[MOAB-dev] mbconvert and HDF5-1.10

[Vijay S. Mahadevan]

Ok, looks like configuration passed cleanly. And certainly looked like
your linkage didn't have problems either. Can you try running make
check in interactive mode to see if that passes in test/io build
folder ? If these fail, then it may point to the root cause.

Either way, I'll try to build MOAB and point to your HDF5 version to
replicate issues locally. More soon.

Vijay

On Thu, Jun 9, 2016 at 1:49 PM, Rob Latham <robl at mcs.anl.gov> wrote:
>
>
> 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