Added resource specs to PBS executor, which were somehow missing.

Also split PBS executor into pbs_classic (the one using `:ppn` to specify
processes per node) and the modern pbspro/openpbs (using `select=:ncpus=`).

src/psij-descriptors/pbs_descriptor.py

@@ -0,0 +1,11 @@
+from distutils.version import StrictVersion
+
+from psij.descriptor import Descriptor
+
+
+__PSI_J_EXECUTORS__ = [Descriptor(name='pbs', nice_name='PBS Pro', aliases=['pbspro'],
+                                  version=StrictVersion('0.0.2'),
+                                  cls='psij.executors.batch.pbs.PBSJobExecutor'),
+                       Descriptor(name='pbs_classic', nice_name='PBS Classic', aliases=['torque'],
+                                  version=StrictVersion('0.0.2'),
+                                  cls='psij.executors.batch.pbs_classic.PBSClassicJobExecutor')]

src/psij/executors/batch/pbs.py

@@ -0,0 +1,27 @@
+from pathlib import Path
+from typing import Optional
+
+from psij.executors.batch.pbs_base import PBSExecutorConfig, GenericPBSJobExecutor
+from psij.executors.batch.script_generator import TemplatedScriptGenerator
+
+
+class PBSJobExecutor(GenericPBSJobExecutor):
+    """A :class:`~psij.JobExecutor` for PBS Pro and friends.
+
+    This executor uses resource specifications specific to PBS Pro
+    """
+
+    def __init__(self, url: Optional[str] = None, config: Optional[PBSExecutorConfig] = None):
+        """
+        Parameters
+        ----------
+        url
+            Not used, but required by the spec for automatic initialization.
+        config
+            An optional configuration for this executor.
+        """
+        if not config:
+            config = PBSExecutorConfig()
+        generator = TemplatedScriptGenerator(config, Path(__file__).parent / 'pbspro'
+                                             / 'pbspro.mustache')
+        super().__init__(generator, url=url, config=config)

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

@@ -0,0 +1,71 @@
+#!/bin/bash
+
+
+{{#job.name}}
+#PBS -N="{{.}}"
+{{/job.name}}
+
+{{#job.spec.inherit_environment}}
+#PBS -V
+{{/job.spec.inherit_environment}}
+
+{{#job.spec.resources}}
+    {{#process_count}}
+#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}}
+    {{/process_count}}
+    {{#exclusive_node_use}}
+#PBS -n
+    {{/exclusive_node_use}}
+{{/job.spec.resources}}
+
+{{#formatted_job_duration}}
+#PBS -l walltime={{.}}
+{{/formatted_job_duration}}
+
+{{#job.spec.attributes}}
+    {{#project_name}}
+#PBS -P {{.}}
+    {{/project_name}}
+    {{#queue_name}}
+#PBS -q {{.}}
+    {{/queue_name}}
+    {{!PBS uses specially named queues for reservations, so we send the job to the respective
+    queue when a reservation ID is specified.}}
+    {{#reservation_id}}
+#PBS -q {{.}}
+    {{/reservation_id}}
+{{/job.spec.attributes}}
+
+{{#custom_attributes}}
+    {{#pbs}}
+#PBS -{{key}} "{{value}}"
+    {{/pbs}}
+{{/custom_attributes}}
+
+
+{{!since we redirect the output manually, below, tell pbs not to do its own thing, since it
+only results in empty files that are not cleaned up}}
+#PBS -e /dev/null
+#PBS -o /dev/null
+
+{{#job.spec.inherit_environment}}
+#PBS -V
+{{/job.spec.inherit_environment}}
+{{#env}}
+#PBS -v {{name}}={{value}}
+{{/env}}
+
+PSIJ_NODEFILE="$PBS_NODEFILE"
+export PSIJ_NODEFILE
+
+
+{{#job.spec.directory}}
+cd "{{.}}"
+{{/job.spec.directory}}
+
+exec &>> "{{psij.script_dir}}/$PBS_JOBID.out"
+
+{{#psij.launch_command}}{{.}} {{/psij.launch_command}}
+
+{{!we redirect to a file tied to the native ID so that we can reach the file with attach().}}
+echo "$?" > "{{psij.script_dir}}/$PBS_JOBID.ec"

src/psij/executors/batch/pbspro/pbspro.mustache → src/psij/executors/batch/pbs/pbspro.mustache

@@ -1,7 +1,5 @@
 #!/bin/bash
 
-# TODO: job.spec.resources
-# TODO: job.spec.attributes
 
 {{#job.name}}
 #PBS -N="{{.}}"
@@ -11,6 +9,18 @@
 #PBS -V
 {{/job.spec.inherit_environment}}
 
+{{#job.spec.resources}}
+    {{#process_count}}
+#PBS -l select={{job.spec.resources.computed_node_count}}:ncpus={{.}}
+    {{/process_count}}
+    {{#exclusive_node_use}}
+#PBS -l place=scatter:exclhost
+    {{/exclusive_node_use}}
+    {{^exclusive_node_use}}
+#PBS -l place=scatter:shared
+    {{/exclusive_node_use}}
+{{/job.spec.resources}}
+
 {{#formatted_job_duration}}
 #PBS -l walltime={{.}}
 {{/formatted_job_duration}}

src/psij/executors/batch/pbspro.py → src/psij/executors/batch/pbs_base.py

@@ -11,7 +11,7 @@
 
 _QSTAT_COMMAND = 'qstat'
 
-# This table maps PBS Pro state codes to the corresponding PSI/J
+# This table maps PBS state codes to the corresponding PSI/J
 # JobState.
 # See https://www.altair.com/pdfs/pbsworks/PBSReferenceGuide2021.1.pdf
 # page 361, section 8.1 "Job States"
@@ -39,14 +39,14 @@
 }
 
 
-class PBSProExecutorConfig(BatchSchedulerExecutorConfig):
-    """A configuration class for the PBS executor."""
+class PBSExecutorConfig(BatchSchedulerExecutorConfig):
+    """A generic configuration class for PBS-type executors."""
 
     pass
 
 
-class PBSProJobExecutor(BatchSchedulerExecutor):
-    """A :class:`~psij.JobExecutor` for PBS.
+class GenericPBSJobExecutor(BatchSchedulerExecutor):
+    """A generic :class:`~psij.JobExecutor` for PBS-type schedulers.
 
     PBS, originally developed by NASA, is one of the oldest resource managers still in use.
     A number of variations are available: `PBS Pro <https://www.altair.com/pbs-professional/>`_,
@@ -60,7 +60,8 @@ class PBSProJobExecutor(BatchSchedulerExecutor):
     Creates a batch script with #PBS directives when submitting a job.
     """
 
-    def __init__(self, url: Optional[str] = None, config: Optional[PBSProExecutorConfig] = None):
+    def __init__(self, generator: TemplatedScriptGenerator, url: Optional[str] = None,
+                 config: Optional[PBSExecutorConfig] = None) -> None:
         """
         Parameters
         ----------
@@ -69,11 +70,8 @@ def __init__(self, url: Optional[str] = None, config: Optional[PBSProExecutorCon
         config
             An optional configuration for this executor.
         """
-        if not config:
-            config = PBSProExecutorConfig()
         super().__init__(url=url, config=config)
-        self.generator = TemplatedScriptGenerator(config, Path(__file__).parent / 'pbspro'
-                                                  / 'pbspro.mustache')
+        self.generator = generator
 
     # Submit methods
 

src/psij/executors/batch/pbs_classic.py

@@ -0,0 +1,29 @@
+from pathlib import Path
+from typing import Optional
+
+from psij.executors.batch.pbs_base import PBSExecutorConfig, GenericPBSJobExecutor
+from psij.executors.batch.script_generator import TemplatedScriptGenerator
+
+
+class PBSClassicJobExecutor(GenericPBSJobExecutor):
+    """A :class:`~psij.JobExecutor` for classic PBS systems.
+
+    This executor uses resource specifications specific to Open PBS. Specifically,
+    this executor uses the `-l nodes=n:ppn=m` way of specifying nodes, which
+    differs from the scheme used by PBS Pro.
+    """
+
+    def __init__(self, url: Optional[str] = None, config: Optional[PBSExecutorConfig] = None):
+        """
+        Parameters
+        ----------
+        url
+            Not used, but required by the spec for automatic initialization.
+        config
+            An optional configuration for this executor.
+        """
+        if not config:
+            config = PBSExecutorConfig()
+        generator = TemplatedScriptGenerator(config, Path(__file__).parent / 'pbs'
+                                             / 'pbs_classic.mustache')
+        super().__init__(generator, url=url, config=config)

tests/test_executor.py

@@ -194,7 +194,7 @@ def _check_str_attrs(ex: BatchSchedulerExecutor, job: Job, names: List[str],
                 pytest.fail('Script generation failed for %s' % name)
 
 
-_PREFIX_TR = {'pbspro': 'pbs'}
+_PREFIX_TR = {'pbspro': 'pbs', 'pbs_classic': 'pbs'}
 
 
 def _get_attr_prefix(exec_name: str) -> str: