Rob, Thanks a lot for your suggestions, I will try them and keep the list updated. And yes, I meant mvapich2... I too heard about unconfirmed mvapich sightings in the wild so thanks for checking :)
Oh, also, I installed a no-romio version of mvapich2 and recompiled HDF5 with it, but still seeing the same problem :( -Mehmet On May 6, 2013, at 10:47 AM, Rob Latham wrote: > 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 _______________________________________________ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
