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"waiting on" vs "waiting to lock" vs "locked" in java thread dumps

Looking through a thread dump I see several BLOCKED threads but some have "waiting to lock " and some have "waiting on " while there is only one RUNNABLE thread that has presumably acquired the lock. The question I have is why are some "waiting to lock" and others "waiting on"? Also the thread that is "waiting on" appears to have the lock but is not the RUNNABLE thread that actually holds the lock as it says it locked the object at address lower in the stack trace, so why is it blocking if it has the lock (or does it not have the lock)?
Examples below:
The locked object is at 0x00000000c2ad4be8
waiting on
"ajp-bio-10032-exec-15" daemon prio=10 tid=0x00007f888c02d000 nid=0x74c8 in Object.wait() [0x00007f8821792000]
java.lang.Thread.State: BLOCKED (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000c2ad4be8> (a java.lang.Object)
at java.lang.Object.wait(Object.java:503)
at com.tibco.tibjms.TibjmsxLinkTcp.disconnect(TibjmsxLinkTcp.java:1026)
waiting to lock
"ajp-bio-10032-exec-95" daemon prio=10 tid=0x00007f888c089800 nid=0x1e66 in Object.wait() [0x00007f881df4b000]
java.lang.Thread.State: BLOCKED (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000c2ad4be8> (a java.lang.Object)
at java.lang.Object.wait(Object.java:503)
at com.tibco.tibjms.TibjmsxLinkTcp.disconnect(TibjmsxLinkTcp.java:1026)
- locked <0x00000000c2ad4be8> (a java.lang.Object)
at com.tibco.tibjms.TibjmsConnection._close(TibjmsConnection.java:2430)
and finally the RUNNABLE thread
"ajp-bio-10032-exec-142" daemon prio=10 tid=0x00007f888c0b7000 nid=0x3657 runnable [0x00007f88167d4000]
java.lang.Thread.State: RUNNABLE
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Thread.java:713)
- locked <0x00000000f022c5e0> (a com.tibco.tibjms.TibjmsxLinkTcp$LinkReader)
at com.tibco.tibjms.TibjmsxLinkTcp.start(TibjmsxLinkTcp.java:968)
- locked <0x00000000c2ad4be8> (a java.lang.Object)

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().

How to handle a SSLSocketImpl Deadlock properly?

Very rarely I get a deadlock while using wiki-java. Having a look at the full thread dump (acquired via kill -3 $JAVA-PID) suggests that the deadlock seems to be originating somewhere in the SSLSocketImpl. I'd prefer to avoid this deadlock in the first place (instead of doing some hacky recovery) but I am unsure how to find the cause and prevent it. Is there a way to set a timeout in the SSLSocketImpl or throw an exception in case of the deadlock? (It would be pretty straightforward to catch it in the main loop and redo the last call)
Full thread dump OpenJDK 64-Bit Server VM (24.51-b03 mixed mode):
"Service Thread" daemon prio=10 tid=0x00007f3cd816b000 nid=0x102c runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread1" daemon prio=10 tid=0x00007f3cd8168800 nid=0x102b waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread0" daemon prio=10 tid=0x00007f3cd8165800 nid=0x102a waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0x00007f3cd8163800 nid=0x1029 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0x00007f3cd8140800 nid=0x1028 waiting on condition [0x00007f3ccb9f7000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000007d77a9080> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:834)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireQueued(AbstractQueuedSynchronizer.java:867)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquire(AbstractQueuedSynchronizer.java:1197)
at java.util.concurrent.locks.ReentrantLock$NonfairSync.lock(ReentrantLock.java:214)
at java.util.concurrent.locks.ReentrantLock.lock(ReentrantLock.java:290)
at sun.security.ssl.SSLSocketImpl.writeRecord(SSLSocketImpl.java:799)
at sun.security.ssl.SSLSocketImpl.writeRecord(SSLSocketImpl.java:672)
at sun.security.ssl.SSLSocketImpl.sendAlert(SSLSocketImpl.java:2005)
at sun.security.ssl.SSLSocketImpl.warning(SSLSocketImpl.java:1832)
at sun.security.ssl.SSLSocketImpl.closeInternal(SSLSocketImpl.java:1600)
- locked <0x00000007d77a8d78> (a sun.security.ssl.SSLSocketImpl)
at sun.security.ssl.SSLSocketImpl.close(SSLSocketImpl.java:1538)
at sun.security.ssl.BaseSSLSocketImpl.finalize(BaseSSLSocketImpl.java:249)
at java.lang.ref.Finalizer.invokeFinalizeMethod(Native Method)
at java.lang.ref.Finalizer.runFinalizer(Finalizer.java:101)
at java.lang.ref.Finalizer.access$100(Finalizer.java:32)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:190)
"Reference Handler" daemon prio=10 tid=0x00007f3cd813e800 nid=0x1027 in Object.wait() [0x00007f3ccbaf9000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x000000078495a2c8> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:503)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
- locked <0x000000078495a2c8> (a java.lang.ref.Reference$Lock)
"main" prio=10 tid=0x00007f3cd8008000 nid=0x1021 waiting for monitor entry [0x00007f3cdfdb7000]
java.lang.Thread.State: BLOCKED (on object monitor)
at sun.security.ssl.SSLSocketImpl.getConnectionState(SSLSocketImpl.java:649)
- waiting to lock <0x00000007d77a8d78> (a sun.security.ssl.SSLSocketImpl)
at sun.security.ssl.SSLSocketImpl.isClosed(SSLSocketImpl.java:1446)
at java.net.Socket.getTcpNoDelay(Socket.java:965)
at sun.security.ssl.BaseSSLSocketImpl.getTcpNoDelay(BaseSSLSocketImpl.java:345)
at sun.security.ssl.SSLSocketImpl.writeRecordInternal(SSLSocketImpl.java:819)
at sun.security.ssl.SSLSocketImpl.writeRecord(SSLSocketImpl.java:801)
at sun.security.ssl.AppOutputStream.write(AppOutputStream.java:122)
- locked <0x00000007d77a8d60> (a sun.security.ssl.AppOutputStream)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
- locked <0x00000007d77a8d48> (a java.io.BufferedOutputStream)
at java.io.PrintStream.flush(PrintStream.java:338)
- locked <0x00000007d77a8d28> (a java.io.PrintStream)
at sun.net.www.MessageHeader.print(MessageHeader.java:297)
- locked <0x00000007d6d057b0> (a sun.net.www.MessageHeader)
at sun.net.www.http.HttpClient.writeRequests(HttpClient.java:599)
at sun.net.www.http.HttpClient.writeRequests(HttpClient.java:610)
at sun.net.www.protocol.http.HttpURLConnection.writeRequests(HttpURLConnection.java:619)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1321)
- locked <0x00000007d6d05640> (a sun.net.www.protocol.https.DelegateHttpsURLConnection)
at sun.net.www.protocol.http.HttpURLConnection.getHeaderFieldKey(HttpURLConnection.java:2731)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getHeaderFieldKey(HttpsURLConnectionImpl.java:307)
at shared.Wiki.grabCookies(Wiki.java:6907)
at shared.Wiki.fetch(Wiki.java:6462)
at shared.Wiki.getPageText(Wiki.java:1465)
at smallBots.Bot1.getText(Bot1.java:204)
at smallBots.Bot1.crawlCategory(Bot1.java:74)
at smallBots.Bot1.main(Bot1.java:49)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
"VM Thread" prio=10 tid=0x00007f3cd813a000 nid=0x1026 runnable
"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f3cd801d800 nid=0x1022 runnable
"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f3cd801f800 nid=0x1023 runnable
"GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f3cd8021800 nid=0x1024 runnable
"GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f3cd8023000 nid=0x1025 runnable
"VM Periodic Task Thread" prio=10 tid=0x00007f3cd8175800 nid=0x102d waiting on condition
JNI global references: 205
Found one Java-level deadlock:
=============================
"Finalizer":
waiting for ownable synchronizer 0x00000007d77a9080, (a java.util.concurrent.locks.ReentrantLock$NonfairSync),
which is held by "main"
"main":
waiting to lock monitor 0x00007f3cac0015c8 (object 0x00000007d77a8d78, a sun.security.ssl.SSLSocketImpl),
which is held by "Finalizer"
Java stack information for the threads listed above:
===================================================
"Finalizer":
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000007d77a9080> (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:186)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:834)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireQueued(AbstractQueuedSynchronizer.java:867)
at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquire(AbstractQueuedSynchronizer.java:1197)
at java.util.concurrent.locks.ReentrantLock$NonfairSync.lock(ReentrantLock.java:214)
at java.util.concurrent.locks.ReentrantLock.lock(ReentrantLock.java:290)
at sun.security.ssl.SSLSocketImpl.writeRecord(SSLSocketImpl.java:799)
at sun.security.ssl.SSLSocketImpl.writeRecord(SSLSocketImpl.java:672)
at sun.security.ssl.SSLSocketImpl.sendAlert(SSLSocketImpl.java:2005)
at sun.security.ssl.SSLSocketImpl.warning(SSLSocketImpl.java:1832)
at sun.security.ssl.SSLSocketImpl.closeInternal(SSLSocketImpl.java:1600)
- locked <0x00000007d77a8d78> (a sun.security.ssl.SSLSocketImpl)
at sun.security.ssl.SSLSocketImpl.close(SSLSocketImpl.java:1538)
at sun.security.ssl.BaseSSLSocketImpl.finalize(BaseSSLSocketImpl.java:249)
at java.lang.ref.Finalizer.invokeFinalizeMethod(Native Method)
at java.lang.ref.Finalizer.runFinalizer(Finalizer.java:101)
at java.lang.ref.Finalizer.access$100(Finalizer.java:32)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:190)
"main":
at sun.security.ssl.SSLSocketImpl.getConnectionState(SSLSocketImpl.java:649)
- waiting to lock <0x00000007d77a8d78> (a sun.security.ssl.SSLSocketImpl)
at sun.security.ssl.SSLSocketImpl.isClosed(SSLSocketImpl.java:1446)
at java.net.Socket.getTcpNoDelay(Socket.java:965)
at sun.security.ssl.BaseSSLSocketImpl.getTcpNoDelay(BaseSSLSocketImpl.java:345)
at sun.security.ssl.SSLSocketImpl.writeRecordInternal(SSLSocketImpl.java:819)
at sun.security.ssl.SSLSocketImpl.writeRecord(SSLSocketImpl.java:801)
at sun.security.ssl.AppOutputStream.write(AppOutputStream.java:122)
- locked <0x00000007d77a8d60> (a sun.security.ssl.AppOutputStream)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
- locked <0x00000007d77a8d48> (a java.io.BufferedOutputStream)
at java.io.PrintStream.flush(PrintStream.java:338)
- locked <0x00000007d77a8d28> (a java.io.PrintStream)
at sun.net.www.MessageHeader.print(MessageHeader.java:297)
- locked <0x00000007d6d057b0> (a sun.net.www.MessageHeader)
at sun.net.www.http.HttpClient.writeRequests(HttpClient.java:599)
at sun.net.www.http.HttpClient.writeRequests(HttpClient.java:610)
at sun.net.www.protocol.http.HttpURLConnection.writeRequests(HttpURLConnection.java:619)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1321)
- locked <0x00000007d6d05640> (a sun.net.www.protocol.https.DelegateHttpsURLConnection)
at sun.net.www.protocol.http.HttpURLConnection.getHeaderFieldKey(HttpURLConnection.java:2731)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getHeaderFieldKey(HttpsURLConnectionImpl.java:307)
at shared.Wiki.grabCookies(Wiki.java:6907)
at shared.Wiki.fetch(Wiki.java:6462)
at shared.Wiki.getPageText(Wiki.java:1465)
at smallBots.Bot1.getText(Bot1.java:204)
at smallBots.Bot1.crawlCategory(Bot1.java:74)
at smallBots.Bot1.main(Bot1.java:49)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Found 1 deadlock.
Heap
PSYoungGen total 10752K, used 801K [0x00000007d6d00000, 0x00000007d7880000, 0x0000000800000000)
eden space 9728K, 1% used [0x00000007d6d00000,0x00000007d6d1fc20,0x00000007d7680000)
from space 1024K, 65% used [0x00000007d7780000,0x00000007d7828b40,0x00000007d7880000)
to space 1024K, 0% used [0x00000007d7680000,0x00000007d7680000,0x00000007d7780000)
ParOldGen total 93696K, used 69956K [0x0000000784800000, 0x000000078a380000, 0x00000007d6d00000)
object space 93696K, 74% used [0x0000000784800000,0x0000000788c51160,0x000000078a380000)
PSPermGen total 21504K, used 9537K [0x000000077a200000, 0x000000077b700000, 0x0000000784800000)
object space 21504K, 44% used [0x000000077a200000,0x000000077ab50720,0x000000077b700000)

The asker's answer: update to Java 8 to fix it.

Why is eclipse eating almost all of CPU for no apparent reason

I tried to follow this question High CPU usage in Eclipse when idle and find out why Eclipse is being such a CPU hog
Here are the threads consuming a double digit processor share, can somebody make sense of them? One thread eating ~80% seems to be related to workbench, but the rest are a mystery.
I do have a decent proc and SSD drive, and most of the time eclipse is running smoothly.
BTW. There was a short lag between executing ps and kill, which might explain it, but I don't understand how a waiting thread could use over 50% of cpu.
"Worker-6" prio=10 tid=0x00007fe9e0036000 nid=0x1caf in Object.wait() [0x00007fe9c2269000]
java.lang.Thread.State: TIMED_WAITING (on object monitor) 16.8%
at java.lang.Object.wait(Native Method)
- waiting on <0x00007fea3fa6d1a0> (a org.eclipse.core.internal.jobs.WorkerPool)
at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
- locked <0x00007fea3fa6d1a0> (a org.eclipse.core.internal.jobs.WorkerPool)
at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:50)
"org.eclipse.jdt.internal.ui.text.JavaReconciler" daemon prio=10 tid=0x00007fea94e3d800 nid=0x1ca1 in Object.wait() [0x00007fe9d65e4000]
java.lang.Thread.State: TIMED_WAITING (on object monitor) 57.4%
at java.lang.Object.wait(Native Method)
- waiting on <0x00007fea39123a28> (a org.eclipse.jface.text.reconciler.DirtyRegionQueue)
at org.eclipse.jface.text.reconciler.AbstractReconciler$BackgroundThread.run(AbstractReconciler.java:179)
- locked <0x00007fea39123a28> (a org.eclipse.jface.text.reconciler.DirtyRegionQueue)
"Java indexing" daemon prio=10 tid=0x00007fea9510f000 nid=0x1c9d in Object.wait() [0x00007fe9fc7bf000]
java.lang.Thread.State: WAITING (on object monitor) 31.9%
at java.lang.Object.wait(Native Method)
- waiting on <0x00007fea3adbe2f8> (a org.eclipse.jdt.internal.core.search.indexing.IndexManager)
at java.lang.Object.wait(Object.java:485)
at org.eclipse.jdt.internal.core.search.processing.JobManager.run(JobManager.java:382)
- locked <0x00007fea3adbe2f8> (a org.eclipse.jdt.internal.core.search.indexing.IndexManager)
at java.lang.Thread.run(Thread.java:662)
"C2 CompilerThread1" daemon prio=10 tid=0x00007fea942fd800 nid=0x1c85 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE 85.6%
"C2 CompilerThread0" daemon prio=10 tid=0x00007fea942fb000 nid=0x1c84 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE 85.6%
"main" prio=10 tid=0x00007fea94009800 nid=0x1c73 runnable [0x00007fea9b93a000]
java.lang.Thread.State: RUNNABLE 72.7%
at org.eclipse.swt.internal.gtk.OS.Call(Native Method)
at org.eclipse.swt.widgets.Display.sleep(Display.java:4233)
at org.eclipse.ui.application.WorkbenchAdvisor.eventLoopIdle(WorkbenchAdvisor.java:364)
at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.eventLoopIdle(IDEWorkbenchAdvisor.java:917)
at org.eclipse.ui.internal.Workbench$3.eventLoopIdle(Workbench.java:487)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$9.run(PartRenderingEngine.java:1117)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:997)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:138)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:610)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:567)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:124)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)

When you use the term "Waiting Thread" the computer assumes that the thread is waiting for something. Thus, the computer keeps checking whether those threads are to be started or ended.
And so, it uses 50% of the CPU memory.

Tomcat webapp error - application started thread [AWT-Windows] but has failed to stop it - memory leak?

I didn't notice it until today during some testing locally on my pc, that Tomcat had posted an error in the log file. I'm using Tomcat 6.0.29 and Java JDK 1.6.
Dec 1, 2010 12:36:57 pm org.apache.catalina.core.StandardContext reload
INFO: Reloading this Context has started
Dec 1, 2010 12:36:57 pm org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVER: The web application [/AutoSpyder] appears to have started a thread named
[AWT-Windows] but has failed to stop it. This is very likely to create a memory
leak.
What? I've never seen this before. So I checked my log file from yesterday, and sure enough, this error was there too. I don't quite understand what's causing this.
Can I assume that it would have to be one of my servlets that uses objects from the java.awt package? If so, how do I pinpoint the code that is causing this?
Edited to add Thread Dump
2010-12-01 14:28:18
Full thread dump Java HotSpot(TM) Client VM (17.1-b03 mixed mode, sharing):
"JMX server connection timeout 34" daemon prio=6 tid=0x03069400 nid=0x960 in Object.wait() [0x0461f000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a [I)
at com.sun.jmx.remote.internal.ServerCommunicatorAdmin$Timeout.run(ServerCommunicatorAdmin.java:150)
- locked (a [I)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"RMI Scheduler(0)" daemon prio=6 tid=0x03069000 nid=0xe88 waiting on condition [0x045cf000]
java.lang.Thread.State: TIMED_WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:198)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2025)
at java.util.concurrent.DelayQueue.take(DelayQueue.java:164)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:609)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:602)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"RMI TCP Connection(1)-192.168.0.102" daemon prio=6 tid=0x0308a400 nid=0xebc runnable [0x0457f000]
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:129)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
at java.io.BufferedInputStream.read(BufferedInputStream.java:237)
- locked (a java.io.BufferedInputStream)
at java.io.FilterInputStream.read(FilterInputStream.java:66)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:517)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:790)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:649)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- (a java.util.concurrent.locks.ReentrantLock$NonfairSync)
"RMI TCP Accept-0" daemon prio=6 tid=0x039e0c00 nid=0xc68 runnable [0x0452f000]
java.lang.Thread.State: RUNNABLE
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
- locked (a java.net.SocksSocketImpl)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at sun.management.jmxremote.LocalRMIServerSocketFactory$1.accept(LocalRMIServerSocketFactory.java:34)
at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:369)
at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:341)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"AWT-Windows" daemon prio=6 tid=0x02b65400 nid=0x7c4 runnable [0x042cf000]
java.lang.Thread.State: RUNNABLE
at sun.awt.windows.WToolkit.eventLoop(Native Method)
at sun.awt.windows.WToolkit.run(WToolkit.java:293)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"Java2D Disposer" daemon prio=10 tid=0x02fccc00 nid=0x93c in Object.wait() [0x039df000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
at sun.java2d.Disposer.run(Disposer.java:127)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"http-8080-6" daemon prio=6 tid=0x03322800 nid=0xfec in Object.wait() [0x0395f000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
- locked (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"http-8080-5" daemon prio=6 tid=0x02ba5c00 nid=0xdbc in Object.wait() [0x0390f000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
- locked (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"http-8080-4" daemon prio=6 tid=0x02ff6400 nid=0xa1c in Object.wait() [0x038bf000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
- locked (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"http-8080-3" daemon prio=6 tid=0x0317e400 nid=0x850 in Object.wait() [0x0386f000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
- locked (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"http-8080-2" daemon prio=6 tid=0x03314800 nid=0xf9c in Object.wait() [0x0381f000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
- locked (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"http-8080-1" daemon prio=6 tid=0x02efe800 nid=0x250 in Object.wait() [0x037cf000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.await(JIoEndpoint.java:458)
- locked (a org.apache.tomcat.util.net.JIoEndpoint$Worker)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:484)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"TP-Monitor" daemon prio=6 tid=0x02eed800 nid=0xd64 in Object.wait() [0x0375f000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.threads.ThreadPool$MonitorRunnable)
at org.apache.tomcat.util.threads.ThreadPool$MonitorRunnable.run(ThreadPool.java:565)
- locked (a org.apache.tomcat.util.threads.ThreadPool$MonitorRunnable)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"TP-Processor4" daemon prio=6 tid=0x0318b000 nid=0x998 runnable [0x0370f000]
java.lang.Thread.State: RUNNABLE
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
- locked (a java.net.SocksSocketImpl)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at org.apache.jk.common.ChannelSocket.accept(ChannelSocket.java:312)
at org.apache.jk.common.ChannelSocket.acceptConnections(ChannelSocket.java:666)
at org.apache.jk.common.ChannelSocket$SocketAcceptor.runIt(ChannelSocket.java:877)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"TP-Processor3" daemon prio=6 tid=0x0308f800 nid=0x92c in Object.wait() [0x036bf000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:662)
- locked (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"TP-Processor2" daemon prio=6 tid=0x03192400 nid=0xfac in Object.wait() [0x0366f000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:662)
- locked (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"TP-Processor1" daemon prio=6 tid=0x03182400 nid=0x8d8 in Object.wait() [0x0361f000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
at java.lang.Object.wait(Object.java:485)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:662)
- locked (a org.apache.tomcat.util.threads.ThreadPool$ControlRunnable)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"http-8080-Acceptor-0" daemon prio=6 tid=0x03172400 nid=0xf04 runnable [0x035cf000]
java.lang.Thread.State: RUNNABLE
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
- locked (a java.net.SocksSocketImpl)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at org.apache.tomcat.util.net.DefaultServerSocketFactory.acceptSocket(DefaultServerSocketFactory.java:61)
at org.apache.tomcat.util.net.JIoEndpoint$Acceptor.run(JIoEndpoint.java:352)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"ContainerBackgroundProcessor[StandardEngine[Catalina]]" daemon prio=6 tid=0x03163400 nid=0xbe8 waiting on condition [0x0357f000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1579)
at java.lang.Thread.run(Thread.java:662)
Locked ownable synchronizers:
- None
"GC Daemon" daemon prio=2 tid=0x0307bc00 nid=0x110 in Object.wait() [0x0349f000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a sun.misc.GC$LatencyLock)
at sun.misc.GC$Daemon.run(GC.java:100)
- locked (a sun.misc.GC$LatencyLock)
Locked ownable synchronizers:
- None
"Low Memory Detector" daemon prio=6 tid=0x02aecc00 nid=0x5b4 runnable [0x00000000]
java.lang.Thread.State: RUNNABLE
Locked ownable synchronizers:
- None
"CompilerThread0" daemon prio=10 tid=0x02ae7000 nid=0x798 waiting on condition [0x00000000]
java.lang.Thread.State: RUNNABLE
Locked ownable synchronizers:
- None
"Attach Listener" daemon prio=10 tid=0x02ae5800 nid=0xddc waiting on condition [0x00000000]
java.lang.Thread.State: RUNNABLE
Locked ownable synchronizers:
- None
"Signal Dispatcher" daemon prio=10 tid=0x02ae4000 nid=0xc00 runnable [0x00000000]
java.lang.Thread.State: RUNNABLE
Locked ownable synchronizers:
- None
"Finalizer" daemon prio=8 tid=0x02add400 nid=0x378 in Object.wait() [0x02caf000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
Locked ownable synchronizers:
- None
"Reference Handler" daemon prio=10 tid=0x02adbc00 nid=0x474 in Object.wait() [0x02c5f000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked (a java.lang.ref.Reference$Lock)
Locked ownable synchronizers:
- None
"main" prio=6 tid=0x002b7000 nid=0x14c runnable [0x0090f000]
java.lang.Thread.State: RUNNABLE
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
- locked (a java.net.SocksSocketImpl)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at org.apache.catalina.core.StandardServer.await(StandardServer.java:389)
at org.apache.catalina.startup.Catalina.await(Catalina.java:662)
at org.apache.catalina.startup.Catalina.start(Catalina.java:614)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
Locked ownable synchronizers:
- None
"VM Thread" prio=10 tid=0x02ada400 nid=0x210 runnable
"VM Periodic Task Thread" prio=10 tid=0x02aefc00 nid=0x79c waiting on condition
JNI global references: 1529

Try taking a thread dump to get a list of all the threads running on your server. From this, you may be able to pinpoint exactly which class started the thread based on the stack traces
Windows
on the console window press ctrl + break
Unix
in a command line enter: kill -3 <pid>

It's to do with Windows (i.e. MS Windows) and native calls to the underlying OS. These would normally be GUI-type window operations, but could be other OS-specific things, e.g Clipboard or Font related, for instance.
If there's nothing obvious that you can see in your code that might relate to why it's being triggered, though, I'd not worry about it - that warning's more for the general case where spinning off new threads in a web-app isn't something you should be explicitly doing without a full appreciation of the potential issues.

We have tomcat server and jsf. JSF client will request images from the server and cause AWT-Windows thread to get started. Appears to cause a memory leak since threads contextClassLoader is the WebappClassLoader.
Looks like calling Java2DResource can caused AWT-Windows thread to be created -
Daemon Thread [http-8080-1] (Suspended (entry into method in Thread))
Thread.(Runnable, String) line: 444 <-- thread name is AWT-Windows
WToolkit.() line: 244
NativeConstructorAccessorImpl.newInstance0(Constructor, Object[]) line: not available [native method]
NativeConstructorAccessorImpl.newInstance(Object[]) line: 39
DelegatingConstructorAccessorImpl.newInstance(Object[]) line: 27
Constructor.newInstance(Object...) line: 513
Class.newInstance0() line: 355
Class.newInstance() line: 308
Toolkit$2.run() line: 846
AccessController.doPrivileged(PrivilegedAction) line: not available [native method]
Toolkit.getDefaultToolkit() line: 826
D3DGraphicsDevice.() line: 47
SurfaceManagerFactory.createCachingManager(BufferedImage) line: 48
SurfaceManager.getManager(Image) line: 54
SurfaceData.getDestSurfaceData(Image) line: 123
Win32GraphicsEnvironment(SunGraphicsEnvironment).createGraphics(BufferedImage) line: 389
HeadlessGraphicsEnvironment.createGraphics(BufferedImage) line: 76
BufferedImage.createGraphics() line: 1137
TabStripeImage(Java2Dresource).getImage(ResourceContext) line: 115
TabStripeImage(Java2Dresource).send(ResourceContext) line: 89
ResourceLifecycle.sendResource(ResourceContext, InternetResource) line: 219
ResourceLifecycle.send(ResourceContext, InternetResource) line: 158
InternetResourceService.load(Object, Object) line: 335
LRUMapCache.load(Object, Object) line: 116
LRUMapCache.get(Object, Object) line: 87
InternetResourceService.serviceResource(String, HttpServletRequest, HttpServletResponse) line: 195
InternetResourceService.serviceResource(HttpServletRequest, HttpServletResponse) line: 141
Filter(BaseFilter).doFilter(ServletRequest, ServletResponse, FilterChain) line: 508
Ajax4jsfFilter.doFilter(ServletRequest, ServletResponse, FilterChain) line: 56
SeamFilter$FilterChainImpl.doFilter(ServletRequest, ServletResponse) line: 69
LoggingFilter.doFilter(ServletRequest, ServletResponse, FilterChain) line: 60
SeamFilter$FilterChainImpl.doFilter(ServletRequest, ServletResponse) line: 69
SeamFilter.doFilter(ServletRequest, ServletResponse, FilterChain) line: 158
ApplicationFilterChain.internalDoFilter(ServletRequest, ServletResponse) line: 235
ApplicationFilterChain.doFilter(ServletRequest, ServletResponse) line: 206
StandardWrapperValve.invoke(Request, Response) line: 233
StandardContextValve.invoke(Request, Response) line: 191
StandardHostValve.invoke(Request, Response) line: 127
ErrorReportValve.invoke(Request, Response) line: 102
AccessLogValve.invoke(Request, Response) line: 555
StandardEngineValve.invoke(Request, Response) line: 109
CoyoteAdapter.service(Request, Response) line: 298
Http11AprProcessor.process(long) line: 861
Http11AprProtocol$Http11ConnectionHandler.process(long) line: 579
AprEndpoint$Worker.run() line: 1584
Thread.run() line: 619 [local variables unavailable]

It looks like you are running JMX and I'm getting the impression that the Tomcat JMX server may be what's actually setting up the timer thread. In addition to the ones you mentioned in your parallel post on the JavaRanch, there's a java2D thread in the dump you have here.
I can't tell 100% because I don't know which threads were the parents for the orphan threads. If you could determine that, it would help.
Your Affine Transform is definitely pulling in graphics, however. It's a graphical function that will attempt to use your video card as a hardware accelerator. If you don't specify headless operation, it will tap into your windowing system to do so.

Inspired by this thread I found the following solution:
You only need to attach the AWT-Window-Thread to System-Classloader instead to Wabapp-Classloader. You can do it in a ServletContextListener like this:
public void contextInitialized(ServletContextEvent evt) {
Thread thread = Thread.currentThread();
ClassLoader ccl = thread.getContextClassLoader(); // PUSH
try {
thread.setContextClassLoader(ClassLoader.getSystemClassLoader());
Toolkit.getDefaultToolkit().createImage(new byte[]{});
} finally {
thread.setContextClassLoader(ccl); // POP
}
}

Are you running including some kind of graphical library like Jasper, JFreechart, LiquidOffice, StyleReport, ... that might interact with AWT ?
Try starting tomcat by providing the -Djava.awt.headless=true property to see that gets rid of the exception