[phenixbb] queueing system support in GUI

Nathaniel Echols nechols at lbl.gov
Sat Jul 3 07:53:24 PDT 2010

The most recent nightly build (dev-457) adds the ability to run jobs on Sun
Grid Engine.  To activate this feature, go to Preferences->Processes and
click "Activate queueing system support"; this will add a queue job option
to the menu that appears when you click the Run button.  I'm hoping that the
default command-line arguments I picked are suitable for most environments.
 Obviously the filesystem that you run jobs on must be visible both to the
host machine and to the machines in the queueing system.  The same PHENIX
installation must also be accessible from both.  You need to be able to
submit jobs from the machine that you're running the GUI on.  (FYI, you
could be running everything on a single multi-core computer - there's no
reason why this has to be done on a cluster, but that's what I'm testing it

You can view the current queue status from the main GUI via "Show queue
status" in the utilities menu.  (You can't actually delete jobs from there
yet, despite the misleading button that I forgot to remove.)

Some caveats:
- This should, in theory, run on heterogeneous clusters, but I haven't tried
this because all of our systems are 64-bit Linux.
- I haven't tried it on Mac either.
- There will probably be some weirdness associated with closing the GUI and
resuming jobs while still running, especially if you try to abort them.
- The built-in parallelization of AutoBuild and the ligand identification
program will not play nice with the queueing system when using this
mechanism (this is really a defect in queueing systems, not AutoBuild).  I
think it will be relatively easy to fix this, but for now, you're better off
using a single multiprocessor machine for parallel AutoBuild runs in the
- If the queueing system or remote host crashes, the GUI will still think
the job is running.

Those of you who are interested in using this, please let me know how it
works and what features are missing.  As always, I fully expect that this
will break on some setups.

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