[POC] Configurable mounting point via config option google.batch.mountRoot

docs/reference/config.md

@@ -878,6 +878,11 @@ The following settings are available for Google Cloud Batch:
 : Max number of execution attempts of a job interrupted by a Compute Engine Spot reclaim event (default: `0`).
 : See also: `google.batch.autoRetryExitCodes`
 
+`google.batch.mountRoot`
+: :::{versionadded} 25.05.0-edge
+  :::
+: The root directory for GCS mounting in the container (default: `/mnt/disks`).
+
 `google.batch.network`
 : The URL of an existing network resource to which the VM will be attached.
 

plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchExecutor.groovy

@@ -168,7 +168,10 @@ class GoogleBatchExecutor extends Executor implements ExtensionPoint, TaskArrayE
     String getArrayWorkDir(TaskHandler handler) {
         return isFusionEnabled() || isWorkDirDefaultFS()
             ? TaskArrayExecutor.super.getArrayWorkDir(handler)
-            : containerMountPath(handler.task.workDir as CloudStoragePath)
+            : containerMountPath(
+                handler.task.workDir as CloudStoragePath, 
+                config.getMountRoot()
+            )
     }
 
     @Override

plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy

@@ -43,8 +43,6 @@ import nextflow.util.TestOnly
 @CompileStatic
 class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatchLauncherSpec {
 
-    private static final String MOUNT_ROOT = '/mnt/disks'
-
     private BatchConfig config
     private CloudStoragePath remoteWorkDir
     private Path remoteBinDir
@@ -55,8 +53,11 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
     @TestOnly
     protected GoogleBatchScriptLauncher() {}
 
-    GoogleBatchScriptLauncher(TaskBean bean, Path remoteBinDir) {
+    GoogleBatchScriptLauncher(TaskBean bean, Path remoteBinDir, BatchConfig config) {
         super(bean)
+        // Initialize config first before using any methods that depend on it
+        this.config = config
+
         // keep track the google storage work dir
         this.remoteWorkDir = (CloudStoragePath) bean.workDir
         this.remoteBinDir = toContainerMount(remoteBinDir)
@@ -116,7 +117,7 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
         if( path instanceof CloudStoragePath ) {
             buckets.add(path.bucket())
             pathTrie.add( (parent ? "/${path.bucket()}${path.parent}" : "/${path.bucket()}${path}").toString() )
-            final containerMount = containerMountPath(path)
+            final containerMount = containerMountPath(path, config.getMountRoot())
             log.trace "Path ${FilesEx.toUriString(path)} to container mount: $containerMount"
             return Paths.get(containerMount)
         }
@@ -135,15 +136,17 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
     @Override
     List<String> getContainerMounts() {
         final result = new ArrayList(10)
+        final mountRoot = config.getMountRoot()
         for( String it : pathTrie.longest() ) {
-            result.add( "${MOUNT_ROOT}${it}:${MOUNT_ROOT}${it}:rw".toString() )
+            result.add( "${mountRoot}${it}:${mountRoot}${it}:rw".toString() )
         }
         return result
     }
 
     @Override
     List<Volume> getVolumes() {
         final result = new ArrayList(10)
+        final mountRoot = config.getMountRoot()
         for( String it : buckets ) {
             final mountOptions = new LinkedList<String>()
             if( config && config.gcsfuseOptions )
@@ -157,7 +160,7 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
                         GCS.newBuilder()
                             .setRemotePath(it)
                     )
-                    .setMountPath( "${MOUNT_ROOT}/${it}".toString() )
+                    .setMountPath( "${mountRoot}/${it}".toString() )
                     .addAllMountOptions( mountOptions )
                     .build()
             )
@@ -184,11 +187,6 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
         return remoteWorkDir.resolve(TaskRun.CMD_INFILE)
     }
 
-    GoogleBatchScriptLauncher withConfig(BatchConfig config) {
-        this.config = config
-        return this
-    }
-
     GoogleBatchScriptLauncher withIsArray(boolean value) {
         this.isArray = value
         return this
@@ -207,7 +205,7 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
         "trap \"{ cp ${TaskRun.CMD_LOG} ${workDir}/${TaskRun.CMD_LOG}; }\" ERR; /bin/bash ${workDir}/${TaskRun.CMD_RUN} 2>&1 | tee ${TaskRun.CMD_LOG}"
     }
 
-    static String containerMountPath(CloudStoragePath path) {
-        return "$MOUNT_ROOT/${path.bucket()}${path}"
+    static String containerMountPath(CloudStoragePath path, String mountRoot) {
+        return "${mountRoot}/${path.bucket()}${path}"
     }
 }

plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy

@@ -37,6 +37,7 @@ import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.cloud.google.batch.client.BatchClient
+import nextflow.cloud.google.batch.client.BatchConfig
 import nextflow.cloud.types.CloudMachineInfo
 import nextflow.cloud.types.PriceModel
 import nextflow.exception.ProcessException
@@ -148,8 +149,8 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         }
         else {
             final taskBean = task.toTaskBean()
-            return new GoogleBatchScriptLauncher(taskBean, executor.remoteBinDir)
-                .withConfig(executor.config)
+            final config = executor.config ?: new BatchConfig()
+            return new GoogleBatchScriptLauncher(taskBean, executor.remoteBinDir, config)
                 .withIsArray(task.isArray())
         }
     }

plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy

@@ -37,6 +37,8 @@ class BatchConfig {
 
     static final private List<String> DEFAULT_GCSFUSE_OPTS = List.<String>of('-o rw', '-implicit-dirs')
 
+    static final private String DEFAULT_MOUNT_ROOT = '/mnt/disks'
+
     private GoogleOpts googleOpts
     private GoogleCredentials credentials
     private List<String> allowedLocations
@@ -55,6 +57,7 @@ class BatchConfig {
     private BatchRetryConfig retryConfig
     private List<Integer> autoRetryExitCodes
     private List<String> gcsfuseOptions
+    private String mountRoot
 
     GoogleOpts getGoogleOpts() { return googleOpts }
     GoogleCredentials getCredentials() { return credentials }
@@ -74,6 +77,7 @@ class BatchConfig {
     BatchRetryConfig getRetryConfig() { retryConfig }
     List<Integer> getAutoRetryExitCodes() { autoRetryExitCodes }
     List<String> getGcsfuseOptions() { gcsfuseOptions }
+    String getMountRoot() { mountRoot }
 
     static BatchConfig create(Session session) {
         final result = new BatchConfig()
@@ -95,6 +99,7 @@ class BatchConfig {
         result.retryConfig = new BatchRetryConfig( session.config.navigate('google.batch.retryPolicy') as Map ?: Map.of() )
         result.autoRetryExitCodes = session.config.navigate('google.batch.autoRetryExitCodes', DEFAULT_RETRY_LIST) as List<Integer>
         result.gcsfuseOptions = session.config.navigate('google.batch.gcsfuseOptions', DEFAULT_GCSFUSE_OPTS) as List<String>
+        result.mountRoot = session.config.navigate('google.batch.mountRoot', DEFAULT_MOUNT_ROOT) as String
         return result
     }