X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9b0de8314d6297df506734844bb2b833ba7d022c..cd6cc155469fb54cd7d868e5bc331f13805b79c9:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index a15c085da7..f048e505e8 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -15,9 +15,10 @@ import datetime import ciso8601 import uuid import math +import re import arvados_cwl.util -import ruamel.yaml as yaml +import ruamel.yaml from cwltool.errors import WorkflowException from cwltool.process import UnsupportedRequirement, shortname @@ -26,6 +27,9 @@ from cwltool.job import JobBase import arvados.collection +import crunchstat_summary.summarizer +import crunchstat_summary.reader + 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, make_builder @@ -56,6 +60,7 @@ class ArvadosContainer(JobBase): self.job_runtime = job_runtime self.running = False self.uuid = None + self.attempt_count = 0 def update_pipeline_component(self, r): pass @@ -88,7 +93,7 @@ class ArvadosContainer(JobBase): container_request["output_path"] = self.outdir container_request["cwd"] = self.outdir container_request["priority"] = runtimeContext.priority - container_request["state"] = "Committed" + container_request["state"] = "Uncommitted" container_request.setdefault("properties", {}) container_request["properties"]["cwl_input"] = self.joborder @@ -250,11 +255,7 @@ class ArvadosContainer(JobBase): container_request["container_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, runtimeContext.pull_image, - runtimeContext.project_uuid, - runtimeContext.force_docker_pull, - runtimeContext.tmp_outdir_prefix, - runtimeContext.match_local_docker, - runtimeContext.copy_deps) + runtimeContext) network_req, _ = self.get_requirement("NetworkAccess") if network_req: @@ -369,6 +370,17 @@ class ArvadosContainer(JobBase): logger.warning("%s API revision is %s, revision %s is required to support setting properties on output collections.", self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510") + ram_multiplier = [1] + + oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry") + if oom_retry_req: + if oom_retry_req.get('memoryRetryMultiplier'): + ram_multiplier.append(oom_retry_req.get('memoryRetryMultiplier')) + elif oom_retry_req.get('memoryRetryMultipler'): + ram_multiplier.append(oom_retry_req.get('memoryRetryMultipler')) + else: + ram_multiplier.append(2) + 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) @@ -376,23 +388,45 @@ class ArvadosContainer(JobBase): container_request["name"] = wfrecord["name"] container_request["properties"]["template_uuid"] = wfuuid - self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback) + if self.attempt_count == 0: + self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback) try: - if runtimeContext.submit_request_uuid: - response = self.arvrunner.api.container_requests().update( - uuid=runtimeContext.submit_request_uuid, - body=container_request, - **extra_submit_params - ).execute(num_retries=self.arvrunner.num_retries) - else: - response = self.arvrunner.api.container_requests().create( - body=container_request, - **extra_submit_params - ).execute(num_retries=self.arvrunner.num_retries) + ram = runtime_constraints["ram"] + + self.uuid = runtimeContext.submit_request_uuid + + for i in ram_multiplier: + runtime_constraints["ram"] = ram * i + + if self.uuid: + response = self.arvrunner.api.container_requests().update( + uuid=self.uuid, + body=container_request, + **extra_submit_params + ).execute(num_retries=self.arvrunner.num_retries) + else: + response = self.arvrunner.api.container_requests().create( + body=container_request, + **extra_submit_params + ).execute(num_retries=self.arvrunner.num_retries) + self.uuid = response["uuid"] + + if response["container_uuid"] is not None: + break + + if response["container_uuid"] is None: + runtime_constraints["ram"] = ram * ram_multiplier[self.attempt_count] + + container_request["state"] = "Committed" + response = self.arvrunner.api.container_requests().update( + uuid=self.uuid, + body=container_request, + **extra_submit_params + ).execute(num_retries=self.arvrunner.num_retries) - self.uuid = response["uuid"] self.arvrunner.process_submitted(self) + self.attempt_count += 1 if response["state"] == "Final": logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"]) @@ -403,8 +437,37 @@ class ArvadosContainer(JobBase): logger.debug("Container request was %s", container_request) self.output_callback({}, "permanentFail") + def out_of_memory_retry(self, record, container): + oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry") + if oom_retry_req is None: + return False + + # Sometimes it gets killed with no warning + if container["exit_code"] == 137: + return True + + logc = arvados.collection.CollectionReader(record["log_uuid"], + api_client=self.arvrunner.api, + keep_client=self.arvrunner.keep_client, + num_retries=self.arvrunner.num_retries) + + loglines = [""] + def callback(v1, v2, v3): + loglines[0] = v3 + + done.logtail(logc, callback, "", maxlen=1000) + + # Check allocation failure + oom_matches = oom_retry_req.get('memoryErrorRegex') or r'(bad_alloc|out ?of ?memory|memory ?error|container using over 9.% of memory)' + if re.search(oom_matches, loglines[0], re.IGNORECASE | re.MULTILINE): + return True + + return False + def done(self, record): outputs = {} + retried = False + rcode = None try: container = self.arvrunner.api.containers().get( uuid=record["container_uuid"] @@ -422,21 +485,33 @@ class ArvadosContainer(JobBase): else: processStatus = "permanentFail" + if processStatus == "permanentFail" and self.attempt_count == 1 and self.out_of_memory_retry(record, container): + logger.warning("%s Container failed with out of memory error, retrying with more RAM.", + self.arvrunner.label(self)) + self.job_runtime.submit_request_uuid = None + self.uuid = None + self.run(None) + retried = True + return + if rcode == 137: - logger.warning("%s Container may have been killed for using too much RAM. Try resubmitting with a higher 'ramMin'.", + logger.warning("%s Container may have been killed for using too much RAM. Try resubmitting with a higher 'ramMin' or use the arv:OutOfMemoryRetry feature.", self.arvrunner.label(self)) else: processStatus = "permanentFail" - 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) + logc = None + if record["log_uuid"]: + logc = arvados.collection.Collection(record["log_uuid"], + api_client=self.arvrunner.api, + keep_client=self.arvrunner.keep_client, + num_retries=self.arvrunner.num_retries) + + if processStatus == "permanentFail" and logc is not None: label = self.arvrunner.label(self) done.logtail( logc, logger.error, - "%s (%s) error log:" % (label, record["uuid"]), maxlen=40) + "%s (%s) error log:" % (label, record["uuid"]), maxlen=40, include_crunchrun=(rcode is None or rcode > 127)) if record["output_uuid"]: if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl: @@ -458,6 +533,28 @@ class ArvadosContainer(JobBase): uuid=self.uuid, body={"container_request": {"properties": properties}} ).execute(num_retries=self.arvrunner.num_retries) + + if logc is not None and self.job_runtime.enable_usage_report is not False: + try: + summarizer = crunchstat_summary.summarizer.ContainerRequestSummarizer( + record, + collection_object=logc, + label=self.name, + arv=self.arvrunner.api) + summarizer.run() + with logc.open("usage_report.html", "wt") as mr: + mr.write(summarizer.html_report()) + logc.save() + + # Post warnings about nodes that are under-utilized. + for rc in summarizer._recommend_gen(lambda x: x): + self.usage_report_notes.append(rc) + + except Exception as e: + logger.warning("%s unable to generate resource usage report", + self.arvrunner.label(self), + exc_info=(e if self.arvrunner.debug else False)) + except WorkflowException as e: # Only include a stack trace if in debug mode. # A stack trace may obfuscate more useful output about the workflow. @@ -468,7 +565,8 @@ class ArvadosContainer(JobBase): logger.exception("%s while getting output object:", self.arvrunner.label(self)) processStatus = "permanentFail" finally: - self.output_callback(outputs, processStatus) + if not retried: + self.output_callback(outputs, processStatus) class RunnerContainer(Runner): @@ -495,13 +593,19 @@ class RunnerContainer(Runner): } self.job_order[param] = {"$include": mnt} + container_image = arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext) + + workflow_runner_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#WorkflowRunnerResources") + if workflow_runner_req and workflow_runner_req.get("acrContainerImage"): + container_image = workflow_runner_req.get("acrContainerImage") + container_req = { "name": self.name, "output_path": "/var/spool/cwl", "cwd": "/var/spool/cwl", "priority": self.priority, "state": "Committed", - "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext), + "container_image": container_image, "mounts": { "/var/lib/cwl/cwl.input.json": { "kind": "json", @@ -522,7 +626,7 @@ class RunnerContainer(Runner): "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)), "API": True }, - "use_existing": False, # Never reuse the runner container - see #15497. + "use_existing": self.reuse_runner, "properties": {} } @@ -536,20 +640,26 @@ class RunnerContainer(Runner): "portable_data_hash": "%s" % workflowcollection } elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"): - workflowpath = "/var/lib/cwl/workflow.json#main" - record = self.arvrunner.api.workflows().get(uuid=self.embedded_tool.tool["id"][6:33]).execute(num_retries=self.arvrunner.num_retries) - packed = yaml.safe_load(record["definition"]) + uuid, frg = urllib.parse.urldefrag(self.embedded_tool.tool["id"]) + workflowpath = "/var/lib/cwl/workflow.json#" + frg + packedtxt = self.loadingContext.loader.fetch_text(uuid) + yaml = ruamel.yaml.YAML(typ='safe', pure=True) + packed = yaml.load(packedtxt) container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", "content": packed } container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33] + elif self.embedded_tool.tool.get("id", "").startswith("file:"): + raise WorkflowException("Tool id '%s' is a local file but expected keep: or arvwf:" % self.embedded_tool.tool.get("id")) else: - packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info) + main = self.loadingContext.loader.idx["_:main"] + if main.get("id") == "_:main": + del main["id"] workflowpath = "/var/lib/cwl/workflow.json#main" container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", - "content": packed + "content": main } container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()}) @@ -622,6 +732,15 @@ class RunnerContainer(Runner): if runtimeContext.prefer_cached_downloads: command.append("--prefer-cached-downloads") + if runtimeContext.enable_usage_report is True: + command.append("--enable-usage-report") + + if runtimeContext.enable_usage_report is False: + command.append("--disable-usage-report") + + if self.fast_parser: + command.append("--fast-parser") + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command @@ -659,14 +778,9 @@ 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)