[Bioclusters] Memory Usage for Blast - question

Dinanath Sulakhe sulakhe at mcs.anl.gov
Wed Mar 9 17:09:41 EST 2005

I am not sure if this is the right place to ask this question !!
I am running Blast (NCBI) parallely on a cluster with 80 nodes. (I am 
running NCBI NR against Itself). Each node is a dual processor.

I am using Condor to submit the jobs to this cluster. The problem I am 
coming across is, whenever two blast jobs (each blast job has 100 
sequences) are assigned on One node (one on each processor), the node 
cannot handle the amount of memory used by the two blast jobs. PBS mom 
daemon on the nodes cannot allocate the memory they need to monitor the 
jobs on the node and they fail, thus killing the jobs.

Condor doesn't recognize this failure and assumes that the job was 
successfully completed, but actually only few sequences get processed 
before the job is killed.

Now the Admin of the Site is asking me if its possible to reduce the amount 
of memory these blast jobs use? He says these jobs are requesting about 
600-700MB of RAM, and he is asking me to reduce it to atmost 500MB.

Is it possible to reduce the amount of RAM it is requesting by tweaking any 
of the parameters in blast??

My blast options are :

blastall -i $input -o $output -d $db -p blastp -m 8 -F F

Please let me know,
Thank you,

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