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Corrected memory handling and jobName formatting issues 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5797 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
dheiman 2011-05-12 17:47:56 +00:00
parent db1f9af679
commit 9e08a699c6
1 changed files with 16 additions and 5 deletions
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21
scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala
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@ -54,8 +54,9 @@ class GridEngineJobRunner(val function: CommandLineFunction) extends CommandLine
// Force the remote environment to inherit local environment settings // Force the remote environment to inherit local environment settings
var nativeSpecString: String = "-V" var nativeSpecString: String = "-V"
// Set the display name to 1024 characters of the description // Set the display name to < 512 characters of the description
gridEngineJob.setJobName(function.description.take(1024)) // NOTE: Not sure if this is configuration specific?
gridEngineJob.setJobName(GridEngineJobRunner.toJobName(function.description.take(500)))
// Set the output file for stdout // Set the output file for stdout
gridEngineJob.setOutputPath(":" + function.jobOutputFile.getPath) gridEngineJob.setOutputPath(":" + function.jobOutputFile.getPath)
@ -83,8 +84,9 @@ class GridEngineJobRunner(val function: CommandLineFunction) extends CommandLine
// If the memory limit is set (GB) specify the memory limit // If the memory limit is set (GB) specify the memory limit
if (function.memoryLimit.isDefined) { if (function.memoryLimit.isDefined) {
val memLim: String = function.memoryLimit.get + "G" val memAvl: String = function.memoryLimit.get + "G"
nativeSpecString += " -l mem_free=" + memLim + ",h_vmem=" + memLim val memMax: String = (function.memoryLimit.get * 1.2 * 1024).ceil.toInt + "M"
nativeSpecString += " -l mem_free=" + memAvl + ",h_rss=" + memMax
} }
// If the priority is set (user specified Int) specify the priority // If the priority is set (user specified Int) specify the priority
@ -144,7 +146,9 @@ object GridEngineJobRunner extends Logging {
try { try {
gridEngineSession.init("") gridEngineSession.init("")
} catch { } catch {
case de: DrmaaException => throw new QException("init() failed", de) case de: DrmaaException =>
logger.error("Issue initializing Grid Engine", de)
throw new QException("init() failed", de)
} }
} }
} }
@ -232,7 +236,14 @@ object GridEngineJobRunner extends Logging {
} }
} }
// Reap what we've sown
override def finalize() { override def finalize() {
gridEngineSession.exit() gridEngineSession.exit()
} }
// Grid Engine disallows certain characters from being in job names.
// This replaces all illegal characters with underscores
private def toJobName(name: String): String = {
name.replaceAll("""[\n\t\r/:@\\*?]""", "_")
}
} }