Interesting links.
Thanks,
Franck - Je suis Charlie : http://www.charliehebdo.fr/index.html
Le 2015-01-07 18:51, Dave Love a écrit :
Emmanuel Florac <[email protected]> writes:
2. Run a code that uses MPI-IO (or HDF5) to read or write (big)
files.
If yes, do I have to modify my code and / or re-compile MPI (or
HDF5) with specific options to account for PVFS ?
If your PVFS cluster is installed with the MPIO libraries, it should
work without code modification. You may need some configuration
though,
like running HDF5 with the proper destination storage parameters,
something like
HDF5_PREFIX=pvfs2:/myorangefs mpiexec /whatever/program
I'm not sure what "MPIO libraries" means, but at least with openmpi
and
using ROMIO, you need to configure it to build against pvfs2 with
something like
./configure ...
--with-io-romio-flags="--with-file_system=ufs+pvfs2"
(Some openmpi versions need patching, but I think the latest 1.8 is
OK.)
I don't know mpich but perhaps Rob Latham will chime in with
authoritative answers.
Then you need to install the parallel version of HDF5 (package
hdf5-{openmpi,mpich} from EPEL for centos) and ensure it's picked up
correctly, of course, and I think had I some trouble at least with
builds against it.
See <http://institutes.lanl.gov/plfs/> for problems and a workaround
concerning hdf-like parallel i/o on gpfs etc., but I don't know how
the
current versions compare. (It's a pity there's no direct comparison,
at
least between lustre and orangefs, on the same hardware that I know
of;
I'd hoped to make one but I didn't get a chance before Lustre was a
fait
acomplis here.) Perhaps the new MPI-IO implementation in openmpi 1.8
for pvfs <http://www.open-mpi.org/papers/euro-mpi-2011-ompio/>
provides
extra improvement too.
Note that you can test off local disks on your cluster as normal user
jobs -- see the recent answers to me here. If you can install
packages
on it, there's orangefs rpm packaging under
<http://copr.fedoraproject.org/coprs/loveshack/orangefs/>. The
binaries
are built against openib, but the source has a flag for that.
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