[phenixbb] Submitting SLURM jobs through PHENIX GUI

Billy Poon BKPoon at lbl.gov
Thu Nov 1 11:33:12 PDT 2018

Hi Tom,

Can you provide your submission script to your cluster? I think we only
call sbatch with no other parameters. We do not have access to a slurm
cluster, so we do not do any real testing.

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 Fri, Oct 26, 2018 at 10:54 AM Thomas Cleveland <
thomas.cleveland at gmail.com> wrote:

> Hi all,
> Has anyone gotten SLURM job submission to work through the PHENIX GUI?
> Under Preferences/Processes, I set Queueing system to SLURM with queue
> submit comand "sbatch." The job does indeed submit to the queue, and I can
> see it in the listing using the "squeue" command. However, there is quickly
> an error, "OSError : [Errno 2] No such file or directory:
> '/home/clevelandt/data/MX/181016_P1_merge/phenix/.phenix/tmp/10.libtbx_info.LOCK'".
> I've attached the full error log. Basically the program is looking for a
> lock file that isn't there. I'm not sure why it's not there. All compute
> nodes should have access to this directory, and there is no caching of any
> kind, so any files placed there should immediately be accessible.
> I can manually submit e.g. phenix.refine jobs to the queue using the
> command line and everything works fine. It would be really nice to have it
> through the GUI though.
> Thanks for any help,
> Tom
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