# Fatal error: Cannot open source file "gnu/stubs-32.h" **URL:** \ **Category:** FreeFEM installation\ **Created:** [February 11, 2022, 10:29am UTC](https://community.freefem.org/t/fatal-error-cannot-open-source-file-gnu-stubs-32-h/1488 "2022-02-11T10:29:18Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![mas](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/mas/32/2160_2.png) [@mas](https://community.freefem.org/u/mas)\ **Post date:** [February 11, 2022, 10:29am UTC](https://community.freefem.org/t/fatal-error-cannot-open-source-file-gnu-stubs-32-h/1488/1 "2022-02-11T10:29:18Z")
I’m installing FreeFEM on my HPC cluster environment, following the discussion " [MPI fail on HPC cluster](https://community.freefem.org/t/mpi-fail-on-hpc-cluster/1303)", but make failed. Final messages (translated from japanese) were > eval ./ff-c++ gsl.cpp -lgsl -lgslcblas -lm -I/usr/include > FCCpx -c -fPIC ‘-I./include’ ‘-I/usr/include’ -g -DNDEBUG -O3 -mmmx -mavx -std=c++14 -DBAMG\_LONG\_LONG -DNCHECKPTR -fPIC ‘gsl.cpp’ > FCCpx: Warning: -mmmx is an unrecognizable option. > FCCpx: Warning: -mavx is an unrecognizable option. > “/usr/include/gnu/stubs.h”, line 7: Fatal error: Cannot open source file “gnu/stubs-32.h” . > # include \ I’m not the root user of this system, so I can not edit “/usr/include/gnu/”. In directory /usr/include/gnu, there is lib-names-64.h lib-names.h libc-version.h stubs-64.h stubs.h How can I solve this problem? Can I compile freefem without “gnu/stubs-32.h”? Run commands are bellow: > module load fj > module load fjmpi > module load odyssey > cd $HOME > export FF\_DIR=${PWD}/FreeFem-sources > export PETSC\_DIR=${PWD}/petsc > export PETSC\_ARCH=arch-FreeFem > export PETSC\_VAR=${PETSC\_DIR}/${PETSC\_ARCH} > cd ${PETSC\_DIR} > export CC=mpifccpx > export CXX=mpiFCCpx > export FC=mpifrtpx > export F77=mpifrtpx > ./configure --enable-download --without-hdf5 --host=aarch64 CC=$CC CXX=$CXX FC=$FC F77=$F77 --with-batch > make PETSC\_DIR=$HOME/petsc PETSC\_ARCH=arch-FreeFem all > > cd $FF\_DIR > autoreconf -i > export CC=fccpx > export CXX=FCCpx > export FC=frtpx > export F77=frtpx > export MPICC=mpifccpx > export MPICXX=mpiFCCpx > export MPIFC=mpifrtpx > > ./configure --without-hdf5 --with-petsc=${PETSC\_VAR}/lib CC=$CC CXX=$CXX FC=$FC F77=$F77 COPTFLAGS=“-Kfast” CXXOPTFLAGS=“-Kfast” FOPTFLAGS=“-Kfast” --prefix=$PWD --host=aarch64 MPICC=$MPICC MPICXX=$MPICXX MPIFC=$MPIFC --build=x86\_64 > > make ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [February 11, 2022, 10:38am UTC](https://community.freefem.org/t/fatal-error-cannot-open-source-file-gnu-stubs-32-h/1488/2 "2022-02-11T10:38:45Z")
If you don’t need the GSL, you can edit `plugin/seq/gsl.cpp` and apply the following patch. ```auto diff --git a/plugin/seq/gsl.cpp b/plugin/seq/gsl.cpp index e9b09630..bc146966 100644 --- a/plugin/seq/gsl.cpp +++ b/plugin/seq/gsl.cpp @@ -23,7 +23,7 @@ // Example C++ function "myfunction", dynamically loaded into "load.edp" /* clang-format off */ -//ff-c++-LIBRARY-dep: gsl +//ff-c++-LIBRARY-dep: broken //ff-c++-cpp-dep: /* clang-format on */ ``` ---
**Author:** ![mas](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/mas/32/2160_2.png) [@mas](https://community.freefem.org/u/mas)\ **Post date:** [February 11, 2022, 1:21pm UTC](https://community.freefem.org/t/fatal-error-cannot-open-source-file-gnu-stubs-32-h/1488/3 "2022-02-11T13:21:24Z")
Thank you very much! Compilation successfully completed. Then, I tested FreeFem++-mpi, > mpiexec FreeFem++-mpi **‘test.edp’** -ng and get > – FreeFem++ v4.1 (2022年 2月 11日 金曜日 19:44:33 JST - git v4.10) > file : test.edp > Load: lg\_fem no UMFPACK → replace by LU or GMRES lg\_mesh lg\_mesh3 parallelempi > 1 : // test.edp > 2 : load “PETSc” > Load error: PETSc > fail: > dlerror : PETSc.so: cannot open shared object file: No such file or directory > list prefix: ‘/xx/username/FreeFem-sources/plugin/seq:/xx/username/FreeFem-sources/plugin/mpi:/xx/username/petsc/arch-FreeFem/lib/’ ‘’ list suffix: ‘’ , ‘.so’ > current line = 2 mpirank 0 / 1 > Load error : PETSc > line number :2, PETSc > error Load error : PETSc > line number :2, PETSc > code = 2 mpirank: 0 Does this mean that the installation of PETSc is failing? Or am I still missing several steps? ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [February 11, 2022, 4:58pm UTC](https://community.freefem.org/t/fatal-error-cannot-open-source-file-gnu-stubs-32-h/1488/4 "2022-02-11T16:58:05Z")
Does the file `/xx/username/FreeFem-sources/plugin/mpi/PETSc.so` exist? ---
**Author:** ![mas](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/mas/32/2160_2.png) [@mas](https://community.freefem.org/u/mas)\ **Post date:** [February 12, 2022, 2:50am UTC](https://community.freefem.org/t/fatal-error-cannot-open-source-file-gnu-stubs-32-h/1488/5 "2022-02-12T02:50:08Z")
No, it doesn’t. It also does not exist in anywhere $HOME/petsc/ The file `$HOME/petsc/arch-FreeFem/lib/libpetsc.so` exist. However, the file `/xx/username/FreeFem-sources/plugin/mpi/medit.so` exists, for example, but `load medit` returns `dlerror : medit.so`. ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [February 12, 2022, 6:55am UTC](https://community.freefem.org/t/fatal-error-cannot-open-source-file-gnu-stubs-32-h/1488/6 "2022-02-12T06:55:23Z")
Then that means you have not compiled or enabled PETSc support, which in turn means you cannot `load "PETSc"` in your file.