[MOAB-dev] mbconvert and HDF5-1.10
Grindeanu, Iulian R.
iulian at mcs.anl.gov
Thu Jun 9 14:45:06 CDT 2016
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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