logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
+def cleanup_name_for_collection(name):
+ return name.replace("/", " ")
+
class ArvadosContainer(JobBase):
"""Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
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
container_request["state"] = "Committed"
container_request.setdefault("properties", {})
+ container_request["properties"]["cwl_input"] = self.joborder
+
runtime_constraints = {}
if runtimeContext.project_uuid:
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:
runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
if runtime_req:
if "keep_cache" in runtime_req:
- runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
+ if self.arvrunner.api.config()["Containers"].get("DefaultKeepCacheDisk", 0) > 0:
+ # If DefaultKeepCacheDisk is non-zero it means we should use disk cache.
+ runtime_constraints["keep_cache_disk"] = math.ceil(runtime_req["keep_cache"] * 2**20)
+ else:
+ runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20)
if "outputDirType" in runtime_req:
if runtime_req["outputDirType"] == "local_output_dir":
# Currently the default behavior.
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:
+ 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
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"] = cleanup_name_for_collection("Output from step %s" % (self.name))
container_request["output_ttl"] = self.output_ttl
container_request["mounts"] = mounts
container_request["secret_mounts"] = secret_mounts
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 revision is %s, revision %s is required to support setting properties on output collections.",
+ self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510")
+
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"
if container["output"]:
outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
+
+ properties = record["properties"].copy()
+ properties["cwl_output"] = outputs
+ self.arvrunner.api.container_requests().update(
+ uuid=self.uuid,
+ body={"container_request": {"properties": properties}}
+ ).execute(num_retries=self.arvrunner.num_retries)
except WorkflowException as e:
# Only include a stack trace if in debug mode.
# A stack trace may obfuscate more useful output about the workflow.
class RunnerContainer(Runner):
"""Submit and manage a container that runs arvados-cwl-runner."""
- def arvados_job_spec(self, runtimeContext):
+ def arvados_job_spec(self, runtimeContext, git_info):
"""Create an Arvados container request for this workflow.
The returned dict can be used to create a container passed as
"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",
"kind": "collection",
"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"])
+ container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
+ "kind": "json",
+ "content": packed
+ }
+ container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
else:
- packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
+ packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info)
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
"content": packed
}
- if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
- container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
+
+ container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
if properties_req:
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")
+
+ if runtimeContext.varying_url_params:
+ command.append("--varying-url-params="+runtimeContext.varying_url_params)
+
+ if runtimeContext.prefer_cached_downloads:
+ command.append("--prefer-cached-downloads")
+
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
+ job_spec = self.arvados_job_spec(runtimeContext, self.git_info)
+ if runtimeContext.project_uuid:
+ job_spec["owner_uuid"] = runtimeContext.project_uuid
extra_submit_params = {}
if runtimeContext.submit_runner_cluster:
projects / arvados.git / blobdiff