add the --shm-size parameter at runtime #1821

cwltool/docker.py

@@ -429,7 +429,10 @@ def create_runtime(
                     "assurance.",
                     self.name,
                 )
-
+        # add ShmSize parameter to docker
+        (shm_size_od, shm_bool) = self.builder.get_requirement("http://commonwl.org/cwltool#ShmSize")
+        if shm_bool:
+            runtime.append("--shm-size=%s" % shm_size_od["shmSize"])
         return runtime, cidfile_path
 
 

cwltool/extensions-v1.2.yml

@@ -240,4 +240,18 @@ $graph:
         - Specify the desired method of dealing with loop outputs
         - Default. Propagates only the last computed element to the subsequent steps when the loop terminates.
         - Propagates a single array with all output values to the subsequent steps when the loop terminates.
+- name: ShmSize
+  type: record
+  extends: cwl:ProcessRequirement
+  inVocab: false
+  fields:
+    class:
+      type: string
+      doc: 'cwltool:ShmSize'
+      jsonldPredicate:
+        "_id": "@type"
+        "_type": "@vocab"
+    shmSize:
+      type: string
+      doc: "Size of /dev/shm. The format is <number><unit>. number must be greater than 0. Unit is optional and can be b (bytes), k (kilobytes), m (megabytes), or g (gigabytes). If you omit the unit, the system uses bytes. If you omit the size entirely, the system uses 64m."
 

cwltool/process.py

@@ -121,6 +121,7 @@ def filter(self, record: logging.LogRecord) -> bool:
     "http://commonwl.org/cwltool#LoadListingRequirement",
     "http://commonwl.org/cwltool#InplaceUpdateRequirement",
     "http://commonwl.org/cwltool#CUDARequirement",
+    "http://commonwl.org/cwltool#ShmSize",
 ]
 
 cwl_files = (

tests/test_docker.py

@@ -264,3 +264,21 @@ def test_singularity_required_missing_secfile(
         "tests/secondary-files-required-missing-container.cwl:16:5: Missing required secondary file"
     )
     assert "file.ext3" in stderr
+
+
+@needs_docker
+def test_docker_shm_size(tmp_path: Path) -> None:
+    result_code, stdout, stderr = get_main_output(
+        [
+            "--enable-ext",
+            "--default-container",
+            "docker.io/debian:stable-slim",
+            "--outdir",
+            str(tmp_path),
+            get_data("tests/wf/shm_size.cwl"),
+        ]
+    )
+    stderr = re.sub(r"\s\s+", " ", stderr)
+    assert result_code == 0
+    assert "--shm-size=128m" in stderr
+

tests/wf/shm_size.cwl

@@ -0,0 +1,17 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.2
+requirements:
+  cwltool:ShmSize:
+    shmSize: 128m
+inputs: []
+
+outputs:
+  output:
+    type: stdout
+
+baseCommand: echo
+
+stdout: shm-size.txt
+
+arguments: [ $(runtime) ]