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Merge branch '19744-acr-crunchstat' refs #19744
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
executor.py
diff --git
a/sdk/cwl/arvados_cwl/executor.py
b/sdk/cwl/arvados_cwl/executor.py
index 22e3f1fdeb124ae6cd0943a18214af73a8f1a1eb..432b380aabcd90c4c91ff3d7d72a9af29ab52823 100644
(file)
--- a/
sdk/cwl/arvados_cwl/executor.py
+++ b/
sdk/cwl/arvados_cwl/executor.py
@@
-34,7
+34,7
@@
from arvados.errors import ApiError
import arvados_cwl.util
from .arvcontainer import RunnerContainer, cleanup_name_for_collection
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, make_workflow_record
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
from .arvworkflow import ArvadosWorkflow, upload_workflow, make_workflow_record
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
@@
-70,7
+70,7
@@
class RuntimeStatusLoggingHandler(logging.Handler):
kind = 'error'
elif record.levelno >= logging.WARNING:
kind = 'warning'
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
# Don't send validation warnings to runtime status,
# they're noisy and unhelpful.
return
@@
-146,6
+146,7
@@
class ArvCwlExecutor(object):
self.stdout = stdout
self.fast_submit = False
self.git_info = arvargs.git_info
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
if keep_client is not None:
self.keep_client = keep_client
@@
-368,9
+369,11
@@
The 'jobs' API is no longer supported.
while keys:
page = keys[:pageSize]
try:
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:
except Exception as e:
- logger.
exception("E
rror checking states on API server: %s", e)
+ logger.
warning("Temporary e
rror checking states on API server: %s", e)
remain_wait = self.poll_interval
continue
remain_wait = self.poll_interval
continue
@@
-602,6
+605,8
@@
The 'jobs' API is no longer supported.
if git_info[g]:
logger.info(" %s: %s", g.split("#", 1)[1], git_info[g])
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"]
workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
@@
-648,6
+653,10
@@
The 'jobs' API is no longer supported.
runtimeContext.copy_deps = True
runtimeContext.match_local_docker = True
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
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
@@
-670,12
+679,10
@@
The 'jobs' API is no longer supported.
# are going to wait for the result, and always_submit_runner
# is false, then we don't submit a runner process.
# 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
(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 = self.loadingContext.copy()
loadingContext.do_validate = False
@@
-701,7
+708,7
@@
The 'jobs' API is no longer supported.
loadingContext.skip_resolve_all = True
workflow_wrapper = None
loadingContext.skip_resolve_all = True
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 = upload_workflow(self, tool, job_order,
# upload workflow and get back the workflow wrapper
workflow_wrapper = upload_workflow(self, tool, job_order,
@@
-724,6
+731,11
@@
The 'jobs' API is no longer supported.
self.stdout.write(uuid + "\n")
return (None, "success")
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()
# Did not register a workflow, we're going to submit
# it instead.
loadingContext.loader.idx.clear()
@@
-866,7
+878,8
@@
The 'jobs' API is no longer supported.
if (self.task_queue.in_flight + len(self.processes)) > 0:
self.workflow_eval_lock.wait(3)
else:
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():
break
if self.stop_polling.is_set():
@@
-916,6
+929,11
@@
The 'jobs' API is no longer supported.
if self.final_output is None:
raise WorkflowException("Workflow did not return a result.")
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:
if runtimeContext.submit and isinstance(tool, Runner):
logger.info("Final output collection %s", tool.final_output)
if workbench2 or workbench1: