Practical Guidelines for Using PBS

Sample Scripts

Practical Guidelines for Using PBS

Use the following guidelines to include comments and PBS options within a shell script: 

• Comments must be preceded by a pound sign (#).
• Embedded PBS options must be preceded by a pound sign, followed by the word PBS (#PBS).
• All embedded options must precede the first executable statement in the script.

The hierarchy for executing PBS command options is as follows: 

• Command-line options have the highest priority, followed by embedded options, then system defaults.
• In cases where the system maximums are more restrictive than the specified options, the specified options will be ignored.
• Note that a batch job always starts in your home directory. Therefore, if the required files for a batch request are in a directory other than your home directory, the batch request must include a command to change directory (cd) to the one containing the required files.

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Sample Scripts

Below is an example of a shell script used to submit a PBS batch job with input from a file. Note that all comments are preceded by a pound sign (#) and that all PBS commands and options are preceded by the #PBS character string and come before the first executable statement.

% cat sample

# Use the C shell
#PBS -S /bin/csh
# request 60MW of memory
#PBS -l mem=60Mw
# request 4 hours of CPU time
#PBS -l cput=4:00:00

% cat bigrun

# Script to run using the local /big file system for faster performance
# Assume a program that reads input from a file called "run_input" and
# uses data from a large master gridfile called "base_grid".

# Cshell | 60MW memory | 4hrs job CPU | 3:55hrs process CPU
#PBS -S /bin/csh
#PBS -l mem=60Mw
#PBS -l cput=4:00:00
#PBS -l pcput=3:55:00

#  combine standard output and standard error
#PBS -j oe

# copy input and required files

rcp tifrc7.tifr.res.in:last_run/restart .
rcp tifrc7.tifr.res.in:last_run/grid_in .
rcp tifrc7.tifr.res.in:last_run/input .