+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
# Copyright (C) The Arvados Authors. All rights reserved.
#
# SPDX-License-Identifier: Apache-2.0
import logging
import json
import os
-import urllib
+import urllib.request, urllib.parse, urllib.error
import time
import datetime
import ciso8601
import uuid
+import math
+import arvados_cwl.util
import ruamel.yaml as yaml
from cwltool.errors import WorkflowException
-from cwltool.process import get_feature, UnsupportedRequirement, shortname
+from cwltool.process import UnsupportedRequirement, shortname
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
from cwltool.utils import aslist
+from cwltool.job import JobBase
import arvados.collection
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
-class ArvadosContainer(object):
+class ArvadosContainer(JobBase):
"""Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
- def __init__(self, runner):
+ def __init__(self, runner, job_runtime,
+ builder, # type: Builder
+ joborder, # type: Dict[Text, Union[Dict[Text, Any], List, Text]]
+ make_path_mapper, # type: Callable[..., PathMapper]
+ requirements, # type: List[Dict[Text, Text]]
+ hints, # type: List[Dict[Text, Text]]
+ name # type: Text
+ ):
+ super(ArvadosContainer, self).__init__(builder, joborder, make_path_mapper, requirements, hints, name)
self.arvrunner = runner
+ self.job_runtime = job_runtime
self.running = False
self.uuid = None
def update_pipeline_component(self, r):
pass
- def run(self, dry_run=False, pull_image=True, **kwargs):
+ def run(self, runtimeContext):
# ArvadosCommandTool subclasses from cwltool.CommandLineTool,
# which calls makeJobRunner() to get a new ArvadosContainer
# object. The fields that define execution such as
# ArvadosContainer object by CommandLineTool.job() before
# run() is called.
+ runtimeContext = self.job_runtime
+
container_request = {
"command": self.command_line,
"name": self.name,
"output_path": self.outdir,
"cwd": self.outdir,
- "priority": kwargs.get("priority"),
+ "priority": runtimeContext.priority,
"state": "Committed",
"properties": {},
}
runtime_constraints = {}
- if self.arvrunner.project_uuid:
- container_request["owner_uuid"] = self.arvrunner.project_uuid
+ if runtimeContext.project_uuid:
+ container_request["owner_uuid"] = runtimeContext.project_uuid
if self.arvrunner.secret_store.has_secret(self.command_line):
raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets")
resources = self.builder.resources
if resources is not None:
- runtime_constraints["vcpus"] = resources.get("cores", 1)
- runtime_constraints["ram"] = resources.get("ram") * 2**20
+ runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
+ runtime_constraints["ram"] = math.ceil(resources.get("ram") * 2**20)
mounts = {
self.outdir: {
"kind": "tmp",
- "capacity": resources.get("outdirSize", 0) * 2**20
+ "capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
},
self.tmpdir: {
"kind": "tmp",
- "capacity": resources.get("tmpdirSize", 0) * 2**20
+ "capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
}
}
secret_mounts = {}
vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
- generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
+ generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
separateDirs=False)
- sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target)
+ sorteditems = sorted(list(generatemapper.items()), None, key=lambda n: n[1].target)
logger.debug("generatemapper is %s", sorteditems)
keepemptydirs(vwd)
- with Perf(metrics, "generatefiles.save_new %s" % self.name):
- vwd.save_new()
+ 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"],
+ owner_uuid=runtimeContext.project_uuid,
+ ensure_unique_name=True,
+ trash_at=info["trash_at"],
+ properties=info["properties"])
prev = None
for f, p in sorteditems:
mounts["stdout"] = {"kind": "file",
"path": "%s/%s" % (self.outdir, self.stdout)}
- (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
+ (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
if not docker_req:
docker_req = {"dockerImageId": "arvados/jobs"}
container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
- docker_req,
- pull_image,
- self.arvrunner.project_uuid)
+ docker_req,
+ runtimeContext.pull_image,
+ runtimeContext.project_uuid)
- api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement")
+ api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
if api_req:
runtime_constraints["API"] = True
- runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
+ runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints")
if runtime_req:
if "keep_cache" in runtime_req:
- runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20
+ 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.
"writable": True
}
- partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
+ partition_req, _ = self.get_requirement("http://arvados.org/cwl#PartitionRequirement")
if partition_req:
scheduling_parameters["partitions"] = aslist(partition_req["partition"])
- intermediate_output_req, _ = get_feature(self, "http://arvados.org/cwl#IntermediateOutput")
+ intermediate_output_req, _ = self.get_requirement("http://arvados.org/cwl#IntermediateOutput")
if intermediate_output_req:
self.output_ttl = intermediate_output_req["outputTTL"]
else:
if self.output_ttl < 0:
raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
+ if self.timelimit is not None:
+ scheduling_parameters["max_run_time"] = self.timelimit
+
+ extra_submit_params = {}
+ 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_ttl"] = self.output_ttl
container_request["mounts"] = mounts
container_request["secret_mounts"] = secret_mounts
container_request["runtime_constraints"] = runtime_constraints
container_request["scheduling_parameters"] = scheduling_parameters
- enable_reuse = kwargs.get("enable_reuse", True)
+ enable_reuse = runtimeContext.enable_reuse
if enable_reuse:
- reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement")
+ reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement")
if reuse_req:
enable_reuse = reuse_req["enableReuse"]
container_request["use_existing"] = enable_reuse
- if kwargs.get("runnerjob", "").startswith("arvwf:"):
- wfuuid = kwargs["runnerjob"][6:kwargs["runnerjob"].index("#")]
+ 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)
if container_request["name"] == "main":
container_request["name"] = wfrecord["name"]
self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
try:
- if kwargs.get("submit_request_uuid"):
+ if runtimeContext.submit_request_uuid:
response = self.arvrunner.api.container_requests().update(
- uuid=kwargs["submit_request_uuid"],
- body=container_request
+ 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
+ body=container_request,
+ **extra_submit_params
).execute(num_retries=self.arvrunner.num_retries)
self.uuid = response["uuid"]
api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
- done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
+ label = self.arvrunner.label(self)
+ done.logtail(
+ logc, logger.error,
+ "%s (%s) error log:" % (label, record["uuid"]), maxlen=40)
if record["output_uuid"]:
if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
class RunnerContainer(Runner):
"""Submit and manage a container that runs arvados-cwl-runner."""
- def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
+ def arvados_job_spec(self, runtimeContext):
"""Create an Arvados container request for this workflow.
The returned dict can be used to create a container passed as
},
"secret_mounts": secret_mounts,
"runtime_constraints": {
- "vcpus": 1,
- "ram": 1024*1024 * self.submit_runner_ram,
+ "vcpus": math.ceil(self.submit_runner_cores),
+ "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
"API": True
},
"use_existing": self.enable_reuse,
"properties": {}
}
- if self.tool.tool.get("id", "").startswith("keep:"):
- sp = self.tool.tool["id"].split('/')
+ if self.embedded_tool.tool.get("id", "").startswith("keep:"):
+ sp = self.embedded_tool.tool["id"].split('/')
workflowcollection = sp[0][5:]
workflowname = "/".join(sp[1:])
workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
"portable_data_hash": "%s" % workflowcollection
}
else:
- packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
+ packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
"content": packed
}
- if self.tool.tool.get("id", "").startswith("arvwf:"):
- container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33]
+ if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
+ container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
# --local means execute the workflow instead of submitting a container request
# --eval-timeout is the timeout for javascript invocation
# --parallel-task-count is the number of threads to use for job submission
# --enable/disable-reuse sets desired job reuse
+ # --collection-cache-size sets aside memory to store collections
command = ["arvados-cwl-runner",
"--local",
"--api=containers",
"--disable-validate",
"--eval-timeout=%s" % self.arvrunner.eval_timeout,
"--thread-count=%s" % self.arvrunner.thread_count,
- "--enable-reuse" if self.enable_reuse else "--disable-reuse"]
+ "--enable-reuse" if self.enable_reuse else "--disable-reuse",
+ "--collection-cache-size=%s" % self.collection_cache_size]
if self.output_name:
command.append("--output-name=" + self.output_name)
if self.output_tags:
command.append("--output-tags=" + self.output_tags)
- if kwargs.get("debug"):
+ if runtimeContext.debug:
command.append("--debug")
+ if runtimeContext.storage_classes != "default":
+ command.append("--storage-classes=" + runtimeContext.storage_classes)
+
if self.on_error:
command.append("--on-error=" + self.on_error)
return container_req
- def run(self, **kwargs):
- kwargs["keepprefix"] = "keep:"
- job_spec = self.arvados_job_spec(**kwargs)
+ 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 kwargs.get("submit_request_uuid"):
+ extra_submit_params = {}
+ if runtimeContext.submit_runner_cluster:
+ extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
+
+ if runtimeContext.submit_request_uuid:
response = self.arvrunner.api.container_requests().update(
- uuid=kwargs["submit_request_uuid"],
- body=job_spec
+ uuid=runtimeContext.submit_request_uuid,
+ body=job_spec,
+ **extra_submit_params
).execute(num_retries=self.arvrunner.num_retries)
else:
response = self.arvrunner.api.container_requests().create(
- body=job_spec
+ body=job_spec,
+ **extra_submit_params
).execute(num_retries=self.arvrunner.num_retries)
self.uuid = response["uuid"]
self.arvrunner.process_submitted(self)
- logger.info("%s submitted container %s", self.arvrunner.label(self), response["uuid"])
+ logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
def done(self, record):
try:
projects / arvados.git / blobdiff