[petsc-users] Problem reading and HDF5 binary file

[fujisan]

It turns out there is nothing in the hdf5 file:

$ h5dump data/matrix3.mat.h5
HDF5 "data/matrix3.mat.h5" {
GROUP "/" {
}
}


On Tue, Oct 4, 2022 at 9:19 AM fujisan <fujisan43 at gmail.com> wrote:

> Hi everyone,
>
> I have written a matrix in an HDF5 binary file without problem using
> PetscViewerHDF5Open function like this:
>
> ! Write
> if (ishdf5) then
>     PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD,trim(filename
> ),FILE_MODE_WRITE,view,ierr))
> else
>     PetscCall(PetscViewerBinaryOpen(PETSC_COMM_WORLD,trim(filename
> ),FILE_MODE_WRITE,view,ierr))
> endif
> PetscCall(MatView(A,view,ierr))
> PetscCall(PetscViewerDestroy(view,ierr))
>
> But when I want to read that HDF5 file like this:
>
> ! Read
> if (ishdf5) then
>     PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD,trim(filename
> ),FILE_MODE_READ,view,ierr))
> else
>     PetscCall(PetscViewerBinaryOpen(PETSC_COMM_WORLD,trim(filename
> ),FILE_MODE_READ,view,ierr))
> endif
> PetscCall(MatCreate(PETSC_COMM_WORLD,A,ierr))
> PetscCall(MatSetType(A,MATMPIAIJ,ierr))
> PetscCall(MatLoad(A,view,ierr))
> PetscCall(PetscViewerDestroy(view,ierr))
>
> I get this kind of error message below.
> I don't have any problem writing / reading using PetscViewerBinaryOpen,
> and no problem writing / reading a vector using PetscViewerHDF5Open either.
>
> What am I missing ?
>
> Fuji
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Unexpected data in file
> [0]PETSC ERROR: Attribute /Mat_0xc4000016_0/MATLAB_sparse does not exist
> and default value not provided
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.18.0, unknown
> [0]PETSC ERROR: ./bin/solve on a x86_64 named master by beauduin Tue Oct
> 4 08:55:55 2022
> [0]PETSC ERROR: Configure options --with-petsc-arch=x86_64 --COPTFLAGS="-g
> -O3" --FOPTFLAGS="-g -O3" --CXXOPTFLAGS="-g -O3" --with-debugging=0
> --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort
> --with-single-library=1 --with-mpiexec=mpiexec --with-precision=double
> --with-fortran-interfaces=1 --with-make=1 --with-mpi=1
> --with-mpi-compilers=1 --download-fblaslapack=0 --download-hypre=1
> --download-cmake=0 --with-cmake=1 --download-metis=1 --download-parmetis=1
> --download-ptscotch=0 --download-suitesparse=1 --download-triangle=1
> --download-superlu=1 --download-superlu_dist=1 --download-scalapack=1
> --download-mumps=1 --download-elemental=1 --download-spai=0
> --download-parms=1 --download-moab=1 --download-chaco=0 --download-fftw=1
> --with-petsc4py=1 --download-mpi4py=1 --download-saws
> --download-concurrencykit=1 --download-revolve=1 --download-cams=1
> --download-p4est=0 --with-zlib=1 --with-hdf5=1 --download-hdf5=1
> --download-mfem=1 --download-glvis=0 --with-opengl=0 --download-libpng=1
> --download-libjpeg=1 --download-slepc=1 --download-hpddm=1
> --download-bamg=1 --download-mmg=0 --download-parmmg=0 --download-htool=1
> --download-egads=0 --download-opencascade=0 PETSC_ARCH=x86_64
> [0]PETSC ERROR: #1 PetscViewerHDF5ReadAttribute() at
> /data/softs/petsc/src/sys/classes/viewer/impls/hdf5/hdf5v.c:1245
> [0]PETSC ERROR: #2 MatLoad_AIJ_HDF5() at
> /data/softs/petsc/src/mat/impls/aij/seq/aijhdf5.c:63
> [0]PETSC ERROR: #3 MatLoad_MPIAIJ() at
> /data/softs/petsc/src/mat/impls/aij/mpi/mpiaij.c:3034
> [0]PETSC ERROR: #4 MatLoad() at
> /data/softs/petsc/src/mat/interface/matrix.c:1304
> [0]PETSC ERROR: #5 bigmat.F90:62
> [0]PETSC ERROR: #6 MatCreateVecs() at
> /data/softs/petsc/src/mat/interface/matrix.c:9336
> [0]PETSC ERROR: #7 solve.F90:143
> Abort(73) on node 0 (rank 0 in comm 16): application called
> MPI_Abort(MPI_COMM_SELF, 73) - process 0
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC                Routine            Line
> Source
> solve              000000000043258A  Unknown               Unknown  Unknown
> libpthread-2.28.s  00007FCAF0B78C20  Unknown               Unknown  Unknown
> libmpi.so.12.0.0   00007FCAF17A09D3  Unknown               Unknown  Unknown
> ....
>
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