[MOAB-dev] mbconvert and HDF5-1.10
Vijay S. Mahadevan
vijay.m at gmail.com
Thu Jun 9 14:46:52 CDT 2016
Rob, all tests work fine with the following options:
../configure CC=mpicc CXX=mpicxx
--with-hdf5=/homes/robl/soft/hdf5-1.10.0-mpich-logfs --with-mpi
--disable-fortran
So I agree with Iulian that your custom MPI installation is messed up.
If you pass CC/CXX, make sure they are consistent with the
"--with-mpi" option.
Vijay
On Thu, Jun 9, 2016 at 2:45 PM, Grindeanu, Iulian R. <iulian at mcs.anl.gov> wrote:
> Hi Rob,
> I think there is some incompatibility with mpi version
>
> /homes/robl/soft/mpich-logfs/bin/mpicxx
>
> does not work
> ________________________________________
> From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf of Rob Latham [robl at mcs.anl.gov]
> Sent: Thursday, June 09, 2016 2:20 PM
> To: Vijay S. Mahadevan
> Cc: moab-dev at mcs.anl.gov
> Subject: Re: [MOAB-dev] mbconvert and HDF5-1.10
>
> On 06/09/2016 01:57 PM, Vijay S. Mahadevan wrote:
>> 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.
>
> all red across the board!
>
> ../../../config/test-driver: line 107: 327 Segmentation fault
> (core dumped) "$@" > $log_file 2>&1
> FAIL: readutil_test
> ../../../config/test-driver: line 107: 334 Segmentation fault
> (core dumped) "$@" > $log_file 2>&1
> FAIL: tqdcfr
> ../../../config/test-driver: line 107: 342 Segmentation fault
> (core dumped) "$@" > $log_file 2>&1
> FAIL: vtk_test
> FAIL: cub_file_test
> FAIL: gmsh_test
> FAIL: nastran_test
> FAIL: ideas_test
> FAIL: stl_test
> FAIL: smf_test
> ============================================================================
> Testsuite summary for MOAB 4.9.2pre
> ============================================================================
> # TOTAL: 9
> # PASS: 0
> # SKIP: 0
> # XFAIL: 0
> # FAIL: 9
> # XPASS: 0
> # ERROR: 0
> ============================================================================
> See test/io/test-suite.log
> Please report to moab-dev at mcs.anl.gov
> ============================================================================
> make[2]: *** [test-suite.log] Error 1
> make[2]: Leaving directory
> `/blues/gpfs/home/robl/src/moab.git/build/test/io'
> make[1]: *** [check-TESTS] Error 2
> make[1]: Leaving directory
> `/blues/gpfs/home/robl/src/moab.git/build/test/io'
> make: *** [check-am] Error 2
>
>
> I can stick with hdf5-1.8.17 for now.
>
> ==rob
>
>> 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
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