X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/47643ae4e47687aa985f0228771579bdc45aa076..9fa635c9dc288317f19471291accecf8690f5718:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 769a63bce3..667f9262f7 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -9,19 +9,21 @@ import urllib import time import datetime import ciso8601 +import uuid import ruamel.yaml as yaml from cwltool.errors import WorkflowException -from cwltool.process import get_feature, UnsupportedRequirement, shortname -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs +from cwltool.process import UnsupportedRequirement, shortname +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class from cwltool.utils import aslist +from cwltool.job import JobBase import arvados.collection from .arvdocker import arv_docker_get_image from . import done -from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location +from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields from .fsaccess import CollectionFetcher from .pathmapper import NoFollowPathMapper, trim_listing from .perf import Perf @@ -29,10 +31,18 @@ from .perf import Perf logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') -class ArvadosContainer(object): +class ArvadosContainer(JobBase): """Submit and manage a Crunch container request for executing a CWL CommandLineTool.""" - def __init__(self, runner): + def __init__(self, runner, + builder, # type: Builder + joborder, # type: Dict[Text, Union[Dict[Text, Any], List, Text]] + make_path_mapper, # type: Callable[..., PathMapper] + requirements, # type: List[Dict[Text, Text]] + hints, # type: List[Dict[Text, Text]] + name # type: Text + ): + super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name) self.arvrunner = runner self.running = False self.uuid = None @@ -40,19 +50,34 @@ class ArvadosContainer(object): def update_pipeline_component(self, r): pass - def run(self, dry_run=False, pull_image=True, **kwargs): + def run(self, runtimeContext): + # ArvadosCommandTool subclasses from cwltool.CommandLineTool, + # which calls makeJobRunner() to get a new ArvadosContainer + # object. The fields that define execution such as + # command_line, environment, etc are set on the + # ArvadosContainer object by CommandLineTool.job() before + # run() is called. + container_request = { "command": self.command_line, - "owner_uuid": self.arvrunner.project_uuid, "name": self.name, "output_path": self.outdir, "cwd": self.outdir, - "priority": 1, + "priority": runtimeContext.priority, "state": "Committed", "properties": {}, } runtime_constraints = {} + if self.arvrunner.project_uuid: + container_request["owner_uuid"] = self.arvrunner.project_uuid + + if self.arvrunner.secret_store.has_secret(self.command_line): + raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets") + + if self.arvrunner.secret_store.has_secret(self.environment): + raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets") + resources = self.builder.resources if resources is not None: runtime_constraints["vcpus"] = resources.get("cores", 1) @@ -68,6 +93,7 @@ class ArvadosContainer(object): "capacity": resources.get("tmpdirSize", 0) * 2**20 } } + secret_mounts = {} scheduling_parameters = {} rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files] @@ -105,27 +131,55 @@ class ArvadosContainer(object): generatemapper = NoFollowPathMapper([self.generatefiles], "", "", separateDirs=False) + sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target) + + logger.debug("generatemapper is %s", sorteditems) + with Perf(metrics, "createfiles %s" % self.name): - for f, p in generatemapper.items(): + for f, p in sorteditems: if not p.target: pass - elif p.type in ("File", "Directory"): - source, path = self.arvrunner.fs_access.get_collection(p.resolved) - vwd.copy(path, p.target, source_collection=source) + elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"): + if p.resolved.startswith("_:"): + vwd.mkdirs(p.target) + else: + source, path = self.arvrunner.fs_access.get_collection(p.resolved) + vwd.copy(path, p.target, source_collection=source) elif p.type == "CreateFile": - with vwd.open(p.target, "w") as n: - n.write(p.resolved.encode("utf-8")) + if self.arvrunner.secret_store.has_secret(p.resolved): + secret_mounts["%s/%s" % (self.outdir, p.target)] = { + "kind": "text", + "content": self.arvrunner.secret_store.retrieve(p.resolved) + } + else: + with vwd.open(p.target, "w") as n: + n.write(p.resolved.encode("utf-8")) + + def keepemptydirs(p): + if isinstance(p, arvados.collection.RichCollectionBase): + if len(p) == 0: + p.open(".keep", "w").close() + else: + for c in p: + keepemptydirs(p[c]) + + keepemptydirs(vwd) with Perf(metrics, "generatefiles.save_new %s" % self.name): vwd.save_new() - for f, p in generatemapper.items(): - if not p.target: + prev = None + for f, p in sorteditems: + if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or + (prev is not None and p.target.startswith(prev))): continue mountpoint = "%s/%s" % (self.outdir, p.target) mounts[mountpoint] = {"kind": "collection", "portable_data_hash": vwd.portable_data_hash(), "path": p.target} + if p.type.startswith("Writable"): + mounts[mountpoint]["writable"] = True + prev = p.target + "/" container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir} if self.environment: @@ -145,20 +199,20 @@ class ArvadosContainer(object): mounts["stdout"] = {"kind": "file", "path": "%s/%s" % (self.outdir, self.stdout)} - (docker_req, docker_is_req) = get_feature(self, "DockerRequirement") + (docker_req, docker_is_req) = self.get_requirement("DockerRequirement") if not docker_req: docker_req = {"dockerImageId": "arvados/jobs"} container_request["container_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, - pull_image, + runtimeContext.pull_image, self.arvrunner.project_uuid) - api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement") + api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement") if api_req: runtime_constraints["API"] = True - runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints") + runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints") if runtime_req: if "keep_cache" in runtime_req: runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20 @@ -172,49 +226,57 @@ class ArvadosContainer(object): "writable": True } - partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement") + partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement") if partition_req: scheduling_parameters["partitions"] = aslist(partition_req["partition"]) - intermediate_output_req, _ = get_feature(self, "http://arvados.org/cwl#IntermediateOutput") + intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput") if intermediate_output_req: self.output_ttl = intermediate_output_req["outputTTL"] else: self.output_ttl = self.arvrunner.intermediate_output_ttl if self.output_ttl < 0: - raise WorkflowError("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"]) + raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"]) container_request["output_ttl"] = self.output_ttl container_request["mounts"] = mounts + container_request["secret_mounts"] = secret_mounts container_request["runtime_constraints"] = runtime_constraints container_request["scheduling_parameters"] = scheduling_parameters - enable_reuse = kwargs.get("enable_reuse", True) + enable_reuse = runtimeContext.enable_reuse if enable_reuse: - reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement") + reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement") if reuse_req: enable_reuse = reuse_req["enableReuse"] container_request["use_existing"] = enable_reuse - if kwargs.get("runnerjob", "").startswith("arvwf:"): - wfuuid = kwargs["runnerjob"][6:kwargs["runnerjob"].index("#")] + if runtimeContext.runnerjob.startswith("arvwf:"): + wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")] wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries) if container_request["name"] == "main": container_request["name"] = wfrecord["name"] container_request["properties"]["template_uuid"] = wfuuid + self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback) + try: - response = self.arvrunner.api.container_requests().create( - body=container_request - ).execute(num_retries=self.arvrunner.num_retries) + if runtimeContext.submit_request_uuid: + response = self.arvrunner.api.container_requests().update( + uuid=runtimeContext.submit_request_uuid, + body=container_request + ).execute(num_retries=self.arvrunner.num_retries) + else: + response = self.arvrunner.api.container_requests().create( + body=container_request + ).execute(num_retries=self.arvrunner.num_retries) self.uuid = response["uuid"] - self.arvrunner.processes[self.uuid] = self + self.arvrunner.process_submitted(self) if response["state"] == "Final": logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"]) - self.done(response) else: logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"]) except Exception as e: @@ -247,7 +309,7 @@ class ArvadosContainer(object): api_client=self.arvrunner.api, keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) - done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self)) + done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40) if record["output_uuid"]: if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl: @@ -271,14 +333,12 @@ class ArvadosContainer(object): processStatus = "permanentFail" finally: self.output_callback(outputs, processStatus) - if record["uuid"] in self.arvrunner.processes: - del self.arvrunner.processes[record["uuid"]] class RunnerContainer(Runner): """Submit and manage a container that runs arvados-cwl-runner.""" - def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs): + def arvados_job_spec(self, runtimeContext): """Create an Arvados container request for this workflow. The returned dict can be used to create a container passed as @@ -286,15 +346,24 @@ class RunnerContainer(Runner): """ adjustDirObjs(self.job_order, trim_listing) - adjustFileObjs(self.job_order, trim_anonymous_location) - adjustDirObjs(self.job_order, trim_anonymous_location) + visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location) + visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields) + + secret_mounts = {} + for param in sorted(self.job_order.keys()): + if self.secret_store.has_secret(self.job_order[param]): + mnt = "/secrets/s%d" % len(secret_mounts) + secret_mounts[mnt] = { + "kind": "text", + "content": self.secret_store.retrieve(self.job_order[param]) + } + self.job_order[param] = {"$include": mnt} container_req = { - "owner_uuid": self.arvrunner.project_uuid, "name": self.name, "output_path": "/var/spool/cwl", "cwd": "/var/spool/cwl", - "priority": 1, + "priority": self.priority, "state": "Committed", "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image), "mounts": { @@ -311,11 +380,13 @@ class RunnerContainer(Runner): "writable": True } }, + "secret_mounts": secret_mounts, "runtime_constraints": { "vcpus": 1, "ram": 1024*1024 * self.submit_runner_ram, "API": True }, + "use_existing": self.enable_reuse, "properties": {} } @@ -329,7 +400,7 @@ class RunnerContainer(Runner): "portable_data_hash": "%s" % workflowcollection } else: - packed = packed_workflow(self.arvrunner, self.tool) + packed = packed_workflow(self.arvrunner, self.tool, self.merged_map) workflowpath = "/var/lib/cwl/workflow.json#main" container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", @@ -338,7 +409,23 @@ class RunnerContainer(Runner): if self.tool.tool.get("id", "").startswith("arvwf:"): container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33] - command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps"] + + # --local means execute the workflow instead of submitting a container request + # --api=containers means use the containers API + # --no-log-timestamps means don't add timestamps (the logging infrastructure does this) + # --disable-validate because we already validated so don't need to do it again + # --eval-timeout is the timeout for javascript invocation + # --parallel-task-count is the number of threads to use for job submission + # --enable/disable-reuse sets desired job reuse + command = ["arvados-cwl-runner", + "--local", + "--api=containers", + "--no-log-timestamps", + "--disable-validate", + "--eval-timeout=%s" % self.arvrunner.eval_timeout, + "--thread-count=%s" % self.arvrunner.thread_count, + "--enable-reuse" if self.enable_reuse else "--disable-reuse"] + if self.output_name: command.append("--output-name=" + self.output_name) container_req["output_name"] = self.output_name @@ -346,13 +433,11 @@ class RunnerContainer(Runner): if self.output_tags: command.append("--output-tags=" + self.output_tags) - if kwargs.get("debug"): + if runtimeContext.debug: command.append("--debug") - if self.enable_reuse: - command.append("--enable-reuse") - else: - command.append("--disable-reuse") + if runtimeContext.storage_classes != "default": + command.append("--storage-classes=" + runtimeContext.storage_classes) if self.on_error: command.append("--on-error=" + self.on_error) @@ -373,23 +458,27 @@ class RunnerContainer(Runner): return container_req - def run(self, *args, **kwargs): - kwargs["keepprefix"] = "keep:" - job_spec = self.arvados_job_spec(*args, **kwargs) - job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid) + def run(self, runtimeContext): + runtimeContext.keepprefix = "keep:" + job_spec = self.arvados_job_spec(runtimeContext) + if self.arvrunner.project_uuid: + job_spec["owner_uuid"] = self.arvrunner.project_uuid - response = self.arvrunner.api.container_requests().create( - body=job_spec - ).execute(num_retries=self.arvrunner.num_retries) + if runtimeContext.submit_request_uuid: + response = self.arvrunner.api.container_requests().update( + uuid=runtimeContext.submit_request_uuid, + body=job_spec + ).execute(num_retries=self.arvrunner.num_retries) + else: + response = self.arvrunner.api.container_requests().create( + body=job_spec + ).execute(num_retries=self.arvrunner.num_retries) self.uuid = response["uuid"] - self.arvrunner.processes[self.uuid] = self + self.arvrunner.process_submitted(self) logger.info("%s submitted container %s", self.arvrunner.label(self), response["uuid"]) - if response["state"] == "Final": - self.done(response) - def done(self, record): try: container = self.arvrunner.api.containers().get( @@ -400,6 +489,3 @@ class RunnerContainer(Runner): self.arvrunner.output_callback({}, "permanentFail") else: super(RunnerContainer, self).done(container) - finally: - if record["uuid"] in self.arvrunner.processes: - del self.arvrunner.processes[record["uuid"]]