update torque support #156
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merge ok? @jan-janssen |
| @@ -19,7 +19,7 @@ | |||
| class TorqueCommands(SchedulerCommands): | |||
| @property | |||
| def submit_job_command(self): | |||
| return ["qsub", "-terse"] | |||
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I am a bit surprised about this one, as it appears in the documentation of the sun grid engine: https://gridscheduler.sourceforge.net/htmlman/manuals.html - can we clarify which systems or system version support this command?
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Here is some comparison for SGE vs. PBS https://softpanorama.org/HPC/PBS_and_derivatives/Reference/pbs_command_vs_sge_commands.shtml
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PBSPro - I can see that PBSPro is the closed-source version of the OpenPBS project, Torque is the continued fork of OpenPBS after it was abandoned.
Do we want to create a new set of templates specifically for PBSPro?
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http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm
Submit PBS job.
Synopsis
qsub [-a date_time] [-A account_string] [-b secs] [-c checkpoint_options]
[-C directive_prefix] [-d path] [-D path] [-e path] [-f] [-F] [-h]
[-I ] [-j join ] [-k keep ] [-l resource_list ]
[-m mail_options] [-M user_list] [-n] [-N name] [-o path]
[-p priority] [-P user[:group]] [-q destination] [-r c] [-S path_to_shell(s)]
[-t array_request] [-u user_list]
[-v variable_list] [-V] [-W additional_attributes] [-x] [-X] [-z] [script]
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at any rate there is no -terse option in torque's documentation, and neither in the PBSPro version:
(base) [hlm562@gadi-login-05 ~]$ qsub -H
qsub: invalid option -- 'H'
usage: qsub [-a date_time] [-A account_string] [-c interval]
[-C directive_prefix] [-e path] [-f ] [-h ] [-I [-X]] [-j oe|eo] [-J X-Y[:Z]]
[-k keep] [-l resource_list] [-m mail_options] [-M user_list]
[-N jobname] [-o path] [-p priority] [-P project] [-q queue] [-r y|n]
[-R o|e|oe] [-S path] [-u user_list] [-W otherattributes=value...]
[-S path] [-u user_list] [-W otherattributes=value...]
[-v variable_list] [-V ] [-z] [script | -- command [arg1 ...]]
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Ok, can we have on version for torque and then derive from there a second version for the sun grid engine?
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I see we already have a separate implementation for the sun grid engine https://github.com/pyiron/pysqa/blob/main/pysqa/wrapper/sge.py
Improves documentation, in the jinja template for torque makes it more "out of the box" for torque users.
Verified installation working on Gadi @ NCI in Australia