[phenixbb] SLURM Batch submission

Heidi Schubert heidi at biochem.utah.edu
Tue Sep 5 13:12:16 PDT 2017


Has anyone successful submitted phenix jobs to a SLURM batch queue?

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.

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).

Anyone know how to get the GUI to read the output files when it loses connection to the run?


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