diff --git a/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala index e584f8a84..57d133dfe 100644 --- a/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala +++ b/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala @@ -56,7 +56,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR * Dispatches the function on the LSF cluster. * @param function Command to run. */ - def start() = { + def start() { Lsf706JobRunner.lsfLibLock.synchronized { val request = new submit for (i <- 0 until LibLsf.LSF_RLIM_NLIMITS) @@ -79,12 +79,6 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR request.options |= LibBat.SUB_ERR_FILE } - // If a project name is set specify the project name - if (function.jobProject != null) { - request.projectName = function.jobProject - request.options |= LibBat.SUB_PROJECT_NAME - } - // If the job queue is set specify the job queue if (function.jobQueue != null) { request.queue = function.jobQueue @@ -103,6 +97,11 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR request.options2 |= LibBat.SUB2_JOB_PRIORITY } + // Broad specific requirement, our esub requires there be a project + // else it will spit out a warning to stdout. see $LSF_SERVERDIR/esub + request.projectName = if (function.jobProject != null) function.jobProject else "Queue" + request.options |= LibBat.SUB_PROJECT_NAME + // LSF specific: get the max runtime for the jobQueue and pass it for this job request.rLimits(LibLsf.LSF_RLIMIT_RUN) = Lsf706JobRunner.getRlimitRun(function.jobQueue) @@ -125,7 +124,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR def status = this.lastStatus - private def updateStatus(updatedStatus: RunnerStatus.Value) = { + private def updateStatus(updatedStatus: RunnerStatus.Value) { this.lastStatus = updatedStatus this.lastStatusUpdate = System.currentTimeMillis }