sdk/cwl/arvados_cwl/arvcontainer.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 import logging
   6 import json
   7 import os
   8 import urllib.request, urllib.parse, urllib.error
   9 import time
  10 import datetime
  11 import ciso8601
  12 import uuid
  13 import math
  14 import re
  15
  16 import arvados_cwl.util
  17 import ruamel.yaml
  18
  19 from cwltool.errors import WorkflowException
  20 from cwltool.process import UnsupportedRequirement, shortname
  21 from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class
  22 from cwltool.job import JobBase
  23
  24 import arvados.collection
  25
  26 import crunchstat_summary.summarizer
  27 import crunchstat_summary.reader
  28
  29 from .arvdocker import arv_docker_get_image
  30 from . import done
  31 from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields, make_builder
  32 from .fsaccess import CollectionFetcher
  33 from .pathmapper import NoFollowPathMapper, trim_listing
  34 from .perf import Perf
  35 from ._version import __version__
  36
  37 logger = logging.getLogger('arvados.cwl-runner')
  38 metrics = logging.getLogger('arvados.cwl-runner.metrics')
  39
  40 def cleanup_name_for_collection(name):
  41     return name.replace("/", " ")
  42
  43 class ArvadosContainer(JobBase):
  44     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
  45
  46     def __init__(self, runner, job_runtime, globpatterns,
  47                  builder,   # type: Builder
  48                  joborder,  # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
  49                  make_path_mapper,  # type: Callable[..., PathMapper]
  50                  requirements,      # type: List[Dict[Text, Text]]
  51                  hints,     # type: List[Dict[Text, Text]]
  52                  name       # type: Text
  53     ):
  54         super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
  55         self.arvrunner = runner
  56         self.job_runtime = job_runtime
  57         self.running = False
  58         self.uuid = None
  59         self.attempt_count = 0
  60         self.globpatterns = globpatterns
  61
  62     def update_pipeline_component(self, r):
  63         pass
  64
  65     def _required_env(self):
  66         env = {}
  67         env["HOME"] = self.outdir
  68         env["TMPDIR"] = self.tmpdir
  69         return env
  70
  71     def run(self, toplevelRuntimeContext):
  72         # ArvadosCommandTool subclasses from cwltool.CommandLineTool,
  73         # which calls makeJobRunner() to get a new ArvadosContainer
  74         # object.  The fields that define execution such as
  75         # command_line, environment, etc are set on the
  76         # ArvadosContainer object by CommandLineTool.job() before
  77         # run() is called.
  78
  79         runtimeContext = self.job_runtime
  80
  81         if runtimeContext.submit_request_uuid:
  82             container_request = self.arvrunner.api.container_requests().get(
  83                 uuid=runtimeContext.submit_request_uuid
  84             ).execute(num_retries=self.arvrunner.num_retries)
  85         else:
  86             container_request = {}
  87
  88         container_request["command"] = self.command_line
  89         container_request["name"] = self.name
  90         container_request["output_path"] = self.outdir
  91         container_request["cwd"] = self.outdir
  92         container_request["priority"] = runtimeContext.priority
  93         container_request["state"] = "Uncommitted"
  94         container_request.setdefault("properties", {})
  95
  96         container_request["properties"]["cwl_input"] = self.joborder
  97
  98         runtime_constraints = {}
  99
 100         if runtimeContext.project_uuid:
 101             container_request["owner_uuid"] = runtimeContext.project_uuid
 102
 103         if self.arvrunner.secret_store.has_secret(self.command_line):
 104             raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
 105
 106         if self.arvrunner.secret_store.has_secret(self.environment):
 107             raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets")
 108
 109         resources = self.builder.resources
 110         if resources is not None:
 111             runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
 112             runtime_constraints["ram"] = math.ceil(resources.get("ram") * 2**20)
 113
 114         mounts = {
 115             self.outdir: {
 116                 "kind": "tmp",
 117                 "capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
 118             },
 119             self.tmpdir: {
 120                 "kind": "tmp",
 121                 "capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
 122             }
 123         }
 124         secret_mounts = {}
 125         scheduling_parameters = {}
 126
 127         rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
 128         rf.sort(key=lambda k: k.resolved)
 129         prevdir = None
 130         for resolved, target, tp, stg in rf:
 131             if not stg:
 132                 continue
 133             if prevdir and target.startswith(prevdir):
 134                 continue
 135             if tp == "Directory":
 136                 targetdir = target
 137             else:
 138                 targetdir = os.path.dirname(target)
 139             sp = resolved.split("/", 1)
 140             pdh = sp[0][5:]   # remove "keep:"
 141             mounts[targetdir] = {
 142                 "kind": "collection",
 143                 "portable_data_hash": pdh
 144             }
 145             if pdh in self.pathmapper.pdh_to_uuid:
 146                 mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
 147             if len(sp) == 2:
 148                 if tp == "Directory":
 149                     path = sp[1]
 150                 else:
 151                     path = os.path.dirname(sp[1])
 152                 if path and path != "/":
 153                     mounts[targetdir]["path"] = path
 154             prevdir = targetdir + "/"
 155
 156         intermediate_collection_info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
 157
 158         with Perf(metrics, "generatefiles %s" % self.name):
 159             if self.generatefiles["listing"]:
 160                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
 161                                                     keep_client=self.arvrunner.keep_client,
 162                                                     num_retries=self.arvrunner.num_retries)
 163                 generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
 164                                                     separateDirs=False)
 165
 166                 sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target)
 167
 168                 logger.debug("generatemapper is %s", sorteditems)
 169
 170                 with Perf(metrics, "createfiles %s" % self.name):
 171                     for f, p in sorteditems:
 172                         if not p.target:
 173                             continue
 174
 175                         if p.target.startswith("/"):
 176                             dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 177                         else:
 178                             dst = p.target
 179
 180                         if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
 181                             if p.resolved.startswith("_:"):
 182                                 vwd.mkdirs(dst)
 183                             else:
 184                                 source, path = self.arvrunner.fs_access.get_collection(p.resolved)
 185                                 vwd.copy(path or ".", dst, source_collection=source)
 186                         elif p.type == "CreateFile":
 187                             if self.arvrunner.secret_store.has_secret(p.resolved):
 188                                 mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 189                                 secret_mounts[mountpoint] = {
 190                                     "kind": "text",
 191                                     "content": self.arvrunner.secret_store.retrieve(p.resolved)
 192                                 }
 193                             else:
 194                                 with vwd.open(dst, "w") as n:
 195                                     n.write(p.resolved)
 196
 197                 def keepemptydirs(p):
 198                     if isinstance(p, arvados.collection.RichCollectionBase):
 199                         if len(p) == 0:
 200                             p.open(".keep", "w").close()
 201                         else:
 202                             for c in p:
 203                                 keepemptydirs(p[c])
 204
 205                 keepemptydirs(vwd)
 206
 207                 if not runtimeContext.current_container:
 208                     runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
 209                 vwd.save_new(name=intermediate_collection_info["name"],
 210                              owner_uuid=runtimeContext.project_uuid,
 211                              ensure_unique_name=True,
 212                              trash_at=intermediate_collection_info["trash_at"],
 213                              properties=intermediate_collection_info["properties"])
 214
 215                 prev = None
 216                 for f, p in sorteditems:
 217                     if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or
 218                         (prev is not None and p.target.startswith(prev))):
 219                         continue
 220                     if p.target.startswith("/"):
 221                         dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
 222                     else:
 223                         dst = p.target
 224                     mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
 225                     mounts[mountpoint] = {"kind": "collection",
 226                                           "portable_data_hash": vwd.portable_data_hash(),
 227                                           "path": dst}
 228                     if p.type.startswith("Writable"):
 229                         mounts[mountpoint]["writable"] = True
 230                     prev = p.target + "/"
 231
 232         container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
 233         if self.environment:
 234             container_request["environment"].update(self.environment)
 235
 236         if self.stdin:
 237             sp = self.stdin[6:].split("/", 1)
 238             mounts["stdin"] = {"kind": "collection",
 239                                 "portable_data_hash": sp[0],
 240                                 "path": sp[1]}
 241
 242         if self.stderr:
 243             mounts["stderr"] = {"kind": "file",
 244                                 "path": "%s/%s" % (self.outdir, self.stderr)}
 245
 246         if self.stdout:
 247             mounts["stdout"] = {"kind": "file",
 248                                 "path": "%s/%s" % (self.outdir, self.stdout)}
 249
 250         (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
 251
 252         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
 253                                                                     docker_req,
 254                                                                     runtimeContext.pull_image,
 255                                                                     runtimeContext)
 256
 257         network_req, _ = self.get_requirement("NetworkAccess")
 258         if network_req:
 259             runtime_constraints["API"] = network_req["networkAccess"]
 260
 261         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
 262         if api_req:
 263             runtime_constraints["API"] = True
 264
 265         use_disk_cache = (self.arvrunner.api.config()["Containers"].get("DefaultKeepCacheRAM", 0) == 0)
 266
 267         keep_cache_type_req, _ = self.get_requirement("http://arvados.org/cwl#KeepCacheTypeRequirement")
 268         if keep_cache_type_req:
 269             if "keepCacheType" in keep_cache_type_req:
 270                 if keep_cache_type_req["keepCacheType"] == "ram_cache":
 271                     use_disk_cache = False
 272
 273         runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
 274         if runtime_req:
 275             if "keep_cache" in runtime_req:
 276                 if use_disk_cache:
 277                     # If DefaultKeepCacheRAM is zero it means we should use disk cache.
 278                     runtime_constraints["keep_cache_disk"] = math.ceil(runtime_req["keep_cache"] * 2**20)
 279                 else:
 280                     runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
 281             if "outputDirType" in runtime_req:
 282                 if runtime_req["outputDirType"] == "local_output_dir":
 283                     # Currently the default behavior.
 284                     pass
 285                 elif runtime_req["outputDirType"] == "keep_output_dir":
 286                     mounts[self.outdir]= {
 287                         "kind": "collection",
 288                         "writable": True
 289                     }
 290
 291         partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
 292         if partition_req:
 293             scheduling_parameters["partitions"] = aslist(partition_req["partition"])
 294
 295         intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
 296         if intermediate_output_req:
 297             self.output_ttl = intermediate_output_req["outputTTL"]
 298         else:
 299             self.output_ttl = self.arvrunner.intermediate_output_ttl
 300
 301         if self.output_ttl < 0:
 302             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 303
 304
 305         if self.arvrunner.api._rootDesc["revision"] >= "20210628":
 306             storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
 307             if storage_class_req and storage_class_req.get("intermediateStorageClass"):
 308                 container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
 309             else:
 310                 container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
 311
 312         cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement")
 313         if cuda_req:
 314             runtime_constraints["cuda"] = {
 315                 "device_count": resources.get("cudaDeviceCount", 1),
 316                 "driver_version": cuda_req["cudaVersionMin"],
 317                 "hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0]
 318             }
 319
 320         if runtimeContext.enable_preemptible is False:
 321             scheduling_parameters["preemptible"] = False
 322         else:
 323             preemptible_req, _ = self.get_requirement("http://arvados.org/cwl#UsePreemptible")
 324             if preemptible_req:
 325                 scheduling_parameters["preemptible"] = preemptible_req["usePreemptible"]
 326             elif runtimeContext.enable_preemptible is True:
 327                 scheduling_parameters["preemptible"] = True
 328             elif runtimeContext.enable_preemptible is None:
 329                 pass
 330
 331         if self.timelimit is not None and self.timelimit > 0:
 332             scheduling_parameters["max_run_time"] = self.timelimit
 333
 334         extra_submit_params = {}
 335         if runtimeContext.submit_runner_cluster:
 336             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 337
 338         container_request["output_name"] = cleanup_name_for_collection("Output from step %s" % (self.name))
 339         container_request["output_ttl"] = self.output_ttl
 340         container_request["mounts"] = mounts
 341         container_request["secret_mounts"] = secret_mounts
 342         container_request["runtime_constraints"] = runtime_constraints
 343         container_request["scheduling_parameters"] = scheduling_parameters
 344
 345         enable_reuse = runtimeContext.enable_reuse
 346         if enable_reuse:
 347             reuse_req, _ = self.get_requirement("WorkReuse")
 348             if reuse_req:
 349                 enable_reuse = reuse_req["enableReuse"]
 350             reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
 351             if reuse_req:
 352                 enable_reuse = reuse_req["enableReuse"]
 353         container_request["use_existing"] = enable_reuse
 354
 355         properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
 356         if properties_req:
 357             for pr in properties_req["processProperties"]:
 358                 container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 359
 360         output_properties_req, _ = self.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
 361         if output_properties_req:
 362             if self.arvrunner.api._rootDesc["revision"] >= "20220510":
 363                 container_request["output_properties"] = {}
 364                 for pr in output_properties_req["outputProperties"]:
 365                     container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 366             else:
 367                 logger.warning("%s API revision is %s, revision %s is required to support setting properties on output collections.",
 368                                self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510")
 369
 370         if self.arvrunner.api._rootDesc["revision"] >= "20240502" and self.globpatterns:
 371             output_glob = []
 372             for gb in self.globpatterns:
 373                 gb = self.builder.do_eval(gb)
 374                 if not gb:
 375                     continue
 376                 for gbeval in aslist(gb):
 377                     if gbeval.startswith(self.outdir+"/"):
 378                         gbeval = gbeval[len(self.outdir)+1:]
 379                     if gbeval in (self.outdir, "", "."):
 380                         output_glob.append("**")
 381                     else:
 382                         output_glob.append(gbeval)
 383                         output_glob.append(gbeval + "/**")
 384
 385             if "**" in output_glob:
 386                 # if it's going to match all, prefer not to provide it
 387                 # at all.
 388                 output_glob.clear()
 389
 390             if output_glob:
 391                 # Tools should either use cwl.output.json or output
 392                 # binding glob. Unfortunately one CWL conformance test
 393                 # has both, but that test uses cwl.output.json return
 394                 # a string, not a File.
 395                 #
 396                 # It could happen that a tool uses cwl.output.json,
 397                 # references a file, but also uses a glob, and that
 398                 # would break, because we don't know about it ahead of
 399                 # time.  However I don't think any conformance tests
 400                 # do this and I'd even be inclined to rule that out of
 401                 # order in the CWL spec if it came up.
 402                 output_glob.append("cwl.output.json")
 403                 container_request["output_glob"] = output_glob
 404
 405         ram_multiplier = [1]
 406
 407         oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
 408         if oom_retry_req:
 409             if oom_retry_req.get('memoryRetryMultiplier'):
 410                 ram_multiplier.append(oom_retry_req.get('memoryRetryMultiplier'))
 411             elif oom_retry_req.get('memoryRetryMultipler'):
 412                 ram_multiplier.append(oom_retry_req.get('memoryRetryMultipler'))
 413             else:
 414                 ram_multiplier.append(2)
 415
 416         if runtimeContext.runnerjob.startswith("arvwf:"):
 417             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 418             wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
 419             if container_request["name"] == "main":
 420                 container_request["name"] = wfrecord["name"]
 421             container_request["properties"]["template_uuid"] = wfuuid
 422
 423         if self.attempt_count == 0:
 424             self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
 425
 426         try:
 427             ram = runtime_constraints["ram"]
 428
 429             self.uuid = runtimeContext.submit_request_uuid
 430
 431             for i in ram_multiplier:
 432                 runtime_constraints["ram"] = ram * i
 433
 434                 if self.uuid:
 435                     response = self.arvrunner.api.container_requests().update(
 436                         uuid=self.uuid,
 437                         body=container_request,
 438                         **extra_submit_params
 439                     ).execute(num_retries=self.arvrunner.num_retries)
 440                 else:
 441                     response = self.arvrunner.api.container_requests().create(
 442                         body=container_request,
 443                         **extra_submit_params
 444                     ).execute(num_retries=self.arvrunner.num_retries)
 445                     self.uuid = response["uuid"]
 446
 447                 if response["container_uuid"] is not None:
 448                     break
 449
 450             if response["container_uuid"] is None:
 451                 runtime_constraints["ram"] = ram * ram_multiplier[self.attempt_count]
 452
 453             container_request["state"] = "Committed"
 454             response = self.arvrunner.api.container_requests().update(
 455                 uuid=self.uuid,
 456                 body=container_request,
 457                 **extra_submit_params
 458             ).execute(num_retries=self.arvrunner.num_retries)
 459
 460             self.arvrunner.process_submitted(self)
 461             self.attempt_count += 1
 462
 463             if response["state"] == "Final":
 464                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
 465             else:
 466                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
 467         except Exception as e:
 468             logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
 469             logger.debug("Container request was %s", container_request)
 470             self.output_callback({}, "permanentFail")
 471
 472     def out_of_memory_retry(self, record, container):
 473         oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
 474         if oom_retry_req is None:
 475             return False
 476
 477         # Sometimes it gets killed with no warning
 478         if container["exit_code"] == 137:
 479             return True
 480
 481         logc = arvados.collection.CollectionReader(record["log_uuid"],
 482                                                    api_client=self.arvrunner.api,
 483                                                    keep_client=self.arvrunner.keep_client,
 484                                                    num_retries=self.arvrunner.num_retries)
 485
 486         loglines = [""]
 487         def callback(v1, v2, v3):
 488             loglines[0] = v3
 489
 490         done.logtail(logc, callback, "", maxlen=1000)
 491
 492         # Check allocation failure
 493         oom_matches = oom_retry_req.get('memoryErrorRegex') or r'(bad_alloc|out ?of ?memory|memory ?error|container using over 9.% of memory)'
 494         if re.search(oom_matches, loglines[0], re.IGNORECASE | re.MULTILINE):
 495             return True
 496
 497         return False
 498
 499     def done(self, record):
 500         outputs = {}
 501         retried = False
 502         rcode = None
 503         try:
 504             container = self.arvrunner.api.containers().get(
 505                 uuid=record["container_uuid"]
 506             ).execute(num_retries=self.arvrunner.num_retries)
 507             if container["state"] == "Complete":
 508                 rcode = container["exit_code"]
 509                 if self.successCodes and rcode in self.successCodes:
 510                     processStatus = "success"
 511                 elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
 512                     processStatus = "temporaryFail"
 513                 elif self.permanentFailCodes and rcode in self.permanentFailCodes:
 514                     processStatus = "permanentFail"
 515                 elif rcode == 0:
 516                     processStatus = "success"
 517                 else:
 518                     processStatus = "permanentFail"
 519
 520                 if processStatus == "permanentFail" and self.attempt_count == 1 and self.out_of_memory_retry(record, container):
 521                     logger.warning("%s Container failed with out of memory error, retrying with more RAM.",
 522                                  self.arvrunner.label(self))
 523                     self.job_runtime.submit_request_uuid = None
 524                     self.uuid = None
 525                     self.run(None)
 526                     retried = True
 527                     return
 528
 529                 if rcode == 137:
 530                     logger.warning("%s Container may have been killed for using too much RAM.  Try resubmitting with a higher 'ramMin' or use the arv:OutOfMemoryRetry feature.",
 531                                  self.arvrunner.label(self))
 532             else:
 533                 processStatus = "permanentFail"
 534
 535             logc = None
 536             if record["log_uuid"]:
 537                 logc = arvados.collection.Collection(record["log_uuid"],
 538                                                      api_client=self.arvrunner.api,
 539                                                      keep_client=self.arvrunner.keep_client,
 540                                                      num_retries=self.arvrunner.num_retries)
 541
 542             if processStatus == "permanentFail" and logc is not None:
 543                 label = self.arvrunner.label(self)
 544                 done.logtail(
 545                     logc, logger.error,
 546                     "%s (%s) error log:" % (label, record["uuid"]), maxlen=40, include_crunchrun=(rcode is None or rcode > 127))
 547
 548             if record["output_uuid"]:
 549                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
 550                     # Compute the trash time to avoid requesting the collection record.
 551                     trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
 552                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
 553                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
 554                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
 555                     logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
 556                         self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
 557                 self.arvrunner.add_intermediate_output(record["output_uuid"])
 558
 559             if container["output"]:
 560                 outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
 561
 562             properties = record["properties"].copy()
 563             properties["cwl_output"] = outputs
 564             self.arvrunner.api.container_requests().update(
 565                 uuid=self.uuid,
 566                 body={"container_request": {"properties": properties}}
 567             ).execute(num_retries=self.arvrunner.num_retries)
 568
 569             if logc is not None and self.job_runtime.enable_usage_report is not False:
 570                 try:
 571                     summarizer = crunchstat_summary.summarizer.ContainerRequestSummarizer(
 572                         record,
 573                         collection_object=logc,
 574                         label=self.name,
 575                         arv=self.arvrunner.api)
 576                     summarizer.run()
 577                     with logc.open("usage_report.html", "wt") as mr:
 578                         mr.write(summarizer.html_report())
 579                     logc.save()
 580
 581                     # Post warnings about nodes that are under-utilized.
 582                     for rc in summarizer._recommend_gen(lambda x: x):
 583                         self.job_runtime.usage_report_notes.append(rc)
 584
 585                 except Exception as e:
 586                     logger.warning("%s unable to generate resource usage report",
 587                                  self.arvrunner.label(self),
 588                                  exc_info=(e if self.arvrunner.debug else False))
 589
 590         except WorkflowException as e:
 591             # Only include a stack trace if in debug mode.
 592             # A stack trace may obfuscate more useful output about the workflow.
 593             logger.error("%s unable to collect output from %s:\n%s",
 594                          self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
 595             processStatus = "permanentFail"
 596         except Exception:
 597             logger.exception("%s while getting output object:", self.arvrunner.label(self))
 598             processStatus = "permanentFail"
 599         finally:
 600             if not retried:
 601                 self.output_callback(outputs, processStatus)
 602
 603
 604 class RunnerContainer(Runner):
 605     """Submit and manage a container that runs arvados-cwl-runner."""
 606
 607     def arvados_job_spec(self, runtimeContext, git_info):
 608         """Create an Arvados container request for this workflow.
 609
 610         The returned dict can be used to create a container passed as
 611         the +body+ argument to container_requests().create().
 612         """
 613
 614         adjustDirObjs(self.job_order, trim_listing)
 615         visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
 616         visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 617
 618         secret_mounts = {}
 619         for param in sorted(self.job_order.keys()):
 620             if self.secret_store.has_secret(self.job_order[param]):
 621                 mnt = "/secrets/s%d" % len(secret_mounts)
 622                 secret_mounts[mnt] = {
 623                     "kind": "text",
 624                     "content": self.secret_store.retrieve(self.job_order[param])
 625                 }
 626                 self.job_order[param] = {"$include": mnt}
 627
 628         container_image = arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext)
 629
 630         workflow_runner_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#WorkflowRunnerResources")
 631         if workflow_runner_req and workflow_runner_req.get("acrContainerImage"):
 632             container_image = workflow_runner_req.get("acrContainerImage")
 633
 634         container_req = {
 635             "name": self.name,
 636             "output_path": "/var/spool/cwl",
 637             "cwd": "/var/spool/cwl",
 638             "priority": self.priority,
 639             "state": "Committed",
 640             "container_image": container_image,
 641             "mounts": {
 642                 "/var/lib/cwl/cwl.input.json": {
 643                     "kind": "json",
 644                     "content": self.job_order
 645                 },
 646                 "stdout": {
 647                     "kind": "file",
 648                     "path": "/var/spool/cwl/cwl.output.json"
 649                 },
 650                 "/var/spool/cwl": {
 651                     "kind": "collection",
 652                     "writable": True
 653                 }
 654             },
 655             "secret_mounts": secret_mounts,
 656             "runtime_constraints": {
 657                 "vcpus": math.ceil(self.submit_runner_cores),
 658                 "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
 659                 "API": True
 660             },
 661             "use_existing": self.reuse_runner,
 662             "properties": {}
 663         }
 664
 665         if self.embedded_tool.tool.get("id", "").startswith("keep:"):
 666             sp = self.embedded_tool.tool["id"].split('/')
 667             workflowcollection = sp[0][5:]
 668             workflowname = "/".join(sp[1:])
 669             workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
 670             container_req["mounts"]["/var/lib/cwl/workflow"] = {
 671                 "kind": "collection",
 672                 "portable_data_hash": "%s" % workflowcollection
 673             }
 674         elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
 675             uuid, frg = urllib.parse.urldefrag(self.embedded_tool.tool["id"])
 676             workflowpath = "/var/lib/cwl/workflow.json#" + frg
 677             packedtxt = self.loadingContext.loader.fetch_text(uuid)
 678             yaml = ruamel.yaml.YAML(typ='safe', pure=True)
 679             packed = yaml.load(packedtxt)
 680             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 681                 "kind": "json",
 682                 "content": packed
 683             }
 684             container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 685         elif self.embedded_tool.tool.get("id", "").startswith("file:"):
 686             raise WorkflowException("Tool id '%s' is a local file but expected keep: or arvwf:" % self.embedded_tool.tool.get("id"))
 687         else:
 688             main = self.loadingContext.loader.idx["_:main"]
 689             if main.get("id") == "_:main":
 690                 del main["id"]
 691             workflowpath = "/var/lib/cwl/workflow.json#main"
 692             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
 693                 "kind": "json",
 694                 "content": main
 695             }
 696
 697         container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
 698
 699         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
 700         if properties_req:
 701             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
 702             for pr in properties_req["processProperties"]:
 703                 container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 704
 705         # --local means execute the workflow instead of submitting a container request
 706         # --api=containers means use the containers API
 707         # --no-log-timestamps means don't add timestamps (the logging infrastructure does this)
 708         # --disable-validate because we already validated so don't need to do it again
 709         # --eval-timeout is the timeout for javascript invocation
 710         # --parallel-task-count is the number of threads to use for job submission
 711         # --enable/disable-reuse sets desired job reuse
 712         # --collection-cache-size sets aside memory to store collections
 713         command = ["arvados-cwl-runner",
 714                    "--local",
 715                    "--api=containers",
 716                    "--no-log-timestamps",
 717                    "--disable-validate",
 718                    "--disable-color",
 719                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
 720                    "--thread-count=%s" % self.arvrunner.thread_count,
 721                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
 722                    "--collection-cache-size=%s" % self.collection_cache_size]
 723
 724         if self.output_name:
 725             command.append("--output-name=" + self.output_name)
 726             container_req["output_name"] = self.output_name
 727
 728         if self.output_tags:
 729             command.append("--output-tags=" + self.output_tags)
 730
 731         if runtimeContext.debug:
 732             command.append("--debug")
 733
 734         if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes:
 735             command.append("--storage-classes=" + runtimeContext.storage_classes)
 736
 737         if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
 738             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 739
 740         if runtimeContext.on_error:
 741             command.append("--on-error=" + self.on_error)
 742
 743         if runtimeContext.intermediate_output_ttl:
 744             command.append("--intermediate-output-ttl=%d" % runtimeContext.intermediate_output_ttl)
 745
 746         if runtimeContext.trash_intermediate:
 747             command.append("--trash-intermediate")
 748
 749         if runtimeContext.project_uuid:
 750             command.append("--project-uuid="+runtimeContext.project_uuid)
 751
 752         if self.enable_dev:
 753             command.append("--enable-dev")
 754
 755         if runtimeContext.enable_preemptible is True:
 756             command.append("--enable-preemptible")
 757
 758         if runtimeContext.enable_preemptible is False:
 759             command.append("--disable-preemptible")
 760
 761         if runtimeContext.varying_url_params:
 762             command.append("--varying-url-params="+runtimeContext.varying_url_params)
 763
 764         if runtimeContext.prefer_cached_downloads:
 765             command.append("--prefer-cached-downloads")
 766
 767         if runtimeContext.enable_usage_report is True:
 768             command.append("--enable-usage-report")
 769
 770         if runtimeContext.enable_usage_report is False:
 771             command.append("--disable-usage-report")
 772
 773         if self.fast_parser:
 774             command.append("--fast-parser")
 775
 776         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 777
 778         container_req["command"] = command
 779
 780         return container_req
 781
 782
 783     def run(self, runtimeContext):
 784         runtimeContext.keepprefix = "keep:"
 785         job_spec = self.arvados_job_spec(runtimeContext, self.git_info)
 786         if runtimeContext.project_uuid:
 787             job_spec["owner_uuid"] = runtimeContext.project_uuid
 788
 789         extra_submit_params = {}
 790         if runtimeContext.submit_runner_cluster:
 791             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 792
 793         if runtimeContext.submit_request_uuid:
 794             if "cluster_id" in extra_submit_params:
 795                 # Doesn't make sense for "update" and actually fails
 796                 del extra_submit_params["cluster_id"]
 797             response = self.arvrunner.api.container_requests().update(
 798                 uuid=runtimeContext.submit_request_uuid,
 799                 body=job_spec,
 800                 **extra_submit_params
 801             ).execute(num_retries=self.arvrunner.num_retries)
 802         else:
 803             response = self.arvrunner.api.container_requests().create(
 804                 body=job_spec,
 805                 **extra_submit_params
 806             ).execute(num_retries=self.arvrunner.num_retries)
 807
 808         self.uuid = response["uuid"]
 809         self.arvrunner.process_submitted(self)
 810
 811         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 812
 813         workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
 814         if workbench2:
 815             url = "{}processes/{}".format(workbench2, response["uuid"])
 816             logger.info("Monitor workflow progress at %s", url)
 817
 818
 819     def done(self, record):
 820         try:
 821             container = self.arvrunner.api.containers().get(
 822                 uuid=record["container_uuid"]
 823             ).execute(num_retries=self.arvrunner.num_retries)
 824             container["log"] = record["log_uuid"]
 825         except Exception:
 826             logger.exception("%s while getting runner container", self.arvrunner.label(self))
 827             self.arvrunner.output_callback({}, "permanentFail")
 828         else:
 829             super(RunnerContainer, self).done(container)