import arvados_cwl.util
from .arvcontainer import RunnerContainer, cleanup_name_for_collection
-from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder, update_from_merged_map
+from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder, update_from_merged_map, print_keep_deps
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
-from .arvworkflow import ArvadosWorkflow, upload_workflow, new_upload_workflow, make_workflow_record
+from .arvworkflow import ArvadosWorkflow, upload_workflow, make_workflow_record
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
from .perf import Perf
from .pathmapper import NoFollowPathMapper
kind = 'error'
elif record.levelno >= logging.WARNING:
kind = 'warning'
- if kind == 'warning' and record.name == "salad":
+ if kind == 'warning' and record.name in ("salad", "crunchstat_summary"):
# Don't send validation warnings to runtime status,
# they're noisy and unhelpful.
return
self.stdout = stdout
self.fast_submit = False
self.git_info = arvargs.git_info
+ self.debug = False
if keep_client is not None:
self.keep_client = keep_client
activity statuses, for example in the RuntimeStatusLoggingHandler.
"""
- if kind not in ('error', 'warning'):
+ if kind not in ('error', 'warning', 'activity'):
# Ignore any other status kind
return
runtime_status = current.get('runtime_status', {})
original_updatemessage = updatemessage = runtime_status.get(kind, "")
- if not updatemessage:
+ if kind == "activity" or not updatemessage:
updatemessage = message
# Subsequent messages tacked on in detail
while keys:
page = keys[:pageSize]
try:
- proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries)
+ proc_states = table.list(filters=[["uuid", "in", page]], select=["uuid", "container_uuid", "state", "log_uuid",
+ "output_uuid", "modified_at", "properties",
+ "runtime_constraints"]).execute(num_retries=self.num_retries)
except Exception as e:
- logger.exception("Error checking states on API server: %s", e)
+ logger.warning("Temporary error checking states on API server: %s", e)
remain_wait = self.poll_interval
continue
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
+ self.runtime_status_update("activity", "initialization")
+
git_info = self.get_git_info(updated_tool) if self.git_info else {}
if git_info:
logger.info("Git provenance")
if git_info[g]:
logger.info(" %s: %s", g.split("#", 1)[1], git_info[g])
+ runtimeContext.git_info = git_info
+
workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
runtimeContext.copy_deps = True
runtimeContext.match_local_docker = True
+ if runtimeContext.print_keep_deps:
+ runtimeContext.copy_deps = False
+ runtimeContext.match_local_docker = False
+
if runtimeContext.update_workflow and self.project_uuid is None:
# If we are updating a workflow, make sure anything that
# gets uploaded goes into the same parent project, unless
self.project_uuid = runtimeContext.project_uuid
+ self.runtime_status_update("activity", "data transfer")
+
# Upload local file references in the job order.
with Perf(metrics, "upload_job_order"):
job_order, jobmapper = upload_job_order(self, "%s input" % runtimeContext.name,
updated_tool, job_order, runtimeContext)
+ # determine if we are submitting or directly executing the workflow.
+ #
# the last clause means: if it is a command line tool, and we
# are going to wait for the result, and always_submit_runner
# is false, then we don't submit a runner process.
- submitting = (runtimeContext.update_workflow or
- runtimeContext.create_workflow or
- (runtimeContext.submit and not
+ submitting = (runtimeContext.submit and not
(updated_tool.tool["class"] == "CommandLineTool" and
runtimeContext.wait and
- not runtimeContext.always_submit_runner)))
+ not runtimeContext.always_submit_runner))
loadingContext = self.loadingContext.copy()
loadingContext.do_validate = False
loadingContext.disable_js_validation = True
- # if submitting and not self.fast_submit:
- # loadingContext.do_update = False
- # # Document may have been auto-updated. Reload the original
- # # document with updating disabled because we want to
- # # submit the document with its original CWL version, not
- # # the auto-updated one.
- # with Perf(metrics, "load_tool original"):
- # tool = load_tool(updated_tool.tool["id"], loadingContext)
- # else:
tool = updated_tool
# Upload direct dependencies of workflow steps, get back mapping of files to keep references.
with Perf(metrics, "upload_workflow_deps"):
merged_map = upload_workflow_deps(self, tool, runtimeContext)
else:
+ # in the fast submit case, we are running a workflow that
+ # has already been uploaded to Arvados, so we assume all
+ # the dependencies have been pinned to keep references and
+ # there is nothing to do.
merged_map = {}
- # Recreate process object (ArvadosWorkflow or
- # ArvadosCommandTool) because tool document may have been
- # updated by upload_workflow_deps in ways that modify
- # hints or requirements.
loadingContext.loader = tool.doc_loader
loadingContext.avsc_names = tool.doc_schema
loadingContext.metadata = tool.metadata
loadingContext.skip_resolve_all = True
- #with Perf(metrics, "load_tool"):
- # tool = load_tool(tool.tool, loadingContext)
workflow_wrapper = None
- if submitting and not self.fast_submit:
+ if (submitting and not self.fast_submit) or runtimeContext.update_workflow or runtimeContext.create_workflow or runtimeContext.print_keep_deps:
# upload workflow and get back the workflow wrapper
- workflow_wrapper = new_upload_workflow(self, tool, job_order,
- runtimeContext.project_uuid,
- runtimeContext,
- uuid=runtimeContext.update_workflow,
- submit_runner_ram=runtimeContext.submit_runner_ram,
- name=runtimeContext.name,
- merged_map=merged_map,
- submit_runner_image=runtimeContext.submit_runner_image,
- git_info=git_info,
- set_defaults=(runtimeContext.update_workflow or runtimeContext.create_workflow),
- jobmapper=jobmapper)
+ workflow_wrapper = upload_workflow(self, tool, job_order,
+ runtimeContext.project_uuid,
+ runtimeContext,
+ uuid=runtimeContext.update_workflow,
+ submit_runner_ram=runtimeContext.submit_runner_ram,
+ name=runtimeContext.name,
+ merged_map=merged_map,
+ submit_runner_image=runtimeContext.submit_runner_image,
+ git_info=git_info,
+ set_defaults=(runtimeContext.update_workflow or runtimeContext.create_workflow),
+ jobmapper=jobmapper)
if runtimeContext.update_workflow or runtimeContext.create_workflow:
- # Now create a workflow record and exit.
+ # We're registering the workflow, so create or update
+ # the workflow record and then exit.
uuid = make_workflow_record(self, workflow_wrapper, runtimeContext.name, tool,
runtimeContext.project_uuid, runtimeContext.update_workflow)
self.stdout.write(uuid + "\n")
return (None, "success")
+ if runtimeContext.print_keep_deps:
+ # Just find and print out all the collection dependencies and exit
+ print_keep_deps(self, runtimeContext, merged_map, tool)
+ return (None, "success")
+
+ # Did not register a workflow, we're going to submit
+ # it instead.
loadingContext.loader.idx.clear()
loadingContext.loader.idx["_:main"] = workflow_wrapper
workflow_wrapper["id"] = "_:main"
- # Reload just the wrapper workflow.
+ # Reload the minimal wrapper workflow.
self.fast_submit = True
tool = load_tool(workflow_wrapper, loadingContext)
loadingContext.loader.idx["_:main"] = workflow_wrapper
if not submitting:
+ # If we are going to run the workflow now (rather than
+ # submit it), we need to update the workflow document
+ # replacing file references with keep references. If we
+ # are just going to construct a run submission, we don't
+ # need to do this.
update_from_merged_map(tool, merged_map)
self.apply_reqs(job_order, tool)
runnerjob = None
if runtimeContext.submit:
- # Submit a runner job to run the workflow for us.
+ # We are submitting instead of running immediately.
+ #
+ # Create a "Runner job" that when run() is invoked,
+ # creates the container request to run the workflow.
if self.work_api == "containers":
if submitting:
loadingContext.metadata = updated_tool.metadata.copy()
runtimeContext)
if runtimeContext.submit and not runtimeContext.wait:
+ # User provided --no-wait so submit the container request,
+ # get the container request uuid, print it out, and exit.
runnerjob = next(jobiter)
runnerjob.run(runtimeContext)
self.stdout.write(runnerjob.uuid+"\n")
return (None, "success")
+ # We either running the workflow directly, or submitting it
+ # and will wait for a final result.
+
+ self.runtime_status_update("activity", "workflow execution")
+
current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
if current_container:
logger.info("Running inside container %s", current_container.get("uuid"))
if (self.task_queue.in_flight + len(self.processes)) > 0:
self.workflow_eval_lock.wait(3)
else:
- logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
+ if self.final_status is None:
+ logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
break
if self.stop_polling.is_set():
if self.final_output is None:
raise WorkflowException("Workflow did not return a result.")
+ if runtimeContext.usage_report_notes:
+ logger.info("Steps with low resource utilization (possible optimization opportunities):")
+ for x in runtimeContext.usage_report_notes:
+ logger.info(" %s", x)
+
if runtimeContext.submit and isinstance(tool, Runner):
logger.info("Final output collection %s", tool.final_output)
if workbench2 or workbench1:
projects / arvados.git / blobdiff