[phenixbb] suggested usage of qsub?

Nathaniel Echols nechols at lbl.gov
Wed Mar 27 14:30:05 PDT 2013

On Wed, Mar 27, 2013 at 12:16 PM, Scott Classen <sclassen at lbl.gov> wrote:
> We have a HPC cluster configured with TORQUE/MAUI. I see in the Phenix GUI that there is some sort of ability to queue jobs to run via qsub. I can't find any documentation on how to set this up.

My fault, sorry.  Will add this to the ever-expanding to-do list.  It
should support PBS-derived queuing systems such as Torque - you will
simply need to enable queuing and specify PBS as the system type in
the preferences (under "Process control").  Caveat: this is not
especially well tested at the moment (we only have SGE on our
systems), some users have had to provide a custom qsub command to get
it to work properly.

> If I'm working at my office computer and I want to submit to a remote server cluster for refinement, is this possible? Or is it assumed that qsub is available on the local machine?

"Probably not" and "yes", respectively.  It may be possible to trick
the GUI into submitting jobs via SSH, but we have not tried this and I
suspect there will be many practical issues that prevent it from
working.  Do you at least have the same filesystem(s) on your office
machine and the cluster?   That is an absolute requirement right now.


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