WX-927 GCP Batch custom mount points tests (#7534)

centaur/src/main/resources/standardTestCases/custom_mount_point.test

@@ -1,20 +1,7 @@
 name: custom_mount_point
 testFormat: workflowsuccess
 
-# Error returned to Centaur:
-#
-# Task custom_mount_point.t:NA:1 failed: Job state is set from RUNNING to FAILED for job projects/blah/locations/us-central1/jobs/job-blah-blah.Job failed due to task failure. Specifically, task with index 0 failed due to the following task event: \"Task state is updated from RUNNING to FAILED on zones/us-central1-b/instances/blah with exit code 125.
-#
-# Exit code 125 appears to be a Docker invocation error. Seeing the following in the logs which seems to suggest the mount point could not be created:
-# docker: Error response from daemon: error while creating mount source path '/some/mnt': mkdir /some: read-only file system.
-#
-# The /some/mnt volume appears to be mounted read-write:
-#              "volumes": [
-#                "/mnt/disks/cromwell_root:/mnt/disks/cromwell_root:rw",
-#                "/some/mnt:/some/mnt:rw"
-#              ]
-
-backends: [Papi, GCPBATCH_FAIL]
+backends: [Papi, GCPBATCH_ALT]
 
 files {
   workflow: custom_mount_point/custom_mount_point.wdl

centaur/src/main/resources/standardTestCases/custom_mount_point/gcpbatch_custom_mount_point.wdl

@@ -0,0 +1,35 @@
+#  1) Mounting a SSD to a custom location and default location with custom disk size
+#  2) Write a file to that mount
+#  3) Changing directory within a command shouldn't break Cromwell
+#  4) Use the file that was written on the mount as an output
+
+# ChrisTM
+task t {
+  String v
+
+  command {
+    echo "bazqux" > some_file
+
+    cd /mnt/disks/some
+    echo "foobar" > some_file
+  }
+
+  output {
+    String out1 = read_string("some_file")
+    String out2 = read_string("/mnt/disks/some/some_file")
+  }
+
+  runtime {
+    docker: "ubuntu:" + v
+    disks: "local-disk 20 SSD, /mnt/disks/some 20 SSD"
+  }
+}
+
+workflow custom_mount_point {
+  call t {input: v="latest"}
+
+  output {
+     String o1 = t.out1
+     String o2 = t.out2
+   }
+}

centaur/src/main/resources/standardTestCases/draft3_custom_mount_point.test

@@ -1,7 +1,6 @@
 name: draft3_custom_mount_point
 testFormat: workflowsuccess
-# probably failing similarly to custom_mount_point
-backends: [Papi, GCPBATCH_FAIL]
+backends: [Papi, GCPBATCH_ALT]
 
 files {
   workflow: wdl_draft3/custom_mount_point/custom_mount_point.wdl

centaur/src/main/resources/standardTestCases/gcpbatch_custom_mount_point.test

@@ -0,0 +1,18 @@
+name: gcpbatch_custom_mount_point
+testFormat: workflowsuccess
+
+backends: [GCPBATCH]
+
+files {
+  workflow: custom_mount_point/gcpbatch_custom_mount_point.wdl
+  # https://github.com/broadinstitute/cromwell/issues/3998
+  options: custom_mount_point/custom_mount_point.options
+}
+
+metadata {
+  "calls.custom_mount_point.t.backend": "GCPBATCH"
+  "calls.custom_mount_point.t.backendStatus": "Success"
+
+  "outputs.custom_mount_point.o1": "bazqux"
+  "outputs.custom_mount_point.o2": "foobar"
+}

centaur/src/main/resources/standardTestCases/gcpbatch_draft3_custom_mount_point.test

@@ -0,0 +1,25 @@
+name: gcpbatch_draft3_custom_mount_point
+testFormat: workflowsuccess
+backends: [GCPBATCH]
+
+files {
+  workflow: wdl_draft3/custom_mount_point/gcpbatch_custom_mount_point.wdl
+  # https://github.com/broadinstitute/cromwell/issues/3998
+  options: wdl_draft3/custom_mount_point/custom_mount_point.options
+}
+
+metadata {
+  "calls.custom_mount_point.local_and_custom.backend": "GCPBATCH"
+  "calls.custom_mount_point.local_and_custom.backendStatus": "Success"
+
+  "calls.custom_mount_point.local_only.backend": "GCPBATCH"
+  "calls.custom_mount_point.local_only.backendStatus": "Success"
+
+  "calls.custom_mount_point.custom_only.backend": "GCPBATCH"
+  "calls.custom_mount_point.custom_only.backendStatus": "Success"
+
+  "outputs.custom_mount_point.o1": "local disk contents"
+  "outputs.custom_mount_point.o2": "custom mount contents"
+  "outputs.custom_mount_point.o3": "local disk contents"
+  "outputs.custom_mount_point.o4": "custom mount contents"
+}

centaur/src/main/resources/standardTestCases/wdl_draft3/custom_mount_point/gcpbatch_custom_mount_point.wdl

@@ -0,0 +1,92 @@
+version 1.0
+
+task local_and_custom {
+  input {
+    String v
+  }
+
+
+  output {
+    String out1 = read_string("some_file")
+    String out2 = read_string("/mnt/disks/some/some_file")
+  }
+  command <<<
+
+    echo "local disk contents" > some_file
+
+    cd /mnt/disks/some
+    echo "custom mount contents" > some_file
+
+  >>>
+  runtime {
+    docker: "ubuntu:" + v
+    disks: "local-disk 20 SSD, /mnt/disks/some 20 SSD"
+  }
+
+}
+
+task local_only {
+
+  input {
+    String v
+  }
+
+  command {
+    echo "local disk contents" > some_file
+  }
+
+  runtime {
+    docker: "ubuntu:" + v
+    disks: "local-disk 20 SSD"
+  }
+
+  output {
+    String out = read_string("some_file")
+  }
+}
+
+task custom_only {
+
+  input {
+    String v
+  }
+
+  command {
+    cd /mnt/disks/some
+    echo "custom mount contents" > some_file
+  }
+
+  runtime {
+    docker: "ubuntu:" + v
+    disks: "/mnt/disks/some 20 SSD"
+  }
+
+  output {
+    String out = read_string("/mnt/disks/some/some_file")
+  }
+}
+
+workflow custom_mount_point {
+
+  call local_and_custom {
+    input:
+      v = "latest"
+  }
+
+  call local_only {
+    input:
+      v = "latest"
+  }
+
+  call custom_only {
+    input:
+      v = "latest"
+  }
+
+  output {
+    String o1 = local_and_custom.out1
+    String o2 = local_and_custom.out2
+    String o3 = local_only.out
+    String o4 = custom_only.out
+  }
+}

docs/backends/GCPBatch.md

@@ -183,6 +183,18 @@ The current default label set automatically applied is:
 
 Any custom labels provided as '`google_labels`' in the [workflow options](../wf_options/Google) are also applied to Google resources by GCP Batch.
 
+### Custom Mount Points
+
+Cromwell's GCP Batch backend supports custom mount points as documented [here](../RuntimeAttributes.md#disks), with the caveat that all custom mount points must be specified under `/mnt/disks`.
+
+e.g. a GCP Batch custom mount point specification should look like:
+
+```
+runtime {
+    disks: "/mnt/disks/my_mnt 30 SSD, /mnt/disks/my_mnt2 500 HDD"
+}
+```
+
 ### Virtual Private Network
 
 Cromwell can arrange for jobs to run in specific GCP private networks via the `config.virtual-private-cloud` stanza of a Batch backend.