[petsc-users] Fwd: Error in HDF5 dumps of DMPlex labels

Tue Apr 2 15:49:40 CDT 2019

Hi there,

I'm not sure if this message got lost (have sent it to petsc-dev, trying
users list now) or if I just did not get the replies.
Anyway, the issue that is attached below is unresolved in the current
master branch and I am curious about your input.

Many Thanks,

Fabian

-------- Weitergeleitete Nachricht --------
Betreff: [petsc-dev] Error in HDF5 dumps of DMPlex labels
Datum: Thu, 14 Feb 2019 14:53:22 +0100
Von: Fabian.Jakub via petsc-dev <petsc-dev at mcs.anl.gov>
Antwort an: Fabian.Jakub <Fabian.Jakub at physik.uni-muenchen.de>
An: petsc-dev <petsc-dev at mcs.anl.gov>

Dear Petsc Team!

I had an issue when writing out DMPlex objects through hdf5.

This comes from a DMLabel that has only entries on non-local mesh points.
The DMLabel write only includes local parts of the label and so leads to
a zero sized write for the index set.
This seems to be fine except that the hdf5 chunksize is set to zero
which is not allowed.

I added a minimal example to illustrate the error.
It creates a 2D DMPlex in serial, distributes it, labels the nonlocal
points in the mesh and dumps it via PetscObjectViewer to HDF5.
Run with:

   make plex.h5

I also attached a quick fix to override the chunksize.

Please let me know if you anything extra and also if this is expected
behavior... I could certainly with the fact that DMLabel is not supposed
to work this way.

Many thanks,

Fabian

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include ${PETSC_DIR}/lib/petsc/conf/variables
include ${PETSC_DIR}/lib/petsc/conf/rules

plex.xmf:: plex.h5
		${PETSC_DIR}/lib/petsc/bin/petsc_gen_xdmf.py plex.h5

plex.h5:: hdf5_issue_nonlocal_only_labels
		mpirun -np 2 ./hdf5_issue_nonlocal_only_labels -show_labeled_plex ::ascii_info_detail
		mpirun -np 2 ./hdf5_issue_nonlocal_only_labels -show_labeled_plex hdf5:plex.h5

hdf5_issue_nonlocal_only_labels:: hdf5_issue_nonlocal_only_labels.F90
		${PETSC_FCOMPILE} -c hdf5_issue_nonlocal_only_labels.F90
		${FLINKER} hdf5_issue_nonlocal_only_labels.o -o hdf5_issue_nonlocal_only_labels ${PETSC_LIB}

clean::
		rm -rf *.o plex.h5 plex.xmf hdf5_issue_nonlocal_only_labels
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HDF5-DIAG: Error detected in HDF5 (1.8.18) MPI-process 0:
#000: H5Pdcpl.c line 870 in H5Pset_chunk(): all chunk dimensions must be positive
major: Invalid arguments to routine
minor: Out of range
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Error in external library
[0]PETSC ERROR: Error in HDF5 call H5Pset_chunk() Status -1
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.10.3-1549-g9b78045  GIT Date: 2019-02-13 11:10:12 -0600
[0]PETSC ERROR: plex_prism on a debug_gcc named met-ws-970r17 by Fabian.Jakub Thu Feb 14 14:39:13 2019
[0]PETSC ERROR: Configure options --with-cc=/usr/bin/mpicc --with-fc=/usr/bin/mpif90 --with-cxx=/usr/bin/mpicxx --with-fortran --with-fortran-interfaces --with-shared-libraries=1 --download-hdf5 --download-netcdf=netcdf-c-4.6.2.tar.gz --download-zlib --download-szlib --download-openblas --download-metis --download-parmetis --download-ptscotch --no-download-petsc4py --download-ml --download-hypre --with-debugging=1 COPTFLAGS="-O2 -g" FOPTFLAGS="-O2 -g"
[0]PETSC ERROR: #1 ISView_General_HDF5() line 288 in /software/meteo/xenial/x86_64/petsc/master/src/vec/is/is/impls/general/general.c
[0]PETSC ERROR: #2 ISView_General() line 513 in /software/meteo/xenial/x86_64/petsc/master/src/vec/is/is/impls/general/general.c
[0]PETSC ERROR: #3 ISView() line 1015 in /software/meteo/xenial/x86_64/petsc/master/src/vec/is/is/interface/index.c
[0]PETSC ERROR: #4 DMPlexWriteLabels_HDF5_Static() line 668 in /software/meteo/xenial/x86_64/petsc/master/src/dm/impls/plex/plexhdf5.c
[0]PETSC ERROR: #5 DMPlexView_HDF5_Internal() line 692 in /software/meteo/xenial/x86_64/petsc/master/src/dm/impls/plex/plexhdf5.c
[0]PETSC ERROR: #6 DMView_Plex() line 1103 in /software/meteo/xenial/x86_64/petsc/master/src/dm/impls/plex/plex.c
[0]PETSC ERROR: #7 DMView() line 904 in /software/meteo/xenial/x86_64/petsc/master/src/dm/interface/dm.c
[0]PETSC ERROR: #8 PetscObjectView() line 100 in /software/meteo/xenial/x86_64/petsc/master/src/sys/objects/destroy.c
[0]PETSC ERROR: #9 PetscObjectViewFromOptions() line 136 in /software/meteo/xenial/x86_64/petsc/master/src/sys/objects/destroy.c
[0]PETSC ERROR: #10 User provided function() line 0 in User file

HDF5-DIAG: Error detected in HDF5 (1.8.18) MPI-process 1:
#000: H5Pdcpl.c line 870 in H5Pset_chunk(): all chunk dimensions must be positive
major: Invalid arguments to routine
minor: Out of range
[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[1]PETSC ERROR: Error in external library
[1]PETSC ERROR: Error in HDF5 call H5Pset_chunk() Status -1
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[1]PETSC ERROR: Petsc Development GIT revision: v3.10.3-1549-g9b78045  GIT Date: 2019-02-13 11:10:12 -0600
[1]PETSC ERROR: plex_prism on a debug_gcc named met-ws-970r17 by Fabian.Jakub Thu Feb 14 14:39:13 2019
[1]PETSC ERROR: Configure options --with-cc=/usr/bin/mpicc --with-fc=/usr/bin/mpif90 --with-cxx=/usr/bin/mpicxx --with-fortran --with-fortran-interfaces --with-shared-libraries=1 --download-hdf5 --download-netcdf=netcdf-c-4.6.2.tar.gz --download-zlib --download-szlib --download-openblas --download-metis --download-parmetis --download-ptscotch --no-download-petsc4py --download-ml --download-hypre --with-debugging=1 COPTFLAGS="-O2 -g" FOPTFLAGS="-O2 -g"
[1]PETSC ERROR: #1 ISView_General_HDF5() line 288 in /software/meteo/xenial/x86_64/petsc/master/src/vec/is/is/impls/general/general.c
[1]PETSC ERROR: #2 ISView_General() line 513 in /software/meteo/xenial/x86_64/petsc/master/src/vec/is/is/impls/general/general.c
[1]PETSC ERROR: #3 ISView() line 1015 in /software/meteo/xenial/x86_64/petsc/master/src/vec/is/is/interface/index.c
[1]PETSC ERROR: #4 DMPlexWriteLabels_HDF5_Static() line 668 in /software/meteo/xenial/x86_64/petsc/master/src/dm/impls/plex/plexhdf5.c
[1]PETSC ERROR: #5 DMPlexView_HDF5_Internal() line 692 in /software/meteo/xenial/x86_64/petsc/master/src/dm/impls/plex/plexhdf5.c
[1]PETSC ERROR: #6 DMView_Plex() line 1103 in /software/meteo/xenial/x86_64/petsc/master/src/dm/impls/plex/plex.c
[1]PETSC ERROR: #7 DMView() line 904 in /software/meteo/xenial/x86_64/petsc/master/src/dm/interface/dm.c
[1]PETSC ERROR: #8 PetscObjectView() line 100 in /software/meteo/xenial/x86_64/petsc/master/src/sys/objects/destroy.c
[1]PETSC ERROR: #9 PetscObjectViewFromOptions() line 136 in /software/meteo/xenial/x86_64/petsc/master/src/sys/objects/destroy.c
[1]PETSC ERROR: #10 User provided function() line 0 in User file
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