error when sending parameters to deuce.genome

[HHmdi]

Hello everyone

we are trying to run Deuce-STM and we need to work on genome but it give us the following errors

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
Creating gene and segments...     at jstamp.genome.Bitmap.isSet(Bitmap.java:100)
    at jstamp.genome.Segments.create(Segments.java:49)
    at jstamp.genome.Genome.<init>(Genome.java:33)
    at jstamp.genome.Genome.main(Genome.java:87)

we are using online methode and when trying to pass  -g  -t  -s  -n  parameters it seems it fail

we hope we can find the answer here, and consider that it is our first time with STMs at all

thank you so much in advance

-------------- genome code------------------


package jstamp.genome;

public class Genome extends Thread {
  int geneLength;
  int segmentLength;
  int minNumSegment;
  int numThread;

  int threadid;

  // add segments, random, etc to member variables
  // include in constructor
  // allows for passing in thread run function
  Random randomPtr;
  Gene genePtr;
  Segments segmentsPtr;
  Sequencer sequencerPtr;

  Genome(String x[]) {
    parseCmdLine(x);
    if(numThread == 0) {
      numThread = 1;
    }

    randomPtr = new Random();
    randomPtr.random_alloc();
    randomPtr.random_seed(0);

    genePtr = new Gene(geneLength);
    genePtr.create(randomPtr);

    segmentsPtr = new Segments(segmentLength, minNumSegment);
    segmentsPtr.create(genePtr, randomPtr);

    sequencerPtr = new Sequencer(geneLength, segmentLength, segmentsPtr);
  }

  Genome(int myThreadid, int myGeneLength, int mySegLength, int myMinNumSegs, int myNumThread, Random myRandomPtr, Gene myGenePtr, Segments mySegmentsPtr, Sequencer mySequencerPtr) {
    threadid = myThreadid;
    geneLength = myGeneLength;
    segmentLength = mySegLength;
    minNumSegment = myMinNumSegs;
    numThread = myNumThread;

    randomPtr = myRandomPtr;
    genePtr = myGenePtr;
    segmentsPtr = mySegmentsPtr;
    sequencerPtr = mySequencerPtr;
  }

  public void parseCmdLine(String args[]) {
    int i = 0;
    String arg;
    while (i < args.length && args[i].startsWith("-")) {
      arg = args[i++];
      //check options
      if(arg.equals("-g")) {
        if(i < args.length) {
          this.geneLength = new Integer(args[i++]).intValue();
        }
      } else if(arg.equals("-s")) {
        if(i < args.length) {
          this.segmentLength = new Integer(args[i++]).intValue();
        }
      } else if(arg.equals("-n")) {
        if(i < args.length) {
          this.minNumSegment = new Integer(args[i++]).intValue();
        }
      } else if(arg.equals("-t")) {
        if(i < args.length) {
          this.numThread = new Integer(args[i++]).intValue();
        }
      }
    }

  }

  public void run() {
    Barrier.enterBarrier();
    Sequencer.run(threadid, numThread, randomPtr, sequencerPtr);
    Barrier.enterBarrier();
  }

  public static void main(String x[]){

    System.out.print("Creating gene and segments... ");
    Genome g = new Genome(x);

    System.out.println("done.");
    System.out.println("Gene length     = " + g.genePtr.length);
    System.out.println("Segment length  = " + g.segmentsPtr.length);
    System.out.println("Number segments = " + g.segmentsPtr.contentsPtr.size());
    System.out.println("Number threads  = " + g.numThread);


    Barrier.setBarrier(g.numThread);

    /* Create and Start Threads */

    ByteString gene = g.genePtr.contents;
    Genome[] gn = new Genome[g.numThread];

    for(int i = 1; i<g.numThread; i++) {
      gn[i] = new Genome(i, g.geneLength, g.segmentLength, g.minNumSegment, g.numThread, g.randomPtr, g.genePtr, g.segmentsPtr, g.sequencerPtr);
    }

    System.out.print("Sequencing gene... ");   

    for(int i = 1; i<g.numThread; i++) {
      gn[i].start();
    }
   
    long start=System.currentTimeMillis();
    Barrier.enterBarrier();
    Sequencer.run(0, g.numThread, g.randomPtr, g.sequencerPtr);
    Barrier.enterBarrier();
    long stop=System.currentTimeMillis();
    long diff=stop-start;
    System.out.println("TIME="+diff);

    System.out.println("done.");

    /* Check result */
    {
      ByteString sequence = g.sequencerPtr.sequence;
      boolean result = gene.compareTo(sequence) == 0;
      System.out.println("Sequence matches gene: " + (result ? "yes" : "no"));
      //DEBUG
      //if (result) {
      // System.out.println("gene     = " + gene);
      // System.out.println("sequence = " + sequence);
      //}
    }

  }
}

[Guy Korland]

Hi,

I'm not sure all the jstamp benchmark were tested with DeuceSTM.

Just to be on the safe side and make sure it's not Deuce's bug, I would have try to run it with global lock (-Dorg.deuce.transaction.global=true).

Regards,
Guy Korland