[GE users] ncbi blast on SGE

axinsoft axinsoft at yahoo.com.cn
Wed May 26 03:41:07 BST 2010


hmmm alright, masters, i give up the wrong expectation on SGE/blast. very appreciated you sharing your knowledge and exp.

the reason we try SGE & cluster is to submit millions of sequence for blasting. it will take a few month if we use normal single cpu workstation. 

i think i should take the way to blastall with "-a $NSLOTS"(this para should be wonderful). so SGE only take my job to run on a --single-- exec node (with NSLOTS cpus/cores), i should do a small script to cut my million seq to a few thousands seq pieces and submit quite a few times to different nodes, am i going to right way now?

when we are talking about thousands of sequence blasting, i test against small swissprot db (only about 200MB), my memory is 1GB/3.5GB, it take up only like 300MB RAM. even with the 7GB NR db(i format it by 1G volume), only 600MB RAM is used. according blast manual, it should read the whole db into memory if there is enough RAM. something wrong? so in my scenario, the CPUs seems to be the only bottleneck? 

so what i need to do, find as many CPU as possible, add them into my cluster, feed them the same number of jobs. correct?

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