[Bioclusters] Re: BLAST job on SGE

Juan Carlos Perin bic at genome.chop.edu
Fri Dec 3 14:52:49 EST 2004

I'm also interested in this, and have been playing with the configuration.
Our friends at Penn have fixed this and created a queue configuration that
allows single jobs to execute on all available nodes, as opposed to running
two jobs per node, which isn't desirable.  It seems to me that the idea was
to run one blast job on each CPU, thus two jobs on each machine, but the
architecture doesn't necessarily work like that, and instead waits for one
to finish, or re-queues the job.

This is a configuration that was suggested by the very kind people at Penn,
that seems to work for this situation:

        # qconf -sp smp
        pe_name           smp
        queue_list        all
        slots             999
        user_lists        NONE
        xuser_lists       NONE
        start_proc_args   NONE
        stop_proc_args    NONE
        allocation_rule   $pe_slots
        control_slaves    FALSE
        job_is_first_task FALSE

I have yet to test it myself.

Juan Perin
Bioinformatics Core
Children's Hospital of Philadelphia

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