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GenomeLocProcessingTracker was using SimpleTimer in a non-thread safe way. No longer providing an interface to time parallel operations. Now issues warning if someone enables distributed GATK, as this is considered an unstable, experimental engine feature. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5842 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-05-23 02:10:27 +00:00
parent a18b0152df
commit d005c4bf09
3 changed files with 20 additions and 25 deletions
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9
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -71,15 +71,6 @@ public class LinearMicroScheduler extends MicroScheduler {
accumulator.accumulate(dataProvider,result);
dataProvider.close();
}
if ( logger.isDebugEnabled() ) {
counter++;
logger.debug(String.format("At %s: processed %d shards. %.2e s / lock (n=%d), %.2e s / read (n=%d), %.2e s / write (n=%d)",
shard.getLocation(), counter,
processingTracker.getTimePerLock(), processingTracker.getNLocks(),
processingTracker.getTimePerRead(), processingTracker.getNReads(),
processingTracker.getTimePerWrite(), processingTracker.getNWrites()));
}
}
Object result = accumulator.finishTraversal();

1
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
View File

@ -165,6 +165,7 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
// create the processing tracker
//
if ( engine.getArguments().processingTrackerFile != null ) {
logger.warn("Distributed GATK is an experimental engine feature, and is likely to not work correctly or reliably.");
if ( engine.getArguments().restartProcessingTracker && engine.getArguments().processingTrackerFile.exists() ) {
engine.getArguments().processingTrackerFile.delete();
logger.info("Deleting ProcessingTracker file " + engine.getArguments().processingTrackerFile);

35
java/src/org/broadinstitute/sting/utils/threading/GenomeLocProcessingTracker.java
View File

@ -82,10 +82,13 @@ public abstract class GenomeLocProcessingTracker {
//
// Timers for recording performance information
// Note -- these cannot be used because this class isn't thread safe, and neither are the
// timers, so they result in invalid operations w.r.t. the SimpleTimer contract
//
protected final SimpleTimer writeTimer = new SimpleTimer("writeTimer");
protected final SimpleTimer readTimer = new SimpleTimer("readTimer");
protected final SimpleTimer lockWaitTimer = new SimpleTimer("lockWaitTimer");
// protected final SimpleTimer writeTimer = new SimpleTimer("writeTimer");
// protected final SimpleTimer readTimer = new SimpleTimer("readTimer");
// protected final SimpleTimer lockWaitTimer = new SimpleTimer("lockWaitTimer");
protected final SimpleTimer timer = new SimpleTimer();
protected long nLocks = 0, nWrites = 0, nReads = 0;
// --------------------------------------------------------------------------------
@ -318,10 +321,10 @@ public abstract class GenomeLocProcessingTracker {
protected final Map<GenomeLoc, ProcessingLoc> updateAndGetProcessingLocs(String myName) {
return new WithLock<Map<GenomeLoc, ProcessingLoc>>(myName) {
public Map<GenomeLoc, ProcessingLoc> doBody() {
readTimer.restart();
// readTimer.restart();
for ( ProcessingLoc p : readNewLocs() )
processingLocs.put(p.getLocation(), p);
readTimer.stop();
// readTimer.stop();
nReads++;
return processingLocs;
}
@ -335,10 +338,10 @@ public abstract class GenomeLocProcessingTracker {
* @param myName
*/
protected final void registerNewLocsWithTimers(Collection<ProcessingLoc> plocs, String myName) {
writeTimer.restart();
// writeTimer.restart();
registerNewLocs(plocs);
nWrites++;
writeTimer.stop();
// writeTimer.stop();
}
private final void printStatusHeader() {
@ -360,15 +363,15 @@ public abstract class GenomeLocProcessingTracker {
* @param id the name of the process doing the locking
*/
private final void lock(String id) {
lockWaitTimer.restart();
//lockWaitTimer.restart();
boolean hadLock = lock.ownsLock();
if ( ! hadLock ) {
nLocks++;
printStatus(id, lockWaitTimer.currentTime(), GOING_FOR_LOCK);
//printStatus(id, lockWaitTimer.currentTime(), GOING_FOR_LOCK);
}
lock.lock();
lockWaitTimer.stop();
if ( ! hadLock ) printStatus(id, lockWaitTimer.currentTime(), HAVE_LOCK);
//lockWaitTimer.stop();
//if ( ! hadLock ) printStatus(id, lockWaitTimer.currentTime(), HAVE_LOCK);
}
/**
@ -376,18 +379,18 @@ public abstract class GenomeLocProcessingTracker {
* @param id the name of the process doing the unlocking
*/
private final void unlock(String id) {
if ( lock.getHoldCount() == 1 ) printStatus(id, lockWaitTimer.currentTime(), RELEASING_LOCK);
if ( lock.getHoldCount() == 1 ) printStatus(id, timer.currentTime(), RELEASING_LOCK);
lock.unlock();
if ( ! lock.ownsLock() ) printStatus(id, lockWaitTimer.currentTime(), RUNNING);
if ( ! lock.ownsLock() ) printStatus(id, timer.currentTime(), RUNNING);
}
// useful code for getting
public final long getNLocks() { return nLocks; }
public final long getNReads() { return nReads; }
public final long getNWrites() { return nWrites; }
public final double getTimePerLock() { return lockWaitTimer.getElapsedTime() / Math.max(nLocks, 1); }
public final double getTimePerRead() { return readTimer.getElapsedTime() / Math.max(nReads,1); }
public final double getTimePerWrite() { return writeTimer.getElapsedTime() / Math.max(nWrites,1); }
// public final double getTimePerLock() { return lockWaitTimer.getElapsedTime() / Math.max(nLocks, 1); }
// public final double getTimePerRead() { return readTimer.getElapsedTime() / Math.max(nReads,1); }
// public final double getTimePerWrite() { return writeTimer.getElapsedTime() / Math.max(nWrites,1); }
// --------------------------------------------------------------------------------
//