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Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts

This commit is contained in:
Mark DePristo 2012-08-17 10:13:40 -04:00
parent 54e7302daf
commit 67ebd65512
1 changed files with 12 additions and 4 deletions
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16
public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
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@ -35,7 +35,7 @@ import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner
import java.util.regex.Pattern import java.util.regex.Pattern
import java.lang.StringBuffer import java.lang.StringBuffer
import java.util.Date import java.util.Date
import com.sun.jna.{Structure, StringArray, NativeLong} import com.sun.jna.{Pointer, Structure, StringArray, NativeLong}
import com.sun.jna.ptr.IntByReference import com.sun.jna.ptr.IntByReference
/** /**
@ -295,9 +295,17 @@ object Lsf706JobRunner extends Logging {
// the platform LSF startTimes are in seconds, not milliseconds, so convert to the java convention // the platform LSF startTimes are in seconds, not milliseconds, so convert to the java convention
runner.getRunInfo.startTime = new Date(jobInfo.startTime.longValue * 1000) runner.getRunInfo.startTime = new Date(jobInfo.startTime.longValue * 1000)
runner.getRunInfo.doneTime = new Date(jobInfo.endTime.longValue * 1000) runner.getRunInfo.doneTime = new Date(jobInfo.endTime.longValue * 1000)
val exHostsRaw = jobInfo.exHosts.getStringArray(0)
//logger.warn("exHostsRaw = " + exHostsRaw) val exHostsList =
val exHostsList = exHostsRaw.toSeq if (jobInfo.numExHosts != 1) {
// this is necessary because
val exHostsString = "multipleHosts_" + jobInfo.numExHosts
logger.debug("numExHosts = " + jobInfo.numExHosts + " != 1 for job " + runner.jobId + ", cannot safely get exhosts, setting to " + exHostsString)
List(exHostsString)
} else {
jobInfo.exHosts.getStringArray(0).toSeq
}
//logger.warn("exHostsList = " + exHostsList) //logger.warn("exHostsList = " + exHostsList)
val exHosts = exHostsList.reduceLeft(_ + "," + _) val exHosts = exHostsList.reduceLeft(_ + "," + _)
//logger.warn("exHosts = " + exHosts) //logger.warn("exHosts = " + exHosts)