[MOAB-dev] mbconvert and HDF5-1.10

[Vijay S. Mahadevan]

Rob,

We haven't tested with the latest HDF5 version yet. We are planning to
do this soon. So it is possible that the configuration is broken or
that parallel HDF5 was not enabled. Can you send the config.log file
so that we can decipher if the configuration was successful to start
with ?

We could try to replicate your configuration and push a fix if there
is a problem.

Vijay

On Thu, Jun 9, 2016 at 1:14 PM, Rob Latham <robl at mcs.anl.gov> wrote:
> I tried running mbconvert with the recently released HDF5-1.10 library.
> That library seems unable to read MeshFiles/unittest/64bricks_12ktet.h5m ?
>
> I built my own HDF5-1.10, so maybe I needed to configure with an extra
> backwards compatibility flag?
>
> HDF5:
> ../configure --prefix=/homes/robl/soft/hdf5-1.10.0 CC=mpicc \
>         --enable-parallel
>
> MOAB:
> ../configure CC=mpicc CXX=mpicxx \
>      --with-hdf5=/homes/robl/soft/hdf5-1.10.0 \
>      --with-mpi=/homes/robl/soft/mpich \
>      --prefix=/homes/robl/soft/moab-logfs
>
> and finally, mbconvert:
>
> mpiexec -np $((PBS_NNODES*4)) ./build-1.8.17/tools/mbconvert \
>                 -O PARALLEL=READ_PART -O PARTITION=PARALLEL_PARTITION \
>                 -O PARALLEL_RESOLVE_SHARED_ENTS -o PARALLEL=WRITE_PART \
>                 MeshFiles/unittest/64bricks_12ktet.h5m
> /lcrc/project/radix/robl/moab/out-gpfs
>
> But when I do that, I get this error:
>
> HDF5-DIAG: Error detected in HDF5 (1.10.0) MPI-process 0:
>   #000: ../../src/H5F.c line 575 in H5Fopen(): can't set access and transfer
> property lists
>     major: File accessibilty
>     minor: Can't set value
>   #001: ../../src/H5Pint.c line 5506 in H5P_verify_apl_and_dxpl(): not the
> required access property list
>     major: Property lists
>     minor: Inappropriate type
>   #002: ../../src/H5Pint.c line 3767 in H5P_isa_class(): not a property list
>     major: Invalid arguments to routine
>     minor: Inappropriate type
> HDF5-DIAG: Error detected in HDF5 (1.10.0) MPI-process 0:
>   #000: ../../src/H5G.c line 464 in H5Gopen2(): not a location
>     major: Invalid arguments to routine
>     minor: Inappropriate type
>   #001: ../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
>     major: Invalid arguments to routine
>     minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.10.0) MPI-process 0:
>   #000: ../../src/H5F.c line 749 in H5Fclose(): not a file ID
>     major: Invalid arguments to routine
>     minor: Inappropriate type
> [0]MOAB ERROR: --------------------- Error Message
> ------------------------------------
> [0]MOAB ERROR: NULL file handle.!
> [0]MOAB ERROR: is_error() line 133 in src/io/ReadHDF5.hpp
> [0]MOAB ERROR: --------------------- Error Message
> ------------------------------------
> [0]MOAB ERROR: Failed to load file after trying all possible readers!
> [0]MOAB ERROR: serial_load_file() line 635 in src/Core.cpp
> [0]MOAB ERROR: --------------------- Error Message
> ------------------------------------
> [0]MOAB ERROR: Failed in step PARALLEL READ PART!
> [0]MOAB ERROR: load_file() line 553 in src/parallel/ReadParallel.cpp
> [0]MOAB ERROR: load_file() line 252 in src/parallel/ReadParallel.cpp
> [0]MOAB ERROR: load_file() line 515 in src/Core.cpp
>
>
> ==rob