--- Ami Klein <ami@genome.kvl.dk> wrote: > when submitting jobs with no delay (or less than 3 > seconds delay) between each submission the system > become unstable: sometimes pbs_sched crash with out > any note in it's log file. > > Should we switch to the PBSPro version? This is a known problem: (http://gridengine.sunsource.net/servlets/ReadMsg?msgId=9921&listName=users) The easiest workaround is to put a sleep in qsub, so that users are forced to wait for 3 or more seconds before another job submission. Before you switch to PBSPro, which cost $$, you should try Scalable PBS, which has *lots* of problem fixed. http://supercluster.org/spbs/ Another batch system that I like is Gridengine: http://gridengine.sunsource.net It has more advanced scheduling algorithms, and better features. One of the examples is "job array", which is actually a group of jobs with the same job id (but different task id), is actually easier for managing genome type of workload. **HOWEVER**, switching to a new batch may require learning a new set of concepts. Both SPBS and Gridengine are free and opensource, download and try them. > stdout and stderr files goes to the $HOME directory > (and not to the > ~/.pbs_spool). Don't know about this problem :( > We also need a "swap out Queue", hence low priority > queue that will suspend running jobs (and swap them > out to the disk) incase some jobs in other queues > needs it's cpu. Does such feature exist under PBS > system? The closest thing you can use is checkpointing. I don't think a batch system can tell the OS to "swap processes to disk". Default PBS may not allow you to do that, may be you need to use Maui+PBS. In SGE, you can use "subordinate queues". -Ron > > Thanks. > > -- > Ami Klein, > System Administrator > Division of Genetics > Institute of Animal Science and Animal Health > The Royal Veterinary and Agricultural University > Email: ami@genome.kvl.dk > > _______________________________________________ > Bioclusters maillist - > Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters __________________________________ Do you Yahoo!? Free Pop-Up Blocker - Get it now http://companion.yahoo.com/