As to MPI, we're both using openmpi 1.4.1. We're both using NFS file systems which are formatted as xfs. As I mentioned, we had problems with ext3 filesystems, which were alleviated when we reformatted as xfs. Unfortunately, that didn't work for the customer.
Thanks, Dave On Oct 26, 2010, at 5:36 PM, Mark Howison wrote: > I guess it could depend on the MPI library, but most likely not. What > parallel file system is used on the customer's machine? Mark > > On Tue, Oct 26, 2010 at 7:25 PM, Dave Wade-Stein <[email protected]> wrote: >> 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 >> > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
