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 > > > > _______________________________________________ > > Bioclusters maillist - Bioclusters at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bioclusters > > >_______________________________________________ >Bioclusters maillist - Bioclusters at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bioclusters =============================== Dinanath Sulakhe Mathematics & Computer Science Division Argonne National Laboratory Ph: (630)-252-7856 Fax: (630)-252-5986