1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
13 import ruamel.yaml as yaml
15 from cwltool.errors import WorkflowException
16 from cwltool.process import get_feature, UnsupportedRequirement, shortname
17 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
18 from cwltool.utils import aslist
20 import arvados.collection
22 from .arvdocker import arv_docker_get_image
24 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
25 from .fsaccess import CollectionFetcher
26 from .pathmapper import NoFollowPathMapper, trim_listing
27 from .perf import Perf
29 logger = logging.getLogger('arvados.cwl-runner')
30 metrics = logging.getLogger('arvados.cwl-runner.metrics')
32 class ArvadosContainer(object):
33 """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
35 def __init__(self, runner):
36 self.arvrunner = runner
40 def update_pipeline_component(self, r):
43 def run(self, dry_run=False, pull_image=True, **kwargs):
45 "command": self.command_line,
46 "owner_uuid": self.arvrunner.project_uuid,
48 "output_path": self.outdir,
54 runtime_constraints = {}
56 resources = self.builder.resources
57 if resources is not None:
58 runtime_constraints["vcpus"] = resources.get("cores", 1)
59 runtime_constraints["ram"] = resources.get("ram") * 2**20
64 "capacity": resources.get("outdirSize", 0) * 2**20
68 "capacity": resources.get("tmpdirSize", 0) * 2**20
71 scheduling_parameters = {}
73 rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
74 rf.sort(key=lambda k: k.resolved)
76 for resolved, target, tp, stg in rf:
79 if prevdir and target.startswith(prevdir):
84 targetdir = os.path.dirname(target)
85 sp = resolved.split("/", 1)
86 pdh = sp[0][5:] # remove "keep:"
89 "portable_data_hash": pdh
95 path = os.path.dirname(sp[1])
96 if path and path != "/":
97 mounts[targetdir]["path"] = path
98 prevdir = targetdir + "/"
100 with Perf(metrics, "generatefiles %s" % self.name):
101 if self.generatefiles["listing"]:
102 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
103 keep_client=self.arvrunner.keep_client,
104 num_retries=self.arvrunner.num_retries)
105 generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
108 logger.debug("generatemapper is %s", generatemapper._pathmap)
110 with Perf(metrics, "createfiles %s" % self.name):
111 for f, p in generatemapper.items():
114 elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
115 if p.resolved.startswith("_:"):
118 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
119 vwd.copy(path, p.target, source_collection=source)
120 elif p.type == "CreateFile":
121 with vwd.open(p.target, "w") as n:
122 n.write(p.resolved.encode("utf-8"))
124 def keepemptydirs(p):
125 if isinstance(p, arvados.collection.RichCollectionBase):
127 p.open(".keep", "w").close()
134 with Perf(metrics, "generatefiles.save_new %s" % self.name):
137 for f, p in generatemapper.items():
140 mountpoint = "%s/%s" % (self.outdir, p.target)
141 mounts[mountpoint] = {"kind": "collection",
142 "portable_data_hash": vwd.portable_data_hash(),
144 if p.type.startswith("Writable"):
145 mounts[mountpoint]["writable"] = True
147 container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
149 container_request["environment"].update(self.environment)
152 sp = self.stdin[6:].split("/", 1)
153 mounts["stdin"] = {"kind": "collection",
154 "portable_data_hash": sp[0],
158 mounts["stderr"] = {"kind": "file",
159 "path": "%s/%s" % (self.outdir, self.stderr)}
162 mounts["stdout"] = {"kind": "file",
163 "path": "%s/%s" % (self.outdir, self.stdout)}
165 (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
167 docker_req = {"dockerImageId": "arvados/jobs"}
169 container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
172 self.arvrunner.project_uuid)
174 api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement")
176 runtime_constraints["API"] = True
178 runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
180 if "keep_cache" in runtime_req:
181 runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20
182 if "outputDirType" in runtime_req:
183 if runtime_req["outputDirType"] == "local_output_dir":
184 # Currently the default behavior.
186 elif runtime_req["outputDirType"] == "keep_output_dir":
187 mounts[self.outdir]= {
188 "kind": "collection",
192 partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
194 scheduling_parameters["partitions"] = aslist(partition_req["partition"])
196 intermediate_output_req, _ = get_feature(self, "http://arvados.org/cwl#IntermediateOutput")
197 if intermediate_output_req:
198 self.output_ttl = intermediate_output_req["outputTTL"]
200 self.output_ttl = self.arvrunner.intermediate_output_ttl
202 if self.output_ttl < 0:
203 raise WorkflowError("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
205 container_request["output_ttl"] = self.output_ttl
206 container_request["mounts"] = mounts
207 container_request["runtime_constraints"] = runtime_constraints
208 container_request["scheduling_parameters"] = scheduling_parameters
210 enable_reuse = kwargs.get("enable_reuse", True)
212 reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement")
214 enable_reuse = reuse_req["enableReuse"]
215 container_request["use_existing"] = enable_reuse
217 if kwargs.get("runnerjob", "").startswith("arvwf:"):
218 wfuuid = kwargs["runnerjob"][6:kwargs["runnerjob"].index("#")]
219 wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
220 if container_request["name"] == "main":
221 container_request["name"] = wfrecord["name"]
222 container_request["properties"]["template_uuid"] = wfuuid
225 response = self.arvrunner.api.container_requests().create(
226 body=container_request
227 ).execute(num_retries=self.arvrunner.num_retries)
229 self.uuid = response["uuid"]
230 self.arvrunner.processes[self.uuid] = self
232 if response["state"] == "Final":
233 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
236 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
237 except Exception as e:
238 logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
239 self.output_callback({}, "permanentFail")
241 def done(self, record):
244 container = self.arvrunner.api.containers().get(
245 uuid=record["container_uuid"]
246 ).execute(num_retries=self.arvrunner.num_retries)
247 if container["state"] == "Complete":
248 rcode = container["exit_code"]
249 if self.successCodes and rcode in self.successCodes:
250 processStatus = "success"
251 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
252 processStatus = "temporaryFail"
253 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
254 processStatus = "permanentFail"
256 processStatus = "success"
258 processStatus = "permanentFail"
260 processStatus = "permanentFail"
262 if processStatus == "permanentFail":
263 logc = arvados.collection.CollectionReader(container["log"],
264 api_client=self.arvrunner.api,
265 keep_client=self.arvrunner.keep_client,
266 num_retries=self.arvrunner.num_retries)
267 done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
269 if record["output_uuid"]:
270 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
271 # Compute the trash time to avoid requesting the collection record.
272 trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
273 aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
274 orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
275 oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
276 logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
277 self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
278 self.arvrunner.add_intermediate_output(record["output_uuid"])
280 if container["output"]:
281 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
282 except WorkflowException as e:
283 logger.error("%s unable to collect output from %s:\n%s",
284 self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
285 processStatus = "permanentFail"
286 except Exception as e:
287 logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
288 processStatus = "permanentFail"
290 self.output_callback(outputs, processStatus)
291 if record["uuid"] in self.arvrunner.processes:
292 del self.arvrunner.processes[record["uuid"]]
295 class RunnerContainer(Runner):
296 """Submit and manage a container that runs arvados-cwl-runner."""
298 def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
299 """Create an Arvados container request for this workflow.
301 The returned dict can be used to create a container passed as
302 the +body+ argument to container_requests().create().
305 adjustDirObjs(self.job_order, trim_listing)
306 visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
307 visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
310 "owner_uuid": self.arvrunner.project_uuid,
312 "output_path": "/var/spool/cwl",
313 "cwd": "/var/spool/cwl",
315 "state": "Committed",
316 "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
318 "/var/lib/cwl/cwl.input.json": {
320 "content": self.job_order
324 "path": "/var/spool/cwl/cwl.output.json"
327 "kind": "collection",
331 "runtime_constraints": {
333 "ram": 1024*1024 * self.submit_runner_ram,
336 "use_existing": self.enable_reuse,
340 if self.tool.tool.get("id", "").startswith("keep:"):
341 sp = self.tool.tool["id"].split('/')
342 workflowcollection = sp[0][5:]
343 workflowname = "/".join(sp[1:])
344 workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
345 container_req["mounts"]["/var/lib/cwl/workflow"] = {
346 "kind": "collection",
347 "portable_data_hash": "%s" % workflowcollection
350 packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
351 workflowpath = "/var/lib/cwl/workflow.json#main"
352 container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
356 if self.tool.tool.get("id", "").startswith("arvwf:"):
357 container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33]
360 command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps"]
362 command.append("--output-name=" + self.output_name)
363 container_req["output_name"] = self.output_name
366 command.append("--output-tags=" + self.output_tags)
368 if kwargs.get("debug"):
369 command.append("--debug")
371 if self.enable_reuse:
372 command.append("--enable-reuse")
374 command.append("--disable-reuse")
377 command.append("--on-error=" + self.on_error)
379 if self.intermediate_output_ttl:
380 command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
382 if self.arvrunner.trash_intermediate:
383 command.append("--trash-intermediate")
385 if self.arvrunner.project_uuid:
386 command.append("--project-uuid="+self.arvrunner.project_uuid)
388 command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
390 container_req["command"] = command
395 def run(self, *args, **kwargs):
396 kwargs["keepprefix"] = "keep:"
397 job_spec = self.arvados_job_spec(*args, **kwargs)
398 job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
400 response = self.arvrunner.api.container_requests().create(
402 ).execute(num_retries=self.arvrunner.num_retries)
404 self.uuid = response["uuid"]
405 self.arvrunner.processes[self.uuid] = self
407 logger.info("%s submitted container %s", self.arvrunner.label(self), response["uuid"])
409 if response["state"] == "Final":
412 def done(self, record):
414 container = self.arvrunner.api.containers().get(
415 uuid=record["container_uuid"]
416 ).execute(num_retries=self.arvrunner.num_retries)
417 except Exception as e:
418 logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
419 self.arvrunner.output_callback({}, "permanentFail")
421 super(RunnerContainer, self).done(container)
423 if record["uuid"] in self.arvrunner.processes:
424 del self.arvrunner.processes[record["uuid"]]