19070: Add integration test for copying dependencies

[arvados.git] / sdk / cwl / arvados_cwl / arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 2a5ff3a13a834861c846769af9407b8b1de10c2a..33b4c90c617711f6c2505bda1be35e93ed74137f 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -63,7 +63,7 @@ class ArvadosContainer(JobBase):
         env["TMPDIR"] = self.tmpdir
         return env
 
-    def run(self, runtimeContext):
+    def run(self, toplevelRuntimeContext):
         # ArvadosCommandTool subclasses from cwltool.CommandLineTool,
         # which calls makeJobRunner() to get a new ArvadosContainer
         # object.  The fields that define execution such as
@@ -247,7 +247,8 @@ class ArvadosContainer(JobBase):
                                                                     runtimeContext.project_uuid,
                                                                     runtimeContext.force_docker_pull,
                                                                     runtimeContext.tmp_outdir_prefix,
-                                                                    runtimeContext.match_local_docker)
+                                                                    runtimeContext.match_local_docker,
+                                                                    runtimeContext.copy_deps)
 
         network_req, _ = self.get_requirement("NetworkAccess")
         if network_req:
@@ -300,6 +301,17 @@ class ArvadosContainer(JobBase):
                 "hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0]
             }
 
+        if runtimeContext.enable_preemptible is False:
+            scheduling_parameters["preemptible"] = False
+        else:
+            preemptible_req, _ = self.get_requirement("http://arvados.org/cwl#UsePreemptible")
+            if preemptible_req:
+                scheduling_parameters["preemptible"] = preemptible_req["usePreemptible"]
+            elif runtimeContext.enable_preemptible is True:
+                scheduling_parameters["preemptible"] = True
+            elif runtimeContext.enable_preemptible is None:
+                pass
+
         if self.timelimit is not None and self.timelimit > 0:
             scheduling_parameters["max_run_time"] = self.timelimit
 
@@ -381,6 +393,10 @@ class ArvadosContainer(JobBase):
                     processStatus = "success"
                 else:
                     processStatus = "permanentFail"
+
+                if rcode == 137:
+                    logger.warning("%s Container may have been killed for using too much RAM.  Try resubmitting with a higher 'ramMin'.",
+                                 self.arvrunner.label(self))
             else:
                 processStatus = "permanentFail"
 
@@ -550,6 +566,12 @@ class RunnerContainer(Runner):
         if self.enable_dev:
             command.append("--enable-dev")
 
+        if runtimeContext.enable_preemptible is True:
+            command.append("--enable-preemptible")
+
+        if runtimeContext.enable_preemptible is False:
+            command.append("--disable-preemptible")
+
         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 
         container_req["command"] = command