hi I'm having trouble reading in a vector on a DMPlex from an HDF5 file. The attached minimal program (readdmvec2.F90) illustrates the problem. What it does is: - reads in a DMPlex from file (ghotcol.exo) and sets it up (distributes, constructs ghost cells and default section) - uses DMGetGlobalVector() to get the vector - sets its object name to 'cell_geometry' - opens the HDF5 file (hotcol_ss.h5) in a viewer and tries to read the vector using VecLoad() The VecLoad() dies, saying "object 'cell_geometry' doesn't exist" in the HDF5 file. (Full error message is below.) But it does exist- it shows up as a dataset in the '/' group in h5dump. I can also read it in from a Python script and h5py, e.g.:

...

...

import h5py f = h5py.File('hotcol_ss.h5') f['cell_geometry'][:]

Any idea why VecLoad() can't find it? I get the same error running on any number of processors. The program that writes 'cell_geometry' to the HDF5 file also subsequently writes time-dependent simulation results to the same file (that's what the other datasets are in there) using DMSetOutputSequenceNumber() and VecView(). I am wondering if the problem is related to this, because if I just write a simple vector out to the file by itself it seems to read back in ok. Cheers, Adrian -- HDF5-DIAG: Error detected in HDF5 (1.8.8) MPI-process 0: #000: ../../../src/H5D.c line 334 in H5Dopen2(): not found major: Dataset minor: Object not found #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find object major: Symbol table minor: Object not found #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 'cell_geometry' doesn't exist major: Symbol table minor: Object not found [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Error in external library [0]PETSC ERROR: Error in HDF5 call H5Dopen2() 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: v3.6.3-3170-g725a008 GIT Date: 2016-01-19 11:34:55 -0600 [0]PETSC ERROR: readdmvec2 `6` on a linux-gnu-c-opt named des108 by acro018 Fri Feb 12 17:36:00 2016 [0]PETSC ERROR: Configure options --download-netcdf --download-exodusii --with-hdf5-dir=/usr --download-triangle --download-ptscotch -- download-chaco [0]PETSC ERROR: #1 VecLoad_HDF5() line 269 in /home/acro018/software/PETSc/code/src/vec/vec/utils/vecio.c [0]PETSC ERROR: #2 VecLoad_Default() line 411 in /home/acro018/software/PETSc/code/src/vec/vec/utils/vecio.c [0]PETSC ERROR: #3 VecLoad_Plex_Local() line 214 in /home/acro018/software/PETSc/code/src/dm/impls/plex/plex.c [0]PETSC ERROR: #4 VecLoad_Plex_HDF5() line 211 in /home/acro018/software/PETSc/code/src/dm/impls/plex/plexhdf5.c [0]PETSC ERROR: #5 VecLoad_Plex() line 238 in /home/acro018/software/PETSc/code/src/dm/impls/plex/plex.c [0]PETSC ERROR: #6 VecLoad() line 975 in /home/acro018/software/PETSc/code/src/vec/vec/interface/vector.c -- Dr Adrian Croucher Senior Research Fellow Department of Engineering Science University of Auckland, New Zealand email: [email protected] tel: +64 (0)9 923 84611