Running with Sun Grid Engine

[Anders Blom]

It has been brought to our attention that if you run ATK using Sun Grid Engine, you need to take care not to over-allocate licenses. If you use the default settings, and run a job over, say, 4 nodes, you will actually consume 4 master licenses, which is not what you want. To avoid this, you should use the setting

Code

#$ -l atk=0.25

or 4 nodes, 0.125 for 8 nodes, etc (that is, in general 1/N where N is the number of nodes). The keyword "atk" here is linked to the "-N" option, i.e. the name of the job. So, a more complete way to start a job on 4 nodes would be

Code

#!/bin/bash
#$ -N atk
#$ -l virtual_free=1G
#$ -l h_cpu=40:00:00
#$ -l atk=0.25
#$ -pe atk=4
module load atk
atk script.py