broadinstitute · mcovarr · Feb 7, 2025 · Jan 31, 2025 · Jan 31, 2025 · Jan 31, 2025
@@ -27,7 +27,7 @@ be found [here](https://cromwell.readthedocs.io/en/stable/backends/HPC/#optional
 - The `genomics` configuration entry was renamed to `batch`, see [ReadTheDocs](https://cromwell.readthedocs.io/en/stable/backends/GCPBatch/) for more information.
 - Fixes a bug with not being able to recover jobs on Cromwell restart.
 - Fixes machine type selection to match the Google Cloud Life Sciences backend, including default n1 non shared-core machine types and correct handling of `cpuPlatform` to select n2 or n2d machine types as appropriate.
-- Fixes the preemption error handling, now, the correct error message is printed, this also handles the other potential exit codes.
+- Fixes preemption and maxRetries behavior. In particular, once a task has exhausted its allowed preemptible attempts, the task will be scheduled again on a non-preemptible VM.
 - Fixes error message reporting for failed jobs.
 - Fixes the "retry with more memory" feature.
 - Fixes the reference disk feature.

@@ -1,6 +1,6 @@
 name: checkpointing
 testFormat: workflowsuccess
-backends: [Papiv2, GCPBATCH]
+backends: [Papiv2, GCPBATCH_ALT]
 
 files {
   workflow: checkpointing/checkpointing.wdl

@@ -0,0 +1,70 @@
+version 1.0
+
+workflow checkpointing {
+  call count { input: count_to = 100 }
+  output {
+    String preempted = count.preempted
+  }
+}
+
+task count {
+  input {
+    Int count_to
+  }
+
+  meta {
+    volatile: true
+  }
+
+  command <<<
+    # Read from the my_checkpoint file if there's content there:
+    FROM_CKPT=$(cat my_checkpoint | tail -n1 | awk '{ print $1 }')
+    FROM_CKPT=${FROM_CKPT:-1}
+
+    # We don't want any single VM run the entire count, so work out the max counter value for this attempt:
+    MAX="$(($FROM_CKPT + 66))"
+
+    INSTANCE_NAME=$(curl -s "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google")
+    echo "Discovered instance: $INSTANCE_NAME"
+
+    # Run the counter:
+    echo '--' >> my_checkpoint
+    for i in $(seq $FROM_CKPT ~{count_to})
+    do
+      echo $i
+      echo $i ${INSTANCE_NAME} $(date) >> my_checkpoint
+
+      # If we're over our max, "preempt" the VM by simulating a maintenance event:
+      if [ "${i}" -gt "${MAX}" ]
+      then
+        fully_qualified_zone=$(curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone)
+        zone=$(basename "$fully_qualified_zone")
+        gcloud beta compute instances simulate-maintenance-event $(curl -s "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google") --zone=$zone -q
+        sleep 60
+      fi
+
+      sleep 1
+    done
+
+    # Prove that we got preempted at least once:
+    FIRST_INSTANCE=$(cat my_checkpoint | head -n1 | awk '{ print $2 }')
+    LAST_INSTANCE=$(cat my_checkpoint | tail -n1 | awk '{ print $2 }')
+    if [ "${FIRST_INSTANCE}" != "LAST_INSTANCE" ]
+    then
+      echo "GOTPREEMPTED" > preempted.txt
+    else
+      echo "NEVERPREEMPTED" > preempted.txt
+    fi
+  >>>
+
+  runtime {
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:slim"
+    preemptible: 3
+    checkpointFile: "my_checkpoint"
+  }
+
+  output {
+    File checkpoint_log = "my_checkpoint"
+    String preempted = read_string("preempted.txt")
+  }
+}
@@ -0,0 +1,13 @@
+name: gcpbatch_checkpointing
+testFormat: workflowsuccess
+backends: [GCPBATCH]
+
+files {
+  workflow: checkpointing/gcpbatch_checkpointing.wdl
+}
+
+metadata {
+  workflowName: checkpointing
+  status: Succeeded
+  "outputs.checkpointing.preempted": "GOTPREEMPTED"
+}
@@ -11,5 +11,5 @@ metadata {
   "calls.required_files.check_it.executionStatus": "Done"
   "calls.required_files.do_it.executionStatus": "Failed"
   "calls.required_files.do_it.retryableFailure": "false"
-  "calls.required_files.do_it.failures.0.message": ~~"failed"
+  "calls.required_files.do_it.failures.0.message": ~~"Job exited without an error, exit code 0. Batch error code 0. Job failed with an unknown reason"
 }
@@ -0,0 +1,13 @@
+name: gcpbatch_papi_preemptible_and_max_retries
+testFormat: workflowfailure
+backends: [GCPBATCH]
+
+files {
+  workflow: papi_preemptible_and_max_retries/gcpbatch_papi_preemptible_and_max_retries.wdl
+}
+
+metadata {
+  workflowName: papi_preemptible_and_max_retries
+  status: Failed
+  "papi_preemptible_and_max_retries.delete_self.-1.attempt": 3
+}
@@ -0,0 +1,28 @@
+name: gcpbatch_preemptible_and_memory_retry
+testFormat: workflowfailure
+# The original version of this test was tailored to the quirks of Papi v2 in depending on the misdiagnosis of its own
+# VM deletion as a preemption event. However GCP Batch perhaps more correctly diagnoses VM deletion as a weird
+# non-preemption event. The GCPBATCH version of this test uses `gcloud beta compute instances simulate-maintenance-event`
+# to simulate a preemption in a way that GCP Batch actually perceives as a preemption.
+backends: [GCPBATCH]
+
+files {
+  workflow: retry_with_more_memory/gcpbatch/preemptible_and_memory_retry.wdl
+  options: retry_with_more_memory/retry_with_more_memory.options
+}
+
+metadata {
+  workflowName: preemptible_and_memory_retry
+  status: Failed
+  "failures.0.message": "Workflow failed"
+  "failures.0.causedBy.0.message": "stderr for job `preemptible_and_memory_retry.imitate_oom_error_on_preemptible:NA:3` contained one of the `memory-retry-error-keys: [OutOfMemory,Killed]` specified in the Cromwell config. Job might have run out of memory."
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.1.preemptible": "true"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.1.executionStatus": "RetryableFailure"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.1.runtimeAttributes.memory": "1 GB"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.2.preemptible": "false"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.2.executionStatus": "RetryableFailure"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.2.runtimeAttributes.memory": "1 GB"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.3.preemptible": "false"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.3.executionStatus": "Failed"
+  "preemptible_and_memory_retry.imitate_oom_error_on_preemptible.-1.3.runtimeAttributes.memory": "1.1 GB"
+}
@@ -0,0 +1,11 @@
+name: gcpbatch_preemptible_basic
+testFormat: workflowsuccess
+backends: [GCPBATCH]
+
+files {
+  workflow: preemptible_basic/gcpbatch_preemptible_basic.wdl
+}
+
+metadata {
+  status: Succeeded
+}
@@ -14,5 +14,5 @@ metadata {
   workflowName: requester_pays_localization
   status: Failed
   "failures.0.message": "Workflow failed"
-  "failures.0.causedBy.0.message": ~~"failed"
+  "failures.0.causedBy.0.message": ~~"The job was stopped before the command finished. Batch error code 0. Job failed with an unknown reason"
 }
@@ -1,5 +1,5 @@
 name: gcpbatch_retry_with_more_memory
-testFormat: workflowfailure
+testFormat: workflowsuccess
 backends: [GCPBATCH]
 
 files {
@@ -9,13 +9,10 @@ files {
 
 metadata {
   workflowName: retry_with_more_memory
-  status: Failed
-  "failures.0.message": "Workflow failed"
-  "failures.0.causedBy.0.message": "stderr for job `retry_with_more_memory.imitate_oom_error:NA:3` contained one of the `memory-retry-error-keys: [OutOfMemory,Killed]` specified in the Cromwell config. Job might have run out of memory."
+  status: Succeeded
   "retry_with_more_memory.imitate_oom_error.-1.1.executionStatus": "RetryableFailure"
   "retry_with_more_memory.imitate_oom_error.-1.1.runtimeAttributes.memory": "1 GB"
   "retry_with_more_memory.imitate_oom_error.-1.2.executionStatus": "RetryableFailure"
   "retry_with_more_memory.imitate_oom_error.-1.2.runtimeAttributes.memory": "1.1 GB"
-  "retry_with_more_memory.imitate_oom_error.-1.3.executionStatus": "Failed"
-  "retry_with_more_memory.imitate_oom_error.-1.3.runtimeAttributes.memory": "1.2100000000000002 GB"
+  "outputs.retry_with_more_memory.memory_output": "1.2100000000000002 GB"
 }
@@ -1,7 +1,7 @@
 name: papi_preemptible_and_max_retries
 testFormat: workflowfailure
-# faking own preemption doesn't work on GCP Batch
-backends: [Papiv2, GCPBATCH_TESTING_PAPIV2_QUIRKS]
+# Faking own preemption has to be done differently on GCP Batch
+backends: [Papiv2, GCPBATCH_ALT]
 
 files {
   workflow: papi_preemptible_and_max_retries/papi_preemptible_and_max_retries.wdl

@@ -0,0 +1,31 @@
+version 1.0
+
+task delete_self {
+
+  command {
+      preemptible=$(curl -H "Metadata-Flavor: Google" "http://metadata.google.internal/computeMetadata/v1/instance/scheduling/preemptible")
+
+      # Simulate a maintenance event on ourselves if running on a preemptible VM, otherwise delete ourselves.
+      fully_qualified_zone=$(curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone)
+      zone=$(basename "$fully_qualified_zone")
+
+      if [ "$preemptible" = "TRUE" ]; then
+        gcloud beta compute instances simulate-maintenance-event $(curl -s "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google") --zone=$zone -q
+        sleep 60
+      else
+        # We need to actually delete ourselves if the VM is not preemptible; simulated maintenance events don't seem to
+        # precipitate the demise of on-demand VMs.
+        gcloud compute instances delete $(curl -s "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google") --zone=$zone -q
+      fi
+  }
+
+  runtime {
+    preemptible: 1
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:slim"
+    maxRetries: 1
+  }
+}
+
+workflow papi_preemptible_and_max_retries {
+  call delete_self
+}
@@ -1,8 +1,10 @@
 name: preemptible_and_memory_retry
 testFormat: workflowfailure
-# The original version of this test seems to have been tailored to the quirks of Papi v2 in depending on the misdiagnosis of its own VM deletion as a preemption event. GCP Batch perhaps more correctly diagnoses the VM deletion as a weird non-preemption happening, but that frustrates the logic of this test.
-# Disabling this as it's not possible to induce a real preemption.
-backends: [Papiv2, GCPBATCH_TESTING_PAPIV2_QUIRKS]
+# The original version of this test was tailored to the quirks of Papi v2 in depending on the misdiagnosis of its own
+# VM deletion as a preemption event. However GCP Batch perhaps more correctly diagnoses VM deletion as a weird
+# non-preemption event. The GCPBATCH version of this test uses `gcloud beta compute instances simulate-maintenance-event`
+# to simulate a preemption in a way that GCP Batch actually perceives as a preemption.
+backends: [Papiv2, GCPBATCH_ALT]
 
 files {
   workflow: retry_with_more_memory/preemptible_and_memory_retry.wdl

@@ -0,0 +1,11 @@
+name: preemptible_basic
+testFormat: workflowsuccess
+backends: [Papiv2, GCPBATCH_ALT]
+
+files {
+  workflow: preemptible_basic/preemptible_basic.wdl
+}
+
+metadata {
+  status: Succeeded
+}
@@ -0,0 +1,33 @@
+version 1.0
+
+task delete_self_if_preemptible {
+
+  command <<<
+    # Prepend date, time and pwd to xtrace log entries.
+    PS4='\D{+%F %T} \w $ '
+    set -o errexit -o nounset -o pipefail -o xtrace
+
+    preemptible=$(curl -H "Metadata-Flavor: Google" "http://metadata.google.internal/computeMetadata/v1/instance/scheduling/preemptible")
+
+    # Perform a maintenance event on this VM if it is preemptible, which should cause it to be preempted.
+    # Since `preemptible: 1` the job should be restarted on a non-preemptible VM.
+    if [ "$preemptible" = "TRUE" ]; then
+      fully_qualified_zone=$(curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone)
+      zone=$(basename "$fully_qualified_zone")
+
+      gcloud beta compute instances simulate-maintenance-event $(curl -s "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google") --zone=$zone -q
+      sleep 60
+    fi
+
+  >>>
+
+  runtime {
+    preemptible: 1
+    docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:slim"
+  }
+}
+
+
+workflow preemptible_basic {
+  call delete_self_if_preemptible
+}
@@ -9,7 +9,7 @@ task delete_self_if_preemptible {
     # Delete self if running on a preemptible VM. This should produce an "error 10" which Cromwell should treat as a preemption.
     # Since `preemptible: 1` the job should be restarted on a non-preemptible VM.
     if [ "$preemptible" = "TRUE" ]; then
-    
+
       fully_qualified_zone=$(curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone)
       zone=$(basename "$fully_qualified_zone")
 
@@ -25,6 +25,6 @@ task delete_self_if_preemptible {
 }
 
 
-workflow error_10_preemptible {
+workflow preemptible_basic {
   call delete_self_if_preemptible
 }
@@ -12,13 +12,14 @@ task imitate_oom_error_on_preemptible {
 
     preemptible=$(curl -H "Metadata-Flavor: Google" "http://metadata.google.internal/computeMetadata/v1/instance/scheduling/preemptible")
 
-    # Delete self if running on a preemptible VM
+    # Simulate a maintenance event on ourselves if running on a preemptible VM
     # Since `preemptible: 1` the job should be restarted on a non-preemptible VM.
     if [ "$preemptible" = "TRUE" ]; then
       fully_qualified_zone=$(curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone)
       zone=$(basename "$fully_qualified_zone")
 
-      gcloud compute instances delete $(curl -s "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google") --zone=$zone -q
+      gcloud beta compute instances simulate-maintenance-event $(curl -s "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google") --zone=$zone -q
+      sleep 60
     fi
 
     # Should reach here on the second attempt

@@ -2,12 +2,21 @@ version 1.0
 
 task imitate_oom_error {
   command {
-    printf "Exception in thread "main" java.lang.OutOfMemoryError: testing\n\tat Test.main(Test.java:1)\n" >&2 && (exit 1)
-    # As a simulation of an OOM condition, do not create the 'foo' file. Cromwell should still be able to delocalize important detritus.
-    # touch foo
+    echo "$MEM_SIZE $MEM_UNIT"
+
+    # Current bashes do not do floating point arithmetic, Python to the rescue.
+    LESS=$(python -c "print($MEM_SIZE < 1.21)")
+
+    if [[ "$LESS" = "True" ]]
+    then
+      printf "Exception in thread "main" java.lang.OutOfMemoryError: testing\n\tat Test.main(Test.java:1)\n" >&2
+      exit 1
+    fi
+
+    echo "$MEM_SIZE $MEM_UNIT" > memory_output.txt
   }
   output {
-    File foo = "foo"
+    String memory_output = read_string("memory_output.txt")
   }
   runtime {
     docker: "python:latest"
@@ -19,4 +28,8 @@ task imitate_oom_error {
 
 workflow retry_with_more_memory {
   call imitate_oom_error
+
+  output {
+    String memory_output = imitate_oom_error.memory_output
+  }
 }