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 >