X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d738b8c32940af71462b8aac9bbfdbbc0f2f2642..0516059abae641ed8a1e95581d070c71f3e943d3:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index f1ae65fc0f..ae3c668895 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -2,10 +2,14 @@ # # SPDX-License-Identifier: Apache-2.0 +from future import standard_library +standard_library.install_aliases() +from builtins import str + import logging import json import os -import urllib +import urllib.request, urllib.parse, urllib.error import time import datetime import ciso8601 @@ -17,18 +21,18 @@ import ruamel.yaml as yaml from cwltool.errors import WorkflowException from cwltool.process import UnsupportedRequirement, shortname -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class -from cwltool.utils import aslist +from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class 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, remove_redundant_fields +from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields, make_builder from .fsaccess import CollectionFetcher from .pathmapper import NoFollowPathMapper, trim_listing from .perf import Perf +from ._version import __version__ logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') @@ -53,6 +57,12 @@ class ArvadosContainer(JobBase): def update_pipeline_component(self, r): pass + def _required_env(self): + env = {} + env["HOME"] = self.outdir + env["TMPDIR"] = self.tmpdir + return env + def run(self, runtimeContext): # ArvadosCommandTool subclasses from cwltool.CommandLineTool, # which calls makeJobRunner() to get a new ArvadosContainer @@ -63,15 +73,21 @@ class ArvadosContainer(JobBase): runtimeContext = self.job_runtime - container_request = { - "command": self.command_line, - "name": self.name, - "output_path": self.outdir, - "cwd": self.outdir, - "priority": runtimeContext.priority, - "state": "Committed", - "properties": {}, - } + if runtimeContext.submit_request_uuid: + container_request = self.arvrunner.api.container_requests().get( + uuid=runtimeContext.submit_request_uuid + ).execute(num_retries=self.arvrunner.num_retries) + else: + container_request = {} + + container_request["command"] = self.command_line + container_request["name"] = self.name + container_request["output_path"] = self.outdir + container_request["cwd"] = self.outdir + container_request["priority"] = runtimeContext.priority + container_request["state"] = "Committed" + container_request.setdefault("properties", {}) + runtime_constraints = {} if runtimeContext.project_uuid: @@ -119,6 +135,8 @@ class ArvadosContainer(JobBase): "kind": "collection", "portable_data_hash": pdh } + if pdh in self.pathmapper.pdh_to_uuid: + mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh] if len(sp) == 2: if tp == "Directory": path = sp[1] @@ -133,32 +151,39 @@ class ArvadosContainer(JobBase): 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], "", "", + generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "", separateDirs=False) - sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target) + sorteditems = sorted(generatemapper.items(), key=lambda n: n[1].target) logger.debug("generatemapper is %s", sorteditems) with Perf(metrics, "createfiles %s" % self.name): for f, p in sorteditems: if not p.target: - pass - elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"): + continue + + if p.target.startswith("/"): + dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:] + else: + dst = p.target + + if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"): if p.resolved.startswith("_:"): - vwd.mkdirs(p.target) + vwd.mkdirs(dst) else: source, path = self.arvrunner.fs_access.get_collection(p.resolved) - vwd.copy(path, p.target, source_collection=source) + vwd.copy(path or ".", dst, source_collection=source) elif p.type == "CreateFile": if self.arvrunner.secret_store.has_secret(p.resolved): - secret_mounts["%s/%s" % (self.outdir, p.target)] = { + mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target) + secret_mounts[mountpoint] = { "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")) + with vwd.open(dst, "w") as n: + n.write(p.resolved) def keepemptydirs(p): if isinstance(p, arvados.collection.RichCollectionBase): @@ -184,10 +209,14 @@ class ArvadosContainer(JobBase): 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) + if p.target.startswith("/"): + dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:] + else: + dst = p.target + mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target) mounts[mountpoint] = {"kind": "collection", "portable_data_hash": vwd.portable_data_hash(), - "path": p.target} + "path": dst} if p.type.startswith("Writable"): mounts[mountpoint]["writable"] = True prev = p.target + "/" @@ -211,13 +240,17 @@ class ArvadosContainer(JobBase): "path": "%s/%s" % (self.outdir, self.stdout)} (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, runtimeContext.pull_image, - runtimeContext.project_uuid) + runtimeContext.project_uuid, + runtimeContext.force_docker_pull, + runtimeContext.tmp_outdir_prefix) + + network_req, _ = self.get_requirement("NetworkAccess") + if network_req: + runtime_constraints["API"] = network_req["networkAccess"] api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement") if api_req: @@ -250,7 +283,15 @@ class ArvadosContainer(JobBase): if self.output_ttl < 0: raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"]) - if self.timelimit is not None: + + if self.arvrunner.api._rootDesc["revision"] >= "20210628": + storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass") + if storage_class_req and storage_class_req.get("intermediateStorageClass"): + container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"]) + else: + container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",") + + if self.timelimit is not None and self.timelimit > 0: scheduling_parameters["max_run_time"] = self.timelimit extra_submit_params = {} @@ -266,11 +307,19 @@ class ArvadosContainer(JobBase): enable_reuse = runtimeContext.enable_reuse if enable_reuse: + reuse_req, _ = self.get_requirement("WorkReuse") + if reuse_req: + enable_reuse = reuse_req["enableReuse"] reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement") if reuse_req: enable_reuse = reuse_req["enableReuse"] container_request["use_existing"] = enable_reuse + properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties") + if properties_req: + for pr in properties_req["processProperties"]: + container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"]) + 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) @@ -301,7 +350,8 @@ class ArvadosContainer(JobBase): 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))) + logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e) + logger.debug("Container request was %s", container_request) self.output_callback({}, "permanentFail") def done(self, record): @@ -325,8 +375,8 @@ class ArvadosContainer(JobBase): else: processStatus = "permanentFail" - if processStatus == "permanentFail": - logc = arvados.collection.CollectionReader(container["log"], + if processStatus == "permanentFail" and record["log_uuid"]: + logc = arvados.collection.CollectionReader(record["log_uuid"], api_client=self.arvrunner.api, keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) @@ -338,7 +388,7 @@ class ArvadosContainer(JobBase): 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) + trash_at = ciso8601.parse_datetime_as_naive(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 "" @@ -349,11 +399,13 @@ class ArvadosContainer(JobBase): if container["output"]: outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep") except WorkflowException as e: + # Only include a stack trace if in debug mode. + # A stack trace may obfuscate more useful output about the workflow. logger.error("%s unable to collect output from %s:\n%s", self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False)) processStatus = "permanentFail" - except Exception as e: - logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e) + except Exception: + logger.exception("%s while getting output object:", self.arvrunner.label(self)) processStatus = "permanentFail" finally: self.output_callback(outputs, processStatus) @@ -407,15 +459,15 @@ class RunnerContainer(Runner): "secret_mounts": secret_mounts, "runtime_constraints": { "vcpus": math.ceil(self.submit_runner_cores), - "ram": math.ceil(1024*1024 * self.submit_runner_ram), + "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)), "API": True }, - "use_existing": self.enable_reuse, + "use_existing": False, # Never reuse the runner container - see #15497. "properties": {} } - if self.tool.tool.get("id", "").startswith("keep:"): - sp = self.tool.tool["id"].split('/') + if self.embedded_tool.tool.get("id", "").startswith("keep:"): + sp = self.embedded_tool.tool["id"].split('/') workflowcollection = sp[0][5:] workflowname = "/".join(sp[1:]) workflowpath = "/var/lib/cwl/workflow/%s" % workflowname @@ -424,15 +476,20 @@ class RunnerContainer(Runner): "portable_data_hash": "%s" % workflowcollection } else: - packed = packed_workflow(self.arvrunner, self.tool, self.merged_map) + packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map) workflowpath = "/var/lib/cwl/workflow.json#main" container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", "content": packed } - if self.tool.tool.get("id", "").startswith("arvwf:"): - container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33] + if self.embedded_tool.tool.get("id", "").startswith("arvwf:"): + container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33] + properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties") + if properties_req: + builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata) + for pr in properties_req["processProperties"]: + container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"]) # --local means execute the workflow instead of submitting a container request # --api=containers means use the containers API @@ -441,14 +498,17 @@ class RunnerContainer(Runner): # --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 + # --collection-cache-size sets aside memory to store collections command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps", "--disable-validate", + "--disable-color", "--eval-timeout=%s" % self.arvrunner.eval_timeout, "--thread-count=%s" % self.arvrunner.thread_count, - "--enable-reuse" if self.enable_reuse else "--disable-reuse"] + "--enable-reuse" if self.enable_reuse else "--disable-reuse", + "--collection-cache-size=%s" % self.collection_cache_size] if self.output_name: command.append("--output-name=" + self.output_name) @@ -460,9 +520,12 @@ class RunnerContainer(Runner): if runtimeContext.debug: command.append("--debug") - if runtimeContext.storage_classes != "default": + if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes: command.append("--storage-classes=" + runtimeContext.storage_classes) + if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes: + command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes) + if self.on_error: command.append("--on-error=" + self.on_error) @@ -475,6 +538,9 @@ class RunnerContainer(Runner): if self.arvrunner.project_uuid: command.append("--project-uuid="+self.arvrunner.project_uuid) + if self.enable_dev: + command.append("--enable-dev") + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command @@ -493,6 +559,9 @@ class RunnerContainer(Runner): extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster if runtimeContext.submit_request_uuid: + if "cluster_id" in extra_submit_params: + # Doesn't make sense for "update" and actually fails + del extra_submit_params["cluster_id"] response = self.arvrunner.api.container_requests().update( uuid=runtimeContext.submit_request_uuid, body=job_spec, @@ -509,13 +578,25 @@ class RunnerContainer(Runner): logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"]) + workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"] + workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"] + url = "" + if workbench2: + url = "{}processes/{}".format(workbench2, response["uuid"]) + elif workbench1: + url = "{}container_requests/{}".format(workbench1, response["uuid"]) + if url: + logger.info("Monitor workflow progress at %s", url) + + def done(self, record): try: container = self.arvrunner.api.containers().get( uuid=record["container_uuid"] ).execute(num_retries=self.arvrunner.num_retries) - except Exception as e: - logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e) + container["log"] = record["log_uuid"] + except Exception: + logger.exception("%s while getting runner container", self.arvrunner.label(self)) self.arvrunner.output_callback({}, "permanentFail") else: super(RunnerContainer, self).done(container)