On 02/02/12 15:50, Reuti wrote: > Can you put the workflow in a loop at submission time? In each loop iteration > you do: > > JOB_ID=$(qsub -terse command1) > > This will give you the JOB_ID of the submitted job. > > Then submit the next steps like: > > qsub -hold_jid $JOB_ID command2 > qsub -hold_jid $JOB_ID command3 > > They will only start, after command1 finished.
On 02/02/12 16:04, William Hay wrote: > I don't know about better but a more conventional way would be to have > the front end script submit three jobs per file. One regular and two > using -hold_jid on the first job. > > To get fancier with it you could have your initial submit script > generate a list of files and the intended name of the corresponding > derived file. Then submit three suitably sized array jobs using > -hold_jid_ad for the second one. Each would then use its $SGE_TASK_ID to > pick the right file to work on from your list. Great, thanks guys, this is exactly the kind of sage advice I was looking for, you've saved me barking up the wrong tree! :) Regards, Rob -- Robert Hutton Senior Systems and Database Administrator Centre for Genomics and Global Health <http://cggh.org> The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Tel: +44 (0)1865 287721 _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
