[petsc-users] Problem reading and HDF5 binary file

[fujisan]

I see from https://petsc.org/main/docs/manualpages/Mat/MatLoad/ that
MatView for HDF5 binary format is not yet implemented.
Any idea when this will be implemented?

F.
Current HDF5 (MAT-File) limitations
<https://petsc.org/main/docs/manualpages/Mat/MatLoad/#current-hdf5-mat-file-limitations>

This reader currently supports only real MATSEQAIJ, MATMPIAIJ, MATSEQDENSE
 and MATMPIDENSE matrices.

Corresponding MatView() is not yet implemented.

The loaded matrix is actually a transpose of the original one in MATLAB,
unless you push PETSC_VIEWER_HDF5_MAT format (see examples above). With
this format, matrix is automatically transposed by PETSc, unless the matrix
is marked as SPD or symmetric (see MatSetOption(), MAT_SPD, MAT_SYMMETRIC).

On Tue, Oct 4, 2022 at 9:42 AM fujisan <fujisan43 at gmail.com> wrote:

> 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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