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update torque support #156
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5f014bc
-terse is a non existent command for qsub
6eeff7f
implement get_job_id_from_output for torque
7f157cd
Update instructs for jinja adjustment for torque
2d2afb5
Format black
pyiron-runner 75162c0
update torque test #1
2e0c469
Merge branch 'torque_fix' of https://github.com/pyiron/pysqa into tor…
1806243
small update for instructions on adjusting your queue
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Original file line number | Diff line number | Diff line change |
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@@ -1,14 +1,21 @@ | ||
#!/bin/bash | ||
#PBS -q queue@host | ||
#PBS -l ppn={{cores}} | ||
#PBS -q normal # Insert the queue that you want to use here | ||
#PBS -l ncpus={{cores}} | ||
#PBS -N {{job_name}} | ||
{%- if memory_max %} | ||
#PBS -l mem={{memory_max}} | ||
#PBS -l mem={{ [16, memory_max]| int |max }}GB # Set minimum 16 GB RAM, or user-set limit | ||
{%- endif %} | ||
{%- if run_time_max %} | ||
#PBS -l walltime={{run_time_max}} | ||
#PBS -l walltime={{ [1*3600, run_time_max*3600]|max }} # Replace 3600 if you want to use seconds as input, currently HOURS | ||
{%- endif %} | ||
#PBS -V | ||
#PBS -d {{working_directory}} | ||
#PBS -l wd | ||
#PBS -l software=vasp # If your system requires this kind of command (check your HPC webpage/ask your admin) | ||
#PBS -l storage=scratch/a01+gdata/a01 # If your system requires you to set visibility of storage partitions | ||
#PBS -P a01 # If you have multiple projects and want to charge to project named "a01" | ||
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{{command}} | ||
# Remove all the trailing # instructions in the headers above before use! | ||
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# Put a command to activate your conda environment with pyiron in it, if required | ||
# e.g. source /software_path/mambaforge/bin/activate pyiron | ||
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{{command}} |
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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:
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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