[Bioclusters] inconsistent output from simple BLAST job

Kumaran Rajaram kums at mpi.mpi-softtech.com
Mon Nov 22 17:21:11 EST 2004


   Use NFSv3 and mount NFS with "noac" option. "noac" disables file
attribute caching and should by default flush write operation to the
disks (on the server). It checks for changes in file attributes for read
operation. The disadvantage with this option is that it degrades the file
write performance.


On Mon, 22 Nov 2004 peter_webb at agilent.com wrote:

> This may be a BLAST question, a Linux question, or a networking question...
> We're running a small cluster (Supermicro dual Xeon, RedHat Enterprise, SGE, gigE switch interconnect).  We observed occasional inconsistent output from BLAST jobs.  Inconsistent means that a few hits in the file are missing, not necessarily at the beginning or end of the file.
> I've tracked it down to writing output from the process running on the nodes to a network file system instead of the local disk.  This happens even when I log into the node and run the BLAST job directly, so I don't believe it has anything to do with SGE.  The problem is intermittent; it will run the test job with identical output hundreds of times, then fail a few times, then run happily again.
> It looks for all the world as if one line of output (using -m 8 in BLAST) has vanished into the ether, without anybody complaining about it.
> Any ideas as to what is up, or suggestions to narrow things down further, would be very welcome.
> Thanks,
> Peter
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