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Running batch jobs from SeqLab

Tim Cutts tjrc1 at mole.bio.cam.ac.uk
Wed Feb 5 12:10:44 EST 1997


Hi.  Today I installed GCG 9 on our main machine (although I haven't
unleashed it on the users yet, obviously).  I am having problems
getting jobs to run from SeqLab with appropriate priority.

In sitequeues, one can define the way that batch programs are run with
the GCGNiceCommand.  On this IRIX system I have this set to "npri -h
129" so that the GCG batch jobs do not impinge on interactive
performance.

This works perfectly, except that SeqLab ignores it, so that as soon
as I start, say, a fasta search from SeqLab, it takes over all the CPU
time on the machine.

Is there something I have to do to make SeqLab take notice of
GCGNiceCommand (and the appropriate FooSubmitCommand entries too?)

It seems that all one can do with !SEQLAB lines is set parameters for
'at'; I can't seem to specify particular queues for particular
programs, as I can for programs started from the command line.

Am I missing something obvious?  I can't believe GCG would not make
these facilities available from SeqLab.  SeqLab looks very nice, but
if it's going to make the machine grind to a halt as soon as anyone
runs anything from it, I will not be impressed.  This machine usually
has 30-40 simultaneous logins, and usually four or five GCG jobs
running at any one time.  I rely on the GCGNiceCommand facility to
keep the machine running smoothly!  Please give me some ideas!

Tim.



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