From: Marc Saric <marc.saric@gm...> - 2004-08-20 09:38:36
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I have a question regarding batch-queue-execution of Pymol-jobs:
I am currently running a Condor batch-queue
(http://www.cs.wisc.edu/condor/) on a bunch of desktop machines, most of
which (unfortunately) run Windows XP and Windows 2k (a few Linux-boxes
as well, but...).
Pymol basically works with Condor, because it can be called via a
batch-file from commandline, so no problem.
I just want to know if there is someone out there who has some more
experience with running Pymol-jobs, like movie-rendering or big
calculations on something (APBS comes to mind) on a batch-queue-system
and is willing to share his experience (or probably a script :-) ).
As I can see it currently, it might be nice to have some sort of
pymol-plugin which gets all the heavy duty stuff and submits it
automatically to the queue. I am willing to write something like that on
my own and contribute it, but maybe someone allready has done it (don't
want to reinvent the wheel)).
Thanks in advance.
Marc Saric http://www.marcsaric.de
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We have a cluster that I would like to use for making images and have
PBS running on there. Can you please share details about how you have
set it up?
Do you have pymol on all nodes? Is it parallelized or each frame (of the
movie) is rendered on individual nodes?
Thanks for any guidance.
> 1. Re: Pymol and batch-queue jobs (Marc Saric)
> Message: 1
> Date: Tue, 24 Aug 2004 09:02:14 +0200
> From: Marc Saric <marc.saric@...>
> To: Jason Thomas Maynes <jason@...>,
> Subject: Re: [PyMOL] Pymol and batch-queue jobs
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> Hash: SHA1
> Hi Jason,
> I have reposted your reply to the list, hope you don't mind.
> Jason Thomas Maynes wrote:
> | Hello:
> | I run movie rendering through PBS but it's nothing fancy.
> | Essentially I have a perl script that takes a pymol movie script as
> | an argument and then sends customized (ie. render frames 40-50 etc)
> | pymol scripts as jobs to the queue. Since pymol can't take a
> | line argument for what frames to render, I couldn't see a away
> | having customized scripts for each job.
> So an applet, which modifies a render-script on the fly (probably as a
> plugin ("remote-rendering" or something) from within Python might be
> I guess, this would be the way people do it -either interactively
> defining a script (probably with manual splitting/parameter-setting
> the job, or automatically if possible), which gets sent to a
> batch-queueing-system from a Tk-GUI or offline (save script for later