[Bioclusters] inconsistent output from simple BLAST job

[Joe Landman]

Hi Peter:

  Could you tell us what your NFS mount options are for the node?  Could 
be a case of async writes and bad flushing of output.

Joe

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 
>_______________________________________________
>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bioclusters
>  
>

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Joseph Landman, Ph.D
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Scalable Informatics LLC,
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