import arvados.events
import arvados.commands.keepdocker
import arvados.commands.run
+import arvados.collection
+import arvados.util
import cwltool.draft2tool
import cwltool.workflow
import cwltool.main
+from cwltool.process import shortname
+from cwltool.errors import WorkflowException
import threading
import cwltool.docker
import fnmatch
import logging
import re
import os
-import copy
+import sys
+
from cwltool.process import get_feature
+from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
logger.setLevel(logging.INFO)
-def arv_docker_get_image(api_client, dockerRequirement, pull_image):
+crunchrunner_pdh = "83db29f08544e1c319572a6bd971088a+140"
+crunchrunner_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/crunchrunner"
+certs_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/ca-certificates.crt"
+
+tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)")
+outdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)")
+keepre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)")
+
+
+def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid):
if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
if not images:
imageId = cwltool.docker.get_image(dockerRequirement, pull_image)
- args = [image_name]
+ args = ["--project-uuid="+project_uuid, image_name]
if image_tag:
args.append(image_tag)
+ logger.info("Uploading Docker image %s", ":".join(args[1:]))
arvados.commands.keepdocker.main(args)
return dockerRequirement["dockerImageId"]
+
class CollectionFsAccess(cwltool.process.StdFsAccess):
def __init__(self, basedir):
self.collections = {}
def get_collection(self, path):
p = path.split("/")
- if arvados.util.keep_locator_pattern.match(p[0]):
- if p[0] not in self.collections:
- self.collections[p[0]] = arvados.collection.CollectionReader(p[0])
- return (self.collections[p[0]], "/".join(p[1:]))
+ if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
+ pdh = p[0][5:]
+ if pdh not in self.collections:
+ self.collections[pdh] = arvados.collection.CollectionReader(pdh)
+ return (self.collections[pdh], "/".join(p[1:]))
else:
return (None, path)
def _match(self, collection, patternsegments, parent):
+ if not patternsegments:
+ return []
+
+ if not isinstance(collection, arvados.collection.RichCollectionBase):
+ return []
+
ret = []
- if len(patternsegments) == 0:
- return ret
+ # iterate over the files and subcollections in 'collection'
for filename in collection:
- if fnmatch.fnmatch(filename, patternsegments[0]):
+ if patternsegments[0] == '.':
+ # Pattern contains something like "./foo" so just shift
+ # past the "./"
+ ret.extend(self._match(collection, patternsegments[1:], parent))
+ elif fnmatch.fnmatch(filename, patternsegments[0]):
cur = os.path.join(parent, filename)
if len(patternsegments) == 1:
ret.append(cur)
else:
ret.extend(self._match(collection[filename], patternsegments[1:], cur))
- elif patternsegments[0] == '.':
- ret.extend(self._match(collection, patternsegments[1:], parent))
return ret
def glob(self, pattern):
collection, rest = self.get_collection(pattern)
patternsegments = rest.split("/")
- return self._match(collection, patternsegments, collection.manifest_locator())
+ return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
def open(self, fn, mode):
collection, rest = self.get_collection(fn)
script_parameters["task.vwd"] = {}
for t in self.generatefiles:
if isinstance(self.generatefiles[t], dict):
- src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"][13:])
+ src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"].replace("$(task.keep)/", "keep:"))
vwd.copy(rest, t, source_collection=src)
else:
with vwd.open(t, "w") as f:
(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)
-
- response = self.arvrunner.api.jobs().create(body={
- "script": "crunchrunner",
- "repository": "peteramstutz/cr",
- "script_version": "master",
- "script_parameters": {"tasks": [script_parameters]},
- "runtime_constraints": runtime_constraints
- }, find_or_create=kwargs.get("enable_reuse", True)).execute()
+ runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
- self.arvrunner.jobs[response["uuid"]] = self
+ 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)
- logger.info("Job %s is %s", response["uuid"], response["state"])
-
- if response["state"] in ("Complete", "Failed", "Cancelled"):
- self.done(response)
+ try:
+ response = self.arvrunner.api.jobs().create(body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "script": "crunchrunner",
+ "repository": "arvados",
+ "script_version": "master",
+ "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
+ "script_parameters": {"tasks": [script_parameters], "crunchrunner": crunchrunner_pdh+"/crunchrunner"},
+ "runtime_constraints": runtime_constraints
+ }, find_or_create=kwargs.get("enable_reuse", True)).execute(num_retries=self.arvrunner.num_retries)
+
+ self.arvrunner.jobs[response["uuid"]] = self
+
+ self.arvrunner.pipeline["components"][self.name] = {"job": response}
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
+ body={
+ "components": self.arvrunner.pipeline["components"]
+ }).execute(num_retries=self.arvrunner.num_retries)
+
+ logger.info("Job %s (%s) is %s", self.name, response["uuid"], response["state"])
+
+ if response["state"] in ("Complete", "Failed", "Cancelled"):
+ self.done(response)
+ except Exception as e:
+ logger.error("Got error %s" % str(e))
+ self.output_callback({}, "permanentFail")
+
+ def update_pipeline_component(self, record):
+ self.arvrunner.pipeline["components"][self.name] = {"job": record}
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
+ body={
+ "components": self.arvrunner.pipeline["components"]
+ }).execute(num_retries=self.arvrunner.num_retries)
def done(self, record):
+ try:
+ self.update_pipeline_component(record)
+ except:
+ pass
+
try:
if record["state"] == "Complete":
processStatus = "success"
try:
outputs = {}
- outputs = self.collect_outputs(record["output"])
+ if record["output"]:
+ logc = arvados.collection.Collection(record["log"])
+ log = logc.open(logc.keys()[0])
+ tmpdir = None
+ outdir = None
+ keepdir = None
+ for l in log.readlines():
+ g = tmpdirre.match(l)
+ if g:
+ tmpdir = g.group(1)
+ g = outdirre.match(l)
+ if g:
+ outdir = g.group(1)
+ g = keepre.match(l)
+ if g:
+ keepdir = g.group(1)
+
+ # 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)
finally:
del self.arvrunner.jobs[record["uuid"]]
+
class ArvPathMapper(cwltool.pathmapper.PathMapper):
- def __init__(self, arvrunner, referenced_files, basedir, **kwargs):
- self._pathmap = copy.copy(arvrunner.uploaded)
+ def __init__(self, arvrunner, referenced_files, basedir,
+ collection_pattern, file_pattern, **kwargs):
+ self._pathmap = arvrunner.get_uploaded()
uploadfiles = []
- pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+/.+')
+ pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+')
for src in referenced_files:
if isinstance(src, basestring) and pdh_path.match(src):
- self._pathmap[src] = (src, "$(task.keep)/%s" % src)
- if src in self._pathmap:
- pass
- else:
+ 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)
+ 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="$(task.keep)/%s/%s")
+ fnPattern=file_pattern,
+ project=arvrunner.project_uuid)
for src, ab, st in uploadfiles:
- arvrunner.uploaded[src] = (ab, st.fn)
+ arvrunner.add_uploaded(src, (ab, st.fn))
self._pathmap[src] = (ab, st.fn)
+ self.keepdir = None
+
+ def reversemap(self, target):
+ if target.startswith("keep:"):
+ return (target, target)
+ elif self.keepdir and target.startswith(self.keepdir):
+ return (target, "keep:" + target[len(self.keepdir)+1:])
+ else:
+ return super(ArvPathMapper, self).reversemap(target)
class ArvadosCommandTool(cwltool.draft2tool.CommandLineTool):
def __init__(self, arvrunner, toolpath_object, **kwargs):
- super(ArvadosCommandTool, self).__init__(toolpath_object, outdir="$(task.outdir)", tmpdir="$(task.tmpdir)", **kwargs)
+ super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
self.arvrunner = arvrunner
def makeJobRunner(self):
return ArvadosJob(self.arvrunner)
def makePathMapper(self, reffiles, input_basedir, **kwargs):
- return ArvPathMapper(self.arvrunner, reffiles, input_basedir, **kwargs)
+ return ArvPathMapper(self.arvrunner, reffiles, input_basedir,
+ "$(task.keep)/%s",
+ "$(task.keep)/%s/%s",
+ **kwargs)
class ArvCwlRunner(object):
self.cond = threading.Condition(self.lock)
self.final_output = None
self.uploaded = {}
+ self.num_retries = 4
def arvMakeTool(self, toolpath_object, **kwargs):
if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
def output_callback(self, out, processStatus):
if processStatus == "success":
logger.info("Overall job status is %s", processStatus)
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Complete"}).execute(num_retries=self.num_retries)
+
else:
logger.warn("Overall job status is %s", processStatus)
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Failed"}).execute(num_retries=self.num_retries)
self.final_output = out
+
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:
- logger.info("Job %s is Running", event["object_uuid"])
- with self.lock:
- self.jobs[event["object_uuid"]].running = True
- elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
- logger.info("Job %s is %s", event["object_uuid"], event["properties"]["new_attributes"]["state"])
- try:
- self.cond.acquire()
- self.jobs[event["object_uuid"]].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:
+ import httplib2
+ h = httplib2.Http(ca_certs=arvados.util.ca_certs_path())
+ resp, content = h.request(crunchrunner_download, "GET")
+ resp2, content2 = h.request(certs_download, "GET")
+ with arvados.collection.Collection() as col:
+ with col.open("crunchrunner", "w") as f:
+ f.write(content)
+ with col.open("ca-certificates.crt", "w") as f:
+ f.write(content2)
+
+ col.save_new("crunchrunner binary", ensure_unique_name=True)
+
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["fs_access"] = self.fs_access
kwargs["enable_reuse"] = args.enable_reuse
+ kwargs["outdir"] = "$(task.outdir)"
+ kwargs["tmpdir"] = "$(task.tmpdir)"
+
+ useruuid = self.api.users().current().execute()["uuid"]
+ self.project_uuid = args.project_uuid if args.project_uuid else useruuid
+
if kwargs.get("conformance_test"):
return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
else:
+ self.pipeline = self.api.pipeline_instances().create(
+ body={
+ "owner_uuid": self.project_uuid,
+ "name": shortname(tool.tool["id"]),
+ "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)
+ input_basedir,
+ self.output_callback,
+ docker_outdir="$(task.outdir)",
+ **kwargs)
- for runnable in jobiter:
- if runnable:
- with self.lock:
+ 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:
runnable.run(**kwargs)
- else:
- if self.jobs:
- try:
- self.cond.acquire()
- self.cond.wait()
- finally:
- self.cond.release()
else:
- logger.error("Workflow cannot make any more progress.")
- break
+ if self.jobs:
+ self.cond.wait(1)
+ else:
+ 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()
- finally:
- self.cond.release()
+ while self.jobs:
+ self.cond.wait(1)
- events.close()
+ events.close()
- if self.final_output is None:
- raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
+ 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 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
def main(args, stdout, stderr, api_client=None):
- runner = ArvCwlRunner(api_client=arvados.api('v1'))
args.insert(0, "--leave-outputs")
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()))
+ except Exception as e:
+ logger.error(e)
+ return 1
return cwltool.main.main(args, executor=runner.arvExecutor, makeTool=runner.arvMakeTool, parser=parser)
projects / arvados.git / blobdiff