Fixes GSA-515 Nanoscheduler GSA-560 / Fix display of NanoScheduler and MonitoringEfficiency
-- Now prints out a single combined NanoScheduler runtime profile report across all nano schedulers in use. So now if you run with -nt 4 you'll get one combined NanoScheduler profiler across all 4 instances of the NanoScheduler within TraverseXNano.
This commit is contained in:
Mark DePristo
parent
64ee0a10fe
commit
e25e617d1a
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@ -42,6 +42,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler;
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import org.broadinstitute.sting.utils.progressmeter.ProgressMeter;
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import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
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@ -315,6 +316,9 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
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for ( final TraversalEngine te : allCreatedTraversalEngines)
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te.shutdown();
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// horrible hack to print nano scheduling information across all nano schedulers, if any were used
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NanoScheduler.printCombinedRuntimeProfile();
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allCreatedTraversalEngines.clear();
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availableTraversalEngines.clear();
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}
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@ -145,4 +145,13 @@ public class SimpleTimer {
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public synchronized long getElapsedTimeNano() {
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return running ? (currentTimeNano() - startTimeNano + elapsedTimeNano) : elapsedTimeNano;
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}
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/**
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* Add the elapsed time from toAdd to this elapsed time
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*
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* @param toAdd the timer whose elapsed time we want to add to this timer
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*/
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public synchronized void addElapsed(final SimpleTimer toAdd) {
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elapsedTimeNano += toAdd.getElapsedTimeNano();
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}
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}
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@ -29,6 +29,7 @@ class InputProducer<InputType> implements Runnable {
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final SimpleTimer inputTimer,
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final BlockingQueue<InputValue> outputQueue) {
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if ( inputReader == null ) throw new IllegalArgumentException("inputReader cannot be null");
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if ( inputTimer == null ) throw new IllegalArgumentException("inputTimer cannot be null");
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if ( outputQueue == null ) throw new IllegalArgumentException("OutputQueue cannot be null");
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this.inputReader = inputReader;
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@ -38,11 +39,16 @@ class InputProducer<InputType> implements Runnable {
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public void run() {
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try {
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while ( inputReader.hasNext() ) {
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if ( inputTimer != null ) inputTimer.restart();
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final InputType input = inputReader.next();
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if ( inputTimer != null ) inputTimer.stop();
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outputQueue.put(new InputValue(input));
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while ( true ) {
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inputTimer.restart();
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if ( ! inputReader.hasNext() ) {
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inputTimer.stop();
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break;
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} else {
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final InputType input = inputReader.next();
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inputTimer.stop();
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outputQueue.put(new InputValue(input));
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}
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}
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// add the EOF object so our consumer knows we are done in all inputs
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@ -0,0 +1,69 @@
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package org.broadinstitute.sting.utils.nanoScheduler;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.utils.AutoFormattingTime;
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import org.broadinstitute.sting.utils.SimpleTimer;
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/**
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* Holds runtime profile (input, read, map) times as tracked by NanoScheduler
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*
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* User: depristo
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* Date: 9/10/12
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* Time: 8:31 PM
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*/
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public class NSRuntimeProfile {
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final SimpleTimer outsideSchedulerTimer = new SimpleTimer("outside");
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final SimpleTimer inputTimer = new SimpleTimer("input");
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final SimpleTimer mapTimer = new SimpleTimer("map");
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final SimpleTimer reduceTimer = new SimpleTimer("reduce");
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/**
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* Combine the elapsed time information from other with this profile
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*
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* @param other a non-null profile
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*/
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public void combine(final NSRuntimeProfile other) {
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outsideSchedulerTimer.addElapsed(other.outsideSchedulerTimer);
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inputTimer.addElapsed(other.inputTimer);
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mapTimer.addElapsed(other.mapTimer);
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reduceTimer.addElapsed(other.reduceTimer);
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}
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/**
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* Print the runtime profiling to logger
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*
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* @param logger
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*/
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public void log(final Logger logger) {
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log1(logger, "Input time", inputTimer);
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log1(logger, "Map time", mapTimer);
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log1(logger, "Reduce time", reduceTimer);
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log1(logger, "Outside time", outsideSchedulerTimer);
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}
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/**
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* @return the total runtime for all functions of this nano scheduler
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*/
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@Ensures("result >= 0.0")
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public double totalRuntimeInSeconds() {
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return inputTimer.getElapsedTime()
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+ mapTimer.getElapsedTime()
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+ reduceTimer.getElapsedTime()
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+ outsideSchedulerTimer.getElapsedTime();
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}
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/**
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* Print to logger.info timing information from timer, with name label
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*
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* @param label the name of the timer to display. Should be human readable
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* @param timer the timer whose elapsed time we will display
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*/
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@Requires({"label != null", "timer != null"})
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private void log1(final Logger logger, final String label, final SimpleTimer timer) {
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final double myTimeInSec = timer.getElapsedTime();
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final double myTimePercent = myTimeInSec / totalRuntimeInSeconds() * 100;
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logger.info(String.format("%s: %s (%5.2f%%)", label, new AutoFormattingTime(myTimeInSec), myTimePercent));
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}
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}
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@ -3,8 +3,6 @@ package org.broadinstitute.sting.utils.nanoScheduler;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.utils.AutoFormattingTime;
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import org.broadinstitute.sting.utils.SimpleTimer;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.threading.NamedThreadFactory;
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@ -46,7 +44,6 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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private final static Logger logger = Logger.getLogger(NanoScheduler.class);
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private final static boolean ALLOW_SINGLE_THREAD_FASTPATH = true;
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private final static boolean LOG_MAP_TIMES = false;
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private final static boolean TIME_CALLS = true;
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private final static int MAP_BUFFER_SIZE_SCALE_FACTOR = 100;
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@ -61,10 +58,15 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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boolean debug = false;
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private NSProgressFunction<InputType> progressFunction = null;
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final SimpleTimer outsideSchedulerTimer = TIME_CALLS ? new SimpleTimer("outside") : null;
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final SimpleTimer inputTimer = TIME_CALLS ? new SimpleTimer("input") : null;
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final SimpleTimer mapTimer = TIME_CALLS ? new SimpleTimer("map") : null;
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final SimpleTimer reduceTimer = TIME_CALLS ? new SimpleTimer("reduce") : null;
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/**
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* Tracks the combined runtime profiles across all created nano schedulers
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*/
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final static private NSRuntimeProfile combinedNSRuntimeProfiler = new NSRuntimeProfile();
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/**
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* The profile specific to this nano scheduler
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*/
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final private NSRuntimeProfile myNSRuntimeProfile = new NSRuntimeProfile();
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/**
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* Create a new nanoscheduler with the desire characteristics requested by the argument
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@ -92,7 +94,7 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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}
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// start timing the time spent outside of the nanoScheduler
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outsideSchedulerTimer.start();
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myNSRuntimeProfile.outsideSchedulerTimer.start();
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}
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/**
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@ -119,21 +121,31 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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* After this call, execute cannot be invoked without throwing an error
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*/
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public void shutdown() {
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outsideSchedulerTimer.stop();
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myNSRuntimeProfile.outsideSchedulerTimer.stop();
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// add my timing information to the combined NS runtime profile
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combinedNSRuntimeProfiler.combine(myNSRuntimeProfile);
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if ( nThreads > 1 ) {
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shutdownExecutor("inputExecutor", inputExecutor);
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shutdownExecutor("mapExecutor", mapExecutor);
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shutdownExecutor("reduceExecutor", reduceExecutor);
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}
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shutdown = true;
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if (TIME_CALLS) {
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printTimerInfo("Input time", inputTimer);
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printTimerInfo("Map time", mapTimer);
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printTimerInfo("Reduce time", reduceTimer);
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printTimerInfo("Outside time", outsideSchedulerTimer);
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}
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shutdown = true;
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}
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public void printRuntimeProfile() {
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myNSRuntimeProfile.log(logger);
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}
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public static void printCombinedRuntimeProfile() {
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if ( combinedNSRuntimeProfiler.totalRuntimeInSeconds() > 0.1 )
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combinedNSRuntimeProfiler.log(logger);
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}
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protected double getTotalRuntime() {
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return myNSRuntimeProfile.totalRuntimeInSeconds();
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}
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/**
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@ -154,21 +166,6 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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throw new IllegalStateException(remaining.size() + " remaining tasks found in an executor " + name + ", unexpected behavior!");
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}
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/**
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* Print to logger.info timing information from timer, with name label
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*
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* @param label the name of the timer to display. Should be human readable
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* @param timer the timer whose elapsed time we will display
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*/
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@Requires({"label != null", "timer != null"})
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private void printTimerInfo(final String label, final SimpleTimer timer) {
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final double total = inputTimer.getElapsedTime() + mapTimer.getElapsedTime()
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+ reduceTimer.getElapsedTime() + outsideSchedulerTimer.getElapsedTime();
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final double myTimeInSec = timer.getElapsedTime();
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final double myTimePercent = myTimeInSec / total * 100;
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logger.info(String.format("%s: %s (%5.2f%%)", label, new AutoFormattingTime(myTimeInSec), myTimePercent));
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}
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/**
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* @return true if this nanoScheduler is shutdown, or false if its still open for business
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*/
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@ -246,7 +243,7 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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if ( map == null ) throw new IllegalArgumentException("map function cannot be null");
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if ( reduce == null ) throw new IllegalArgumentException("reduce function cannot be null");
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outsideSchedulerTimer.stop();
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myNSRuntimeProfile.outsideSchedulerTimer.stop();
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ReduceType result;
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if ( ALLOW_SINGLE_THREAD_FASTPATH && getnThreads() == 1 ) {
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@ -255,7 +252,7 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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result = executeMultiThreaded(inputReader, map, initialValue, reduce);
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}
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outsideSchedulerTimer.restart();
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myNSRuntimeProfile.outsideSchedulerTimer.restart();
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return result;
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}
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@ -272,28 +269,31 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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ReduceType sum = initialValue;
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int i = 0;
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// start timer to ensure that both hasNext and next are caught by the timer
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if ( TIME_CALLS ) inputTimer.restart();
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while ( inputReader.hasNext() ) {
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final InputType input = inputReader.next();
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if ( TIME_CALLS ) inputTimer.stop();
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while ( true ) {
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// start timer to ensure that both hasNext and next are caught by the timer
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myNSRuntimeProfile.inputTimer.restart();
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if ( ! inputReader.hasNext() ) {
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myNSRuntimeProfile.inputTimer.stop();
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break;
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} else {
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final InputType input = inputReader.next();
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myNSRuntimeProfile.inputTimer.stop();
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// map
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if ( TIME_CALLS ) mapTimer.restart();
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final long preMapTime = LOG_MAP_TIMES ? 0 : mapTimer.currentTimeNano();
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final MapType mapValue = map.apply(input);
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if ( LOG_MAP_TIMES ) logger.info("MAP TIME " + (mapTimer.currentTimeNano() - preMapTime));
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if ( TIME_CALLS ) mapTimer.stop();
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// map
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myNSRuntimeProfile.mapTimer.restart();
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final long preMapTime = LOG_MAP_TIMES ? 0 : myNSRuntimeProfile.mapTimer.currentTimeNano();
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final MapType mapValue = map.apply(input);
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if ( LOG_MAP_TIMES ) logger.info("MAP TIME " + (myNSRuntimeProfile.mapTimer.currentTimeNano() - preMapTime));
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myNSRuntimeProfile.mapTimer.stop();
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if ( i++ % inputBufferSize == 0 && progressFunction != null )
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progressFunction.progress(input);
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if ( i++ % inputBufferSize == 0 && progressFunction != null )
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progressFunction.progress(input);
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// reduce
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if ( TIME_CALLS ) reduceTimer.restart();
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sum = reduce.apply(mapValue, sum);
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if ( TIME_CALLS ) reduceTimer.stop();
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if ( TIME_CALLS ) inputTimer.restart();
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// reduce
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myNSRuntimeProfile.reduceTimer.restart();
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sum = reduce.apply(mapValue, sum);
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myNSRuntimeProfile.reduceTimer.stop();
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}
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}
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return sum;
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@ -321,11 +321,11 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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new LinkedBlockingDeque<Future<MapResult<MapType>>>(mapBufferSize);
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// Start running the input reader thread
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inputExecutor.submit(new InputProducer<InputType>(inputReader, inputTimer, inputQueue));
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inputExecutor.submit(new InputProducer<InputType>(inputReader, myNSRuntimeProfile.inputTimer, inputQueue));
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// Start running the reducer thread
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final ReducerThread<MapType, ReduceType> reducer
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= new ReducerThread<MapType, ReduceType>(reduce, reduceTimer, initialValue, mapResultQueue);
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= new ReducerThread<MapType, ReduceType>(reduce, myNSRuntimeProfile.reduceTimer, initialValue, mapResultQueue);
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final Future<ReduceType> reduceResult = reduceExecutor.submit(reducer);
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try {
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@ -382,10 +382,10 @@ public class NanoScheduler<InputType, MapType, ReduceType> {
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@Override
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public MapResult<MapType> call() {
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if ( TIME_CALLS ) mapTimer.restart();
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if ( debug ) debugPrint("\t\tmap " + input);
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myNSRuntimeProfile.mapTimer.restart();
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final MapType result = map.apply(input);
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if ( TIME_CALLS ) mapTimer.stop();
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myNSRuntimeProfile.mapTimer.stop();
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return new MapResult<MapType>(result, id);
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}
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}
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@ -29,6 +29,7 @@ class ReducerThread<MapType, ReduceType> implements Callable<ReduceType> {
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final ReduceType sum,
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final BlockingQueue<Future<MapResult<MapType>>> mapResultQueue) {
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if ( reduce == null ) throw new IllegalArgumentException("Reduce function cannot be null");
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if ( reduceTimer == null ) throw new IllegalArgumentException("reduceTimer cannot be null");
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if ( mapResultQueue == null ) throw new IllegalArgumentException("mapResultQueue cannot be null");
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this.reduce = reduce;
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@ -51,9 +52,9 @@ class ReducerThread<MapType, ReduceType> implements Callable<ReduceType> {
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} else {
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lastJobID = result.getJobID();
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// apply reduce, keeping track of sum
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if ( reduceTimer != null ) reduceTimer.restart();
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reduceTimer.restart();
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sum = reduce.apply(result.getValue(), sum);
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if ( reduceTimer != null ) reduceTimer.stop();
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reduceTimer.stop();
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}
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}
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} catch (ExecutionException ex) {
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@ -1,6 +1,7 @@
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package org.broadinstitute.sting.utils.nanoScheduler;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.SimpleTimer;
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import org.testng.Assert;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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@ -42,7 +43,7 @@ public class InputProducerUnitTest extends BaseTest {
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final LinkedBlockingDeque<InputProducer<Integer>.InputValue> readQueue =
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new LinkedBlockingDeque<InputProducer<Integer>.InputValue>(queueSize);
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final InputProducer<Integer> ip = new InputProducer<Integer>(elements.iterator(), null, readQueue);
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final InputProducer<Integer> ip = new InputProducer<Integer>(elements.iterator(), new SimpleTimer(), readQueue);
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final ExecutorService es = Executors.newSingleThreadExecutor();
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es.submit(ip);
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils.nanoScheduler;
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import org.apache.log4j.BasicConfigurator;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.SimpleTimer;
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import org.testng.Assert;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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@ -86,7 +87,7 @@ public class NanoSchedulerUnitTest extends BaseTest {
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static NanoSchedulerBasicTest exampleTest = null;
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@DataProvider(name = "NanoSchedulerBasicTest")
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public Object[][] createNanoSchedulerBasicTest() {
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for ( final int bufferSize : Arrays.asList(1, 10, 1000, 1000000) ) {
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for ( final int bufferSize : Arrays.asList(1, 10, 1000, 1000000, 10000000) ) {
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for ( final int nt : Arrays.asList(1, 2, 4) ) {
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for ( final int start : Arrays.asList(0) ) {
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for ( final int end : Arrays.asList(0, 1, 2, 11, 10000, 100000) ) {
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@ -114,6 +115,7 @@ public class NanoSchedulerUnitTest extends BaseTest {
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}
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private void testNanoScheduler(final NanoSchedulerBasicTest test) throws InterruptedException {
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final SimpleTimer timer = new SimpleTimer().start();
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final NanoScheduler<Integer, Integer, Integer> nanoScheduler =
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new NanoScheduler<Integer, Integer, Integer>(test.bufferSize, test.nThreads);
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@ -129,6 +131,17 @@ public class NanoSchedulerUnitTest extends BaseTest {
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Assert.assertTrue(callback.callBacks >= test.nExpectedCallbacks(), "Not enough callbacks detected. Expected at least " + test.nExpectedCallbacks() + " but saw only " + callback.callBacks);
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nanoScheduler.shutdown();
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// TODO -- need to enable only in the case where there's serious time spend in
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// TODO -- read /map / reduce, otherwise the "outside" timer doesn't add up
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final double myTimeEstimate = timer.getElapsedTime();
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final double tolerance = 0.1;
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if ( false && myTimeEstimate > 0.1 ) {
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Assert.assertTrue(nanoScheduler.getTotalRuntime() > myTimeEstimate * tolerance,
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"NanoScheduler said that the total runtime was " + nanoScheduler.getTotalRuntime()
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+ " but the overall test time was " + myTimeEstimate + ", beyond our tolerance factor of "
|
||||
+ tolerance);
|
||||
}
|
||||
}
|
||||
|
||||
@Test(enabled = true, dataProvider = "NanoSchedulerBasicTest", dependsOnMethods = "testMultiThreadedNanoScheduler", timeOut = NANO_SCHEDULE_MAX_RUNTIME)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
package org.broadinstitute.sting.utils.nanoScheduler;
|
||||
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.utils.SimpleTimer;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.DataProvider;
|
||||
import org.testng.annotations.Test;
|
||||
|
|
@ -61,7 +62,7 @@ public class ReducerThreadUnitTest extends BaseTest {
|
|||
|
||||
final ReduceSumTest reduce = new ReduceSumTest(mapResultsQueue);
|
||||
final ReducerThread<Integer, Integer> thread
|
||||
= new ReducerThread<Integer, Integer>(reduce, null, 0, mapResultsQueue);
|
||||
= new ReducerThread<Integer, Integer>(reduce, new SimpleTimer(), 0, mapResultsQueue);
|
||||
|
||||
final ExecutorService es = Executors.newSingleThreadExecutor();
|
||||
final Future<Integer> value = es.submit(thread);
|
||||
|
|
|
|||
Loading…
Reference in New Issue