On 2014-04-28 19:08, Imran Ali wrote:
I have recently opened an issue at h5py github repository
(https://github.com/h5py/h5py/issues/434#issuecomment-41567806 [1])
about an error I am having with my Parallel HDF5 install. I have
installed HDF5 through the dorsal script
(https://github.com/FEniCS/dorsal/blob/master/FEniCS/packages/hdf5.package
[2]). The install completes without any error. However, when I try to
use h5py (using a test run script) , I get an odd error :
................EE................................................................................................................sss...........................x.......................s.......................................x.................................s...............................................
======================================================================
ERROR: test_mpi_atomic (h5py.tests.test_file.TestDrivers)
Enable atomic mode for MPIO driver
-------------------------
Traceback (most recent call last):
File
"/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/h5py-2.3.0-py2.7-
linux-x86_64.egg/h5py/tests/test_file.py", line 251, in
test_mpi_atomic
with File(fname, 'w', driver='mpio', comm=MPI.COMM_WORLD) as f:
File
"/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/h5py-2.3.0-py2.7-linux-x86_64.egg/h5py/_hl/files.py",
line 222, in __init__
fid = make_fid(name, mode, userblock_size, fapl)
File
"/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/h5py-2.3.0-py2.7-linux-x86_64.egg/h5py/_hl/files.py",
line 85, in make_fid
fid = h5f.create(name, h5f.ACC_TRUNC, fapl=fapl, fcpl=fcpl)
File "h5f.pyx", line 90, in h5py.h5f.create (h5py/h5f.c:2222)
IOError: Unable to create file (Mpi_err_other: known error not in
list)
======================================================================
ERROR: test_mpio (h5py.tests.test_file.TestDrivers)
MPIO driver and options
-------------------------
Traceback (most recent call last):
File
"/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/h5py-2.3.0-py2.7-linux-x86_64.egg/h5py/tests/test_file.py",
line 241, in test_mpio
with File(fname, 'w', driver='mpio', comm=MPI.COMM_WORLD) as f:
File
"/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/h5py-2.3.0-py2.7-linux-x86_64.egg/h5py/_hl/files.py",
line 222, in __init__
fid = make_fid(name, mode, userblock_size, fapl)
File
"/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/h5py-2.3.0-py2.7-linux-x86_64.egg/h5py/_hl/files.py",
line 85, in make_fid
fid = h5f.create(name, h5f.ACC_TRUNC, fapl=fapl, fcpl=fcpl)
File "h5f.pyx", line 90, in h5py.h5f.create (h5py/h5f.c:2222)
IOError: Unable to create file (Mpi_err_other: known error not in
list)
-------------------------
Ran 306 tests in 0.382s
FAILED (errors=2, skipped=5, expected failures=2)
I am able to use hdf5 just fine when I do not use the mpio driver
along with the mpi communicator.
Links:
------
[1] https://github.com/h5py/h5py/issues/434#issuecomment-41567806
[2]
https://github.com/FEniCS/dorsal/blob/master/FEniCS/packages/hdf5.package
I forgot to mention that I am using Red Hat 4.4.7-4 6 (x86_64) without
root access. My mpi version is
mpirun (Open MPI) 1.6.2
mpiexec (OpenRTE) 1.6.2
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