X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/be4852ec32e5eeed1af9a62017cfc39ed66ac186..6f6ce90eb894bde190fd7522cbec037fe61fc25c:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 657d5927d0..78086ed0cc 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -1,20 +1,27 @@ +# 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 adjustFileObjs, adjustDirObjs +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class 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_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 @@ -42,15 +49,23 @@ 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" + "kind": "tmp", + "capacity": resources.get("tmpdirSize", 0) * 2**20 } } scheduling_parameters = {} @@ -139,11 +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 @@ -152,16 +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) @@ -187,6 +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"] @@ -213,7 +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: @@ -240,8 +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) + visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location) + visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields) container_req = { "owner_uuid": self.arvrunner.project_uuid, @@ -311,6 +357,15 @@ 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") + + 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