Program: 177501
Project: 177501
Buggy source:
/** 
 * Creates a SimpleRegionFile
 * @param filePath the path to the file
 * @param desiredSegmentSize log2(the desired segment size) 
 * @param entries the number of blocks (sub-files) in the RegionFile
 * @param timeout the time in ms until the file times out for auto-closing
 * @throws IOException on error
 */
public SimpleRegionFile(File filePath,int desiredSegmentSize,int entries,int timeout) throws IOException {
  this.filePath=filePath;
  this.closed=new AtomicBoolean(false);
  this.timeout=timeout;
  this.lastAccess=new AtomicLong(0);
  refreshAccess();
  try {
    this.file=new RandomAccessFile(this.filePath,"String_Node_Str");
  }
 catch (  FileNotFoundException e) {
    this.closed.set(true);
    throw new SRFException("String_Node_Str" + this.filePath,e);
  }
  int headerSize=getHeaderSize(entries);
  if (file.length() <= headerSize) {
    file.seek(0);
    file.writeInt(VERSION);
    file.writeInt(desiredSegmentSize);
    file.writeInt(entries);
    for (int i=0; i < entries << 1; i++) {
      file.writeInt(0);
    }
  }
  file.seek(0);
  this.version=file.readInt();
  this.segmentSize=file.readInt();
  this.segmentMask=(1 << this.segmentSize) - 1;
  this.entries=file.readInt();
  if (entries != this.entries) {
    file.close();
    this.closed.set(true);
    throw new SRFException("String_Node_Str" + this.filePath + "String_Node_Str"+ entries+ "String_Node_Str"+ this.entries);
  }
  inuse=new AtomicReference<AtomicBoolean[]>(new AtomicBoolean[0]);
  int headerSegments=sizeToSegments(headerSize);
  int segmentsLocked=reserveSegments(0,headerSegments);
  if (segmentsLocked != headerSegments) {
    throw new SRFException("String_Node_Str");
  }
  blockSegmentStart=new AtomicInteger[entries];
  blockSegmentLength=new AtomicInteger[entries];
  blockActualLength=new AtomicInteger[entries];
  blockLock=new SRFReentrantReadWriteLock[entries];
  numberBlocksLocked=new AtomicInteger(0);
  for (int i=0; i < entries; i++) {
    blockSegmentStart[i]=new AtomicInteger(file.readInt());
    blockActualLength[i]=new AtomicInteger(file.readInt());
    blockSegmentLength[i]=new AtomicInteger(sizeToSegments(blockActualLength[i].get()));
    blockLock[i]=new SRFReentrantReadWriteLock(numberBlocksLocked);
    int length=reserveSegments(blockSegmentStart[i].get(),blockSegmentLength[i].get());
    if (length != blockSegmentLength[i].get()) {
      throw new SRFException("String_Node_Str" + i + "String_Node_Str");
    }
  }
}

Fixed version (ground truth):
/** 
 * Creates a SimpleRegionFile
 * @param filePath the path to the file
 * @param desiredSegmentSize log2(the desired segment size) 
 * @param entries the number of blocks (sub-files) in the RegionFile
 * @param timeout the time in ms until the file times out for auto-closing
 * @throws IOException on error
 */
public SimpleRegionFile(File filePath,int desiredSegmentSize,int entries,int timeout) throws IOException {
  this.filePath=filePath;
  this.closed=new AtomicBoolean(false);
  this.timeout=timeout;
  this.lastAccess=new AtomicLong(0);
  refreshAccess();
  try {
    this.file=new CachedRandomAccessFile(this.filePath,"String_Node_Str");
  }
 catch (  FileNotFoundException e) {
    this.closed.set(true);
    throw new SRFException("String_Node_Str" + this.filePath,e);
  }
  int headerSize=getHeaderSize(entries);
  if (file.length() <= headerSize) {
    file.seek(0);
    file.writeInt(VERSION);
    file.writeInt(desiredSegmentSize);
    file.writeInt(entries);
    for (int i=0; i < entries << 1; i++) {
      file.writeInt(0);
    }
  }
  file.seek(0);
  this.version=file.readInt();
  this.segmentSize=file.readInt();
  this.segmentMask=(1 << this.segmentSize) - 1;
  this.entries=file.readInt();
  if (entries != this.entries) {
    file.close();
    this.closed.set(true);
    throw new SRFException("String_Node_Str" + this.filePath + "String_Node_Str"+ entries+ "String_Node_Str"+ this.entries);
  }
  inuse=new AtomicReference<AtomicBoolean[]>(new AtomicBoolean[0]);
  int headerSegments=sizeToSegments(headerSize);
  int segmentsLocked=reserveSegments(0,headerSegments);
  if (segmentsLocked != headerSegments) {
    throw new SRFException("String_Node_Str");
  }
  blockSegmentStart=new AtomicInteger[entries];
  blockSegmentLength=new AtomicInteger[entries];
  blockActualLength=new AtomicInteger[entries];
  blockLock=new SRFReentrantReadWriteLock[entries];
  numberBlocksLocked=new AtomicInteger(0);
  for (int i=0; i < entries; i++) {
    blockSegmentStart[i]=new AtomicInteger(file.readInt());
    blockActualLength[i]=new AtomicInteger(file.readInt());
    blockSegmentLength[i]=new AtomicInteger(sizeToSegments(blockActualLength[i].get()));
    blockLock[i]=new SRFReentrantReadWriteLock(numberBlocksLocked);
    int length=reserveSegments(blockSegmentStart[i].get(),blockSegmentLength[i].get());
    if (length != blockSegmentLength[i].get()) {
      throw new SRFException("String_Node_Str" + i + "String_Node_Str");
    }
  }
}