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Full Discussion: qsub in a bash script?
Top Forums Shell Programming and Scripting qsub in a bash script? Post 302436620 by kcgb20 on Monday 12th of July 2010 03:20:16 PM
Old 07-12-2010
qsub in a bash script?
I was just wondering if it is permissible to qsub from a bash script as follows:

Code:
#! /bin/sh

echo "altering .txt in dir $DIR with retokenize.py"
for f in $DIR/txt/*.txt; do
  echo $f;
  /l2/nlp/i2b2/retokenize.py < $f > ${f//.txt/.tok};
done


echo "altering .tok in dir $DIR with awk <s> </s>"
for f in $DIR/txt/*.tok; do
  echo $f;
  cat $f | awk '{printf("<s> %s </s>\n",$0)}' > ${f//.tok/.ecIN};
done


echo "altering .tok in dir $DIR with tagger.stayTOK.py "
for f in $DIR/txt/*.tok; do
  echo $f;
  cat $f | /l2/nlp/i2b2/tagger.stayTOK.py < $f > ${f//.tok/.ecIN-POS};
done


export MODEL=/data/nlp/src/charniak/DATA/DATA_DEV24/;
echo "qsubbing for $DIR";
qsub -o $DIR/ecOUT.log -q kiwi.q /l2/nlp/i2b2/runEC.unconstrained.sh;
qsub -o $DIR/ecOUT-POS.log -q kiwi.q l2/nlp/i2b2/runEC.POS.sh;

 

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LEARN ABOUT OSX

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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