X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/49a841a5179307f0c8d84f647a71f44fb2b4b26d..060d38d627bd1e51dd2b3c6e7de9af6aa7d7b6f3:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 9e76cf711e..4ab65d9d87 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -1,22 +1,29 @@ +# 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, adjustDirObjs +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, packed_workflow, trim_listing +from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location from .fsaccess import CollectionFetcher -from .pathmapper import NoFollowPathMapper +from .pathmapper import NoFollowPathMapper, trim_listing from .perf import Perf logger = logging.getLogger('arvados.cwl-runner') @@ -42,43 +49,53 @@ 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(): - pdh, p, tp, stg = self.pathmapper.mapper(f) - if tp == "Directory" and '/' not in pdh: - mounts[p] = { - "kind": "collection", - "portable_data_hash": pdh[5:] - } - dirs.add(pdh) - - for f in self.pathmapper.files(): - res, p, tp, stg = self.pathmapper.mapper(f) - if res.startswith("keep:"): - res = res[5:] - elif res.startswith("/keep/"): - res = res[6:] - else: + 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 - sp = res.split("/", 1) - pdh = sp[0] - if pdh not in dirs: - mounts[p] = { - "kind": "collection", - "portable_data_hash": pdh - } - if len(sp) == 2: - mounts[p]["path"] = urllib.unquote(sp[1]) + 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"]: @@ -137,11 +154,6 @@ class ArvadosContainer(object): 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 @@ -150,16 +162,41 @@ class ArvadosContainer(object): if runtime_req: if "keep_cache" in runtime_req: 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) @@ -185,6 +222,7 @@ class ArvadosContainer(object): self.output_callback({}, "permanentFail") def done(self, record): + outputs = {} try: container = self.arvrunner.api.containers().get( uuid=record["container_uuid"] @@ -211,7 +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: @@ -238,6 +286,8 @@ class RunnerContainer(Runner): """ 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, @@ -307,6 +357,12 @@ class RunnerContainer(Runner): 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") + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command