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
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,
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:
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:
else:
container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
- cuda_req, _ = self.get_requirement("http://arvados.org/cwl#CUDARequirement")
+ cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement")
if cuda_req:
runtime_constraints["cuda"] = {
- "device_count": cuda_req.get("minDeviceCount", 1),
- "driver_version": cuda_req["minCUDADriverVersion"],
- "hardware_capability": cuda_req["minCUDAHardwareCapability"]
+ "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:
+ 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
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)
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"
"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",
"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",
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
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:
projects / arvados.git / blobdiff