[MOAB-dev] mbconvert and HDF5-1.10

[Rob Latham]

On 06/09/2016 01:18 PM, Vijay S. Mahadevan wrote:
> 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.

I'm happy to include the config.log.  It's attached to this email.

An identically-configured HDF5-1.8.17 works well.

What version of HDF5 created the unit test files?  git tells me they 
were committed in July 2013, but HDF5 libraries are supposed to be 
backwards compatible.

==rob

>
> 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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: config-moab-hdf5-1.10.log
Type: text/x-log
Size: 155135 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/moab-dev/attachments/20160609/dd8d9c90/attachment-0001.bin>