Hi Intikhab, We've never run mpiBLAST on Score, but I highly doubt that that is where the problem lays. Could you run mpiblast with the --debug option and post the output after 24hrs? Are the processors really using >90% CPU or are they stuck in system or iowait states? If you can login to the worker nodes top can tell you this. Looking at your command line, you don't want to use both 44 mpi proceses and the '-m 8' option. Try mpiblast without the '-m 8' option. Lucas
On 2/20/07, intikhab alam <[EMAIL PROTECTED]> wrote: > Hi everybody, > > I have a dataset of 347899 protein sequences which I want to compare > to each other (all-against-all blast). I have access to the compute > cluster which is running Score (version 5.8.4.r3) as an mpi > environment and have 25 nodes, each with 4 cores and 8 GB of RAM. > > We have the latest version of mpiblast installed. I started a mpiblast > job, (for comparing 347899 sequences against each other), on 44 > processors using the following commandline: > > > mpiformatdb -i 36FungalJGIanigNbcin_M40 --nfrags=42 -p > T --skip-reorder > > mpisub 44 /usr/local/mpiblast_tool/bin/mpiblast -p blastp -d > 36FungalJGIanigNbcin_M40 -i > /users/zzalssn4/scratch/mpiblast/work/36FungalJGIanigNbcin_M40 -m 8 -e > 1e-5 -o > /users/zzalssn4/scratch/mpiblast/work/36FungalJGIanigNbcin_M40.outF42C44 > > This job was running for about 12 days and only 22% or 10122202 > matches of the total 47342483 known significant matches were received, > still all the processes running to the full (>90% usage) on all > specified processors. > > > The same all-against-all blast job using standard blast on 36 > processors, where I made 36 chunks of the dataset and blasted each > chunk against the complete dataset on a single processor, got > completed in less than 24hrs, resulting in 47342483 significant > sequence matches. > > May be I am missing something in running mpiblast properly, so here I > need some help in whether I could improve the running time of mpiblast > on the size of the datasets mentioned above. > > Hope to hear from you soon. > > Regards, > > Intikhab > > > -- > Dr. Intikhab Alam > > Research Associate > School of Computer Science > University of Manchester > LF7, Kilburn Building, > Oxford Road Manchester, M13 9PL > United Kingdom > http://www.cs.man.ac.uk/~ialam ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
