[GE users] ncbi blast on SGE

axinsoft axinsoft at yahoo.com.cn
Sat May 22 18:42:01 BST 2010


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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