ADL: Submitting an AutoDock job in a Linux cluster

Wilfred Li 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.

Regards,
 
Wilfred
 

	-----Original Message-----
	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
	
	Dear all,
	
	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 
	AutoDock jobs. 
	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:
	
	cd $PBS_O_WORKDIR
	autodock3 -p DPF_FILE -l DLG_FILE &
	
	and I submit the jobs using the following command:
	
	qsub -N AutoDock -l 
	walltime=01:00:00,nodes=1:ppn=1:bionode1 autodockJob.sh
	
	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,
	 
	Christos 
	
	
	
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