On Fri, Jan 28, 2011 at 5:08 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> > Is there anyway we can get this into the petsc-dev source so it is fixed > for everyone in the future? > Brad already pushed it :) Matt > Thanks > > Barry > > On Jan 28, 2011, at 2:54 PM, Brad Aagaard wrote: > > > Barry- > > > > It turns out the workaround was explained deep in some of the HDF5 > documentation. I pushed the fix. If the local Vec size is zero, then I > created a null memspace and reset the filespace to none. > > > > Brad > > > > > > On 01/28/2011 10:00 AM, Barry Smith wrote: > >> > >> Sounds like a bug report/inquiry to HDF5 folks. > >> > >> Barry > >> > >> > >> On Jan 28, 2011, at 10:23 AM, Brad Aagaard wrote: > >> > >>> We are trying to get HDF5 output working in PyLith using the PETSc HDF5 > viewer. I get an HDF5 error > >>> > >>> H5Screate_simple(): zero sized dimension for non-unlimited dimension, > >>> VecView_MPI_HDF5() line 771 in petsc-dev/src/vec/vec/impls/mpi/pdvec.c > >>> > >>> when I have a Vec that has a zero local size on a processor (the global > size is nonzero). The Vec layout is correct in that we expect some > processors to have a local size of zero (the field is over only a portion of > the domain). > >>> > >>> The collective write of the Vec creates the filespace using the global > size and the memspace using the local size. It is in trying to create the > memspace that the error occurs. I tried adjusting pdvec.c so that it creates > a null memspace when the local size is zero but then I get an error during > the write about differences in dimensions (the number of dimensions in the > filespace and memspace don't agree). I was unable to find any info on this > type of use case in the HDF5 documentation. > >>> > >>> I have attached a toy example that illustrates the problem. > >>> mpiexec -n 1 test_view [creates the expected test.h5 file] > >>> mpiexec -n 2 test_view [generates the above error] > >>> > >>> Thanks, > >>> Brad > >>> <test_view.tgz> > >> > >> > > > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20110128/f9060ac0/attachment.html>