[phenixbb] Slurm/qsub queue usage

Billy Poon BKPoon at lbl.gov
Wed Mar 18 10:40:58 PDT 2020

Hi Michael,

Do you get any output about any jobs being submitted? Is there a way to
query what the GUI is trying to submit? We don't have a SLURM queueing
system for testing, so I'm not sure how functional our implementation.

The GUI should be submitting jobs using "sbatch", but the script might be
dynamically generated and passed through the command line. Do you need
#SBATCH directives for choosing a specific queue or setting a wall time?
That is not supported with the way jobs are currently submitted to queueing

However, submission to more queueing systems seems like something we should
overhaul so that users can submit custom parameters specific to the
queueing system. That would be a longer term project, though.

Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Wed, Mar 11, 2020 at 8:55 AM Michael Weyand <
michael.weyand at uni-bayreuth.de> wrote:

> Dear Phenixer,
> I would like to use Phenix GUI queue execution option. We have access to
> cluster nodes via Slurm/qsub.
> https://slurm.schedmd.com/documentation.html
> The reason is that we have severe problems to run Coot/PyMol form the
> Phenix GUI if Phenix is executed on our number cruncher.
> This direct Coot usage GUI option is HIGHLY preferred by my young
> colleagues... Therefore my Slurm queue installation.
> But I have no clue how to add the needed first qsub script line (
> "#!/bin/bash" or "#!/bin/tcsh" )  to the final Phenix command script
> from the Phenix GUI, which is to my knowledge a must for the qsub/sbatch
> command.
> Same holds true for the CCP4i GUI  ... :-(
> This line is added to avoid cross positing to CCP4BB ... ;-)
> Is there any simple hint / command which I have missed ?
> Kind regards,
> Michael
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