Drill down on metrics on job submission.

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index abb41f4f17553a4fe68600a3fa0f15681260e942..0818d5d62b4dcd023153daf1e69ace6b34175655 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -38,21 +38,27 @@ class ArvadosJob(object):
         }
         runtime_constraints = {}
 
-        if self.generatefiles["listing"]:
-            vwd = arvados.collection.Collection()
-            script_parameters["task.vwd"] = {}
-            generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
-                                        separateDirs=False)
-            for f, p in generatemapper.items():
-                if p.type == "CreateFile":
-                    with vwd.open(p.target, "w") as n:
-                        n.write(p.resolved.encode("utf-8"))
-            vwd.save_new()
-            for f, p in generatemapper.items():
-                if p.type == "File":
-                    script_parameters["task.vwd"][p.target] = p.resolved
-                if p.type == "CreateFile":
-                    script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
+        with Perf(metrics, "generatefiles %s" % self.name):
+            if self.generatefiles["listing"]:
+                vwd = arvados.collection.Collection()
+                script_parameters["task.vwd"] = {}
+                generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
+                                                          separateDirs=False)
+
+                with Perf(metrics, "createfiles %s" % self.name):
+                    for f, p in generatemapper.items():
+                        if p.type == "CreateFile":
+                            with vwd.open(p.target, "w") as n:
+                                n.write(p.resolved.encode("utf-8"))
+
+                with Perf(metrics, "generatefiles.save_new %s" % self.name):
+                    vwd.save_new()
+
+                for f, p in generatemapper.items():
+                    if p.type == "File":
+                        script_parameters["task.vwd"][p.target] = p.resolved
+                    if p.type == "CreateFile":
+                        script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
 
         script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
         if self.environment:
@@ -74,11 +80,12 @@ class ArvadosJob(object):
         if self.permanentFailCodes:
             script_parameters["task.permanentFailCodes"] = self.permanentFailCodes
 
-        (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.arvrunner.project_uuid)
-        else:
-            runtime_constraints["docker_image"] = "arvados/jobs"
+        with Perf(metrics, "arv_docker_get_image %s" % self.name):
+            (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.arvrunner.project_uuid)
+            else:
+                runtime_constraints["docker_image"] = "arvados/jobs"
 
         resources = self.builder.resources
         if resources is not None:

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index f4ce44670dd7f1f9dd282158196af8b214874982..8eb8fe6fee50e0722ee7066171ff7b7bbc4a10c5 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -13,8 +13,10 @@ import ruamel.yaml as yaml
 
 from .runner import upload_docker, upload_dependencies, trim_listing
 from .arvtool import ArvadosCommandTool
+from .perf import Perf
 
 logger = logging.getLogger('arvados.cwl-runner')
+metrics = logging.getLogger('arvados.cwl-runner.metrics')
 
 def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
     upload_docker(arvRunner, tool)
@@ -62,40 +64,42 @@ class ArvadosWorkflow(Workflow):
         if req:
             document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
 
-            workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
-            workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
-            packed = pack(document_loader, workflowobj, uri, self.metadata)
-
-            upload_dependencies(self.arvrunner,
-                                kwargs.get("name", ""),
-                                document_loader,
-                                packed,
-                                uri,
-                                False)
-
-            upload_dependencies(self.arvrunner,
-                                os.path.basename(joborder.get("id", "#")),
-                                document_loader,
-                                joborder,
-                                joborder.get("id", "#"),
-                                False)
-
-            joborder_keepmount = copy.deepcopy(joborder)
-
-            def keepmount(obj):
-                if obj["location"].startswith("keep:"):
-                    obj["location"] = "/keep/" + obj["location"][5:]
-                    if "listing" in obj:
-                        del obj["listing"]
-                elif obj["location"].startswith("_:"):
-                    del obj["location"]
-                else:
-                    raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
-
-            adjustFileObjs(joborder_keepmount, keepmount)
-            adjustDirObjs(joborder_keepmount, keepmount)
-            adjustFileObjs(packed, keepmount)
-            adjustDirObjs(packed, keepmount)
+            with Perf(metrics, "subworkflow upload_deps"):
+                workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
+                workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
+                packed = pack(document_loader, workflowobj, uri, self.metadata)
+
+                upload_dependencies(self.arvrunner,
+                                    kwargs.get("name", ""),
+                                    document_loader,
+                                    packed,
+                                    uri,
+                                    False)
+
+                upload_dependencies(self.arvrunner,
+                                    os.path.basename(joborder.get("id", "#")),
+                                    document_loader,
+                                    joborder,
+                                    joborder.get("id", "#"),
+                                    False)
+
+            with Perf(metrics, "subworkflow adjust"):
+                joborder_keepmount = copy.deepcopy(joborder)
+
+                def keepmount(obj):
+                    if obj["location"].startswith("keep:"):
+                        obj["location"] = "/keep/" + obj["location"][5:]
+                        if "listing" in obj:
+                            del obj["listing"]
+                    elif obj["location"].startswith("_:"):
+                        del obj["location"]
+                    else:
+                        raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
+
+                adjustFileObjs(joborder_keepmount, keepmount)
+                adjustDirObjs(joborder_keepmount, keepmount)
+                adjustFileObjs(packed, keepmount)
+                adjustDirObjs(packed, keepmount)
 
             wf_runner = {
                 "class": "CommandLineTool",
@@ -104,7 +108,6 @@ class ArvadosWorkflow(Workflow):
                 "outputs": self.tool["outputs"],
                 "stdout": "cwl.output.json",
                 "requirements": workflowobj["requirements"]+[
-                    {"class": "InlineJavascriptRequirement"},
                     {
                     "class": "InitialWorkDirRequirement",
                     "listing": [{
@@ -116,7 +119,7 @@ class ArvadosWorkflow(Workflow):
                         }]
                 }],
                 "hints": workflowobj["hints"],
-                "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.yml"]
+                "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
             }
             kwargs["loader"] = self.doc_loader
             kwargs["avsc_names"] = self.doc_schema