<div dir="ltr">Hi Tom,<div><br></div><div>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.</div><div><br clear="all"><div><div dir="ltr" class="m_7911344598499593037gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Oct 26, 2018 at 10:54 AM Thomas Cleveland <<a href="mailto:thomas.cleveland@gmail.com" target="_blank">thomas.cleveland@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr"><div>Hi all,<br><br></div>Has anyone gotten SLURM job submission to work through the PHENIX GUI? <br><br>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'".<br><br></div><div>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.<br><br></div><div>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.<br></div><div><br></div><div>Thanks for any help,<br></div><div>Tom<br></div></div>
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