Coverage for python/lsst/ctrl/bps/transform.py: 8%
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« prev ^ index » next coverage.py v6.5.0, created at 2023-01-12 02:13 -0800
1# This file is part of ctrl_bps.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
22"""Driver for the transformation of a QuantumGraph into a generic workflow.
23"""
25import copy
26import dataclasses
27import logging
28import math
29import os
30import re
32from lsst.utils.logging import VERBOSE
33from lsst.utils.timer import time_this, timeMethod
35from . import (
36 DEFAULT_MEM_RETRIES,
37 BpsConfig,
38 GenericWorkflow,
39 GenericWorkflowExec,
40 GenericWorkflowFile,
41 GenericWorkflowJob,
42)
43from .bps_utils import (
44 WhenToSaveQuantumGraphs,
45 _create_execution_butler,
46 create_job_quantum_graph_filename,
47 save_qg_subgraph,
48)
50# All available job attributes.
51_ATTRS_ALL = frozenset([field.name for field in dataclasses.fields(GenericWorkflowJob)])
53# Job attributes that need to be set to their maximal value in the cluster.
54_ATTRS_MAX = frozenset(
55 {
56 "memory_multiplier",
57 "number_of_retries",
58 "request_cpus",
59 "request_memory",
60 "request_memory_max",
61 }
62)
64# Job attributes that need to be set to sum of their values in the cluster.
65_ATTRS_SUM = frozenset(
66 {
67 "request_disk",
68 "request_walltime",
69 }
70)
72# Job attributes do not fall into a specific category
73_ATTRS_MISC = frozenset(
74 {
75 "cmdvals",
76 "profile",
77 "attrs",
78 }
79)
81# Attributes that need to be the same for each quanta in the cluster.
82_ATTRS_UNIVERSAL = frozenset(_ATTRS_ALL - (_ATTRS_MAX | _ATTRS_MISC | _ATTRS_SUM))
84_LOG = logging.getLogger(__name__)
87@timeMethod(logger=_LOG, logLevel=VERBOSE)
88def transform(config, cqgraph, prefix):
89 """Transform a ClusteredQuantumGraph to a GenericWorkflow.
91 Parameters
92 ----------
93 config : `lsst.ctrl.bps.BpsConfig`
94 BPS configuration.
95 cqgraph : `lsst.ctrl.bps.ClusteredQuantumGraph`
96 A clustered quantum graph to transform into a generic workflow.
97 prefix : `str`
98 Root path for any output files.
100 Returns
101 -------
102 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
103 The generic workflow transformed from the clustered quantum graph.
104 generic_workflow_config : `lsst.ctrl.bps.BpsConfig`
105 Configuration to accompany GenericWorkflow.
106 """
107 _, when_create = config.search(".executionButler.whenCreate")
108 if when_create.upper() == "TRANSFORM":
109 _, execution_butler_dir = config.search(".bps_defined.executionButlerDir")
110 _LOG.info("Creating execution butler in '%s'", execution_butler_dir)
111 with time_this(log=_LOG, level=logging.INFO, prefix=None, msg="Creating execution butler completed"):
112 _create_execution_butler(config, config["runQgraphFile"], execution_butler_dir, prefix)
114 if cqgraph.name is not None:
115 name = cqgraph.name
116 else:
117 _, name = config.search("uniqProcName", opt={"required": True})
119 generic_workflow = create_generic_workflow(config, cqgraph, name, prefix)
120 generic_workflow_config = create_generic_workflow_config(config, prefix)
122 return generic_workflow, generic_workflow_config
125def add_workflow_init_nodes(config, qgraph, generic_workflow):
126 """Add nodes to workflow graph that perform initialization steps.
128 Assumes that all of the initialization should be executed prior to any
129 of the current workflow.
131 Parameters
132 ----------
133 config : `lsst.ctrl.bps.BpsConfig`
134 BPS configuration.
135 qgraph : `lsst.pipe.base.graph.QuantumGraph`
136 The quantum graph the generic workflow represents.
137 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
138 Generic workflow to which the initialization steps should be added.
139 """
140 # Create a workflow graph that will have task and file nodes necessary for
141 # initializing the pipeline execution
142 init_workflow = create_init_workflow(config, qgraph, generic_workflow.get_file("runQgraphFile"))
143 _LOG.debug("init_workflow nodes = %s", init_workflow.nodes())
144 generic_workflow.add_workflow_source(init_workflow)
147def create_init_workflow(config, qgraph, qgraph_gwfile):
148 """Create workflow for running initialization job(s).
150 Parameters
151 ----------
152 config : `lsst.ctrl.bps.BpsConfig`
153 BPS configuration.
154 qgraph : `lsst.pipe.base.graph.QuantumGraph`
155 The quantum graph the generic workflow represents.
156 qgraph_gwfile : `lsst.ctrl.bps.GenericWorkflowFile`
157 File object for the full run QuantumGraph file.
159 Returns
160 -------
161 init_workflow : `lsst.ctrl.bps.GenericWorkflow`
162 GenericWorkflow consisting of job(s) to initialize workflow.
163 """
164 _LOG.debug("creating init subgraph")
165 _LOG.debug("creating init task input(s)")
166 search_opt = {
167 "curvals": {"curr_pipetask": "pipetaskInit"},
168 "replaceVars": False,
169 "expandEnvVars": False,
170 "replaceEnvVars": True,
171 "required": False,
172 }
173 found, value = config.search("computeSite", opt=search_opt)
174 if found:
175 search_opt["curvals"]["curr_site"] = value
176 found, value = config.search("computeCloud", opt=search_opt)
177 if found:
178 search_opt["curvals"]["curr_cloud"] = value
180 init_workflow = GenericWorkflow("init")
181 init_workflow.add_file(qgraph_gwfile)
183 # create job for executing --init-only
184 gwjob = GenericWorkflowJob("pipetaskInit")
186 job_values = _get_job_values(config, search_opt, "runQuantumCommand")
187 job_values["name"] = "pipetaskInit"
188 job_values["label"] = "pipetaskInit"
190 # Adjust job attributes values if necessary.
191 _handle_job_values(job_values, gwjob)
193 # Pick a node id for each task (not quantum!) to avoid reading the entire
194 # quantum graph during the initialization stage.
195 node_ids = []
196 for task in qgraph.iterTaskGraph():
197 task_def = qgraph.findTaskDefByLabel(task.label)
198 node = next(iter(qgraph.getNodesForTask(task_def)))
199 node_ids.append(node.nodeId)
200 gwjob.cmdvals["qgraphId"] = qgraph.graphID
201 gwjob.cmdvals["qgraphNodeId"] = ",".join(sorted([f"{node_id}" for node_id in node_ids]))
203 init_workflow.add_job(gwjob)
205 # Lookup butler values
206 _, when_create = config.search(".executionButler.whenCreate", opt=search_opt)
207 _, butler_config = config.search("butlerConfig", opt=search_opt)
208 _, execution_butler_dir = config.search(".bps_defined.executionButlerDir", opt=search_opt)
209 prefix = config["submitPath"]
210 butler_gwfile = _get_butler_gwfile(prefix, when_create, butler_config, execution_butler_dir)
212 init_workflow.add_job_inputs(gwjob.name, [qgraph_gwfile, butler_gwfile])
213 _enhance_command(config, init_workflow, gwjob, {})
215 return init_workflow
218def _enhance_command(config, generic_workflow, gwjob, cached_job_values):
219 """Enhance command line with env and file placeholders
220 and gather command line values.
222 Parameters
223 ----------
224 config : `lsst.ctrl.bps.BpsConfig`
225 BPS configuration.
226 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
227 Generic workflow that contains the job.
228 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
229 Generic workflow job to which the updated executable, arguments,
230 and values should be saved.
231 cached_job_values : `dict` [`str`, dict[`str`, `Any`]]
232 Cached values common across jobs with same label. Updated if values
233 aren't already saved for given gwjob's label.
234 """
235 _LOG.debug("gwjob given to _enhance_command: %s", gwjob)
237 search_opt = {
238 "curvals": {"curr_pipetask": gwjob.label},
239 "replaceVars": False,
240 "expandEnvVars": False,
241 "replaceEnvVars": True,
242 "required": False,
243 }
245 if gwjob.label not in cached_job_values:
246 cached_job_values[gwjob.label] = {}
247 # Allowing whenSaveJobQgraph and useLazyCommands per pipetask label.
248 key = "whenSaveJobQgraph"
249 _, when_save = config.search(key, opt=search_opt)
250 cached_job_values[gwjob.label][key] = WhenToSaveQuantumGraphs[when_save.upper()]
252 key = "useLazyCommands"
253 search_opt["default"] = True
254 _, cached_job_values[gwjob.label][key] = config.search(key, opt=search_opt)
255 del search_opt["default"]
257 # Change qgraph variable to match whether using run or per-job qgraph
258 # Note: these are lookup keys, not actual physical filenames.
259 if cached_job_values[gwjob.label]["whenSaveJobQgraph"] == WhenToSaveQuantumGraphs.NEVER:
260 gwjob.arguments = gwjob.arguments.replace("{qgraphFile}", "{runQgraphFile}")
261 elif gwjob.name == "pipetaskInit":
262 gwjob.arguments = gwjob.arguments.replace("{qgraphFile}", "{runQgraphFile}")
263 else: # Needed unique file keys for per-job QuantumGraphs
264 gwjob.arguments = gwjob.arguments.replace("{qgraphFile}", f"{{qgraphFile_{gwjob.name}}}")
266 # Replace files with special placeholders
267 for gwfile in generic_workflow.get_job_inputs(gwjob.name):
268 gwjob.arguments = gwjob.arguments.replace(f"{{{gwfile.name}}}", f"<FILE:{gwfile.name}>")
269 for gwfile in generic_workflow.get_job_outputs(gwjob.name):
270 gwjob.arguments = gwjob.arguments.replace(f"{{{gwfile.name}}}", f"<FILE:{gwfile.name}>")
272 # Save dict of other values needed to complete command line.
273 # (Be careful to not replace env variables as they may
274 # be different in compute job.)
275 search_opt["replaceVars"] = True
277 for key in re.findall(r"{([^}]+)}", gwjob.arguments):
278 if key not in gwjob.cmdvals:
279 if key not in cached_job_values[gwjob.label]:
280 _, cached_job_values[gwjob.label][key] = config.search(key, opt=search_opt)
281 gwjob.cmdvals[key] = cached_job_values[gwjob.label][key]
283 # backwards compatibility
284 if not cached_job_values[gwjob.label]["useLazyCommands"]:
285 if "bpsUseShared" not in cached_job_values[gwjob.label]:
286 key = "bpsUseShared"
287 search_opt["default"] = True
288 _, cached_job_values[gwjob.label][key] = config.search(key, opt=search_opt)
289 del search_opt["default"]
291 gwjob.arguments = _fill_arguments(
292 cached_job_values[gwjob.label]["bpsUseShared"], generic_workflow, gwjob.arguments, gwjob.cmdvals
293 )
296def _fill_arguments(use_shared, generic_workflow, arguments, cmdvals):
297 """Replace placeholders in command line string in job.
299 Parameters
300 ----------
301 use_shared : `bool`
302 Whether using shared filesystem.
303 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
304 Generic workflow containing the job.
305 arguments : `str`
306 String containing placeholders.
307 cmdvals : `dict` [`str`, `Any`]
308 Any command line values that can be used to replace placeholders.
310 Returns
311 -------
312 arguments : `str`
313 Command line with FILE and ENV placeholders replaced.
314 """
315 # Replace file placeholders
316 for file_key in re.findall(r"<FILE:([^>]+)>", arguments):
317 gwfile = generic_workflow.get_file(file_key)
318 if not gwfile.wms_transfer:
319 # Must assume full URI if in command line and told WMS is not
320 # responsible for transferring file.
321 uri = gwfile.src_uri
322 elif use_shared:
323 if gwfile.job_shared:
324 # Have shared filesystems and jobs can share file.
325 uri = gwfile.src_uri
326 else:
327 # Taking advantage of inside knowledge. Not future-proof.
328 # Temporary fix until have job wrapper that pulls files
329 # within job.
330 if gwfile.name == "butlerConfig" and os.path.splitext(gwfile.src_uri)[1] != ".yaml":
331 uri = "butler.yaml"
332 else:
333 uri = os.path.basename(gwfile.src_uri)
334 else: # Using push transfer
335 uri = os.path.basename(gwfile.src_uri)
337 arguments = arguments.replace(f"<FILE:{file_key}>", uri)
339 # Replace env placeholder with submit-side values
340 arguments = re.sub(r"<ENV:([^>]+)>", r"$\1", arguments)
341 arguments = os.path.expandvars(arguments)
343 # Replace remaining vars
344 arguments = arguments.format(**cmdvals)
346 return arguments
349def _get_butler_gwfile(prefix, when_create, butler_config, execution_butler_dir):
350 """Get butler location to be used by job.
352 Parameters
353 ----------
354 prefix : `str`
355 Root path for any output files.
356 when_create : `str`
357 When to create the execution butler used to determine whether job is
358 using execution butler or not.
359 butler_config : `str`
360 Location of central butler repositories config file.
361 execution_butler_dir : `str`
362 Location of execution butler repository.
364 Returns
365 -------
366 gwfile : `lsst.ctrl.bps.GenericWorkflowFile`
367 Representation of butler location.
368 """
369 if when_create.upper() == "NEVER":
370 wms_transfer = False
371 job_access_remote = True
372 job_shared = True
373 else:
374 butler_config = execution_butler_dir
375 if not butler_config.startswith("/"):
376 butler_config = f"{prefix}/{butler_config}"
377 wms_transfer = True
378 job_access_remote = False
379 job_shared = False
381 gwfile = GenericWorkflowFile(
382 "butlerConfig",
383 src_uri=butler_config,
384 wms_transfer=wms_transfer,
385 job_access_remote=job_access_remote,
386 job_shared=job_shared,
387 )
389 return gwfile
392def _get_qgraph_gwfile(config, save_qgraph_per_job, gwjob, run_qgraph_file, prefix):
393 """Get qgraph location to be used by job.
395 Parameters
396 ----------
397 config : `lsst.ctrl.bps.BpsConfig`
398 Bps configuration.
399 save_qgraph_per_job: `lsst.ctrl.bps.bps_utils.WhenToSaveQuantumGraphs`
400 What submission stage to save per-job qgraph files (or NEVER)
401 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
402 Job for which determining QuantumGraph file.
403 run_qgraph_file : `lsst.ctrl.bps.GenericWorkflowFile`
404 File representation of the full run QuantumGraph.
405 prefix : `str`
406 Path prefix for any files written.
408 Returns
409 -------
410 gwfile : `lsst.ctrl.bps.GenericWorkflowFile`
411 Representation of butler location (may not include filename).
412 """
413 qgraph_gwfile = None
414 if save_qgraph_per_job != WhenToSaveQuantumGraphs.NEVER:
415 qgraph_gwfile = GenericWorkflowFile(
416 f"qgraphFile_{gwjob.name}",
417 src_uri=create_job_quantum_graph_filename(config, gwjob, prefix),
418 wms_transfer=True,
419 job_access_remote=True,
420 job_shared=True,
421 )
422 else:
423 qgraph_gwfile = run_qgraph_file
425 return qgraph_gwfile
428def _get_job_values(config, search_opt, cmd_line_key):
429 """Gather generic workflow job values from the bps config.
431 Parameters
432 ----------
433 config : `lsst.ctrl.bps.BpsConfig`
434 Bps configuration.
435 search_opt : `dict` [`str`, `Any`]
436 Search options to be used when searching config.
437 cmd_line_key : `str` or None
438 Which command line key to search for (e.g., "runQuantumCommand").
440 Returns
441 -------
442 job_values : `dict` [ `str`, `Any` ]`
443 A mapping between job attributes and their values.
444 """
445 _LOG.debug("cmd_line_key=%s, search_opt=%s", cmd_line_key, search_opt)
447 # Create a dummy job to easily access the default values.
448 default_gwjob = GenericWorkflowJob("default_job")
450 job_values = {}
451 for attr in _ATTRS_ALL:
452 # Variable names in yaml are camel case instead of snake case.
453 yaml_name = re.sub(r"_(\S)", lambda match: match.group(1).upper(), attr)
454 found, value = config.search(yaml_name, opt=search_opt)
455 if found:
456 job_values[attr] = value
457 else:
458 job_values[attr] = getattr(default_gwjob, attr)
460 # If the automatic memory scaling is enabled (i.e. the memory multiplier
461 # is set and it is a positive number greater than 1.0), adjust number
462 # of retries when necessary. If the memory multiplier is invalid, disable
463 # automatic memory scaling.
464 if job_values["memory_multiplier"] is not None:
465 if math.ceil(float(job_values["memory_multiplier"])) > 1:
466 if job_values["number_of_retries"] is None:
467 job_values["number_of_retries"] = DEFAULT_MEM_RETRIES
468 else:
469 job_values["memory_multiplier"] = None
471 if cmd_line_key:
472 found, cmdline = config.search(cmd_line_key, opt=search_opt)
473 # Make sure cmdline isn't None as that could be sent in as a
474 # default value in search_opt.
475 if found and cmdline:
476 cmd, args = cmdline.split(" ", 1)
477 job_values["executable"] = GenericWorkflowExec(os.path.basename(cmd), cmd, False)
478 if args:
479 job_values["arguments"] = args
481 return job_values
484def _handle_job_values(quantum_job_values, gwjob, attributes=_ATTRS_ALL):
485 """Set the job attributes in the cluster to their correct values.
487 Parameters
488 ----------
489 quantum_job_values : `dict` [`str`, Any]
490 Job values for running single Quantum.
491 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
492 Generic workflow job in which to store the universal values.
493 attributes: `Iterable` [`str`], optional
494 Job attributes to be set in the job following different rules.
495 The default value is _ATTRS_ALL.
496 """
497 _LOG.debug("Call to _handle_job_values")
498 _handle_job_values_universal(quantum_job_values, gwjob, attributes)
499 _handle_job_values_max(quantum_job_values, gwjob, attributes)
500 _handle_job_values_sum(quantum_job_values, gwjob, attributes)
503def _handle_job_values_universal(quantum_job_values, gwjob, attributes=_ATTRS_UNIVERSAL):
504 """Handle job attributes that must have the same value for every quantum
505 in the cluster.
507 Parameters
508 ----------
509 quantum_job_values : `dict` [`str`, Any]
510 Job values for running single Quantum.
511 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
512 Generic workflow job in which to store the universal values.
513 attributes: `Iterable` [`str`], optional
514 Job attributes to be set in the job following different rules.
515 The default value is _ATTRS_UNIVERSAL.
516 """
517 for attr in _ATTRS_UNIVERSAL & set(attributes):
518 _LOG.debug(
519 "Handling job %s (job=%s, quantum=%s)",
520 attr,
521 getattr(gwjob, attr),
522 quantum_job_values.get(attr, "MISSING"),
523 )
524 current_value = getattr(gwjob, attr)
525 try:
526 quantum_value = quantum_job_values[attr]
527 except KeyError:
528 continue
529 else:
530 if not current_value:
531 setattr(gwjob, attr, quantum_value)
532 elif current_value != quantum_value:
533 _LOG.error(
534 "Inconsistent value for %s in Cluster %s Quantum Number %s\n"
535 "Current cluster value: %s\n"
536 "Quantum value: %s",
537 attr,
538 gwjob.name,
539 quantum_job_values.get("qgraphNodeId", "MISSING"),
540 current_value,
541 quantum_value,
542 )
543 raise RuntimeError(f"Inconsistent value for {attr} in cluster {gwjob.name}.")
546def _handle_job_values_max(quantum_job_values, gwjob, attributes=_ATTRS_MAX):
547 """Handle job attributes that should be set to their maximum value in
548 the in cluster.
550 Parameters
551 ----------
552 quantum_job_values : `dict` [`str`, `Any`]
553 Job values for running single Quantum.
554 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
555 Generic workflow job in which to store the aggregate values.
556 attributes: `Iterable` [`str`], optional
557 Job attributes to be set in the job following different rules.
558 The default value is _ATTR_MAX.
559 """
560 for attr in _ATTRS_MAX & set(attributes):
561 current_value = getattr(gwjob, attr)
562 try:
563 quantum_value = quantum_job_values[attr]
564 except KeyError:
565 continue
566 else:
567 needs_update = False
568 if current_value is None:
569 if quantum_value is not None:
570 needs_update = True
571 else:
572 if quantum_value is not None and current_value < quantum_value:
573 needs_update = True
574 if needs_update:
575 setattr(gwjob, attr, quantum_value)
577 # When updating memory requirements for a job, check if memory
578 # autoscaling is enabled. If it is, always use the memory
579 # multiplier and the number of retries which comes with the
580 # quantum.
581 #
582 # Note that as a result, the quantum with the biggest memory
583 # requirements will determine whether the memory autoscaling
584 # will be enabled (or disabled) depending on the value of its
585 # memory multiplier.
586 if attr == "request_memory":
587 gwjob.memory_multiplier = quantum_job_values["memory_multiplier"]
588 if gwjob.memory_multiplier is not None:
589 gwjob.number_of_retries = quantum_job_values["number_of_retries"]
592def _handle_job_values_sum(quantum_job_values, gwjob, attributes=_ATTRS_SUM):
593 """Handle job attributes that are the sum of their values in the cluster.
595 Parameters
596 ----------
597 quantum_job_values : `dict` [`str`, `Any`]
598 Job values for running single Quantum.
599 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
600 Generic workflow job in which to store the aggregate values.
601 attributes: `Iterable` [`str`], optional
602 Job attributes to be set in the job following different rules.
603 The default value is _ATTRS_SUM.
604 """
605 for attr in _ATTRS_SUM & set(attributes):
606 current_value = getattr(gwjob, attr)
607 if not current_value:
608 setattr(gwjob, attr, quantum_job_values[attr])
609 else:
610 setattr(gwjob, attr, current_value + quantum_job_values[attr])
613def create_generic_workflow(config, cqgraph, name, prefix):
614 """Create a generic workflow from a ClusteredQuantumGraph such that it
615 has information needed for WMS (e.g., command lines).
617 Parameters
618 ----------
619 config : `lsst.ctrl.bps.BpsConfig`
620 BPS configuration.
621 cqgraph : `lsst.ctrl.bps.ClusteredQuantumGraph`
622 ClusteredQuantumGraph for running a specific pipeline on a specific
623 payload.
624 name : `str`
625 Name for the workflow (typically unique).
626 prefix : `str`
627 Root path for any output files.
629 Returns
630 -------
631 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
632 Generic workflow for the given ClusteredQuantumGraph + config.
633 """
634 # Determine whether saving per-job QuantumGraph files in the loop.
635 _, when_save = config.search("whenSaveJobQgraph", {"default": WhenToSaveQuantumGraphs.TRANSFORM.name})
636 save_qgraph_per_job = WhenToSaveQuantumGraphs[when_save.upper()]
638 search_opt = {"replaceVars": False, "expandEnvVars": False, "replaceEnvVars": True, "required": False}
640 # Lookup butler values once
641 _, when_create = config.search(".executionButler.whenCreate", opt=search_opt)
642 _, butler_config = config.search("butlerConfig", opt=search_opt)
643 _, execution_butler_dir = config.search(".bps_defined.executionButlerDir", opt=search_opt)
645 generic_workflow = GenericWorkflow(name)
647 # Save full run QuantumGraph for use by jobs
648 generic_workflow.add_file(
649 GenericWorkflowFile(
650 "runQgraphFile",
651 src_uri=config["runQgraphFile"],
652 wms_transfer=True,
653 job_access_remote=True,
654 job_shared=True,
655 )
656 )
658 # Cache pipetask specific or more generic job values to minimize number
659 # on config searches.
660 cached_job_values = {}
661 cached_pipetask_values = {}
663 for cluster in cqgraph.clusters():
664 _LOG.debug("Loop over clusters: %s, %s", cluster, type(cluster))
665 _LOG.debug(
666 "cqgraph: name=%s, len=%s, label=%s, ids=%s",
667 cluster.name,
668 len(cluster.qgraph_node_ids),
669 cluster.label,
670 cluster.qgraph_node_ids,
671 )
673 gwjob = GenericWorkflowJob(cluster.name)
675 # First get job values from cluster or cluster config
676 search_opt["curvals"] = {"curr_cluster": cluster.label}
677 found, value = config.search("computeSite", opt=search_opt)
678 if found:
679 search_opt["curvals"]["curr_site"] = value
680 found, value = config.search("computeCloud", opt=search_opt)
681 if found:
682 search_opt["curvals"]["curr_cloud"] = value
684 # If some config values are set for this cluster
685 if cluster.label not in cached_job_values:
686 _LOG.debug("config['cluster'][%s] = %s", cluster.label, config["cluster"][cluster.label])
687 cached_job_values[cluster.label] = {}
689 # Allowing whenSaveJobQgraph and useLazyCommands per cluster label.
690 key = "whenSaveJobQgraph"
691 _, when_save = config.search(key, opt=search_opt)
692 cached_job_values[cluster.label][key] = WhenToSaveQuantumGraphs[when_save.upper()]
694 key = "useLazyCommands"
695 search_opt["default"] = True
696 _, cached_job_values[cluster.label][key] = config.search(key, opt=search_opt)
697 del search_opt["default"]
699 if cluster.label in config["cluster"]:
700 # Don't want to get global defaults here so only look in
701 # cluster section.
702 cached_job_values[cluster.label].update(
703 _get_job_values(config["cluster"][cluster.label], search_opt, "runQuantumCommand")
704 )
705 cluster_job_values = copy.copy(cached_job_values[cluster.label])
707 cluster_job_values["name"] = cluster.name
708 cluster_job_values["label"] = cluster.label
709 cluster_job_values["quanta_counts"] = cluster.quanta_counts
710 cluster_job_values["tags"] = cluster.tags
711 _LOG.debug("cluster_job_values = %s", cluster_job_values)
712 _handle_job_values(cluster_job_values, gwjob, cluster_job_values.keys())
714 # For purposes of whether to continue searching for a value is whether
715 # the value evaluates to False.
716 unset_attributes = {attr for attr in _ATTRS_ALL if not getattr(gwjob, attr)}
718 _LOG.debug("unset_attributes=%s", unset_attributes)
719 _LOG.debug("set=%s", _ATTRS_ALL - unset_attributes)
721 # For job info not defined at cluster level, attempt to get job info
722 # either common or aggregate for all Quanta in cluster.
723 for node_id in iter(cluster.qgraph_node_ids):
724 _LOG.debug("node_id=%s", node_id)
725 qnode = cqgraph.get_quantum_node(node_id)
727 if qnode.taskDef.label not in cached_pipetask_values:
728 search_opt["curvals"]["curr_pipetask"] = qnode.taskDef.label
729 cached_pipetask_values[qnode.taskDef.label] = _get_job_values(
730 config, search_opt, "runQuantumCommand"
731 )
733 _handle_job_values(cached_pipetask_values[qnode.taskDef.label], gwjob, unset_attributes)
735 # Update job with workflow attribute and profile values.
736 qgraph_gwfile = _get_qgraph_gwfile(
737 config, save_qgraph_per_job, gwjob, generic_workflow.get_file("runQgraphFile"), prefix
738 )
739 butler_gwfile = _get_butler_gwfile(prefix, when_create, butler_config, execution_butler_dir)
741 generic_workflow.add_job(gwjob)
742 generic_workflow.add_job_inputs(gwjob.name, [qgraph_gwfile, butler_gwfile])
744 gwjob.cmdvals["qgraphId"] = cqgraph.qgraph.graphID
745 gwjob.cmdvals["qgraphNodeId"] = ",".join(
746 sorted([f"{node_id}" for node_id in cluster.qgraph_node_ids])
747 )
748 _enhance_command(config, generic_workflow, gwjob, cached_job_values)
750 # If writing per-job QuantumGraph files during TRANSFORM stage,
751 # write it now while in memory.
752 if save_qgraph_per_job == WhenToSaveQuantumGraphs.TRANSFORM:
753 save_qg_subgraph(cqgraph.qgraph, qgraph_gwfile.src_uri, cluster.qgraph_node_ids)
755 # Create job dependencies.
756 for parent in cqgraph.clusters():
757 for child in cqgraph.successors(parent):
758 generic_workflow.add_job_relationships(parent.name, child.name)
760 # Add initial workflow.
761 if config.get("runInit", "{default: False}"):
762 add_workflow_init_nodes(config, cqgraph.qgraph, generic_workflow)
764 generic_workflow.run_attrs.update(
765 {
766 "bps_isjob": "True",
767 "bps_project": config["project"],
768 "bps_campaign": config["campaign"],
769 "bps_run": generic_workflow.name,
770 "bps_operator": config["operator"],
771 "bps_payload": config["payloadName"],
772 "bps_runsite": config["computeSite"],
773 }
774 )
776 # Add final job
777 add_final_job(config, generic_workflow, prefix)
779 return generic_workflow
782def create_generic_workflow_config(config, prefix):
783 """Create generic workflow configuration.
785 Parameters
786 ----------
787 config : `lsst.ctrl.bps.BpsConfig`
788 Bps configuration.
789 prefix : `str`
790 Root path for any output files.
792 Returns
793 -------
794 generic_workflow_config : `lsst.ctrl.bps.BpsConfig`
795 Configuration accompanying the GenericWorkflow.
796 """
797 generic_workflow_config = BpsConfig(config)
798 generic_workflow_config["workflowName"] = config["uniqProcName"]
799 generic_workflow_config["workflowPath"] = prefix
800 return generic_workflow_config
803def add_final_job(config, generic_workflow, prefix):
804 """Add final workflow job depending upon configuration.
806 Parameters
807 ----------
808 config : `lsst.ctrl.bps.BpsConfig`
809 Bps configuration.
810 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
811 Generic workflow to which attributes should be added.
812 prefix : `str`
813 Directory in which to output final script.
814 """
815 _, when_create = config.search(".executionButler.whenCreate")
816 _, when_merge = config.search(".executionButler.whenMerge")
818 search_opt = {"searchobj": config[".executionButler"], "curvals": {}, "default": None}
819 found, value = config.search("computeSite", opt=search_opt)
820 if found:
821 search_opt["curvals"]["curr_site"] = value
822 found, value = config.search("computeCloud", opt=search_opt)
823 if found:
824 search_opt["curvals"]["curr_cloud"] = value
826 if when_create.upper() != "NEVER" and when_merge.upper() != "NEVER":
827 # create gwjob
828 gwjob = GenericWorkflowJob("mergeExecutionButler")
829 gwjob.label = "mergeExecutionButler"
831 # Set job attributes based on the values find in the config excluding
832 # the ones in the _ATTRS_MISC group. The attributes in this group are
833 # somewhat "special":
834 # * HTCondor plugin, which uses 'attrs' and 'profile', has its own
835 # mechanism for setting them,
836 # * 'cmdvals' is being set internally, not via config.
837 job_values = _get_job_values(config, search_opt, None)
838 for attr in _ATTRS_ALL - _ATTRS_MISC:
839 if not getattr(gwjob, attr) and job_values.get(attr, None):
840 setattr(gwjob, attr, job_values[attr])
842 # Create script and add command line to job.
843 gwjob.executable, gwjob.arguments = _create_final_command(config, prefix)
845 # Determine inputs from command line.
846 for file_key in re.findall(r"<FILE:([^>]+)>", gwjob.arguments):
847 gwfile = generic_workflow.get_file(file_key)
848 generic_workflow.add_job_inputs(gwjob.name, gwfile)
850 _enhance_command(config, generic_workflow, gwjob, {})
852 # Put transfer repo job in appropriate location in workflow.
853 if when_merge.upper() == "ALWAYS":
854 # add as special final job
855 generic_workflow.add_final(gwjob)
856 elif when_merge.upper() == "SUCCESS":
857 # add as regular sink node
858 add_final_job_as_sink(generic_workflow, gwjob)
859 else:
860 raise ValueError(f"Invalid value for executionButler.when_merge {when_merge}")
863def _create_final_command(config, prefix):
864 """Create the command and shell script for the final job.
866 Parameters
867 ----------
868 config : `lsst.ctrl.bps.BpsConfig`
869 Bps configuration.
870 prefix : `str`
871 Directory in which to output final script.
873 Returns
874 -------
875 executable : `lsst.ctrl.bps.GenericWorkflowExec`
876 Executable object for the final script.
877 arguments : `str`
878 Command line needed to call the final script.
879 """
880 search_opt = {
881 "replaceVars": False,
882 "replaceEnvVars": False,
883 "expandEnvVars": False,
884 "searchobj": config["executionButler"],
885 }
887 script_file = os.path.join(prefix, "final_job.bash")
888 with open(script_file, "w") as fh:
889 print("#!/bin/bash\n", file=fh)
890 print("set -e", file=fh)
891 print("set -x", file=fh)
893 print("butlerConfig=$1", file=fh)
894 print("executionButlerDir=$2", file=fh)
896 i = 1
897 found, command = config.search(f".executionButler.command{i}", opt=search_opt)
898 while found:
899 # Temporarily replace any env vars so formatter doesn't try to
900 # replace them.
901 command = re.sub(r"\${([^}]+)}", r"<BPSTMP:\1>", command)
903 # executionButlerDir and butlerConfig will be args to script and
904 # set to env vars
905 command = command.replace("{executionButlerDir}", "<BPSTMP:executionButlerDir>")
906 command = command.replace("{butlerConfig}", "<BPSTMP:butlerConfig>")
908 # Replace all other vars in command string
909 search_opt["replaceVars"] = True
910 command = config.formatter.format(command, config, search_opt)
911 search_opt["replaceVars"] = False
913 # Replace any temporary env place holders.
914 command = re.sub(r"<BPSTMP:([^>]+)>", r"${\1}", command)
916 print(command, file=fh)
917 i += 1
918 found, command = config.search(f".executionButler.command{i}", opt=search_opt)
919 os.chmod(script_file, 0o755)
920 executable = GenericWorkflowExec(os.path.basename(script_file), script_file, True)
922 _, orig_butler = config.search("butlerConfig")
923 # The execution butler was saved as butlerConfig in the workflow.
924 return executable, f"{orig_butler} <FILE:butlerConfig>"
927def add_final_job_as_sink(generic_workflow, final_job):
928 """Add final job as the single sink for the workflow.
930 Parameters
931 ----------
932 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
933 Generic workflow to which attributes should be added.
934 final_job : `lsst.ctrl.bps.GenericWorkflowJob`
935 Job to add as new sink node depending upon all previous sink nodes.
936 """
937 # Find sink nodes of generic workflow graph.
938 gw_sinks = [n for n in generic_workflow if generic_workflow.out_degree(n) == 0]
939 _LOG.debug("gw_sinks = %s", gw_sinks)
941 generic_workflow.add_job(final_job)
942 generic_workflow.add_job_relationships(gw_sinks, final_job.name)