[petsc-users] HDF5 DM and VecView with MPI :: Crash

[Barry Smith]

   Please send the error message that is printed to the screen. 

    Also please send the exact PETSc version you are using.   If possible also a code that reproduces the problem. 

   Can you view other simpler things with HDF5? Like say just a vector? 

   Barry



> On Jul 5, 2021, at 11:50 AM, Thibault Bridel-Bertomeu <thibault.bridelbertomeu at gmail.com> wrote:
> 
> Dear all,
> 
> I keep having this error on one of the supercomputers I have access to :
> 
> [1]PETSC ERROR: The EXACT line numbers in the error traceback are not available.
> [1]PETSC ERROR: instead the line number of the start of the function is given.
> [1]PETSC ERROR: #1 H5Dcreate2() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:690
> [1]PETSC ERROR: #2 VecView_MPI_HDF5() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:594
> [1]PETSC ERROR: #3 VecView_MPI() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/impls/mpi/pdvec.c:787
> [1]PETSC ERROR: #4 VecView() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/vec/vec/interface/vector.c:576
> [1]PETSC ERROR: #5 DMPlexCoordinatesView_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:560
> [1]PETSC ERROR: #6 DMPlexView_HDF5_Internal() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plexhdf5.c:802
> [1]PETSC ERROR: #7 DMView_Plex() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/impls/plex/plex.c:1366
> [1]PETSC ERROR: #8 DMView() at /ccc/work/cont001/ocre/bridelbert/05-PETSC/src/dm/interface/dm.c:954
> [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> 
> The configure options are as follow :
> 
> [1]PETSC ERROR: Configure options --with-clean=1 --prefix=/ccc/work/cont001/ocre/bridelbert/05-PETSC/build_uns3D_inti --with-make-np=8 --with-windows-graphics=0 --with-debugging=1 --download-mpich-shared=0 --with-x=0 --with-pthread=0 --with-valgrind=0 --PETSC_ARCH=INTI_UNS3D --with-fc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpifort --with-cc=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicc --with-cxx=/ccc/products/openmpi-4.0.3/gcc--8.3.0/default/bin/mpicxx --with-openmp=0 --download-sowing=/ccc/work/cont001/ocre/bridelbert/v1.1.26-p2.tar.gz --download-metis=/ccc/work/cont001/ocre/bridelbert/git.metis.tar.gz --download-parmetis=/ccc/work/cont001/ocre/bridelbert/git.parmetis.tar.gz --download-fblaslapack=/ccc/work/cont001/ocre/bridelbert/git.fblaslapack.tar.gz --with-cmake-dir=/ccc/products/cmake-3.13.3/system/default --download-hdf5=/ccc/work/cont001/ocre/bridelbert/hdf5-1.12.0.tar.bz2 --download-netcdf=/ccc/work/cont001/ocre/bridelbert/netcdf-4.5.0.tar.gz --download-pnetcdf=/ccc/work/cont001/ocre/bridelbert/pnetcdf-1.12.1.tar.gz --download-exodusii=/ccc/work/cont001/ocre/bridelbert/v2021-01-20.tar.gz --download-zlib=/ccc/work/cont001/ocre/bridelbert/zlib-1.2.11.tar.gz
> 
> The piece of code that is responsible is that one :
> 
>                 call PetscViewerHDF5Open(PETSC_COMM_WORLD, "debug_initmesh.h5", FILE_MODE_WRITE, hdf5Viewer, ierr); CHKERRA(ierr)
>                 call PetscViewerPushFormat(hdf5Viewer, PETSC_VIEWER_HDF5_XDMF, ierr); CHKERRA(ierr)
>                 call DMView(dm, hdf5Viewer, ierr); CHKERRA(ierr)
>                 call PetscViewerPopFormat(hdf5Viewer, ierr); CHKERRA(ierr)
>                 call PetscViewerDestroy(hdf5Viewer, ierr); CHKERRA(ierr)
> 
> I tried with gcc, intel compiler, openmpi 2.x.x or openmpi 4.x.x ... same problems ... can anyone please advise ? It's starting to make me quite crazy ... x(
> 
> Thank you !!!
> 
> Thibault

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