import cwltool.workflow
import cwltool.main
from cwltool.process import shortname
+from cwltool.errors import WorkflowException
import threading
import cwltool.docker
import fnmatch
if not images:
imageId = cwltool.docker.get_image(dockerRequirement, pull_image)
- args = ["--project-uuid", project_uuid, image_name]
+ args = ["--project-uuid="+project_uuid, image_name]
if image_tag:
args.append(image_tag)
- logger.info("Uploading Docker image %s", ":".join(args))
+ logger.info("Uploading Docker image %s", ":".join(args[1:]))
arvados.commands.keepdocker.main(args)
return dockerRequirement["dockerImageId"]
(docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
if docker_req and kwargs.get("use_container") is not False:
- runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvruner.project_uuid)
+ runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
+
+ resources = self.builder.resources
+ if resources is not None:
+ runtime_constraints["min_cores_per_node"] = resources.get("cores", 1)
+ runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
+ runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
try:
response = self.arvrunner.api.jobs().create(body={
g = keepre.match(l)
if g:
keepdir = g.group(1)
- if tmpdir and outdir and keepdir:
- break
+
+ # It turns out if the job fails and restarts it can
+ # come up on a different compute node, so we have to
+ # read the log to the end to be sure instead of taking the
+ # easy way out.
+ #
+ #if tmpdir and outdir and keepdir:
+ # break
self.builder.outdir = outdir
self.builder.pathmapper.keepdir = keepdir
outputs = self.collect_outputs("keep:" + record["output"])
+ except WorkflowException as e:
+ logger.error("Error while collecting job outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
+ processStatus = "permanentFail"
except Exception as e:
- logger.exception("Got exception while collecting job outputs:")
+ logger.exception("Got unknown exception while collecting job outputs:")
processStatus = "permanentFail"
self.output_callback(outputs, processStatus)
class ArvPathMapper(cwltool.pathmapper.PathMapper):
- def __init__(self, arvrunner, referenced_files, basedir, **kwargs):
+ def __init__(self, arvrunner, referenced_files, basedir,
+ collection_pattern, file_pattern, **kwargs):
self._pathmap = arvrunner.get_uploaded()
uploadfiles = []
for src in referenced_files:
if isinstance(src, basestring) and pdh_path.match(src):
- self._pathmap[src] = (src, "$(task.keep)/%s" % src[5:])
+ self._pathmap[src] = (src, collection_pattern % src[5:])
if src not in self._pathmap:
ab = cwltool.pathmapper.abspath(src, basedir)
- st = arvados.commands.run.statfile("", ab, fnPattern="$(task.keep)/%s/%s")
+ st = arvados.commands.run.statfile("", ab, fnPattern=file_pattern)
if kwargs.get("conformance_test"):
self._pathmap[src] = (src, ab)
elif isinstance(st, arvados.commands.run.UploadFile):
arvrunner.api,
dry_run=kwargs.get("dry_run"),
num_retries=3,
- fnPattern="$(task.keep)/%s/%s",
+ fnPattern=file_pattern,
project=arvrunner.project_uuid)
for src, ab, st in uploadfiles:
return ArvadosJob(self.arvrunner)
def makePathMapper(self, reffiles, input_basedir, **kwargs):
- return ArvPathMapper(self.arvrunner, reffiles, input_basedir, **kwargs)
+ return ArvPathMapper(self.arvrunner, reffiles, input_basedir,
+ "$(task.keep)/%s",
+ "$(task.keep)/%s/%s",
+ **kwargs)
class ArvCwlRunner(object):
def on_message(self, event):
if "object_uuid" in event:
- if event["object_uuid"] in self.jobs and event["event_type"] == "update":
- if event["properties"]["new_attributes"]["state"] == "Running" and self.jobs[event["object_uuid"]].running is False:
- uuid = event["object_uuid"]
- with self.lock:
- j = self.jobs[uuid]
- logger.info("Job %s (%s) is Running", j.name, uuid)
- j.running = True
- j.update_pipeline_component(event["properties"]["new_attributes"])
- elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
- uuid = event["object_uuid"]
- try:
- self.cond.acquire()
- j = self.jobs[uuid]
- logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"])
- j.done(event["properties"]["new_attributes"])
- self.cond.notify()
- finally:
- self.cond.release()
+ if event["object_uuid"] in self.jobs and event["event_type"] == "update":
+ if event["properties"]["new_attributes"]["state"] == "Running" and self.jobs[event["object_uuid"]].running is False:
+ uuid = event["object_uuid"]
+ with self.lock:
+ j = self.jobs[uuid]
+ logger.info("Job %s (%s) is Running", j.name, uuid)
+ j.running = True
+ j.update_pipeline_component(event["properties"]["new_attributes"])
+ elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
+ uuid = event["object_uuid"]
+ try:
+ self.cond.acquire()
+ j = self.jobs[uuid]
+ logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"])
+ j.done(event["properties"]["new_attributes"])
+ self.cond.notify()
+ finally:
+ self.cond.release()
def get_uploaded(self):
return self.uploaded.copy()
def add_uploaded(self, src, pair):
self.uploaded[src] = pair
+ def upload_docker(self, tool):
+ pass
+
+ def submit(self, tool, job_order, input_basedir, args, **kwargs):
+ files = set()
+ def visitFiles(self, path):
+ files.add(path)
+
+ adjustFiles(process.scandeps("", tool.tool,
+ set(("run")),
+ set(("$schemas", "path"))),
+ visitFiles)
+ adjustFiles(job_order, visitFiles)
+
+ mapper = ArvPathMapper(self, files, "",
+ "$(task.keep)/%s",
+ "$(task.keep)/%s/%s",
+ **kwargs)
+
+ job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
+
+ response = self.api.jobs().create(body={
+ "script": "cwl-runner",
+ "script_version": "8654-arv-jobs-cwl-runner",
+ "repository": "arvados",
+ "script_parameters": job_order,
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs"
+ }
+ }, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
+ print response["uuid"]
+ return None
+
+
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+ if args.submit:
+ self.submit(tool, job_order, input_basedir, args, **kwargs)
+ return
+
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
+ self.debug = args.debug
+
try:
self.api.collections().get(uuid=crunchrunner_pdh).execute()
except arvados.errors.ApiError as e:
"components": {},
"state": "RunningOnClient"}).execute(num_retries=self.num_retries)
+ logger.info("Pipeline instance %s", self.pipeline["uuid"])
+
jobiter = tool.job(job_order,
input_basedir,
self.output_callback,
**kwargs)
try:
+ self.cond.acquire()
+ # Will continue to hold the lock for the duration of this code
+ # except when in cond.wait(), at which point on_message can update
+ # job state and process output callbacks.
+
for runnable in jobiter:
if runnable:
- with self.lock:
- runnable.run(**kwargs)
+ runnable.run(**kwargs)
else:
if self.jobs:
- try:
- self.cond.acquire()
- self.cond.wait(1)
- except RuntimeError:
- pass
- finally:
- self.cond.release()
+ self.cond.wait(1)
else:
- logger.error("Workflow cannot make any more progress.")
+ logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.")
break
while self.jobs:
- try:
- self.cond.acquire()
- self.cond.wait(1)
- except RuntimeError:
- pass
- finally:
- self.cond.release()
+ self.cond.wait(1)
events.close()
if self.final_output is None:
raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
+ # create final output collection
except:
- if sys.exc_info()[0] is not KeyboardInterrupt:
- logger.exception("Caught unhandled exception, marking pipeline as failed")
+ if sys.exc_info()[0] is KeyboardInterrupt:
+ logger.error("Interrupted, marking pipeline as failed")
+ else:
+ logger.error("Caught unhandled exception, marking pipeline as failed. Error was: %s", sys.exc_info()[0], exc_info=(sys.exc_info()[1] if self.debug else False))
self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
body={"state": "Failed"}).execute(num_retries=self.num_retries)
+ finally:
+ self.cond.release()
return self.final_output
parser = cwltool.main.arg_parser()
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--enable-reuse", action="store_true",
- default=False, dest="enable_reuse",
+ default=True, dest="enable_reuse",
help="")
exgroup.add_argument("--disable-reuse", action="store_false",
- default=False, dest="enable_reuse",
+ default=True, dest="enable_reuse",
help="")
parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
+ parser.add_argument("--submit", type=str, help="Submit job and print job uuid.")
try:
runner = ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
projects / arvados.git / blobdiff