[Bioclusters] Reasonable blast runtime

Paul Mc Kenna cluster_boy at pmckenna.net
Fri Feb 3 14:07:32 EST 2006

We are trying to get the hang of a small cluster we just built. A 
co-worker launched a 10K query against the whole human genome. It has 
been running for 3 days now! He had previously launched a 1K query which 
took about 1hr. We are trying to understand what might have happened 
when we scaled up. Is a 10K query really that unreasonable or is 
something else likely to be going on. Is there anyway to check on 
exactly how much of a Blast job has been completed.

Process currently running on 6 compute nodes, 4 are dual processor 
boards. Most have have 2G or more of memory. A quick look of the stats 
showed no more than 12% of available memory being used, less on most 
machines. Essentially no swap has been used to the best of my knowledge.

We used the following syntax to launch the job:

P4_GLOBMEMSIZE=268435456 time  /opt/mpich/gnu/bin/mpirun -np 14 /usr/local/bin/mpiblast -p blastn -d whole_genome.fa -i /home/kieran/rnd.seq



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