Program: 3108
Project: 3108
Buggy source:
private boolean doStart(BTraceTask task){
  final AtomicBoolean result=new AtomicBoolean(false);
  final BTraceTaskImpl btrace=(BTraceTaskImpl)task;
  try {
    final CountDownLatch latch=new CountDownLatch(1);
    final BTraceCompiler compiler=compilerFactory.newCompiler(btrace);
    btrace.setState(BTraceTask.State.COMPILING);
    final byte[] bytecode=compiler.compile(btrace.getScript(),task.getClassPath(),outputProvider.getStdErr(task));
    if (bytecode.length == 0) {
      btrace.setState(BTraceTask.State.FAILED);
      return false;
    }
    btrace.setState(BTraceTask.State.COMPILED);
    LOGGER.log(Level.FINEST,"String_Node_Str",bytecode.length);
    commQueue.submit(new Runnable(){
      public void run(){
        int port=portLocator.getTaskPort(btrace);
        LOGGER.log(Level.FINEST,"String_Node_Str",port);
        BTraceSettings settings=settingsProvider.getSettings();
        final Client client=new Client(port,"String_Node_Str",settings.isDebugMode(),true,btrace.isUnsafe(),settings.isDumpClasses(),settings.getDumpClassPath());
        try {
          client.attach(String.valueOf(btrace.getPid()),compiler.getAgentJarPath(),compiler.getToolsJarPath(),null);
          Thread.sleep(200);
          client.submit(bytecode,new String[]{},new CommandListener(){
            private boolean retransforming=false;
            public void onCommand(            Command cmd) throws IOException {
              LOGGER.log(Level.FINEST,"String_Node_Str",cmd.toString());
switch (cmd.getType()) {
case Command.SUCCESS:
{
                  if (retransforming) {
                    clientMap.put(btrace,client);
                    result.set(true);
                    latch.countDown();
                    retransforming=false;
                  }
                  break;
                }
case Command.EXIT:
{
                latch.countDown();
                stop(btrace);
                break;
              }
case Command.RETRANSFORMATION_START:
{
              int numClasses=((RetransformationStartNotification)cmd).getNumClasses();
              btrace.setInstrClasses(numClasses);
              btrace.setState(BTraceTask.State.INSTRUMENTING);
              retransforming=true;
              break;
            }
        }
        btrace.dispatchCommand(cmd);
      }
    }
);
  }
 catch (  Exception e) {
    LOGGER.log(Level.FINE,e.getLocalizedMessage(),e);
    result.set(false);
    latch.countDown();
  }
}
}
);
latch.await();
}
 catch (InterruptedException ex) {
LOGGER.log(Level.WARNING,null,ex);
}
return result.get();
}

Fixed version (ground truth):
private boolean doStart(BTraceTask task){
  final AtomicBoolean result=new AtomicBoolean(false);
  final BTraceTaskImpl btrace=(BTraceTaskImpl)task;
  try {
    final CountDownLatch latch=new CountDownLatch(1);
    final BTraceCompiler compiler=compilerFactory.newCompiler(btrace);
    btrace.setState(BTraceTask.State.COMPILING);
    final byte[] bytecode=compiler.compile(btrace.getScript(),task.getClassPath(),outputProvider.getStdErr(task));
    if (bytecode.length == 0) {
      btrace.setState(BTraceTask.State.FAILED);
      return false;
    }
    btrace.setState(BTraceTask.State.COMPILED);
    LOGGER.log(Level.FINEST,"String_Node_Str",bytecode.length);
    commQueue.submit(new Runnable(){
      public void run(){
        int port=portLocator.getTaskPort(btrace);
        LOGGER.log(Level.FINEST,"String_Node_Str",port);
        BTraceSettings settings=settingsProvider.getSettings();
        final Client client=new Client(port,"String_Node_Str",settings.isDebugMode(),true,btrace.isUnsafe(),settings.isDumpClasses(),settings.getDumpClassPath());
        try {
          client.attach(String.valueOf(btrace.getPid()),compiler.getAgentJarPath(),compiler.getToolsJarPath(),null);
          Thread.sleep(200);
          client.submit(bytecode,new String[]{},new CommandListener(){
            private boolean retransforming=false;
            public void onCommand(            Command cmd) throws IOException {
              LOGGER.log(Level.FINEST,"String_Node_Str",cmd.toString());
switch (cmd.getType()) {
case Command.SUCCESS:
{
                  if (!retransforming) {
                    result.set(true);
                    clientMap.put(btrace,client);
                    latch.countDown();
                  }
                  break;
                }
case Command.EXIT:
{
                latch.countDown();
                stop(btrace);
                break;
              }
case Command.RETRANSFORMATION_START:
{
              int numClasses=((RetransformationStartNotification)cmd).getNumClasses();
              btrace.setInstrClasses(numClasses);
              btrace.setState(BTraceTask.State.INSTRUMENTING);
              retransforming=true;
              break;
            }
case Command.RETRANSFORMATION_END:
{
            if (retransforming) {
              btrace.setState(BTraceTask.State.RUNNING);
              retransforming=false;
            }
            break;
          }
      }
      btrace.dispatchCommand(cmd);
    }
  }
);
}
 catch (Exception e) {
  LOGGER.log(Level.FINE,e.getLocalizedMessage(),e);
  result.set(false);
  latch.countDown();
}
}
}
);
latch.await();
}
 catch (InterruptedException ex) {
LOGGER.log(Level.WARNING,null,ex);
}
return result.get();
}