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 1029ca0e05bff2e0bf501f61fa65f19ea482b2e6..f75bde81e6cebd655a8378fbd382f18b3bf18d2f 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -57,7 +57,13 @@ class ArvadosContainer(JobBase):
     def update_pipeline_component(self, r):
         pass
 
-    def run(self, runtimeContext):
+    def _required_env(self):
+        env = {}
+        env["HOME"] = self.outdir
+        env["TMPDIR"] = self.tmpdir
+        return env
+
+    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
@@ -234,15 +240,14 @@ class ArvadosContainer(JobBase):
                                 "path": "%s/%s" % (self.outdir, self.stdout)}
 
         (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
-        if not docker_req:
-            docker_req = {"dockerImageId": "arvados/jobs:"+__version__}
 
         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
                                                                     docker_req,
                                                                     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:
@@ -279,11 +284,32 @@ class ArvadosContainer(JobBase):
         if self.output_ttl < 0:
             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 
-        storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
-        if storage_class_req and storage_class_req.get("intermediateStorageClass"):
-            container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
+
+        if self.arvrunner.api._rootDesc["revision"] >= "20210628":
+            storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
+            if storage_class_req and storage_class_req.get("intermediateStorageClass"):
+                container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
+            else:
+                container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
+
+        cuda_req, _ = self.get_requirement("http://commonwl.org/cwltool#CUDARequirement")
+        if cuda_req:
+            runtime_constraints["cuda"] = {
+                "device_count": resources.get("cudaDeviceCount", 1),
+                "driver_version": cuda_req["cudaVersionMin"],
+                "hardware_capability": aslist(cuda_req["cudaComputeCapability"])[0]
+            }
+
+        if runtimeContext.enable_preemptible is False:
+            scheduling_parameters["preemptible"] = False
         else:
-            container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
+            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
@@ -366,6 +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"
 
@@ -514,10 +544,10 @@ class RunnerContainer(Runner):
         if runtimeContext.debug:
             command.append("--debug")
 
-        if runtimeContext.storage_classes != "default":
+        if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes:
             command.append("--storage-classes=" + runtimeContext.storage_classes)
 
-        if runtimeContext.intermediate_storage_classes != "default":
+        if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 
         if self.on_error:
@@ -535,6 +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