import logging
import json
import os
+import urllib
+
+import ruamel.yaml as yaml
from cwltool.errors import WorkflowException
from cwltool.process import get_feature, UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFiles
+from cwltool.pathmapper import adjustFiles, adjustDirObjs
from cwltool.utils import aslist
import arvados.collection
from .arvdocker import arv_docker_get_image
from . import done
-from .runner import Runner, arvados_jobs_image
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
+from .fsaccess import CollectionFetcher
+from .pathmapper import NoFollowPathMapper
+from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
+metrics = logging.getLogger('arvados.cwl-runner.metrics')
class ArvadosContainer(object):
"""Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
"output_path": self.outdir,
"cwd": self.outdir,
"priority": 1,
- "state": "Committed"
+ "state": "Committed",
+ "properties": {}
}
runtime_constraints = {}
mounts = {
dirs = set()
for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if tp == "Directory" and '/' not in p[6:]:
+ pdh, p, tp, stg = self.pathmapper.mapper(f)
+ if tp == "Directory" and '/' not in pdh:
mounts[p] = {
"kind": "collection",
- "portable_data_hash": p[6:]
+ "portable_data_hash": pdh[5:]
}
- dirs.add(p[6:])
+ dirs.add(pdh)
+
for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if p[6:].split("/")[0] not in dirs:
+ res, p, tp, stg = self.pathmapper.mapper(f)
+ if res.startswith("keep:"):
+ res = res[5:]
+ elif res.startswith("/keep/"):
+ res = res[6:]
+ else:
+ continue
+ sp = res.split("/", 1)
+ pdh = sp[0]
+ if pdh not in dirs:
mounts[p] = {
"kind": "collection",
- "portable_data_hash": p[6:]
+ "portable_data_hash": pdh
}
-
- if self.generatefiles["listing"]:
- raise UnsupportedRequirement("Generate files not supported")
+ if len(sp) == 2:
+ mounts[p]["path"] = urllib.unquote(sp[1])
+
+ with Perf(metrics, "generatefiles %s" % self.name):
+ if self.generatefiles["listing"]:
+ 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], "", "",
+ separateDirs=False)
+
+ with Perf(metrics, "createfiles %s" % self.name):
+ for f, p in generatemapper.items():
+ if not p.target:
+ pass
+ elif p.type in ("File", "Directory"):
+ source, path = self.arvrunner.fs_access.get_collection(p.resolved)
+ vwd.copy(path, p.target, source_collection=source)
+ elif p.type == "CreateFile":
+ with vwd.open(p.target, "w") as n:
+ n.write(p.resolved.encode("utf-8"))
+
+ with Perf(metrics, "generatefiles.save_new %s" % self.name):
+ vwd.save_new()
+
+ for f, p in generatemapper.items():
+ if not p.target:
+ continue
+ mountpoint = "%s/%s" % (self.outdir, p.target)
+ mounts[mountpoint] = {"kind": "collection",
+ "portable_data_hash": vwd.portable_data_hash(),
+ "path": p.target}
container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
if self.environment:
(docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
if not docker_req:
- docker_req = {"dockerImageId": arvados_jobs_image(self.arvrunner)}
+ docker_req = {"dockerImageId": "arvados/jobs"}
container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
docker_req,
runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
if runtime_req:
if "keep_cache" in runtime_req:
- runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"]
+ runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20
partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
if partition_req:
container_request["use_existing"] = kwargs.get("enable_reuse", True)
container_request["scheduling_parameters"] = scheduling_parameters
+ if kwargs.get("runnerjob", "").startswith("arvwf:"):
+ wfuuid = kwargs["runnerjob"][6:kwargs["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"]
+ container_request["properties"]["template_uuid"] = wfuuid
+
try:
response = self.arvrunner.api.container_requests().create(
body=container_request
).execute(num_retries=self.arvrunner.num_retries)
- self.arvrunner.processes[response["uuid"]] = response["uuid"]
-
- logger.info("Container request %s (%s) state is %s with container %s %s", self.name, response["uuid"], response["state"])
+ self.uuid = response["uuid"]
+ self.arvrunner.processes[self.uuid] = self
if response["state"] == "Final":
+ logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
self.done(response)
+ else:
+ logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
except Exception as e:
- logger.error("Got error %s" % str(e))
+ logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
self.output_callback({}, "permanentFail")
def done(self, record):
else:
processStatus = "permanentFail"
- outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
- self.output_callback(outputs, processStatus)
+ if processStatus == "permanentFail":
+ logc = arvados.collection.CollectionReader(container["log"],
+ 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))
+
+ outputs = {}
+ if container["output"]:
+ outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
+ except WorkflowException as e:
+ logger.error("%s unable to collect output from %s:\n%s",
+ self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
+ processStatus = "permanentFail"
+ except Exception as e:
+ logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
+ processStatus = "permanentFail"
finally:
- del self.arvrunner.processes[record["uuid"]]
+ self.output_callback(outputs, processStatus)
+ if record["uuid"] in self.arvrunner.processes:
+ del self.arvrunner.processes[record["uuid"]]
class RunnerContainer(Runner):
the +body+ argument to container_requests().create().
"""
- workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
-
- with arvados.collection.Collection(api_client=self.arvrunner.api,
- keep_client=self.arvrunner.keep_client,
- num_retries=self.arvrunner.num_retries) as jobobj:
- with jobobj.open("cwl.input.json", "w") as f:
- json.dump(self.job_order, f, sort_keys=True, indent=4)
- jobobj.save_new(owner_uuid=self.arvrunner.project_uuid)
-
- workflowname = os.path.basename(self.tool.tool["id"])
- workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
- workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
- workflowcollection = workflowcollection[5:workflowcollection.index('/')]
- jobpath = "/var/lib/cwl/job/cwl.input.json"
-
- command = ["arvados-cwl-runner", "--local", "--api=containers"]
- if self.output_name:
- command.append("--output-name=" + self.output_name)
-
- if self.output_tags:
- command.append("--output-tags=" + self.output_tags)
+ adjustDirObjs(self.job_order, trim_listing)
- if self.enable_reuse:
- command.append("--enable-reuse")
- else:
- command.append("--disable-reuse")
-
- command.extend([workflowpath, jobpath])
-
- return {
- "command": command,
+ container_req = {
"owner_uuid": self.arvrunner.project_uuid,
"name": self.name,
"output_path": "/var/spool/cwl",
"cwd": "/var/spool/cwl",
"priority": 1,
"state": "Committed",
- "container_image": arvados_jobs_image(self.arvrunner),
+ "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
"mounts": {
- "/var/lib/cwl/workflow": {
- "kind": "collection",
- "portable_data_hash": "%s" % workflowcollection
- },
- jobpath: {
- "kind": "collection",
- "portable_data_hash": "%s/cwl.input.json" % jobobj.portable_data_hash()
+ "/var/lib/cwl/cwl.input.json": {
+ "kind": "json",
+ "content": self.job_order
},
"stdout": {
"kind": "file",
},
"runtime_constraints": {
"vcpus": 1,
- "ram": 1024*1024*256,
+ "ram": 1024*1024 * self.submit_runner_ram,
"API": True
- }
+ },
+ "properties": {}
}
+ if self.tool.tool.get("id", "").startswith("keep:"):
+ sp = self.tool.tool["id"].split('/')
+ workflowcollection = sp[0][5:]
+ workflowname = "/".join(sp[1:])
+ workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
+ container_req["mounts"]["/var/lib/cwl/workflow"] = {
+ "kind": "collection",
+ "portable_data_hash": "%s" % workflowcollection
+ }
+ else:
+ packed = packed_workflow(self.arvrunner, self.tool)
+ 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]
+
+ command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps"]
+ if self.output_name:
+ command.append("--output-name=" + self.output_name)
+ container_req["output_name"] = self.output_name
+
+ if self.output_tags:
+ command.append("--output-tags=" + self.output_tags)
+
+ if kwargs.get("debug"):
+ command.append("--debug")
+
+ if self.enable_reuse:
+ command.append("--enable-reuse")
+ else:
+ command.append("--disable-reuse")
+
+ if self.on_error:
+ command.append("--on-error=" + self.on_error)
+
+ command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
+
+ container_req["command"] = command
+
+ return container_req
+
+
def run(self, *args, **kwargs):
kwargs["keepprefix"] = "keep:"
job_spec = self.arvados_job_spec(*args, **kwargs)
).execute(num_retries=self.arvrunner.num_retries)
self.uuid = response["uuid"]
- self.arvrunner.processes[response["uuid"]] = response["uuid"]
+ self.arvrunner.processes[self.uuid] = self
- logger.info("Submitted container %s", response["uuid"])
+ logger.info("%s submitted container %s", self.arvrunner.label(self), response["uuid"])
if response["state"] == "Final":
self.done(response)
+
+ def done(self, record):
+ try:
+ container = self.arvrunner.api.containers().get(
+ uuid=record["container_uuid"]
+ ).execute(num_retries=self.arvrunner.num_retries)
+ except Exception as e:
+ logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
+ self.arvrunner.output_callback({}, "permanentFail")
+ else:
+ super(RunnerContainer, self).done(container)
+ finally:
+ if record["uuid"] in self.arvrunner.processes:
+ del self.arvrunner.processes[record["uuid"]]
projects / arvados.git / blobdiff