Oh. You want to kill program A from outside of itself.

So find the java process that's running it and kill it.

"ps aux" and then "kill <pid>"

That's right. Starting java twice results in two java processes. Stopping one
doesn't ( necessarily ;) ) stop the other. But you can stop it anyway.

If you have access to program-A's console, you can just press Control+C.

Otherwise...

1. If you run some flavor of Linux (Unix?), you do the following:

1.1. Find out what program-A's pid is:

ps -A | grep java
(where -A is a switch, not program-A's name)

or

ps x | grep java

1.2. and then

kill <pid>

If the process doesn't want to die, you turn the radical-gauge nine notches up
;-) and

kill -9 <pid>

See also: killall.

2. If, on the other hand, you use Windows, just use Task Manager (End Process,
End Process Tree).

According to
http://java.sun.com/j2se/1.3/docs/api/java/lang/Thread.html the JVM
will terminate when System.exit() is called, regardless of the type of
threads still running, or when the only threads running are daemon
threads

No,  or at least not that I know of.  Normally when you start a java
program it maintains it's own JVM for execution.  This provides a layer
of separation between instances of a program running, even if it is run
from the same code base.

I just wrote something (may be a better way to do it, so here goes ...) ,
Every thread registers itself with the ShutdownManager at a certain
shutdown level..
If the thread is blocking on a socket then it registers that socket..

Then the thread goes about its busienss like this..

try
  ShutdownManager.register(socket,1);
  while(!ShutdownManager.shuttingDown(socket) && other stuff ) {
        process input
  }
  ShutdownManager.unregister(socket);
} catch (Exception e) {
  ShutdownManager.unregister(socket);
}

Then the ShutdownManger. will cycle through the shutdown levels calling
either  Thread.interrupt(), Socket.close() etc..

Generally the server sockets are at level 1.
SessionSockets level 2.
Output threads etc. level 3.
Core processes (eg internal hsqldb) at highest level.

The ShutdownManager enters a sleep, loop waiting for a shutdownRequest
from the rest of the app... This sets a flag and interrupts the sleep
loop.

There's probably a nice class out there that does this properly!

Lordy