Hi Larry, Everything below is with the filesystem mounted with localflock.
This does indeed look a lot like the bug referred to by David Dillow (thanks!) Chris On 5/4/11 10:05 PM, Larry wrote: > try mounting the lustre filesystem with -o flock or -o localflock > > On Thu, May 5, 2011 at 4:47 AM, Christopher Walker > <cwal...@fas.harvard.edu> wrote: >> Hello, >> >> We have a user who is trying to post-process HDF files in R. Her script >> goes through a number (~2500) of files in a directory, opening and >> reading the contents. This usually goes fine, but occasionally the >> script dies with: >> >> >> HDF5-DIAG: Error detected in HDF5 (1.9.4) thread 46944713368080: >> #000: H5F.c line 1560 in H5Fopen(): unable to open file >> major: File accessability >> minor: Unable to open file >> #001: H5F.c line 1337 in H5F_open(): unable to read superblock >> major: File accessability >> minor: Read failed >> #002: H5Fsuper.c line 542 in H5F_super_read(): truncated file >> major: File accessability >> minor: File has been truncated >> Error in hdf5load(file = myfile, load = FALSE, verbosity = 0, tidy = >> TRUE) : >> unable to open HDF file: >> /n/scratch2/moorcroft_lab/nlevine/Moore_sites_final/met/LT_spinup/ms67/analy/s67-E-1628-04-00-000000-g01.h5 >> HDF5-DIAG: Error detected in HDF5 (1.9.4) thread 46944713368080: >> #000: H5F.c line 2012 in H5Fclose(): decrementing file ID failed >> major: Object atom >> minor: Unable to close file >> #001: H5I.c line 1340 in H5I_dec_ref(): can't locate ID >> major: Object atom >> minor: Unable to find atom information (already closed?) >> Error in hdf5cleanup(16778754L) : unable to close HDF file >> >> >> But this file definitely does exist -- any stat or ls command shows it >> without a problem. Further, once I 'ls' this file, if I rerun the same >> script, it successfully reads this file, but then dies on the next one >> with the same error. If I 'ls' the entire directory, the script runs to >> completion without a problem. strace output shows: >> >> open("/n/scratch2/moorcroft_lab/nlevine/Moore_sites_final/met/LT_spinup/ms67/analy/s67-E-1628-04-00-000000-g01.h5", >> O_RDONLY) = 3 >> fstat(3, {st_mode=S_IFREG|0644, st_size=0, ...}) = 0 >> lseek(3, 0, SEEK_SET) = 0 >> read(3, "\211HDF\r\n\32\n", 8) = 8 >> read(3, "\0", 1) = 1 >> read(3, >> "\0\0\0\0\10\10\0\4\0\20\0\0\0\0\0\0\0\0\0\0\0\0\0\377\377\377\377\377\377\377\377@"..., >> 87) = 87 >> close(3) = 0 >> write(2, "HDF5-DIAG: Error detected in HDF"..., 42) = 42 >> etc >> >> which initially looks fine to me, followed by an abrupt close. >> >> NFS filesystems and our 1.6.7.2 filesystem have no such problems -- any >> suggestions? >> >> Thanks very much, >> Chris >> _______________________________________________ >> Lustre-discuss mailing list >> Lustre-discuss@lists.lustre.org >> http://lists.lustre.org/mailman/listinfo/lustre-discuss >> _______________________________________________ Lustre-discuss mailing list Lustre-discuss@lists.lustre.org http://lists.lustre.org/mailman/listinfo/lustre-discuss