[Bioclusters] Memory Usage for Blast - question

Dinanath Sulakhe sulakhe at mcs.anl.gov
Wed Mar 9 18:23:51 EST 2005

At 05:06 PM 3/9/2005, Lucas Carey wrote:
>Hi Dina,
>I don't know how many of the results you actually need. You may free up 
>some memory by limiting e-value, returned results, and aligned results.
>blastall -e 0.0001 -b 25 -v 25

would limiting the e-value and other parameters reduce the RAM usage??

>Another option, if you can limit Condor to a single job per machine, would 
>be to run 'blastall -a 2' to use both CPUs with only one process.

These jobs are assigned by the scheduler. Initially i had used '-a 2' 
option, but when this job is running on a node, the scheduler would assign 
another job by some other user on the same node, assuming the other 
processor to be free, but then blast would starve the other job. So we 
can't use 'a -n' option here.


>On Wednesday, March 09, 2005 at 16:09 -0600, 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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>Bioclusters maillist  -  Bioclusters at bioinformatics.org

Dinanath Sulakhe
Mathematics & Computer Science Division
Argonne National Laboratory
Ph: (630)-252-7856      Fax: (630)-252-5986

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