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Full Discussion: Problem Running qsub multiple jobs
Top Forums UNIX for Advanced & Expert Users Problem Running qsub multiple jobs Post 302376470 by InfoSeeker on Tuesday 1st of December 2009 12:28:59 PM
Old 12-01-2009
Question Problem Running qsub multiple jobs
Hello,
I have a perl script that takes in one file of input and outputs to a file. I would like to run this script on several input files, and I would like to run it with qsub, something like this:

Input files:

FileListDssp.txt.numaa
FileListDssp.txt.numab
FileListDssp.txt.numac
etc..

and code

[tcsh shell]
foreach file ( FileListDssp.txt.num* )
qsub -cwd PerlScript.pl $file
## this outputs to a file Output.txt (command is within PerlScript)
echo DONE $file >>Status.txt ##be aware whether job submitted or not
end

If I do this, I get multiple jobs submitted, which is fine, but the output is jumbled because everything is sent to one file in no particular order.
Accordingly, I want to run a loop that executes each qsub job one at a time (to get the ordered output).

Can anyone kindly advise as to how to use qhold or qrls to prevent a new job from executing until the previous one is done? And how do I incorporate them into the loop?

OR, do I need to run all the jobs and then develop a different loop with qhold and qrls? How would I do that?

Your advice is greatly appreciated!
Thanks,
DG
 

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LEARN ABOUT HPUX

qsub

QSUB(1) 						User Contributed Perl Documentation						   QSUB(1)

NAME

       qsub - submit a batch job in a familiar pbs format

SYNOPSIS

       qsub  [-a date_time]
	     [-A account_string]
	     [-b secs]
	     [-C directive_prefix]
	     [-e path]
	     [-I]
	     [-l resource_list]
	     [-m mail_options] [-M  user_list]
	     [-N name]
	     [-o path]
	     [-p priority]
	     [-q destination]
	     [-W additional_attributes]
	     [-h]
	     [script]

DESCRIPTION

       The qsub command displays information about nodes. It is aimed to be feature-compatible with PBS' qsub.

OPTIONS

       -a  Display information for all nodes. This is the default if no node name is specified.

       -I  Interactive execution.

       -j join
	   It is not necessary (currently also not possible) since stderr/stdout are always joined.

       -v [variable_list]
	   Exporting single variables via -v is not supported, since the entire login environment is exported by the default.

       -V  The -V option to export the current environment is not required since it is done by default.

       -? | --help
	   brief help message

       --man
	   full documentation

perl v5.14.2							    2012-04-10								   QSUB(1)
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