Mark, The same code hangs on the customer machine, but works fine on our clusters. Would that be possible if some subset aren't participating in the I/O?
Thanks, Dave On Oct 26, 2010, at 5:14 PM, Mark Howison wrote: > Hi Dave, > > One common hang with collective-mode parallel I/O in HDF5 is when only > a subset of processes are participating in the I/O, but the other > processes haven't made an empty selection (to say that they are not > participating) using H5Sselect_none(). Also, have you tried > experimenting with collective vs. independent mode? > > Mark > > On Tue, Oct 26, 2010 at 6:52 PM, Dave Wade-Stein <[email protected]> wrote: >> We use hdf5 for parallel I/O in VORPAL, our laser plasma simulation code. >> For the most part, it works fine, but on certain machines (e.g., early Cray >> and BG/P) and certain types of filesystems, we've noticed that parallel I/O >> hangs, so we instituted a -id (individual dump) option which causes each MPI >> rank to dump its own hdf5 file, and once the simulation is complete, we >> merge the individual dump files. >> >> We have a customer for whom parallel I/O is hanging, and they are using -id >> as described above. We're trying to pinpoint why parallel I/O is not working >> on their system, which is CentOS 5.5 cluster. >> >> In the past we ourselves have had problems with parallel I/O failing on ext3 >> filesystems, so we reformatted as XFS and the problem went away. Our >> customer did this, but the problem still persists. >> >> Anyone have any words of wisdom as to what other things could cause parallel >> I/O to hang? >> >> Thanks for any help! >> Dave _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
