X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b417e845a53ffe207314108b3d1c813fe09e32a9..60e38e35f49de11b5752c2bfb7f9f10443d82c49:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 1e79566f40..7964486ff2 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -63,7 +63,7 @@ class ArvadosContainer(JobBase): env["TMPDIR"] = self.tmpdir return env - def run(self, runtimeContext): + def run(self, toplevelRuntimeContext): # ArvadosCommandTool subclasses from cwltool.CommandLineTool, # which calls makeJobRunner() to get a new ArvadosContainer # object. The fields that define execution such as @@ -246,7 +246,9 @@ class ArvadosContainer(JobBase): runtimeContext.pull_image, runtimeContext.project_uuid, runtimeContext.force_docker_pull, - runtimeContext.tmp_outdir_prefix) + runtimeContext.tmp_outdir_prefix, + runtimeContext.match_local_docker, + runtimeContext.copy_deps) network_req, _ = self.get_requirement("NetworkAccess") if network_req: @@ -283,11 +285,32 @@ 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"]) - 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"]) + + 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(",") + + cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement") + if cuda_req: + runtime_constraints["cuda"] = { + "device_count": resources.get("cudaDeviceCount", 1), + "driver_version": cuda_req["cudaVersionMin"], + "hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0] + } + + if runtimeContext.enable_preemptible is False: + scheduling_parameters["preemptible"] = False else: - container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",") + preemptible_req, _ = self.get_requirement("http://arvados.org/cwl#UsePreemptible") + if preemptible_req: + scheduling_parameters["preemptible"] = preemptible_req["usePreemptible"] + elif runtimeContext.enable_preemptible is True: + scheduling_parameters["preemptible"] = True + elif runtimeContext.enable_preemptible is None: + pass if self.timelimit is not None and self.timelimit > 0: scheduling_parameters["max_run_time"] = self.timelimit @@ -318,6 +341,11 @@ class ArvadosContainer(JobBase): for pr in properties_req["processProperties"]: container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"]) + output_properties_req, _ = self.get_requirement("http://arvados.org/cwl#OutputCollectionProperties") + if output_properties_req: + for pr in output_properties_req["processProperties"]: + container_request["output_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) @@ -370,6 +398,10 @@ class ArvadosContainer(JobBase): processStatus = "success" else: processStatus = "permanentFail" + + if rcode == 137: + logger.warning("%s Container may have been killed for using too much RAM. Try resubmitting with a higher 'ramMin'.", + self.arvrunner.label(self)) else: processStatus = "permanentFail" @@ -439,7 +471,7 @@ class RunnerContainer(Runner): "cwd": "/var/spool/cwl", "priority": self.priority, "state": "Committed", - "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image), + "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext), "mounts": { "/var/lib/cwl/cwl.input.json": { "kind": "json", @@ -474,7 +506,7 @@ class RunnerContainer(Runner): "portable_data_hash": "%s" % workflowcollection } else: - packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map) + packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext) workflowpath = "/var/lib/cwl/workflow.json#main" container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", @@ -518,27 +550,33 @@ 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": + if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes: command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes) - if self.on_error: + if runtimeContext.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 runtimeContext.intermediate_output_ttl: + command.append("--intermediate-output-ttl=%d" % runtimeContext.intermediate_output_ttl) - if self.arvrunner.trash_intermediate: + if runtimeContext.trash_intermediate: command.append("--trash-intermediate") - if self.arvrunner.project_uuid: - command.append("--project-uuid="+self.arvrunner.project_uuid) + if runtimeContext.project_uuid: + command.append("--project-uuid="+runtimeContext.project_uuid) if self.enable_dev: command.append("--enable-dev") + if runtimeContext.enable_preemptible is True: + command.append("--enable-preemptible") + + if runtimeContext.enable_preemptible is False: + command.append("--disable-preemptible") + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command @@ -549,8 +587,8 @@ class RunnerContainer(Runner): def run(self, runtimeContext): runtimeContext.keepprefix = "keep:" job_spec = self.arvados_job_spec(runtimeContext) - if self.arvrunner.project_uuid: - job_spec["owner_uuid"] = self.arvrunner.project_uuid + if runtimeContext.project_uuid: + job_spec["owner_uuid"] = runtimeContext.project_uuid extra_submit_params = {} if runtimeContext.submit_runner_cluster: