README.md

sublime

Easy job submission to Torque-based clusters

Sublime is a light helper script for submitting jobs to a cluster. sub automatically keeps track of what was run, important file locations, preserves virtualenv, and switches to your current working directory. For instance, to submit a job that calls the command hostname, just use:

$ sub hostname

Additionally, you can specify the name of the job:

$ sub -n testjob hostname

Walltime and queue is also available:

$ sub -q friendlyq -m 2 -w 12:34:56 hostname

If submitting a command that also takes arguments, a POSIX separator must be used to indicate the the split. For instance:

$ sub -n testjob -- grep -i -n export ~/.bash_profile

Installation

You can install sub easily! THe only dependency is Click, which is one of best designed Python packages around.

$ pip install sublime

Practical example

In the example below, we're going to submit a simple job in a new directory, and then show the files created and the contents of notes.

$ workon some-virtualenv
$ mkdir sub-testing
$ cd sub-testing/
$ ls
total 0
$ sub hostname
Success! This job is named sub_jxwLOz with job id 112730.
$ cat sub.notes
time=10:01:49 on 27 Mar 2015
id=sub_jxwLOz
job_id=112730
cmd=echo "cd `pwd`; source ~/.bash_profile;workon some-virtualenv; hostname" | qsub -o sub.oe -e sub.oe -N sub_jxwLOz -q route -l nodes=1:ppn=1
resub=/Users/mcdonadt/bin/sub hostname
expected_stdout=/Users/mcdonadt/sub-testing/sub.oe/sub_jxwLOz.o112730
expected_stderr=/Users/mcdonadt/sub-testing/sub.oe/sub_jxwLOz.e112730

$ ls sub.oe
total 2.0K
-rw-------+ 1 mcdonadt knightlab 0 Mar 27 10:01 sub_jxwLOz.e112730
-rw-------+ 1 mcdonadt knightlab 8 Mar 27 10:01 sub_jxwLOz.o112730

Running multiple commands in a job

It is possible to build up a list of commands to execute within a single job as well. By using --prime, you can build up a list of commands. These commands are stored in a file within the current working directory. The commands can then be submitted by issuing a --purge. The --purge will create a PBS script, store it under the sub.primed/ directory, and submit the script to the cluster. The script includes a wait command at the end to ensure that all executed commands complete.

Running commands in serial

Below is an example that will run 3 commands serially:

$ sub --prime -- hostname
$ sub --prime -- uname -a
$ sub --prime -- date
$ sub --purge -q route -w 12:34:56

Running commands in parallel

Below is the same example as the serial commands, except that we're adding an ampersand (&) to the end of each command. Note that the command needs to be encased in quotes. We're also indicating that our resource request needs 3 processors.

$ sub --prime -- "hostname &"
$ sub --prime -- "uname -a &"
$ sub --prime -- "date &"
$ sub --purge -p 3 -q route -w 12:34:56