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Fixed bug where the command directory was not being set to an absolute path, leading LSF to write some .done files to /tmp. 

No longer using the command directory for temporary .done files, and instead using the user specified temporary directory.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4678 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-11-15 17:59:39 +00:00
parent 62be55376b
commit 302e8f0239
2 changed files with 12 additions and 9 deletions
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19
scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala
View File

@ -13,6 +13,9 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
var job: LsfJob = new LsfJob var job: LsfJob = new LsfJob
/** Which directory to use for the job status files. */
private def jobStatusDir = function.jobTempDir
/** A file to look for to validate that the function ran to completion. */ /** A file to look for to validate that the function ran to completion. */
private var jobStatusPath: String = _ private var jobStatusPath: String = _
@ -45,7 +48,7 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
job.project = function.jobProject job.project = function.jobProject
job.queue = function.jobQueue job.queue = function.jobQueue
if (function.commandDirectory != new File(".").getAbsoluteFile) if (IOUtils.absolute(new File(".")) != function.commandDirectory)
job.workingDir = function.commandDirectory job.workingDir = function.commandDirectory
job.extraBsubArgs ++= function.extraArgs job.extraBsubArgs ++= function.extraArgs
@ -78,7 +81,7 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
runStatus = RunnerStatus.RUNNING runStatus = RunnerStatus.RUNNING
Retry.attempt(() => job.run(), 1, 5, 10) Retry.attempt(() => job.run(), 1, 5, 10)
jobStatusPath = IOUtils.absolute(new File(function.commandDirectory, "." + job.bsubJobId)).toString jobStatusPath = IOUtils.absolute(new File(jobStatusDir, "." + job.bsubJobId)).toString
logger.info("Submitted LSF job id: " + job.bsubJobId) logger.info("Submitted LSF job id: " + job.bsubJobId)
} catch { } catch {
case e => case e =>
@ -166,7 +169,7 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
* @return the file path to the pre-exec. * @return the file path to the pre-exec.
*/ */
private def writeExec() = { private def writeExec() = {
IOUtils.writeTempFile(function.commandLine, ".exec", "", function.jobTempDir) IOUtils.writeTempFile(function.commandLine, ".exec", "", jobStatusDir)
} }
/** /**
@ -177,15 +180,15 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
private def writePreExec() = { private def writePreExec() = {
val preExec = new StringBuilder val preExec = new StringBuilder
preExec.append("rm -f '%s/'.$LSB_JOBID.done%n".format(function.commandDirectory)) preExec.append("rm -f '%s/'.$LSB_JOBID.done%n".format(jobStatusDir))
function.doneOutputs.foreach(file => preExec.append("rm -f '%s'%n".format(file))) function.doneOutputs.foreach(file => preExec.append("rm -f '%s'%n".format(file)))
preExec.append("rm -f '%s/'.$LSB_JOBID.fail%n".format(function.commandDirectory)) preExec.append("rm -f '%s/'.$LSB_JOBID.fail%n".format(jobStatusDir))
function.failOutputs.foreach(file => preExec.append("rm -f '%s'%n".format(file))) function.failOutputs.foreach(file => preExec.append("rm -f '%s'%n".format(file)))
mountCommand(function).foreach(command => mountCommand(function).foreach(command =>
preExec.append("%s%n".format(command))) preExec.append("%s%n".format(command)))
IOUtils.writeTempFile(preExec.toString, ".preExec", "", function.jobTempDir) IOUtils.writeTempFile(preExec.toString, ".preExec", "", jobStatusDir)
} }
/** /**
@ -209,8 +212,8 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
|else |else
|%stouch "$JOB_STAT_ROOT".fail |%stouch "$JOB_STAT_ROOT".fail
|fi |fi
|""".stripMargin.format(function.commandDirectory, touchDone, touchFail)) |""".stripMargin.format(jobStatusDir, touchDone, touchFail))
IOUtils.writeTempFile(postExec.toString, ".postExec", "", function.jobTempDir) IOUtils.writeTempFile(postExec.toString, ".postExec", "", jobStatusDir)
} }
} }

2
scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
View File

@ -283,7 +283,7 @@ trait QFunction extends Logging {
jobTempDir = qSettings.tempDirectory jobTempDir = qSettings.tempDirectory
// If the command directory is relative, insert the run directory ahead of it. // If the command directory is relative, insert the run directory ahead of it.
commandDirectory = new File(qSettings.runDirectory, commandDirectory.getPath) commandDirectory = IOUtils.absolute(new File(qSettings.runDirectory, commandDirectory.getPath))
} }
/** /**