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 systems. 

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


On Wed, Mar 11, 2020 at 8:55 AM Michael Weyand <michael.weyand@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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