From e93052a51e88ddb77c8ce71cf6a14a449ca3b1aa Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Mon, 11 Jul 2011 19:17:58 -0400
Subject: [PATCH] When generating the QGraph, don't regenerate if there aren't
 scatter/gather jobs. Fixed a display issue with the number of milliseconds
 that Queue has tried to contact LSF.

---
 .../sting/queue/engine/QGraph.scala           | 44 ++++++++++---------
 .../queue/engine/lsf/Lsf706JobRunner.scala    |  6 +--
 2 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
index bfcc4d48c..8ed3f84c1 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
@@ -138,30 +138,32 @@ class QGraph extends Logging {
     validate()
 
     if (running && numMissingValues == 0) {
-      logger.info("Generating scatter gather jobs.")
       val scatterGathers = jobGraph.edgeSet.filter(edge => scatterGatherable(edge))
+      if (!scatterGathers.isEmpty) {
+        logger.info("Generating scatter gather jobs.")
 
-      var addedFunctions = List.empty[QFunction]
-      for (scatterGather <- scatterGathers) {
-        val functions = scatterGather.asInstanceOf[FunctionEdge]
-                .function.asInstanceOf[ScatterGatherableFunction]
-                .generateFunctions()
-        addedFunctions ++= functions
+        var addedFunctions = List.empty[QFunction]
+        for (scatterGather <- scatterGathers) {
+          val functions = scatterGather.asInstanceOf[FunctionEdge]
+                  .function.asInstanceOf[ScatterGatherableFunction]
+                  .generateFunctions()
+          addedFunctions ++= functions
+        }
+
+        logger.info("Removing original jobs.")
+        this.jobGraph.removeAllEdges(scatterGathers)
+        prune()
+
+        logger.info("Adding scatter gather jobs.")
+        addedFunctions.foreach(function => if (running) this.add(function))
+
+        logger.info("Regenerating graph.")
+        fill
+        val scatterGatherDotFile = if (settings.expandedDotFile != null) settings.expandedDotFile else settings.dotFile
+        if (scatterGatherDotFile != null)
+          renderToDot(scatterGatherDotFile)
+        validate()
       }
-
-      logger.info("Removing original jobs.")
-      this.jobGraph.removeAllEdges(scatterGathers)
-      prune()
-
-      logger.info("Adding scatter gather jobs.")
-      addedFunctions.foreach(function => if (running) this.add(function))
-
-      logger.info("Regenerating graph.")
-      fill
-      val scatterGatherDotFile = if (settings.expandedDotFile != null) settings.expandedDotFile else settings.dotFile
-      if (scatterGatherDotFile != null)
-        renderToDot(scatterGatherDotFile)
-      validate()
     }
   }
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
index 57d133dfe..ac2f036b4 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
@@ -286,11 +286,11 @@ object Lsf706JobRunner extends Logging {
     // LSB_SHAREDIR/cluster_name/logdir/lsb.acct (man bacct)
     // LSB_SHAREDIR/cluster_name/logdir/lsb.events (man bhist)
     logger.debug("Job Id %s status / exitStatus / exitInfo: ??? / ??? / ???".format(runner.jobId))
-    val unknownStatusSeconds = (System.currentTimeMillis - runner.lastStatusUpdate)
-    if (unknownStatusSeconds > (unknownStatusMaxSeconds * 1000L)) {
+    val unknownStatusMillis = (System.currentTimeMillis - runner.lastStatusUpdate)
+    if (unknownStatusMillis > (unknownStatusMaxSeconds * 1000L)) {
       // Unknown status has been returned for a while now.
       runner.updateStatus(RunnerStatus.FAILED)
-      logger.error("Unable to read LSF status for %d minutes: job id %d: %s".format(unknownStatusSeconds/60, runner.jobId, runner.function.description))
+      logger.error("Unable to read LSF status for %0.2f minutes: job id %d: %s".format(unknownStatusMillis/(60 * 1000D), runner.jobId, runner.function.description))
     }
   }