Problem when compiling SCALAPACK

nabil3achour · September 22, 2020, 8:45am

Dear all
We are trying to install FreeFem (from git) on a MacBook (macOS 10.15.6). We have a problem at the 'make petsc-slepc ’ stage when compiling SCALAPACK.
Below is the error message. We don’t understand why the compiler wants to use c99 at this stage.
Is this problem identified ?

Thanks for help
Nabil & David

igsum2d_.c:153:7: error: implicit declaration of function ‘BI_imvcopy’ is invalid in C99 [-Werror,-Wimplicit-function-declaration]

BI_imvcopy(Mpval(m), Mpval(n), A, tlda, bp->Buff);

^

igsum2d_.c:166:6: error: implicit declaration of function ‘BI_ivmcopy’ is invalid in C99 [-Werror,-Wimplicit-function-declaration]

BI_ivmcopy(Mpval(m), Mpval(n), A, tlda, bp2->Buff);

^

igsum2d_.c:172:3: error: implicit declaration of function ‘BI_ivmcopy’ is invalid in C99 [-Werror,-Wimplicit-function-declaration]

BI_ivmcopy(Mpval(m), Mpval(n), A, tlda, bp2->Buff);

^

igsum2d_.c:226:10: error: implicit declaration of function ‘BI_ivmcopy’ is invalid in C99 [-Werror,-Wimplicit-function-declaration]

BI_ivmcopy(Mpval(m), Mpval(n), A, tlda, bp->Buff);

prj · September 22, 2020, 8:52am

Are you voluntarily using the -Werror flag? This should be fixed in PETSc 3.14.0 coming at the end of the month.

david.fabre · September 22, 2020, 9:07am

Thanks Pierre For answer.
I don’t think we volontarily use Werror flag, how can we disable this ?

prj · September 22, 2020, 9:10am

I’m cooking something for you, please give me a couple of minutes

prj · September 22, 2020, 9:43am

Could you please try the branch petsc-3.14.0? This branch installs a very recent snapshot of PETSc (from this morning), which should fix this issue, and which is very close to the upcoming PETSc release 3.14.0. So if you agree to be a guinea pig, I’d be really grateful if you report FreeFEM/PETSc error with this branch (I’ve made a good deal of troubleshooting myself, so it should be a clean process, but you never know…)
By the way, it will also install ARPACK from SLEPc, so it would be interesting to see if you still have make check failures in examples/eigen.

$ git clone -b petsc-3.14.0 https://github.com/FreeFem/FreeFem-sources
$ cd FreeFem-sources && autoreconf -i
$ ./configure --enable-download --prefix=~/FreeFem-install
$ cd 3rdparty/ff-petsc && make petsc-slepc
$ cd - && ./reconfigure
$ make && make check

nabil3achour · September 22, 2020, 11:53am

Hello,

At the stage “make petsc-slepc”, it show me this error message:

>     **************************ERROR*************************************
> 
>     Error building SLEPc. Check fr/lib/petsc/conf/slepc.log
> 
>     ********************************************************************
> 
>     make[3]: *** [slepcbuild] Error 1
> 
>     make[2]: *** [install] Error 2
> 
>     make[1]: *** [install] Error 2
> 
>     make: *** [petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/tag-install-real] Error 2

The fr/lib/petsc/conf/slepc.log file contains :

*Checking environment… *
Cleaning arch dir /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt…
done
Checking PETSc installation… done
Checking LAPACK library… done
Checking SCALAPACK… done
*Installing ARPACK version 3.7.0… *
ERROR: Installation of ARPACK failed
ERROR: See “installed-arch-darwin-c-opt/lib/slepc/conf/configure.log” file for details

Could you help me to fix this problem please?

Thanks

Nabil

prj · September 22, 2020, 11:56am

Could you please share /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt/lib/slepc/conf/configure.log here?

BTW, that’s a “good” error, it means that ScaLAPACK was successfully installed (SLEPc is installed after ScaLAPACK).

david.fabre · September 22, 2020, 12:13pm

Thanks Pierre !
i will also try your branch tonight
(I prefer if my computer plays the ginea pig while I’l sleeping )

nabil3achour · September 22, 2020, 12:27pm

Thank,
you may find the configure.log file in the following link: configure.log

prj · September 22, 2020, 12:28pm

Unfortunately, that’s not at all the file I asked for.

nabil3achour · September 22, 2020, 12:30pm

================================================================================
Starting Configure Run at Tue Sep 22 13:36:31 2020
Configure Options: --with-clean=1 --prefix=/Users/nabilachour/FreeFem-install/ff-petsc/r --download-arpack=https://github.com/prj-/arpack-ng/archive/94a5e1128dce0630cf26725247e18c787ce7f877.tar.gz
Working directory: /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc
Python version:
3.8.5 (default, Jul 21 2020, 10:48:26)
[Clang 11.0.3 (clang-1103.0.32.62)]
make: /usr/bin/make
PETSc source directory: /Users/nabilachour/FreeFem-install/ff-petsc/r
PETSc install directory: /Users/nabilachour/FreeFem-install/ff-petsc/r
PETSc version: 3.13.5
SLEPc source directory: /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc
SLEPc install directory: /Users/nabilachour/FreeFem-install/ff-petsc/r
SLEPc version: 3.13.4

Cleaning arch dir /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt…

Checking PETSc installation…

Checking link with code:

#include “petscsnes.h”
int main() {
Vec v; Mat m; KSP k;
PetscInitializeNoArguments();
VecCreate(PETSC_COMM_WORLD,&v);
MatCreate(PETSC_COMM_WORLD,&m);
KSPCreate(PETSC_COMM_WORLD,&k);
return 0;
}

Running command:
cd /var/folders/4p/4lsnvzr955j0wmrcj9tjtgkm0000gn/T/slepc-h1o8etrk;/usr/bin/make checklink LINKFLAGS=""

Output:
/usr/local/bin/mpicc -o checklink.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/include -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/include -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include pwd/checklink.c
/usr/local/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -o checklink checklink.o -Wl,-rpath,/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -L/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -framework Accelerate -Wl,-rpath,/usr/local/Cellar/mpich/3.3.2_1/lib -L/usr/local/Cellar/mpich/3.3.2_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lumfpack -lklu -lcholmod -lbtf -lccolamd -lcolamd -lcamd -lamd -lsuitesparseconfig -lsuperlu -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltet -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl

================================================================================
Checking LAPACK library…
=== Checking all LAPACK functions…

Checking link with code:

extern void dlaev2_();
extern void dgehrd_();
extern void dlanhs_();
extern void dtrexc_();
extern void dtrevc_();
extern void dtgexc_();
extern void dtgevc_();
extern void dstedc_();
extern void dhsein_();
extern void dlarfg_();
extern void dlarf_();
extern void dlascl_();
extern void dtrsyl_();
extern void dorghr_();
extern void dsytrd_();
extern void dorgtr_();
extern void dstevr_();
extern void dbdsdc_();
extern void dlag2_();
extern void dlasv2_();
extern void dlartg_();
extern void dlaed4_();
extern void dlamrg_();
int main() {
dlaev2_();
dgehrd_();
dlanhs_();
dtrexc_();
dtrevc_();
dtgexc_();
dtgevc_();
dstedc_();
dhsein_();
dlarfg_();
dlarf_();
dlascl_();
dtrsyl_();
dorghr_();
dsytrd_();
dorgtr_();
dstevr_();
dbdsdc_();
dlag2_();
dlasv2_();
dlartg_();
dlaed4_();
dlamrg_();
return 0;
}

Running command:
cd /var/folders/4p/4lsnvzr955j0wmrcj9tjtgkm0000gn/T/slepc-0c3x1xwy;/usr/bin/make checklink LINKFLAGS=""

Output:
/usr/local/bin/mpicc -o checklink.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/include -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/include -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include pwd/checklink.c
/usr/local/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -o checklink checklink.o -Wl,-rpath,/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -L/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -framework Accelerate -Wl,-rpath,/usr/local/Cellar/mpich/3.3.2_1/lib -L/usr/local/Cellar/mpich/3.3.2_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lumfpack -lklu -lcholmod -lbtf -lccolamd -lcolamd -lcamd -lamd -lsuitesparseconfig -lsuperlu -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltet -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl

================================================================================
Checking SCALAPACK…

Running command:
cd /var/folders/4p/4lsnvzr955j0wmrcj9tjtgkm0000gn/T/slepc-t_z_4rpm;/usr/bin/make checklink LINKFLAGS=""

Output:
/usr/local/bin/mpicc -o checklink.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/include -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/include -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include pwd/checklink.c
/usr/local/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -o checklink checklink.o -Wl,-rpath,/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -L/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -framework Accelerate -Wl,-rpath,/usr/local/Cellar/mpich/3.3.2_1/lib -L/usr/local/Cellar/mpich/3.3.2_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lumfpack -lklu -lcholmod -lbtf -lccolamd -lcolamd -lcamd -lamd -lsuitesparseconfig -lsuperlu -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltet -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl

====== With underscore Fortran names
#include “petscsnes.h”
PETSC_EXTERN int
pdsyev_();
PETSC_EXTERN int
pdsygvx_();
PETSC_EXTERN int
pdgesvd_();
int main() {
Vec v; Mat m; KSP k;
PetscInitializeNoArguments();
VecCreate(PETSC_COMM_WORLD,&v);
MatCreate(PETSC_COMM_WORLD,&m);
KSPCreate(PETSC_COMM_WORLD,&k);
pdsyev_();
pdsygvx_();
pdgesvd_();
return 0;
}
/usr/local/bin/mpicc -o checklink.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/include -I/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/include -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include `pwd`/checklink.c
/usr/local/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native -o checklink checklink.o -Wl,-rpath,/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -L/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/lib -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -framework Accelerate -Wl,-rpath,/usr/local/Cellar/mpich/3.3.2_1/lib -L/usr/local/Cellar/mpich/3.3.2_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lumfpack -lklu -lcholmod -lbtf -lccolamd -lcolamd -lcamd -lamd -lsuitesparseconfig -lsuperlu -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltet -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl

Installing ARPACK version 3.7.0…
Downloading https://github.com/prj-/arpack-ng/archive/94a5e1128dce0630cf26725247e18c787ce7f877.tar.gz to /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt/externalpackages/arpack-ng-3.7.0.tar.gz
Uncompressing /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt/externalpackages/arpack-ng-3.7.0.tar.gz to directory /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt/externalpackages/arpack-ng-3.7.0

Running command:
cd /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt/externalpackages; chmod -R a+r arpack-ng-94a5e1128dce0630cf26725247e18c787ce7f877; find arpack-ng-94a5e1128dce0630cf26725247e18c787ce7f877 -type d -name “*” -exec chmod a+rx {} ;

Output:

Running command:
autoreconf --help

Output:
Usage: /usr/local/autoconf/bin/autoreconf [OPTION]… [DIRECTORY]…

Run autoconf' (and autoheader’, aclocal', automake’, autopoint' (formerly gettextize’), and libtoolize' where appropriate) repeatedly to remake the GNU Build System files in specified DIRECTORIES and their subdirectories (defaulting to .’).

By default, it only remakes those files that are older than their
sources. If you install new versions of the GNU Build System,
you can make autoreconf' remake all of the files by giving it the –force’ option.

Operation modes:
-h, --help print this help, then exit
-V, --version print version number, then exit
-v, --verbose verbosely report processing
-d, --debug don’t remove temporary files
-f, --force consider all files obsolete
-i, --install copy missing auxiliary files
–no-recursive don’t rebuild sub-packages
-s, --symlink with -i, install symbolic links instead of copies
-m, --make when applicable, re-run ./configure && make
-W, --warnings=CATEGORY report the warnings falling in CATEGORY [syntax]

Warning categories include:
cross' cross compilation issues gnu’ GNU coding standards (default in gnu and gnits modes)
obsolete' obsolete features or constructions override’ user redefinitions of Automake rules or variables
portability' portability issues (default in gnu and gnits modes) syntax’ dubious syntactic constructs (default)
unsupported' unsupported or incomplete features (default) all’ all the warnings
no-CATEGORY' turn off warnings in CATEGORY none’ turn off all the warnings
`error’ treat warnings as errors

The environment variable WARNINGS' is honored. Some subtools might support other warning types, using all’ is encouraged.

Library directories:
-B, --prepend-include=DIR prepend directory DIR to search path
-I, --include=DIR append directory DIR to search path

The environment variables AUTOM4TE, AUTOCONF, AUTOHEADER, AUTOMAKE,
ACLOCAL, AUTOPOINT, LIBTOOLIZE, M4, and MAKE are honored.

Report bugs to bug-autoconf@gnu.org.
GNU Autoconf home page: http://www.gnu.org/software/autoconf/.
General help using GNU software: http://www.gnu.org/gethelp/.

Running command:
/usr/local/bin/mpif90 --version

Output:
GNU Fortran (Homebrew GCC 10.2.0) 10.2.0
Copyright © 2020 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.

Running command:
cd /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt/externalpackages/arpack-ng-94a5e1128dce0630cf26725247e18c787ce7f877&& sh bootstrap && ./configure --prefix=/Users/nabilachour/FreeFem-install/ff-petsc/r CC="/usr/local/bin/mpicc" CFLAGS="-Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -O3 -mtune=native" F77="/usr/local/bin/mpif90" FFLAGS=" -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native -fallow-argument-mismatch" FC="/usr/local/bin/mpif90" FCFLAGS=" -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mtune=native -fallow-argument-mismatch" LIBS="-framework Accelerate" --enable-mpi MPICC="/usr/local/bin/mpicc" MPIF77="/usr/local/bin/mpif90" MPIFC="/usr/local/bin/mpif90" && /usr/bin/make && /usr/bin/make install

Output:
autoreconf: Entering directory `.’
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force -I m4
error: you must have libtool 2.4.2 or a more recent version
error: you must have libtool 2.4.2 or a more recent version
autoreconf: configure.ac: tracing
error: you must have libtool 2.4.2 or a more recent version
autoreconf: configure.ac: creating directory build-aux
autoreconf: configure.ac: not using Libtool
autoreconf: running: /usr/local/mac-dev-env/autoconf-2.69/bin/autoconf --force
error: you must have libtool 2.4.2 or a more recent version
configure.ac:18: error: possibly undefined macro: AC_MSG_ERROR
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
autoreconf: /usr/local/mac-dev-env/autoconf-2.69/bin/autoconf failed with exit status: 1

ERROR: Installation of ARPACK failed

prj · September 22, 2020, 12:31pm

Better! Please do brew install libtool, or something like that.

nabil3achour · September 22, 2020, 12:41pm

Despite the installation of libtool it show me the same error message

prj · September 22, 2020, 12:42pm

Did you run make petsc-slepc in a new shell? I’ll try to find a work around, because I don’t want to force people to install libtool, but are you sure it’s the same message?

nabil3achour · September 22, 2020, 12:51pm

Yes I did that!
configure.log (17.7 KB)

prj · September 22, 2020, 1:20pm

OK, I think this is fixed.

$ brew uninstall libtool
$ cd /Users/nabilachour/FF++/FreeFem-sources 
$ git fetch
$ git reset --hard origin/petsc-3.14.0
$ cd 3rdparty/ff-petsc && unlink petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/tag-conf-real
$ make petsc-slepc

And we should be good to go! Thank you for bearing with me.

nabil3achour · September 22, 2020, 1:34pm

Thank you!
Now it shows this message:

> ====================================

Install complete.

Now to check if the libraries are working do (in current directory):

make PETSC_DIR=/Users/nabilachour/FreeFem-install/ff-petsc/c PETSC_ARCH="" check

====================================

/usr/bin/make --no-print-directory -f makefile PETSC_ARCH=fc PETSC_DIR=/Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd mpi4py-install petsc4py-install libmesh-install mfem-install slepc-install hpddm-install amrex-install bamg-install

make[4]: Nothing to be done for `mpi4py-install'.

make[4]: Nothing to be done for `petsc4py-install'.

make[4]: Nothing to be done for `libmesh-install'.

make[4]: Nothing to be done for `mfem-install'.

*** Building SLEPc ***

*** Installing SLEPc ***

*** Building and installing HPDDM ***

make[4]: Nothing to be done for `amrex-install'.

make[4]: Nothing to be done for `bamg-install'.

test -x "`type -p otool`" && make changec

diri=/Users/nabilachour/FreeFem-install/ff-petsc/c/lib ; \

libpp=$diri/libslepc.3.13.3.dylib ; \

opblibpp=`otool -L $libpp | awk '/3rdparty/ {print $1}'` ; \

npblibpp=$diri/`basename $opblibpp` ; \

echo -- $opblibpp ; \

echo -- $npblibpp ; \

test -n "$opblibpp" && install_name_tool -change $opblibpp $npblibpp $libpp ; \

otool -L $libpp | awk '/libpetsc/ {print "**",$1}'

/Library/Developer/CommandLineTools/usr/bin/objdump: **error:** '/Users/nabilachour/FreeFem-install/ff-petsc/c/lib/libslepc.3.13.3.dylib': No such file or directory

usage: basename string [suffix]

basename [-a] [-s suffix] string [...]

--

-- /Users/nabilachour/FreeFem-install/ff-petsc/c/lib/

/Library/Developer/CommandLineTools/usr/bin/objdump: **error:** '/Users/nabilachour/FreeFem-install/ff-petsc/c/lib/libslepc.3.13.3.dylib': No such file or directory

test -e /Users/nabilachour/FreeFem-install/ff-petsc/c/include/petsc.h

touch petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/tag-install-complex

test -e /Users/nabilachour/FreeFem-install/ff-petsc/c/include/petsc.h

mkdir ../lib

mkdir: ../lib: File exists

make[1]: [../lib/WHERE.PETSc-complex] Error 1 (ignored)

echo 'petsccomplex LD -Wl,-rpath,"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -L"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -lpetsc' > ../lib/WHERE.PETSc-complex

echo 'petsccomplex INCLUDE -I"/Users/nabilachour/FreeFem-install/ff-petsc/c/include"' >> ../lib/WHERE.PETSc-complex

echo done ../lib/WHERE.PETSc-complex

done ../lib/WHERE.PETSc-complex

test -e /Users/nabilachour/FreeFem-install/ff-petsc/c/include/slepc.h

mkdir ../lib

mkdir: ../lib: File exists

make[1]: [../lib/WHERE.SLEPc-complex] Error 1 (ignored)

echo 'slepccomplex LD -Wl,-rpath,"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -L"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -lslepc' > ../lib/WHERE.SLEPc-complex

echo 'slepccomplex INCLUDE -I"/Users/nabilachour/FreeFem-install/ff-petsc/c/include"' >> ../lib/WHERE.SLEPc-complex

echo done ../lib/WHERE.SLEPc-complex

done ../lib/WHERE.SLEPc-complex

echo >WHERE-all

test -z '-Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lscalapack' || echo scalapack LD -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lscalapack >>WHERE-all

test -z '' || echo scalapack INCLUDE -I >>WHERE-all

test -z '-Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lmetis' || echo metis LD -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lmetis >>WHERE-all

test -z '/Users/nabilachour/FreeFem-install/ff-petsc/r/include' || echo metis INCLUDE -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include >>WHERE-all

test -z '-Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord' || echo mumps LD -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord >>WHERE-all

test -z '/Users/nabilachour/FreeFem-install/ff-petsc/r/include' || echo mumps INCLUDE -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include >>WHERE-all

test -z '-Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lsuperlu' || echo superlu LD -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lsuperlu >>WHERE-all

test -z '/Users/nabilachour/FreeFem-install/ff-petsc/r/include' || echo superlu INCLUDE -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include >>WHERE-all

test -z '-Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr' || echo ptscotch LD -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr >>WHERE-all

test -z '/Users/nabilachour/FreeFem-install/ff-petsc/r/include' || echo ptscotch INCLUDE -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include >>WHERE-all

test -z '-Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -ltet' || echo tetgen LD -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -ltet >>WHERE-all

test -z '/Users/nabilachour/FreeFem-install/ff-petsc/r/include' || echo tetgen INCLUDE -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include >>WHERE-all

test -z '-Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lparmetis' || echo parmetis LD -Wl,-rpath,/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -L/Users/nabilachour/FreeFem-install/ff-petsc/r/lib -lparmetis >>WHERE-all

test -z '/Users/nabilachour/FreeFem-install/ff-petsc/r/include' || echo parmetis INCLUDE -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include >>WHERE-all

test -z '' || echo hpddm LD >>WHERE-all

test -z '/Users/nabilachour/FreeFem-install/ff-petsc/r/include' || echo hpddm INCLUDE -I/Users/nabilachour/FreeFem-install/ff-petsc/r/include >>WHERE-all

echo 'petsc LD -Wl,-rpath,"/Users/nabilachour/FreeFem-install/ff-petsc/r/lib" -L"/Users/nabilachour/FreeFem-install/ff-petsc/r/lib" -lpetsc' >>WHERE-all

echo 'petsc INCLUDE -I"/Users/nabilachour/FreeFem-install/ff-petsc/r/include"' >>WHERE-all

echo 'petsccomplex LD -Wl,-rpath,"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -L"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -lpetsc' >>WHERE-all

echo 'petsccomplex INCLUDE -I"/Users/nabilachour/FreeFem-install/ff-petsc/c/include"' >> WHERE-all

echo 'slepc LD -Wl,-rpath,"/Users/nabilachour/FreeFem-install/ff-petsc/r/lib" -L"/Users/nabilachour/FreeFem-install/ff-petsc/r/lib" -lslepc' >>WHERE-all

echo 'slepc INCLUDE -I"/Users/nabilachour/FreeFem-install/ff-petsc/r/include"' >>WHERE-all

echo 'slepccomplex LD -Wl,-rpath,"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -L"/Users/nabilachour/FreeFem-install/ff-petsc/c/lib" -lslepc' >>WHERE-all

echo 'slepccomplex INCLUDE -I"/Users/nabilachour/FreeFem-install/ff-petsc/c/include"' >>WHERE-all

nabilachour@MacBook-Pro-de-Nabil ff-petsc %

prj · September 22, 2020, 1:37pm

Things are looking good, you can resume the procedure from this earlier post.

nabil3achour · September 22, 2020, 1:43pm

At the last stage it shows this:

/Users/nabilachour/FF++/FreeFem-sources/3rdparty/yams/freeyams.2012.02.05/sourceslib/colar2.c:105:9: error: implicit declaration of

function ‘hippop’ is invalid in C99 [-Werror,-Wimplicit-function-declaration]

k = hippop(sm->tria);

^

1 error generated.

make[7]: *** [/Users/nabilachour/FF++/FreeFem-sources/3rdparty/yams/freeyams.2012.02.05/objects/colar2.o] Error 1

make[6]: *** [freeyams.2012.02.05/FAIT] Error 2

make[5]: *** [FAIRE] Error 2

make[4]: *** [compile-dir] Error 2

make[3]: *** [tag-compile-pkg] Error 1

make[2]: *** [all-recursive] Error 1

make[1]: *** [all-recursive] Error 1

make: *** [all] Error 2

prj · September 22, 2020, 1:46pm

OK, then do the following. Disclaimer: some packages won’t be installed.

$ ./reconfigure --disable-download
$ make && make check

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Problem when compiling SCALAPACK

Cleaning arch dir /Users/nabilachour/FF++/FreeFem-sources/3rdparty/ff-petsc/petsc-6f7728a9761c25b7b2c7be97feaf14de71316cbd/fr/externalpackages/git.slepc/installed-arch-darwin-c-opt…

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