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.shyou 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.