58 lines
1.7 KiB
Scala
58 lines
1.7 KiB
Scala
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package org.broadinstitute.sting.queue.engine
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import collection.JavaConversions._
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import edu.mit.broad.core.lsf.LocalLsfJob
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import org.broadinstitute.sting.queue.function.DispatchFunction
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import java.io.File
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import java.util.ArrayList
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import org.broadinstitute.sting.queue.util.Logging
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trait LsfJobRunner extends DispatchJobRunner with Logging {
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type DispatchJobType = LocalLsfJob
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def dispatch(function: DispatchFunction, qGraph: QGraph) = {
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var jobName = function.jobName
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if (jobName == null)
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jobName = newJobName
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var jobOutputFile = function.jobOutputFile
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if (jobOutputFile == null)
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jobOutputFile = new File(jobName + ".out")
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var jobErrorFile = function.jobErrorFile
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if (jobErrorFile == null)
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jobErrorFile = new File(jobName + ".err")
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val job = new LocalLsfJob
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job.setName(jobName)
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job.setOutputFile(jobOutputFile)
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job.setErrFile(jobErrorFile)
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job.setWorkingDir(function.commandDirectory)
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job.setProject(function.jobProject)
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job.setQueue(function.jobQueue)
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job.setCommand(function.commandLine)
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var extraArgs = List("-r")
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if (function.memoryLimit.isDefined)
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extraArgs :::= List("-R", "rusage[mem=" + function.memoryLimit.get + "]")
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val previous = previousJobs(function, qGraph)
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if (previous.size > 0)
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extraArgs :::= List("-w", dependencyExpression(previous))
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job.setExtraBsubArgs(new ArrayList(extraArgs))
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addJob(function, job)
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logger.info(job.getBsubCommand.mkString(" "))
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if (!qGraph.dryRun)
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job.start
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}
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private def dependencyExpression(jobs: List[LocalLsfJob]) = {
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jobs.toSet[LocalLsfJob].map(_.getName).mkString("ended(\"", "\") && ended(\"", "\")")
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}
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}
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