On Wednesday, March 09, 2005 at 17:23 -0600, Dinanath Sulakhe wrote: > 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 > >after would limiting the e-value and other parameters reduce the RAM usage?? with mpiBLAST -e & -b can limit the memory usage for the master node. I don't have a free cpu right now to check blastall. > > >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. I used to use an OpenPBS cluster that would do that, but allowed me to specify which nodes I wanted to run on. I would start up my compute job on one processor, and while (1){ sleep (1000); } one the second. -Lucas > > > Thanks, > Dina > > >-Lucas > > > >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 > >> 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 > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters