segmentation fault when trying to install OpenCMISS iron on ubuntu 18.04

[vraj004]

Trying to install opencmiss iron on ubuntu 18.04, gnu toolchain, gcc-7, gfortran-7, g++-7, mpich (compiled against gcc-7). Note, this issue occurs with gcc-8 toolchain as well.

After executing inside setup-build/:
cmake -DOPENCMISS_LIBRARIES=iron -DOPENCMISS_ROOT=../opencmiss ../setup
make VERBOSE=1

I get the following error at OC_IRON:
[ 0%] Building Fortran object CMakeFiles/iron.dir/src/fieldml_output_routines.F90.o
/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/iron/src/fieldml_output_routines.F90:182:0:

   FIELDML_OUTPUT_IMPORT_FML = Fieldml_AddImport( FML_HANDLE, IMPORT_INDEX, cchar(REMOTE_NAME), cchar(REMOTE_NAME) )

internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See file:///usr/share/doc/gcc-7/README.Bugs for instructions.
CMakeFiles/iron.dir/build.make:1739: recipe for target 'CMakeFiles/iron.dir/src/fieldml_output_routines.F90.o' failed
make[2]: *** [CMakeFiles/iron.dir/src/fieldml_output_routines.F90.o] Error 1
CMakeFiles/Makefile2:77: recipe for target 'CMakeFiles/iron.dir/all' failed
make[1]: *** [CMakeFiles/iron.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2

[chrispbradley]

Hi Vijay,
yes, there appears to be a bug with the compilers on 18.04. You can install the gcc-9 compilers to fix this. Try something like

sudo apt-get install gcc-9 g++-9 gfortran-9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 90 --slave /usr/bin/g++ g++ /usr/bin/g++-
sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortan-9 90

then test it with

gcc --version
gfortran --version

[sgenie68]

Hi, Vijay Yes, the compiler has a bug that crashes it during Fieldml processing. You need to update your GCC to v 9 Cheers, Gene

…

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On 24/11/19 13:50, Vijay Rajagopal wrote: Trying to install opencmiss iron on ubuntu 18.04, gnu toolchain, gcc-7, gfortran-7, g++-7, mpich (compiled against gcc-7). Note, this issue occurs with gcc-8 toolchain as well. After executing inside setup-build/: cmake -DOPENCMISS_LIBRARIES=iron -DOPENCMISS_ROOT=../opencmiss ../setup make VERBOSE=1 I get the following error at OC_IRON: [ 0%] Building Fortran object CMakeFiles/iron.dir/src/fieldml_output_routines.F90.o /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/iron/src/fieldml_output_routines.F90:182:0: |FIELDML_OUTPUT_IMPORT_FML = Fieldml_AddImport( FML_HANDLE, IMPORT_INDEX, cchar(REMOTE_NAME), cchar(REMOTE_NAME) ) | internal compiler error: Segmentation fault Please submit a full bug report, with preprocessed source if appropriate. See file:///usr/share/doc/gcc-7/README.Bugs for instructions. CMakeFiles/iron.dir/build.make:1739: recipe for target 'CMakeFiles/iron.dir/src/fieldml_output_routines.F90.o' failed make[2]: *** [CMakeFiles/iron.dir/src/fieldml_output_routines.F90.o] Error 1 CMakeFiles/Makefile2:77: recipe for target 'CMakeFiles/iron.dir/all' failed make[1]: *** [CMakeFiles/iron.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#186?email_source=notifications&email_token=AAGJIDUPOMYZ2KPR4B2V4ITQVHFVFA5CNFSM4JQ4UZU2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H3TAHRA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDSXIR2RK5LYGC6ZBELQVHFVFANCNFSM4JQ4UZUQ>.

[vraj004]

This suggestion resolved the issue, thanks.