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
> <[email protected]> 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
