[petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)

[Satish Balay]

On Sun, 31 Mar 2024, Zongze Yang wrote:
> > ---
> > petsc at npro petsc % ./configure --download-bison --download-chaco --download-ctetgen --download-eigen --download-fftw --download-hdf5 --download-hpddm --download-hwloc --download-hypre --download-libpng --download-metis --download-mmg --download-mumps --download-netcdf --download-openblas
>  --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" --download-p4est --download-parmmg --download-pnetcdf --download-pragmatic --download-ptscotch --download-scalapack --download-slepc --download-suitesparse --download-superlu_dist --download-tetgen --download-tri
> angle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 --with-shared-libraries=1 --with-x=0 --with-zlib --download-openmpi=https://urldefense.us/v3/__https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.3rc1.tar.bz2__;!!G_uCfscf7eWS!aCLPUhLfLFG5UwNlUWgGGhXZlw905gJwDd
> AryIrltDIXJcdmOP6Is44FzBVrY5ndwzmIqMhI515mnNjTuHoR-tzq$ --download-pastix=https://urldefense.us/v3/__https://web.cels.anl.gov/projects/petsc/download/externalpackages/pastix_5.2.3-p1.tar.bz2__;!!G_uCfscf7eWS!aCLPUhLfLFG5UwNlUWgGGhXZlw905gJwDdAryIrltDIXJcdmOP6Is44FzBVrY5ndwzmIqMhI515mnNjTuA
> fJ49xl$ && make && make check
> 
> There's an error encountered during configuration with the above options:
> ```
> TESTING: FortranMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:676)
> *********************************************************************************************
>            UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
> ---------------------------------------------------------------------------------------------
>                        Fortran error! mpi_init() could not be located!
> *********************************************************************************************
> ```
> Please refer to the attached file for further information.

So I'm getting:

>>>>>>
*** Fortran compiler
checking whether the compiler supports GNU Fortran... yes
checking whether gfortran accepts -g... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking if Fortran compiler works... yes
checking for extra arguments to build a shared library... impossible -- -static
checking for gfortran warnings flags... none
checking for Fortran flag to compile .f files... none
checking for Fortran flag to compile .f90 files... none
checking if Fortran compilers preprocess .F90 files without additional flag... yes
checking to see if Fortran compilers need additional linker flags... -Wl,-flat_namespace
checking  external symbol convention... single underscore
checking if C and Fortran are link compatible... yes
checking to see if Fortran compiler likes the C++ exception flags... skipped (no C++ exceptions flags)
checking to see if mpifort compiler needs additional linker flags... none
<<<<

However you are getting:

>>>>
*** Fortran compiler
checking whether the compiler supports GNU Fortran... yes
checking whether gfortran accepts -g... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking if Fortran compiler works... yes
checking for extra arguments to build a shared library... impossible -- -static
checking for gfortran warnings flags... none
checking for Fortran flag to compile .f files... none
checking for Fortran flag to compile .f90 files... none
checking if Fortran compilers preprocess .F90 files without additional flag... yes
checking to see if Fortran compilers need additional linker flags... -Wl,-flat_namespace
checking  external symbol convention... single underscore
checking if C and Fortran are link compatible... yes
checking to see if Fortran compiler likes the C++ exception flags... skipped (no C++ exceptions flags)
checking to see if mpifort compiler needs additional linker flags... -Wl,-commons,use_dylibs
<<<<

So gfortran [or ld from this newer xcode?] is behaving differently - and openmpi is picking up and using this broken/unsupported option - and likely triggering subsequent errors.

>>>
ld: warning: -commons use_dylibs is no longer supported, using error treatment instead
ld: common symbol '_mpi_fortran_argv_null_' from '/private/var/folders/tf/v4zjvtw12yb3tszk813gmnvw0000gn/T/petsc-xyn64q55/config.libraries/conftest.o' conflicts with definition from dylib '_mpi_fortran_argv_null_' from '/Users/zzyang/workspace/repos/petsc/arch-darwin-c-debug/lib/libmpi_usempif08.40.dylib'
<<<

Or perhaps openmpi configure is affected by this new warning that this newer xcode spews
>>>
ld: warning: duplicate -rpath '/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc' ignored
<<<

I'm not sure what to suggest here [other than using Linux - and avoiding these hassles with MacOS :( ]..

Satish