How to wait for a number of threads to complete?

instead of join(), which is an old API, you can use CountDownLatch. I have modified your code as below to fulfil your requirement.

import java.util.concurrent.*;
class DoSomethingInAThread implements Runnable{
    CountDownLatch latch;
    public DoSomethingInAThread(CountDownLatch latch){
        this.latch = latch;
    } 
    public void run() {
        try{
            System.out.println("Do some thing");
            latch.countDown();
        }catch(Exception err){
            err.printStackTrace();
        }
    }
}

public class CountDownLatchDemo {
    public static void main(String[] args) {
        try{
            CountDownLatch latch = new CountDownLatch(1000);
            for (int n=0; n<1000; n++) {
                Thread t = new Thread(new DoSomethingInAThread(latch));
                t.start();
            }
            latch.await();
            System.out.println("In Main thread after completion of 1000 threads");
        }catch(Exception err){
            err.printStackTrace();
        }
    }
}

Explanation:

1. CountDownLatch has been initialized with given count 1000 as per your requirement.

2. Each worker thread DoSomethingInAThread will decrement the CountDownLatch, which has been passed in constructor.

3. Main thread CountDownLatchDemo await() till the count has become zero. Once the count has become zero, you will get below line in output.

   In Main thread after completion of 1000 threads
   

More info from oracle documentation page

public void await()
           throws InterruptedException

Causes the current thread to wait until the latch has counted down to zero, unless the thread is interrupted.

Refer to related SE question for other options:

wait until all threads finish their work in java

One way would be to make a List of Threads, create and launch each thread, while adding it to the list. Once everything is launched, loop back through the list and call join() on each one. It doesn't matter what order the threads finish executing in, all you need to know is that by the time that second loop finishes executing, every thread will have completed.

A better approach is to use an ExecutorService and its associated methods:

List<Callable> callables = ... // assemble list of Callables here
                               // Like Runnable but can return a value
ExecutorService execSvc = Executors.newCachedThreadPool();
List<Future<?>> results = execSvc.invokeAll(callables);
// Note: You may not care about the return values, in which case don't
//       bother saving them

Using an ExecutorService (and all of the new stuff from Java 5's concurrency utilities) is incredibly flexible, and the above example barely even scratches the surface.

import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;

public class DoSomethingInAThread implements Runnable
{
   public static void main(String[] args) throws ExecutionException, InterruptedException
   {
      //limit the number of actual threads
      int poolSize = 10;
      ExecutorService service = Executors.newFixedThreadPool(poolSize);
      List<Future<Runnable>> futures = new ArrayList<Future<Runnable>>();

      for (int n = 0; n < 1000; n++)
      {
         Future f = service.submit(new DoSomethingInAThread());
         futures.add(f);
      }

      // wait for all tasks to complete before continuing
      for (Future<Runnable> f : futures)
      {
         f.get();
      }

      //shut down the executor service so that this thread can exit
      service.shutdownNow();
   }

   public void run()
   {
      // do something here
   }
}

You put all threads in an array, start them all, and then have a loop

for(i = 0; i < threads.length; i++)
  threads[i].join();

Each join will block until the respective thread has completed. Threads may complete in a different order than you joining them, but that's not a problem: when the loop exits, all threads are completed.