ADL: Submitting an AutoDock job in a Linux cluster
wilfred at sdsc.edu
Tue Apr 3 23:10:48 PDT 2007
Try get rid of the '&' sign at the end of your autodock3 command line,
which sends the job to the background, and is considered 'done' to PBS.
From: autodock-bounces at scripps.edu
[mailto:autodock-bounces at scripps.edu] On Behalf Of
cdeligka at purdue.edu
Sent: Wednesday, April 04, 2007 2:08 PM
To: autodock at scripps.edu
Subject: ADL: Submitting an AutoDock job in a Linux cluster
I am using a simple PBS script to submit AutoGrid and
AutoDock jobs in a Linux cluster. The jobs are launched
succesfully and I do get the results and all the output files.
However, PBS fails to keep track of the AutoGrid and
Immediately after I submit the job the job is running
and after a few seconds the job is exitting (although
it is still running on the node).
So, after a few seconds, according to PBS the node is
free but in reality there is an AutoDock job running.
I know that the AutoDock job is still running because
the output file is not complete.
This is the executable script (autodockJob.sh) that I use:
autodock3 -p DPF_FILE -l DLG_FILE &
and I submit the jobs using the following command:
qsub -N AutoDock -l
I just started using PBS and I do not know why PBS
fails to keep track of the jobs,
any help would be greatly appreciated,
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