Coverage for python/lsst/ctrl/bps/transform.py: 8%
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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 "cmdline",
76 "cmdvals",
77 "environment",
78 "pre_cmdline",
79 "post_cmdline",
80 "profile",
81 "attrs",
82 }
83)
85# Attributes that need to be the same for each quanta in the cluster.
86_ATTRS_UNIVERSAL = frozenset(_ATTRS_ALL - (_ATTRS_MAX | _ATTRS_MISC | _ATTRS_SUM))
88_LOG = logging.getLogger(__name__)
91@timeMethod(logger=_LOG, logLevel=VERBOSE)
92def transform(config, cqgraph, prefix):
93 """Transform a ClusteredQuantumGraph to a GenericWorkflow.
95 Parameters
96 ----------
97 config : `lsst.ctrl.bps.BpsConfig`
98 BPS configuration.
99 cqgraph : `lsst.ctrl.bps.ClusteredQuantumGraph`
100 A clustered quantum graph to transform into a generic workflow.
101 prefix : `str`
102 Root path for any output files.
104 Returns
105 -------
106 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
107 The generic workflow transformed from the clustered quantum graph.
108 generic_workflow_config : `lsst.ctrl.bps.BpsConfig`
109 Configuration to accompany GenericWorkflow.
110 """
111 _, when_create = config.search(".executionButler.whenCreate")
112 if when_create.upper() == "TRANSFORM":
113 _, execution_butler_dir = config.search(".bps_defined.executionButlerDir")
114 _LOG.info("Creating execution butler in '%s'", execution_butler_dir)
115 with time_this(log=_LOG, level=logging.INFO, prefix=None, msg="Creating execution butler completed"):
116 _create_execution_butler(config, config["runQgraphFile"], execution_butler_dir, prefix)
118 if cqgraph.name is not None:
119 name = cqgraph.name
120 else:
121 _, name = config.search("uniqProcName", opt={"required": True})
123 generic_workflow = create_generic_workflow(config, cqgraph, name, prefix)
124 generic_workflow_config = create_generic_workflow_config(config, prefix)
126 return generic_workflow, generic_workflow_config
129def add_workflow_init_nodes(config, qgraph, generic_workflow):
130 """Add nodes to workflow graph that perform initialization steps.
132 Assumes that all of the initialization should be executed prior to any
133 of the current workflow.
135 Parameters
136 ----------
137 config : `lsst.ctrl.bps.BpsConfig`
138 BPS configuration.
139 qgraph : `lsst.pipe.base.graph.QuantumGraph`
140 The quantum graph the generic workflow represents.
141 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
142 Generic workflow to which the initialization steps should be added.
143 """
144 # Create a workflow graph that will have task and file nodes necessary for
145 # initializing the pipeline execution
146 init_workflow = create_init_workflow(config, qgraph, generic_workflow.get_file("runQgraphFile"))
147 _LOG.debug("init_workflow nodes = %s", init_workflow.nodes())
148 generic_workflow.add_workflow_source(init_workflow)
151def create_init_workflow(config, qgraph, qgraph_gwfile):
152 """Create workflow for running initialization job(s).
154 Parameters
155 ----------
156 config : `lsst.ctrl.bps.BpsConfig`
157 BPS configuration.
158 qgraph : `lsst.pipe.base.graph.QuantumGraph`
159 The quantum graph the generic workflow represents.
160 qgraph_gwfile : `lsst.ctrl.bps.GenericWorkflowFile`
161 File object for the full run QuantumGraph file.
163 Returns
164 -------
165 init_workflow : `lsst.ctrl.bps.GenericWorkflow`
166 GenericWorkflow consisting of job(s) to initialize workflow.
167 """
168 _LOG.debug("creating init subgraph")
169 _LOG.debug("creating init task input(s)")
170 search_opt = {
171 "curvals": {"curr_pipetask": "pipetaskInit"},
172 "replaceVars": False,
173 "expandEnvVars": False,
174 "replaceEnvVars": True,
175 "required": False,
176 }
178 init_workflow = GenericWorkflow("init")
179 init_workflow.add_file(qgraph_gwfile)
181 # create job for executing --init-only
182 gwjob = GenericWorkflowJob("pipetaskInit")
184 job_values = _get_job_values(config, search_opt, "runQuantumCommand")
185 job_values["name"] = "pipetaskInit"
186 job_values["label"] = "pipetaskInit"
188 # Adjust job attributes values if necessary.
189 _handle_job_values(job_values, gwjob)
191 # Pick a node id for each task (not quantum!) to avoid reading the entire
192 # quantum graph during the initialization stage.
193 node_ids = []
194 for task in qgraph.iterTaskGraph():
195 task_def = qgraph.findTaskDefByLabel(task.label)
196 node = next(iter(qgraph.getNodesForTask(task_def)))
197 node_ids.append(node.nodeId)
198 gwjob.cmdvals["qgraphId"] = qgraph.graphID
199 gwjob.cmdvals["qgraphNodeId"] = ",".join(sorted([f"{node_id}" for node_id in node_ids]))
201 init_workflow.add_job(gwjob)
203 # Lookup butler values
204 _, when_create = config.search(".executionButler.whenCreate", opt=search_opt)
205 _, butler_config = config.search("butlerConfig", opt=search_opt)
206 _, execution_butler_dir = config.search(".bps_defined.executionButlerDir", opt=search_opt)
207 prefix = config["submitPath"]
208 butler_gwfile = _get_butler_gwfile(prefix, when_create, butler_config, execution_butler_dir)
210 init_workflow.add_job_inputs(gwjob.name, [qgraph_gwfile, butler_gwfile])
211 _enhance_command(config, init_workflow, gwjob, {})
213 return init_workflow
216def _enhance_command(config, generic_workflow, gwjob, cached_job_values):
217 """Enhance command line with env and file placeholders
218 and gather command line values.
220 Parameters
221 ----------
222 config : `lsst.ctrl.bps.BpsConfig`
223 BPS configuration.
224 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
225 Generic workflow that contains the job.
226 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
227 Generic workflow job to which the updated executable, arguments,
228 and values should be saved.
229 cached_job_values : `dict` [`str`, dict[`str`, `Any`]]
230 Cached values common across jobs with same label. Updated if values
231 aren't already saved for given gwjob's label.
232 """
233 _LOG.debug("gwjob given to _enhance_command: %s", gwjob)
235 search_opt = {
236 "curvals": {"curr_pipetask": gwjob.label},
237 "replaceVars": False,
238 "expandEnvVars": False,
239 "replaceEnvVars": True,
240 "required": False,
241 }
243 if gwjob.label not in cached_job_values:
244 cached_job_values[gwjob.label] = {}
245 # Allowing whenSaveJobQgraph and useLazyCommands per pipetask label.
246 key = "whenSaveJobQgraph"
247 _, when_save = config.search(key, opt=search_opt)
248 cached_job_values[gwjob.label][key] = WhenToSaveQuantumGraphs[when_save.upper()]
250 key = "useLazyCommands"
251 search_opt["default"] = True
252 _, cached_job_values[gwjob.label][key] = config.search(key, opt=search_opt)
253 del search_opt["default"]
255 # Change qgraph variable to match whether using run or per-job qgraph
256 # Note: these are lookup keys, not actual physical filenames.
257 if cached_job_values[gwjob.label]["whenSaveJobQgraph"] == WhenToSaveQuantumGraphs.NEVER:
258 gwjob.arguments = gwjob.arguments.replace("{qgraphFile}", "{runQgraphFile}")
259 elif gwjob.name == "pipetaskInit":
260 gwjob.arguments = gwjob.arguments.replace("{qgraphFile}", "{runQgraphFile}")
261 else: # Needed unique file keys for per-job QuantumGraphs
262 gwjob.arguments = gwjob.arguments.replace("{qgraphFile}", f"{{qgraphFile_{gwjob.name}}}")
264 # Replace files with special placeholders
265 for gwfile in generic_workflow.get_job_inputs(gwjob.name):
266 gwjob.arguments = gwjob.arguments.replace(f"{{{gwfile.name}}}", f"<FILE:{gwfile.name}>")
267 for gwfile in generic_workflow.get_job_outputs(gwjob.name):
268 gwjob.arguments = gwjob.arguments.replace(f"{{{gwfile.name}}}", f"<FILE:{gwfile.name}>")
270 # Save dict of other values needed to complete command line.
271 # (Be careful to not replace env variables as they may
272 # be different in compute job.)
273 search_opt["replaceVars"] = True
275 for key in re.findall(r"{([^}]+)}", gwjob.arguments):
276 if key not in gwjob.cmdvals:
277 if key not in cached_job_values[gwjob.label]:
278 _, cached_job_values[gwjob.label][key] = config.search(key, opt=search_opt)
279 gwjob.cmdvals[key] = cached_job_values[gwjob.label][key]
281 # backwards compatibility
282 if not cached_job_values[gwjob.label]["useLazyCommands"]:
283 if "bpsUseShared" not in cached_job_values[gwjob.label]:
284 key = "bpsUseShared"
285 search_opt["default"] = True
286 _, cached_job_values[gwjob.label][key] = config.search(key, opt=search_opt)
287 del search_opt["default"]
289 gwjob.arguments = _fill_arguments(
290 cached_job_values[gwjob.label]["bpsUseShared"], generic_workflow, gwjob.arguments, gwjob.cmdvals
291 )
294def _fill_arguments(use_shared, generic_workflow, arguments, cmdvals):
295 """Replace placeholders in command line string in job.
297 Parameters
298 ----------
299 use_shared : `bool`
300 Whether using shared filesystem.
301 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
302 Generic workflow containing the job.
303 arguments : `str`
304 String containing placeholders.
305 cmdvals : `dict` [`str`, `Any`]
306 Any command line values that can be used to replace placeholders.
308 Returns
309 -------
310 arguments : `str`
311 Command line with FILE and ENV placeholders replaced.
312 """
313 # Replace file placeholders
314 for file_key in re.findall(r"<FILE:([^>]+)>", arguments):
315 gwfile = generic_workflow.get_file(file_key)
316 if not gwfile.wms_transfer:
317 # Must assume full URI if in command line and told WMS is not
318 # responsible for transferring file.
319 uri = gwfile.src_uri
320 elif use_shared:
321 if gwfile.job_shared:
322 # Have shared filesystems and jobs can share file.
323 uri = gwfile.src_uri
324 else:
325 # Taking advantage of inside knowledge. Not future-proof.
326 # Temporary fix until have job wrapper that pulls files
327 # within job.
328 if gwfile.name == "butlerConfig" and os.path.splitext(gwfile.src_uri)[1] != ".yaml":
329 uri = "butler.yaml"
330 else:
331 uri = os.path.basename(gwfile.src_uri)
332 else: # Using push transfer
333 uri = os.path.basename(gwfile.src_uri)
335 arguments = arguments.replace(f"<FILE:{file_key}>", uri)
337 # Replace env placeholder with submit-side values
338 arguments = re.sub(r"<ENV:([^>]+)>", r"$\1", arguments)
339 arguments = os.path.expandvars(arguments)
341 # Replace remaining vars
342 arguments = arguments.format(**cmdvals)
344 return arguments
347def _get_butler_gwfile(prefix, when_create, butler_config, execution_butler_dir):
348 """Get butler location to be used by job.
350 Parameters
351 ----------
352 prefix : `str`
353 Root path for any output files.
354 when_create : `str`
355 When to create the execution butler used to determine whether job is
356 using execution butler or not.
357 butler_config : `str`
358 Location of central butler repositories config file.
359 execution_butler_dir : `str`
360 Location of execution butler repository.
362 Returns
363 -------
364 gwfile : `lsst.ctrl.bps.GenericWorkflowFile`
365 Representation of butler location.
366 """
367 if when_create.upper() == "NEVER":
368 wms_transfer = False
369 job_access_remote = True
370 job_shared = True
371 else:
372 butler_config = execution_butler_dir
373 if not butler_config.startswith("/"):
374 butler_config = f"{prefix}/{butler_config}"
375 wms_transfer = True
376 job_access_remote = False
377 job_shared = False
379 gwfile = GenericWorkflowFile(
380 "butlerConfig",
381 src_uri=butler_config,
382 wms_transfer=wms_transfer,
383 job_access_remote=job_access_remote,
384 job_shared=job_shared,
385 )
387 return gwfile
390def _get_qgraph_gwfile(config, save_qgraph_per_job, gwjob, run_qgraph_file, prefix):
391 """Get qgraph location to be used by job.
393 Parameters
394 ----------
395 config : `lsst.ctrl.bps.BpsConfig`
396 Bps configuration.
397 save_qgraph_per_job: `lsst.ctrl.bps.bps_utils.WhenToSaveQuantumGraphs`
398 What submission stage to save per-job qgraph files (or NEVER)
399 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
400 Job for which determining QuantumGraph file.
401 run_qgraph_file : `lsst.ctrl.bps.GenericWorkflowFile`
402 File representation of the full run QuantumGraph.
403 prefix : `str`
404 Path prefix for any files written.
406 Returns
407 -------
408 gwfile : `lsst.ctrl.bps.GenericWorkflowFile`
409 Representation of butler location (may not include filename).
410 """
411 qgraph_gwfile = None
412 if save_qgraph_per_job != WhenToSaveQuantumGraphs.NEVER:
413 qgraph_gwfile = GenericWorkflowFile(
414 f"qgraphFile_{gwjob.name}",
415 src_uri=create_job_quantum_graph_filename(config, gwjob, prefix),
416 wms_transfer=True,
417 job_access_remote=True,
418 job_shared=True,
419 )
420 else:
421 qgraph_gwfile = run_qgraph_file
423 return qgraph_gwfile
426def _get_job_values(config, search_opt, cmd_line_key):
427 """Gather generic workflow job values from the bps config.
429 Parameters
430 ----------
431 config : `lsst.ctrl.bps.BpsConfig`
432 Bps configuration.
433 search_opt : `dict` [`str`, `Any`]
434 Search options to be used when searching config.
435 cmd_line_key : `str` or None
436 Which command line key to search for (e.g., "runQuantumCommand").
438 Returns
439 -------
440 job_values : `dict` [ `str`, `Any` ]`
441 A mapping between job attributes and their values.
442 """
443 job_values = {}
444 for attr in _ATTRS_ALL:
445 # Variable names in yaml are camel case instead of snake case.
446 yaml_name = re.sub(r"_(\S)", lambda match: match.group(1).upper(), attr)
447 found, value = config.search(yaml_name, opt=search_opt)
448 if found:
449 job_values[attr] = value
450 else:
451 job_values[attr] = None
453 # If the automatic memory scaling is enabled (i.e. the memory multiplier
454 # is set and it is a positive number greater than 1.0), adjust number
455 # of retries when necessary. If the memory multiplier is invalid, disable
456 # automatic memory scaling.
457 if job_values["memory_multiplier"] is not None:
458 if math.ceil(float(job_values["memory_multiplier"])) > 1:
459 if job_values["number_of_retries"] is None:
460 job_values["number_of_retries"] = DEFAULT_MEM_RETRIES
461 else:
462 job_values["memory_multiplier"] = None
464 if cmd_line_key:
465 found, cmdline = config.search(cmd_line_key, opt=search_opt)
466 # Make sure cmdline isn't None as that could be sent in as a
467 # default value in search_opt.
468 if found and cmdline:
469 cmd, args = cmdline.split(" ", 1)
470 job_values["executable"] = GenericWorkflowExec(os.path.basename(cmd), cmd, False)
471 if args:
472 job_values["arguments"] = args
474 return job_values
477def _handle_job_values(quantum_job_values, gwjob, attributes=_ATTRS_ALL):
478 """Set the job attributes in the cluster to their correct values.
480 Parameters
481 ----------
482 quantum_job_values : `dict` [`str`, Any]
483 Job values for running single Quantum.
484 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
485 Generic workflow job in which to store the universal values.
486 attributes: `Iterable` [`str`], optional
487 Job attributes to be set in the job following different rules.
488 The default value is _ATTRS_ALL.
489 """
490 _LOG.debug("Call to _handle_job_values")
491 _handle_job_values_universal(quantum_job_values, gwjob, attributes)
492 _handle_job_values_max(quantum_job_values, gwjob, attributes)
493 _handle_job_values_sum(quantum_job_values, gwjob, attributes)
496def _handle_job_values_universal(quantum_job_values, gwjob, attributes=_ATTRS_UNIVERSAL):
497 """Handle job attributes that must have the same value for every quantum
498 in the cluster.
500 Parameters
501 ----------
502 quantum_job_values : `dict` [`str`, Any]
503 Job values for running single Quantum.
504 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
505 Generic workflow job in which to store the universal values.
506 attributes: `Iterable` [`str`], optional
507 Job attributes to be set in the job following different rules.
508 The default value is _ATTRS_UNIVERSAL.
509 """
510 for attr in _ATTRS_UNIVERSAL & set(attributes):
511 _LOG.debug(
512 "Handling job %s (job=%s, quantum=%s)",
513 attr,
514 getattr(gwjob, attr),
515 quantum_job_values.get(attr, "MISSING"),
516 )
517 current_value = getattr(gwjob, attr)
518 try:
519 quantum_value = quantum_job_values[attr]
520 except KeyError:
521 continue
522 else:
523 if not current_value:
524 setattr(gwjob, attr, quantum_value)
525 elif current_value != quantum_value:
526 _LOG.error(
527 "Inconsistent value for %s in Cluster %s Quantum Number %s\n"
528 "Current cluster value: %s\n"
529 "Quantum value: %s",
530 attr,
531 gwjob.name,
532 quantum_job_values.get("qgraphNodeId", "MISSING"),
533 current_value,
534 quantum_value,
535 )
536 raise RuntimeError(f"Inconsistent value for {attr} in cluster {gwjob.name}.")
539def _handle_job_values_max(quantum_job_values, gwjob, attributes=_ATTRS_MAX):
540 """Handle job attributes that should be set to their maximum value in
541 the in cluster.
543 Parameters
544 ----------
545 quantum_job_values : `dict` [`str`, `Any`]
546 Job values for running single Quantum.
547 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
548 Generic workflow job in which to store the aggregate values.
549 attributes: `Iterable` [`str`], optional
550 Job attributes to be set in the job following different rules.
551 The default value is _ATTR_MAX.
552 """
553 for attr in _ATTRS_MAX & set(attributes):
554 current_value = getattr(gwjob, attr)
555 try:
556 quantum_value = quantum_job_values[attr]
557 except KeyError:
558 continue
559 else:
560 needs_update = False
561 if current_value is None:
562 if quantum_value is not None:
563 needs_update = True
564 else:
565 if quantum_value is not None and current_value < quantum_value:
566 needs_update = True
567 if needs_update:
568 setattr(gwjob, attr, quantum_value)
570 # When updating memory requirements for a job, check if memory
571 # autoscaling is enabled. If it is, always use the memory
572 # multiplier and the number of retries which comes with the
573 # quantum.
574 #
575 # Note that as a result, the quantum with the biggest memory
576 # requirements will determine whether the memory autoscaling
577 # will be enabled (or disabled) depending on the value of its
578 # memory multiplier.
579 if attr == "request_memory":
580 gwjob.memory_multiplier = quantum_job_values["memory_multiplier"]
581 if gwjob.memory_multiplier is not None:
582 gwjob.number_of_retries = quantum_job_values["number_of_retries"]
585def _handle_job_values_sum(quantum_job_values, gwjob, attributes=_ATTRS_SUM):
586 """Handle job attributes that are the sum of their values in the cluster.
588 Parameters
589 ----------
590 quantum_job_values : `dict` [`str`, `Any`]
591 Job values for running single Quantum.
592 gwjob : `lsst.ctrl.bps.GenericWorkflowJob`
593 Generic workflow job in which to store the aggregate values.
594 attributes: `Iterable` [`str`], optional
595 Job attributes to be set in the job following different rules.
596 The default value is _ATTRS_SUM.
597 """
598 for attr in _ATTRS_SUM & set(attributes):
599 current_value = getattr(gwjob, attr)
600 if not current_value:
601 setattr(gwjob, attr, quantum_job_values[attr])
602 else:
603 setattr(gwjob, attr, current_value + quantum_job_values[attr])
606def create_generic_workflow(config, cqgraph, name, prefix):
607 """Create a generic workflow from a ClusteredQuantumGraph such that it
608 has information needed for WMS (e.g., command lines).
610 Parameters
611 ----------
612 config : `lsst.ctrl.bps.BpsConfig`
613 BPS configuration.
614 cqgraph : `lsst.ctrl.bps.ClusteredQuantumGraph`
615 ClusteredQuantumGraph for running a specific pipeline on a specific
616 payload.
617 name : `str`
618 Name for the workflow (typically unique).
619 prefix : `str`
620 Root path for any output files.
622 Returns
623 -------
624 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
625 Generic workflow for the given ClusteredQuantumGraph + config.
626 """
627 # Determine whether saving per-job QuantumGraph files in the loop.
628 _, when_save = config.search("whenSaveJobQgraph", {"default": WhenToSaveQuantumGraphs.TRANSFORM.name})
629 save_qgraph_per_job = WhenToSaveQuantumGraphs[when_save.upper()]
631 search_opt = {"replaceVars": False, "expandEnvVars": False, "replaceEnvVars": True, "required": False}
633 # Lookup butler values once
634 _, when_create = config.search(".executionButler.whenCreate", opt=search_opt)
635 _, butler_config = config.search("butlerConfig", opt=search_opt)
636 _, execution_butler_dir = config.search(".bps_defined.executionButlerDir", opt=search_opt)
638 generic_workflow = GenericWorkflow(name)
640 # Save full run QuantumGraph for use by jobs
641 generic_workflow.add_file(
642 GenericWorkflowFile(
643 "runQgraphFile",
644 src_uri=config["runQgraphFile"],
645 wms_transfer=True,
646 job_access_remote=True,
647 job_shared=True,
648 )
649 )
651 # Cache pipetask specific or more generic job values to minimize number
652 # on config searches.
653 cached_job_values = {}
654 cached_pipetask_values = {}
656 for cluster in cqgraph.clusters():
657 _LOG.debug("Loop over clusters: %s, %s", cluster, type(cluster))
658 _LOG.debug(
659 "cqgraph: name=%s, len=%s, label=%s, ids=%s",
660 cluster.name,
661 len(cluster.qgraph_node_ids),
662 cluster.label,
663 cluster.qgraph_node_ids,
664 )
666 gwjob = GenericWorkflowJob(cluster.name)
668 # First get job values from cluster or cluster config
669 search_opt["curvals"] = {"curr_cluster": cluster.label}
671 # If some config values are set for this cluster
672 if cluster.label not in cached_job_values:
673 _LOG.debug("config['cluster'][%s] = %s", cluster.label, config["cluster"][cluster.label])
674 cached_job_values[cluster.label] = {}
676 # Allowing whenSaveJobQgraph and useLazyCommands per cluster label.
677 key = "whenSaveJobQgraph"
678 _, when_save = config.search(key, opt=search_opt)
679 cached_job_values[cluster.label][key] = WhenToSaveQuantumGraphs[when_save.upper()]
681 key = "useLazyCommands"
682 search_opt["default"] = True
683 _, cached_job_values[cluster.label][key] = config.search(key, opt=search_opt)
684 del search_opt["default"]
686 if cluster.label in config["cluster"]:
687 # Don't want to get global defaults here so only look in
688 # cluster section.
689 cached_job_values[cluster.label].update(
690 _get_job_values(config["cluster"][cluster.label], search_opt, "runQuantumCommand")
691 )
692 cluster_job_values = copy.copy(cached_job_values[cluster.label])
694 cluster_job_values["name"] = cluster.name
695 cluster_job_values["label"] = cluster.label
696 cluster_job_values["quanta_counts"] = cluster.quanta_counts
697 cluster_job_values["tags"] = cluster.tags
698 _LOG.debug("cluster_job_values = %s", cluster_job_values)
699 _handle_job_values(cluster_job_values, gwjob, cluster_job_values.keys())
701 # For purposes of whether to continue searching for a value is whether
702 # the value evaluates to False.
703 unset_attributes = {attr for attr in _ATTRS_ALL if not getattr(gwjob, attr)}
705 _LOG.debug("unset_attributes=%s", unset_attributes)
706 _LOG.debug("set=%s", _ATTRS_ALL - unset_attributes)
708 # For job info not defined at cluster level, attempt to get job info
709 # either common or aggregate for all Quanta in cluster.
710 for node_id in iter(cluster.qgraph_node_ids):
711 _LOG.debug("node_id=%s", node_id)
712 qnode = cqgraph.get_quantum_node(node_id)
714 if qnode.taskDef.label not in cached_pipetask_values:
715 search_opt["curvals"] = {"curr_pipetask": qnode.taskDef.label}
716 cached_pipetask_values[qnode.taskDef.label] = _get_job_values(
717 config, search_opt, "runQuantumCommand"
718 )
720 _handle_job_values(cached_pipetask_values[qnode.taskDef.label], gwjob, unset_attributes)
722 # Update job with workflow attribute and profile values.
723 qgraph_gwfile = _get_qgraph_gwfile(
724 config, save_qgraph_per_job, gwjob, generic_workflow.get_file("runQgraphFile"), prefix
725 )
726 butler_gwfile = _get_butler_gwfile(prefix, when_create, butler_config, execution_butler_dir)
728 generic_workflow.add_job(gwjob)
729 generic_workflow.add_job_inputs(gwjob.name, [qgraph_gwfile, butler_gwfile])
731 gwjob.cmdvals["qgraphId"] = cqgraph.qgraph.graphID
732 gwjob.cmdvals["qgraphNodeId"] = ",".join(
733 sorted([f"{node_id}" for node_id in cluster.qgraph_node_ids])
734 )
735 _enhance_command(config, generic_workflow, gwjob, cached_job_values)
737 # If writing per-job QuantumGraph files during TRANSFORM stage,
738 # write it now while in memory.
739 if save_qgraph_per_job == WhenToSaveQuantumGraphs.TRANSFORM:
740 save_qg_subgraph(cqgraph.qgraph, qgraph_gwfile.src_uri, cluster.qgraph_node_ids)
742 # Create job dependencies.
743 for parent in cqgraph.clusters():
744 for child in cqgraph.successors(parent):
745 generic_workflow.add_job_relationships(parent.name, child.name)
747 # Add initial workflow.
748 if config.get("runInit", "{default: False}"):
749 add_workflow_init_nodes(config, cqgraph.qgraph, generic_workflow)
751 generic_workflow.run_attrs.update(
752 {
753 "bps_isjob": "True",
754 "bps_project": config["project"],
755 "bps_campaign": config["campaign"],
756 "bps_run": generic_workflow.name,
757 "bps_operator": config["operator"],
758 "bps_payload": config["payloadName"],
759 "bps_runsite": config["computeSite"],
760 }
761 )
763 # Add final job
764 add_final_job(config, generic_workflow, prefix)
766 return generic_workflow
769def create_generic_workflow_config(config, prefix):
770 """Create generic workflow configuration.
772 Parameters
773 ----------
774 config : `lsst.ctrl.bps.BpsConfig`
775 Bps configuration.
776 prefix : `str`
777 Root path for any output files.
779 Returns
780 -------
781 generic_workflow_config : `lsst.ctrl.bps.BpsConfig`
782 Configuration accompanying the GenericWorkflow.
783 """
784 generic_workflow_config = BpsConfig(config)
785 generic_workflow_config["workflowName"] = config["uniqProcName"]
786 generic_workflow_config["workflowPath"] = prefix
787 return generic_workflow_config
790def add_final_job(config, generic_workflow, prefix):
791 """Add final workflow job depending upon configuration.
793 Parameters
794 ----------
795 config : `lsst.ctrl.bps.BpsConfig`
796 Bps configuration.
797 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
798 Generic workflow to which attributes should be added.
799 prefix : `str`
800 Directory in which to output final script.
801 """
802 _, when_create = config.search(".executionButler.whenCreate")
803 _, when_merge = config.search(".executionButler.whenMerge")
805 search_opt = {"searchobj": config[".executionButler"], "default": None}
806 if when_create.upper() != "NEVER" and when_merge.upper() != "NEVER":
807 # create gwjob
808 gwjob = GenericWorkflowJob("mergeExecutionButler")
809 gwjob.label = "mergeExecutionButler"
811 job_values = _get_job_values(config, search_opt, None)
812 for attr in _ATTRS_ALL:
813 if not getattr(gwjob, attr) and job_values.get(attr, None):
814 setattr(gwjob, attr, job_values[attr])
816 # Create script and add command line to job.
817 gwjob.executable, gwjob.arguments = _create_final_command(config, prefix)
819 # Determine inputs from command line.
820 for file_key in re.findall(r"<FILE:([^>]+)>", gwjob.arguments):
821 gwfile = generic_workflow.get_file(file_key)
822 generic_workflow.add_job_inputs(gwjob.name, gwfile)
824 _enhance_command(config, generic_workflow, gwjob, {})
826 # Put transfer repo job in appropriate location in workflow.
827 if when_merge.upper() == "ALWAYS":
828 # add as special final job
829 generic_workflow.add_final(gwjob)
830 elif when_merge.upper() == "SUCCESS":
831 # add as regular sink node
832 add_final_job_as_sink(generic_workflow, gwjob)
833 else:
834 raise ValueError(f"Invalid value for executionButler.when_merge {when_merge}")
837def _create_final_command(config, prefix):
838 """Create the command and shell script for the final job.
840 Parameters
841 ----------
842 config : `lsst.ctrl.bps.BpsConfig`
843 Bps configuration.
844 prefix : `str`
845 Directory in which to output final script.
847 Returns
848 -------
849 executable : `lsst.ctrl.bps.GenericWorkflowExec`
850 Executable object for the final script.
851 arguments : `str`
852 Command line needed to call the final script.
853 """
854 search_opt = {
855 "replaceVars": False,
856 "replaceEnvVars": False,
857 "expandEnvVars": False,
858 "searchobj": config["executionButler"],
859 }
861 script_file = os.path.join(prefix, "final_job.bash")
862 with open(script_file, "w") as fh:
863 print("#!/bin/bash\n", file=fh)
864 print("set -e", file=fh)
865 print("set -x", file=fh)
867 print("butlerConfig=$1", file=fh)
868 print("executionButlerDir=$2", file=fh)
870 i = 1
871 found, command = config.search(f".executionButler.command{i}", opt=search_opt)
872 while found:
873 # Temporarily replace any env vars so formatter doesn't try to
874 # replace them.
875 command = re.sub(r"\${([^}]+)}", r"<BPSTMP:\1>", command)
877 # executionButlerDir and butlerConfig will be args to script and
878 # set to env vars
879 command = command.replace("{executionButlerDir}", "<BPSTMP:executionButlerDir>")
880 command = command.replace("{butlerConfig}", "<BPSTMP:butlerConfig>")
882 # Replace all other vars in command string
883 search_opt["replaceVars"] = True
884 command = config.formatter.format(command, config, search_opt)
885 search_opt["replaceVars"] = False
887 # Replace any temporary env place holders.
888 command = re.sub(r"<BPSTMP:([^>]+)>", r"${\1}", command)
890 print(command, file=fh)
891 i += 1
892 found, command = config.search(f".executionButler.command{i}", opt=search_opt)
893 os.chmod(script_file, 0o755)
894 executable = GenericWorkflowExec(os.path.basename(script_file), script_file, True)
896 _, orig_butler = config.search("butlerConfig")
897 # The execution butler was saved as butlerConfig in the workflow.
898 return executable, f"{orig_butler} <FILE:butlerConfig>"
901def add_final_job_as_sink(generic_workflow, final_job):
902 """Add final job as the single sink for the workflow.
904 Parameters
905 ----------
906 generic_workflow : `lsst.ctrl.bps.GenericWorkflow`
907 Generic workflow to which attributes should be added.
908 final_job : `lsst.ctrl.bps.GenericWorkflowJob`
909 Job to add as new sink node depending upon all previous sink nodes.
910 """
911 # Find sink nodes of generic workflow graph.
912 gw_sinks = [n for n in generic_workflow if generic_workflow.out_degree(n) == 0]
913 _LOG.debug("gw_sinks = %s", gw_sinks)
915 generic_workflow.add_job(final_job)
916 generic_workflow.add_job_relationships(gw_sinks, final_job.name)