[petsc-users] hdf5 viewer and zero sized local vectors

Matthew Knepley knepley at gmail.com
Thu Jan 19 22:19:36 CST 2012 

On Thu, Jan 19, 2012 at 9:54 PM, Mohamad M. Nasr-Azadani
<mmnasr at gmail.com>wrote:

> Hi,
>
> I am trying to use VecView() and hdf5 viewer.
> I am trying to create a "parallel" vector of size N which has N elements
> on only processor zero and 0 elements on all other processors.
>
> This is the code that I have (if it helps):
>
>     PetscViewer    H5viewer;
>
>     // Create the HDF5 viewer
>
>     int ierr = PetscViewerHDF5Open(PCW, "temp.h5", FILE_MODE_WRITE, &H5viewer); PETScErrAct(ierr);
>
>      Vec x;
>
>     ierr = VecCreate(PCW, &x); PETScErrAct(ierr);
>
>     int n_local = 0;
>
> /* Rank of current processor */
>
>     if (params->rank == MASTER) {
>
>         n_local = N;
>
>     }
>
>     ierr = VecSetSizes(x,n_local, N); PETScErrAct(ierr);
>
>     ierr = VecSetFromOptions(x); PETScErrAct(ierr);
>
>      double *vcoord;
>
>     ierr = VecGetArray(x, &vcoord); PETScErrAct(ierr);
>
>      int i;
>
>     for (i=0; i<n_local; i++) {
>
>         vcoord[i] = coord[i];
>
>     }
>
>     ierr = VecRestoreArray(x, vcoord); PETScErrAct(ierr);
>
>     ierr = PetscObjectSetName((PetscObject) x, gridname); PETScErrAct(ierr);
>
>     // Write the H5 file
>
>     ierr = VecView(x, H5viewer); PETScErrAct(ierr);
>
>     ierr = VecDestroy(x); PETScErrAct(ierr);
>
>      ierr = PetscViewerDestroy(H5viewer); PETScErrAct(ierr);
>
>
>
> When I create a viewer and use VecView() to write this vector to file,
> this is the error I get. Apparently, it seems it does not like it that
> other processors do not have any elements.
> Any ideas how to fix that?
>
> HDF5-DIAG: Error detected in HDF5 (1.8.4) HDF5-DIAG: Error detected in
> HDF5 (1.8.4) HDF5-DIAG: Error detected in HDF5 (1.8.4) MPI-process
> 2MPI-process 3:
>   #000: H5S.c line 1335 in H5Screate_simple(): zero sized dimension for
> non-unlimited dimension
>

It appears that HDF5 has some limitations.

   Matt


> :
>   #000: H5S.c line 1335 in H5Screate_simple(): zero sized dimension for
> non-unlimited dimension
>     major: Invalid arguments to routine
>     minor: Bad value
>     major: Invalid arguments to routine
>     minor: Bad value
> [2]PETSC ERROR: MPI-process 1--------------------- Error Message
> ------------------------------------
> [3]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [2]PETSC ERROR: Error in external library!
> [3]PETSC ERROR: Error in external library!
> [2]PETSC ERROR: Cannot H5Screate_simple()!
> [3]PETSC ERROR: Cannot H5Screate_simple()!
> [2]PETSC ERROR: [3]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> :
>   #000: H5S.c line 1335 in H5Screate_simple(): zero sized dimension for
> non-unlimited dimension
>     major: Invalid arguments to routine
>     minor: Bad value
> [1]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [1]PETSC ERROR: Error in external library!
> [1]PETSC ERROR: Cannot H5Screate_simple()!
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48
> CDT 2011
> [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [1]PETSC ERROR: See docs/index.html for manual pages.
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: ./gvg on a linux-gnu named mylaptop by mmnasr Thu Jan 19
> 19:47:49 2012
> [1]PETSC ERROR: Libraries linked from
> /home/mmnasr/Softwares/petsc-3.1-p8/linux-gnuPetsc Release Version 3.1.0,
> Patch 8, Thu Mar 17 13:37:48 CDT 2011
> -hdf5/lib
> [1]PETSC ERROR: Configure run at Tue Sep  6 18:38:57 2011
> [1]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-hdf5 --with-cc=gcc
> --with-fc=gfortran --download-f-blas-lapack=1 --download-mpich=1
> --with-debugging=0 COPTFLAGS=-O3 FOPTFLAGS=-O3
> --download-hypre=/home/mmnasr/Softwares/hypre-2.7.0b.tar.gz
> --download-hdf5=1
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: VecView_MPI_HDF5() line 748 in
> src/vec/vec/impls/mpi/pdvec.c
> [1]PETSC ERROR: VecView_MPI() line 840 in src/vec/vec/impls/mpi/pdvec.c
> [1]PETSC ERROR: VecView() line 710 in src/vec/vec/interface/vector.c
> [1]PETSC ERROR: Output_grid_hdf5() line 2358 in "unknowndirectory/"Output.c
> [2]PETSC ERROR: See docs/changes/index.html for recent updates.
> [3]PETSC ERROR: [2]PETSC ERROR: See docs/faq.html for hints about trouble
> shooting.
> Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 CDT 2011
> [2]PETSC ERROR: See docs/index.html for manual pages.
> [2]PETSC ERROR: [3]PETSC ERROR: See docs/changes/index.html for recent
> updates.
> [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [3]PETSC ERROR: See docs/index.html for manual pages.
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
> [3]PETSC ERROR: ./gvg on a linux-gnu named mylaptop by mmnasr Thu Jan 19
> 19:47:49 2012
> [3]PETSC ERROR: Libraries linked from
> /home/mmnasr/Softwares/petsc-3.1-p8/linux-gnu-hdf5/lib
> [3]PETSC ERROR: Configure run at Tue Sep  6 18:38:57 2011
> [3]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-hdf5 --with-cc=gcc
> --with-fc=gfortran --download-f-blas-lapack=1 --download-mpich=1
> --with-debugging=0 COPTFLAGS=-O3 FOPTFLAGS=-O3
> --download-hypre=/home/mmnasr/Softwares/hypre-2.7.0b.tar.gz
> --download-hdf5=1
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
> [3]PETSC ERROR: VecView_MPI_HDF5() line 748 in
> src/vec/vec/impls/mpi/pdvec.c
> [3]PETSC ERROR: VecView_MPI() line 840 in src/vec/vec/impls/mpi/pdvec.c
> [3]PETSC
> ------------------------------------------------------------------------
> ERROR: VecView() line 710 in src/vec/vec/interface/vector.c
> [3]PETSC ERROR: Output_grid_hdf5() line 2358 in "unknowndirectory/"Output.c
> [2]PETSC ERROR: ./gvg on a linux-gnu named mylaptop by mmnasr Thu Jan 19
> 19:47:49 2012
> [2]PETSC ERROR: Libraries linked from
> /home/mmnasr/Softwares/petsc-3.1-p8/linux-gnu-hdf5/lib
> [2]PETSC ERROR: Configure run at Tue Sep  6 18:38:57 2011
> [2]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-hdf5 --with-cc=gcc
> --with-fc=gfortran --download-f-blas-lapack=1 --download-mpich=1
> --with-debugging=0 COPTFLAGS=-O3 FOPTFLAGS=-O3
> --download-hypre=/home/mmnasr/Softwares/hypre-2.7.0b.tar.gz
> --download-hdf5=1
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: VecView_MPI_HDF5() line 748 in
> src/vec/vec/impls/mpi/pdvec.c
> [2]PETSC ERROR: VecView_MPI() line 840 in src/vec/vec/impls/mpi/pdvec.c
> [2]PETSC ERROR: VecView() line 710 in src/vec/vec/interface/vector.c
> [2]PETSC ERROR: Output_grid_hdf5() line 2358 in "unknowndirectory/"Output.c
>
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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