[GE users] Re: [HPC] Running Array job only one per node

mhanby mhanby at uab.edu
Fri Mar 13 14:35:17 GMT 2009


One possible solution would be to request a large amount of RAM (say
your nodes have 16GB you might request 15GB). That should ensure that
only one task per node is started. This will also prevent other jobs
from using those remaining 7 slots per node as well if I'm not mistaken.

-l mem_free=15G

-----Original Message-----
From: rkrug [mailto:R.M.Krug at gmail.com] 
Sent: Friday, March 13, 2009 3:42 AM
To: users at gridengine.sunsource.net
Subject: [GE users] Re: [HPC] Running Array job only one per node

Hi

I want to submit an array job which should run 25 times, but only
one instance at each node at the same time. When I submit the script as
below, it starts all instances at the same time and up to 8 per node
(one per core). Is it possible to state that only one instance should
run at the same time on one node? This has to do with resources use and
disk access.

Thanks,

Rainer


@@@@@@@@@@@@@@@@@@@@@@@
#!/bin/bash
#$ -t 1-25
#$ -cwd -j y

export MPIEXEC_RSH=ssh
export
LD_LIBRARY_PATH=$HOME/lib:/usr/local/openmpi_gnu/lib:$LD_LIBRARY_PATH
export PATH=$HOME/bin:/usr/local/openmpi_gnu/bin:$PATH
.
.
.
@@@@@@@@@@@@@@@@@@@@@@@



-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Cell:		+27 - (0)83 9479 042
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Skype:		RMkrug
Google:		R.M.Krug at gmail.com

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