[GE users] ncbi blast on SGE

murple andreas.kuntzagk at mdc-berlin.de
Tue May 25 09:58:17 BST 2010

If you want to boost blast performance by parallelization across nodes 
you should install mpiblast (http://www.mpiblast.org/).
Setting it up requires installation of the openMPI library and 
integration of it into SGE.
SGE does not make your programs running parallel by some kind of magic. 
And the vanilla-NCBI-blast is not cable of running parallel across 
multiple nodes (don't know if it can do multi-core)

So in your tests SGE was doing what it is supposed to do - distribute 
your jobs to empty nodes/slots. Bummer is, each of these jobs was the 
same blast run as the others - so no speedup.

So if you just want to run blast across multiple nodes as the only user 
and the only jobs you only need to install mpiblast without SGE and do 
the management of starting the jobs manual.
If you will run it in a multiple user scenario and/or on many more 
nodes, you should consider SGE with openMPI integration.

regards, Andreas

axinsoft wrote:
> hi masters:
> I just installed Rocks clusters 5.3(the lastest) with default SGE package on a small 2 nodes cluster for testing purpose. Everything seems working. But the ncbi blast is not working with performance double as expecting.
> example here a long time ago, seems blast is working with SGE very well already.
> http://developers.sun.com/solaris/articles/integrating_blast.html
> follow the instruction to create the job, it submit to one node only.
> i try qsub with array option (-t 1-2), job is dispatch to 2 nodes to utilize all cpus. but the execution time do not even reduce a second, compare to running job in one node. (the test run is 15 min with 1000 seq blastx)
> i try other option -pe orte 4, then qstat could see the job also spread to 2 nodes, but one of the host the cpu do not boost up at all. so the performance is still same as before.
> I google and seems all other people are happy and quiet. Do I need to config or setup anything?
> I install Rocks 5.3 with default setting. only config i did was to add 'execd' into the qmaster host to make it exec node also. (as instruction in Rocks guide.)
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