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Slightly more tolerant timing setting. Main() method in GenomeLocProcessTracker to generating timing data for trackers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5097 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-01-27 15:16:07 +00:00
parent 61c29d550d
commit 5ed128f839
2 changed files with 58 additions and 4 deletions
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58
java/src/org/broadinstitute/sting/utils/threading/GenomeLocProcessingTracker.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.utils.threading;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.apache.log4j.BasicConfigurator;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
@ -11,10 +13,8 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.io.RandomAccessFile;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.concurrent.locks.ReentrantLock;
/**
*
@ -338,4 +338,58 @@ public abstract class GenomeLocProcessingTracker {
protected abstract void registerNewLocs(Collection<ProcessingLoc> plocs);
protected abstract Collection<ProcessingLoc> readNewLocs();
// --------------------------------------------------------------------------------
//
// main function for testing performance
//
// --------------------------------------------------------------------------------
public static void main(String[] args) {
//BasicConfigurator.configure();
final String ref = args[0];
final File file = new File(args[1]);
final int cycles = Integer.valueOf(args[2]);
File referenceFile = new File(ref);
try {
final IndexedFastaSequenceFile fasta = new IndexedFastaSequenceFile(referenceFile);
final String chr1 = fasta.getSequenceDictionary().getSequence(1).getSequenceName();
final GenomeLocParser genomeLocParser = new GenomeLocParser(fasta);
final class MyTest {
String name;
GenomeLocProcessingTracker tracker;
MyTest(String name, GenomeLocProcessingTracker tracker) {
this.name = name;
this.tracker = tracker;
}
public void execute(int cycles) {
SimpleTimer delta = new SimpleTimer("delta");
SimpleTimer timer = new SimpleTimer("none");
if ( file.exists() ) file.delete();
timer.start();
delta.start();
for ( int i = 1; i < cycles; i++ ) {
tracker.claimOwnership(genomeLocParser.createGenomeLoc(chr1, i, i+1), "ABCDEFGHIJKL");
if ( i % 1000 == 0 ) {
System.out.printf("%s\t%d\t%d\t%.4f\t%.4f%n", name, i, timer.currentTime(), timer.getElapsedTime(), delta.getElapsedTime() );
delta.restart();
}
}
}
}
System.out.printf("name\tcycle\tcurrent.time\telapsed.time\tdelta%n");
new MyTest("in-memory", new SharedMemoryGenomeLocProcessingTracker(new ClosableReentrantLock())).execute(cycles);
new MyTest("nio", new FileBackedGenomeLocProcessingTracker(file, genomeLocParser, new ClosableReentrantLock(), null)).execute(cycles);
new MyTest("nio-file-lock", new FileBackedGenomeLocProcessingTracker(file, genomeLocParser, new SharedFileThreadSafeLock(file,1), null)).execute(cycles);
}
catch(FileNotFoundException ex) {
throw new UserException.CouldNotReadInputFile(referenceFile,ex);
}
}
}

4
java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java
View File

@ -27,9 +27,9 @@ public class SharedFileLock extends ClosableReentrantLock { // todo -- kinda gro
private static final boolean VERIFY = false;
private static final int VERIFY_PORT = 5050;
// 100 seconds of trying -> failure
// 5 minutes => 360 seconds of trying -> failure
protected static final int DEFAULT_N_TRIES = 1000;
protected static final long DEFAULT_MILLISECONDS_PER_TRY = 100;
protected static final long DEFAULT_MILLISECONDS_PER_TRY = 360;
/** The file we are locking */
private final File file;