Hi Chuming, How much of that 17 seconds is startup time? -- if you run with a single short query on the database how long does mpiblast take? You're probably reaching a lowerlimit for time at very small query sizes. How many nodes are you running on? How long does it take to run an mpi-hello_world on that number of nodes? If you'd like you can post or look through the output produced when running with --debug and see where the most time is spent for the short run.
additionally, please don't double-post to mpiblast-users and bioclusters. A question like this is for the mpiblast list. -Lucas On Wednesday, March 15, 2006 at 08:17 -0500, Chuming Chen wrote: > Hi all, > > Does the query size of mpiblast effect the total performance? > > It took about 17 seconds per sequence when I run 721 sequences (542K) > against 22G database. > But when I run 88532 sequences (47M) against the same database, it took > about 1 minute. > > Can the performance be improved if the query sequence is in a > relatively smaller size? > > Thank you for your kind comments and suggestions. > > Chuming Chen ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
