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Merge pull request #439 from ExaWorks/pbs_fixes
Added resource specs to PBS executor, which were somehow missing.
2 parents 991a6a0 + 5706789 commit 391eb6b

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8 files changed

+159
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‎src/psij-descriptors/pbs_descriptor.py‎

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from distutils.version import StrictVersion
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from psij.descriptor import Descriptor
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__PSI_J_EXECUTORS__ = [Descriptor(name='pbs', nice_name='PBS Pro', aliases=['pbspro'],
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version=StrictVersion('0.0.2'),
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cls='psij.executors.batch.pbs.PBSJobExecutor'),
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Descriptor(name='pbs_classic', nice_name='PBS Classic', aliases=['torque'],
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version=StrictVersion('0.0.2'),
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cls='psij.executors.batch.pbs_classic.PBSClassicJobExecutor')]

‎src/psij-descriptors/pbspro_descriptor.py‎

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‎src/psij/executors/batch/pbs.py‎

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from pathlib import Path
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from typing import Optional
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from psij.executors.batch.pbs_base import PBSExecutorConfig, GenericPBSJobExecutor
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from psij.executors.batch.script_generator import TemplatedScriptGenerator
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class PBSJobExecutor(GenericPBSJobExecutor):
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"""A :class:`~psij.JobExecutor` for PBS Pro and friends.
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This executor uses resource specifications specific to PBS Pro
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"""
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def __init__(self, url: Optional[str] = None, config: Optional[PBSExecutorConfig] = None):
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"""
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Parameters
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----------
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url
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Not used, but required by the spec for automatic initialization.
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config
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An optional configuration for this executor.
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"""
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if not config:
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config = PBSExecutorConfig()
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generator = TemplatedScriptGenerator(config, Path(__file__).parent / 'pbspro'
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/ 'pbspro.mustache')
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super().__init__(generator, url=url, config=config)

‎src/psij/executors/batch/pbs/pbs_classic.mustache‎

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#!/bin/bash
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{{#job.name}}
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#PBS -N="{{.}}"
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{{/job.name}}
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{{#job.spec.inherit_environment}}
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#PBS -V
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{{/job.spec.inherit_environment}}
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{{#job.spec.resources}}
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{{#process_count}}
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#PBS -l nodes={{job.spec.resources.computed_node_count}}:ppn={{.}}{{#job.spec.resources.gpu_cores_per_process}}:gpus={{.}}{{/job.spec.resources.gpu_cores_per_process}}
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{{/process_count}}
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{{#exclusive_node_use}}
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#PBS -n
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{{/exclusive_node_use}}
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{{/job.spec.resources}}
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{{#formatted_job_duration}}
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#PBS -l walltime={{.}}
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{{/formatted_job_duration}}
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{{#job.spec.attributes}}
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{{#project_name}}
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#PBS -P {{.}}
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{{/project_name}}
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{{#queue_name}}
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#PBS -q {{.}}
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{{/queue_name}}
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{{!PBS uses specially named queues for reservations, so we send the job to the respective
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queue when a reservation ID is specified.}}
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{{#reservation_id}}
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#PBS -q {{.}}
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{{/reservation_id}}
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{{/job.spec.attributes}}
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{{#custom_attributes}}
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{{#pbs}}
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#PBS -{{key}} "{{value}}"
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{{/pbs}}
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{{/custom_attributes}}
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{{!since we redirect the output manually, below, tell pbs not to do its own thing, since it
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only results in empty files that are not cleaned up}}
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#PBS -e /dev/null
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#PBS -o /dev/null
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{{#job.spec.inherit_environment}}
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#PBS -V
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{{/job.spec.inherit_environment}}
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{{#env}}
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#PBS -v {{name}}={{value}}
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{{/env}}
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PSIJ_NODEFILE="$PBS_NODEFILE"
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export PSIJ_NODEFILE
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{{#job.spec.directory}}
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cd "{{.}}"
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{{/job.spec.directory}}
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exec &>> "{{psij.script_dir}}/$PBS_JOBID.out"
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{{#psij.launch_command}}{{.}} {{/psij.launch_command}}
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{{!we redirect to a file tied to the native ID so that we can reach the file with attach().}}
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echo "$?" > "{{psij.script_dir}}/$PBS_JOBID.ec"

src/psij/executors/batch/pbspro/pbspro.mustache renamed to src/psij/executors/batch/pbs/pbspro.mustache

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#!/bin/bash
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# TODO: job.spec.resources
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# TODO: job.spec.attributes
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{{#job.name}}
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#PBS -N="{{.}}"
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#PBS -V
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{{/job.spec.inherit_environment}}
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{{#job.spec.resources}}
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{{#process_count}}
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#PBS -l select={{job.spec.resources.computed_node_count}}:ncpus={{.}}
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{{/process_count}}
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{{#exclusive_node_use}}
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#PBS -l place=scatter:exclhost
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{{/exclusive_node_use}}
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{{^exclusive_node_use}}
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#PBS -l place=scatter:shared
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{{/exclusive_node_use}}
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{{/job.spec.resources}}
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{{#formatted_job_duration}}
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#PBS -l walltime={{.}}
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{{/formatted_job_duration}}

src/psij/executors/batch/pbspro.py renamed to src/psij/executors/batch/pbs_base.py

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_QSTAT_COMMAND = 'qstat'
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# This table maps PBS Pro state codes to the corresponding PSI/J
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# This table maps PBS state codes to the corresponding PSI/J
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# JobState.
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# See https://www.altair.com/pdfs/pbsworks/PBSReferenceGuide2021.1.pdf
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# page 361, section 8.1 "Job States"
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}
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class PBSProExecutorConfig(BatchSchedulerExecutorConfig):
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"""A configuration class for the PBS executor."""
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class PBSExecutorConfig(BatchSchedulerExecutorConfig):
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"""A generic configuration class for PBS-type executors."""
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pass
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class PBSProJobExecutor(BatchSchedulerExecutor):
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"""A :class:`~psij.JobExecutor` for PBS.
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class GenericPBSJobExecutor(BatchSchedulerExecutor):
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"""A generic :class:`~psij.JobExecutor` for PBS-type schedulers.
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PBS, originally developed by NASA, is one of the oldest resource managers still in use.
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A number of variations are available: `PBS Pro <https://www.altair.com/pbs-professional/>`_,
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Creates a batch script with #PBS directives when submitting a job.
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"""
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def __init__(self, url: Optional[str] = None, config: Optional[PBSProExecutorConfig] = None):
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def __init__(self, generator: TemplatedScriptGenerator, url: Optional[str] = None,
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config: Optional[PBSExecutorConfig] = None) -> None:
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"""
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Parameters
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----------
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config
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An optional configuration for this executor.
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"""
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if not config:
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config = PBSProExecutorConfig()
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super().__init__(url=url, config=config)
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self.generator = TemplatedScriptGenerator(config, Path(__file__).parent / 'pbspro'
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/ 'pbspro.mustache')
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self.generator = generator
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# Submit methods
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‎src/psij/executors/batch/pbs_classic.py‎

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from pathlib import Path
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from typing import Optional
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from psij.executors.batch.pbs_base import PBSExecutorConfig, GenericPBSJobExecutor
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from psij.executors.batch.script_generator import TemplatedScriptGenerator
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class PBSClassicJobExecutor(GenericPBSJobExecutor):
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"""A :class:`~psij.JobExecutor` for classic PBS systems.
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This executor uses resource specifications specific to Open PBS. Specifically,
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this executor uses the `-l nodes=n:ppn=m` way of specifying nodes, which
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differs from the scheme used by PBS Pro.
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"""
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def __init__(self, url: Optional[str] = None, config: Optional[PBSExecutorConfig] = None):
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"""
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Parameters
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----------
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url
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Not used, but required by the spec for automatic initialization.
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config
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An optional configuration for this executor.
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"""
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if not config:
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config = PBSExecutorConfig()
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generator = TemplatedScriptGenerator(config, Path(__file__).parent / 'pbs'
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/ 'pbs_classic.mustache')
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super().__init__(generator, url=url, config=config)

‎tests/test_executor.py‎

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pytest.fail('Script generation failed for %s' % name)
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_PREFIX_TR = {'pbspro': 'pbs'}
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_PREFIX_TR = {'pbspro': 'pbs', 'pbs_classic': 'pbs'}
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def _get_attr_prefix(exec_name: str) -> str:

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