[Bioclusters] Memory Usage for Blast - question

[Dinanath Sulakhe]

This is a blast run for NCBI NR against itself. So the sequence size varies.
Thanks for the reply, i will look into the wordsize.

Dina

At 04:50 PM 3/9/2005, Hrishikesh Deshmukh wrote:
>Hi,
>
>You haven't told how long each sequence is!, you can tweak wordsize -W
>to make it faster but then BLAST becomes less sensitive.I suggest you
>take a look at the book BLAST by Ian Korf et al.
>
>Thanks,
>Hrishi
>
>
>On Wed, 09 Mar 2005 16:09:41 -0600, Dinanath Sulakhe
><sulakhe at mcs.anl.gov> 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
> >
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> >
>_______________________________________________
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===============================
Dinanath Sulakhe
Mathematics & Computer Science Division
Argonne National Laboratory
Ph: (630)-252-7856      Fax: (630)-252-5986