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
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 Web: https://phenix-online.org On Wed, Mar 11, 2020 at 8:55 AM Michael Weyand < michael.weyand@uni-bayreuth.de> wrote:
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Michael Weyand