Aaron, Thanks for the reply. I am referring to the workers, which all seem to be chugging along. They all seem to have plenty of memory, and I'm not seeing local I/O or network traffic (iostat and netstat). The mpiPBLAST search is blastn on the nt database, with 100 fragments, and I asked for 102 MPI tasks. The query file is 92MB and I'm running on dual-CPU dual-core Opterons (anyone have any prediction of how long this should take with everything running optimally?).
So you can see what I'm talking about, here's the vmstat output for 3 nodes: (1) 2GB node with 1 worker, (2) 4GB node with 3 workers, and (3) 8GB node with 4 workers. I'm using a beta-version of Open-MPI 1.2, and I had the thought that maybe Open-MPI might be causing mis-representation of user v.s. system time. Thanks, Todd procs -----------memory---------- ---swap-- -----io---- --system-- ----cpu---- r b swpd free buff cache si so bi bo in cs us sy id wa 1 0 0 606540 88732 977100 0 0 0 1 2 2 1 3 96 0 1 0 0 606540 88732 977100 0 0 0 0 1004 20 2 23 75 0 1 0 0 606396 88732 977100 0 0 0 0 1005 24 3 22 75 0 1 0 0 606396 88732 977100 0 0 0 14 1006 21 3 23 75 0 procs -----------memory---------- ---swap-- -----io---- --system-- ----cpu---- r b swpd free buff cache si so bi bo in cs us sy id wa 4 1 4 2130840 85972 988492 0 0 0 1 2 2 1 9 90 0 3 0 4 2130840 85972 988492 0 0 0 88 1008 27 7 68 24 1 3 0 4 2130840 85972 988492 0 0 0 0 1004 19 7 68 25 0 3 0 4 2130848 85972 988492 0 0 0 0 1003 18 8 67 25 0 procs -----------memory---------- ---swap-- -----io---- --system-- ----cpu---- r b swpd free buff cache si so bi bo in cs us sy id wa 4 1 0 4794384 96300 1384740 0 0 0 1 2 0 2 12 86 0 4 0 0 4794384 96300 1384740 0 0 0 90 1039 340 8 92 0 0 4 0 0 4794344 96300 1384740 0 0 0 0 1064 424 10 90 0 0 4 0 0 4794352 96300 1384740 0 0 0 0 1056 360 9 91 0 0 -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Aaron Darling Sent: Friday, March 02, 2007 1:31 AM To: [email protected] Subject: Re: [Mpiblast-users] cpu time partitioning Hi Todd... Heywood, Todd wrote: > I'm just starting to run mpiBLAST jobs, and I'm noticing, using vmstat, that the vast majority of CPU time is system time, not user time. Is this normal? > > Thanks. > > Todd Heywood > Whether that's normal depends on which mpiblast process you were monitoring and a few other details. mpiblast processes have three roles: writer, scheduler, and worker. For a perfectly load-balanced search, the workers should probably be more user-time than system time. The writer can have substantial system time because it does lots of disk I/O and communication, and what little CPU time the scheduler uses will probably be system time for communication overhead. Depending on the search type and database, i.e. blastn, blastp, tblastx etc, the relative amounts of system time to user time for workers can change substantially. blastn can be extremely I/O intensive, while tblastx tends to be compute intensive. -Aaron ------------------------------------------------------------------------ - 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=DEVDE V _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users ------------------------------------------------------------------------- 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
