Merge branch '18947-githttpd'

[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 3c7e9cfaa6d5e91eed03b03222522db9a96c83f9..f75bde81e6cebd655a8378fbd382f18b3bf18d2f 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
@@ -246,7 +246,8 @@ class ArvadosContainer(JobBase):
                                                                     runtimeContext.pull_image,
                                                                     runtimeContext.project_uuid,
                                                                     runtimeContext.force_docker_pull,
-                                                                    runtimeContext.tmp_outdir_prefix)
+                                                                    runtimeContext.tmp_outdir_prefix,
+                                                                    runtimeContext.match_local_docker)
 
         network_req, _ = self.get_requirement("NetworkAccess")
         if network_req:
@@ -294,11 +295,22 @@ class ArvadosContainer(JobBase):
         cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement")
         if cuda_req:
             runtime_constraints["cuda"] = {
-                "device_count": cuda_req.get("deviceCountMin", 1),
+                "device_count": resources.get("cudaDeviceCount", 1),
                 "driver_version": cuda_req["cudaVersionMin"],
-                "hardware_capability": cuda_req["cudaComputeCapabilityMin"]
+                "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
 
@@ -380,6 +392,10 @@ 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"
 
@@ -549,6 +565,12 @@ 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