TimeOut for Individual Threads in ExecutorService

Question

Hello all,
I am using a FixedThreadPool to execute a number of individual jobs. The jobs are using an external chemistry library (CDK) to calculate various properties on a set of molecules. The problem is that for a small number of the molecules, this calculation does not terminate in a reasonable time. I'm not sure if it is a bug with the program or a property of the algorithm they are using or what. The problem is that once thread pool starts a number of these non-terminating jobs equal to the max pools, the entire pool is locked up on these non-terminating calculations, meaning the program comes to a standstill.
So what I need to do is terminate the jobs if they take longer than a TimeOut value. There doesn't seem to be a way to do this with the concurrency API - you can terminate the entire ExecutorService if it runs for too long, but not on an individual thread level, from what I can see. So how would I go about doing this?
Cheers,
nfitzgerald
String nstmt = new String("SELECT mol_id FROM " + infotablename + " WHERE XLogP IS NULL ORDER BY mol_id DESC");
          PreparedStatement stmt = con.prepareStatement(nstmt, ResultSet.TYPE_FORWARD_ONLY,
                    ResultSet.CONCUR_READ_ONLY);
          ResultSet rs = stmt
                    .executeQuery();
          ExecutorService pool = Executors.newFixedThreadPool(workers);
          while (rs.next()) {
               String mol_id = rs.getString("mol_id");
               pool.submit(new CalculationHandler(hostname, user, password, infotable, structable, mol_id));
          System.out.println("All Submitted.");
          pool.shutdown();
          pool.awaitTermination(36000, TimeUnit.SECONDS);
          pool.shutdownNow();

Answer 1

Is there anything wrong with doing it this way:
public class TimeOutWrapper implements Runnable {
     Runnable runnable;
     long timeout;
     public TimeOutWrapper(Runnable runnable, long timeout){
          this.runnable = runnable;
          this.timeout = timeout;
     public void run(){
          Thread thread = new Thread(runnable);
          thread.start();
          //check every .1 second to see if it is done, return if done
          for(int i = 0; i < (timeout/1000); i++){
               try {
                    Thread.sleep(1000);
               } catch (InterruptedException e) {
                    e.printStackTrace();
               if(!thread.isAlive()){
                    return;
          //if it makes it the whole timeout
          thread.interrupt();
     return;          
}And then setting up the pool like this:
ExecutorService pool = Executors.newFixedThreadPool(workers);
String mol_id = rs.getString("mol_id");
TimeOutWrapper timeOutJob = new TimeOutWrapper(new SomeRunnable(args),  30000);
pool.submit(timeOutJob);Is this a "bad" way of doing it? Am I breaking some law here, or is this a valid work-around?
Edited by: nfitzgerald on Aug 7, 2008 3:09 PM
Edited by: nfitzgerald on Aug 7, 2008 3:11 PM