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update torque support #156

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merged 7 commits into from
Apr 17, 2023
Merged

update torque support #156

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5f014bc
-terse is a non existent command for qsub
Apr 15, 2023
6eeff7f
implement get_job_id_from_output for torque
Apr 15, 2023
7f157cd
Update instructs for jinja adjustment for torque
Apr 15, 2023
2d2afb5
Format black
pyiron-runner Apr 15, 2023
75162c0
update torque test #1
Apr 15, 2023
2e0c469
Merge branch 'torque_fix' of https://github.com/pyiron/pysqa into tor…
Apr 15, 2023
1806243
small update for instructions on adjusting your queue
Apr 15, 2023
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12 changes: 11 additions & 1 deletion pysqa/wrapper/torque.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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 ...]]
       qsub --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

return ["qsub"]

@property
def delete_job_command(self):
Expand All @@ -28,3 +28,13 @@ def delete_job_command(self):
@property
def get_queue_status_command(self):
return ["qstat", "-x"]

@staticmethod
def get_job_id_from_output(queue_submit_output):
# strip last line from output, leading and trailing whitespaces, and separates the queue id from the stuff after "."
# Adjust if your system doesn't have output like below!
# e.g. qsub run_queue.sh -> "12347673.gadi-pbs", the below returns 12347673
# It must return an integer for it to not raise an exception later.
return int(
queue_submit_output.splitlines()[-1].rstrip().lstrip().split(sep=".")[0]
)
21 changes: 14 additions & 7 deletions tests/config/torque/torque.sh
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Original file line number Diff line number Diff line change
@@ -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"

{{command}}
# Remove all the trailing # instructions in the headers above before use!

# Put a command to activate your conda environment with pyiron in it, if required
# e.g. source /software_path/mambaforge/bin/activate pyiron

{{command}}
4 changes: 2 additions & 2 deletions tests/test_queueadapter.py
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Expand Up @@ -118,7 +118,7 @@ def test_interfaces(self):
self.sge._adapter._commands.get_queue_status_command, ["qstat", "-xml"]
)
self.assertEqual(
self.torque._adapter._commands.submit_job_command, ["qsub", "-terse"]
self.torque._adapter._commands.submit_job_command, ["qsub"]
)
self.assertEqual(self.torque._adapter._commands.delete_job_command, ["qdel"])
self.assertEqual(
Expand Down Expand Up @@ -170,7 +170,7 @@ def test__list_command_to_be_executed(self):
with self.subTest("torque"):
self.assertEqual(
self.torque._adapter._list_command_to_be_executed(None, "here"),
["qsub", "-terse", "here"],
["qsub", "here"],
)
with self.subTest("torque with dependency"):
self.assertRaises(
Expand Down