diff --git a/scala/qscript/playground/MultiFullCallingPipeline.scala b/scala/qscript/playground/MultiFullCallingPipeline.scala
index 2650f5b5c..0f61747eb 100644
--- a/scala/qscript/playground/MultiFullCallingPipeline.scala
+++ b/scala/qscript/playground/MultiFullCallingPipeline.scala
@@ -28,6 +28,9 @@ class MultiFullCallingPipeline extends QScript {
   @Argument(doc="pipeline priority", shortName="PP", required = false)
   var pipelinePriority: Option[Int] = None
 
+  @Argument(doc="pipeline retry", shortName="PR", required = false)
+  var pipelineRetry: Option[Int] = None
+
   @Argument(doc="run with -tearScript", shortName="TS")
   var runWithTearScript = false
 
@@ -85,6 +88,7 @@ class MultiFullCallingPipeline extends QScript {
         optional(" -jobQueue ", qscript.pipelineJobQueue) +
         optional(" -shortJobQueue ", qscript.pipelineShortQueue) +
         optional(" -jobPriority ", qscript.pipelinePriority) +
+        optional(" -retry ", qscript.pipelineRetry) +
         optional(" -tearScript ", tearScript) +
         " -S %s --gatkjar %s -jobProject %s -jobPrefix %s -Y %s -bsub -run"
           .format(pipelineScript, gatkJar, yamlName, yamlName, yamlFile)
diff --git a/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala b/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
index 6af376810..a70276bef 100644
--- a/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
+++ b/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
@@ -40,8 +40,8 @@ class QScriptManager() extends Logging {
 
       reporter.printSummary()
       if (reporter.hasErrors) {
-        val msg = "Compile failed with %d error%s".format(
-          reporter.ERROR.count, plural(reporter.ERROR.count))
+        val msg = "Compile of %s failed with %d error%s".format(
+          scripts.mkString(", "), reporter.ERROR.count, plural(reporter.ERROR.count))
         throw new QException(msg)
       }
       else if (reporter.WARNING.count > 0)
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala
index 70fdf2d48..1107c1b25 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala
@@ -8,9 +8,9 @@ import org.broadinstitute.sting.jna.lsf.v7_0_6.{LibLsf, LibBat}
 import org.broadinstitute.sting.utils.Utils
 import org.broadinstitute.sting.jna.clibrary.LibC
 import java.util.Date
-import org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.{signalBulkJobs, submitReply, submit}
+import org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.{submitReply, submit}
 import com.sun.jna.ptr.IntByReference
-import com.sun.jna.{StringArray, NativeLong, Memory}
+import com.sun.jna.{StringArray, NativeLong}
 
 /**
  * Runs jobs on an LSF compute cluster.
@@ -107,9 +107,12 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
       var exitInfo = 0
       var endTime: NativeLong = null
 
-      val result = LibBat.lsb_openjobinfo(jobId, null, null, null, null, LibBat.ALL_JOB)
-      if (result < 0)
-        throw new QException(LibBat.lsb_sperror("Unable to open LSF job info for job id: " + jobId))
+      var result = 0
+      Retry.attempt(() => {
+        result = LibBat.lsb_openjobinfo(jobId, null, null, null, null, LibBat.ALL_JOB)
+        if (result < 0)
+          throw new QException(LibBat.lsb_sperror("Unable to open LSF job info for job id: " + jobId))
+      }, 0.5, 1, 2)
       try {
         if (result > 1)
           throw new QException(LibBat.lsb_sperror("Recieved " + result + " LSF results for job id: " + jobId))
@@ -179,6 +182,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
 
 object Lsf706JobRunner extends Logging {
   private val lsfLibLock = new Object
+  private val SIGTERM = 15
 
   init()
 
@@ -244,23 +248,15 @@ object Lsf706JobRunner extends Logging {
    */
   def tryStop(runners: List[Lsf706JobRunner]) {
     lsfLibLock.synchronized {
-      for (jobRunners <- runners.filterNot(_.jobId < 0).grouped(10)) {
+      // lsb_killbulkjobs does not seem to forward SIGTERM,
+      // only SIGKILL, so send the Ctrl-C (SIGTERM) one by one.
+      for (jobRunner <- runners.filterNot(_.jobId < 0)) {
         try {
-          val njobs = jobRunners.size
-          val signalJobs = new signalBulkJobs
-          signalJobs.jobs = {
-            val jobIds = new Memory(8 * njobs)
-            jobIds.write(0, jobRunners.map(_.jobId).toArray, 0, njobs)
-            jobIds
-          }
-          signalJobs.njobs = njobs
-          signalJobs.signal = 9
-
-          if (LibBat.lsb_killbulkjobs(signalJobs) < 0)
-            throw new QException(LibBat.lsb_sperror("lsb_killbulkjobs failed"))
+          if (LibBat.lsb_signaljob(jobRunner.jobId, SIGTERM) < 0)
+            logger.error(LibBat.lsb_sperror("Unable to kill job " + jobRunner.jobId))
         } catch {
           case e =>
-            logger.error("Unable to kill all jobs.", e)
+            logger.error("Unable to kill job " + jobRunner.jobId, e)
         }
       }
     }
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
index 987f393f8..2d81a6955 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
@@ -67,7 +67,7 @@ class MultiFullCallingPipelineTest {
 
     // Run the pipeline with the expected inputs.
     val pipelineCommand = ("-retry 1 -BS 3 -PP 100 -S scala/qscript/playground/MultiFullCallingPipeline.scala" +
-            " -jobProject %s -YL %s -PJQ %s -stingHome %s")
+            " -jobProject %s -YL %s -PJQ %s -PR 2 -stingHome %s")
             .format(projectName, yamlList, dataset.pipelineJobQueue, PipelineTest.currentStingDir)
 
     val pipelineSpec = new PipelineTestSpec