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java Finalizer thread blocked

Java's large number of threads are in a blocked state, waiting for a lock, but there is no thread to have this lock
blocked thread
[root#xxx xxx]# grep BLOCKED 11.txt -C5
at java.lang.ref.Reference.waitForReferencePendingList(java.base#12.0.2/Native Method)
at java.lang.ref.Reference.processPendingReferences(java.base#12.0.2/Reference.java:241)
at java.lang.ref.Reference$ReferenceHandler.run(java.base#12.0.2/Reference.java:213)
"Finalizer" #3 daemon prio=8 os_prio=0 cpu=273.67ms elapsed=1139.36s tid=0x00007fabf2c6a000 nid=0x11 waiting for monitor entry [0x00007fabb19fd000]
java.lang.Thread.State: BLOCKED (on object monitor)
at java.lang.ref.Finalizer.runFinalizer(java.base#12.0.2/Finalizer.java:70)
- waiting to lock <0x000000048046f6f0> (a java.lang.Object)
at java.lang.ref.Finalizer$FinalizerThread.run(java.base#12.0.2/Finalizer.java:171)
"Signal Dispatcher" #4 daemon prio=9 os_prio=0 cpu=1.42ms elapsed=1139.36s tid=0x00007fabf2c6b000 nid=0x12 runnable [0x0000000000000000]
--
at java.util.concurrent.LinkedBlockingQueue.take(java.base#12.0.2/LinkedBlockingQueue.java:433)
at com.alipay.remoting.ReconnectManager$HealConnectionRunner.run(ReconnectManager.java:144)
at java.lang.Thread.run(java.base#12.0.2/Thread.java:835)
"Init-TX-Disruptor-0" #26 prio=5 os_prio=0 cpu=4732.71ms elapsed=1122.35s tid=0x00007fabb40c5800 nid=0x5d waiting for monitor entry [0x00007fab939ec000]
java.lang.Thread.State: BLOCKED (on object monitor)
at java.lang.ref.Finalizer.<init>(java.base#12.0.2/Finalizer.java:51)
- waiting to lock <0x000000048046f6f0> (a java.lang.Object)
at java.lang.ref.Finalizer.register(java.base#12.0.2/Finalizer.java:66)
at java.lang.Object.<init>(java.base#12.0.2/Object.java:50)
at org.rocksdb.AbstractNativeReference.<init>(AbstractNativeReference.java:25)
--
at xx.xxxx.xxx.xx.xxxx.xx.xx.onEvent(InitTxWorkHandler.java:24)
at com.lmax.disruptor.WorkProcessor.run(WorkProcessor.java:143)
at java.lang.Thread.run(java.base#12.0.2/Thread.java:835)
"Init-TX-Disruptor-1" #27 prio=5 os_prio=0 cpu=4698.53ms elapsed=1122.35s tid=0x00007faba7b1a000 nid=0x5e waiting for monitor entry [0x00007fab9236b000]
java.lang.Thread.State: BLOCKED (on object monitor)
at java.lang.ref.Finalizer.<init>(java.base#12.0.2/Finalizer.java:51)
- waiting to lock <0x000000048046f6f0> (a java.lang.Object)
at java.lang.ref.Finalizer.register(java.base#12.0.2/Finalizer.java:66)
at java.lang.Object.<init>(java.base#12.0.2/Object.java:50)
at org.rocksdb.AbstractNativeReference.<init>(AbstractNativeReference.java:25)
grep 0x000000048046f6f0 not found owns the monitor on 0x000000048046f6f0
grep 0x000000048046f6f0
The thread has been blocked for a long time, I want to know why

What are threads (i.e. lightweight processes) named `{java}` created for?

I wrote a Java program that sleeps for a while:
package com.mycompany.app;
import java.lang.System;
import java.util.concurrent.TimeUnit;
public class Main {
public static void main(String[] args) {
System.out.println("the current process's pid is " + ProcessHandle.current().pid());
try {
TimeUnit.SECONDS.sleep(200);
} catch (InterruptedException e) {
e.printStackTrace();
}
System.out.println("Hello World!"); // Prints the string to the console.
}
}
I run the program with:
$ java -cp target com.mycompany.app.Main
the current process's pid is 10172
I inspect the processes that Ubuntu creates to run it:
$ pstree -pau -l -G -s 10172
systemd,1 splash
└─lxterminal,3194,t
└─bash,12150
└─java,10172 -cp target com.mycompany.app.Main
├─{java},10173
├─{java},10174
├─{java},10175
├─{java},10176
├─{java},10177
├─{java},10178
├─{java},10179
├─{java},10180
├─{java},10181
├─{java},10182
├─{java},10183
├─{java},10184
├─{java},10185
├─{java},10186
├─{java},10187
├─{java},10188
├─{java},10189
└─{java},10190
What are those threads (i.e. lightweight processes) named {java} created for?
Is it possible to find out what programs they run from shell using some commands?
Which processes (and LWPs) are running JVM?
Which processes (and LWPs) are running my Java program?

All of these threads belong to JVM.
Run jstack <pid> to get the thread list.
"main" #1 prio=5 os_prio=0 cpu=150.00ms elapsed=8.04s tid=0x00007f9f90011000 nid=0x107 waiting on condition [0x00007f9f99f9f000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(java.base#11.0.1/Native Method)
at java.lang.Thread.sleep(java.base#11.0.1/Thread.java:339)
at java.util.concurrent.TimeUnit.sleep(java.base#11.0.1/TimeUnit.java:446)
at com.mycompany.app.Main.main(Main.java:10)
"Reference Handler" #2 daemon prio=10 os_prio=0 cpu=0.00ms elapsed=7.95s tid=0x00007f9f901f9000 nid=0x10e waiting on condition [0x00007f9f6c10f000]
java.lang.Thread.State: RUNNABLE
at java.lang.ref.Reference.waitForReferencePendingList(java.base#11.0.1/Native Method)
at java.lang.ref.Reference.processPendingReferences(java.base#11.0.1/Reference.java:241)
at java.lang.ref.Reference$ReferenceHandler.run(java.base#11.0.1/Reference.java:213)
"Finalizer" #3 daemon prio=8 os_prio=0 cpu=0.00ms elapsed=7.95s tid=0x00007f9f901fd800 nid=0x10f in Object.wait() [0x00007f9f65fef000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(java.base#11.0.1/Native Method)
- waiting on <0x0000000712108f80> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(java.base#11.0.1/ReferenceQueue.java:155)
- waiting to re-lock in wait() <0x0000000712108f80> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(java.base#11.0.1/ReferenceQueue.java:176)
at java.lang.ref.Finalizer$FinalizerThread.run(java.base#11.0.1/Finalizer.java:170)
"Signal Dispatcher" #4 daemon prio=9 os_prio=0 cpu=0.00ms elapsed=7.93s tid=0x00007f9f90210000 nid=0x110 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread0" #5 daemon prio=9 os_prio=0 cpu=40.00ms elapsed=7.93s tid=0x00007f9f90212000 nid=0x111 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
No compile task
"C1 CompilerThread0" #7 daemon prio=9 os_prio=0 cpu=40.00ms elapsed=7.93s tid=0x00007f9f90214000 nid=0x112 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
No compile task
"Sweeper thread" #8 daemon prio=9 os_prio=0 cpu=10.00ms elapsed=7.93s tid=0x00007f9f90216000 nid=0x113 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Service Thread" #9 daemon prio=9 os_prio=0 cpu=0.00ms elapsed=7.90s tid=0x00007f9f902d3800 nid=0x114 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Common-Cleaner" #10 daemon prio=8 os_prio=0 cpu=0.00ms elapsed=7.89s tid=0x00007f9f902df800 nid=0x116 in Object.wait() [0x00007f9f656ef000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(java.base#11.0.1/Native Method)
- waiting on <0x0000000712002df0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(java.base#11.0.1/ReferenceQueue.java:155)
- waiting to re-lock in wait() <0x0000000712002df0> (a java.lang.ref.ReferenceQueue$Lock)
at jdk.internal.ref.CleanerImpl.run(java.base#11.0.1/CleanerImpl.java:148)
at java.lang.Thread.run(java.base#11.0.1/Thread.java:834)
at jdk.internal.misc.InnocuousThread.run(java.base#11.0.1/InnocuousThread.java:134)
"Attach Listener" #11 daemon prio=9 os_prio=0 cpu=0.00ms elapsed=0.21s tid=0x00007f9f44001000 nid=0x126 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"VM Thread" os_prio=0 cpu=0.00ms elapsed=7.95s tid=0x00007f9f901f1000 nid=0x10d runnable
"GC Thread#0" os_prio=0 cpu=0.00ms elapsed=8.01s tid=0x00007f9f90038800 nid=0x108 runnable
"G1 Main Marker" os_prio=0 cpu=0.00ms elapsed=8.00s tid=0x00007f9f90097800 nid=0x109 runnable
"G1 Conc#0" os_prio=0 cpu=0.00ms elapsed=8.00s tid=0x00007f9f90099800 nid=0x10a runnable
"G1 Refine#0" os_prio=0 cpu=0.00ms elapsed=8.00s tid=0x00007f9f9018d000 nid=0x10b runnable
"G1 Young RemSet Sampling" os_prio=0 cpu=0.00ms elapsed=8.00s tid=0x00007f9f9018f000 nid=0x10c runnable
"VM Periodic Task Thread" os_prio=0 cpu=0.00ms elapsed=7.90s tid=0x00007f9f902d6000 nid=0x115 waiting on condition
Here nid is the hexadecimal ID of a thread in the OS - you may match it to the output of pstree.
The first thread named main is the thread executing your code.
Reference Handler thread is responsible for adding Weak, Soft and Phantom references discovered by Garbage Collector into their registered ReferenceQueues.
Finalizer thread runs finalize method of the objects ready to be finalized.
Signal Dispatcher waits for specific OS signals and handles them. In particular, it makes thread dump on SIGQUIT, and also initiates VM shutdown process on SIGTERM, SIGINT and SIGHUP.
CompilerThreads perform JIT compilation of the bytecode.
Sweeper thread cleans up obsolete compiled methods.
Service Thread runs several background JVM tasks: detects low memory condition, cleans up StringTable and SymbolTable, sends deferred JVMTI events and GC notifications and so on.
Common-Cleaner runs cleaning actions of java.lang.ref.Cleaner instances.
Attach Listener thread supports Dynamic Attach mechanism. It listens for incoming Dynamic Attach connections and executes VM commands. For example, it is used by jstack, jmap and jcmd utilities.
VM Thread runs internal VM operations that require a safepoint. The examples of such operations are deoptimization, class redifinition, biased lock revocation, thread dump, heap inspection etc.
G1 threads are involved in Garbage Collection.
VM Periodic Task Thread is used to simulate timer interrupts.

Using BufferedReader.lines() breaks in parallel

I'm writing some code that will be reading log lines and doing some processing in the background on that data. This processing would probably benifit from parallelization, such as what is offered by the Stream.parallel methods, and I was attempting to use this. This is the code I started out with that works perfectly.
public static void main(String[] args) {
try {
final Socket socket = new Socket(ADDRESS, PORT);
final BufferedReader reader = new BufferedReader(new InputStreamReader(socket.getInputStream()));
socket.getOutputStream().write(QUERY);
reader.lines().forEach(System.out::println);
} catch (IOException e) {
e.printStackTrace();
}
}
This code connects and prints out all of my data. I would very much like to restructure this code as follows:
public static void main(String[] args) {
try (Socket socket = new Socket(ADDRESS, PORT);
BufferedReader reader = new BufferedReader(new InputStreamReader(socket.getInputStream()))) {
socket.getOutputStream().write(QUERY);
reader.lines().forEach(System.out::println);
} catch (IOException e) {
e.printStackTrace();
}
}
But sadly this doesn't work. Even worse, going back to the original code, this doesn't even work:
public static void main(String[] args) {
try {
final Socket socket = new Socket(ADDRESS, PORT);
final BufferedReader reader = new BufferedReader(new InputStreamReader(socket.getInputStream()));
socket.getOutputStream().write(QUERY);
reader.lines().parallel().forEach(System.out::println);
} catch (IOException e) {
e.printStackTrace();
}
}
All that was added here was a .parallel call and this completely doesn't work. It just sits there and nothing is printed out.
I can live perfectly well and good without the 2nd version using the modified try(A a = new A()) {} as that doesn't look too good in this case. What I can't live without is figuring out why this .parallel call breaks everything.
I'm assuming the modified try statement is closing the streams as soon as I fall out of them (right after we start the forEach) so they are being killed and GC'd before operation. I can't for the life of me figure out what the hell is going on with the .parallel call.
As requested here is the output of jstack running on the .parellel() version of this code.
Full thread dump OpenJDK 64-Bit Server VM (25.112-b15 mixed mode):
"Attach Listener" #9 daemon prio=9 os_prio=0 tid=0x00007fd4f4001000 nid=0x4907 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Service Thread" #8 daemon prio=9 os_prio=0 tid=0x00007fd5280be000 nid=0x48d2 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C1 CompilerThread2" #7 daemon prio=9 os_prio=0 tid=0x00007fd5280bb000 nid=0x48d1 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007fd5280b9800 nid=0x48d0 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007fd5280b6800 nid=0x48cf waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007fd5280b5000 nid=0x48ce runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007fd528082000 nid=0x48cd in Object.wait() [0x00007fd515c6d000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000ec008e98> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
- locked <0x00000000ec008e98> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)
"Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007fd52807d800 nid=0x48cc in Object.wait() [0x00007fd515d6e000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000ec006b40> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:502)
at java.lang.ref.Reference.tryHandlePending(Reference.java:191)
- locked <0x00000000ec006b40> (a java.lang.ref.Reference$Lock)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153)
"main" #1 prio=5 os_prio=0 tid=0x00007fd528008000 nid=0x48c2 runnable [0x00007fd52fd9f000]
java.lang.Thread.State: RUNNABLE
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
- locked <0x00000000ec086790> (a java.net.SocksSocketImpl)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:211)
at com.gravypod.Test.main(Test.java:48)
"VM Thread" os_prio=0 tid=0x00007fd528075800 nid=0x48ca runnable
"GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007fd52801d800 nid=0x48c4 runnable
"GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007fd52801f000 nid=0x48c5 runnable
"GC task thread#2 (ParallelGC)" os_prio=0 tid=0x00007fd528021000 nid=0x48c6 runnable
"GC task thread#3 (ParallelGC)" os_prio=0 tid=0x00007fd528022800 nid=0x48c7 runnable
"VM Periodic Task Thread" os_prio=0 tid=0x00007fd5280c0800 nid=0x48d3 waiting on condition
JNI global references: 18
The Test.java:48 line is the Socket socket = new Socket line. This is the result of the fully-working non-parallel code (just using .lines()).
Full thread dump OpenJDK 64-Bit Server VM (25.112-b15 mixed mode):
"Attach Listener" #9 daemon prio=9 os_prio=0 tid=0x00007f9048001000 nid=0x4982 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Service Thread" #8 daemon prio=9 os_prio=0 tid=0x00007f90800be800 nid=0x496f runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C1 CompilerThread2" #7 daemon prio=9 os_prio=0 tid=0x00007f90800bb000 nid=0x496e waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007f90800b9800 nid=0x496d waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007f90800b6800 nid=0x496c waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007f90800b5000 nid=0x496b runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007f9080082000 nid=0x496a in Object.wait() [0x00007f907018d000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000ec008e98> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
- locked <0x00000000ec008e98> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)
"Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007f908007d800 nid=0x4969 in Object.wait() [0x00007f907028e000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000ec006b40> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:502)
at java.lang.ref.Reference.tryHandlePending(Reference.java:191)
- locked <0x00000000ec006b40> (a java.lang.ref.Reference$Lock)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153)
"main" #1 prio=5 os_prio=0 tid=0x00007f9080008000 nid=0x4961 runnable [0x00007f90884c3000]
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
at java.net.SocketInputStream.read(SocketInputStream.java:170)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
- locked <0x00000000ec08e890> (a java.io.InputStreamReader)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.fill(BufferedReader.java:161)
at java.io.BufferedReader.readLine(BufferedReader.java:324)
- locked <0x00000000ec08e890> (a java.io.InputStreamReader)
at java.io.BufferedReader.readLine(BufferedReader.java:389)
at java.io.BufferedReader$1.hasNext(BufferedReader.java:571)
at java.util.Iterator.forEachRemaining(Iterator.java:115)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at com.gravypod.Test.main(Test.java:51)
"VM Thread" os_prio=0 tid=0x00007f9080075800 nid=0x4968 runnable
"GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007f908001d800 nid=0x4963 runnable
"GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007f908001f000 nid=0x4964 runnable
"GC task thread#2 (ParallelGC)" os_prio=0 tid=0x00007f9080021000 nid=0x4965 runnable
"GC task thread#3 (ParallelGC)" os_prio=0 tid=0x00007f9080022800 nid=0x4966 runnable
"VM Periodic Task Thread" os_prio=0 tid=0x00007f90800c1000 nid=0x4970 waiting on condition
JNI global references: 319
The line Test.java:51 is the reader.lines().forEach line.

I imagine that parallel() or the forEach() on a parallel stream waits to read all the input before parallelising the task. Because the server never closes the connection, it will wait forever.
Your task is not really parallelizable. Data comes sequentially over the wire, so reading it in parallel cannot work.

It seems, your application isn’t hanging, technically, but just waiting for a lot of input, before performing observable work. This is a combination of two implementation details. When you are starting a parallel stream operation, it will first try to split the workload until every CPU core has something to do, before actually starting to process elements. This combines with the Reader#lines() parallelizes badly due to nonconfigurable batch size issue.
Simply said, when a Stream has an unknown size, the implementation will try to buffer batches of sizes that are multiples of 1024, growing on each split. This great answer shows, how the splitting will happen for a stream of an unknown size with multiple cores, showing that multiples of 1024 elements will get buffered in the process. This can take a very long time, before the consumer passed to forEach is ever invoked.
Note that processing an infinite source via the non-short-circuiting forEach is outside the scope of the Stream API anyway. Assuming a timely side effect is an assumption about the processing order of the Stream, but there is no guaranty about it.
This answer guides you to a work-around. You can use something like
try(Socket socket = new Socket(ADDRESS, PORT);
BufferedReader reader = new BufferedReader(
new InputStreamReader(socket.getInputStream()))) {
socket.getOutputStream().write(QUERY);
Stream.generate(() -> {
try { return reader.readLine(); }
catch (IOException ex) { throw new UncheckedIOException(ex); }
}).parallel().forEach(System.out::println);
} catch(IOException|UncheckedIOException e) {
e.printStackTrace();
}
But, as said, this isn’t the intended use case of the Stream API…

how to interprete this thread dump from a hung Java Swing application?

I have the following thread dump from a hung java swing application. It hung after a button is clicked and the GUI changed to blank. Other threads in socket communication and task management are still working (from the log file I can tell). I have removed some non-relevant output.
The #13 AW-EventQueue-0 should send out a command through the socket but it seems failed there. The #20 and #21 are AW-EventQueue-0-SharedResourceRunner which is not the same as the #13? It seems there is no deadlock but the GUI is not responsive and became blank.
do you see any useful information about the cause of the hanging?
Full thread dump Java HotSpot(TM) 64-Bit Server VM (25.20-b23 mixed mode):
"DestroyJavaVM" #32 prio=5 os_prio=0 tid=0x00007f286c009800 nid=0xa41 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"TimerQueue" #22 daemon prio=5 os_prio=0 tid=0x00007f28002a8800 nid=0xa65 waiting on condition [0x00007f284c56f000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x0000000088a8f5c0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
at java.util.concurrent.DelayQueue.take(DelayQueue.java:211)
at javax.swing.TimerQueue.run(TimerQueue.java:171)
at java.lang.Thread.run(Thread.java:745)
"AWT-EventQueue-0-SharedResourceRunner" #21 daemon prio=6 os_prio=0 tid=0x00007f280021d000 nid=0xa64 in Object.wait() [0x00007f284d434000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x0000000088aec748> (a jogamp.opengl.SharedResourceRunner)
at java.lang.Object.wait(Object.java:502)
at jogamp.opengl.SharedResourceRunner.run(SharedResourceRunner.java:276)
- locked <0x0000000088aec748> (a jogamp.opengl.SharedResourceRunner)
at java.lang.Thread.run(Thread.java:745)
"AWT-EventQueue-0-SharedResourceRunner" #20 daemon prio=6 os_prio=0 tid=0x00007f28001f3000 nid=0xa63 in Object.wait() [0x00007f284f7f5000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x0000000088aed588> (a jogamp.opengl.SharedResourceRunner)
at java.lang.Object.wait(Object.java:502)
at jogamp.opengl.SharedResourceRunner.run(SharedResourceRunner.java:276)
- locked <0x0000000088aed588> (a jogamp.opengl.SharedResourceRunner)
at java.lang.Thread.run(Thread.java:745)
"AWT-EventQueue-0" #13 prio=6 os_prio=0 tid=0x00007f286c444800 nid=0xa59 in Object.wait() [0x00007f2858913000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000dc467018> (a java.lang.Object)
at java.lang.Object.wait(Object.java:502)
at com.mycp.common.task.BMBTaskBase.startTask(BMBTaskBase.java:551)
- locked <0x00000000dc467018> (a java.lang.Object)
at com.mycp.uiapp.workmgmt.WorkMgmtMgr.sendBegCmd(WorkMgmtMgr.java:334)
at com.mycp.uiapp.workmgmt.WorkMgmtPanelBase.prepareAndSendBegWork(WorkMgmtPanelBase.java:559)
at com.mycp.uiapp.workmmgmt.WorkMgmtPanel.prepareAndSendBegWork(WorkMgmtPanel.java:1479)
at com.mycp.uiapp.workmgmt.WorkMgmtPanelBase.btnPrepareClicked(WorkMgmtPanelBase.java:363)
at com.mycp.uiapp.workmgmt.WorkMgmtPanel.btnPrepareClicked(WorkMgmtPanel.java:1412)
at com.mycp.uiapp.workmgmt.WorkMgmtPanel.actionPerformed(WorkMgmtPanel.java:1336)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
"AWT-Shutdown" #14 prio=5 os_prio=0 tid=0x00007f286c443000 nid=0xa58 in Object.wait() [0x00007f2858a17000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x0000000088ae8c28> (a java.lang.Object)
at java.lang.Object.wait(Object.java:502)
at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
- locked <0x0000000088ae8c28> (a java.lang.Object)
at java.lang.Thread.run(Thread.java:745)
"AWT-XAWT" #12 daemon prio=6 os_prio=0 tid=0x00007f286c384000 nid=0xa51 runnable [0x00007f285914f000]
java.lang.Thread.State: RUNNABLE
at sun.awt.X11.XToolkit.waitForEvents(Native Method)
at sun.awt.X11.XToolkit.run(XToolkit.java:559)
at sun.awt.X11.XToolkit.run(XToolkit.java:523)
at java.lang.Thread.run(Thread.java:745)
"Java2D Disposer" #10 daemon prio=10 os_prio=0 tid=0x00007f286c35e000 nid=0xa50 in Object.wait() [0x00007f2859250000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x0000000087ab7ec0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:142)
- locked <0x0000000087ab7ec0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:158)
at sun.java2d.Disposer.run(Disposer.java:148)
at java.lang.Thread.run(Thread.java:745)
"Thread-0" #9 prio=5 os_prio=0 tid=0x00007f286c234800 nid=0xa4f waiting on condition [0x00007f2859af5000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at com.mycp.logging.BMBLogging$Task.run(BMBLogging.java:1072)
at java.lang.Thread.run(Thread.java:745)
"Service Thread" #8 daemon prio=9 os_prio=0 tid=0x00007f286c0cf800 nid=0xa4d runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C1 CompilerThread2" #7 daemon prio=9 os_prio=0 tid=0x00007f286c0b2000 nid=0xa4c waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007f286c0b0000 nid=0xa4b waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007f286c0ad800 nid=0xa4a waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007f286c0ab000 nid=0xa49 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007f286c07c000 nid=0xa48 in Object.wait() [0x00007f285a2dd000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x0000000087a7e6c8> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:142)
- locked <0x0000000087a7e6c8> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:158)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)
"Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007f286c07a000 nid=0xa47 in Object.wait() [0x00007f285a3de000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x0000000087a7e708> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:502)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)
- locked <0x0000000087a7e708> (a java.lang.ref.Reference$Lock)
"VM Thread" os_prio=0 tid=0x00007f286c072800 nid=0xa46 runnable
"GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007f286c01e800 nid=0xa42 runnable
"GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007f286c020800 nid=0xa43 runnable
"GC task thread#2 (ParallelGC)" os_prio=0 tid=0x00007f286c022000 nid=0xa44 runnable
"GC task thread#3 (ParallelGC)" os_prio=0 tid=0x00007f286c024000 nid=0xa45 runnable
"VM Periodic Task Thread" os_prio=0 tid=0x00007f286c0d2000 nid=0xa4e waiting on condition
JNI global references: 485
Heap
PSYoungGen total 118272K, used 98176K [0x00000000d6e00000, 0x00000000de700000, 0x0000000100000000)
eden space 113152K, 82% used [0x00000000d6e00000,0x00000000dc8e00c8,0x00000000ddc80000)
from space 5120K, 100% used [0x00000000de180000,0x00000000de680000,0x00000000de680000)
to space 5120K, 0% used [0x00000000ddc80000,0x00000000ddc80000,0x00000000de180000)
ParOldGen total 159744K, used 76671K [0x0000000084a00000, 0x000000008e600000, 0x00000000d6e00000)
object space 159744K, 47% used [0x0000000084a00000,0x00000000894dfc50,0x000000008e600000)
Metaspace used 30027K, capacity 30212K, committed 30464K, reserved 1077248K
class space used 3528K, capacity 3582K, committed 3584K, reserved 1048576K

The thread dump shows stack traces from about 22 different threads. Many of them look like application threads (as opposed to JVM internal threads). Most of the application threads are waiting for something. Which of those threads should not be waiting?
I'd start by looking at thread 13: Looks like the Swing EDT, and it's waiting inside a call to a button's actionPerformed(...) handler. That can't be good.

I think I am late in the game. Anyways, from your logs we could see that a thread is in Parking Waiting state.
"TimerQueue" #22 daemon prio=5 os_prio=0 tid=0x00007f28002a8800 nid=0xa65 waiting on condition [0x00007f284c56f000]
java.lang.Thread.State: WAITING (parking)
We could see that this thread is expecting something from DelayQueue.
DelayQueue-An unbounded blocking queue of Delayed elements, in which an element can only be taken when its delay has expired.
So In the same TimerQueue, we have
at java.util.concurrent.DelayQueue.take(DelayQueue.java:211)
This take() function waits if an element with expired delay is available on this queue.
This could be the reason for application hanging issue as this thread is still waiting and doesn't shutdown. So, there are still threads alive. To resolve this you will need to kill these threads.
For this you could just use ExecutorServices.shutdown() method. OR Simply you could use System.exit().
I would recommend you to use System.exit().

My program will not stop after run() method in main thread finishes

I am using Java. The main thread sends data, while a worker thread listens to responses. I also have Timer in case timeout occurs. In main(), I am calling run(), which can finish, according to the output. Here is what it looks like:
class Send {
Worker w;
run() {
// w was initialized in constructor
w.start();
....
w.join();
}
main(args) {
Send s = new Send();
s.run();
}
private class Worker extend Thread {
public void run() {
....
}
}
}
In s.run(), every time I need to cancel the Timer or restart the Timer, I would do
timer.cancel();
timer.purge();
timer = new Timer();
timer.schdule(...);
The TimerTask is simply calling a static method in Send to handle the timeout.
So what did I do wrong to cause my program hanging after the main thread finishes?
Thank you.
EDIT: the out put of kill -3 process-id:
Full thread dump OpenJDK 64-Bit Server VM (19.0-b09 mixed mode):
"DestroyJavaVM" prio=10 tid=0x00007f9f20035000 nid=0x73f1 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Timer-10" prio=10 tid=0x0000000001a7d800 nid=0x740f in Object.wait() [0x00007f9f1e39c000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x000000075833fe78> (a java.util.TaskQueue)
at java.lang.Object.wait(Object.java:502)
at java.util.TimerThread.mainLoop(Timer.java:505)
- locked <0x000000075833fe78> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:484)
"Low Memory Detector" daemon prio=10 tid=0x00007f9f20004800 nid=0x7402 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread1" daemon prio=10 tid=0x0000000001a70000 nid=0x7401 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread0" daemon prio=10 tid=0x00007f9f20001000 nid=0x7400 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0x0000000001a6e800 nid=0x73ff waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0x0000000001a49000 nid=0x73fe in Object.wait() [0x00007f9f1f3f2000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000007580b1310> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:133)
- locked <0x00000007580b1310> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:149)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:177)
"Reference Handler" daemon prio=10 tid=0x0000000001a47000 nid=0x73fd in Object.wait() [0x00007f9f1f4f3000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000007580b11e8> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:502)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
- locked <0x00000007580b11e8> (a java.lang.ref.Reference$Lock)
"VM Thread" prio=10 tid=0x0000000001a40000 nid=0x73fc runnable
"GC task thread#0 (ParallelGC)" prio=10 tid=0x00000000019d7000 nid=0x73f2 runnable
"GC task thread#1 (ParallelGC)" prio=10 tid=0x00000000019d9000 nid=0x73f3 runnable
"GC task thread#2 (ParallelGC)" prio=10 tid=0x00000000019da800 nid=0x73f4 runnable
"GC task thread#3 (ParallelGC)" prio=10 tid=0x00000000019dc800 nid=0x73f5 runnable
"GC task thread#4 (ParallelGC)" prio=10 tid=0x00000000019de800 nid=0x73f6 runnable
"GC task thread#5 (ParallelGC)" prio=10 tid=0x00000000019e0000 nid=0x73f7 runnable
"GC task thread#6 (ParallelGC)" prio=10 tid=0x00000000019e2000 nid=0x73f8 runnable
"GC task thread#7 (ParallelGC)" prio=10 tid=0x00000000019e4000 nid=0x73f9 runnable
"GC task thread#8 (ParallelGC)" prio=10 tid=0x00000000019e5800 nid=0x73fa runnable
"GC task thread#9 (ParallelGC)" prio=10 tid=0x00000000019e7800 nid=0x73fb runnable
"VM Periodic Task Thread" prio=10 tid=0x00007f9f20007800 nid=0x7403 waiting on condition
JNI global references: 886
Heap
PSYoungGen total 150528K, used 7745K [0x00000007580b0000, 0x00000007628a0000, 0x0000000800000000)
eden space 129088K, 6% used [0x00000007580b0000,0x00000007588405b8,0x000000075fec0000)
from space 21440K, 0% used [0x00000007613b0000,0x00000007613b0000,0x00000007628a0000)
to space 21440K, 0% used [0x000000075fec0000,0x000000075fec0000,0x00000007613b0000)
PSOldGen total 343936K, used 0K [0x0000000608200000, 0x000000061d1e0000, 0x00000007580b0000)
object space 343936K, 0% used [0x0000000608200000,0x0000000608200000,0x000000061d1e0000)
PSPermGen total 21248K, used 3130K [0x00000005fdc00000, 0x00000005ff0c0000, 0x0000000608200000)
object space 21248K, 14% used [0x00000005fdc00000,0x00000005fdf0ea30,0x00000005ff0c0000)

A Java program will exit after the last thread finishes.
To prevent that, mark the other threads as daemon threads.

Get a thread dump by running kill -3 <process id>. This will tell you which threads are hanging around & preventing the java process from exiting. Feel free to post (some of) the thread dump & folks can help you figure out what to do next.

It looks like you are creating several Timer threads. Check that all of them have exited properly, that is probably the problem.
If you check the Timer JavaDoc - http://download.oracle.com/javase/6/docs/api/java/util/Timer.html - you will notice the following note:
By default, the task execution thread does not run as a daemon thread
You can use a debugger (both Eclipse and NetBeans have excellent ones) to see which threads are still alive.