Hi Juan: You might want to trim you cc list ... :) You should have a look at mpiBLAST. It might be able to handle what you want, and we have a nice run script to drive it (works great with gridengine). See http://www.scalableinformatics.com/metadot/index.pl?id=2213&isa=Category&op=show for more details. We have a web-ified version of this for another customer, somewhat specialized to their environment. Joe Juan Carlos Perin wrote: > > Sun Grid Engine doesn't seem to utilize all the empty resources that > it should. When I run btblastall on the command line on a search > against NT ( which has been partitioned into 15 segments), only three > machines actually get queued up for blastall jobs. Also, during this > process I do not see processor usage ever going above 24%. I would > hope, or expect that more, idle nodes, would receive blastall jobs > with one of the 15 segments of the DB. This is very disappointing > considering a single G5 can search the NT database in under 3 minutes, > while running on multiple nodes actually takes well over ten minutes. > > I would also hope, but don't know how, to tweak or configure SGE to > allow more efficient usage of idle resources. On the same note, it > seems that even running a regular blastall job from the command line > on a single machine is also somehow restricted to a certain amount of > CPU usage. (usually no more than 60% CPU usage). I'm wondering if > there is a way to allow greater CPU usage overall. > > The only work-around that seems to really work is running btblastall > on the command line with a database that has been forced to segment > into many more segments, rather than 15 (one for every node) into 30 > or 32 (one for every processor). This, on the command line, seems to > distribute jobs a little more efficiently, as well as utilizing more > CPU power than any other run. > > Any thoughts would be VERY helpful. > > Thanks, > Juan > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman@scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 612 4615