Hi,
I am trying to install freefem on a remote machine (Compute Canada) with Linux.
|Distributor ID:|CentOS|
|Description:|CentOS Linux release 7.8.2003 (Core)|
|Release:|7.8.2003|
|Codename:|Core|
I followed the documentation in link https://doc.freefem.org/introduction/installation.html,
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Under heading, Compilation on Ubuntu, there are some packages which needs to be downloaded by apt-get command which is not possible in remote machines. Compilers are already installed in these machines but some other packages like freeglut3, patch etc. mayn’t be in their software stack. So, is there a way I use some other means to download and install these packages ? or can I proceed without them ?
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When I proceeded to the next steps without these packages it breaks at the make step for FreeFem (7th step). I am not able to upload the configure logs since I am a new user. The final part of error is copied below.
gcc -rdynamic -L/home/sudhipv/software/FreeFem-sources/3rdparty/lib -lMesh /home/sudhipv/software/FreeFem-sources/3rdparty/yams/freeyams.2012.02.05/objects/yams.o -o /home/sudhipv/software/FreeFem-sources/3rdparty/bin/yams2 /home/sudhipv/software/FreeFem-sources/3rdparty/yams/freeyams.2012.02.05/objects/libyams.a -lm -L…/…/…/src/libMesh/ -lMesh -ldl -lm -lrt /cvmfs/soft.computecanada.ca/nix/store/c9qaklf3dvjvlbky3fiakmafb1p8l106-gfortran-7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/…/…/…/libgfortran.a /cvmfs/soft.computecanada.ca/nix/store/c9qaklf3dvjvlbky3fiakmafb1p8l106-gfortran-7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/…/…/…/libquadmath.a -L/usr/lib64 -lm -ldl -lz -lsz -lhdf5
/cvmfs/soft.computecanada.ca/nix/store/aj0bl3ac193y0y66iaj258n3z8hvz19f-binutils-2.28/bin/ld: warning: libaec.so.0, needed by /usr/lib64/libsz.so, not found (try using -rpath or -rpath-link)
/usr/lib64/libsz.so: undefined reference to `aec_buffer_decode’
/usr/lib64/libsz.so: undefined reference to `aec_buffer_encode’
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libpthread.so.0: undefined reference to `__twalk@GLIBC_PRIVATE’
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libpthread.so.0: undefined reference to `__tsearch@GLIBC_PRIVATE’
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libpthread.so.0: undefined reference to `__tfind@GLIBC_PRIVATE’
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libpthread.so.0: undefined reference to `__libc_vfork@GLIBC_PRIVATE’
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libpthread.so.0: undefined reference to `__call_tls_dtors@GLIBC_PRIVATE’
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libpthread.so.0: undefined reference to `__tdelete@GLIBC_PRIVATE’
collect2: error: ld returned 1 exit status
make[7]: *** [makefile:32: /home/sudhipv/software/FreeFem-sources/3rdparty/bin/yams2] Error 1
make[7]: Leaving directory ‘/home/sudhipv/software/FreeFem-sources/3rdparty/yams/freeyams.2012.02.05’
make[6]: *** [Makefile:42: freeyams.2012.02.05/FAIT] Error 2
make[6]: Leaving directory ‘/home/sudhipv/software/FreeFem-sources/3rdparty/yams’
make[5]: *** [Makefile:36: FAIRE] Error 2
make[5]: Leaving directory ‘/home/sudhipv/software/FreeFem-sources/3rdparty/yams’
make[4]: *** [Makefile:987: compile-dir] Error 2
make[4]: Leaving directory ‘/home/sudhipv/software/FreeFem-sources/3rdparty’
make[3]: *** [Makefile:996: tag-compile-pkg] Error 1
make[3]: Leaving directory ‘/home/sudhipv/software/FreeFem-sources/3rdparty’
make[2]: *** [Makefile:592: all-recursive] Error 1
make[2]: Leaving directory ‘/home/sudhipv/software/FreeFem-sources/3rdparty’
make[1]: *** [Makefile:796: all-recursive] Error 1
make[1]: Leaving directory ‘/home/sudhipv/software/FreeFem-sources’
make: *** [Makefile:746: all] Error 2
The modules I loaded before starting the installation are :
Currently Loaded Modules:
- nixpkgs/16.09 (S) 3) gcccore/.7.3.0 (H) 5) ifort/.2018.3.222 (H) 7) openmpi/3.1.2 (m)
- imkl/2018.3.222 (math) 4) icc/.2018.3.222 (H) 6) intel/2018.3 (t) 8) StdEnv/2018.3 (S)
If anyone have any comments on how to resolve this, please help.