qsub-wrapper

A simple wrapper to execute qsub commands from CLI avoiding the creation of complicated PBS scripts. An intermediate PBS configuration in a shell string is generated automatically by the wrapper and passed directly to qsub command.

It can be executed as follows:

$ ./qsub-wrapper.sh -N SLEEP_TEST -- sleep 4
# NCORES:     1
# QSUB ARGS:  -d /public/ -N SLEEP_TEST
# RUNNING:    sleep 10
733631.server01

And produces as result:

$ cat SLEEP_TEST.o733631
# HOST: worker_hostname
# DATE: Sat Sep 24 19:03:01 CEST 2016
# NCORES: 1
# QSUB ARGS: -d /public/ -N SLEEP_TEST
# RUNNING: sleep 10
# ELAPSED_TIME: 10 seconds

When executed without arguments it shows a simple help screen:

$ ./qsub-wrapper.sh
Error: a double dash (--) followed by a command is mandatory.
    qsub-wrapper.sh [--ncores=N] [qsub_args ...] -- command [args ...]

The syntax of this wrapper is:

• After ./qsub_wrapper.sh you include as many qsub arguments as you want (output name, node properties, resources, ...)
• Next you should write -- (double dash) indicating the end of qsub arguments and the start of the command you want to execute.
• Finally you write your command and all the arguments required by this command.

Currently, all jobs are enqueued with nice=19, the working directory will be retrieved by pwd command in the moment you execute the wrapper. There is an optional argument --ncores=N which allow to indicate how many cores your program uses. Given ncores option automatically sets the property -l nodes=1:ppn=N in the list of qsub arguments. If ncores option is not given, this wrapper won't set any job property/resource.