Manage AWS Batch Unscheduled jobs (nextflow-io#5936)

---------

Signed-off-by: jorgee <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Co-authored-by: Paolo Di Tommaso <[email protected]>
Co-authored-by: Chris Hakkaart <[email protected]>
Co-authored-by: Ben Sherman <[email protected]>
Signed-off-by: Dietmar Rieder <[email protected]>

Author: 4 people

docs/reference/config.md

@@ -180,6 +180,11 @@ The following settings are available:
   :::
 : The share identifier for all tasks when using [fair-share scheduling for AWS Batch](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/)
 
+`aws.batch.terminateUnschedulableJobs`
+: :::{versionadded} 25.03.0-edge
+:::
+: When `true`, jobs that cannot be scheduled for lack of resources or misconfiguration are terminated automatically (default: `false`). The pipeline may complete with an error status depending on the error strategy defined for the corresponding jobs.
+
 `aws.batch.volumes`
 : One or more container mounts. Mounts can be specified as simple e.g. `/some/path` or canonical format e.g. `/host/path:/mount/path[:ro|rw]`. Multiple mounts can be specified separating them with a comma or using a list object.
 

modules/nf-lang/src/main/java/nextflow/config/scopes/AwsBatchConfig.java

@@ -104,6 +104,12 @@ Max number of downloads attempts from S3 (default: `1`).
     """)
     public String shareIdentifier;
 
+    @ConfigOption
+    @Description("""
+        When true, jobs that cannot be scheduled for lack of resources or misconfiguration are terminated automatically (default: `false`).
+    """)
+    public boolean terminateUnschedulableJobs;
+
     @ConfigOption
     @Description("""
         One or more container mounts. Mounts can be specified as simple e.g. `/some/path` or canonical format e.g. `/host/path:/mount/path[:ro|rw]`.

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy

@@ -116,6 +116,11 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
 
     final static private Map<String,String> jobDefinitions = [:]
 
+    final static private List<String> MISCONFIGURATION_REASONS = List.of(
+        "MISCONFIGURATION:JOB_RESOURCE_REQUIREMENT",
+        "MISCONFIGURATION:COMPUTE_ENVIRONMENT_MAX_RESOURCE"
+    )
+
     /**
      * Batch context shared between multiple task handlers
      */
@@ -232,12 +237,40 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         final result = job?.status in ['RUNNING', 'SUCCEEDED', 'FAILED']
         if( result )
             this.status = TaskStatus.RUNNING
+        else
+            checkIfUnschedulable(job)
         // fetch the task arn
         if( !taskArn )
             taskArn = job?.getContainer()?.getTaskArn()
         return result
     }
 
+    protected void checkIfUnschedulable(JobDetail job) {
+        if( job ) try {
+            checkIfUnschedulable0(job)
+        }
+        catch (Throwable e) {
+            log.warn "Unable to check if job is unschedulable - ${e.message}", e
+        }
+    }
+
+    private void checkIfUnschedulable0(JobDetail job) {
+        final reason = errReason(job)
+        if( MISCONFIGURATION_REASONS.any((it) -> reason.contains(it)) ) {
+            final msg = "unschedulable AWS Batch job ${jobId} (${task.lazyName()}) - $reason"
+            // If indicated in aws.batch config kill the job an produce a failure
+            if( executor.awsOptions.terminateUnschedulableJobs() ){
+                log.warn("Terminating ${jobId}")
+                kill()
+                task.error = new ProcessException("Unschedulable AWS Batch job ${jobId} - $reason")
+                status = TaskStatus.COMPLETED
+            }
+            else {
+                log.warn "Detected $msg"
+            }
+        }
+    }
+
     protected String errReason(JobDetail job){
         if(!job)
             return "(unknown)"
@@ -256,6 +289,10 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
     @Override
     boolean checkIfCompleted() {
         assert jobId
+        if( isCompleted() ) {
+            //Task can be marked as completed before running by unschedulable reason. Return true
+            return true
+        }
         if( !isRunning() )
             return false
         final job = describeJob(jobId)

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy

@@ -161,4 +161,8 @@ class AwsOptions implements CloudTransferOptions {
         return awsConfig.batchConfig.getExecutionRole()
     }
 
+    boolean terminateUnschedulableJobs() {
+        return awsConfig.batchConfig.terminateUnschedulableJobs
+    }
+
 }

plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy

@@ -92,6 +92,11 @@ class AwsBatchConfig implements CloudTransferOptions {
      */
     boolean fargateMode
 
+    /**
+     * Flag to fail and terminate unscheduled jobs.
+     */
+    boolean terminateUnschedulableJobs
+
     /*
      * only for testing
      */
@@ -112,11 +117,11 @@ class AwsBatchConfig implements CloudTransferOptions {
         shareIdentifier = opts.shareIdentifier
         schedulingPriority = opts.schedulingPriority as Integer ?: 0
         executionRole = opts.executionRole
+        terminateUnschedulableJobs = opts.terminateUnschedulableJobs as boolean
         if( retryMode == 'built-in' )
             retryMode = null // this force falling back on NF built-in retry mode instead of delegating to AWS CLI tool
         if( retryMode && retryMode !in AwsOptions.VALID_RETRY_MODES )
             log.warn "Unexpected value for 'aws.batch.retryMode' config setting - offending value: $retryMode - valid values: ${AwsOptions.VALID_RETRY_MODES.join(',')}"
-
     }
 
     // ====  getters =====

plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsBatchConfigTest.groovy

@@ -46,6 +46,7 @@ class AwsBatchConfigTest extends Specification {
         !batch.isFargateMode()
         !batch.s5cmdPath
         batch.schedulingPriority == 0
+        !batch.terminateUnschedulableJobs
     }
 
     def 'should create config with options' () {
@@ -139,4 +140,17 @@ class AwsBatchConfigTest extends Specification {
         [platformType: 'fargate', cliPath: "/opt/s5cmd --foo"]      | null              | '/opt/s5cmd --foo'| true
     }
 
+    def 'should parse unschedulable flag' () {
+        given:
+        def opts = new AwsBatchConfig(OPTS)
+
+        expect:
+        opts.terminateUnschedulableJobs == UNSCHEDULABLE
+
+        where:
+        OPTS                                    | UNSCHEDULABLE
+        [:]                                     | false
+        [terminateUnschedulableJobs: false]     | false
+        [terminateUnschedulableJobs: true]      | true
+    }
 }