X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6599088b45103087b4be743fd51a8330e694e57f..47643ae4e47687aa985f0228771579bdc45aa076:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index c1e1a26b1b..769a63bce3 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -1,22 +1,33 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + import logging import json import os +import urllib +import time +import datetime +import ciso8601 import ruamel.yaml as yaml from cwltool.errors import WorkflowException from cwltool.process import get_feature, UnsupportedRequirement, shortname -from cwltool.pathmapper import adjustFiles +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs from cwltool.utils import aslist import arvados.collection from .arvdocker import arv_docker_get_image from . import done -from .runner import Runner, arvados_jobs_image +from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location from .fsaccess import CollectionFetcher +from .pathmapper import NoFollowPathMapper, trim_listing +from .perf import Perf logger = logging.getLogger('arvados.cwl-runner') +metrics = logging.getLogger('arvados.cwl-runner.metrics') class ArvadosContainer(object): """Submit and manage a Crunch container request for executing a CWL CommandLineTool.""" @@ -38,45 +49,97 @@ class ArvadosContainer(object): "cwd": self.outdir, "priority": 1, "state": "Committed", - "properties": {} + "properties": {}, } runtime_constraints = {} + + resources = self.builder.resources + if resources is not None: + runtime_constraints["vcpus"] = resources.get("cores", 1) + runtime_constraints["ram"] = resources.get("ram") * 2**20 + mounts = { self.outdir: { - "kind": "tmp" + "kind": "tmp", + "capacity": resources.get("outdirSize", 0) * 2**20 + }, + self.tmpdir: { + "kind": "tmp", + "capacity": resources.get("tmpdirSize", 0) * 2**20 } } scheduling_parameters = {} - dirs = set() - for f in self.pathmapper.files(): - _, p, tp = self.pathmapper.mapper(f) - if tp == "Directory" and '/' not in p[6:]: - mounts[p] = { - "kind": "collection", - "portable_data_hash": p[6:] - } - dirs.add(p[6:]) - for f in self.pathmapper.files(): - _, p, tp = self.pathmapper.mapper(f) - if p[6:].split("/")[0] not in dirs: - mounts[p] = { - "kind": "collection", - "portable_data_hash": p[6:] - } - - if self.generatefiles["listing"]: - raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers") + rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files] + rf.sort(key=lambda k: k.resolved) + prevdir = None + for resolved, target, tp, stg in rf: + if not stg: + continue + if prevdir and target.startswith(prevdir): + continue + if tp == "Directory": + targetdir = target + else: + targetdir = os.path.dirname(target) + sp = resolved.split("/", 1) + pdh = sp[0][5:] # remove "keep:" + mounts[targetdir] = { + "kind": "collection", + "portable_data_hash": pdh + } + if len(sp) == 2: + if tp == "Directory": + path = sp[1] + else: + path = os.path.dirname(sp[1]) + if path and path != "/": + mounts[targetdir]["path"] = path + prevdir = targetdir + "/" + + with Perf(metrics, "generatefiles %s" % self.name): + if self.generatefiles["listing"]: + vwd = arvados.collection.Collection(api_client=self.arvrunner.api, + keep_client=self.arvrunner.keep_client, + num_retries=self.arvrunner.num_retries) + generatemapper = NoFollowPathMapper([self.generatefiles], "", "", + separateDirs=False) + + with Perf(metrics, "createfiles %s" % self.name): + for f, p in generatemapper.items(): + 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 == "CreateFile": + with vwd.open(p.target, "w") as n: + n.write(p.resolved.encode("utf-8")) + + with Perf(metrics, "generatefiles.save_new %s" % self.name): + vwd.save_new() + + for f, p in generatemapper.items(): + if not p.target: + continue + mountpoint = "%s/%s" % (self.outdir, p.target) + mounts[mountpoint] = {"kind": "collection", + "portable_data_hash": vwd.portable_data_hash(), + "path": p.target} container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir} if self.environment: container_request["environment"].update(self.environment) if self.stdin: - raise UnsupportedRequirement("Stdin redirection currently not suppported") + sp = self.stdin[6:].split("/", 1) + mounts["stdin"] = {"kind": "collection", + "portable_data_hash": sp[0], + "path": sp[1]} if self.stderr: - raise UnsupportedRequirement("Stderr redirection currently not suppported") + mounts["stderr"] = {"kind": "file", + "path": "%s/%s" % (self.outdir, self.stderr)} if self.stdout: mounts["stdout"] = {"kind": "file", @@ -84,18 +147,13 @@ class ArvadosContainer(object): (docker_req, docker_is_req) = get_feature(self, "DockerRequirement") if not docker_req: - docker_req = {"dockerImageId": arvados_jobs_image(self.arvrunner)} + docker_req = {"dockerImageId": "arvados/jobs"} container_request["container_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid) - resources = self.builder.resources - if resources is not None: - runtime_constraints["vcpus"] = resources.get("cores", 1) - runtime_constraints["ram"] = resources.get("ram") * 2**20 - api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement") if api_req: runtime_constraints["API"] = True @@ -103,17 +161,42 @@ class ArvadosContainer(object): runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints") if runtime_req: if "keep_cache" in runtime_req: - runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] + runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20 + if "outputDirType" in runtime_req: + if runtime_req["outputDirType"] == "local_output_dir": + # Currently the default behavior. + pass + elif runtime_req["outputDirType"] == "keep_output_dir": + mounts[self.outdir]= { + "kind": "collection", + "writable": True + } partition_req, _ = get_feature(self, "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") + 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"]) + + container_request["output_ttl"] = self.output_ttl container_request["mounts"] = mounts container_request["runtime_constraints"] = runtime_constraints - container_request["use_existing"] = kwargs.get("enable_reuse", True) container_request["scheduling_parameters"] = scheduling_parameters + enable_reuse = kwargs.get("enable_reuse", True) + if enable_reuse: + reuse_req, _ = get_feature(self, "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("#")] wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries) @@ -129,15 +212,17 @@ class ArvadosContainer(object): self.uuid = response["uuid"] self.arvrunner.processes[self.uuid] = self - logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"]) - 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: logger.error("%s got error %s" % (self.arvrunner.label(self), str(e))) self.output_callback({}, "permanentFail") def done(self, record): + outputs = {} try: container = self.arvrunner.api.containers().get( uuid=record["container_uuid"] @@ -164,7 +249,17 @@ class ArvadosContainer(object): num_retries=self.arvrunner.num_retries) done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self)) - outputs = {} + if record["output_uuid"]: + if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl: + # Compute the trash time to avoid requesting the collection record. + trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl) + aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else "" + orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else "" + oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else "" + logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % ( + self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete)) + self.arvrunner.add_intermediate_output(record["output_uuid"]) + if container["output"]: outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep") except WorkflowException as e: @@ -173,10 +268,9 @@ class ArvadosContainer(object): processStatus = "permanentFail" except Exception as e: logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e) - self.output_callback({}, "permanentFail") - else: - self.output_callback(outputs, processStatus) + processStatus = "permanentFail" finally: + self.output_callback(outputs, processStatus) if record["uuid"] in self.arvrunner.processes: del self.arvrunner.processes[record["uuid"]] @@ -191,7 +285,9 @@ class RunnerContainer(Runner): the +body+ argument to container_requests().create(). """ - workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs) + adjustDirObjs(self.job_order, trim_listing) + adjustFileObjs(self.job_order, trim_anonymous_location) + adjustDirObjs(self.job_order, trim_anonymous_location) container_req = { "owner_uuid": self.arvrunner.project_uuid, @@ -200,7 +296,7 @@ class RunnerContainer(Runner): "cwd": "/var/spool/cwl", "priority": 1, "state": "Committed", - "container_image": arvados_jobs_image(self.arvrunner), + "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image), "mounts": { "/var/lib/cwl/cwl.input.json": { "kind": "json", @@ -223,27 +319,24 @@ class RunnerContainer(Runner): "properties": {} } - workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1] - if workflowcollection.startswith("keep:"): - workflowcollection = workflowcollection[5:workflowcollection.index('/')] - workflowname = os.path.basename(self.tool.tool["id"]) + if self.tool.tool.get("id", "").startswith("keep:"): + sp = self.tool.tool["id"].split('/') + workflowcollection = sp[0][5:] + workflowname = "/".join(sp[1:]) workflowpath = "/var/lib/cwl/workflow/%s" % workflowname container_req["mounts"]["/var/lib/cwl/workflow"] = { "kind": "collection", "portable_data_hash": "%s" % workflowcollection - } - elif workflowcollection.startswith("arvwf:"): + } + else: + packed = packed_workflow(self.arvrunner, self.tool) workflowpath = "/var/lib/cwl/workflow.json#main" - wfuuid = workflowcollection[6:workflowcollection.index("#")] - wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries) - wfobj = yaml.safe_load(wfrecord["definition"]) - if container_req["name"].startswith("arvwf:"): - container_req["name"] = wfrecord["name"] container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", - "json": wfobj + "content": packed } - container_req["properties"]["template_uuid"] = wfuuid + 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"] if self.output_name: @@ -261,6 +354,18 @@ class RunnerContainer(Runner): else: command.append("--disable-reuse") + if self.on_error: + command.append("--on-error=" + self.on_error) + + if self.intermediate_output_ttl: + command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl) + + if self.arvrunner.trash_intermediate: + command.append("--trash-intermediate") + + if self.arvrunner.project_uuid: + command.append("--project-uuid="+self.arvrunner.project_uuid) + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command