPFLAGS to Initialized HIPPPFLAGS to -Wno-deprecated-gpu-targets Initialized SYCLPPFLAGS to -Wno-deprecated-gpu-targets Initialized CC_LINKER_FLAGS to [] Initialized CXX_LINKER_FLAGS to [] Initialized FC_LINKER_FLAGS to [] Initialized CUDAC_LINKER_FLAGS to [] Initialized HIPC_LINKER_FLAGS to [] Initialized SYCLCXX_LINKER_FLAGS to [] Initialized sharedLibraryFlags to [] Initialized dynamicLibraryFlags to [] ============================================================================================= TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:701) Locate a functional C compiler Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc...found Defined make macro "CC" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Testing executable /tmp/petsc-EaoSnO/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc --version stdout: gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Since MPI c compiler starts with mpi, force searches for other compilers to only look for MPI compilers ============================================================================================= TESTING: checkCPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:740) Locate a functional C preprocessor Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc...found Defined make macro "CPP" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : ============================================================================================= TESTING: checkCUDACompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:776) Locate a functional CUDA compiler ============================================================================================= TESTING: checkCUDAPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:816) Locate a functional CUDA preprocessor ============================================================================================= TESTING: checkHIPCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:850) Locate a functional HIP compiler Checking for program /cm/local/apps/cmake/3.9.6/bin/hipcc...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/hipcc...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/hipcc...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/hipcc...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/hipcc...not found Checking for program /usr/local/bin/hipcc...not found Checking for program /usr/bin/hipcc...not found Checking for program /usr/local/sbin/hipcc...not found Checking for program /usr/sbin/hipcc...not found Checking for program /opt/ibutils/bin/hipcc...not found Checking for program /sbin/hipcc...not found Checking for program /usr/sbin/hipcc...not found Checking for program /cm/local/apps/environment-modules/3.2.10/bin/hipcc...not found Checking for program ./hipcc...not found Checking for program /home2/barretk3/.local/bin/hipcc...not found Checking for program /home2/barretk3/bin/hipcc...not found Checking for program /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/lib/petsc/bin/win32fe/hipcc...not found Checking for program /cm/local/apps/cmake/3.9.6/bin/opt/rocm/bin/hipcc...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/opt/rocm/bin/hipcc...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/opt/rocm/bin/hipcc...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/opt/rocm/bin/hipcc...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/opt/rocm/bin/hipcc...not found Checking for program /usr/local/bin/opt/rocm/bin/hipcc...not found Checking for program /usr/bin/opt/rocm/bin/hipcc...not found Checking for program /usr/local/sbin/opt/rocm/bin/hipcc...not found Checking for program /usr/sbin/opt/rocm/bin/hipcc...not found Checking for program /opt/ibutils/bin/opt/rocm/bin/hipcc...not found Checking for program /sbin/opt/rocm/bin/hipcc...not found Checking for program /usr/sbin/opt/rocm/bin/hipcc...not found Checking for program /cm/local/apps/environment-modules/3.2.10/bin/opt/rocm/bin/hipcc...not found Checking for program ./opt/rocm/bin/hipcc...not found Checking for program /home2/barretk3/.local/bin/opt/rocm/bin/hipcc...not found Checking for program /home2/barretk3/bin/opt/rocm/bin/hipcc...not found Checking for program /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/lib/petsc/bin/win32fe/opt/rocm/bin/hipcc...not found ============================================================================================= TESTING: checkHIPPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:886) Placeholder for now ============================================================================================= TESTING: checkSYCLCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:907) Locate a functional SYCL compiler ============================================================================================= TESTING: checkSYCLPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:933) Placeholder for now ============================================================================================= TESTING: checkCxxCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1020) Locate a functional Cxx compiler Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx...found Defined make macro "CXX" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Testing executable /tmp/petsc-EaoSnO/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx --version stdout: g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ============================================================================================= TESTING: checkCxxPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:1061) Locate a functional Cxx preprocessor Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx...found Defined make macro "CXXPP" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -E -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Preprocess stderr before filtering: : Preprocess stderr after filtering: : ============================================================================================= TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1160) Locate a functional Fortran compiler Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90...found Defined make macro "FC" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Testing executable /tmp/petsc-EaoSnO/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING ============================================================================================= TESTING: checkFortranPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:1197) Locate a functional Fortran preprocessor Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90...found Defined make macro "FPP" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -E" Deleting "FPP" Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90...found Defined make macro "FPP" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --use cpp32" Deleting "FPP" ============================================================================================= TESTING: checkFortranComments from config.setCompilers(config/BuildSystem/config/setCompilers.py:1219) Make sure fortran comment "!" works ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main ! comment end Fortran comments can use ! in column 1 ============================================================================================= TESTING: checkLargeFileIO from config.setCompilers(config/BuildSystem/config/setCompilers.py:1355) ============================================================================================= TESTING: checkArchiver from config.setCompilers(config/BuildSystem/config/setCompilers.py:1454) Check that the archiver exists and can make a library usable by the compiler Executing: ar -V stdout: GNU ar version 2.25.1-32.base.el7_4.1 Copyright (C) 2014 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar version 2.25.1-32.base.el7_4.1 Copyright (C) 2014 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /cm/local/apps/cmake/3.9.6/bin/ar...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/ar...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/ar...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/ar...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /cm/local/apps/cmake/3.9.6/bin/ranlib...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/ranlib...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/ranlib...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/ranlib...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib -c" Executing: /usr/bin/ar cr /tmp/petsc-EaoSnO/config.setCompilers/libconf1.a /tmp/petsc-EaoSnO/config.setCompilers/conf1.o Executing: /usr/bin/ranlib -c /tmp/petsc-EaoSnO/config.setCompilers/libconf1.a Possible ERROR while running ranlib: stderr: /usr/bin/ranlib: invalid option -- 'c' Ranlib is not functional with your archiver. Try --with-ranlib=true if ranlib is unnecessary. Executing: ar -V stdout: GNU ar version 2.25.1-32.base.el7_4.1 Copyright (C) 2014 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar version 2.25.1-32.base.el7_4.1 Copyright (C) 2014 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /cm/local/apps/cmake/3.9.6/bin/ar...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/ar...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/ar...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/ar...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /cm/local/apps/cmake/3.9.6/bin/ranlib...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/ranlib...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/ranlib...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/ranlib...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib" Executing: /usr/bin/ar cr /tmp/petsc-EaoSnO/config.setCompilers/libconf1.a /tmp/petsc-EaoSnO/config.setCompilers/conf1.o Executing: /usr/bin/ranlib /tmp/petsc-EaoSnO/config.setCompilers/libconf1.a ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern int foo(int); int main() { int b = foo(1); if (b); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -L/tmp/petsc-EaoSnO/config.setCompilers -lconf1 Defined make macro "AR_FLAGS" to "cr" Defined make macro "AR_LIB_SUFFIX" to "a" ============================================================================================= TESTING: checkArchiverRecipeArgfile from config.setCompilers(config/BuildSystem/config/setCompilers.py:1518) Checks if AR handles @ notation Executing: /usr/bin/ar cr checkRecipeArgfile.a @checkRecipeArgfile.args Defined make macro "AR_ARGFILE" to "yes" ============================================================================================= TESTING: checkSharedLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1598) Check that the linker can produce shared libraries Executing: uname -s stdout: Linux Checking shared linker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc using flags ['-shared'] Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc...found Defined make macro "LD_SHARED" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" Trying C compiler flag Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -shared /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Valid C linker flag -shared ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /tmp/petsc-EaoSnO/config.setCompilers/conftest.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o: error adding symbols: Bad value collect2: error: ld returned 1 exit status Rejected C compiler flag because it was not compatible with shared linker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc using flags ['-shared'] Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc --help | head -n 20 stdout: Usage: gcc [options] file... Options: -pass-exit-codes Exit with highest error code from a phase --help Display this information --target-help Display target specific command line options --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...] Display specific types of command line options (Use '-v --help' to display command line options of sub-processes) --version Display compiler version information -dumpspecs Display all of the built in spec strings -dumpversion Display the version of the compiler -dumpmachine Display the compiler's target processor -print-search-dirs Display the directories in the compiler's search path -print-libgcc-file-name Display the name of the compiler's companion library -print-file-name= Display the full path to library -print-prog-name= Display the full path to compiler component -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path -print-multi-directory Display the root directory for versions of libgcc -print-multi-lib Display the mapping between command line options and Detected GNU compiler Trying C compiler flag -fPIC Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC Added C compiler flag -fPIC Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Valid C linker flag -shared ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(void); int main() { int ret = foo(); if (ret) {} ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -L/tmp/petsc-EaoSnO/config.setCompilers -lconftest Using shared linker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc with flags ['-shared'] and library extension so Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux ============================================================================================= TESTING: checkPIC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1298) Determine the PIC option for each compiler Trying Cxx for PIC code without any compiler flag Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /tmp/petsc-EaoSnO/config.setCompilers/conftest.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o: error adding symbols: Bad value collect2: error: ld returned 1 exit status Rejected Cxx compiler flag because shared linker cannot handle it Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx --help | head -n 20 stdout: Usage: g++ [options] file... Options: -pass-exit-codes Exit with highest error code from a phase --help Display this information --target-help Display target specific command line options --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...] Display specific types of command line options (Use '-v --help' to display command line options of sub-processes) --version Display compiler version information -dumpspecs Display all of the built in spec strings -dumpversion Display the version of the compiler -dumpmachine Display the compiler's target processor -print-search-dirs Display the directories in the compiler's search path -print-libgcc-file-name Display the name of the compiler's companion library -print-file-name= Display the full path to library -print-prog-name= Display the full path to compiler component -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path -print-multi-directory Display the root directory for versions of libgcc -print-multi-lib Display the mapping between command line options and Detected GNU compiler Trying Cxx compiler flag -fPIC for PIC code Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC Added Cxx compiler flag -fPIC ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Accepted Cxx compiler flag -fPIC for PIC code Trying FC for PIC code without any compiler flag Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Output from compiling with ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /tmp/petsc-EaoSnO/config.setCompilers/conftest.o: relocation R_X86_64_32 against `xx_' can not be used when making a shared object; recompile with -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o: error adding symbols: Bad value collect2: error: ld returned 1 exit status Rejected FC compiler flag because shared linker cannot handle it Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --help | head -n 20 stdout: Usage: gfortran [options] file... Options: -pass-exit-codes Exit with highest error code from a phase --help Display this information --target-help Display target specific command line options --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...] Display specific types of command line options (Use '-v --help' to display command line options of sub-processes) --version Display compiler version information -dumpspecs Display all of the built in spec strings -dumpversion Display the version of the compiler -dumpmachine Display the compiler's target processor -print-search-dirs Display the directories in the compiler's search path -print-libgcc-file-name Display the name of the compiler's companion library -print-file-name= Display the full path to library -print-prog-name= Display the full path to compiler component -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path -print-multi-directory Display the root directory for versions of libgcc -print-multi-lib Display the mapping between command line options and Detected GNU compiler Trying FC compiler flag -fPIC for PIC code Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Output from compiling with -fPIC Added FC compiler flag -fPIC ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Accepted FC compiler flag -fPIC for PIC code ============================================================================================= TESTING: checkSharedLinkerPaths from config.setCompilers(config/BuildSystem/config/setCompilers.py:1711) Determine the shared linker path options - IRIX: -rpath - Linux, OSF: -Wl,-rpath, - Solaris: -R - FreeBSD: -Wl,-R, Executing: uname -s stdout: Linux Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -V Trying C linker flag -Wl,-rpath, Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -Wl,-rpath,/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Valid C linker flag -Wl,-rpath,/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 Executing: uname -s stdout: Linux Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -V Trying Cxx linker flag -Wl,-rpath, Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -Wl,-rpath,/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Valid Cxx linker flag -Wl,-rpath,/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 Executing: uname -s stdout: Linux Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -V Trying FC linker flag -Wl,-rpath, Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -Wl,-rpath,/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Valid FC linker flag -Wl,-rpath,/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 ============================================================================================= TESTING: checkLibC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1750) Test whether we need to explicitly include libc in shared linking - Mac OSX requires an explicit reference to libc for shared linking ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {void *chunk = malloc(31); free(chunk); return 0;} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o Shared linking does not require an explicit libc reference ============================================================================================= TESTING: checkDynamicLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1796) Check that the linker can dynamicaly load shared libraries Checking for header: dlfcn.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_DLFCN_H" to "1" Checking for functions [dlopen dlsym dlclose] in library ['dl'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.libraries -fPIC /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } char dlsym(); static void _check_dlsym() { dlsym(); } char dlclose(); static void _check_dlclose() { dlclose(); } int main() { _check_dlopen(); _check_dlsym(); _check_dlclose();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC /tmp/petsc-EaoSnO/config.libraries/conftest.o -ldl Defined "HAVE_LIBDL" to "1" Adding ['dl'] to LIBS Executing: uname -s stdout: Linux Checking dynamic linker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc using flags ['-shared'] Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc...found Defined make macro "DYNAMICLINKER" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -ldl Valid C linker flag -shared ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {printf("test");return 0;} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -ldl ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { void *handle = dlopen("/tmp/petsc-EaoSnO/config.setCompilers/libconftest.so", 0); int (*foo)(void) = (int (*)(void)) dlsym(handle, "foo"); if (!foo) { printf("Could not load symbol\n"); return -1; } if ((*foo)()) { printf("Invalid return from foo()\n"); return -1; } if (dlclose(handle)) { printf("Could not close library\n"); return -1; } ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -ldl Using dynamic linker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc with flags ['-shared'] and library extension so ============================================================================================= TESTING: output from config.setCompilers(config/BuildSystem/config/setCompilers.py:1845) Output module data as defines and substitutions Substituting "CC" with "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" Substituting "CFLAGS" with " -fPIC" Defined make macro "CC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "CPP" with "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E" Substituting "CPPFLAGS" with "" Substituting "CXX" with "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx" Substituting "CXX_CXXFLAGS" with " -fPIC" Substituting "CXXFLAGS" with "" Substituting "CXX_LINKER_SLFLAG" with "-Wl,-rpath," Substituting "CXXPP" with "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -E" Substituting "CXXPPFLAGS" with "" Substituting "FC" with "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90" Substituting "FFLAGS" with " -fPIC" Defined make macro "FC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "LDFLAGS" with "" Substituting "LIBS" with "-ldl " Substituting "SHARED_LIBRARY_FLAG" with "-shared" child config.setCompilers 8.417705 ============================================================================================= TESTING: configureIndexSize from PETSc.options.indexTypes(config/PETSc/options/indexTypes.py:39) Defined make macro "PETSC_INDEX_SIZE" to "32" child PETSc.options.indexTypes 0.001401 ============================================================================================= TESTING: configureCompilerFlags from config.compilerFlags(config/BuildSystem/config/compilerFlags.py:82) Get the default compiler flags Defined make macro "C_VERSION" to "gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)" Defined make macro "MPICC_SHOW" to "gcc -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl" Trying C compiler flag -Wall Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall Added C compiler flag -Wall Trying C compiler flag -Wwrite-strings Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings Added C compiler flag -Wwrite-strings Trying C compiler flag -Wno-strict-aliasing Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing Added C compiler flag -Wno-strict-aliasing Trying C compiler flag -Wno-unknown-pragmas Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas Added C compiler flag -Wno-unknown-pragmas Trying C compiler flag -fstack-protector Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector Added C compiler flag -fstack-protector Trying C compiler flag -mfp16-format=ieee Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -mfp16-format=ieee /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: gcc: error: unrecognized command line option ‘-mfp16-format=ieee’ Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -mfp16-format=ieee gcc: error: unrecognized command line option ‘-mfp16-format=ieee’ PETSc Error: No output file produced Rejecting compiler flag -mfp16-format=ieee due to nonzero status from link Rejecting compiler flag -mfp16-format=ieee due to gcc: error: unrecognized command line option ‘-mfp16-format=ieee’ PETSc Error: No output file produced Rejected C compiler flag -mfp16-format=ieee Trying C compiler flag -fvisibility=hidden Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden Added C compiler flag -fvisibility=hidden Trying C compiler flag -O3 -mtune=native Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native Added C compiler flag -O3 -mtune=native Defined make macro "Cxx_VERSION" to "g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)" Defined make macro "MPICXX_SHOW" to "g++ -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpicxx -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl" Trying Cxx compiler flag -Wall Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -Wall Added Cxx compiler flag -Wall Trying Cxx compiler flag -Wwrite-strings Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -Wwrite-strings -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -Wall -Wwrite-strings Added Cxx compiler flag -Wwrite-strings Trying Cxx compiler flag -Wno-strict-aliasing Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing Added Cxx compiler flag -Wno-strict-aliasing Trying Cxx compiler flag -Wno-unknown-pragmas Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas Added Cxx compiler flag -Wno-unknown-pragmas Trying Cxx compiler flag -fstack-protector Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector Added Cxx compiler flag -fstack-protector Trying Cxx compiler flag -fvisibility=hidden Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden Added Cxx compiler flag -fvisibility=hidden Trying Cxx compiler flag -O3 -mtune=native Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native Added Cxx compiler flag -O3 -mtune=native Defined make macro "FC_VERSION" to "GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)" Defined make macro "MPIFC_SHOW" to "gfortran -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl" Trying FC compiler flag -Wall Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Output from compiling with -fPIC -Wall Added FC compiler flag -Wall Trying FC compiler flag -ffree-line-length-0 Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -ffree-line-length-0 /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Output from compiling with -fPIC -Wall -ffree-line-length-0 Added FC compiler flag -ffree-line-length-0 Trying FC compiler flag -Wno-unused-dummy-argument Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Output from compiling with -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument Added FC compiler flag -Wno-unused-dummy-argument Trying FC compiler flag -O3 -mtune=native Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Output from compiling with -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native Added FC compiler flag -O3 -mtune=native ============================================================================================= TESTING: checkIntelHardwareSupport from config.compilerFlags(config/BuildSystem/config/compilerFlags.py:175) Use Linux/MacOS commands to determine what operations the hardware supports Executing: lscpu stdout: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 36 On-line CPU(s) list: 0-35 Thread(s) per core: 1 Core(s) per socket: 18 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 79 Model name: Intel(R) Xeon(R) CPU E5-2697 v4 @ 2.30GHz Stepping: 1 CPU MHz: 1200.042 CPU max MHz: 3600.0000 CPU min MHz: 1200.0000 BogoMIPS: 4589.30 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 46080K NUMA node0 CPU(s): 0-17 NUMA node1 CPU(s): 18-35 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts ============================================================================================= TESTING: checkCompilerMacros from config.compilerFlags(config/BuildSystem/config/compilerFlags.py:166) Save the list of CPP macros defined by the C and C++ compiler, does not work for all compilers Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilerFlags -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilerFlags/conftest.c -E -dM stdout: #define __DBL_MIN_EXP__ (-1021) #define __UINT_LEAST16_MAX__ 65535 #define __ATOMIC_ACQUIRE 2 #define __FLT_MIN__ 1.17549435082228750797e-38F #define __UINT_LEAST8_TYPE__ unsigned char #define __INTMAX_C(c) c ## L #define __CHAR_BIT__ 8 #define __UINT8_MAX__ 255 #define __WINT_MAX__ 4294967295U #define __ORDER_LITTLE_ENDIAN__ 1234 #define __SIZE_MAX__ 18446744073709551615UL #define __WCHAR_MAX__ 2147483647 #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_1 1 #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_2 1 #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_4 1 #define __DBL_DENORM_MIN__ ((double)4.94065645841246544177e-324L) #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_8 1 #define __GCC_ATOMIC_CHAR_LOCK_FREE 2 #define __FLT_EVAL_METHOD__ 0 #define __unix__ 1 #define __GCC_ATOMIC_CHAR32_T_LOCK_FREE 2 #define __x86_64 1 #define __UINT_FAST64_MAX__ 18446744073709551615UL #define __SIG_ATOMIC_TYPE__ int #define __DBL_MIN_10_EXP__ (-307) #define __FINITE_MATH_ONLY__ 0 #define __GNUC_PATCHLEVEL__ 5 #define __UINT_FAST8_MAX__ 255 #define __DEC64_MAX_EXP__ 385 #define __INT8_C(c) c #define __UINT_LEAST64_MAX__ 18446744073709551615UL #define __SHRT_MAX__ 32767 #define __LDBL_MAX__ 1.18973149535723176502e+4932L #define __UINT_LEAST8_MAX__ 255 #define __GCC_ATOMIC_BOOL_LOCK_FREE 2 #define __UINTMAX_TYPE__ long unsigned int #define __linux 1 #define __DEC32_EPSILON__ 1E-6DF #define __OPTIMIZE__ 1 #define __unix 1 #define __UINT32_MAX__ 4294967295U #define __LDBL_MAX_EXP__ 16384 #define __WINT_MIN__ 0U #define __linux__ 1 #define __SCHAR_MAX__ 127 #define __WCHAR_MIN__ (-__WCHAR_MAX__ - 1) #define __INT64_C(c) c ## L #define __DBL_DIG__ 15 #define __GCC_ATOMIC_POINTER_LOCK_FREE 2 #define __SIZEOF_INT__ 4 #define __SIZEOF_POINTER__ 8 #define __USER_LABEL_PREFIX__ #define __STDC_HOSTED__ 1 #define __LDBL_HAS_INFINITY__ 1 #define __FLT_EPSILON__ 1.19209289550781250000e-7F #define __LDBL_MIN__ 3.36210314311209350626e-4932L #define __DEC32_MAX__ 9.999999E96DF #define __INT32_MAX__ 2147483647 #define __SIZEOF_LONG__ 8 #define __STDC_IEC_559__ 1 #define __STDC_ISO_10646__ 201103L #define __UINT16_C(c) c #define __DECIMAL_DIG__ 21 #define __gnu_linux__ 1 #define __LDBL_HAS_QUIET_NAN__ 1 #define __GNUC__ 4 #define __MMX__ 1 #define __FLT_HAS_DENORM__ 1 #define __SIZEOF_LONG_DOUBLE__ 16 #define __BIGGEST_ALIGNMENT__ 16 #define __DBL_MAX__ ((double)1.79769313486231570815e+308L) #define __INT_FAST32_MAX__ 9223372036854775807L #define __DBL_HAS_INFINITY__ 1 #define __DEC32_MIN_EXP__ (-94) #define __INT_FAST16_TYPE__ long int #define __LDBL_HAS_DENORM__ 1 #define __DEC128_MAX__ 9.999999999999999999999999999999999E6144DL #define __INT_LEAST32_MAX__ 2147483647 #define __DEC32_MIN__ 1E-95DF #define __DBL_MAX_EXP__ 1024 #define __DEC128_EPSILON__ 1E-33DL #define __SSE2_MATH__ 1 #define __ATOMIC_HLE_RELEASE 131072 #define __PTRDIFF_MAX__ 9223372036854775807L #define __amd64 1 #define __STDC_NO_THREADS__ 1 #define __ATOMIC_HLE_ACQUIRE 65536 #define __LONG_LONG_MAX__ 9223372036854775807LL #define __SIZEOF_SIZE_T__ 8 #define __SIZEOF_WINT_T__ 4 #define __GCC_HAVE_DWARF2_CFI_ASM 1 #define __GXX_ABI_VERSION 1002 #define __FLT_MIN_EXP__ (-125) #define __INT_FAST64_TYPE__ long int #define __DBL_MIN__ ((double)2.22507385850720138309e-308L) #define __LP64__ 1 #define __DECIMAL_BID_FORMAT__ 1 #define __DEC128_MIN__ 1E-6143DL #define __REGISTER_PREFIX__ #define __UINT16_MAX__ 65535 #define __DBL_HAS_DENORM__ 1 #define __UINT8_TYPE__ unsigned char #define __FLT_MANT_DIG__ 24 #define __VERSION__ "4.8.5 20150623 (Red Hat 4.8.5-16)" #define __UINT64_C(c) c ## UL #define _STDC_PREDEF_H 1 #define __GCC_ATOMIC_INT_LOCK_FREE 2 #define __FLOAT_WORD_ORDER__ __ORDER_LITTLE_ENDIAN__ #define __STDC_IEC_559_COMPLEX__ 1 #define __INT32_C(c) c #define __DEC64_EPSILON__ 1E-15DD #define __ORDER_PDP_ENDIAN__ 3412 #define __DEC128_MIN_EXP__ (-6142) #define __INT_FAST32_TYPE__ long int #define __UINT_LEAST16_TYPE__ short unsigned int #define unix 1 #define __INT16_MAX__ 32767 #define __SIZE_TYPE__ long unsigned int #define __UINT64_MAX__ 18446744073709551615UL #define __INT8_TYPE__ signed char #define __ELF__ 1 #define __FLT_RADIX__ 2 #define __INT_LEAST16_TYPE__ short int #define __LDBL_EPSILON__ 1.08420217248550443401e-19L #define __UINTMAX_C(c) c ## UL #define __GNUC_RH_RELEASE__ 16 #define __SSE_MATH__ 1 #define __k8 1 #define __SIG_ATOMIC_MAX__ 2147483647 #define __GCC_ATOMIC_WCHAR_T_LOCK_FREE 2 #define __SIZEOF_PTRDIFF_T__ 8 #define __x86_64__ 1 #define __DEC32_SUBNORMAL_MIN__ 0.000001E-95DF #define __INT_FAST16_MAX__ 9223372036854775807L #define __UINT_FAST32_MAX__ 18446744073709551615UL #define __UINT_LEAST64_TYPE__ long unsigned int #define __FLT_HAS_QUIET_NAN__ 1 #define __FLT_MAX_10_EXP__ 38 #define __LONG_MAX__ 9223372036854775807L #define __DEC128_SUBNORMAL_MIN__ 0.000000000000000000000000000000001E-6143DL #define __FLT_HAS_INFINITY__ 1 #define __UINT_FAST16_TYPE__ long unsigned int #define __DEC64_MAX__ 9.999999999999999E384DD #define __CHAR16_TYPE__ short unsigned int #define __PRAGMA_REDEFINE_EXTNAME 1 #define __INT_LEAST16_MAX__ 32767 #define __DEC64_MANT_DIG__ 16 #define __INT64_MAX__ 9223372036854775807L #define __UINT_LEAST32_MAX__ 4294967295U #define __GCC_ATOMIC_LONG_LOCK_FREE 2 #define __INT_LEAST64_TYPE__ long int #define __INT16_TYPE__ short int #define __INT_LEAST8_TYPE__ signed char #define __DEC32_MAX_EXP__ 97 #define __INT_FAST8_MAX__ 127 #define __INTPTR_MAX__ 9223372036854775807L #define linux 1 #define __SSE2__ 1 #define __LDBL_MANT_DIG__ 64 #define __DBL_HAS_QUIET_NAN__ 1 #define __SIG_ATOMIC_MIN__ (-__SIG_ATOMIC_MAX__ - 1) #define __code_model_small__ 1 #define __k8__ 1 #define __INTPTR_TYPE__ long int #define __UINT16_TYPE__ short unsigned int #define __WCHAR_TYPE__ int #define __SIZEOF_FLOAT__ 4 #define __pic__ 2 #define __UINTPTR_MAX__ 18446744073709551615UL #define __DEC64_MIN_EXP__ (-382) #define __INT_FAST64_MAX__ 9223372036854775807L #define __GCC_ATOMIC_TEST_AND_SET_TRUEVAL 1 #define __FLT_DIG__ 6 #define __UINT_FAST64_TYPE__ long unsigned int #define __INT_MAX__ 2147483647 #define __amd64__ 1 #define __INT64_TYPE__ long int #define __FLT_MAX_EXP__ 128 #define __ORDER_BIG_ENDIAN__ 4321 #define __DBL_MANT_DIG__ 53 #define __INT_LEAST64_MAX__ 9223372036854775807L #define __GCC_ATOMIC_CHAR16_T_LOCK_FREE 2 #define __DEC64_MIN__ 1E-383DD #define __WINT_TYPE__ unsigned int #define __UINT_LEAST32_TYPE__ unsigned int #define __SIZEOF_SHORT__ 2 #define __SSE__ 1 #define __LDBL_MIN_EXP__ (-16381) #define __INT_LEAST8_MAX__ 127 #define __SSP__ 1 #define __SIZEOF_INT128__ 16 #define __LDBL_MAX_10_EXP__ 4932 #define __ATOMIC_RELAXED 0 #define __DBL_EPSILON__ ((double)2.22044604925031308085e-16L) #define _LP64 1 #define __UINT8_C(c) c #define __INT_LEAST32_TYPE__ int #define __SIZEOF_WCHAR_T__ 4 #define __UINT64_TYPE__ long unsigned int #define __INT_FAST8_TYPE__ signed char #define __DBL_DECIMAL_DIG__ 17 #define __FXSR__ 1 #define __DEC_EVAL_METHOD__ 2 #define __UINT32_C(c) c ## U #define __INTMAX_MAX__ 9223372036854775807L #define __BYTE_ORDER__ __ORDER_LITTLE_ENDIAN__ #define __FLT_DENORM_MIN__ 1.40129846432481707092e-45F #define __INT8_MAX__ 127 #define __PIC__ 2 #define __UINT_FAST32_TYPE__ long unsigned int #define __CHAR32_TYPE__ unsigned int #define __FLT_MAX__ 3.40282346638528859812e+38F #define __INT32_TYPE__ int #define __SIZEOF_DOUBLE__ 8 #define __FLT_MIN_10_EXP__ (-37) #define __INTMAX_TYPE__ long int #define __DEC128_MAX_EXP__ 6145 #define __ATOMIC_CONSUME 1 #define __GNUC_MINOR__ 8 #define __UINTMAX_MAX__ 18446744073709551615UL #define __DEC32_MANT_DIG__ 7 #define __DBL_MAX_10_EXP__ 308 #define __LDBL_DENORM_MIN__ 3.64519953188247460253e-4951L #define __INT16_C(c) c #define __STDC__ 1 #define __PTRDIFF_TYPE__ long int #define __ATOMIC_SEQ_CST 5 #define __UINT32_TYPE__ unsigned int #define __UINTPTR_TYPE__ long unsigned int #define __DEC64_SUBNORMAL_MIN__ 0.000000000000001E-383DD #define __DEC128_MANT_DIG__ 34 #define __LDBL_MIN_10_EXP__ (-4931) #define __SIZEOF_LONG_LONG__ 8 #define __GCC_ATOMIC_LLONG_LOCK_FREE 2 #define __LDBL_DIG__ 18 #define __FLT_DECIMAL_DIG__ 9 #define __UINT_FAST16_MAX__ 18446744073709551615UL #define __GNUC_GNU_INLINE__ 1 #define __GCC_ATOMIC_SHORT_LOCK_FREE 2 #define __UINT_FAST8_TYPE__ unsigned char #define __ATOMIC_ACQ_REL 4 #define __ATOMIC_RELEASE 3 Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilerFlags -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -fPIC /tmp/petsc-EaoSnO/config.compilerFlags/conftest.cc -E -dM stdout: #define __DBL_MIN_EXP__ (-1021) #define __UINT_LEAST16_MAX__ 65535 #define __ATOMIC_ACQUIRE 2 #define __FLT_MIN__ 1.17549435082228750797e-38F #define __UINT_LEAST8_TYPE__ unsigned char #define __INTMAX_C(c) c ## L #define __CHAR_BIT__ 8 #define __UINT8_MAX__ 255 #define __WINT_MAX__ 4294967295U #define __ORDER_LITTLE_ENDIAN__ 1234 #define __SIZE_MAX__ 18446744073709551615UL #define __WCHAR_MAX__ 2147483647 #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_1 1 #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_2 1 #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_4 1 #define __DBL_DENORM_MIN__ double(4.94065645841246544177e-324L) #define __GCC_HAVE_SYNC_COMPARE_AND_SWAP_8 1 #define __GCC_ATOMIC_CHAR_LOCK_FREE 2 #define __FLT_EVAL_METHOD__ 0 #define __unix__ 1 #define __GCC_ATOMIC_CHAR32_T_LOCK_FREE 2 #define __x86_64 1 #define __UINT_FAST64_MAX__ 18446744073709551615UL #define __SIG_ATOMIC_TYPE__ int #define __DBL_MIN_10_EXP__ (-307) #define __FINITE_MATH_ONLY__ 0 #define __GNUC_PATCHLEVEL__ 5 #define __UINT_FAST8_MAX__ 255 #define __DEC64_MAX_EXP__ 385 #define __INT8_C(c) c #define __UINT_LEAST64_MAX__ 18446744073709551615UL #define __SHRT_MAX__ 32767 #define __LDBL_MAX__ 1.18973149535723176502e+4932L #define __UINT_LEAST8_MAX__ 255 #define __GCC_ATOMIC_BOOL_LOCK_FREE 2 #define __UINTMAX_TYPE__ long unsigned int #define __linux 1 #define __DEC32_EPSILON__ 1E-6DF #define __OPTIMIZE__ 1 #define __unix 1 #define __UINT32_MAX__ 4294967295U #define __LDBL_MAX_EXP__ 16384 #define __WINT_MIN__ 0U #define __linux__ 1 #define __SCHAR_MAX__ 127 #define __WCHAR_MIN__ (-__WCHAR_MAX__ - 1) #define __INT64_C(c) c ## L #define __DBL_DIG__ 15 #define __GCC_ATOMIC_POINTER_LOCK_FREE 2 #define __SIZEOF_INT__ 4 #define __SIZEOF_POINTER__ 8 #define __GCC_ATOMIC_CHAR16_T_LOCK_FREE 2 #define __USER_LABEL_PREFIX__ #define __STDC_HOSTED__ 1 #define __LDBL_HAS_INFINITY__ 1 #define __FLT_EPSILON__ 1.19209289550781250000e-7F #define __GXX_WEAK__ 1 #define __LDBL_MIN__ 3.36210314311209350626e-4932L #define __DEC32_MAX__ 9.999999E96DF #define __INT32_MAX__ 2147483647 #define __SIZEOF_LONG__ 8 #define __STDC_IEC_559__ 1 #define __STDC_ISO_10646__ 201103L #define __UINT16_C(c) c #define __DECIMAL_DIG__ 21 #define __gnu_linux__ 1 #define __LDBL_HAS_QUIET_NAN__ 1 #define __GNUC__ 4 #define __GXX_RTTI 1 #define __MMX__ 1 #define __FLT_HAS_DENORM__ 1 #define __SIZEOF_LONG_DOUBLE__ 16 #define __BIGGEST_ALIGNMENT__ 16 #define __DBL_MAX__ double(1.79769313486231570815e+308L) #define __INT_FAST32_MAX__ 9223372036854775807L #define __DBL_HAS_INFINITY__ 1 #define __INT64_MAX__ 9223372036854775807L #define __DEC32_MIN_EXP__ (-94) #define __INT_FAST16_TYPE__ long int #define __LDBL_HAS_DENORM__ 1 #define __cplusplus 199711L #define __DEC128_MAX__ 9.999999999999999999999999999999999E6144DL #define __INT_LEAST32_MAX__ 2147483647 #define __DEC32_MIN__ 1E-95DF #define __DEPRECATED 1 #define __DBL_MAX_EXP__ 1024 #define __DEC128_EPSILON__ 1E-33DL #define __SSE2_MATH__ 1 #define __ATOMIC_HLE_RELEASE 131072 #define __PTRDIFF_MAX__ 9223372036854775807L #define __amd64 1 #define __STDC_NO_THREADS__ 1 #define __ATOMIC_HLE_ACQUIRE 65536 #define __GNUG__ 4 #define __LONG_LONG_MAX__ 9223372036854775807LL #define __SIZEOF_SIZE_T__ 8 #define __SIZEOF_WINT_T__ 4 #define __GCC_HAVE_DWARF2_CFI_ASM 1 #define __GXX_ABI_VERSION 1002 #define __FLT_MIN_EXP__ (-125) #define __INT_FAST64_TYPE__ long int #define __DBL_MIN__ double(2.22507385850720138309e-308L) #define __LP64__ 1 #define __DECIMAL_BID_FORMAT__ 1 #define __DEC128_MIN__ 1E-6143DL #define __REGISTER_PREFIX__ #define __UINT16_MAX__ 65535 #define __DBL_HAS_DENORM__ 1 #define __UINT8_TYPE__ unsigned char #define __FLT_MANT_DIG__ 24 #define __VERSION__ "4.8.5 20150623 (Red Hat 4.8.5-16)" #define __UINT64_C(c) c ## UL #define _STDC_PREDEF_H 1 #define __GCC_ATOMIC_INT_LOCK_FREE 2 #define __FLOAT_WORD_ORDER__ __ORDER_LITTLE_ENDIAN__ #define __STDC_IEC_559_COMPLEX__ 1 #define __INT32_C(c) c #define __DEC64_EPSILON__ 1E-15DD #define __ORDER_PDP_ENDIAN__ 3412 #define __DEC128_MIN_EXP__ (-6142) #define __INT_FAST32_TYPE__ long int #define __UINT_LEAST16_TYPE__ short unsigned int #define unix 1 #define __INT16_MAX__ 32767 #define __SIZE_TYPE__ long unsigned int #define __UINT64_MAX__ 18446744073709551615UL #define __INT8_TYPE__ signed char #define __ELF__ 1 #define __FLT_RADIX__ 2 #define __INT_LEAST16_TYPE__ short int #define __LDBL_EPSILON__ 1.08420217248550443401e-19L #define __UINTMAX_C(c) c ## UL #define __GNUC_RH_RELEASE__ 16 #define __k8 1 #define __SIG_ATOMIC_MAX__ 2147483647 #define __GCC_ATOMIC_WCHAR_T_LOCK_FREE 2 #define __SIZEOF_PTRDIFF_T__ 8 #define __x86_64__ 1 #define __DEC32_SUBNORMAL_MIN__ 0.000001E-95DF #define __INT_FAST16_MAX__ 9223372036854775807L #define __UINT_FAST32_MAX__ 18446744073709551615UL #define __UINT_LEAST64_TYPE__ long unsigned int #define __FLT_HAS_QUIET_NAN__ 1 #define __FLT_MAX_10_EXP__ 38 #define __LONG_MAX__ 9223372036854775807L #define __DEC128_SUBNORMAL_MIN__ 0.000000000000000000000000000000001E-6143DL #define __FLT_HAS_INFINITY__ 1 #define __UINT_FAST16_TYPE__ long unsigned int #define __DEC64_MAX__ 9.999999999999999E384DD #define __CHAR16_TYPE__ short unsigned int #define __PRAGMA_REDEFINE_EXTNAME 1 #define __INT_LEAST16_MAX__ 32767 #define __DEC64_MANT_DIG__ 16 #define __UINT_LEAST32_MAX__ 4294967295U #define __GCC_ATOMIC_LONG_LOCK_FREE 2 #define __INT_LEAST64_TYPE__ long int #define __INT16_TYPE__ short int #define __INT_LEAST8_TYPE__ signed char #define __DEC32_MAX_EXP__ 97 #define __INT_FAST8_MAX__ 127 #define __INTPTR_MAX__ 9223372036854775807L #define linux 1 #define __SSE2__ 1 #define __EXCEPTIONS 1 #define __LDBL_MANT_DIG__ 64 #define __DBL_HAS_QUIET_NAN__ 1 #define __SIG_ATOMIC_MIN__ (-__SIG_ATOMIC_MAX__ - 1) #define __code_model_small__ 1 #define __k8__ 1 #define __INTPTR_TYPE__ long int #define __UINT16_TYPE__ short unsigned int #define __WCHAR_TYPE__ int #define __SIZEOF_FLOAT__ 4 #define __pic__ 2 #define __UINTPTR_MAX__ 18446744073709551615UL #define __DEC64_MIN_EXP__ (-382) #define __INT_FAST64_MAX__ 9223372036854775807L #define __GCC_ATOMIC_TEST_AND_SET_TRUEVAL 1 #define __FLT_DIG__ 6 #define __UINT_FAST64_TYPE__ long unsigned int #define __INT_MAX__ 2147483647 #define __amd64__ 1 #define __INT64_TYPE__ long int #define __FLT_MAX_EXP__ 128 #define __ORDER_BIG_ENDIAN__ 4321 #define __DBL_MANT_DIG__ 53 #define __INT_LEAST64_MAX__ 9223372036854775807L #define __DEC64_MIN__ 1E-383DD #define __WINT_TYPE__ unsigned int #define __UINT_LEAST32_TYPE__ unsigned int #define __SIZEOF_SHORT__ 2 #define __SSE__ 1 #define __LDBL_MIN_EXP__ (-16381) #define __INT_LEAST8_MAX__ 127 #define __SSP__ 1 #define __SIZEOF_INT128__ 16 #define __LDBL_MAX_10_EXP__ 4932 #define __ATOMIC_RELAXED 0 #define __DBL_EPSILON__ double(2.22044604925031308085e-16L) #define _LP64 1 #define __UINT8_C(c) c #define __INT_LEAST32_TYPE__ int #define __SIZEOF_WCHAR_T__ 4 #define __UINT64_TYPE__ long unsigned int #define __INT_FAST8_TYPE__ signed char #define __DBL_DECIMAL_DIG__ 17 #define __FXSR__ 1 #define __DEC_EVAL_METHOD__ 2 #define __UINT32_C(c) c ## U #define __INTMAX_MAX__ 9223372036854775807L #define __BYTE_ORDER__ __ORDER_LITTLE_ENDIAN__ #define __FLT_DENORM_MIN__ 1.40129846432481707092e-45F #define __INT8_MAX__ 127 #define __PIC__ 2 #define __UINT_FAST32_TYPE__ long unsigned int #define __CHAR32_TYPE__ unsigned int #define __FLT_MAX__ 3.40282346638528859812e+38F #define __INT32_TYPE__ int #define __SIZEOF_DOUBLE__ 8 #define __INTMAX_TYPE__ long int #define __DEC128_MAX_EXP__ 6145 #define __ATOMIC_CONSUME 1 #define __GNUC_MINOR__ 8 #define __UINTMAX_MAX__ 18446744073709551615UL #define __DEC32_MANT_DIG__ 7 #define __DBL_MAX_10_EXP__ 308 #define __LDBL_DENORM_MIN__ 3.64519953188247460253e-4951L #define __INT16_C(c) c #define __STDC__ 1 #define __PTRDIFF_TYPE__ long int #define __ATOMIC_SEQ_CST 5 #define __UINT32_TYPE__ unsigned int #define __UINTPTR_TYPE__ long unsigned int #define __DEC64_SUBNORMAL_MIN__ 0.000000000000001E-383DD #define __DEC128_MANT_DIG__ 34 #define __LDBL_MIN_10_EXP__ (-4931) #define __SSE_MATH__ 1 #define __SIZEOF_LONG_LONG__ 8 #define __GCC_ATOMIC_LLONG_LOCK_FREE 2 #define __LDBL_DIG__ 18 #define __FLT_DECIMAL_DIG__ 9 #define __UINT_FAST16_MAX__ 18446744073709551615UL #define __GNUC_GNU_INLINE__ 1 #define __FLT_MIN_10_EXP__ (-37) #define __GCC_ATOMIC_SHORT_LOCK_FREE 2 #define __UINT_FAST8_TYPE__ unsigned char #define _GNU_SOURCE 1 #define __ATOMIC_ACQ_REL 4 #define __ATOMIC_RELEASE 3 child config.compilerFlags 1.821919 Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc --help | head -n 20 stdout: Usage: gcc [options] file... Options: -pass-exit-codes Exit with highest error code from a phase --help Display this information --target-help Display target specific command line options --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...] Display specific types of command line options (Use '-v --help' to display command line options of sub-processes) --version Display compiler version information -dumpspecs Display all of the built in spec strings -dumpversion Display the version of the compiler -dumpmachine Display the compiler's target processor -print-search-dirs Display the directories in the compiler's search path -print-libgcc-file-name Display the name of the compiler's companion library -print-file-name= Display the full path to library -print-prog-name= Display the full path to compiler component -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path -print-multi-directory Display the root directory for versions of libgcc -print-multi-lib Display the mapping between command line options and Detected GNU compiler ============================================================================================= TESTING: checkC99Flag from config.compilers(config/BuildSystem/config/compilers.py:1429) Check for -std=c99 or equivalent flag Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.setCompilers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:11:5: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i=0; i<2; i++){ ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:11:5: note: use option -std=c99 or -std=gnu99 to compile your code /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:7:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] float x[2],y; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { float x[2],y; y = FLT_ROUNDS; // c++ comment int j = 2; for (int i=0; i<2; i++){ x[i] = i*j*y; } ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:11:5: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i=0; i<2; i++){ ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:11:5: note: use option -std=c99 or -std=gnu99 to compile your code /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:7:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] float x[2],y; ^ PETSc Error: No output file produced Rejecting compiler flag due to nonzero status from link Rejecting compiler flag due to /tmp/petsc-EaoSnO/config.setCompilers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:11:5: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i=0; i<2; i++){ ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:11:5: note: use option -std=c99 or -std=gnu99 to compile your code /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:7:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] float x[2],y; ^ PETSc Error: No output file produced Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.setCompilers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:7:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] float x[2],y; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { float x[2],y; y = FLT_ROUNDS; // c++ comment int j = 2; for (int i=0; i<2; i++){ x[i] = i*j*y; } ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.c:7:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] float x[2],y; ^ Accepted C99 compile flag: -std=c99 ============================================================================================= TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:158) Check for the C/CXX restrict keyword Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -V ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.compilers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.compilers/conftest.c:5:20: warning: unused variable ‘x’ [-Wunused-variable] float * __restrict x;; ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set C restrict keyword to __restrict Defined "C_RESTRICT" to "__restrict" ============================================================================================= TESTING: checkCFormatting from config.compilers(config/BuildSystem/config/compilers.py:413) Activate format string checking if using the GNU compilers ============================================================================================= TESTING: checkCInline from config.compilers(config/BuildSystem/config/compilers.py:128) Check for C inline keyword ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set C Inline keyword to inline Defined "C_INLINE" to "inline" ============================================================================================= TESTING: checkDynamicLoadFlag from config.compilers(config/BuildSystem/config/compilers.py:424) Checks that dlopen() takes RTLD_XXX, and defines PETSC_HAVE_RTLD_XXX if it does ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include char *libname; int main() { dlopen(libname, RTLD_LAZY);dlopen(libname, RTLD_NOW);dlopen(libname, RTLD_LOCAL);dlopen(libname, RTLD_GLOBAL); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o -ldl Defined "HAVE_RTLD_LAZY" to "1" Defined "HAVE_RTLD_NOW" to "1" Defined "HAVE_RTLD_LOCAL" to "1" Defined "HAVE_RTLD_GLOBAL" to "1" ============================================================================================= TESTING: checkCLibraries from config.compilers(config/BuildSystem/config/compilers.py:222) Determines the libraries needed to link with C compiled code ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -ldl C libraries are not needed when using Fortran linker ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -fPIC /tmp/petsc-EaoSnO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.compilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -ldl C libraries are not needed when using C++ linker ============================================================================================= TESTING: checkDependencyGenerationFlag from config.compilers(config/BuildSystem/config/compilers.py:1380) Check if -MMD works for dependency generation, and add it if it does Trying C compiler flag -MMD -MP Defined make macro "C_DEPFLAGS" to "-MMD -MP" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -MMD -MP -std=c99 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -MMD -MP Trying Cxx compiler flag -MMD -MP Defined make macro "CXX_DEPFLAGS" to "-MMD -MP" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -fPIC -MMD -MP /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Output from compiling with -fPIC -MMD -MP Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx --help | head -n 20 stdout: Usage: g++ [options] file... Options: -pass-exit-codes Exit with highest error code from a phase --help Display this information --target-help Display target specific command line options --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...] Display specific types of command line options (Use '-v --help' to display command line options of sub-processes) --version Display compiler version information -dumpspecs Display all of the built in spec strings -dumpversion Display the version of the compiler -dumpmachine Display the compiler's target processor -print-search-dirs Display the directories in the compiler's search path -print-libgcc-file-name Display the name of the compiler's companion library -print-file-name= Display the full path to library -print-prog-name= Display the full path to compiler component -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path -print-multi-directory Display the root directory for versions of libgcc -print-multi-lib Display the mapping between command line options and Detected GNU compiler ============================================================================================= TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:158) Check for the C/CXX restrict keyword Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -V ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -fPIC /tmp/petsc-EaoSnO/config.compilers/conftest.cc Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.compilers/conftest.cc: In function ‘int main()’: /tmp/petsc-EaoSnO/config.compilers/conftest.cc:5:20: warning: unused variable ‘x’ [-Wunused-variable] float * __restrict x;; ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set Cxx restrict keyword to __restrict Defined "CXX_RESTRICT" to "__restrict" ============================================================================================= TESTING: checkCxxDialect from config.compilers(config/BuildSystem/config/compilers.py:471) Determine the CXX dialect supported by the compiler(language) [and correspoding compiler option - if any]. isGNU indicates if the compiler is g++. -with--dialect can take options: auto: use highest dialect configure can determine cxx17: [future?] cxx14: gnu++14 or c++14 cxx11: gnu++11 or c++11 0: disable CxxDialect check and use compiler default checkCxxDialect: checking CXX11 for Cxx with flag: Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Possible ERROR while running compiler: exit code 1 stderr: In file included from /usr/include/c++/4.8.2/random:35:0, from /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:4: /usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support for the \ ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:11: warning: identifier ‘constexpr’ is a keyword in C++11 [-Wc++0x-compat] template constexpr T Cubed( T x ) { return x*x*x; } ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:32: error: ‘constexpr’ does not name a type template constexpr T Cubed( T x ) { return x*x*x; } ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:32: note: C++11 ‘constexpr’ only available with -std=c++11 or -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc: In function ‘int main()’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:12:11: error: ‘random_device’ is not a member of ‘std’ std::random_device rd; ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:12:30: error: expected ‘;’ before ‘rd’ std::random_device rd; ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:13:11: error: ‘mt19937’ is not a member of ‘std’ std::mt19937 mt(rd()); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:13:24: error: expected ‘;’ before ‘mt’ std::mt19937 mt(rd()); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:11: error: ‘normal_distribution’ is not a member of ‘std’ std::normal_distribution dist(0,1); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:36: error: expected primary-expression before ‘double’ std::normal_distribution dist(0,1); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:36: error: expected ‘;’ before ‘double’ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:15:33: error: ‘mt’ was not declared in this scope const double x = dist(mt); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:15:35: error: ‘dist’ was not declared in this scope const double x = dist(mt); ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include template constexpr T Cubed( T x ) { return x*x*x; } int main() { std::random_device rd; std::mt19937 mt(rd()); std::normal_distribution dist(0,1); const double x = dist(mt); std::cout << x; ; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native In file included from /usr/include/c++/4.8.2/random:35:0, from /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:4: /usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support for the \ ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:11: warning: identifier ‘constexpr’ is a keyword in C++11 [-Wc++0x-compat] template constexpr T Cubed( T x ) { return x*x*x; } ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:32: error: ‘constexpr’ does not name a type template constexpr T Cubed( T x ) { return x*x*x; } ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:32: note: C++11 ‘constexpr’ only available with -std=c++11 or -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc: In function ‘int main()’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:12:11: error: ‘random_device’ is not a member of ‘std’ std::random_device rd; ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:12:30: error: expected ‘;’ before ‘rd’ std::random_device rd; ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:13:11: error: ‘mt19937’ is not a member of ‘std’ std::mt19937 mt(rd()); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:13:24: error: expected ‘;’ before ‘mt’ std::mt19937 mt(rd()); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:11: error: ‘normal_distribution’ is not a member of ‘std’ std::normal_distribution dist(0,1); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:36: error: expected primary-expression before ‘double’ std::normal_distribution dist(0,1); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:36: error: expected ‘;’ before ‘double’ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:15:33: error: ‘mt’ was not declared in this scope const double x = dist(mt); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:15:35: error: ‘dist’ was not declared in this scope const double x = dist(mt); ^ PETSc Error: No output file produced Rejecting compiler flag due to nonzero status from link Rejecting compiler flag due to In file included from /usr/include/c++/4.8.2/random:35:0, from /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:4: /usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. #error This file requires compiler and library support for the \ ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:11: warning: identifier ‘constexpr’ is a keyword in C++11 [-Wc++0x-compat] template constexpr T Cubed( T x ) { return x*x*x; } ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:32: error: ‘constexpr’ does not name a type template constexpr T Cubed( T x ) { return x*x*x; } ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:7:32: note: C++11 ‘constexpr’ only available with -std=c++11 or -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc: In function ‘int main()’: /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:12:11: error: ‘random_device’ is not a member of ‘std’ std::random_device rd; ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:12:30: error: expected ‘;’ before ‘rd’ std::random_device rd; ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:13:11: error: ‘mt19937’ is not a member of ‘std’ std::mt19937 mt(rd()); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:13:24: error: expected ‘;’ before ‘mt’ std::mt19937 mt(rd()); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:11: error: ‘normal_distribution’ is not a member of ‘std’ std::normal_distribution dist(0,1); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:36: error: expected primary-expression before ‘double’ std::normal_distribution dist(0,1); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:14:36: error: expected ‘;’ before ‘double’ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:15:33: error: ‘mt’ was not declared in this scope const double x = dist(mt); ^ /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc:15:35: error: ‘dist’ was not declared in this scope const double x = dist(mt); ^ PETSc Error: No output file produced checkCxxDialect: checking CXX11 for Cxx with flag: -std=gnu++11 Defined "HAVE_CXX_DIALECT_CXX11" to "1" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include template constexpr T Cubed( T x ) { return x*x*x; } int main() { std::random_device rd; std::mt19937 mt(rd()); std::normal_distribution dist(0,1); const double x = dist(mt); std::cout << x; ; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 ============================================================================================= TESTING: checkCxxOptionalExtensions from config.compilers(config/BuildSystem/config/compilers.py:443) Check whether the C++ compiler (IBM xlC, OSF5) need special flag for .c files which contain C++ Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { class somename { int i; };; return 0; } Output from compiling with -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 ============================================================================================= TESTING: checkCxxInline from config.compilers(config/BuildSystem/config/compilers.py:143) Check for C++ inline keyword ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set Cxx Inline keyword to inline Defined "CXX_INLINE" to "inline" ============================================================================================= TESTING: checkCxxLibraries from config.compilers(config/BuildSystem/config/compilers.py:566) Determines the libraries needed to link with C++ from C and Fortran ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.compilers/confc.o: In function `asub()': conftest.cc:(.text+0x7): undefined reference to `__cxa_allocate_exception' conftest.cc:(.text+0xe): undefined reference to `typeinfo for int' conftest.cc:(.text+0x1e): undefined reference to `__cxa_throw' conftest.cc:(.text+0x2c): undefined reference to `__cxa_begin_catch' conftest.cc:(.text+0x33): undefined reference to `std::cout' conftest.cc:(.text+0x3f): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' conftest.cc:(.text+0x4d): undefined reference to `__cxa_end_catch' conftest.cc:(.text+0x45): undefined reference to `__cxa_end_catch' /tmp/petsc-EaoSnO/config.compilers/confc.o: In function `_GLOBAL__sub_I_conftest.cc': conftest.cc:(.text.startup+0xc): undefined reference to `std::ios_base::Init::Init()' conftest.cc:(.text.startup+0x13): undefined reference to `std::ios_base::Init::~Init()' /tmp/petsc-EaoSnO/config.compilers/confc.o:(.data.DW.ref._ZTIi[DW.ref._ZTIi]+0x0): undefined reference to `typeinfo for int' /tmp/petsc-EaoSnO/config.compilers/confc.o:(.data.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0' collect2: error: ld returned 1 exit status Executing: uname -s stdout: Linux ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -lstdc++ -ldl compilers: C++ requires -lstdc++ to link with C compiler ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -lstdc++ -ldl C++ libraries are not needed when using FC linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -V ============================================================================================= TESTING: checkFortranNameMangling from config.compilers(config/BuildSystem/config/compilers.py:873) Checks Fortran name mangling, and defines HAVE_FORTRAN_UNDERSCORE, HAVE_FORTRAN_NOUNDERSCORE, HAVE_FORTRAN_CAPS Testing Fortran mangling type underscore with code void d1chk_(void){return;} ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1chk_(void){return;} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran name mangling is underscore Defined "HAVE_FORTRAN_UNDERSCORE" to "1" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Defined "FORTRAN_CHARLEN_T" to "int" ============================================================================================= TESTING: checkFortranNameManglingDouble from config.compilers(config/BuildSystem/config/compilers.py:911) Checks if symbols containing an underscore append an extra underscore, and defines HAVE_FORTRAN_UNDERSCORE_UNDERSCORE if necessary ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1_chk__(void){return;} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: program main call d1_chk() end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.compilers/conftest.o: In function `main': conftest.F90:(.text.startup+0x1d): undefined reference to `d1_chk_' collect2: error: ld returned 1 exit status ============================================================================================= TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:921) Substitutes for FLIBS the libraries needed to link with Fortran This macro is intended to be used in those situations when it is necessary to mix, e.g. C++ and Fortran 77, source code into a single program or shared library. For example, if object files from a C++ and Fortran 77 compiler must be linked together, then the C++ compiler/linker must be used for linking (since special C++-ish things need to happen at link time like calling global constructors, instantiating templates, enabling exception support, etc.). However, the Fortran 77 intrinsic and run-time libraries must be linked in as well, but the C++ compiler/linker does not know how to add these Fortran 77 libraries. This code was translated from the autoconf macro which was packaged in its current form by Matthew D. Langston . However, nearly all of this macro came from the OCTAVE_FLIBS macro in octave-2.0.13/aclocal.m4, and full credit should go to John W. Eaton for writing this extremely useful macro. ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: program main #include call MPI_Allreduce() end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o -lstdc++ -ldl ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: subroutine asub() print*,'testing' call MPI_Allreduce() return end ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern void asub_(void); int main(int argc,char **args) { asub_(); return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.compilers/confc.o: In function `asub_': conftest.F90:(.text+0x2f): undefined reference to `_gfortran_st_write' conftest.F90:(.text+0x43): undefined reference to `_gfortran_transfer_character_write' conftest.F90:(.text+0x4b): undefined reference to `_gfortran_st_write_done' collect2: error: ld returned 1 exit status Fortran code cannot directly be linked with C linker, therefore will determine needed Fortran libraries Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: program main end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o -lstdc++ -ldl stdout: mpif90 for the Intel(R) MPI Library 2019 Update 5 for Linux* Copyright 2003-2019, Intel Corporation. Possible ERROR while running linker: stdout: mpif90 for the Intel(R) MPI Library 2019 Update 5 for Linux* Copyright 2003-2019, Intel Corporation.stderr: Driving: gfortran -o /tmp/petsc-EaoSnO/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o -lstdc++ -ldl -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -Wl,-z,now -Wl,-z,relro -Wl,-z,noexecstack -Xlinker --enable-new-dtags -ldl -l gfortran -l m -shared-libgcc Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-16) (GCC) Reading specs from /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libgfortran.spec rename spec lib to liborig COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-EaoSnO/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O3' '-mtune=native' '-I' '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0' '-I' '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include' '-L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release' '-L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib' '-shared-libgcc' '-march=x86-64' COMPILER_PATH=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/ LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/cm/shared/apps/lapack/gcc/64/3.7.0/:/cm/shared/apps/openblas/0.2.18/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib/:/cm/shared/apps/hdf5/1.10.0/lib/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-EaoSnO/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O3' '-mtune=native' '-I' '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0' '-I' '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include' '-L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release' '-L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib' '-shared-libgcc' '-march=x86-64' /usr/libexec/gcc/x86_64-redhat-linux/4.8.5/collect2 --build-id --no-add-needed --eh-frame-hdr --hash-style=gnu -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o /tmp/petsc-EaoSnO/config.compilers/conftest /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/cm/shared/apps/lapack/gcc/64/3.7.0 -L/cm/shared/apps/openblas/0.2.18/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -L/cm/shared/apps/hdf5/1.10.0/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. /tmp/petsc-EaoSnO/config.compilers/conftest.o -lstdc++ -ldl --enable-new-dtags -rpath /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -rpath /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -z now -z relro -z noexecstack --enable-new-dtags -ldl -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crtn.o compilers: Checking arg mpif90 compilers: Unknown arg mpif90 compilers: Checking arg for compilers: Unknown arg for compilers: Checking arg the compilers: Unknown arg the compilers: Checking arg Intel(R) compilers: Unknown arg Intel(R) compilers: Checking arg MPI compilers: Unknown arg MPI compilers: Checking arg Library compilers: Unknown arg Library compilers: Checking arg 2019 compilers: Unknown arg 2019 compilers: Checking arg Update compilers: Unknown arg Update compilers: Checking arg 5 compilers: Unknown arg 5 compilers: Checking arg for compilers: Unknown arg for compilers: Checking arg Linux* compilers: Unknown arg Linux* compilers: Checking arg Copyright compilers: Unknown arg Copyright compilers: Checking arg 2003-2019, compilers: Unknown arg 2003-2019, compilers: Checking arg Intel compilers: Unknown arg Intel compilers: Checking arg Corporation. compilers: Unknown arg Corporation. compilers: Checking arg Driving: compilers: Unknown arg Driving: compilers: Checking arg gfortran compilers: Unknown arg gfortran compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-EaoSnO/config.compilers/conftest compilers: Unknown arg /tmp/petsc-EaoSnO/config.compilers/conftest compilers: Checking arg -v compilers: Unknown arg -v compilers: Checking arg -fPIC compilers: Unknown arg -fPIC compilers: Checking arg -Wall compilers: Unknown arg -Wall compilers: Checking arg -ffree-line-length-0 compilers: Unknown arg -ffree-line-length-0 compilers: Checking arg -Wno-unused-dummy-argument compilers: Unknown arg -Wno-unused-dummy-argument compilers: Checking arg -O3 compilers: Unknown arg -O3 compilers: Checking arg -mtune=native compilers: Unknown arg -mtune=native compilers: Checking arg /tmp/petsc-EaoSnO/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-EaoSnO/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Found library: -lstdc++ compilers: Checking arg -ldl compilers: Found library: -ldl compilers: Checking arg -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 compilers: Found include directory: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 compilers: Checking arg -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include compilers: Found include directory: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include compilers: Checking arg -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Found library directory: -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Checking arg -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Found library directory: -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Checking arg -Xlinker compilers: Unknown arg -Xlinker compilers: Checking arg --enable-new-dtags compilers: Unknown arg --enable-new-dtags compilers: Checking arg -Xlinker compilers: Unknown arg -Xlinker compilers: Checking arg -rpath compilers: Checking arg /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Unknown arg /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Checking arg -Xlinker compilers: Unknown arg -Xlinker compilers: Checking arg -rpath compilers: Checking arg /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Unknown arg /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Checking arg -lmpifort compilers: Found library: -lmpifort compilers: Checking arg -lmpi compilers: Found library: -lmpi compilers: Checking arg -lrt compilers: Found library: -lrt compilers: Checking arg -lpthread compilers: Found library: -lpthread compilers: Checking arg -Wl,-z,now compilers: Unknown arg -Wl,-z,now compilers: Checking arg -Wl,-z,relro compilers: Unknown arg -Wl,-z,relro compilers: Checking arg -Wl,-z,noexecstack compilers: Unknown arg -Wl,-z,noexecstack compilers: Checking arg -Xlinker compilers: Unknown arg -Xlinker compilers: Checking arg --enable-new-dtags compilers: Unknown arg --enable-new-dtags compilers: Checking arg -ldl compilers: Already in lflags: -ldl compilers: Checking arg -l compilers: Found canonical library: -lgfortran compilers: Checking arg -l compilers: Found canonical library: -lm compilers: Checking arg -shared-libgcc compilers: Unknown arg -shared-libgcc compilers: Checking arg Using compilers: Unknown arg Using compilers: Checking arg built-in compilers: Unknown arg built-in compilers: Checking arg specs. compilers: Unknown arg specs. compilers: Checking arg COLLECT_GCC=gfortran compilers: Unknown arg COLLECT_GCC=gfortran compilers: Checking arg COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper compilers: Unknown arg COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper compilers: Checking arg Target: compilers: Unknown arg Target: compilers: Checking arg x86_64-redhat-linux compilers: Unknown arg x86_64-redhat-linux compilers: Checking arg Configured compilers: Unknown arg Configured compilers: Checking arg with: compilers: Unknown arg with: compilers: Checking arg ../configure compilers: Unknown arg ../configure compilers: Checking arg --prefix=/usr compilers: Unknown arg --prefix=/usr compilers: Checking arg --mandir=/usr/share/man compilers: Unknown arg --mandir=/usr/share/man compilers: Checking arg --infodir=/usr/share/info compilers: Unknown arg --infodir=/usr/share/info compilers: Checking arg --with-bugurl=http://bugzilla.redhat.com/bugzilla compilers: Unknown arg --with-bugurl=http://bugzilla.redhat.com/bugzilla compilers: Checking arg --enable-bootstrap compilers: Unknown arg --enable-bootstrap compilers: Checking arg --enable-shared compilers: Unknown arg --enable-shared compilers: Checking arg --enable-threads=posix compilers: Unknown arg --enable-threads=posix compilers: Checking arg --enable-checking=release compilers: Unknown arg --enable-checking=release compilers: Checking arg --with-system-zlib compilers: Unknown arg --with-system-zlib compilers: Checking arg --enable-__cxa_atexit compilers: Unknown arg --enable-__cxa_atexit compilers: Checking arg --disable-libunwind-exceptions compilers: Unknown arg --disable-libunwind-exceptions compilers: Checking arg --enable-gnu-unique-object compilers: Unknown arg --enable-gnu-unique-object compilers: Checking arg --enable-linker-build-id compilers: Unknown arg --enable-linker-build-id compilers: Checking arg --with-linker-hash-style=gnu compilers: Unknown arg --with-linker-hash-style=gnu compilers: Checking arg --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto compilers: Unknown arg --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto compilers: Checking arg --enable-plugin compilers: Unknown arg --enable-plugin compilers: Checking arg --enable-initfini-array compilers: Unknown arg --enable-initfini-array compilers: Checking arg --disable-libgcj compilers: Unknown arg --disable-libgcj compilers: Checking arg --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install compilers: Unknown arg --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install compilers: Checking arg --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install compilers: Unknown arg --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install compilers: Checking arg --enable-gnu-indirect-function compilers: Unknown arg --enable-gnu-indirect-function compilers: Checking arg --with-tune=generic compilers: Unknown arg --with-tune=generic compilers: Checking arg --with-arch_32=x86-64 compilers: Unknown arg --with-arch_32=x86-64 compilers: Checking arg --build=x86_64-redhat-linux compilers: Unknown arg --build=x86_64-redhat-linux compilers: Checking arg Thread compilers: Unknown arg Thread compilers: Checking arg model: compilers: Unknown arg model: compilers: Checking arg posix compilers: Unknown arg posix compilers: Checking arg gcc compilers: Unknown arg gcc compilers: Checking arg version compilers: Unknown arg version compilers: Checking arg 4.8.5 compilers: Unknown arg 4.8.5 compilers: Checking arg 20150623 compilers: Unknown arg 20150623 compilers: Checking arg (Red compilers: Unknown arg (Red compilers: Checking arg Hat compilers: Unknown arg Hat compilers: Checking arg 4.8.5-16) compilers: Unknown arg 4.8.5-16) compilers: Checking arg (GCC) compilers: Unknown arg (GCC) compilers: Checking arg Reading compilers: Unknown arg Reading compilers: Checking arg specs compilers: Unknown arg specs compilers: Checking arg from compilers: Unknown arg from compilers: Checking arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libgfortran.spec compilers: Unknown arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libgfortran.spec compilers: Checking arg rename compilers: Unknown arg rename compilers: Checking arg spec compilers: Unknown arg spec compilers: Checking arg lib compilers: Unknown arg lib compilers: Checking arg to compilers: Unknown arg to compilers: Checking arg liborig compilers: Unknown arg liborig compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg COMPILER_PATH=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/ compilers: Skipping arg COMPILER_PATH=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/ compilers: Checking arg LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/cm/shared/apps/lapack/gcc/64/3.7.0/:/cm/shared/apps/openblas/0.2.18/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib/:/cm/shared/apps/hdf5/1.10.0/lib/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../:/lib/:/usr/lib/ compilers: Skipping arg LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.8.5/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/cm/shared/apps/lapack/gcc/64/3.7.0/:/cm/shared/apps/openblas/0.2.18/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib/:/cm/shared/apps/hdf5/1.10.0/lib/:/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../:/lib/:/usr/lib/ compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg /usr/libexec/gcc/x86_64-redhat-linux/4.8.5/collect2 compilers: Unknown arg /usr/libexec/gcc/x86_64-redhat-linux/4.8.5/collect2 compilers: Checking arg --build-id compilers: Unknown arg --build-id compilers: Checking arg --no-add-needed compilers: Unknown arg --no-add-needed compilers: Checking arg --eh-frame-hdr compilers: Unknown arg --eh-frame-hdr compilers: Checking arg --hash-style=gnu compilers: Unknown arg --hash-style=gnu compilers: Checking arg -m compilers: Unknown arg -m compilers: Checking arg elf_x86_64 compilers: Unknown arg elf_x86_64 compilers: Checking arg -dynamic-linker compilers: Unknown arg -dynamic-linker compilers: Checking arg /lib64/ld-linux-x86-64.so.2 compilers: Unknown arg /lib64/ld-linux-x86-64.so.2 compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-EaoSnO/config.compilers/conftest compilers: Unknown arg /tmp/petsc-EaoSnO/config.compilers/conftest compilers: Checking arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o compilers: Unknown arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o compilers: Checking arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crti.o compilers: Unknown arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crti.o compilers: Checking arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o compilers: Unknown arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o compilers: Checking arg -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Already in lflags so skipping: -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Checking arg -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Already in lflags so skipping: -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Checking arg -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 compilers: Found library directory: -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 compilers: Checking arg -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 compilers: Checking arg -L/lib/../lib64 compilers: Checking arg -L/usr/lib/../lib64 compilers: Checking arg -L/cm/shared/apps/lapack/gcc/64/3.7.0 compilers: Found library directory: -L/cm/shared/apps/lapack/gcc/64/3.7.0 compilers: Checking arg -L/cm/shared/apps/openblas/0.2.18/lib compilers: Found library directory: -L/cm/shared/apps/openblas/0.2.18/lib compilers: Checking arg -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib compilers: Found library directory: -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib compilers: Checking arg -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Already in lflags so skipping: -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Checking arg -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Already in lflags so skipping: -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Checking arg -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib compilers: Found library directory: -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib compilers: Checking arg -L/cm/shared/apps/hdf5/1.10.0/lib compilers: Found library directory: -L/cm/shared/apps/hdf5/1.10.0/lib compilers: Checking arg -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. compilers: Checking arg /tmp/petsc-EaoSnO/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-EaoSnO/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Already in lflags: -lstdc++ compilers: Checking arg -ldl compilers: Already in lflags: -ldl compilers: Checking arg --enable-new-dtags compilers: Unknown arg --enable-new-dtags compilers: Checking arg -rpath compilers: Found -rpath library: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release compilers: Checking arg -rpath compilers: Found -rpath library: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib compilers: Checking arg -lmpifort compilers: Already in lflags: -lmpifort compilers: Checking arg -lmpi compilers: Already in lflags: -lmpi compilers: Checking arg -lrt compilers: Already in lflags: -lrt compilers: Checking arg -lpthread compilers: Already in lflags: -lpthread compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg now compilers: Unknown arg now compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg relro compilers: Unknown arg relro compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg noexecstack compilers: Unknown arg noexecstack compilers: Checking arg --enable-new-dtags compilers: Unknown arg --enable-new-dtags compilers: Checking arg -ldl compilers: Already in lflags: -ldl compilers: Checking arg -lgfortran compilers: Found library: -lgfortran compilers: Checking arg -lm compilers: Found library: -lm compilers: Checking arg -lgcc_s compilers: Found library: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lquadmath compilers: Found library: -lquadmath compilers: Checking arg -lm compilers: Already in lflags: -lm compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lc compilers: Found system library therefore skipping: -lc compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o compilers: Unknown arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o compilers: Checking arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crtn.o compilers: Unknown arg /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crtn.o compilers: Libraries needed to link Fortran code with the C linker: ['-lstdc++', '-ldl', '-Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release', '-L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release', '-Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib', '-L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib', '-lmpifort', '-lmpi', '-lrt', '-lpthread', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-Wl,-rpath,/cm/shared/apps/lapack/gcc/64/3.7.0', '-L/cm/shared/apps/lapack/gcc/64/3.7.0', '-Wl,-rpath,/cm/shared/apps/openblas/0.2.18/lib', '-L/cm/shared/apps/openblas/0.2.18/lib', '-Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib', '-L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib', '-Wl,-rpath,/cm/shared/apps/intel/itac/2019.5.075/intel64/slib', '-L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib', '-Wl,-rpath,/cm/shared/apps/hdf5/1.10.0/lib', '-L/cm/shared/apps/hdf5/1.10.0/lib', '-Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release', '-Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath'] compilers: Libraries needed to link Fortran main with the C linker: [] compilers: Check that Fortran libraries can be used with C as the linker ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/cm/shared/apps/lapack/gcc/64/3.7.0 -L/cm/shared/apps/lapack/gcc/64/3.7.0 -Wl,-rpath,/cm/shared/apps/openblas/0.2.18/lib -L/cm/shared/apps/openblas/0.2.18/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -Wl,-rpath,/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -Wl,-rpath,/cm/shared/apps/hdf5/1.10.0/lib -L/cm/shared/apps/hdf5/1.10.0/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/cm/shared/apps/lapack/gcc/64/3.7.0 -L/cm/shared/apps/lapack/gcc/64/3.7.0 -Wl,-rpath,/cm/shared/apps/openblas/0.2.18/lib -L/cm/shared/apps/openblas/0.2.18/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -Wl,-rpath,/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -Wl,-rpath,/cm/shared/apps/hdf5/1.10.0/lib -L/cm/shared/apps/hdf5/1.10.0/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/cm/shared/apps/lapack/gcc/64/3.7.0 -L/cm/shared/apps/lapack/gcc/64/3.7.0 -Wl,-rpath,/cm/shared/apps/openblas/0.2.18/lib -L/cm/shared/apps/openblas/0.2.18/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -Wl,-rpath,/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -Wl,-rpath,/cm/shared/apps/hdf5/1.10.0/lib -L/cm/shared/apps/hdf5/1.10.0/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-EaoSnO/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest compilers: Check that Fortran libraries can be used with C++ as linker compilers: Fortran libraries can be used from C++ ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/cm/shared/apps/lapack/gcc/64/3.7.0 -L/cm/shared/apps/lapack/gcc/64/3.7.0 -Wl,-rpath,/cm/shared/apps/openblas/0.2.18/lib -L/cm/shared/apps/openblas/0.2.18/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -Wl,-rpath,/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -Wl,-rpath,/cm/shared/apps/hdf5/1.10.0/lib -L/cm/shared/apps/hdf5/1.10.0/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/cm/shared/apps/lapack/gcc/64/3.7.0 -L/cm/shared/apps/lapack/gcc/64/3.7.0 -Wl,-rpath,/cm/shared/apps/openblas/0.2.18/lib -L/cm/shared/apps/openblas/0.2.18/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -Wl,-rpath,/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -Wl,-rpath,/cm/shared/apps/hdf5/1.10.0/lib -L/cm/shared/apps/hdf5/1.10.0/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/cm/shared/apps/lapack/gcc/64/3.7.0 -L/cm/shared/apps/lapack/gcc/64/3.7.0 -Wl,-rpath,/cm/shared/apps/openblas/0.2.18/lib -L/cm/shared/apps/openblas/0.2.18/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -L/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib -Wl,-rpath,/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -L/cm/shared/apps/intel/itac/2019.5.075/intel64/slib -Wl,-rpath,/cm/shared/apps/hdf5/1.10.0/lib -L/cm/shared/apps/hdf5/1.10.0/lib -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release -Wl,-rpath,/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-EaoSnO/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.setCompilers/conftest ============================================================================================= TESTING: checkFortranLinkingCxx from config.compilers(config/BuildSystem/config/compilers.py:1345) Check that Fortran can link C++ libraries ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void foo(void){d1chk_();} ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void d1chk_(void){return;} ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilers/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilers/conftest.o /tmp/petsc-EaoSnO/config.compilers/cxxobj.o /tmp/petsc-EaoSnO/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran can link C++ functions ============================================================================================= TESTING: setupFrameworkCompilers from config.compilers(config/BuildSystem/config/compilers.py:1506) child config.compilers 8.869160 ============================================================================================= TESTING: configureClosure from config.utilities.closure(config/BuildSystem/config/utilities/closure.py:17) Determine if Apple ^close syntax is supported in C ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.closure/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.closure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.utilities.closure/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.utilities.closure/conftest.c:6:6: error: expected identifier or ‘(’ before ‘^’ token int (^closure)(int);; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int (^closure)(int);; return 0; } Compile failed inside link child config.utilities.closure 0.062779 ============================================================================================= TESTING: checkFortranTypeSizes from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:56) Check whether real*8 is supported and suggest flags which will allow support Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:2.21: real*8 variable 1 Warning: Unused variable 'variable' declared at (1) Source: program main real*8 variable end ============================================================================================= TESTING: checkFortranPreprocessor from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:73) Determine if Fortran handles preprocessing properly Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef dummy fooey #endif end Output from compiling with -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native compilers: Fortran uses preprocessor ============================================================================================= TESTING: checkFortranDefineCompilerOption from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:96) Check if -WF,-Dfoobar or -Dfoobar is the compiler option to define a macro Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native -DTesting /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef Testing fooey #endif end Output from compiling with -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native -DTesting Defined make macro "FC_DEFINE_FLAG" to "-D" compilers: Fortran uses -D for defining macro ============================================================================================= TESTING: checkFortran90 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:146) Determine whether the Fortran compiler handles F90 ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:3.43: REAL(KIND=SELECTED_REAL_KIND(10)) d 1 Warning: Unused variable 'd' declared at (1) Source: program main REAL(KIND=SELECTED_REAL_KIND(10)) d INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8) INTEGER (KIND=int) :: ierr ierr = 1 end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -lstdc++ -ldl Fortran compiler supports F90 ============================================================================================= TESTING: checkFortran90FreeForm from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:162) Determine whether the Fortran compiler handles F90FreeForm We also require that the compiler handles lines longer than 132 characters ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Successful compile: Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8); INTEGER (KIND=int) :: ierr; ierr = 1 end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F90FREEFORM" to "1" Fortran compiler supports F90FreeForm ============================================================================================= TESTING: checkFortran2003 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:176) Determine whether the Fortran compiler handles F2003 ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90: In function ‘main’: /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:21:0: warning: ‘carray.dim[0].lbound’ may be used uninitialized in this function [-Wmaybe-uninitialized] CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) ^ /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:16:0: note: ‘carray.dim[0].lbound’ was declared here Type(C_Ptr),Dimension(:),Pointer :: CArray ^ /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:21:0: warning: ‘carray.dim[0].stride’ may be used uninitialized in this function [-Wmaybe-uninitialized] CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) ^ /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:16:0: note: ‘carray.dim[0].stride’ was declared here Type(C_Ptr),Dimension(:),Pointer :: CArray ^ /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:21:0: warning: ‘carray.offset’ may be used uninitialized in this function [-Wmaybe-uninitialized] CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) ^ /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90:16:0: note: ‘carray.offset’ was declared here Type(C_Ptr),Dimension(:),Pointer :: CArray ^ Source: module Base_module type, public :: base_type integer :: A contains procedure, public :: Print => BasePrint end type base_type contains subroutine BasePrint(this) class(base_type) :: this end subroutine BasePrint end module Base_module program main use,intrinsic :: iso_c_binding Type(C_Ptr),Dimension(:),Pointer :: CArray character(kind=c_char),pointer :: nullc => null() character(kind=c_char,len=5),dimension(:),pointer::list1 allocate(list1(5)) CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F2003" to "1" Fortran compiler supports F2003 ============================================================================================= TESTING: checkFortran90Array from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:211) Check for F90 array interfaces Executing: uname -s stdout: Linux ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.compilersFortran/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void f90arraytest_(void* a1, void* a2,void* a3, void* i) { printf("arrays [%p %p %p]\n",a1,a2,a3); fflush(stdout); return; } void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void* p2, void* p3) { printf("arrays [%p %p %p]\n",a1,a2,a3); if ((p1 == p3) && (p1 != p2)) { printf("pointers match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); } else { printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); exit(111); } return; } ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Successful compile: Source: program main Interface Subroutine f90ptrtest(p1,p2,p3,i) integer, pointer :: p1(:,:) integer, pointer :: p2(:,:) integer, pointer :: p3(:,:) integer i End Subroutine End Interface integer, pointer :: ptr1(:,:),ptr2(:,:) integer, target :: array(6:8,9:21) integer in in = 25 ptr1 => array ptr2 => array call f90arraytest(ptr1,ptr2,ptr1,in) call f90ptrtest(ptr1,ptr2,ptr1,in) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o /tmp/petsc-EaoSnO/config.compilersFortran/fooobj.o -lstdc++ -ldl Testing executable /tmp/petsc-EaoSnO/config.compilersFortran/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.compilersFortran/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.compilersFortran/conftest stdout: arrays [0x7fffffffd100 0x7fffffffd100 0x7fffffffd100] arrays [0x7fffffffd060 0x7fffffffd0b0 0x7fffffffd060] pointers do not match! [0x2aaaaaaebe80 0x19] [0x7fffffff] ERROR while running executable: Could not execute "['/tmp/petsc-EaoSnO/config.compilersFortran/conftest']": arrays [0x7fffffffd100 0x7fffffffd100 0x7fffffffd100] arrays [0x7fffffffd060 0x7fffffffd0b0 0x7fffffffd060] pointers do not match! [0x2aaaaaaebe80 0x19] [0x7fffffff] compilers: F90 uses a single argument for array pointers ============================================================================================= TESTING: checkFortran90AssumedType from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:298) Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -qversion ============================================================================================= TESTING: checkFortranModuleInclude from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:303) Figures out what flag is used to specify the include path for Fortran modules ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Successful compile: Source: program main use configtest write(*,*) testint end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest -I/tmp/petsc-EaoSnO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o /tmp/petsc-EaoSnO/config.compilersFortran/configtest.o -lstdc++ -ldl compilers: Fortran module include flag -I found ============================================================================================= TESTING: checkFortranModuleOutput from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:369) Figures out what flag is used to specify the output path for Fortran modules ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -module /tmp/petsc-EaoSnO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ‘-module’ Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module compile failed ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -module:/tmp/petsc-EaoSnO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ‘-module:/tmp/petsc-EaoSnO/config.compilersFortran/confdir’ Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module: compile failed ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fmod=/tmp/petsc-EaoSnO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ‘-fmod=/tmp/petsc-EaoSnO/config.compilersFortran/confdir’ Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -fmod= compile failed ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -J/tmp/petsc-EaoSnO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -J found ============================================================================================= TESTING: checkFortranTypeStar from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:135) Determine whether the Fortran compiler handles type(*) ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Successful compile: Source: program main interface subroutine a(b) type(*) :: b(:) end subroutine end interface end Defined "HAVE_FORTRAN_TYPE_STAR" to "1" Fortran compiler supports type(*) ============================================================================================= TESTING: checkFortranTypeInitialize from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:125) Determines if PETSc objects in Fortran are initialized by default (doesn't work with common blocks) Defined "FORTRAN_TYPE_INITIALIZE" to " = -2" Initializing Fortran objects ============================================================================================= TESTING: configureFortranFlush from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:116) ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.F90 Successful compile: Source: program main call flush(6) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_FLUSH" to "1" ============================================================================================= TESTING: checkDependencyGenerationFlag from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:414) Check if -MMD works for dependency generation, and add it if it does Trying FC compiler flag -MMD -MP Defined make macro "FC_DEPFLAGS" to "-MMD -MP" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.setCompilers/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native -MMD -MP /tmp/petsc-EaoSnO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Output from compiling with -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native -MMD -MP child config.compilersFortran 3.431226 ============================================================================================= TESTING: checkStdC from config.headers(config/BuildSystem/config/headers.py:105) ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.headers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.headers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #define ISLOWER(c) ('a' <= (c) && (c) <= 'z') #define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main() { int i; for(i = 0; i < 256; i++) if (XOR(islower(i), ISLOWER(i)) || toupper(i) != TOUPPER(i)) exit(2); exit(0); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.headers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.headers/conftest.o -lstdc++ -ldl Testing executable /tmp/petsc-EaoSnO/config.headers/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.headers/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.headers/conftest ============================================================================================= TESTING: checkStat from config.headers(config/BuildSystem/config/headers.py:138) Checks whether stat file-mode macros are broken, and defines STAT_MACROS_BROKEN if they are Preprocessing source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(S_ISBLK) && defined(S_IFDIR) # if S_ISBLK (S_IFDIR) You lose. # endif #endif #if defined(S_ISBLK) && defined(S_IFCHR) # if S_ISBLK (S_IFCHR) You lose. # endif #endif #if defined(S_ISLNK) && defined(S_IFREG) # if S_ISLNK (S_IFREG) You lose. # endif #endif #if defined(S_ISSOCK) && defined(S_IFREG) # if S_ISSOCK (S_IFREG) You lose. # endif #endif Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c ============================================================================================= TESTING: checkSysWait from config.headers(config/BuildSystem/config/headers.py:173) Check for POSIX.1 compatible sys/wait.h, and defines HAVE_SYS_WAIT_H if found ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.headers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #ifndef WEXITSTATUS #define WEXITSTATUS(stat_val) ((unsigned)(stat_val) >> 8) #endif #ifndef WIFEXITED #define WIFEXITED(stat_val) (((stat_val) & 255) == 0) #endif int main() { int s; wait (&s); s = WIFEXITED (s) ? WEXITSTATUS (s) : 1; ; return 0; } Defined "HAVE_SYS_WAIT_H" to "1" ============================================================================================= TESTING: checkTime from config.headers(config/BuildSystem/config/headers.py:195) Checks if you can safely include both and , and if so defines TIME_WITH_SYS_TIME Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_TIME_H" to "1" Checking for header: sys/time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_TIME_H" to "1" ============================================================================================= TESTING: checkMath from config.headers(config/BuildSystem/config/headers.py:201) Checks for the math headers and defines Checking for header: math.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.headers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.headers/conftest.c:6:13: error: ‘M_PI’ undeclared (first use in this function) double pi = M_PI; ^ /tmp/petsc-EaoSnO/config.headers/conftest.c:6:13: note: each undeclared identifier is reported only once for each function it appears in Source: #include "confdefs.h" #include "conffix.h" #include int main() { double pi = M_PI; if (pi); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.headers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.headers/conftest.c:7:13: error: ‘M_PI’ undeclared (first use in this function) double pi = M_PI; ^ /tmp/petsc-EaoSnO/config.headers/conftest.c:7:13: note: each undeclared identifier is reported only once for each function it appears in Source: #include "confdefs.h" #include "conffix.h" #define _USE_MATH_DEFINES 1 #include int main() { double pi = M_PI; if (pi); ; return 0; } Missing math #defines, like M_PI ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SETJMP_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:17: fatal error: dos.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:17: fatal error: dos.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:17: fatal error: dos.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_FCNTL_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_FLOAT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:16: fatal error: io.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:16: fatal error: io.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:16: fatal error: io.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_MALLOC_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_PWD_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_STRINGS_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_UNISTD_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_SYSINFO_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: machine/endian.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: machine/endian.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: machine/endian.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_PARAM_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_PROCFS_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_RESOURCE_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_TIMES_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_UTSNAME_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_SOCKET_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_WAIT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_NETINET_IN_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_NETDB_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: direct.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: direct.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: direct.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_TIME_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: Ws2tcpip.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: Ws2tcpip.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: Ws2tcpip.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_TYPES_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: WindowsX.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: WindowsX.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: WindowsX.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_FLOAT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: ieeefp.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: ieeefp.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: ieeefp.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_STDINT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_PTHREAD_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_INTTYPES_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_IMMINTRIN_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:23: fatal error: zmmintrin.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:23: fatal error: zmmintrin.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:23: fatal error: zmmintrin.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SETJMP_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:17: fatal error: dos.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:17: fatal error: dos.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:17: fatal error: dos.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_FCNTL_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_FLOAT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:16: fatal error: io.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:16: fatal error: io.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:16: fatal error: io.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_MALLOC_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_PWD_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_STRINGS_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_UNISTD_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_SYSINFO_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: machine/endian.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: machine/endian.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: machine/endian.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_PARAM_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_PROCFS_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_RESOURCE_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_TIMES_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_UTSNAME_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_SOCKET_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_WAIT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_NETINET_IN_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_NETDB_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: direct.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: direct.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: direct.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_TIME_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: Ws2tcpip.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: Ws2tcpip.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: Ws2tcpip.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_TYPES_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: WindowsX.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: WindowsX.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:22: fatal error: WindowsX.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_FLOAT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: ieeefp.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: ieeefp.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: ieeefp.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_STDINT_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_PTHREAD_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_INTTYPES_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_IMMINTRIN_H" to "1" ============================================================================================= TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:23: fatal error: zmmintrin.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:23: fatal error: zmmintrin.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:23: fatal error: zmmintrin.h: No such file or directory #include ^compilation terminated.: ============================================================================================= TESTING: checkRecursiveMacros from config.headers(config/BuildSystem/config/headers.py:216) Checks that the preprocessor allows recursive macros, and if not defines HAVE_BROKEN_RECURSIVE_MACRO ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.headers/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void a(int i, int j) {} #define a(b) a(b,__LINE__) int main() { a(0); ; return 0; } child config.headers 6.757668 ============================================================================================= TESTING: configureCacheDetails from config.utilities.cacheDetails(config/BuildSystem/config/utilities/cacheDetails.py:78) Try to determine the size and associativity of the cache. ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { ; return 0; } ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { FILE *output = fopen("conftestval","w"); if (!output) return 1; fprintf(output,"%ld",getconf_LEVEL1_DCACHE_LINESIZE()); fclose(output);; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest.o -lstdc++ -ldl Testing executable /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest to see if it can be run Executing: /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest Running Executable with threads to time it out at 60 Executing: /tmp/petsc-EaoSnO/config.utilities.cacheDetails/conftest Defined "LEVEL1_DCACHE_LINESIZE" to "64" child config.utilities.cacheDetails 0.617423 ============================================================================================= TESTING: check_struct_sigaction from config.types(config/BuildSystem/config/types.py:42) Checks if "struct sigaction" exists in signal.h. This check is for C89 check. Checking for type: struct sigaction ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:11:18: error: storage size of ‘a’ isn’t known struct sigaction a;; ^ /tmp/petsc-EaoSnO/config.types/conftest.c:11:18: warning: unused variable ‘a’ [-Wunused-variable] Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { struct sigaction a;; return 0; } struct sigaction found ============================================================================================= TESTING: check__int64 from config.types(config/BuildSystem/config/types.py:48) Checks if __int64 exists. This is primarily for windows. Checking for type: __int64 ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:11:1: error: unknown type name ‘__int64’ __int64 a;; ^ /tmp/petsc-EaoSnO/config.types/conftest.c:11:9: warning: unused variable ‘a’ [-Wunused-variable] __int64 a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { __int64 a;; return 0; } __int64 found ============================================================================================= TESTING: checkSizeTypes from config.types(config/BuildSystem/config/types.py:54) Checks for types associated with sizes, such as size_t. Checking for type: size_t ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:11:8: warning: unused variable ‘a’ [-Wunused-variable] size_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { size_t a;; return 0; } size_t found ============================================================================================= TESTING: checkFileTypes from config.types(config/BuildSystem/config/types.py:64) Checks for types associated with files, such as mode_t, off_t, etc. Checking for type: mode_t ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:11:8: warning: unused variable ‘a’ [-Wunused-variable] mode_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { mode_t a;; return 0; } mode_t found Checking for type: off_t ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:11:7: warning: unused variable ‘a’ [-Wunused-variable] off_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { off_t a;; return 0; } off_t found ============================================================================================= TESTING: checkIntegerTypes from config.types(config/BuildSystem/config/types.py:59) Checks for types associated with integers, such as int32_t. Checking for type: int32_t ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:11:9: warning: unused variable ‘a’ [-Wunused-variable] int32_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { int32_t a;; return 0; } int32_t found ============================================================================================= TESTING: checkPID from config.types(config/BuildSystem/config/types.py:70) Checks for pid_t, and defines it if necessary Checking for type: pid_t ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:11:7: warning: unused variable ‘a’ [-Wunused-variable] pid_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { pid_t a;; return 0; } pid_t found ============================================================================================= TESTING: checkUID from config.types(config/BuildSystem/config/types.py:74) Checks for uid_t and gid_t, and defines them if necessary Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c ============================================================================================= TESTING: checkC99Complex from config.types(config/BuildSystem/config/types.py:81) Check for complex numbers in in C99 std Note that since PETSc source code uses _Complex we test specifically for that, not complex ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:6:17: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] double _Complex x; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:6:17: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] double _Complex x; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.types/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_C99_COMPLEX" to "1" ============================================================================================= TESTING: checkCxxComplex from config.types(config/BuildSystem/config/types.py:92) Check for complex numbers in namespace std ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { std::complex x; ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.types/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_CXX_COMPLEX" to "1" ============================================================================================= TESTING: checkConst from config.types(config/BuildSystem/config/types.py:103) Checks for working const, and if not found defines it to empty string ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.types/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.types/conftest.c:30:9: warning: ‘t’ is used uninitialized in this function [-Wuninitialized] *t++ = 0; ^ /tmp/petsc-EaoSnO/config.types/conftest.c:46:25: warning: ‘b’ is used uninitialized in this function [-Wuninitialized] struct s *b; b->j = 5; ^ Source: #include "confdefs.h" #include "conffix.h" int main() { /* Ultrix mips cc rejects this. */ typedef int charset[2]; const charset x; /* SunOS 4.1.1 cc rejects this. */ char const *const *ccp; char **p; /* NEC SVR4.0.2 mips cc rejects this. */ struct point {int x, y;}; static struct point const zero = {0,0}; /* AIX XL C 1.02.0.0 rejects this. It does not let you subtract one const X* pointer from another in an arm of an if-expression whose if-part is not a constant expression */ const char *g = "string"; ccp = &g + (g ? g-g : 0); /* HPUX 7.0 cc rejects these. */ ++ccp; p = (char**) ccp; ccp = (char const *const *) p; /* This section avoids unused variable warnings */ if (zero.x); if (x[0]); { /* SCO 3.2v4 cc rejects this. */ char *t; char const *s = 0 ? (char *) 0 : (char const *) 0; *t++ = 0; if (*s); } { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ int x[] = {25, 17}; const int *foo = &x[0]; ++foo; } { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ typedef const int *iptr; iptr p = 0; ++p; } { /* AIX XL C 1.02.0.0 rejects this saying "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ struct s { int j; const int *ap[3]; }; struct s *b; b->j = 5; } { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ const int foo = 10; /* Get rid of unused variable warning */ if (foo); } ; return 0; } ============================================================================================= TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:159) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: short ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(short)==2)*2-1]; Defined "SIZEOF_SHORT" to "2" ============================================================================================= TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:159) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: int ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(int)==4)*2-1]; Defined "SIZEOF_INT" to "4" ============================================================================================= TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:159) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: enum ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(enum{ENUM_DUMMY})==4)*2-1]; Defined "SIZEOF_ENUM" to "4" ============================================================================================= TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:159) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long)==8)*2-1]; Defined "SIZEOF_LONG" to "8" ============================================================================================= TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:159) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: void * ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(void *)==8)*2-1]; Defined "SIZEOF_VOID_P" to "8" ============================================================================================= TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:159) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long long ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long long)==8)*2-1]; Defined "SIZEOF_LONG_LONG" to "8" ============================================================================================= TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:159) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: size_t ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(size_t)==8)*2-1]; Defined "SIZEOF_SIZE_T" to "8" Defined "USING_64BIT_PTR" to "1" ============================================================================================= TESTING: checkVisibility from config.types(config/BuildSystem/config/types.py:193) ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_C" to "1" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.types -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_CXX" to "1" ============================================================================================= TESTING: checkMaxPathLen from config.types(config/BuildSystem/config/types.py:215) Determining PETSC_MAX_PATH_LEN ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.types/conftest.o -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(MAXPATHLEN) # define PETSC_MAX_PATH_LEN MAXPATHLEN #elif defined(MAX_PATH) # define PETSC_MAX_PATH_LEN MAX_PATH #elif defined(_MAX_PATH) # define PETSC_MAX_PATH_LEN _MAX_PATH #else # define PETSC_MAX_PATH_LEN 4096 #endif #define xstr(s) str(s) #define str(s) #s char petsc_max_path_len[] = xstr(PETSC_MAX_PATH_LEN); int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(MAXPATHLEN) # define PETSC_MAX_PATH_LEN MAXPATHLEN #elif defined(MAX_PATH) # define PETSC_MAX_PATH_LEN MAX_PATH #elif defined(_MAX_PATH) # define PETSC_MAX_PATH_LEN _MAX_PATH #else # define PETSC_MAX_PATH_LEN 4096 #endif #define xstr(s) str(s) #define str(s) #s char petsc_max_path_len[] = xstr(PETSC_MAX_PATH_LEN); Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.types -std=c99 /tmp/petsc-EaoSnO/config.types/conftest.c Defined "MAX_PATH_LEN" to "4096" child config.types 3.096251 ============================================================================================= TESTING: configureMemAlign from PETSc.options.memAlign(config/PETSc/options/memAlign.py:29) Choose alignment Defined "MEMALIGN" to "16" Memory alignment is 16 child PETSc.options.memAlign 0.002467 ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ============================================================================================= TESTING: checkMath from config.libraries(config/BuildSystem/config/libraries.py:264) Check for sin() in libm, the math library Checking for functions [sin floor log10 pow] in library [''] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /tmp/petsc-EaoSnO/config.libraries/conftest.o: undefined reference to symbol 'floor@@GLIBC_2.2.5' /usr/lib64/libm.so.6: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status Checking for functions [sin floor log10 pow] in library ['m'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" CheckMath: using math library ['libm.a'] ============================================================================================= TESTING: checkMathErf from config.libraries(config/BuildSystem/config/libraries.py:283) Check for erf() in libm, the math library Checking for functions [erf] in library ['libm.a'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.c: In function ‘_check_erf’: /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:74: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } int main() { _check_erf();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" erf() found Defined "HAVE_ERF" to "1" ============================================================================================= TESTING: checkMathTgamma from config.libraries(config/BuildSystem/config/libraries.py:292) Check for tgamma() in libm, the math library Checking for functions [tgamma] in library ['libm.a'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.c: In function ‘_check_tgamma’: /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:83: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } int main() { _check_tgamma();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" tgamma() found Defined "HAVE_TGAMMA" to "1" ============================================================================================= TESTING: checkMathLgamma from config.libraries(config/BuildSystem/config/libraries.py:301) Check for lgamma() in libm, the math library Checking for functions [lgamma] in library ['libm.a'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include #include static void _check_lgamma() { double (*checkLgamma)(double) = lgamma;double x = 1,y; y = (*checkLgamma)(x);if (y != 0.) abort(); } int main() { _check_lgamma();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" lgamma() found Defined "HAVE_LGAMMA" to "1" ============================================================================================= TESTING: checkMathFenv from config.libraries(config/BuildSystem/config/libraries.py:314) Checks if can be used with FE_DFL_ENV Checking for functions [fesetenv] in library ['libm.a'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_fesetenv() { fesetenv(FE_DFL_ENV);; } int main() { _check_fesetenv();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" Defined "HAVE_FENV_H" to "1" ============================================================================================= TESTING: checkMathLog2 from config.libraries(config/BuildSystem/config/libraries.py:322) Check for log2() in libm, the math library Checking for functions [log2] in library ['libm.a'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.c: In function ‘_check_log2’: /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:81: warning: unused variable ‘y’ [-Wunused-variable] static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } int main() { _check_log2();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" log2() found Defined "HAVE_LOG2" to "1" ============================================================================================= TESTING: checkRealtime from config.libraries(config/BuildSystem/config/libraries.py:331) Check for presence of clock_gettime() in realtime library (POSIX Realtime extensions) Checking for functions [clock_gettime] in library [''] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.c: In function ‘_check_clock_gettime’: /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:54: error: storage size of ‘tp’ isn’t known static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:45: warning: implicit declaration of function ‘clock_gettime’ [-Wimplicit-function-declaration] static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:72: error: ‘CLOCK_REALTIME’ undeclared (first use in this function) static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:72: note: each undeclared identifier is reported only once for each function it appears in /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:54: warning: unused variable ‘tp’ [-Wunused-variable] static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } int main() { _check_clock_gettime();; return 0; } Compile failed inside link Checking for functions [clock_gettime] in library ['rt'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.c: In function ‘_check_clock_gettime’: /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:54: error: storage size of ‘tp’ isn’t known static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:45: warning: implicit declaration of function ‘clock_gettime’ [-Wimplicit-function-declaration] static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:72: error: ‘CLOCK_REALTIME’ undeclared (first use in this function) static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:72: note: each undeclared identifier is reported only once for each function it appears in /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:54: warning: unused variable ‘tp’ [-Wunused-variable] static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } int main() { _check_clock_gettime();; return 0; } Compile failed inside link Warning: No realtime library found ============================================================================================= TESTING: checkDynamic from config.libraries(config/BuildSystem/config/libraries.py:347) Check for the header and libraries necessary for dynamic library manipulation Checking for functions [dlopen] in library ['dl'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } int main() { _check_dlopen();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -ldl -lstdc++ -ldl Defined "HAVE_LIBDL" to "1" Checking for header: dlfcn.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_DLFCN_H" to "1" child config.libraries 3.766784 ============================================================================================= TESTING: configureLibraryOptions from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:38) Sets PETSC_USE_DEBUG, PETSC_USE_INFO, PETSC_USE_LOG, PETSC_USE_CTABLE, PETSC_USE_FORTRAN_KERNELS, and PETSC_USE_AVX512_KERNELS Defined "USE_LOG" to "1" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -qversion Defined "USE_MALLOC_COALESCED" to "1" Defined "USE_INFO" to "1" Defined "USE_CTABLE" to "1" Defined "USE_BACKWARD_LOOP" to "1" **********Checking if running on BGL/IBM detected Checking for functions [bgl_perfctr_void] in library [''] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char bgl_perfctr_void(); static void _check_bgl_perfctr_void() { bgl_perfctr_void(); } int main() { _check_bgl_perfctr_void();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `bgl_perfctr_void' collect2: error: ld returned 1 exit status Checking for functions [ADIOI_BGL_Open] in library [''] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ADIOI_BGL_Open(); static void _check_ADIOI_BGL_Open() { ADIOI_BGL_Open(); } int main() { _check_ADIOI_BGL_Open();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `ADIOI_BGL_Open' collect2: error: ld returned 1 exit status *********BGL/IBM test failure Defined "USE_AVX512_KERNELS" to "1" Defined "Alignx(a,b)" to " " ============================================================================================= TESTING: configureISColorValueType from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:99) Sets PETSC_IS_COLORING_VALUE_TYPE, PETSC_MPIU_IS_COLORING_VALUE_TYPE, and PETSC_IS_COLORING_MAX as required by ISColoring Defined "MPIU_IS_COLORING_VALUE_TYPE" to "MPI_UNSIGNED_SHORT" Defined "IS_COLORING_MAX" to "USHRT_MAX" Defined "IS_COLORING_VALUE_TYPE" to "short" Defined "IS_COLORING_VALUE_TYPE_F" to "integer2" child PETSc.options.libraryOptions 0.528378 child config.atomics 0.000014 ============================================================================================= TESTING: checkSysinfo from config.functions(config/BuildSystem/config/functions.py:106) Check whether sysinfo takes three arguments, and if it does define HAVE_SYSINFO_3ARG Checking for functions [sysinfo] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sysinfo(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sysinfo) || defined (__stub___sysinfo) sysinfo_will_always_fail_with_ENOSYS(); #else sysinfo(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SYSINFO" to "1" Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_SYSINFO_H" to "1" Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:28: fatal error: sys/systeminfo.h: No such file or directory #include ^compilation terminated.: ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.c:9:4: error: #error "Cannot check sysinfo without special headers" # error "Cannot check sysinfo without special headers" ^ /tmp/petsc-EaoSnO/config.functions/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.functions/conftest.c:13:1: warning: implicit declaration of function ‘sysinfo’ [-Wimplicit-function-declaration] char buf[10]; long count=10; sysinfo(1, buf, count); ^ Source: #include "confdefs.h" #include "conffix.h" #ifdef HAVE_SYS_SYSINFO_H # include #elif defined(HAVE_SYS_SYSTEMINFO_H) # include #else # error "Cannot check sysinfo without special headers" #endif int main() { char buf[10]; long count=10; sysinfo(1, buf, count); ; return 0; } Compile failed inside link ============================================================================================= TESTING: checkVPrintf from config.functions(config/BuildSystem/config/functions.py:125) Checks whether vprintf requires a char * last argument, and if it does defines HAVE_VPRINTF_CHAR ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vprintf( "%d", Argp ); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl ============================================================================================= TESTING: checkVFPrintf from config.functions(config/BuildSystem/config/functions.py:131) Checks whether vfprintf requires a char * last argument, and if it does defines HAVE_VFPRINTF_CHAR ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vfprintf(stdout, "%d", Argp ); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl ============================================================================================= TESTING: checkVSNPrintf from config.functions(config/BuildSystem/config/functions.py:137) Checks whether vsnprintf requires a char * last argument, and if it does defines HAVE_VSNPRINTF_CHAR ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp;char str[6]; vsnprintf(str,5, "%d", Argp ); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VSNPRINTF" to "1" ============================================================================================= TESTING: checkNanosleep from config.functions(config/BuildSystem/config/functions.py:167) Check for functional nanosleep() - as time.h behaves differently for different compiler flags - like -std=c89 ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.functions/conftest.c:6:17: error: storage size of ‘tp’ isn’t known struct timespec tp; ^ /tmp/petsc-EaoSnO/config.functions/conftest.c:9:2: warning: implicit declaration of function ‘nanosleep’ [-Wimplicit-function-declaration] nanosleep(&tp,0); ^ /tmp/petsc-EaoSnO/config.functions/conftest.c:6:17: warning: unused variable ‘tp’ [-Wunused-variable] struct timespec tp; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { struct timespec tp; tp.tv_sec = 0; tp.tv_nsec = (long)(1e9); nanosleep(&tp,0); ; return 0; } Compile failed inside link ============================================================================================= TESTING: checkMemmove from config.functions(config/BuildSystem/config/functions.py:173) Check for functional memmove() - as MS VC requires correct includes to for this test ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char c1[1], c2[1] = "c"; size_t n=1; memmove(c1,c2,n); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MEMMOVE" to "1" ============================================================================================= TESTING: checkSignalHandlerType from config.functions(config/BuildSystem/config/functions.py:143) Checks the type of C++ signals handlers, and defines SIGNAL_CAST to the correct value ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.functions/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include static void myhandler(int sig) {} int main() { signal(SIGFPE,myhandler); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.functions/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "SIGNAL_CAST" to " " ============================================================================================= TESTING: checkFreeReturnType from config.functions(config/BuildSystem/config/functions.py:153) Checks whether free returns void or int, and defines HAVE_FREE_RETURN_INT ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.functions/conftest.c:6:25: error: void value not ignored as it ought to be int ierr; void *p; ierr = free(p); return 0; ^ /tmp/petsc-EaoSnO/config.functions/conftest.c:6:5: warning: variable ‘ierr’ set but not used [-Wunused-but-set-variable] int ierr; void *p; ierr = free(p); return 0; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ierr; void *p; ierr = free(p); return 0; ; return 0; } Compile failed inside link ============================================================================================= TESTING: checkVariableArgumentLists from config.functions(config/BuildSystem/config/functions.py:159) Checks whether the variable argument list functionality is working ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { va_list l1, l2; va_copy(l1, l2); return 0; ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VA_COPY" to "1" ============================================================================================= TESTING: checkClassify from config.functions(config/BuildSystem/config/functions.py:85) Recursive decompose to rapidly classify functions as found or missing To confirm that a function is missing, we require a compile/link failure with only that function in a compilation unit. In contrast, we can confirm that many functions are present by compiling them all together in a large compilation unit. We optimistically compile everything together, then trim all functions that were named in the error message and bisect the result. The trimming is only an optimization to increase the likelihood of a big-batch compile succeeding; we do not rely on the compiler naming missing functions. Checking for functions [rand getdomainname _access snprintf realpath dlsym bzero _getcwd _pipe getwd uname _lseek sleep _sleep lseek usleep dlclose gethostname clock access _snprintf dlerror fork getpagesize sbreak memalign getcwd gethostbyname readlink _set_output_format PXFGETARG strcasecmp dlopen fpresetsticky drand48 socket popen getrusage _mkdir time fpsetsticky stricmp] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.functions/conftest.c:16:6: warning: conflicting types for built-in function ‘snprintf’ [enabled by default] char snprintf(); ^ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char _access(); char snprintf(); char realpath(); char dlsym(); char bzero(); char _getcwd(); char _pipe(); char getwd(); char uname(); char _lseek(); char sleep(); char _sleep(); char lseek(); char usleep(); char dlclose(); char gethostname(); char clock(); char access(); char _snprintf(); char dlerror(); char fork(); char getpagesize(); char sbreak(); char memalign(); char getcwd(); char gethostbyname(); char readlink(); char _set_output_format(); char PXFGETARG(); char strcasecmp(); char dlopen(); char fpresetsticky(); char drand48(); char socket(); char popen(); char getrusage(); char _mkdir(); char time(); char fpsetsticky(); char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif #if defined (__stub__pipe) || defined (__stub____pipe) _pipe_will_always_fail_with_ENOSYS(); #else _pipe(); #endif #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_fpresetsticky) || defined (__stub___fpresetsticky) fpresetsticky_will_always_fail_with_ENOSYS(); #else fpresetsticky(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif #if defined (__stub_fpsetsticky) || defined (__stub___fpsetsticky) fpsetsticky_will_always_fail_with_ENOSYS(); #else fpsetsticky(); #endif #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x46): warning: the `getwd' function is dangerous and should not be used. conftest.c:(.text.startup+0x15): undefined reference to `_access' conftest.c:(.text.startup+0x38): undefined reference to `_getcwd' conftest.c:(.text.startup+0x3f): undefined reference to `_pipe' conftest.c:(.text.startup+0x54): undefined reference to `_lseek' conftest.c:(.text.startup+0x62): undefined reference to `_sleep' conftest.c:(.text.startup+0x93): undefined reference to `_snprintf' conftest.c:(.text.startup+0xaf): undefined reference to `sbreak' conftest.c:(.text.startup+0xd2): undefined reference to `_set_output_format' conftest.c:(.text.startup+0xd9): undefined reference to `PXFGETARG' conftest.c:(.text.startup+0xee): undefined reference to `fpresetsticky' conftest.c:(.text.startup+0x111): undefined reference to `_mkdir' conftest.c:(.text.startup+0x11f): undefined reference to `fpsetsticky' conftest.c:(.text.startup+0x126): undefined reference to `stricmp' collect2: error: ld returned 1 exit status Checking for functions [rand getdomainname realpath dlsym bzero uname usleep dlclose gethostname clock dlerror] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char realpath(); char dlsym(); char bzero(); char uname(); char usleep(); char dlclose(); char gethostname(); char clock(); char dlerror(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_RAND" to "1" Defined "HAVE_GETDOMAINNAME" to "1" Defined "HAVE_REALPATH" to "1" Defined "HAVE_DLSYM" to "1" Defined "HAVE_BZERO" to "1" Defined "HAVE_UNAME" to "1" Defined "HAVE_USLEEP" to "1" Defined "HAVE_DLCLOSE" to "1" Defined "HAVE_GETHOSTNAME" to "1" Defined "HAVE_CLOCK" to "1" Defined "HAVE_DLERROR" to "1" Checking for functions [fork getpagesize memalign gethostbyname readlink strcasecmp dlopen drand48 socket popen getrusage time] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char fork(); char getpagesize(); char memalign(); char gethostbyname(); char readlink(); char strcasecmp(); char dlopen(); char drand48(); char socket(); char popen(); char getrusage(); char time(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_FORK" to "1" Defined "HAVE_GETPAGESIZE" to "1" Defined "HAVE_MEMALIGN" to "1" Defined "HAVE_GETHOSTBYNAME" to "1" Defined "HAVE_READLINK" to "1" Defined "HAVE_STRCASECMP" to "1" Defined "HAVE_DLOPEN" to "1" Defined "HAVE_DRAND48" to "1" Defined "HAVE_SOCKET" to "1" Defined "HAVE_POPEN" to "1" Defined "HAVE_GETRUSAGE" to "1" Defined "HAVE_TIME" to "1" Checking for functions [_access] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_access' collect2: error: ld returned 1 exit status Checking for functions [snprintf] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.functions/conftest.c:13:6: warning: conflicting types for built-in function ‘snprintf’ [enabled by default] char snprintf(); ^ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SNPRINTF" to "1" Checking for functions [_getcwd] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_getcwd' collect2: error: ld returned 1 exit status Checking for functions [_pipe] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _pipe(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__pipe) || defined (__stub____pipe) _pipe_will_always_fail_with_ENOSYS(); #else _pipe(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_pipe' collect2: error: ld returned 1 exit status Checking for functions [getwd] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): warning: the `getwd' function is dangerous and should not be used. Defined "HAVE_GETWD" to "1" Checking for functions [_lseek] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_lseek' collect2: error: ld returned 1 exit status Checking for functions [sleep] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SLEEP" to "1" Checking for functions [_sleep] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_sleep' collect2: error: ld returned 1 exit status Checking for functions [lseek] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_LSEEK" to "1" Checking for functions [access] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_ACCESS" to "1" Checking for functions [_snprintf] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_snprintf' collect2: error: ld returned 1 exit status Checking for functions [sbreak] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sbreak(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `sbreak' collect2: error: ld returned 1 exit status Checking for functions [getcwd] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_GETCWD" to "1" Checking for functions [_set_output_format] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _set_output_format(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_set_output_format' collect2: error: ld returned 1 exit status Checking for functions [PXFGETARG] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char PXFGETARG(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `PXFGETARG' collect2: error: ld returned 1 exit status Checking for functions [fpresetsticky] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char fpresetsticky(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_fpresetsticky) || defined (__stub___fpresetsticky) fpresetsticky_will_always_fail_with_ENOSYS(); #else fpresetsticky(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `fpresetsticky' collect2: error: ld returned 1 exit status Checking for functions [_mkdir] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _mkdir(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `_mkdir' collect2: error: ld returned 1 exit status Checking for functions [fpsetsticky] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char fpsetsticky(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_fpsetsticky) || defined (__stub___fpsetsticky) fpsetsticky_will_always_fail_with_ENOSYS(); #else fpsetsticky(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `fpsetsticky' collect2: error: ld returned 1 exit status Checking for functions [stricmp] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.functions/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `stricmp' collect2: error: ld returned 1 exit status ============================================================================================= TESTING: checkMmap from config.functions(config/BuildSystem/config/functions.py:179) Check for functional mmap() to allocate shared memory and define HAVE_MMAP ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.functions/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { int fd; fd=open("/tmp/file",O_RDWR); mmap((void*)0,100,PROT_READ|PROT_WRITE,MAP_SHARED,fd,0); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MMAP" to "1" child config.functions 7.364149 ============================================================================================= TESTING: configureMemorySize from config.utilities.getResidentSetSize(config/BuildSystem/config/utilities/getResidentSetSize.py:31) Try to determine how to measure the memory usage Defined "USE_PROC_FOR_SIZE" to "1" Using /proc for PetscMemoryGetCurrentUsage() child config.utilities.getResidentSetSize 0.001605 ============================================================================================= TESTING: configureFortranCommandLine from config.utilities.fortranCommandLine(config/BuildSystem/config/utilities/fortranCommandLine.py:27) Check for the mechanism to retrieve command line arguments in Fortran Checking for functions [] in library [''] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.F90 Successful compile: Source: program main integer i character*(80) arg i = command_argument_count() call get_command_argument(i,arg) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_GET_COMMAND_ARGUMENT" to "1" child config.utilities.fortranCommandLine 0.172187 ============================================================================================= TESTING: configureFPTrap from config.utilities.FPTrap(config/BuildSystem/config/utilities/FPTrap.py:27) Checking the handling of floating point traps Checking for header: sigfpe.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: sigfpe.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: sigfpe.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:20: fatal error: sigfpe.h: No such file or directory #include ^compilation terminated.: Checking for header: fpxcp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:19: fatal error: fpxcp.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:19: fatal error: fpxcp.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:19: fatal error: fpxcp.h: No such file or directory #include ^compilation terminated.: Checking for header: floatingpoint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:27: fatal error: floatingpoint.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:27: fatal error: floatingpoint.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:27: fatal error: floatingpoint.h: No such file or directory #include ^compilation terminated.: child config.utilities.FPTrap 0.285991 ============================================================================================= TESTING: configureFeatureTestMacros from config.utilities.featureTestMacros(config/BuildSystem/config/utilities/featureTestMacros.py:13) Checks if certain feature test macros are support ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.c:4:20: fatal error: sysctl.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #define _POSIX_C_SOURCE 200112L #include int main() { ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _BSD_SOURCE #include int main() { ; return 0; } Defined "_BSD_SOURCE" to "1" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _DEFAULT_SOURCE #include int main() { ; return 0; } Defined "_DEFAULT_SOURCE" to "1" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include int main() { cpu_set_t mset; CPU_ZERO(&mset);; return 0; } Defined "_GNU_SOURCE" to "1" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include #include int main() { Dl_info info; if (dladdr(exit, &info));; return 0; } Defined "_GNU_SOURCE" to "1" child config.utilities.featureTestMacros 0.574164 ============================================================================================= TESTING: configureMissingUtypeTypedefs from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:55) Checks if u_short is undefined ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c:6:1: error: unknown type name ‘u_short’ u_short foo; ^ /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c:6:9: warning: unused variable ‘foo’ [-Wunused-variable] u_short foo; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { u_short foo; ; return 0; } Defined "NEEDS_UTYPE_TYPEDEFS" to "1" ============================================================================================= TESTING: configureMissingFunctions from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:61) Checks for SOCKETS ============================================================================================= TESTING: configureMissingSignals from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:79) Check for missing signals, and define MISSING_ if necessary ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGABRT; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGALRM; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGBUS; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCHLD; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCONT; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGFPE; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGHUP; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGILL; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGINT; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGKILL; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGPIPE; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGQUIT; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSEGV; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSTOP; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSYS; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTERM; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTRAP; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTSTP; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGURG; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR1; if (i); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR2; if (i); ; return 0; } ============================================================================================= TESTING: configureMissingGetdomainnamePrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:96) ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -lstdc++ -ldl ============================================================================================= TESTING: configureMissingSrandPrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:121) ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.utilities.missing/conftest.o -lstdc++ -ldl child config.utilities.missing 3.284375 ============================================================================================= TESTING: checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:34) ============================================================================================= TESTING: configureSharedLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:49) Checks whether shared libraries should be used, for which you must - Specify --with-shared-libraries - Have found a working shared linker Defines PETSC_USE_SHARED_LIBRARIES if they are used Executing: uname -s stdout: Linux Defined make rule "shared_arch" with dependencies "shared_linux" and code [] Defined make macro "SONAME_FUNCTION" to "$(1).so.$(2)" Defined make macro "SL_LINKER_FUNCTION" to "-shared -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2))" Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -v stdout: mpigcc for the Intel(R) MPI Library 2019 Update 5 for Linux* Copyright 2003-2019, Intel Corporation. Defined make macro "BUILDSHAREDLIB" to "yes" Defined "USE_SHARED_LIBRARIES" to "1" ============================================================================================= TESTING: configureDynamicLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:94) Checks whether dynamic loading is available (with dlfcn.h and libdl) Defined "HAVE_DYNAMIC_LIBRARIES" to "1" ============================================================================================= TESTING: configureSerializedFunctions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:100) Defines PETSC_SERIALIZE_FUNCTIONS if they are used Requires shared libraries ============================================================================================= TESTING: checkSymbolResolution from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:109) Checks that dladdr() works ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/PETSc.options.sharedLibraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/PETSc.options.sharedLibraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include #include int main() { Dl_info info; if (dladdr(exit, &info)); ; return 0; } Defined "HAVE_DLADDR" to "1" child PETSc.options.sharedLibraries 0.134030 ============================================================================================= TESTING: configureScalarType from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:40) Choose between real and complex numbers Scalar type is real ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ‘a’ [-Wunused-variable] double b = 2.0; int a = isnormal(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnormal(b); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNORMAL" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ‘a’ [-Wunused-variable] double b = 2.0; int a = isnan(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnan(b); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNAN" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ‘a’ [-Wunused-variable] double b = 2.0; int a = isinf(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isinf(b); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISINF" to "1" ============================================================================================= TESTING: configurePrecision from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:81) Set the default real number precision for PETSc objects Checking C compiler works with __float128 Checking for functions [logq] in library ['quadmath'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.c: In function ‘_check_logq’: /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:47: warning: ‘f’ is used uninitialized in this function [-Wuninitialized] static void _check_logq() { __float128 f; logq(f);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:40: note: ‘f’ was declared here static void _check_logq() { __float128 f; logq(f);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" C compiler with quadmath library Checking Fortran works with quadmath library Checking for functions [ ] in library ['quadmath'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.F90 Successful compile: Source: program main real*16 s,w; w = 2.0 ;s = cos(w) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Fortran works with quadmath library Checking for functions [logq] in library ['quadmath'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.c: In function ‘_check_logq’: /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:47: warning: ‘f’ is used uninitialized in this function [-Wuninitialized] static void _check_logq() { __float128 f; logq(f);; } ^ /tmp/petsc-EaoSnO/config.libraries/conftest.c:5:40: note: ‘f’ was declared here static void _check_logq() { __float128 f; logq(f);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Adding ['quadmath'] to LIBS Defined "HAVE_REAL___FLOAT128" to "1" Defined "USE_REAL_DOUBLE" to "1" Defined make macro "PETSC_SCALAR_SIZE" to "64" Precision is double child PETSc.options.scalarTypes 1.508039 ============================================================================================= TESTING: configureMkdir from config.programs(config/BuildSystem/config/programs.py:22) Make sure we can have mkdir automatically make intermediate directories Checking for program /cm/local/apps/cmake/3.9.6/bin/mkdir...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/mkdir...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mkdir...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/mkdir...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/mkdir...not found Checking for program /usr/local/bin/mkdir...not found Checking for program /usr/bin/mkdir...found Executing: /usr/bin/mkdir -p .conftest/tmp Adding -p flag to /usr/bin/mkdir -p to automatically create directories Defined make macro "MKDIR" to "/usr/bin/mkdir -p" ============================================================================================= TESTING: configureAutoreconf from config.programs(config/BuildSystem/config/programs.py:44) Check for autoreconf Checking for program /cm/local/apps/cmake/3.9.6/bin/autoreconf...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/autoreconf...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/autoreconf...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/autoreconf...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/autoreconf...not found Checking for program /usr/local/bin/autoreconf...not found Checking for program /usr/bin/autoreconf...found Executing: ['/usr/bin/autoreconf'] autoreconf test successful! Checking for program /cm/local/apps/cmake/3.9.6/bin/libtoolize...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/libtoolize...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/libtoolize...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/libtoolize...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/libtoolize...not found Checking for program /usr/local/bin/libtoolize...not found Checking for program /usr/bin/libtoolize...found ============================================================================================= TESTING: configurePrograms from config.programs(config/BuildSystem/config/programs.py:71) Check for the programs needed to build and run PETSc Checking for program /cm/local/apps/cmake/3.9.6/bin/bash...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/bash...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/bash...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/bash...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/bash...not found Checking for program /usr/local/bin/bash...not found Checking for program /usr/bin/bash...found Defined make macro "SHELL" to "/usr/bin/bash" Checking for program /cm/local/apps/cmake/3.9.6/bin/sed...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/sed...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/sed...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/sed...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/sed...not found Checking for program /usr/local/bin/sed...not found Checking for program /usr/bin/sed...found Defined make macro "SED" to "/usr/bin/sed" Executing: /usr/bin/sed -i s/sed/sd/g "/tmp/petsc-EaoSnO/config.programs/sed1" Adding SEDINPLACE cmd: /usr/bin/sed -i Defined make macro "SEDINPLACE" to "/usr/bin/sed -i" Checking for program /cm/local/apps/cmake/3.9.6/bin/mv...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/mv...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mv...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/mv...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/mv...not found Checking for program /usr/local/bin/mv...not found Checking for program /usr/bin/mv...found Defined make macro "MV" to "/usr/bin/mv" Checking for program /cm/local/apps/cmake/3.9.6/bin/cp...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/cp...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/cp...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/cp...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/cp...not found Checking for program /usr/local/bin/cp...not found Checking for program /usr/bin/cp...found Defined make macro "CP" to "/usr/bin/cp" Checking for program /cm/local/apps/cmake/3.9.6/bin/grep...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/grep...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/grep...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/grep...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/grep...not found Checking for program /usr/local/bin/grep...not found Checking for program /usr/bin/grep...found Defined make macro "GREP" to "/usr/bin/grep" Checking for program /cm/local/apps/cmake/3.9.6/bin/rm...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/rm...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/rm...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/rm...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/rm...not found Checking for program /usr/local/bin/rm...not found Checking for program /usr/bin/rm...found Defined make macro "RM" to "/usr/bin/rm -f" Checking for program /cm/local/apps/cmake/3.9.6/bin/diff...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/diff...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/diff...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/diff...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/diff...not found Checking for program /usr/local/bin/diff...not found Checking for program /usr/bin/diff...found Executing: "/usr/bin/diff" -w "/tmp/petsc-EaoSnO/config.programs/diff1" "/tmp/petsc-EaoSnO/config.programs/diff2" Defined make macro "DIFF" to "/usr/bin/diff -w" Checking for program /usr/ucb/ps...not found Checking for program /usr/usb/ps...not found Checking for program /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/lib/petsc/bin/win32fe/ps...not found Unable to find programs ['ps'] providing listing of the specific search path Warning accessing /usr/ucb gives errors: cannot concatenate 'str' and 'builtin_function_or_method' objects Warning accessing /usr/usb gives errors: cannot concatenate 'str' and 'builtin_function_or_method' objects Defined make macro "PYTHON" to "/usr/bin/python" Checking for program /cm/local/apps/cmake/3.9.6/bin/m4...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/m4...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/m4...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/m4...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/m4...not found Checking for program /usr/local/bin/m4...not found Checking for program /usr/bin/m4...found Defined make macro "M4" to "/usr/bin/m4" child config.programs 2.215650 ============================================================================================= TESTING: consistencyChecks from config.packages.make(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.make(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default ============================================================================================= TESTING: configureMake from config.packages.make(config/BuildSystem/config/packages/make.py:96) Check Guesses for GNU make Executing: gmake --version stdout: GNU Make 3.82 Built for x86_64-redhat-linux-gnu Copyright (C) 2010 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Checking for program /cm/local/apps/cmake/3.9.6/bin/gmake...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/gmake...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/gmake...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/gmake...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/gmake...not found Checking for program /usr/local/bin/gmake...not found Checking for program /usr/bin/gmake...found Defined make macro "MAKE" to "/usr/bin/gmake" Checking for program /cm/local/apps/cmake/3.9.6/bin/make...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/make...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/make...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/make...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/make...not found Checking for program /usr/local/bin/make...not found Checking for program /usr/bin/make...found Defined make macro "MAKE_USER" to "make" ============================================================================================= ***** WARNING: You have a version of GNU make older than 4.0. It will work, but may not support all the parallel testing options. You can install the latest GNU make with your package manager, such as brew or macports, or use the --download-make option to get the latest GNU make ***** ============================================================================================= ============================================================================================= TESTING: setupGNUMake from config.packages.make(config/BuildSystem/config/packages/make.py:150) Setup other GNU make stuff Defined make rule "libc" with dependencies "${LIBNAME}(${OBJSC})" and code [] Defined make rule "libcxx" with dependencies "${LIBNAME}(${OBJSCXX})" and code [] Defined make rule "libcu" with dependencies "${LIBNAME}(${OBJSCU})" and code [] Defined make rule "libf" with dependencies "${OBJSF}" and code -${AR} ${AR_FLAGS} ${LIBNAME} ${OBJSF} Defined make macro "OMAKE_PRINTDIR " to "/usr/bin/gmake --print-directory" Defined make macro "OMAKE" to "/usr/bin/gmake --no-print-directory" Defined make macro "MAKE_PAR_OUT_FLG" to "" ============================================================================================= TESTING: configureMakeNP from config.packages.make(config/BuildSystem/config/packages/make.py:197) check no of cores on the build machine [perhaps to do make '-j ncores'] module multiprocessing found 36 cores: using make_np = 26 Defined make macro "MAKE_NP" to "26" Defined make macro "MAKE_TEST_NP" to "17" Defined make macro "MAKE_LOAD" to "54.0" Defined make macro "NPMAX" to "36" child config.packages.make 0.043576 ============================================================================================= TESTING: consistencyChecks from config.packages.X(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.X(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.X 0.002508 ============================================================================================= TESTING: consistencyChecks from config.packages.hwloc(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.hwloc(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.hwloc 0.002989 ============================================================================================= TESTING: consistencyChecks from config.packages.valgrind(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: configureLibrary from config.packages.valgrind(config/BuildSystem/config/package.py:897) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional valgrind Not checking for library in Compiler specific search VALGRIND: [] because no functions given to check for ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library [] [] Checking for optional headers [] in Compiler specific search VALGRIND: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['valgrind/valgrind.h'] in Compiler specific search VALGRIND: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['valgrind/valgrind.h'] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^compilation terminated.: Not checking for library in Package specific search directory VALGRIND: [] because no functions given to check for ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library [] [] Checking for optional headers [] in Package specific search directory VALGRIND: ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['valgrind/valgrind.h'] in Package specific search directory VALGRIND: ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['valgrind/valgrind.h'] in ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 -I/usr/local/include -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^compilation terminated.: Not checking for library in Package specific search directory VALGRIND: [] because no functions given to check for ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library [] [] Checking for optional headers [] in Package specific search directory VALGRIND: ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['valgrind/valgrind.h'] in Package specific search directory VALGRIND: ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['valgrind/valgrind.h'] in ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/usr/local/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 -I/usr/local/include -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conftest.c" # 1 "/tmp/petsc-EaoSnO/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 # 1 "/tmp/petsc-EaoSnO/config.headers/conffix.h" 1 # 3 "/tmp/petsc-EaoSnO/config.headers/conftest.c" 2 stderr: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^ compilation terminated. : Preprocess stderr after filtering: /tmp/petsc-EaoSnO/config.headers/conftest.c:3:31: fatal error: valgrind/valgrind.h: No such file or directory #include ^compilation terminated.: VALGRIND: SearchDir DirPath not found.. skipping: /opt/local Executing: uname -s stdout: Linux Detected Linux OS ============================================================================================= It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure ============================================================================================= child config.packages.valgrind 0.620275 ============================================================================================= TESTING: consistencyChecks from config.packages.thrust(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.thrust(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.thrust 0.003558 ============================================================================================= TESTING: consistencyChecks from config.packages.cuda(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.cuda(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.cuda 0.002600 ============================================================================================= TESTING: consistencyChecks from config.packages.OpenMPI(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.OpenMPI(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.OpenMPI 0.002602 Executing: uname -s stdout: Linux ============================================================================================= TESTING: consistencyChecks from config.packages.MPICH(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.MPICH(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.MPICH 0.017799 ============================================================================================= TESTING: consistencyChecks from config.packages.MPI(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.MPI(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:691) ================================================================================== Checking for a functional MPI Checking for library in Compiler specific search MPI: [] ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [MPI_Init MPI_Comm_create] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Init(); static void _check_MPI_Init() { MPI_Init(); } char MPI_Comm_create(); static void _check_MPI_Comm_create() { MPI_Comm_create(); } int main() { _check_MPI_Init(); _check_MPI_Comm_create();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for optional headers [] in Compiler specific search MPI: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['mpi.h'] in Compiler specific search MPI: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['mpi.h'] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -std=c99 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Found header files ['mpi.h'] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Defined "HAVE_MPI_F90MODULE_VISIBILITY" to "1" ============================================================================================= TESTING: checkMPIDistro from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:544) Determine if MPICH_NUMVERSION, OMPI_MAJOR_VERSION or MSMPI_VER exist in mpi.h Used for consistency checking of MPI installation at compile time ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include const char *mpich_ver = I_MPI_VERSION; int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include const char *mpich_ver = I_MPI_VERSION; Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.MPI -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Unable to parse I_MPI version from header. Probably a buggy preprocessor ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:4:1: warning: overflow in implicit constant conversion [-Woverflow] int mpich_ver = I_MPI_NUMVERSION; ^ Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = I_MPI_NUMVERSION; int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = I_MPI_NUMVERSION; Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.MPI -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Defined "HAVE_I_MPI_NUMVERSION" to "20190005300" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:4:17: error: ‘MVAPICH2_NUMVERSION’ undeclared here (not in a function) int mpich_ver = MVAPICH2_NUMVERSION; ^ Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MVAPICH2_NUMVERSION; int main() { ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MPICH_NUMVERSION; int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MPICH_NUMVERSION; Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.MPI -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Defined "HAVE_MPICH_NUMVERSION" to "30300300" Executing: uname -s stdout: Linux ============================================================================================= TESTING: configureMPI2 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:332) Check for functions added to the interface in MPI-2 ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int flag;if (MPI_Finalized(&flag)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_FINALIZED" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Allreduce(MPI_IN_PLACE,0, 1, MPI_INT, MPI_SUM, MPI_COMM_SELF)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_IN_PLACE" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={MPI_INT,MPI_DOUBLE}; MPI_Datatype *newtype = 0; if (MPI_Type_create_struct(count, blocklens, indices, old_types, newtype)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Comm_set_errhandler(MPI_COMM_WORLD,MPI_ERRORS_RETURN)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Reduce_local(0, 0, 0, MPI_INT, MPI_SUM));; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_REDUCE_LOCAL" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char version[MPI_MAX_LIBRARY_VERSION_STRING];int verlen;if (MPI_Get_library_version(version,&verlen)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_GET_LIBRARY_VERSION" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int base[100]; MPI_Win win; if (MPI_Win_create(base,100,4,MPI_INFO_NULL,MPI_COMM_WORLD,&win)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_WIN_CREATE" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:6:44: warning: ‘win’ is used uninitialized in this function [-Wuninitialized] int ptr[1]; MPI_Win win; if (MPI_Accumulate(ptr,1,MPI_INT,0,0,1,MPI_INT,MPI_REPLACE,win)); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ptr[1]; MPI_Win win; if (MPI_Accumulate(ptr,1,MPI_INT,0,0,1,MPI_INT,MPI_REPLACE,win)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_ONE_SIDED" to "1" ============================================================================================= TESTING: configureMPI3 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:379) Check for functions added to the interface in MPI-3 ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm scomm; MPI_Aint size=128; int disp_unit=8,*baseptr; MPI_Win win; if (MPI_Comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &scomm)); if (MPI_Win_allocate_shared(size,disp_unit,MPI_INFO_NULL,MPI_COMM_WORLD,&baseptr,&win)); if (MPI_Win_shared_query(win,0,&size,&disp_unit,&baseptr)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_PROCESS_SHARED_MEMORY" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int send=0,recv,counts[2]={1,1},displs[2]={1,2}; MPI_Request req; if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igather(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iallgather(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Iallgatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Ialltoall(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NONBLOCKING_COLLECTIVES" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm distcomm; MPI_Request req; if (MPI_Dist_graph_create_adjacent(MPI_COMM_WORLD,0,0,MPI_WEIGHTS_EMPTY,0,0,MPI_WEIGHTS_EMPTY,MPI_INFO_NULL,0,&distcomm)); if (MPI_Neighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm)); if (MPI_Ineighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm,&req)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NEIGHBORHOOD_COLLECTIVES" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:6:48: warning: ‘win’ is used uninitialized in this function [-Wuninitialized] int ptr[1]; MPI_Win win; if (MPI_Get_accumulate(ptr,1,MPI_INT,ptr,1,MPI_INT,0,0,1,MPI_INT,MPI_SUM,win)); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ptr[1]; MPI_Win win; if (MPI_Get_accumulate(ptr,1,MPI_INT,ptr,1,MPI_INT,0,0,1,MPI_INT,MPI_SUM,win)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_GET_ACCUMULATE" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:6:55: warning: ‘win’ is used uninitialized in this function [-Wuninitialized] int ptr[1]; MPI_Win win; MPI_Request req; if (MPI_Rget(ptr,1,MPI_INT,0,1,1,MPI_INT,win,&req)); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ptr[1]; MPI_Win win; MPI_Request req; if (MPI_Rget(ptr,1,MPI_INT,0,1,1,MPI_INT,win,&req)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_RGET" to "1" ============================================================================================= TESTING: configureMPIEXEC from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:177) Checking for location of mpiexec Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec...found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec...found Defined make macro "MPIEXECEXECUTABLE" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec" Running Executable with threads to time it out at 120 Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec -n 1 printenv stdout: MODULE_VERSION_STACK=3.2.10 CPLUS_INCLUDE_PATH=/cm/shared/apps/openblas/0.2.18/include MANPATH=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/man:/cm/shared/apps/intel/itac/2019.5.075/man:/usr/local/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man:/opt/ibutils/share/man:/cm/local/apps/environment-modules/current/share/man XDG_SESSION_ID=124879 HOSTNAME=vegaln1 VT_MPI=impi4 INTEL_LICENSE_FILE=/cm/shared/licenses/intel TERM=xterm-256color SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=155.31.114.10 41362 22 I_MPI_HYDRA_CLEANUP=enable LIBRARY_PATH=/cm/shared/apps/lapack/gcc/64/3.7.0:/cm/shared/apps/openblas/0.2.18/lib/:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib:/cm/shared/apps/hdf5/1.10.0/lib SSH_TTY=/dev/pts/9 QT_GRAPHICSSYSTEM_CHECKED=1 USER=barretk3 LD_LIBRARY_PATH=/cm/shared/apps/lapack/gcc/64/3.7.0:/cm/shared/apps/openblas/0.2.18/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib:/cm/shared/apps/hdf5/1.10.0/lib LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: BLASLIB=openblas FI_PROVIDER_PATH=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib/prov CPATH=/cm/shared/apps/openblas/0.2.18/include:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include MAKELEVEL=1 PE_PRODUCT_LIST=CRAYPE_BROADWELL COLUMNS=210 MFLAGS= MPIRUN=mpiexec MODULE_VERSION=3.2.10 MAIL=/var/spool/mail/barretk3 VT_ADD_LIBS=-ldwarf -lelf -lvtunwind -lnsl -lm -ldl -lpthread PATH=/cm/local/apps/cmake/3.9.6/bin:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin:/cm/shared/apps/intel/itac/2019.5.075/intel64/bin:/cm/shared/apps/hdf5/1.10.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:.:/home2/barretk3/.local/bin:/home2/barretk3/bin I_MPI_TMPDIR=/tmp LD_RUN_PATH=/cm/shared/apps/openblas/0.2.18/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/lib:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/release:/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib:/cm/shared/apps/intel/itac/2019.5.075/intel64/slib:/cm/shared/apps/hdf5/1.10.0/lib C_INCLUDE_PATH=/cm/shared/apps/openblas/0.2.18/include PWD=/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0 _LMFILES_=/opt/cray/craype/default/modulefiles/craype-network-infiniband:/opt/cray/craype/default/modulefiles/craype-broadwell:/cm/shared/modulefiles/hdf5/1.10.0:/cm/shared/modulefiles/intel/itac/2019/5.075:/cm/shared/modulefiles/intel/mpi/64/2019/5.075:/cm/shared/modulefiles/cmake/3.9.6:/cm/shared/modulefiles/openblas/dynamic/0.2.18:/cm/shared/modulefiles/lapack/gcc/64/3.7.0 HDF5_ROOT=/cm/shared/apps/hdf5/1.10.0 LANG=en_US.UTF-8 MODULEPATH=/opt/cray/craype/default/modulefiles:/opt/cray/modulefiles:/cm/local/modulefiles:/opt/modulefiles:/cm/shared/modulefiles LOADEDMODULES=craype-network-infiniband:craype-broadwell:hdf5/1.10.0:intel/itac/2019/5.075:intel/mpi/64/2019/5.075:cmake/3.9.6:openblas/dynamic/0.2.18:lapack/gcc/64/3.7.0 VT_LIB_DIR=/cm/shared/apps/intel/itac/2019.5.075/intel64/lib ENABLE_LMOD=0 LINES=58 HDF5INCLUDE=/cm/shared/apps/hdf5/1.10.0/include VT_ROOT=/cm/shared/apps/intel/itac/2019.5.075 LAPACK_DIR=/cm/shared/apps/lapack/gcc/64/3.7.0 HISTCONTROL=ignoredups SHLVL=3 HOME=/home2/barretk3 HDF5LIB=hdf5 CRAYPE_NETWORK_TARGET=infiniband VT_ARCH=intel64 VT_SLIB_DIR=/cm/shared/apps/intel/itac/2019.5.075/intel64/slib LOGNAME=barretk3 CLASSPATH=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/lib/mpi.jar SSH_CONNECTION=155.31.114.10 41362 155.31.18.51 22 MODULESHOME=/cm/local/apps/environment-modules/3.2.10/Modules/3.2.10 LESSOPEN=||/usr/bin/lesspipe.sh %s HDF5DIR=/cm/shared/apps/hdf5/1.10.0/lib CRAY_CPU_TARGET=broadwell XDG_RUNTIME_DIR=/run/user/23069 MPI_RUN=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpirun BLASDIR=/cm/shared/apps/openblas/0.2.18/lib SCRATCH=/scratch/barretk3 I_MPI_ROOT=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi BASH_FUNC_module()=() { eval `/cm/local/apps/environment-modules/3.2.10/Modules/$MODULE_VERSION/bin/modulecmd bash $*` } _=/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec I_MPI_HYDRA_TOPOLIB=hwloc I_MPI_HYDRA_TREE_LEVEL=1 HYDRA_BSTRAP_PGID=0 HYDRA_BSTRAP_PROXY_ID=0 HYDRA_BSTRAP_NODE_ID=0 HYDRA_BSTRAP_UPSTREAM_FD=10 HYDRA_BSTRAP_SUBTREE_SIZE=1 HYDRA_BSTRAP_TREE_WIDTH=16 HYDRA_BSTRAP_NUM_DOWNSTREAM_PROXIES=0 HYDRA_BSTRAP_DOWNSTREAM_CONTROL= HYDRA_BSTRAP_DOWNSTREAM_STDOUT= HYDRA_BSTRAP_DOWNSTREAM_STDERR= HYDRA_BSTRAP_DOWNSTREAM_PID= HYDRA_BSTRAP_LOCALHOST=vegaln1 HYDRA_BSTRAP_DEBUG=0 HYDRA_BSTRAP_NUM_LAUNCHES=-1 HYDRA_IP_VERSION=2 HYDRA_BSTRAP_DOWNSTREAM_HOSTS= HYDRA_BSTRAP_LAUNCHER=ssh HYDRA_COLLECTIVE_LAUNCH=1 I_MPI_INFO_NUMA_NODE_NUM=2 I_MPI_INFO_NUMA_NODE_MAP=,mlx4_0:1,mlx5_0:0 PMI_SIZE=1 PMI_RANK=0 PMI_FD=12 MPI_LOCALNRANKS=1 MPI_LOCALRANKID=0 GFORTRAN_UNBUFFERED_PRECONNECTED=y I_MPI_INTERNAL_MEM_POLICY=default I_MPI_INFO_STATE=0 I_MPI_INFO_MODE=263 I_MPI_INFO_VEND=1 I_MPI_INFO_FLGB=35438523 I_MPI_INFO_FLGC=2147417087 I_MPI_INFO_FLGD=-1075053569 I_MPI_INFO_FLGCEXT=0 I_MPI_INFO_FLGDEXT=0 I_MPI_INFO_DESC=1342177285 I_MPI_INFO_BRAND=Intel(R) Xeon(R) I_MPI_INFO_SERIAL=E5-2697 v4 I_MPI_INFO_C_NAME=Unknown I_MPI_INFO_SIGN=263921 I_MPI_INFO_LCPU=36 I_MPI_INFO_PACK=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 I_MPI_INFO_CORE=0,1,2,3,4,8,9,10,11,16,17,18,19,20,24,25,26,27,0,1,2,3,4,8,9,10,11,16,17,18,19,20,24,25,26,27 I_MPI_INFO_THREAD=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 I_MPI_INFO_CACHE1=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35 I_MPI_INFO_CACHE2=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35 I_MPI_INFO_CACHE3=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 I_MPI_INFO_CACHES=3 I_MPI_INFO_CACHE_SHARE=2,2,64 I_MPI_INFO_CACHE_SIZE=32768,262144,47185920 I_MPI_INFO_NC=36 I_MPI_INFO_NP=2 I_MPI_PIN_MAPPING=1:0 0 I_MPI_PIN_INFO=x0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35 Defined make macro "MPIEXEC" to "/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec" Checking for program /usr/libexec/ApplicationFirewall/socketfilterfw...not found Checking for program /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/lib/petsc/bin/win32fe/socketfilterfw...not found Unable to find programs ['socketfilterfw'] providing listing of the specific search path Warning accessing /usr/libexec/ApplicationFirewall gives errors: cannot concatenate 'str' and 'builtin_function_or_method' objects Checking for program /cm/local/apps/cmake/3.9.6/bin/hostname...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/hostname...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/hostname...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/hostname...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/hostname...not found Checking for program /usr/local/bin/hostname...not found Checking for program /usr/bin/hostname...found Defined make macro "HOSTNAME" to "hostname" Running Executable with threads to time it out at 60 Executing: hostname stdout: vegaln1 Return code from hostname: 0 Hostname works, running network checks Checking for program /sbin/ping...not found Checking for program /cm/local/apps/cmake/3.9.6/bin/ping...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/ping...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/ping...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/ping...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/ping...not found Checking for program /usr/local/bin/ping...not found Checking for program /usr/bin/ping...found Defined make macro "PING" to "ping" Executing: uname -s stdout: Linux Running Executable with threads to time it out at 60 Executing: ping -c 2 vegaln1 stdout: PING vegaln1.cm.cluster (10.10.0.1) 56(84) bytes of data. 64 bytes from vegaln1.cm.cluster (10.10.0.1): icmp_seq=1 ttl=64 time=0.039 ms 64 bytes from vegaln1.cm.cluster (10.10.0.1): icmp_seq=2 ttl=64 time=0.031 ms --- vegaln1.cm.cluster ping statistics --- 2 packets transmitted, 2 received, 0% packet loss, time 999ms rtt min/avg/max/mdev = 0.031/0.035/0.039/0.004 ms Return code from ping: 0 ============================================================================================= ======== Checking running linked program ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Init(0,0); MPI_Finalize(); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-EaoSnO/config.packages.MPI/conftest to see if it can be run Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec -n 1 /tmp/petsc-EaoSnO/config.packages.MPI/conftest Running Executable with threads to time it out at 120 Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpiexec -n 1 /tmp/petsc-EaoSnO/config.packages.MPI/conftest ============================================================================================= TESTING: configureMPITypes from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:426) Checking for MPI Datatype handles ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Defined "HAVE_MPI_LONG_DOUBLE" to "1" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Defined "HAVE_MPI_INT64_T" to "1" ============================================================================================= TESTING: SGIMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:472) Returns true if SGI MPI is used Checking for functions [MPI_SGI_barrier] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_SGI_barrier(); static void _check_MPI_SGI_barrier() { MPI_SGI_barrier(); } int main() { _check_MPI_SGI_barrier();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `MPI_SGI_barrier' collect2: error: ld returned 1 exit status SGI MPI test failure ============================================================================================= TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:482) Make sure C++ can compile and link Checking for header mpi.h Checking for C++ MPI_Finalize() Checking for functions [MPI_Finalize] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/config.libraries -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 /tmp/petsc-EaoSnO/config.libraries/conftest.cc Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.cc: In function ‘void _check_MPI_Finalize()’: /tmp/petsc-EaoSnO/config.libraries/conftest.cc:5:41: warning: variable ‘ierr’ set but not used [-Wunused-but-set-variable] static void _check_MPI_Finalize() { int ierr; ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_MPI_Finalize() { int ierr; ierr = MPI_Finalize();; } int main() { _check_MPI_Finalize();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.libraries/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl ============================================================================================= TESTING: FortranMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:498) Make sure fortran include [mpif.h] and library symbols are found Checking for fortran mpi_init() Checking for functions [] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.F90 Successful compile: Source: program main #include "mpif.h" integer ierr call mpi_init(ierr) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for mpi.mod Checking for functions [] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.F90 Successful compile: Source: program main use mpi integer(kind=selected_int_kind(5)) ierr,rank call mpi_init(ierr) call mpi_comm_rank(MPI_COMM_WORLD,rank,ierr) end Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_F90MODULE" to "1" ============================================================================================= TESTING: configureIO from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:520) Check for the functions in MPI/IO - Define HAVE_MPIIO if they are present - Some older MPI 1 implementations are missing these ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:12:23: warning: ‘buf’ is used uninitialized in this function [-Wuninitialized] if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); ^ /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:18:22: warning: ‘disp’ is used uninitialized in this function [-Wuninitialized] if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); ^ /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:18:22: warning: ‘info’ is used uninitialized in this function [-Wuninitialized] Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Aint lb, extent; if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); MPI_File fh; void *buf; MPI_Status status; if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); MPI_Offset disp; MPI_Info info; if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); if (MPI_File_close(&fh)); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPIIO" to "1" ============================================================================================= TESTING: findMPIInc from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:624) Find MPI include paths from "mpicc -show" and use with CUDAC_FLAGS ============================================================================================= TESTING: PetscArchMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:666) Checking for functions [MPI_Type_get_envelope MPI_Type_dup MPI_Init_thread MPI_Iallreduce MPI_Ibarrier MPI_Finalized MPI_Exscan MPI_Reduce_scatter MPI_Reduce_scatter_block] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Type_get_envelope(); static void _check_MPI_Type_get_envelope() { MPI_Type_get_envelope(); } char MPI_Type_dup(); static void _check_MPI_Type_dup() { MPI_Type_dup(); } char MPI_Init_thread(); static void _check_MPI_Init_thread() { MPI_Init_thread(); } char MPI_Iallreduce(); static void _check_MPI_Iallreduce() { MPI_Iallreduce(); } char MPI_Ibarrier(); static void _check_MPI_Ibarrier() { MPI_Ibarrier(); } char MPI_Finalized(); static void _check_MPI_Finalized() { MPI_Finalized(); } char MPI_Exscan(); static void _check_MPI_Exscan() { MPI_Exscan(); } char MPI_Reduce_scatter(); static void _check_MPI_Reduce_scatter() { MPI_Reduce_scatter(); } char MPI_Reduce_scatter_block(); static void _check_MPI_Reduce_scatter_block() { MPI_Reduce_scatter_block(); } int main() { _check_MPI_Type_get_envelope(); _check_MPI_Type_dup(); _check_MPI_Init_thread(); _check_MPI_Iallreduce(); _check_MPI_Ibarrier(); _check_MPI_Finalized(); _check_MPI_Exscan(); _check_MPI_Reduce_scatter(); _check_MPI_Reduce_scatter_block();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_TYPE_GET_ENVELOPE" to "1" Defined "HAVE_MPI_TYPE_DUP" to "1" Defined "HAVE_MPI_INIT_THREAD" to "1" Defined "HAVE_MPI_IALLREDUCE" to "1" Defined "HAVE_MPI_IBARRIER" to "1" Defined "HAVE_MPI_FINALIZED" to "1" Defined "HAVE_MPI_EXSCAN" to "1" Defined "HAVE_MPI_REDUCE_SCATTER" to "1" Defined "HAVE_MPI_REDUCE_SCATTER_BLOCK" to "1" Checking for functions [MPIX_Iallreduce] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPIX_Iallreduce(); static void _check_MPIX_Iallreduce() { MPIX_Iallreduce(); } int main() { _check_MPIX_Iallreduce();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `MPIX_Iallreduce' collect2: error: ld returned 1 exit status Checking for functions [MPIX_Ibarrier] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPIX_Ibarrier(); static void _check_MPIX_Ibarrier() { MPIX_Ibarrier(); } int main() { _check_MPIX_Ibarrier();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /tmp/petsc-EaoSnO/config.libraries/conftest.o: In function `main': conftest.c:(.text.startup+0x7): undefined reference to `MPIX_Ibarrier' collect2: error: ld returned 1 exit status ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:6:5: warning: unused variable ‘combiner’ [-Wunused-variable] int combiner = MPI_COMBINER_DUP;; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_DUP;; return 0; } Defined "HAVE_MPI_COMBINER_DUP" to "1" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:6:5: warning: unused variable ‘combiner’ [-Wunused-variable] int combiner = MPI_COMBINER_CONTIGUOUS;; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_CONTIGUOUS;; return 0; } Defined "HAVE_MPI_COMBINER_CONTIGUOUS" to "1" ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.MPI/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c:6:5: warning: unused variable ‘combiner’ [-Wunused-variable] int combiner = MPI_COMBINER_NAMED;; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_NAMED;; return 0; } Defined "HAVE_MPI_COMBINER_NAMED" to "1" ============================================================================================= TESTING: checkVersion from config.packages.MPI(config/BuildSystem/config/package.py:1026) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version Preprocessing source: #include "confdefs.h" #include "conffix.h" #include "mpi.h" ;petscpkgver(MPI_VERSION); Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.MPI -std=c99 /tmp/petsc-EaoSnO/config.packages.MPI/conftest.c For mpi need 2 <= 3 <= ============================================================================================= TESTING: checkSharedLibrary from config.packages.MPI(config/BuildSystem/config/package.py:955) By default we don't care about checking if the library is shared child config.packages.MPI 10.841773 ============================================================================================= TESTING: consistencyChecks from config.packages.zstd(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.zstd(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.zstd 0.002589 ============================================================================================= TESTING: consistencyChecks from config.packages.yaml(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.yaml(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.yaml 0.002231 ============================================================================================= TESTING: consistencyChecks from config.packages.sycl(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.sycl(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.sycl 0.001809 ============================================================================================= TESTING: consistencyChecks from config.packages.ssl(config/BuildSystem/config/packages/ssl.py:31) ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.ssl(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.ssl 0.002155 ============================================================================================= TESTING: consistencyChecks from config.packages.sprng(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.sprng(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.sprng 0.002140 Not a clone of PETSc or no Fortran compiler or fortran-bindings disabled, don't need Sowing child config.packages.sowing 0.000386 ============================================================================================= TESTING: consistencyChecks from config.packages.revolve(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.revolve(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.revolve 0.002045 ============================================================================================= TESTING: consistencyChecks from config.packages.radau5(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.radau5(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.radau5 0.001968 ============================================================================================= TESTING: consistencyChecks from config.packages.pami(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.pami(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.pami 0.001955 ============================================================================================= TESTING: consistencyChecks from config.packages.opengles(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.opengles(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.opengles 0.001815 ============================================================================================= TESTING: consistencyChecks from config.packages.opencl(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.opencl(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.opencl 0.001811 ============================================================================================= TESTING: consistencyChecks from config.packages.muparser(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.muparser(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.muparser 0.001983 ============================================================================================= TESTING: consistencyChecks from config.packages.mpe(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.mpe(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.mpe 0.002074 ============================================================================================= TESTING: consistencyChecks from config.packages.memkind(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.memkind(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.memkind 0.001783 ============================================================================================= TESTING: consistencyChecks from config.packages.libmesh(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.libmesh(config/BuildSystem/config/packages/libmesh.py:76) Defined make rule "libmesh-build" with dependencies "" and code [] Defined make rule "libmesh-install" with dependencies "" and code [] child config.packages.libmesh 0.002474 ============================================================================================= TESTING: consistencyChecks from config.packages.moose(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.moose(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.moose 0.001899 ============================================================================================= TESTING: consistencyChecks from config.packages.libjpeg(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.libjpeg(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.libjpeg 0.001786 Not a clone of PETSc, don't need Lgrind child config.packages.lgrind 0.000377 ============================================================================================= TESTING: consistencyChecks from config.packages.hip(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.hip(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.hip 0.001637 child config.packages.gmsh 0.000244 ============================================================================================= TESTING: consistencyChecks from config.packages.gmp(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.gmp(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.gmp 0.001858 ============================================================================================= TESTING: consistencyChecks from config.packages.mpfr(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.mpfr(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.mpfr 0.001796 ============================================================================================= TESTING: consistencyChecks from config.packages.giflib(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.giflib 0.001821 ============================================================================================= TESTING: consistencyChecks from config.packages.cub(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.cub(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.cub 0.001763 ============================================================================================= TESTING: consistencyChecks from config.packages.ctetgen(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.ctetgen(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.ctetgen 0.001681 ============================================================================================= TESTING: consistencyChecks from config.packages.concurrencykit(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.concurrencykit(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.concurrencykit 0.001824 ============================================================================================= TESTING: locateC2html from config.packages.c2html(config/BuildSystem/config/packages/c2html.py:30) Looking for default C2html executable Checking for program /cm/local/apps/cmake/3.9.6/bin/c2html...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/c2html...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/c2html...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/c2html...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/c2html...not found Checking for program /usr/local/bin/c2html...not found Checking for program /usr/bin/c2html...not found Checking for program /usr/local/sbin/c2html...not found Checking for program /usr/sbin/c2html...not found Checking for program /opt/ibutils/bin/c2html...not found Checking for program /sbin/c2html...not found Checking for program /usr/sbin/c2html...not found Checking for program /cm/local/apps/environment-modules/3.2.10/bin/c2html...not found Checking for program ./c2html...not found Checking for program /home2/barretk3/.local/bin/c2html...not found Checking for program /home2/barretk3/bin/c2html...not found Checking for program /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/lib/petsc/bin/win32fe/c2html...not found child config.packages.c2html 0.001861 ============================================================================================= TESTING: consistencyChecks from config.packages.boost(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.boost(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.boost 0.001768 ============================================================================================= TESTING: consistencyChecks from config.packages.silo(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.silo(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.silo 0.001683 ============================================================================================= TESTING: consistencyChecks from config.packages.Random123(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.Random123(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.Random123 0.001741 ============================================================================================= TESTING: consistencyChecks from config.packages.PARTY(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.PARTY(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.PARTY 0.001695 ============================================================================================= TESTING: consistencyChecks from config.packages.NVSHMEM(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.NVSHMEM(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.NVSHMEM 0.001219 ============================================================================================= TESTING: consistencyChecks from config.packages.Matlab(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.Matlab(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.Matlab 0.001088 ============================================================================================= TESTING: consistencyChecks from config.packages.MatlabEngine(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.MatlabEngine(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.MatlabEngine 0.001225 ============================================================================================= TESTING: consistencyChecks from config.packages.Mathematica(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.Mathematica(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.Mathematica 0.001085 ============================================================================================= TESTING: consistencyChecks from config.packages.regex(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.regex(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.regex(config/BuildSystem/config/package.py:897) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional regex Checking for library in Compiler specific search REGEX: [] ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [regexec regcomp regfree] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char regexec(); static void _check_regexec() { regexec(); } char regcomp(); static void _check_regcomp() { regcomp(); } char regfree(); static void _check_regfree() { regfree(); } int main() { _check_regexec(); _check_regcomp(); _check_regfree();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for optional headers [] in Compiler specific search REGEX: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['regex.h'] in Compiler specific search REGEX: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['regex.h'] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.MPI -std=c99 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Found header files ['regex.h'] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkVersion from config.packages.regex(config/BuildSystem/config/package.py:1026) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ============================================================================================= TESTING: checkSharedLibrary from config.packages.regex(config/BuildSystem/config/package.py:955) By default we don't care about checking if the library is shared child config.packages.regex 0.231661 ============================================================================================= TESTING: consistencyChecks from config.packages.libceed(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.libceed(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.libceed 0.002999 Defined "PYTHON_EXE" to ""/usr/bin/python"" Executing: /usr/bin/python -c "import Cython" Executing: /usr/bin/python -c "import numpy" child config.packages.python 0.050320 ============================================================================================= TESTING: consistencyChecks from config.packages.petsc4py(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.petsc4py(config/BuildSystem/config/packages/petsc4py.py:120) Defined make rule "petsc4py-build" with dependencies "" and code [] Defined make rule "petsc4py-install" with dependencies "" and code [] Defined make rule "petsc4pytest" with dependencies "" and code [] child config.packages.petsc4py 0.004610 ============================================================================================= TESTING: consistencyChecks from config.packages.mpi4py(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.mpi4py(config/BuildSystem/config/packages/mpi4py.py:79) Defined make rule "mpi4py-build" with dependencies "" and code [] Defined make rule "mpi4py-install" with dependencies "" and code [] child config.packages.mpi4py 0.004070 ============================================================================================= TESTING: consistencyChecks from config.packages.slepc(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.slepc(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.slepc(config/BuildSystem/config/package.py:897) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional slepc Looking for SLEPC at git.slepc, hg.slepc or a directory starting with ['slepc'] Found a copy of SLEPC in git.slepc Executing: ['git', 'rev-parse', '--git-dir'] stdout: .git Executing: ['git', 'cat-file', '-e', '36355849444d1e7f855f863bb249f6241dde0898^{commit}'] Executing: ['git', 'rev-parse', '36355849444d1e7f855f863bb249f6241dde0898'] stdout: 36355849444d1e7f855f863bb249f6241dde0898 Executing: ['git', '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'] stdout: No local changes to save Executing: ['git', 'clean', '-f', '-d', '-x'] stdout: Removing pkg.gitcommit Executing: ['git', 'checkout', '-f', '36355849444d1e7f855f863bb249f6241dde0898'] Defined "HAVE_SLEPC" to "1" Defined make macro "SLEPC" to "yes" Defined make rule "slepcbuild" with dependencies "" and code ['@echo "*** Building SLEPc ***"', '@${RM} -f ${PETSC_ARCH}/lib/petsc/conf/slepc.errorflg', '@(cd /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.slepc && \\\n SLEPC_DIR=/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.slepc PETSC_DIR=/home2/barretk3/ff-petsc/r PETSC_ARCH="" /usr/bin/python ./configure --with-clean --prefix=/home2/barretk3/ff-petsc/r --download-arpack=https://github.com/prj-/arpack-ng/archive/b64dccb.tar.gz && \\\n SLEPC_DIR=/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.slepc PETSC_DIR=/home2/barretk3/ff-petsc/r PETSC_ARCH=installed-arch-linux2-c-opt ${OMAKE} SLEPC_DIR=/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.slepc PETSC_DIR=/home2/barretk3/ff-petsc/r PETSC_ARCH=installed-arch-linux2-c-opt ) || \\\n (echo "**************************ERROR*************************************" && \\\n echo "Error building SLEPc." && \\\n echo "********************************************************************" && \\\n touch ${PETSC_ARCH}/lib/petsc/conf/slepc.errorflg && \\\n exit 1)'] Defined make rule "slepcinstall" with dependencies "" and code ['@echo "*** Installing SLEPc ***"', '@(cd /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.slepc && \\\n SLEPC_DIR=/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.slepc PETSC_DIR=/home2/barretk3/ff-petsc/r PETSC_ARCH=installed-arch-linux2-c-opt ${OMAKE} install SLEPC_DIR=/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.slepc PETSC_DIR=/home2/barretk3/ff-petsc/r PETSC_ARCH=installed-arch-linux2-c-opt ) || \\\n (echo "**************************ERROR*************************************" && \\\n echo "Error building SLEPc." && \\\n echo "********************************************************************" && \\\n exit 1)'] Defined make rule "slepc-build" with dependencies "" and code [] Defined make rule "slepc-install" with dependencies "slepcbuild slepcinstall" and code [] ============================================================================================= SLEPc examples are available at ${PETSC_DIR}/fr/externalpackages/git.slepc export SLEPC_DIR=/home2/barretk3/ff-petsc/r ============================================================================================= ============================================================================================= TESTING: checkSharedLibrary from config.packages.slepc(config/BuildSystem/config/package.py:955) By default we don't care about checking if the library is shared child config.packages.slepc 1.892249 ============================================================================================= TESTING: consistencyChecks from config.packages.opengl(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.opengl(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.opengl 0.002671 ============================================================================================= TESTING: consistencyChecks from config.packages.glut(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.glut 0.002594 ============================================================================================= TESTING: consistencyChecks from config.packages.GLVis(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.GLVis(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.GLVis 0.002818 ============================================================================================= TESTING: consistencyChecks from config.packages.CoDiPack(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.CoDiPack(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.CoDiPack 0.002731 ============================================================================================= TESTING: consistencyChecks from config.packages.adblaslapack(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.adblaslapack(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.adblaslapack 0.002588 child config.packages.cxxlibs 0.000049 ============================================================================================= TESTING: locateCMake from config.packages.cmake(config/BuildSystem/config/packages/cmake.py:48) Looking for default CMake executable Checking for program /cm/local/apps/cmake/3.9.6/bin/cmake...found Defined make macro "CMAKE" to "/cm/local/apps/cmake/3.9.6/bin/cmake" Looking for default CTest executable Checking for program /cm/local/apps/cmake/3.9.6/bin/ctest...found Defined make macro "CTEST" to "/cm/local/apps/cmake/3.9.6/bin/ctest" Executing: /cm/local/apps/cmake/3.9.6/bin/cmake --version stdout: cmake version 3.9.6 CMake suite maintained and supported by Kitware (kitware.com/cmake). cmake version found 3.9.6 child config.packages.cmake 0.175704 ============================================================================================= TESTING: consistencyChecks from config.packages.unittestcpp(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.unittestcpp(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.unittestcpp 0.003891 ============================================================================================= TESTING: consistencyChecks from config.packages.googletest(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.googletest(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.googletest 0.003049 ============================================================================================= TESTING: consistencyChecks from config.packages.eigen(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.eigen(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.eigen 0.002897 ============================================================================================= TESTING: consistencyChecks from config.packages.szlib(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.szlib(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.szlib 0.002830 ============================================================================================= TESTING: consistencyChecks from config.packages.zlib(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.zlib(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.zlib 0.002815 child config.packages.mathlib 0.000043 ============================================================================================= TESTING: consistencyChecks from config.packages.tetgen(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.tetgen(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.tetgen(config/BuildSystem/config/packages/tetgen.py:83) ================================================================================== Checking for a functional tetgen Looking for TETGEN at git.tetgen, hg.tetgen or a directory starting with ['tetgen'] Found a copy of TETGEN in tetgen1.5.1 Makefile /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/lib/petsc/conf/pkg.conf.tetgen has correct checksum Do not need to rebuild TETGEN Not checking for library in Download TETGEN: ['/home2/barretk3/ff-petsc/r/lib/libtet.a'] because no functions given to check for ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library ['/home2/barretk3/ff-petsc/r/lib/libtet.a'] ['libm.a'] Checking for optional headers [] in Download TETGEN: ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['tetgen.h'] in Download TETGEN: ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['tetgen.h'] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CXXPPFLAGS ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.headers -std=gnu++11 -I/home2/barretk3/ff-petsc/r/include -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.cc Preprocess stderr before filtering: : Preprocess stderr after filtering: : Found header files ['tetgen.h'] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.tetgen -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 -I/home2/barretk3/ff-petsc/r/include /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.cc Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.cc: In function ‘int main()’: /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.cc:9:33: error: cannot convert ‘char*’ to ‘tetgenbehavior*’ for argument ‘1’ to ‘void tetrahedralize(tetgenbehavior*, tetgenio*, tetgenio*, tetgenio*, tetgenio*)’ tetrahedralize(args, &in, &out); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { char args[] = ""; tetgenio in,out; tetrahedralize(args, &in, &out); ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.tetgen -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 -I/home2/barretk3/ff-petsc/r/include -DTETLIBRARY /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char args[] = ""; tetgenio in,out; tetrahedralize(args, &in, &out); ; return 0; } Defined "HAVE_TETGEN_TETLIBRARY_NEEDED" to "1" ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -c -o /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.tetgen -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 -fPIC -std=gnu++11 -I/home2/barretk3/ff-petsc/r/include -DTETLIBRARY /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char args[] = ""; tetgenio in,out; tetrahedralize(args, &in, &out); ; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx -o /tmp/petsc-EaoSnO/config.packages.tetgen/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=gnu++11 /tmp/petsc-EaoSnO/config.packages.tetgen/conftest.o -Wl,-rpath,/home2/barretk3/ff-petsc/r/lib -L/home2/barretk3/ff-petsc/r/lib -ltet -lquadmath -lstdc++ -ldl ============================================================================================= TESTING: checkVersion from config.packages.tetgen(config/BuildSystem/config/package.py:1026) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ============================================================================================= TESTING: checkSharedLibrary from config.packages.tetgen(config/BuildSystem/config/package.py:955) By default we don't care about checking if the library is shared child config.packages.tetgen 0.885636 ============================================================================================= TESTING: consistencyChecks from config.packages.tchem(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.tchem(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.tchem 0.002992 ============================================================================================= TESTING: consistencyChecks from config.packages.saws(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.saws(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.saws 0.002940 ============================================================================================= TESTING: consistencyChecks from config.packages.libpng(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.libpng(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.libpng 0.002677 ============================================================================================= TESTING: consistencyChecks from config.packages.combblas(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.combblas(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.combblas 0.002688 ============================================================================================= TESTING: consistencyChecks from config.packages.Triangle(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.Triangle(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.Triangle 0.002695 ============================================================================================= TESTING: consistencyChecks from config.packages.metis(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.metis(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.metis(config/BuildSystem/config/packages/metis.py:52) ================================================================================== Checking for a functional metis Looking for METIS at git.metis, hg.metis or a directory starting with ['petsc-pkg-metis'] Found a copy of METIS in git.metis Executing: ['git', 'rev-parse', '--git-dir'] stdout: .git Executing: ['git', 'cat-file', '-e', 'v5.1.0-p10^{commit}'] Executing: ['git', 'rev-parse', 'v5.1.0-p10'] stdout: c8d2dc1e751ef7ebe5e221156d7572d7cea26990 Executing: ['git', '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'] stdout: No local changes to save Executing: ['git', 'clean', '-f', '-d', '-x'] stdout: Removing metis.petscconf Removing petsc-build/ Removing pkg.gitcommit Executing: ['git', 'checkout', '-f', 'c8d2dc1e751ef7ebe5e221156d7572d7cea26990'] Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -V Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -V Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -V Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Removing configure arguments ['-DCMAKE_CXX_COMPILER="/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicxx"', '-DCMAKE_C_COMPILER="/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc"'] Makefile /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/lib/petsc/conf/pkg.conf.metis has correct checksum Commit file /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/lib/petsc/conf/pkg.gitcommit.metis has correct checksum Do not need to rebuild METIS Checking for library in Download METIS: ['/home2/barretk3/ff-petsc/r/lib/libmetis.a'] Contents: ['lib', 'include'] ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [METIS_PartGraphKway] in library ['/home2/barretk3/ff-petsc/r/lib/libmetis.a'] ['libm.a'] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char METIS_PartGraphKway(); static void _check_METIS_PartGraphKway() { METIS_PartGraphKway(); } int main() { _check_METIS_PartGraphKway();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -Wl,-rpath,/home2/barretk3/ff-petsc/r/lib -L/home2/barretk3/ff-petsc/r/lib -lmetis -lm -lquadmath -lstdc++ -ldl Defined "HAVE_LIBMETIS" to "1" Checking for optional headers [] in Download METIS: ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['metis.h'] in Download METIS: ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['metis.h'] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.MPI -std=c99 -I/home2/barretk3/ff-petsc/r/include -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Found header files ['metis.h'] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.metis/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 -I/home2/barretk3/ff-petsc/r/include /tmp/petsc-EaoSnO/config.packages.metis/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.metis/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.metis/conftest.c:8:7: warning: extra tokens at end of #endif directive [enabled by default] #endif; ^ Source: #include "confdefs.h" #include "conffix.h" #include "metis.h" int main() { #if (IDXTYPEWIDTH != 32) #error incompatible IDXTYPEWIDTH #endif; return 0; } ============================================================================================= TESTING: checkVersion from config.packages.metis(config/BuildSystem/config/package.py:1026) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version Preprocessing source: #include "confdefs.h" #include "conffix.h" #include "metis.h" ;petscpkgver(METIS_VER_MAJOR.METIS_VER_MINOR.METIS_VER_SUBMINOR); Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -std=c99 -I/home2/barretk3/ff-petsc/r/include /tmp/petsc-EaoSnO/config.packages.metis/conftest.c For metis need <= 5.1.0 <= ============================================================================================= TESTING: checkSharedLibrary from config.packages.metis(config/BuildSystem/config/package.py:955) By default we don't care about checking if the library is shared child config.packages.metis 1.260601 ============================================================================================= TESTING: consistencyChecks from config.packages.pragmatic(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.pragmatic(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.pragmatic 0.003597 ============================================================================================= TESTING: consistencyChecks from config.packages.parmetis(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.parmetis(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.parmetis(config/BuildSystem/config/packages/parmetis.py:41) ================================================================================== Checking for a functional parmetis Looking for PARMETIS at git.parmetis, hg.parmetis or a directory starting with ['petsc-pkg-parmetis'] Found a copy of PARMETIS in git.parmetis Executing: ['git', 'rev-parse', '--git-dir'] stdout: .git Executing: ['git', 'cat-file', '-e', 'v4.0.3-p6^{commit}'] Executing: ['git', 'rev-parse', 'v4.0.3-p6'] stdout: 475d8facbb324527c205f1f78a7c90bd160bddcd Executing: ['git', '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'] stdout: No local changes to save Executing: ['git', 'clean', '-f', '-d', '-x'] stdout: Removing parmetis.petscconf Removing petsc-build/ Removing pkg.gitcommit Executing: ['git', 'checkout', '-f', '475d8facbb324527c205f1f78a7c90bd160bddcd'] Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -V Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -V Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 -V Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpif90 --version stdout: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Makefile /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/lib/petsc/conf/pkg.conf.parmetis has correct checksum Commit file /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/lib/petsc/conf/pkg.gitcommit.parmetis has correct checksum Do not need to rebuild PARMETIS Checking for library in Download PARMETIS: ['/home2/barretk3/ff-petsc/r/lib/libparmetis.a'] Contents: ['lib', 'include'] ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [ParMETIS_V3_PartKway] in library ['/home2/barretk3/ff-petsc/r/lib/libparmetis.a'] ['/home2/barretk3/ff-petsc/r/lib/libmetis.a', 'libm.a'] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ParMETIS_V3_PartKway(); static void _check_ParMETIS_V3_PartKway() { ParMETIS_V3_PartKway(); } int main() { _check_ParMETIS_V3_PartKway();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -Wl,-rpath,/home2/barretk3/ff-petsc/r/lib -L/home2/barretk3/ff-petsc/r/lib -lparmetis -Wl,-rpath,/home2/barretk3/ff-petsc/r/lib -L/home2/barretk3/ff-petsc/r/lib -lmetis -lm -lquadmath -lstdc++ -ldl Defined "HAVE_LIBPARMETIS" to "1" Checking for optional headers [] in Download PARMETIS: ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['parmetis.h'] in Download PARMETIS: ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['parmetis.h'] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include', '/home2/barretk3/ff-petsc/r/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.headers -std=c99 -I/home2/barretk3/ff-petsc/r/include -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include -I/home2/barretk3/ff-petsc/r/include /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Found header files ['parmetis.h'] in ['/home2/barretk3/ff-petsc/r/include', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for functions [ParMETIS_ComputeVertexSeparator] in library ['/home2/barretk3/ff-petsc/r/lib/libparmetis.a'] ['/home2/barretk3/ff-petsc/r/lib/libmetis.a', 'libm.a'] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ParMETIS_ComputeVertexSeparator(); static void _check_ParMETIS_ComputeVertexSeparator() { ParMETIS_ComputeVertexSeparator(); } int main() { _check_ParMETIS_ComputeVertexSeparator();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -Wl,-rpath,/home2/barretk3/ff-petsc/r/lib -L/home2/barretk3/ff-petsc/r/lib -lparmetis -Wl,-rpath,/home2/barretk3/ff-petsc/r/lib -L/home2/barretk3/ff-petsc/r/lib -lmetis -lm -lquadmath -lstdc++ -ldl Defined "HAVE_LIBPARMETIS" to "1" ============================================================================================= TESTING: checkVersion from config.packages.parmetis(config/BuildSystem/config/package.py:1026) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version Preprocessing source: #include "confdefs.h" #include "conffix.h" #include "parmetis.h" ;petscpkgver(PARMETIS_MAJOR_VERSION.PARMETIS_MINOR_VERSION.PARMETIS_SUBMINOR_VERSION); Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.parmetis -std=c99 -I/home2/barretk3/ff-petsc/r/include /tmp/petsc-EaoSnO/config.packages.parmetis/conftest.c For parmetis need <= 4.0.3 <= ============================================================================================= TESTING: checkSharedLibrary from config.packages.parmetis(config/BuildSystem/config/package.py:955) By default we don't care about checking if the library is shared child config.packages.parmetis 1.166155 ============================================================================================= TESTING: consistencyChecks from config.packages.Chaco(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.Chaco(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.Chaco 0.002663 Executing: uname -s stdout: Linux ============================================================================================= TESTING: consistencyChecks from config.packages.hdf5(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.hdf5(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.hdf5 0.080893 ============================================================================================= TESTING: consistencyChecks from config.packages.med(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.med(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.med 0.003092 ============================================================================================= TESTING: consistencyChecks from config.packages.cgns(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.cgns(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.cgns 0.002746 ============================================================================================= TESTING: consistencyChecks from config.packages.ascem-io(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.ascem-io(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.ascem-io 0.002825 ============================================================================================= TESTING: consistencyChecks from config.packages.pflotran(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.pflotran(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.pflotran 0.002811 ============================================================================================= TESTING: consistencyChecks from config.packages.alquimia(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.alquimia(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.alquimia 0.002798 ============================================================================================= TESTING: consistencyChecks from config.packages.SAMRAI(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.SAMRAI(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.SAMRAI 0.002714 ============================================================================================= TESTING: consistencyChecks from config.packages.ADIOS2(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.ADIOS2(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.ADIOS2 0.002639 child config.packages.flibs 0.000039 ============================================================================================= TESTING: consistencyChecks from config.packages.pnetcdf(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.pnetcdf(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.pnetcdf 0.002600 ============================================================================================= TESTING: consistencyChecks from config.packages.netcdf(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.netcdf(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.netcdf 0.002606 ============================================================================================= TESTING: consistencyChecks from config.packages.exodusii(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.exodusii(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.exodusii 0.002605 ============================================================================================= TESTING: consistencyChecks from config.packages.fblaslapack(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.fblaslapack(config/BuildSystem/config/packages/fblaslapack.py:27) The Apple Accelerate library uses threads that valgrind cannot handle child config.packages.fblaslapack 0.002568 ============================================================================================= TESTING: consistencyChecks from config.packages.pthread(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.pthread(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.pthread(config/BuildSystem/config/packages/pthread.py:20) Checks for pthread_barrier_t, cpu_set_t, and sys/sysctl.h ================================================================================== Checking for a functional pthread Checking for library in Compiler specific search PTHREAD: [] ============================================================================================= TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [pthread_create] in library [] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char pthread_create(); static void _check_pthread_create() { pthread_create(); } int main() { _check_pthread_create();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for optional headers [] in Compiler specific search PTHREAD: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Found header files [] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking for headers ['pthread.h'] in Compiler specific search PTHREAD: ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ============================================================================================= TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['pthread.h'] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Checking include with compiler flags var CPPFLAGS ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.packages.parmetis -I/tmp/petsc-EaoSnO/config.headers -std=c99 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0 -I/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include /tmp/petsc-EaoSnO/config.headers/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Found header files ['pthread.h'] in ['/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include/gfortran/4.8.0', '/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/include'] ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.pthread/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c:6:1: error: unknown type name ‘pthread_barrier_t’ pthread_barrier_t *a; ^ /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c:6:20: warning: unused variable ‘a’ [-Wunused-variable] pthread_barrier_t *a; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { pthread_barrier_t *a; ; return 0; } ===== Checking compiler Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.packages.pthread/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c: In function ‘main’: /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c:6:12: warning: unused variable ‘a’ [-Wunused-variable] cpu_set_t *a; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { cpu_set_t *a; ; return 0; } Defined "HAVE_SCHED_CPU_SET_T" to "1" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -E -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.packages.parmetis -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.packages.pthread -std=c99 /tmp/petsc-EaoSnO/config.packages.pthread/conftest.c Preprocess stderr before filtering: : Preprocess stderr after filtering: : Defined "HAVE_SYS_SYSCTL_H" to "1" ============================================================================================= TESTING: checkVersion from config.packages.pthread(config/BuildSystem/config/package.py:1026) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ============================================================================================= TESTING: checkSharedLibrary from config.packages.pthread(config/BuildSystem/config/package.py:955) By default we don't care about checking if the library is shared child config.packages.pthread 0.997744 ============================================================================================= TESTING: consistencyChecks from config.packages.egads(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: alternateConfigureLibrary from config.packages.egads(config/BuildSystem/config/package.py:959) Called if --with-packagename=0; does nothing by default child config.packages.egads 0.003383 ============================================================================================= TESTING: consistencyChecks from config.packages.PTScotch(config/BuildSystem/config/package.py:963) Checks run on the system and currently installed packages that need to be correct for the package now being configured ============================================================================================= TESTING: checkDependencies from config.packages.PTScotch(config/BuildSystem/config/package.py:872) ============================================================================================= TESTING: configureLibrary from config.packages.PTScotch(config/BuildSystem/config/package.py:897) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional PTScotch Looking for PTSCOTCH at git.ptscotch, hg.ptscotch or a directory starting with ['scotch', 'petsc-pkg-scotch'] Found a copy of PTSCOTCH in git.ptscotch Executing: ['git', 'rev-parse', '--git-dir'] stdout: .git Executing: ['git', 'cat-file', '-e', 'v6.1.0^{commit}'] Executing: ['git', 'rev-parse', 'v6.1.0'] stdout: efc9416ca2cff3409fb464e56caacbec295d8c00 Executing: ['git', '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'] stdout: No local changes to save Executing: ['git', 'clean', '-f', '-d', '-x'] stdout: Removing bin/ Removing include/ Removing lib/ Removing pkg.gitcommit Removing src/Makefile.inc Removing src/libscotch/arch.o Removing src/libscotch/arch_build.o Removing src/libscotch/arch_build2.o Removing src/libscotch/arch_cmplt.o Removing src/libscotch/arch_cmpltw.o Removing src/libscotch/arch_deco.o Removing src/libscotch/arch_deco2.o Removing src/libscotch/arch_dist.o Removing src/libscotch/arch_hcub.o Removing src/libscotch/arch_mesh.o Removing src/libscotch/arch_sub.o Removing src/libscotch/arch_tleaf.o Removing src/libscotch/arch_torus.o Removing src/libscotch/arch_vcmplt.o Removing src/libscotch/arch_vhcub.o Removing src/libscotch/bgraph.o Removing src/libscotch/bgraph_bipart_bd.o Removing src/libscotch/bgraph_bipart_df.o Removing src/libscotch/bgraph_bipart_ex.o Removing src/libscotch/bgraph_bipart_fm.o Removing src/libscotch/bgraph_bipart_gg.o Removing src/libscotch/bgraph_bipart_gp.o Removing src/libscotch/bgraph_bipart_ml.o Removing src/libscotch/bgraph_bipart_st.o Removing src/libscotch/bgraph_bipart_zr.o Removing src/libscotch/bgraph_check.o Removing src/libscotch/bgraph_store.o Removing src/libscotch/common.o Removing src/libscotch/common_file.o Removing src/libscotch/common_file_compress.o Removing src/libscotch/common_file_decompress.o Removing src/libscotch/common_integer.o Removing src/libscotch/common_memory.o Removing src/libscotch/dummysizes Removing src/libscotch/scotch.h Removing src/libscotch/scotchf.h Executing: ['git', 'checkout', '-f', 'efc9416ca2cff3409fb464e56caacbec295d8c00'] Creating PTScotch /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/Makefile.inc Checking for program /cm/local/apps/cmake/3.9.6/bin/bison...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/bison...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/bison...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/bison...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/bison...not found Checking for program /usr/local/bin/bison...not found Checking for program /usr/bin/bison...found Defined make macro "BISON" to "/usr/bin/bison" Checking for program /cm/local/apps/cmake/3.9.6/bin/flex...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/libfabric/bin/flex...not found Checking for program /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/flex...not found Checking for program /cm/shared/apps/intel/itac/2019.5.075/intel64/bin/flex...not found Checking for program /cm/shared/apps/hdf5/1.10.0/bin/flex...not found Checking for program /usr/local/bin/flex...not found Checking for program /usr/bin/flex...found Defined make macro "FLEX" to "/usr/bin/flex" Checking for functions [timer_create] in library ['-lrt'] [] ===== Checking linker Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -c -o /tmp/petsc-EaoSnO/config.libraries/conftest.o -I/tmp/petsc-EaoSnO/config.compilerFlags -I/tmp/petsc-EaoSnO/config.utilities.closure -I/tmp/petsc-EaoSnO/config.setCompilers -I/tmp/petsc-EaoSnO/config.compilers -I/tmp/petsc-EaoSnO/config.compilersFortran -I/tmp/petsc-EaoSnO/config.headers -I/tmp/petsc-EaoSnO/config.utilities.cacheDetails -I/tmp/petsc-EaoSnO/config.types -I/tmp/petsc-EaoSnO/config.functions -I/tmp/petsc-EaoSnO/config.utilities.featureTestMacros -I/tmp/petsc-EaoSnO/config.utilities.missing -I/tmp/petsc-EaoSnO/PETSc.options.sharedLibraries -I/tmp/petsc-EaoSnO/PETSc.options.scalarTypes -I/tmp/petsc-EaoSnO/config.packages.metis -I/tmp/petsc-EaoSnO/config.packages.MPI -I/tmp/petsc-EaoSnO/config.libraries -I/tmp/petsc-EaoSnO/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native -std=c99 /tmp/petsc-EaoSnO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char timer_create(); static void _check_timer_create() { timer_create(); } int main() { _check_timer_create();; return 0; } Executing: /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -o /tmp/petsc-EaoSnO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mtune=native /tmp/petsc-EaoSnO/config.libraries/conftest.o -lrt -lquadmath -lstdc++ -ldl Defined "HAVE_LIBRT" to "1" Adding ['-lrt'] to LIBS Executing: uname -s stdout: Linux Have to rebuild PTSCOTCH, /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/Makefile.inc != /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/lib/petsc/conf/pkg.conf.ptscotch ============================================================================================= Compiling PTScotch; this may take several minutes ============================================================================================= Executing: cd /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src && make clean ptesmumps esmumps stdout: make[1]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src' /usr/bin/mkdir -p ../bin /usr/bin/mkdir -p ../include /usr/bin/mkdir -p ../lib (cd libscotch ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' rm -f *~ *.o lib*.a parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output *dummysizes make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' (cd scotch ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/scotch' rm -f *~ *.o acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv gdump *ggath *gmap gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst *gord gotst gout *gpart *gscat *gtst mcv mmk_m2 mmk_m3 mord mtst make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/scotch' (cd libscotchmetis ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotchmetis' rm -f *~ *.o lib*.a metis.h parmetis.h make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotchmetis' (cd check ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/check' rm -f *~ *.o make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/check' (cd esmumps ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/esmumps' rm -f *~ common.h *.o lib*.a main_esmumps make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/esmumps' (cd libscotch ; make VERSION=6 RELEASE=1 PATCHLEVEL=0 scotch && make install) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' make \ CC="/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" \ CCD="/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" \ scotch.h \ scotchf.h \ libscotch.a \ libscotcherr.a \ libscotcherrexit.a make[3]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch.c -o arch.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 dummysizes.c -o dummysizes -lm -lrt ./dummysizes "-s" library.h scotch.h ./dummysizes "-s" library_f.h scotchf.h /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_build.c -o arch_build.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_build2.c -o arch_build2.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_cmplt.c -o arch_cmplt.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_cmpltw.c -o arch_cmpltw.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_deco.c -o arch_deco.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_deco2.c -o arch_deco2.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_dist.c -o arch_dist.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_hcub.c -o arch_hcub.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_mesh.c -o arch_mesh.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_sub.c -o arch_sub.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_tleaf.c -o arch_tleaf.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_torus.c -o arch_torus.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_vcmplt.c -o arch_vcmplt.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_vhcub.c -o arch_vhcub.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph.c -o bgraph.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_bd.c -o bgraph_bipart_bd.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_df.c -o bgraph_bipart_df.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_ex.c -o bgraph_bipart_ex.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_fm.c -o bgraph_bipart_fm.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_gg.c -o bgraph_bipart_gg.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_gp.c -o bgraph_bipart_gp.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_ml.c -o bgraph_bipart_ml.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_st.c -o bgraph_bipart_st.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_zr.c -o bgraph_bipart_zr.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_check.c -o bgraph_check.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_store.c -o bgraph_store.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common.c -DSCOTCH_COMMON_RENAME -o common.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_file.c -DSCOTCH_COMMON_RENAME -o common_file.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_file_compress.c -DSCOTCH_COMMON_RENAME -o common_file_compress.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_file_decompress.c -DSCOTCH_COMMON_RENAME -o common_file_decompress.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_integer.c -DSCOTCH_COMMON_RENAME -o common_integer.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_memory.c -DSCOTCH_COMMON_RENAME -o common_memory.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_string.c -DSCOTCH_COMMON_RENAME -o common_string.o make[3]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' make[1]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src' **** Configure header /tmp/petsc-EaoSnO/confdefs.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #define PETSC_Alignx(a,b) #define PETSC_CLANGUAGE_C 1 #define PETSC_CXX_INLINE inline #define PETSC_CXX_RESTRICT __restrict #define PETSC_C_INLINE inline #define PETSC_C_RESTRICT __restrict #define PETSC_FORTRAN_CHARLEN_T int #define PETSC_FORTRAN_TYPE_INITIALIZE = -2 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_CXX_COMPLEX 1 #define PETSC_HAVE_CXX_DIALECT_CXX11 1 #define PETSC_HAVE_DLADDR 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_DYNAMIC_LIBRARIES 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_FORTRAN_FLUSH 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_HAVE_FORTRAN_TYPE_STAR 1 #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_IMMINTRIN_H 1 #define PETSC_HAVE_INTTYPES_H 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_HAVE_ISNORMAL 1 #define PETSC_HAVE_I_MPI_NUMVERSION 20190005300 #define PETSC_HAVE_LGAMMA 1 #define PETSC_HAVE_LOG2 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_MALLOC_H 1 #define PETSC_HAVE_MEMALIGN 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE_MMAP 1 #define PETSC_HAVE_MPICH_NUMVERSION 30300300 #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_COMBINER_CONTIGUOUS 1 #define PETSC_HAVE_MPI_COMBINER_DUP 1 #define PETSC_HAVE_MPI_COMBINER_NAMED 1 #define PETSC_HAVE_MPI_EXSCAN 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_F90MODULE_VISIBILITY 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_GET_ACCUMULATE 1 #define PETSC_HAVE_MPI_GET_LIBRARY_VERSION 1 #define PETSC_HAVE_MPI_IALLREDUCE 1 #define PETSC_HAVE_MPI_IBARRIER 1 #define PETSC_HAVE_MPI_INIT_THREAD 1 #define PETSC_HAVE_MPI_INT64_T 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_HAVE_MPI_LONG_DOUBLE 1 #define PETSC_HAVE_MPI_NEIGHBORHOOD_COLLECTIVES 1 #define PETSC_HAVE_MPI_NONBLOCKING_COLLECTIVES 1 #define PETSC_HAVE_MPI_ONE_SIDED 1 #define PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY 1 #define PETSC_HAVE_MPI_REDUCE_LOCAL 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER_BLOCK 1 #define PETSC_HAVE_MPI_RGET 1 #define PETSC_HAVE_MPI_TYPE_DUP 1 #define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_REAL___FLOAT128 1 #define PETSC_HAVE_RTLD_GLOBAL 1 #define PETSC_HAVE_RTLD_LAZY 1 #define PETSC_HAVE_RTLD_LOCAL 1 #define PETSC_HAVE_RTLD_NOW 1 #define PETSC_HAVE_SCHED_CPU_SET_T 1 #define PETSC_HAVE_SETJMP_H 1 #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_SLEPC 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_SYSINFO 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_SYS_PROCFS_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_SYS_SYSCTL_H 1 #define PETSC_HAVE_SYS_SYSINFO_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_TETGEN_TETLIBRARY_NEEDED 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_IS_COLORING_MAX USHRT_MAX #define PETSC_IS_COLORING_VALUE_TYPE short #define PETSC_IS_COLORING_VALUE_TYPE_F integer2 #define PETSC_LEVEL1_DCACHE_LINESIZE 64 #define PETSC_MAX_PATH_LEN 4096 #define PETSC_MEMALIGN 16 #define PETSC_MPIU_IS_COLORING_VALUE_TYPE MPI_UNSIGNED_SHORT #define PETSC_NEEDS_UTYPE_TYPEDEFS 1 #define PETSC_PYTHON_EXE "/usr/bin/python" #define PETSC_SIGNAL_CAST #define PETSC_SIZEOF_ENUM 4 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG 8 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_USE_AVX512_KERNELS 1 #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_CTABLE 1 #define PETSC_USE_DEBUGGER "gdb" #define PETSC_USE_INFO 1 #define PETSC_USE_LOG 1 #define PETSC_USE_MALLOC_COALESCED 1 #define PETSC_USE_PROC_FOR_SIZE 1 #define PETSC_USE_REAL_DOUBLE 1 #define PETSC_USE_SHARED_LIBRARIES 1 #define PETSC_USE_VISIBILITY_C 1 #define PETSC_USE_VISIBILITY_CXX 1 #define PETSC_USING_64BIT_PTR 1 #define PETSC_USING_F2003 1 #define PETSC_USING_F90FREEFORM 1 #define PETSC__BSD_SOURCE 1 #define PETSC__DEFAULT_SOURCE 1 #define PETSC__GNU_SOURCE 1 #endif **** C specific Configure header /tmp/petsc-EaoSnO/conffix.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #if defined(__cplusplus) extern "C" { } #else #endif #endif ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error running make on PTScotch: Could not execute "['cd /home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src && make clean ptesmumps esmumps']": make[1]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src' /usr/bin/mkdir -p ../bin /usr/bin/mkdir -p ../include /usr/bin/mkdir -p ../lib (cd libscotch ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' rm -f *~ *.o lib*.a parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output *dummysizes make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' (cd scotch ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/scotch' rm -f *~ *.o acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv gdump *ggath *gmap gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst *gord gotst gout *gpart *gscat *gtst mcv mmk_m2 mmk_m3 mord mtst make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/scotch' (cd libscotchmetis ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotchmetis' rm -f *~ *.o lib*.a metis.h parmetis.h make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotchmetis' (cd check ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/check' rm -f *~ *.o make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/check' (cd esmumps ; make clean) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/esmumps' rm -f *~ common.h *.o lib*.a main_esmumps make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/esmumps' (cd libscotch ; make VERSION=6 RELEASE=1 PATCHLEVEL=0 scotch && make install) make[2]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' make \ CC="/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" \ CCD="/cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc" \ scotch.h \ scotchf.h \ libscotch.a \ libscotcherr.a \ libscotcherrexit.a make[3]: Entering directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch.c -o arch.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 dummysizes.c -o dummysizes -lm -lrt ./dummysizes "-s" library.h scotch.h ./dummysizes "-s" library_f.h scotchf.h /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_build.c -o arch_build.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_build2.c -o arch_build2.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_cmplt.c -o arch_cmplt.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_cmpltw.c -o arch_cmpltw.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_deco.c -o arch_deco.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_deco2.c -o arch_deco2.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_dist.c -o arch_dist.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_hcub.c -o arch_hcub.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_mesh.c -o arch_mesh.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_sub.c -o arch_sub.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_tleaf.c -o arch_tleaf.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_torus.c -o arch_torus.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_vcmplt.c -o arch_vcmplt.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c arch_vhcub.c -o arch_vhcub.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph.c -o bgraph.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_bd.c -o bgraph_bipart_bd.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_df.c -o bgraph_bipart_df.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_ex.c -o bgraph_bipart_ex.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_fm.c -o bgraph_bipart_fm.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_gg.c -o bgraph_bipart_gg.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_gp.c -o bgraph_bipart_gp.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_ml.c -o bgraph_bipart_ml.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_st.c -o bgraph_bipart_st.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_bipart_zr.c -o bgraph_bipart_zr.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_check.c -o bgraph_check.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c bgraph_store.c -o bgraph_store.o -DSCOTCH_VERSION_NUM=6 -DSCOTCH_RELEASE_NUM=1 -DSCOTCH_PATCHLEVEL_NUM=0 /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common.c -DSCOTCH_COMMON_RENAME -o common.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_file.c -DSCOTCH_COMMON_RENAME -o common_file.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_file_compress.c -DSCOTCH_COMMON_RENAME -o common_file_compress.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_file_decompress.c -DSCOTCH_COMMON_RENAME -o common_file_decompress.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_integer.c -DSCOTCH_COMMON_RENAME -o common_integer.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_memory.c -DSCOTCH_COMMON_RENAME -o common_memory.o /cm/shared/apps/intel/compilers_and_libraries/2019.5.075/mpi/intel64/bin/mpicc -fPIC -fstack-protector -O3 -mtune=native -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict="__restrict" -DINTSIZE32 -DSCOTCH_METIS_PREFIX -c common_string.c -DSCOTCH_COMMON_RENAME -o common_string.o make[3]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' make[2]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src/libscotch' make[1]: Leaving directory `/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/fr/externalpackages/git.ptscotch/src'In file included from /usr/include/sys/wait.h:30:0, from common.h:130, from common_string.c:57: /usr/include/signal.h:156:1: error: unknown type name ‘siginfo_t’ extern void psiginfo (const siginfo_t *__pinfo, const char *__s); ^ make[3]: *** [common_string.o] Error 1 make[2]: *** [scotch] Error 2 make[1]: *** [libscotch] Error 2 ******************************************************************************* File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/configure.py", line 458, in petsc_configure framework.configure(out = sys.stdout) File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/framework.py", line 1289, in configure self.processChildren() File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/framework.py", line 1277, in processChildren self.serialEvaluation(self.childGraph) File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/framework.py", line 1252, in serialEvaluation child.configure() File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/package.py", line 1146, in configure self.executeTest(self.configureLibrary) File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/base.py", line 138, in executeTest ret = test(*args,**kargs) File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/package.py", line 904, in configureLibrary for location, directory, lib, incl in self.generateGuesses(): File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/package.py", line 478, in generateGuesses d = self.checkDownload() File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/package.py", line 612, in checkDownload return self.getInstallDir() File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/package.py", line 367, in getInstallDir installDir = self.Install() File "/home2/barretk3/FreeFem-sources/3rdparty/ff-petsc/petsc-3.15.0/config/BuildSystem/config/packages/PTScotch.py", line 105, in Install raise RuntimeError('Error running make on PTScotch: '+str(e)) ================================================================================ Finishing configure run at Mon, 26 Apr 2021 14:50:49 -0400 ================================================================================