Introducing dqsub

Wed, 05 Aug 2015 14:48:39 -0700
biology, cluster, debian, tech

I've been using qsub for a while now on the cluster here at the IGB at UofI. qsub is a command line program which is used to submit jobs to a scheduler to eventually be run on one (or more) nodes of a cluster.

Unfortunately, qsub's interface is horrible. It requires that you write a shell script for every single little thing you run, and doesn't do simple things like providing defaults or running multiple jobs at once with slightly different arguments. I've dealt with this for a while using some rudimentary shell scripting, but I finally had enough.

So instead, I wrote a wrapper around qsub called dqsub.

What used to require a complicated invocation like:

echo -e '#!/bin/bash\nmake foo'| \
 qsub -q default -S /bin/bash -d $(pwd) \
  -l mem=8G,nodes=1:ppn=4 -;

can now be run with

dqsub --mem 8G --ppn 4 make foo;

Want to run some command in every single directory which starts with SRX? That's easy:

ls -1 SRX*|dqsub --mem 8G --ppn 4 --array chdir make bar;

Want instead to behave like xargs but do the same thing?

ls -1 SRX*|dqsub --mem 8G --ppn 4 --array xargs make bar -C;

Now, this wrapper isn't complete yet, but it's already more than enough to do what I require, and has saved me quite a bit of time already.

You can steal dqsub for yourself

Feel free to request specific features, too.