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What is a preferred way of closing a third-application thread without waiting for it to complete?

I am currently running the JAR that I cannot change, and sometimes it simply gets stuck for no good reason. I have tried finding the ways to interrupt the thread, stop the thread, etceteras, but no luck.
Each solution offered was about doing the complete exit or waiting for a thread to complete.
What I want to do is to simply close the thread, exactly when the timeout completes, and carry on with the program.
What I do not want to do is use the while loop with a timeout, java.util.concurrent.Future, System.exit, and make a Thread.interrupt call.
None of these will help!

You can't forcibly stop a thread in mid-execution. The Thread.destroy() method would have done that, but it was never implemented, and its documentation explains why it would be unsafe to use even if it worked.
There are some other deprecated methods like Thread.stop() and Thread.suspend() which may actually work, but they're also unsafe to use; again, their documentation explains why.
Telling the thread that it should terminate itself, and then waiting for it to do so, is the only safe way to stop a thread.
As an workaround, you could run your task in an entirely separate process, so that you can destroy it when you want it to stop. That is safe, since processes are isolated from each other and destroying the child process can't leave the parent process in an unstable state.
Interacting with a separate process is more difficult, though, since you can't share variables between processes like you can with threads. You'd need to send messages through the process's input and output streams.

Actually, you can't really solve this!
What I mean is: even if you would manage to kill "your" thread that you used to trigger the 3rd party code - you have no way of killing threads or processes created by the code you are invoking.
If you want to be absolutely sure to kill all and anything, you might have to look into rather complex solutions like:
instead of just using a thread, you create a new process with a new JVM B
in that JVM B, you can call that library
but of course, that requires that you put additional code around; so that "your" code in JVM A can talk to "your" code in JVM B
And now you might be able to tear down that process, and all artifacts belonging to it. Maybe.
And seriously: to be really really sure that the 3rd party library didn't kick of anything that you can't stop; you might even have to run that JVM inside some kind of container (for example a docker instance). That you could tear down and be sure that everything is gone.
Long story short: I think there is no way to absolutely control the threads created in a thread. If you need that level of control, you need to look into "outsourcing" those calls.

You can use Executor for this. It allows you to submit tasks (e.g. runnable) and executes those tasks parallely. Also, once you call shutdown(), it lets you configure the timeout and kills all the workers if they are not finished by that time. An example would look like this:
ExecutorService executor = Executors.newFixedThreadPool(1);
executor.execute(() -> {
//logic to call the method of third party jar
});
//Other business logic
executor.awaitTermination(1, TimeUnit.MINUTES);
executor.shutdownNow();
TimeUnit is an enum, with values like SECONDS, HOURS, MINUTES etc (here's javadoc) so you can configure different time units. A couple of points:
Once shutdownNow is called, no new tasks will be accepted (i.e. you can't call execute or submit) and existing tasks will be stopped. So, we are basically waiting for a minute for tasks to be complete and if it is not complete, we are killing that task.
awaitTermination throws InterruptedException (as it interrupts the threads internally if they are not finished) so you will have to wrap it inside try-catch block.
Here's javadoc for Executor.

Is Thread to be favoured over Executor here?

As far as I understand Executors help handling the execution of runnables. E.g. I would choose using an executor when I have several worker threads that do their job and then terminate.
The executor would handle the creation and the termination of the Threads needed to execute the worker runnables.
However now I am facing another situation. A fixed number of classes/objects shall encapsulate their own thread. So the thread is started at the creation of those objects and the Thread shall continue running for the whole life time of these objects.
The few objects in turn are created at the start of the programm and exist for the whole run time.
I guess Threads are preferable over Executors in this situation, however when I read the internet everybody seems to suggest using Executors over Threads in any possible situation.
Can somebody please tell me if I want to choose Executors or Threads here and why?
Thanks

You're somewhat mixing things. Executor is just an interface. Thread is a core class. There's nothing which directly implies that Executor implementations execute tasks in separate threads.
Read the first few lines of the JavaDoc.
Executor
So if you want full control, just use Thread and do things on your own.

Without knowing more about the context, it's hard to give a good answer, but generally speaking I'd say that the situations that calls for using Thread are pretty few and far between. If you start trying to synchronize your program "manually" using synchronized I bet things will get out of hand quickly. (Not to mention how hard it will be to debug the code.)
Last time I used a thread was when I wanted to record some audio in the background. It was a "start"/"stop" kind of thing, and not "task oriented". (I tried long and hard to try to find an audio library that would encapsulate that for me but failed.)
If you choose to go for a thread-solution, I suggest you try to limit the scope of the thread to only execute within the associated object. This will to an as large extent as possible avoid forcing you to think about happens-before relations, thread-safe publishing of values etc throughout the code.

ExecutorService can have thread pool
It optimizes performance, because creating a Thread is expensive.
ExecutorService has life cycle control
shutdown(), shutdownNow() etc are provided.
ExecutorService is flexible
You could invoke variety of behaviors: customize ThreadFactory, set thread pool size, delay behavior ScheduledThreadPoolExecutor etc...

How to manage java threads by sleep function? [duplicate]

and excuse the lack of knowledge on multithreaded apps, but I am new to the field.
Is there a pattern or common used methodology for monitoring the 'job completion' or 'job status' of worker threads from a monitor (a class that acts as a monitor)?
What I have currently done is create a list of workers and create one thread for each worker. After all threads have started i am looping over the worker list and 'checking their status' by making a call to a method.
At that time I couldn't come up with a different solution, but being new to the field, I don't know if this is the way to go, or if there are other solutions or patterns that I should study.

Depending on what you want, there are many ways that you can do this.
If you just want to wait until all the threads finish (i.e. all you care about is having everything finish before moving on), you can use Thread.join():
try {
for (Thread t: threadsIWaitOn)
t.join();
} catch (InterruptedException iex) {
/* ... handle error ...
}
If you want a more fine-grained control over the thread status and want to be able, at any time, to know what threads are doing, you can use the Thread.getState() function. This returns a Thread.State object that describes whether the thread is running, blocked, new, etc., and the Javadoc specifically says that it's designed for monitoring the state of a thread rather than trying to synchronize on it. This might be want you want to do.
If you want even more information than that - say, how to get a progress indicator for each thread that counts up from 0 to 100 as the thread progresses - then another option might be to create a Map from Threads to AtomicIntegers associating each thread with a counter, then pass the AtomicInteger into the constructor of each thread. That way, each thread can continuously increment the counters, and you can have another thread that continuously polls the progress.
In short, you have a lot of options based on what it is that you're trying to accomplish. Hopefully something in here helps out!

Use a ThreadPool and Executor, then you get a Future<> and you can poll for their completion and some more nice stuff, too. I can appreciate this book for you: Java Concurrency in Practice

Try to use any kind of synchronization. For example, wait on some kind of monitor/semaphore until job is done / whatever you need.

Analysing a multi-threaded Java application

In an open source application I'm participating, we've got a bug, where the application doesn't always close properly. That's what I'd like to solve.
Experience has shown that this happens most of the time when threads and processes are being started, but not managed correctly (e.g. a thread is waiting on a socket connection, the application is being shut down and the thread keeps on waiting).
With this in mind I've searched for '.start()' in the entire source and found 53 occurrences (which scared me a bit).
As a first step, I wanted to create a helper class (ThreadExecutor) where the current code 'thread.start()' would be replaced by 'ThreadExecutor.Execute(thread)' to have a) only a few changes in the existing source and b) a single class where I can easily check which threads don't end as they should. To do this I wanted to
add the thread to be executed to a list called activeThreads when calling the Execute method
start the thread
remove it from the activeThreads list when it ends.
This way I'd have an up to date list of all executing threads and when the app hangs on shutdown I could see in there which thread(s) is(are) causing it.
Questions:
What do you think about the concept? I'm usually coding c# and know how I'd do it using .NET with workers, but am not too sure what's best in Java (I'd like to modify as few lines of code as possible in the existing source).
If the concept seems ok, how can I get notified of a thread terminating. I'd like to avoid having an additional thread checking every once in a while what the state of all threads contained in activeThreads is, to remove them if they terminated.
Just to clarify: Before figuring out how to terminate the application properly, what I'm asking here is what's the best/easiest way to find which threads are at cause for certain test cases which are pretty hard to reproduce.

I would attempt to analyze your application's behavior before changing any code. Code changes can introduce new problems - not what you want to do if you're trying to solve problems.
The easiest way to introspect the state of your application with regard to which threads are currently running is to obtain a thread dump. You said that your problem is that the application hangs on shutdown. This is the perfect scenario to apply a thread dump. You'll be able to see which threads are blocked.
You can read more about thread dumps here.

Try to make all threads daemon(when all remaining threads are daemon the JVM terminates). Use thread.setDaemon(true) before starting each thread.

You could try to look into your application using jvisualvm (which is shipped with the jdk, find it in the bin folder of your jdk). JVisualVM can connect to your application and display a lot of interesting information, including which processes are still running. I'd give that a shot before starting down the road you describe.
Here is some documentation on JVisualVM should you need it.

The best way in java is to use Thread pools instead of Threads directly (although using threads directly is accepted). Thread pools accept Runnable objects, which you can see as Tasks. The idea is that most threads would do a small task and then end, because making a Thread is expensive and harder to manager you can use the threadpool, which allows things like 'ThreadPoolExecutor.awaitTermination()`. If you have more tasks than Threads in the pool, remaining tasks will just be queued.
Changing a Thread into a Runnable is easy, and you can even execute a runnable on a Thread you make yourself.
Note that this might not work for threads that run a long time, but your question seems to suggest that they will eventually finish.
As for your second question, the best way to find out which threads are running at a certain point is to run the application in a debugger (such as Eclipse) and pause all threads on a breakpoint in the close function.

I would try the trial edition of jprofiler or something similar, which gives you a lot of insight into what your application and its threads actually do.
Don't change the code yet, but try to reproduce and understand when this happens.

Create yourself a static thread pool.
static ExecutorService threads = Executors.newCachedThreadPool();
For every start of thread change:
new Thread(new AThread()).start();
to
threads.submit(new AThread ());
When your code exits, list all running threads with:
List<Runnable> runningThreads = threads.shutdownNow();
for ( Runnable t : runningThreads ) {
System.out.println("Thread running at shutdown: "+t.toString());
}
This will not only shut down all running threads, it will list them out for you to see what their issue is.
EDIT: Added
If you want to keep track of all running threads use:
Future f = threads.submit(new AThread ());
and store it in a list somewhere. You can then find out about its state with calls like:
f.isDone();
... etc.

Java daemon - handling shutdown requests

I'm currently working on a daemon that will be doing A LOT of different tasks. It's multi threaded and is being built to handle almost any kind of internal-error without crashing. Well I'm getting to the point of handling a shutdown request and I'm not sure how I should go about doing it.
I have a shutdown hook setup, and when it's called it sets a variable telling the main daemon loop to stop running. The problem is, this daemon spawns multiple threads and they can take a long time. For instance, one of these threads could be converting a document. Most of them will be quick (I'm guessing under 10 seconds), but there will be threads that can last as long as 10+ minutes.
What I'm thinking of doing right now is when a shutdown hook has been sent, do a loop for like 5 seconds on ThreadGroup.activeCount() with a 500ms (or so) Sleep (all these threads are in a ThreadGroup) and before this loop, I will send a notification to all threads telling them a shutdown request has been called. Then they will have to instantly no matter what they're doing cleanup and shutdown.
Anyone else have any suggestions? I'm interested in what a daemon like MySQL for instance does when it gets told to stop, it stops instantly. What happens if like 10 query's are running that are very slow are being called? Does it wait or does it just end them. I mean servers are really quick, so there really isn't any kind of operation that I shouldn't be able to do in less than a second. You can do A LOT in 1000ms now days.
Thanks

The java.util.concurrent package provides a number of utilities, such as ThreadPoolExecutor (along with various specialized types of other Executor implementations from the Executors class) and ThreadPoolExecutor.awaitTermination(), which you might want to look into - as they provide the same exact functionality you are looking to implement. This way you can concentrate on implementing the actual functionality of your application/tasks instead of worrying about things like thread and task scheduling.

Are your thread jobs amenable to interruption via Thread#interrupt()? Do they mostly call on functions that themselves advertise throwing InterruptedException? If so, then the aforementioned java.util.concurrent.ExecutorService#shutdownNow() is the way to go. It will interrupt any running threads and return the list of jobs that were never started.
Similarly, if you hang on to the Futures produced by ExecutorService#submit(), you can use Future#cancel(boolean) and pass true to request that a running job be interrupted.
Unless you're calling on code out of your control that swallows interrupt signals (say, by catching InterruptedException without calling Thread.currentThread().interrupt()), using the built-in cooperative interruption facility is a better choice than introducing your own flags to approximate what's already there.