<div dir="ltr">Hi Heidi,<div><br></div><div>Sorry, we don't have a SLURM environment for any rigorous testing, so we just use "sbatch" for submitting jobs by default. We use some default flags for job names ("-J") and files for the output/error logs ("-o", "-e"), but other than that, the job submission step is not really customizable.</div><div><br></div><div>When you say that the job took a while to start, do you mean that the Phenix jobs showed up in the queue (by checking "squeue -u <user name>"), but was in the pending state ("PD") instead of the running state ("R")? Or does the job take a while to even show up in the queue?</div><div><br></div><div>Lastly, for the output to show up in the GUI, did the jobs finish successfully? If you restart the GUI and try to restore the job after it finished, do you see any output? For example, in phenix.refine, you should see graphs for the progress and some final statistics. Another thing to check is the hidden directory in the project directory that stores information for the GUI. Again, for phenix.refine, if that is your first job, you would see 3 files (refine_1.eff, refine_1.log, and refine_1.pkl) in your "<project directory>/.phenix/project_data" directory. The number just refers to the job number. If those files are not there, the GUI cannot update.</div><div><br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_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 class="gmail_quote">On Tue, Sep 5, 2017 at 1:12 PM, Heidi Schubert <span dir="ltr"><<a href="mailto:heidi@biochem.utah.edu" target="_blank">heidi@biochem.utah.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Has anyone successful submitted phenix jobs to a SLURM batch queue?
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I guess, in theory, I did successfully submit a job but it took a while to start and after completion the log files did not successfully link back to the interface losing the graphic feedback.
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I can’t tell how the job was submitted. Our submission command is sbatch, which is what I put in the Phenix Preference > Processes queue command. But locally we have a header on our sbatch submission which
spells out our wall time, account and MPI expectations/requests. Is there an environment file that Phenix reads to provide this information or does it submit generically? I wondered if this was responsible for the long delay of the start of our job (sure
– could have been a busy queue). <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Anyone know how to get the GUI to read the output files when it loses connection to the run?
<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></span></p><span class="HOEnZb"><font color="#888888">
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Heidi<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><u></u> <u></u></span></p>
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