Find and delete files before a job is submitted to queue Post: 302420045

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Top Forums Shell Programming and Scripting Find and delete files before a job is submitted to queue Post 302420045 by marcozd on Monday 10th of May 2010 11:57:38 AM

05-10-2010

Registered User

Find and delete files before a job is submitted to queue

Hello all.

I need some help modifying the following script:

Code:

#!/bin/bash
#PBS -l nodes=1:ppn=8,walltime=48:00:00,os=centos53computeA

## To submit type: qsub x.sh

# If not an interactive job (i.e. -I), then cd into the directory where
# I typed qsub.
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then
   if [ -n "$PBS_O_WORKDIR" ]; then
     cd $PBS_O_WORKDIR
   fi
fi

# the input file is typically named something like "gamesjob.inp"
# so the script will be run like "$SCINET_RUNGMS gamessjob 00 8 8"

# load the gamess module if not in .bashrc already
# actually, it MUST be in .bashrc
# module load gamess

# run the program

/scratch/mzd/rungms $NAME 00 8 8 >& $NAME.log

This script is used to submit jobs to a computer cluster to run quantum chemistry programs. I define the $NAME variable in the command line when I run the script.

The trouble is that the program I am running requires that any files with the same name as the file that is submitted must be deleted. That is, it will not overwrite any files with the same name.

That is, I need the script to check in "/scratch/mzd/gamess-scratch/" for any files with the same name as the file that I am submitting ($NAME). If it does find any files, regardless of extension, I need the script to delete them before the job is submitted to the queue. I also need it to check the directory where the input file is for any files that have the same name ($NAME) and delete them as well, also before submitting the job to the queue.

Looking forward to working with you again and thanks in advance.

marcozd

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LEARN ABOUT DEBIAN

nqs2pbs

nqs2pbs(1B)								PBS							       nqs2pbs(1B)

NAME

       nqs2pbs - convert NQS job scripts to PBS

SYNOPSIS

       nqs2pbs nqs_script [pbs_script]

DESCRIPTION

       This  utility  converts	a  existing NQS job script to work with PBS and NQS.  The existing script is copied and PBS directives, #PBS , are
       inserted prior to each NQS directive #QSUB or #@$ , in the original script.

       Certain NQS date specification and options are not supported by PBS.  A warning message will be displayed indicating the  problem  and  the
       line of the script on which it occurred.

       If  any	unrecognizable	NQS  directives  are encountered, an error message is displayed.  The new PBS script will be deleted if any errors
       occur.

OPERANDS

       nqs_script
	      Specifies the file name of the NQS script to convert.  This file is not changed.

       pbs_script
	      If specified, it is the name of the new PBS script.   If not specified, the new file name is nqs_script.new .

NOTES

       Converting NQS date specifications to the PBS form may result in a warning message and an incompleted converted date.  PBS does not support
       date  specifications  of  "today",  "tomorrow", or the name of the days of the week such as "Monday".  If any of these are encountered in a
       script, the PBS specification will contain only the time portion of the NQS specification, i.e. #PBS -a hhmm[.ss].   It is  suggested  that
       you specify the execution time on the qsub command line rather than in the script.

       Note that PBS will interpret a time specification without a date in the following way:

       -  If the time specified has not yet been reached, the job will become eligible to run at that time today.

       -  If the specified time has already passed when the job is submitted, the job will become eligible to run at that time tomorrow.

       PBS does not support time zone identifiers.  All times are taken as local time.

SEE ALSO

       qsub(1B)

Local																       nqs2pbs(1B)

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