[GE users] ncbi blast on SGE

reuti reuti at staff.uni-marburg.de
Tue May 25 11:40:42 BST 2010


Hi,

Am 22.05.2010 um 19:42 schrieb axinsoft:

> 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)

-t will submit an array job, i.e. two times the same job with index number 1 and 2. When you speak below of orte, I assume you want to submit the job in parallel instead.


> 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.

Did you compile blast on your own with Open MPI? Specifying only a parallel environment without any adjustements of the jobscript won't execute in parallel automatically, you can even submit serial jobs with an attached PE, but this will only block slots as only the one from the master process is used. Do you use mpiexec/mpirun in your jobscript?

-- Reuti


> 
> 
> 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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