[Bioclusters] Memory Usage for Blast - question

Malay mbasu at mail.nih.gov
Thu Mar 10 10:30:23 EST 2005

Dinanath Sulakhe wrote:
> Hi,
> 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,
> Dina
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
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I am not very sure what's the installation setup is but in many cases it 
can be solved by fragmenting the database into smaller sizes using -v 
while running formatdb.


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