[ImageJ-bugs] [Bug 1166] Oval Profile plugin runs really slow - possible Java issue?

bugzilla at fiji.sc bugzilla at fiji.sc
Tue Sep 29 11:34:38 CDT 2015 

http://fiji.sc/bugzilla/show_bug.cgi?id=1166

--- Comment #2 from jmesquib at gmail.com ---
Attempted recommendations. Unsure if I compiled correctly. Couldn't find how to
do that in FIJI by command as compile and run is not supported. When I run the
"oval profile" I see from console that it compiled it so I tracked down that
.class file and transferred as recommended. 

When I run "oval profile" the console still pops up with compiling info as the
first time. Recommended suggestions did not appear to change anything. 

Have added stack trace: 
"AWT-EventQueue-0" prio=6 id=15 group=main
   java.lang.Thread.State: RUNNABLE
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at java.awt.EventQueue.getNextEvent(EventQueue.java:485)
    at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:236)
    at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

"AWT-Shutdown" prio=5 id=12 group=main
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
    at java.lang.Thread.run(Thread.java:662)

"AWT-Windows" daemon prio=6 id=13 group=main
   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)

"Attach Listener" daemon prio=5 id=6 group=system
   java.lang.Thread.State: RUNNABLE

"DestroyJavaVM" prio=5 id=24 group=main
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=8 id=3 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"GC Daemon" daemon prio=2 id=22 group=system
   java.lang.Thread.State: TIMED_WAITING
    at java.lang.Object.wait(Native Method)
    at sun.misc.GC$Daemon.run(GC.java:100)

"Image Fetcher 0" daemon prio=8 id=55 group=main
   java.lang.Thread.State: TIMED_WAITING
    at java.lang.Object.wait(Native Method)
    at sun.awt.image.ImageFetcher.nextImage(ImageFetcher.java:114)
    at sun.awt.image.ImageFetcher.fetchloop(ImageFetcher.java:167)
    at sun.awt.image.ImageFetcher.run(ImageFetcher.java:136)

"Java2D Disposer" daemon prio=10 id=11 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
    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)

"RMI Reaper" prio=5 id=21 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
    at sun.rmi.transport.ObjectTable$Reaper.run(ObjectTable.java:333)
    at java.lang.Thread.run(Thread.java:662)

"RMI TCP Accept-0" daemon prio=5 id=20 group=system
   java.lang.Thread.State: RUNNABLE
    at java.net.PlainSocketImpl.socketAccept(Native Method)
    at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408)
    at java.net.ServerSocket.implAccept(ServerSocket.java:462)
    at java.net.ServerSocket.accept(ServerSocket.java:430)
    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)

"Reference Handler" daemon prio=10 id=2 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)

"Run$_Macro$" prio=4 id=52 group=main
   java.lang.Thread.State: WAITING
    at sun.misc.Unsafe.park(Native Method)
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
    at
java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:811)
    at
java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireSharedInterruptibly(AbstractQueuedSynchronizer.java:969)
    at
java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireSharedInterruptibly(AbstractQueuedSynchronizer.java:1281)
    at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:218)
    at java.util.concurrent.FutureTask.get(FutureTask.java:83)
    at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:282)
    at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:161)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:132)
    at ij.Executer.run(Executer.java:65)
    at ij.IJ.run(IJ.java:292)
    at ij.macro.Functions.doRun(Functions.java:601)
    at ij.macro.Functions.doFunction(Functions.java:96)
    at ij.macro.Interpreter.doStatement(Interpreter.java:227)
    at ij.macro.Interpreter.doBlock(Interpreter.java:605)
    at ij.macro.Interpreter.doStatement(Interpreter.java:269)
    at ij.macro.Interpreter.doFor(Interpreter.java:527)
    at ij.macro.Interpreter.doStatement(Interpreter.java:251)
    at ij.macro.Interpreter.doStatements(Interpreter.java:215)
    at ij.macro.Interpreter.run(Interpreter.java:112)
    at ij.macro.Interpreter.run(Interpreter.java:82)
    at ij.macro.MacroRunner.run(MacroRunner.java:139)
    at java.lang.Thread.run(Thread.java:662)

"SciJava-f1a47df-Thread-0" prio=5 id=17 group=main
   java.lang.Thread.State: RUNNABLE
    at java.lang.StringBuilder.append(StringBuilder.java:119)
    at org.scijava.minimaven.Coordinate.getKey(Coordinate.java:99)
    at
org.scijava.minimaven.BuildEnvironment.containsProject(BuildEnvironment.java:281)
    at
org.scijava.minimaven.BuildEnvironment.containsProject(BuildEnvironment.java:277)
    at
org.scijava.plugins.scripting.java.JavaEngine.fakeArtifactId(JavaEngine.java:657)
    at
org.scijava.plugins.scripting.java.JavaEngine.fakeDependency(JavaEngine.java:827)
    at
org.scijava.plugins.scripting.java.JavaEngine.getAllDependencies(JavaEngine.java:804)
    at
org.scijava.plugins.scripting.java.JavaEngine.fakePOM(JavaEngine.java:720)
    at
org.scijava.plugins.scripting.java.JavaEngine.writeTemporaryProject(JavaEngine.java:631)
    at
org.scijava.plugins.scripting.java.JavaEngine.getMavenProject(JavaEngine.java:532)
    at
org.scijava.plugins.scripting.java.JavaEngine.access$600(JavaEngine.java:95)
    at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:410)
    at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:372)
    at
org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:198)
    at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
    at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
    at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    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)

"SciJava-f1a47df-Thread-7" prio=5 id=36 group=main
   java.lang.Thread.State: RUNNABLE
    at java.lang.Thread.dumpThreads(Native Method)
    at java.lang.Thread.getAllStackTraces(Thread.java:1530)
    at org.scijava.plugins.commands.debug.DumpStack.run(DumpStack.java:80)
    at org.scijava.command.CommandModule.run(CommandModule.java:201)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
    at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    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)

"SciJava-f1a47df-Thread-9" prio=5 id=56 group=main
   java.lang.Thread.State: RUNNABLE
    at java.lang.Object.hashCode(Native Method)
    at java.util.WeakHashMap.put(WeakHashMap.java:401)
    at
org.scijava.thread.DefaultThreadService$1.run(DefaultThreadService.java:173)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:662)

"Signal Dispatcher" daemon prio=9 id=5 group=system
   java.lang.Thread.State: RUNNABLE

"TimerQueue" daemon prio=5 id=26 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at javax.swing.TimerQueue.run(TimerQueue.java:232)
    at java.lang.Thread.run(Thread.java:662)

"zSelector" prio=5 id=43 group=main
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at ij.gui.StackWindow.run(StackWindow.java:228)
    at java.lang.Thread.run(Thread.java:662)

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