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=DEVDEV _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
