[petsc-users] hdf5 viewer and zero sized local vectors
Mohamad M. Nasr-Azadani
mmnasr at gmail.com
Thu Jan 19 21:54:33 CST 2012
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
:
#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
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