X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f30e59af90558e47a4156566d0209bc8efacd85a..cf9afd31cf9bc682ea3f8c0d59012fa7080b0e9b:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 3c7e9cfaa6..ec9c52c59a 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 @@ -146,6 +146,8 @@ class ArvadosContainer(JobBase): mounts[targetdir]["path"] = path prevdir = targetdir + "/" + intermediate_collection_info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl) + with Perf(metrics, "generatefiles %s" % self.name): if self.generatefiles["listing"]: vwd = arvados.collection.Collection(api_client=self.arvrunner.api, @@ -197,12 +199,11 @@ class ArvadosContainer(JobBase): if not runtimeContext.current_container: runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) - info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl) - vwd.save_new(name=info["name"], + vwd.save_new(name=intermediate_collection_info["name"], owner_uuid=runtimeContext.project_uuid, ensure_unique_name=True, - trash_at=info["trash_at"], - properties=info["properties"]) + trash_at=intermediate_collection_info["trash_at"], + properties=intermediate_collection_info["properties"]) prev = None for f, p in sorteditems: @@ -246,7 +247,9 @@ 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: @@ -294,11 +297,22 @@ class ArvadosContainer(JobBase): cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement") if cuda_req: runtime_constraints["cuda"] = { - "device_count": cuda_req.get("deviceCountMin", 1), + "device_count": resources.get("cudaDeviceCount", 1), "driver_version": cuda_req["cudaVersionMin"], - "hardware_capability": cuda_req["cudaComputeCapabilityMin"] + "hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0] } + if runtimeContext.enable_preemptible is False: + scheduling_parameters["preemptible"] = False + else: + 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 @@ -306,7 +320,7 @@ class ArvadosContainer(JobBase): if runtimeContext.submit_runner_cluster: extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster - container_request["output_name"] = "Output for step %s" % (self.name) + container_request["output_name"] = "Output from step %s" % (self.name) container_request["output_ttl"] = self.output_ttl container_request["mounts"] = mounts container_request["secret_mounts"] = secret_mounts @@ -328,6 +342,16 @@ 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: + if self.arvrunner.api._rootDesc["revision"] >= "20220510": + container_request["output_properties"] = {} + for pr in output_properties_req["outputProperties"]: + container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"]) + else: + logger.warning("%s API server is too old to support setting properties on output collections.", + self.arvrunner.label(self)) + 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) @@ -380,6 +404,10 @@ 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" @@ -449,7 +477,7 @@ 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", @@ -484,7 +512,7 @@ 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", @@ -534,21 +562,27 @@ class RunnerContainer(Runner): 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 @@ -559,8 +593,8 @@ 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: