1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
15 from arvados_cwl.util import get_current_container, get_intermediate_collection_info
16 import ruamel.yaml as yaml
18 from cwltool.errors import WorkflowException
19 from cwltool.process import UnsupportedRequirement, shortname
20 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
21 from cwltool.utils import aslist
22 from cwltool.job import JobBase
24 import arvados.collection
26 from .arvdocker import arv_docker_get_image
28 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
29 from .fsaccess import CollectionFetcher
30 from .pathmapper import NoFollowPathMapper, trim_listing
31 from .perf import Perf
33 logger = logging.getLogger('arvados.cwl-runner')
34 metrics = logging.getLogger('arvados.cwl-runner.metrics')
36 class ArvadosContainer(JobBase):
37 """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
39 def __init__(self, runner,
40 builder, # type: Builder
41 joborder, # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
42 make_path_mapper, # type: Callable[..., PathMapper]
43 requirements, # type: List[Dict[Text, Text]]
44 hints, # type: List[Dict[Text, Text]]
47 super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
48 self.arvrunner = runner
52 def update_pipeline_component(self, r):
55 def run(self, runtimeContext):
56 # ArvadosCommandTool subclasses from cwltool.CommandLineTool,
57 # which calls makeJobRunner() to get a new ArvadosContainer
58 # object. The fields that define execution such as
59 # command_line, environment, etc are set on the
60 # ArvadosContainer object by CommandLineTool.job() before
64 "command": self.command_line,
66 "output_path": self.outdir,
68 "priority": runtimeContext.priority,
72 runtime_constraints = {}
74 if self.arvrunner.project_uuid:
75 container_request["owner_uuid"] = self.arvrunner.project_uuid
77 if self.arvrunner.secret_store.has_secret(self.command_line):
78 raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
80 if self.arvrunner.secret_store.has_secret(self.environment):
81 raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets")
83 resources = self.builder.resources
84 if resources is not None:
85 runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
86 runtime_constraints["ram"] = math.ceil(resources.get("ram") * 2**20)
91 "capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
95 "capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
99 scheduling_parameters = {}
101 rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
102 rf.sort(key=lambda k: k.resolved)
104 for resolved, target, tp, stg in rf:
107 if prevdir and target.startswith(prevdir):
109 if tp == "Directory":
112 targetdir = os.path.dirname(target)
113 sp = resolved.split("/", 1)
114 pdh = sp[0][5:] # remove "keep:"
115 mounts[targetdir] = {
116 "kind": "collection",
117 "portable_data_hash": pdh
120 if tp == "Directory":
123 path = os.path.dirname(sp[1])
124 if path and path != "/":
125 mounts[targetdir]["path"] = path
126 prevdir = targetdir + "/"
128 with Perf(metrics, "generatefiles %s" % self.name):
129 if self.generatefiles["listing"]:
130 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
131 keep_client=self.arvrunner.keep_client,
132 num_retries=self.arvrunner.num_retries)
133 generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
136 sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target)
138 logger.debug("generatemapper is %s", sorteditems)
140 with Perf(metrics, "createfiles %s" % self.name):
141 for f, p in sorteditems:
144 elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
145 if p.resolved.startswith("_:"):
148 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
149 vwd.copy(path, p.target, source_collection=source)
150 elif p.type == "CreateFile":
151 if self.arvrunner.secret_store.has_secret(p.resolved):
152 secret_mounts["%s/%s" % (self.outdir, p.target)] = {
154 "content": self.arvrunner.secret_store.retrieve(p.resolved)
157 with vwd.open(p.target, "w") as n:
158 n.write(p.resolved.encode("utf-8"))
160 def keepemptydirs(p):
161 if isinstance(p, arvados.collection.RichCollectionBase):
163 p.open(".keep", "w").close()
170 if not runtimeContext.current_container:
171 runtimeContext.current_container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
172 info = get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
173 vwd.save_new(name=info["name"],
174 owner_uuid=self.arvrunner.project_uuid,
175 ensure_unique_name=True,
176 trash_at=info["trash_at"],
177 properties=info["properties"])
180 for f, p in sorteditems:
181 if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
182 (prev is not None and p.target.startswith(prev))):
184 mountpoint = "%s/%s" % (self.outdir, p.target)
185 mounts[mountpoint] = {"kind": "collection",
186 "portable_data_hash": vwd.portable_data_hash(),
188 if p.type.startswith("Writable"):
189 mounts[mountpoint]["writable"] = True
190 prev = p.target + "/"
192 container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
194 container_request["environment"].update(self.environment)
197 sp = self.stdin[6:].split("/", 1)
198 mounts["stdin"] = {"kind": "collection",
199 "portable_data_hash": sp[0],
203 mounts["stderr"] = {"kind": "file",
204 "path": "%s/%s" % (self.outdir, self.stderr)}
207 mounts["stdout"] = {"kind": "file",
208 "path": "%s/%s" % (self.outdir, self.stdout)}
210 (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
212 docker_req = {"dockerImageId": "arvados/jobs"}
214 container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
216 runtimeContext.pull_image,
217 self.arvrunner.project_uuid,
218 runtimeContext.submit_runner_cluster)
220 api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
222 runtime_constraints["API"] = True
224 runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
226 if "keep_cache" in runtime_req:
227 runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
228 if "outputDirType" in runtime_req:
229 if runtime_req["outputDirType"] == "local_output_dir":
230 # Currently the default behavior.
232 elif runtime_req["outputDirType"] == "keep_output_dir":
233 mounts[self.outdir]= {
234 "kind": "collection",
238 partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
240 scheduling_parameters["partitions"] = aslist(partition_req["partition"])
242 intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
243 if intermediate_output_req:
244 self.output_ttl = intermediate_output_req["outputTTL"]
246 self.output_ttl = self.arvrunner.intermediate_output_ttl
248 if self.output_ttl < 0:
249 raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
251 if self.timelimit is not None:
252 scheduling_parameters["max_run_time"] = self.timelimit
254 extra_submit_params = {}
255 cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget")
256 if cluster_target_req:
257 cluster_id = cluster_target_req.get("clusterID")
259 extra_submit_params["cluster_id"] = cluster_id
260 if cluster_target_req.get("ownerUUID"):
261 container_request["owner_uuid"] = cluster_target_req.get("ownerUUID")
263 container_request["output_name"] = "Output for step %s" % (self.name)
264 container_request["output_ttl"] = self.output_ttl
265 container_request["mounts"] = mounts
266 container_request["secret_mounts"] = secret_mounts
267 container_request["runtime_constraints"] = runtime_constraints
268 container_request["scheduling_parameters"] = scheduling_parameters
270 enable_reuse = runtimeContext.enable_reuse
272 reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
274 enable_reuse = reuse_req["enableReuse"]
275 container_request["use_existing"] = enable_reuse
277 if runtimeContext.runnerjob.startswith("arvwf:"):
278 wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
279 wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
280 if container_request["name"] == "main":
281 container_request["name"] = wfrecord["name"]
282 container_request["properties"]["template_uuid"] = wfuuid
284 self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
287 if runtimeContext.submit_request_uuid:
288 response = self.arvrunner.api.container_requests().update(
289 uuid=runtimeContext.submit_request_uuid,
290 body=container_request,
291 **extra_submit_params
292 ).execute(num_retries=self.arvrunner.num_retries)
294 response = self.arvrunner.api.container_requests().create(
295 body=container_request,
296 **extra_submit_params
297 ).execute(num_retries=self.arvrunner.num_retries)
299 self.uuid = response["uuid"]
300 self.arvrunner.process_submitted(self)
302 if response["state"] == "Final":
303 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
305 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
306 except Exception as e:
307 logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
308 self.output_callback({}, "permanentFail")
310 def done(self, record):
313 container = self.arvrunner.api.containers().get(
314 uuid=record["container_uuid"]
315 ).execute(num_retries=self.arvrunner.num_retries)
316 if container["state"] == "Complete":
317 rcode = container["exit_code"]
318 if self.successCodes and rcode in self.successCodes:
319 processStatus = "success"
320 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
321 processStatus = "temporaryFail"
322 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
323 processStatus = "permanentFail"
325 processStatus = "success"
327 processStatus = "permanentFail"
329 processStatus = "permanentFail"
331 if processStatus == "permanentFail":
332 logc = arvados.collection.CollectionReader(container["log"],
333 api_client=self.arvrunner.api,
334 keep_client=self.arvrunner.keep_client,
335 num_retries=self.arvrunner.num_retries)
336 label = self.arvrunner.label(self)
339 "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
341 if record["output_uuid"]:
342 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
343 # Compute the trash time to avoid requesting the collection record.
344 trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
345 aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
346 orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
347 oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
348 logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
349 self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
350 self.arvrunner.add_intermediate_output(record["output_uuid"])
352 if container["output"]:
353 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
354 except WorkflowException as e:
355 logger.error("%s unable to collect output from %s:\n%s",
356 self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
357 processStatus = "permanentFail"
358 except Exception as e:
359 logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
360 processStatus = "permanentFail"
362 self.output_callback(outputs, processStatus)
365 class RunnerContainer(Runner):
366 """Submit and manage a container that runs arvados-cwl-runner."""
368 def arvados_job_spec(self, runtimeContext):
369 """Create an Arvados container request for this workflow.
371 The returned dict can be used to create a container passed as
372 the +body+ argument to container_requests().create().
375 adjustDirObjs(self.job_order, trim_listing)
376 visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
377 visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
380 for param in sorted(self.job_order.keys()):
381 if self.secret_store.has_secret(self.job_order[param]):
382 mnt = "/secrets/s%d" % len(secret_mounts)
383 secret_mounts[mnt] = {
385 "content": self.secret_store.retrieve(self.job_order[param])
387 self.job_order[param] = {"$include": mnt}
391 "output_path": "/var/spool/cwl",
392 "cwd": "/var/spool/cwl",
393 "priority": self.priority,
394 "state": "Committed",
395 "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
397 "/var/lib/cwl/cwl.input.json": {
399 "content": self.job_order
403 "path": "/var/spool/cwl/cwl.output.json"
406 "kind": "collection",
410 "secret_mounts": secret_mounts,
411 "runtime_constraints": {
412 "vcpus": math.ceil(self.submit_runner_cores),
413 "ram": math.ceil(1024*1024 * self.submit_runner_ram),
416 "use_existing": self.enable_reuse,
420 if self.tool.tool.get("id", "").startswith("keep:"):
421 sp = self.tool.tool["id"].split('/')
422 workflowcollection = sp[0][5:]
423 workflowname = "/".join(sp[1:])
424 workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
425 container_req["mounts"]["/var/lib/cwl/workflow"] = {
426 "kind": "collection",
427 "portable_data_hash": "%s" % workflowcollection
430 packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
431 workflowpath = "/var/lib/cwl/workflow.json#main"
432 container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
436 if self.tool.tool.get("id", "").startswith("arvwf:"):
437 container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33]
440 # --local means execute the workflow instead of submitting a container request
441 # --api=containers means use the containers API
442 # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
443 # --disable-validate because we already validated so don't need to do it again
444 # --eval-timeout is the timeout for javascript invocation
445 # --parallel-task-count is the number of threads to use for job submission
446 # --enable/disable-reuse sets desired job reuse
447 command = ["arvados-cwl-runner",
450 "--no-log-timestamps",
451 "--disable-validate",
452 "--eval-timeout=%s" % self.arvrunner.eval_timeout,
453 "--thread-count=%s" % self.arvrunner.thread_count,
454 "--enable-reuse" if self.enable_reuse else "--disable-reuse"]
457 command.append("--output-name=" + self.output_name)
458 container_req["output_name"] = self.output_name
461 command.append("--output-tags=" + self.output_tags)
463 if runtimeContext.debug:
464 command.append("--debug")
466 if runtimeContext.storage_classes != "default":
467 command.append("--storage-classes=" + runtimeContext.storage_classes)
470 command.append("--on-error=" + self.on_error)
472 if self.intermediate_output_ttl:
473 command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
475 if self.arvrunner.trash_intermediate:
476 command.append("--trash-intermediate")
478 if self.arvrunner.project_uuid:
479 command.append("--project-uuid="+self.arvrunner.project_uuid)
481 command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
483 container_req["command"] = command
488 def run(self, runtimeContext):
489 runtimeContext.keepprefix = "keep:"
490 job_spec = self.arvados_job_spec(runtimeContext)
491 if self.arvrunner.project_uuid:
492 job_spec["owner_uuid"] = self.arvrunner.project_uuid
494 extra_submit_params = {}
495 if runtimeContext.submit_runner_cluster:
496 extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
498 if runtimeContext.submit_request_uuid:
499 response = self.arvrunner.api.container_requests().update(
500 uuid=runtimeContext.submit_request_uuid,
502 **extra_submit_params
503 ).execute(num_retries=self.arvrunner.num_retries)
505 response = self.arvrunner.api.container_requests().create(
507 **extra_submit_params
508 ).execute(num_retries=self.arvrunner.num_retries)
510 self.uuid = response["uuid"]
511 self.arvrunner.process_submitted(self)
513 logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
515 def done(self, record):
517 container = self.arvrunner.api.containers().get(
518 uuid=record["container_uuid"]
519 ).execute(num_retries=self.arvrunner.num_retries)
520 except Exception as e:
521 logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
522 self.arvrunner.output_callback({}, "permanentFail")
524 super(RunnerContainer, self).done(container)