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N1 Grid Engine 6 User's Guide

Extensions to Regular Shell Scripts

Some extensions to regular shell scripts influence the behavior of scripts that run under grid engine system control. The following sections describe these extensions.

How a Command Interpreter Is Selected

At submit time, you can specify the command interpreter to use to process the job script file. See, for example, Figure 3–5. However, if nothing is specified, the configuration variable shell_start_mode determines how the command interpreter is selected:

Output Redirection

Since batch jobs do not have a terminal connection, their standard output and their standard error output must be redirected into files. The grid engine system enables the user to define the location of the files to which the output is redirected. Defaults are used if no output files are specified.

The standard location for the files is in the current working directory where the jobs run. The default standard output file name is job-name.ojob-id, the default standard error output is redirected to job-name>.ejob-id. The job-name is built from the script file name, or the job-name can be defined by the user. See for example the -N option in the submit(1) man page. job-id is a unique identifier that is assigned to the job by the grid engine system.

In case of array job tasks , the task identifier is added to these filenames, separated by a dot. Hence the resulting standard redirection paths are job-name.ojob-id.task-id> and job-name.ejob-id.task-id. For more information, see Submitting Array Jobs.

In case the standard locations are not suitable, the user can specify output directions with QMON, as shown in Figure 3–6. Or the user can use the -e and -o options to the qsub command to specify output directions. Standard output and standard error output can be merged into one file. The redirections can be specified on a per execution host basis. That is, depending on the host on which the job is executed, the location of the output redirection files is different. To build custom but unique redirection file paths, dummy environment variables are available that can be used together with the qsub -e and -o options. A list of these variables follows.

When the job runs, these variables are expanded into the actual values, and the redirection path is built with these values.

See the qsub(1) man page for further details.

Active Comments

Lines with a leading # sign are treated as comments in shell scripts. However, the grid engine system recognizes special comment lines and uses these lines in a special way. The rest of such a script line is treated as part of the command line argument list of the qsub command. The qsub options that are supplied within these special comment lines are also interpreted by the QMON Submit Job dialog box. The corresponding parameters are preset when a script file is selected.

By default, the special comment lines are identified by the #$ prefix string. You can redefine the prefix string with the qsub -C command.

This use of special comments is called script embedding of submit arguments. The following is an example of a script file that makes use of script-embedded command-line options.

Example 3–2 Using Script-Embedded Command Line Options


#!/bin/csh

#Force csh if not Grid Engine default 
#shell

#$ -S /bin/csh

# This is a sample script file for compiling and
# running a sample FORTRAN program under N1 Grid Engine 6
# We want Grid Engine to send mail
# when the job begins
# and when it ends.

#$ -M EmailAddress
#$ -m b,e

# We want to name the file for the standard output
# and standard error.

#$ -o flow.out -j y

# Change to the directory where the files are located.

cd TEST

# Now we need to compile the program "flow.f" and
# name the executable "flow".

f77 flow.f -o flow

# Once it is compiled, we can run the program.

flow

Environment Variables

When a job runs, a number of variables are preset into the job's environment. The following is a list of these variables: