[Bioclusters] Blast Problems

[david speed (RI)]

Hi all,

We have installed Sun Grid Engine onto our 15-node Linux (Red Hat 7.1) cluster (30 Intel CPUs). There is an NFS export mounted from the head node to each slave node solely to contain the SGE tools and directories.  We have installed the ncbi blast tools (blastall version 2.2.6) and the databases to be blasted against locally on each node.

This set up works fine for most of the jobs we run however sometimes a blast job will continue to run even though the output file contains output for all the sequences in the input file the job just runs using 99.9 %cpu until the queue is cleaned.  After the queue is cleaned sometimes the queue will become unusable.

For a long time we thought this was a problem with our SGE set-up now we are thinking it may be a problem with ncbi blast has anyone else had similar problems with blast failing to exit?

Would there be any benefit in switching to Wu-Blast?

Thanks for your time

David Speed
Programmer
Roslin Institute
Bioinformatics Group
Roslin, 
Midlothian, 
EH25 9PS, 
UK
Telephone: +44 (0)131 527 4200 (switchboard) 
Fax: +44 (0)131 440 0434

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