Queue: add -qsub-broad argument

When -qsub-broad is specified instead of -qsub, use the "h_vmem" parameter
instead of "h_rss" to specify memory limit requests.

Also cause the GridEngine native arguments to be output by default to the logger,
instead of only when in debug mode.

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala

@@ -98,4 +98,9 @@ class QSettings {
   
   @Argument(fullName="log_directory", shortName="logDir", doc="Directory to write log files into.", required=false)
   var logDirectory: File = _
+
+  /**
+   * If set, use Broad-specific cluster settings in the GridEngine job runner. Activated via the -qsub-broad argument in QGraphSettings.
+   */
+  var useBroadClusterSettings: Boolean = false
 }

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala

@@ -395,12 +395,18 @@ class QGraph extends Logging {
    */
   private def runJobs() {
     try {
-      if (settings.bsub)
+      if (settings.bsub) {
         settings.jobRunner = "Lsf706"
-      else if (settings.qsub)
+      }
+      else if (settings.qsub || settings.qsubBroad) {
         settings.jobRunner = "GridEngine"
-      else if (settings.jobRunner == null)
+        if ( settings.qsubBroad ) {
+          settings.qSettings.useBroadClusterSettings = true
+        }
+      }
+      else if (settings.jobRunner == null) {
         settings.jobRunner = "Shell"
+      }
       commandLineManager = commandLinePluginManager.createByName(settings.jobRunner)
 
       for (mgr <- managers) {

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala

@@ -46,6 +46,9 @@ class QGraphSettings {
   @Argument(fullName="qsub", shortName="qsub", doc="Equivalent to -jobRunner GridEngine", required=false)
   var qsub = false
 
+  @Argument(fullName="qsub-broad", shortName="qsub-broad", doc="Equivalent to -qsub, but uses GridEngine parameters specific to the Broad GridEngine cluster", required=false)
+  var qsubBroad = false
+
   @Argument(fullName="status",shortName="status",doc="Get status of jobs for the qscript",required=false)
   var getStatus = false
 

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala

@@ -58,8 +58,14 @@ class GridEngineJobRunner(session: Session, function: CommandLineFunction) exten
       nativeSpec += " -l %s=%dM".format(function.qSettings.residentRequestParameter, function.residentRequest.map(_ * 1024).get.ceil.toInt)
 
     // If the resident set size limit is defined specify the memory limit
-    if (function.residentLimit.isDefined)
+    if (function.residentLimit.isDefined) {
-      nativeSpec += " -l h_rss=%dM".format(function.residentLimit.map(_ * 1024).get.ceil.toInt)
+      var memoryLimitParameter : String = "h_rss"
+      if (function.qSettings.useBroadClusterSettings) {
+        memoryLimitParameter = "h_vmem"
+      }
+
+      nativeSpec += " -l %s=%dM".format(memoryLimitParameter, function.residentLimit.map(_ * 1024).get.ceil.toInt)
+    }
 
     // If more than 1 core is requested, set the proper request
     // if we aren't being jerks and just stealing cores (previous behavior)
@@ -82,7 +88,7 @@ class GridEngineJobRunner(session: Session, function: CommandLineFunction) exten
     if (priority.isDefined)
       nativeSpec += " -p " + priority.get
 
-    logger.debug("Native spec is: %s".format(nativeSpec))
+    logger.info("Native spec is: %s".format(nativeSpec))
     (nativeSpec + " " + super.functionNativeSpec).trim()
   }
 }