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[don.git] / posts / introducing_dqsub.mdwn

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+[[!meta title="Introducing dqsub"]]
+
+I've been using qsub for a while now on the cluster here at the
+[IGB at UofI](http://www.igb.illinois.edu). 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 it for yourself: [http://git.donarmstrong.com/uiuc_igb_scripts.git/f/dqsub]
+
+Feel free to request specific features, too.
+
+
+[[!tag debian tech biology cluster]]