On Fri, Apr 19, 2013 at 12:47:40PM -0400, Mehmet Belgin wrote: > Hello everyone, > > We cannot use parallel HDF5 on any of our systems. The processes either crash > or hang (and they work with sequential HDF5). > > On NFS, we are getting: > > ADIOI_Set_lock:: No locks available > ADIOI_Set_lock:offset 69744, length 256 > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 124 > File locking failed in ADIOI_Set_lock(fd 25,cmd F_SETLKW/7,type > F_WRLCK/1,whence 0) with return value FFFFFFFF and errno 25. > If the file system is NFS, you need to use NFS version 3, ensure that the > lockd daemon is running on all the machines, and mount the directory with the > 'noac' option (no attribute caching).
NFS is tricky to get right, and often requires turning off any and all caching. Let's set the NFS issue aside for now. > On Panasas: > > ADIOI_PANFS_RESIZE: Rank 13: Resize failed: requested=46996328 actual=9187464. > > We are using intel 12.1.4, mvapich1.6 (tested with 1.8 and 1.9 as well) and > HDF5 1.8.10. > > Is this a known problem, and do you know any workarounds without turning of > the parallel capabilities of HDF5? Parallel HDF5 works on a lot of other environments, but I don't have any experience with Panasas or the Panasas-contributed ADIO driver. > Any suggestions you may have will be appreciated! The simplest workaround will be to select other ROMIO drivers. - When accessing the Panasas file system, try prefixing the file name you pass to HDF5 with "ufs:". This will turn off any panasas-specific optimizations, unfortunately, but lots of folks use the default "unix file system" driver. Also, nvapic1.6 is based on an ancient version of ROMIO. If you've got any way to use mvapich2, there are undoubtedly some fixes that might make your life better. Perhaps you meant 'mvapich2' .. I've seen mvapich 1 "in the wild" enough times, though, that I thought I should double-check. ==rob -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA _______________________________________________ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
