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ClearVolume / clearvolume

ClearVolume is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With ClearVolume you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data.
http://clearvolume.github.io
GNU Lesser General Public License v3.0
44 stars 11 forks source link

ClearVolume crashes #24

Closed ctrueden closed 8 years ago

ctrueden commented 9 years ago

From @acardona:

When opening the ClearVolume Network Client the whole JVM segfaults:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f28a2d62d80, pid=27327, tid=139811869296384
#
# JRE version: Java(TM) SE Runtime Environment (7.0_67-b01) (build 1.7.0_67-b01)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.65-b04 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [ld-linux-x86-64.so.2+0x9d80]  _dl_rtld_di_serinfo+0x670
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/albert/Programming/fiji-linux64-20091014/Fiji.app/hs_err_pid27327.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
#
Aborted

Additionally, when using the "Open in ClearVolume", it fails with an exception if no images are open, and it throws an exception if an RGB stack is open, leaving the splash screen looping forever. Eventually the whole of Fiji freezes. The exception in the case of no images:

(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_67 [64-bit]; Linux 3.13.11-031311ckt16-generic; 59MB of 4096MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException
  at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)
  at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)
  at ij.IJ.runPlugIn(IJ.java)
  at ij.Executer.runCommand(Executer.java:131)
  at ij.Executer.run(Executer.java:64)
  at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException
  at java.util.concurrent.FutureTask.report(FutureTask.java:122)
  at java.util.concurrent.FutureTask.get(FutureTask.java:188)
  at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)
  ... 5 more
Caused by: java.lang.NullPointerException
  at net.imagej.legacy.translate.ImagePlusDatasetConverter.populateInputCandidates(ImagePlusDatasetConverter.java:126)
  at org.scijava.convert.DefaultConvertService.getCompatibleInputs(DefaultConvertService.java:111)
  at org.scijava.widget.AbstractInputHarvester.getObjects(AbstractInputHarvester.java:153)
  at org.scijava.widget.AbstractInputHarvester.addInput(AbstractInputHarvester.java:128)
  at org.scijava.widget.AbstractInputHarvester.buildPanel(AbstractInputHarvester.java:94)
  at org.scijava.widget.AbstractInputHarvester.harvest(AbstractInputHarvester.java:75)
  at org.scijava.ui.AbstractInputHarvesterPlugin.process(AbstractInputHarvesterPlugin.java:76)
  at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:104)
  at org.scijava.module.ModuleRunner.run(ModuleRunner.java:156)
  at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
  at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
  at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)
  at java.util.concurrent.FutureTask.run(FutureTask.java:262)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
  ... 1 more

And the exception in the case of an RGB image stack being open:

(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_67 [64-bit]; Linux 3.13.11-031311ckt16-generic; 75MB of 4096MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException
  at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)
  at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)
  at ij.IJ.runPlugIn(IJ.java)
  at ij.Executer.runCommand(Executer.java:131)
  at ij.Executer.run(Executer.java:64)
  at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException
  at java.util.concurrent.FutureTask.report(FutureTask.java:122)
  at java.util.concurrent.FutureTask.get(FutureTask.java:188)
  at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)
  ... 5 more
Caused by: java.lang.NullPointerException
  at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:264)
  at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:418)
  at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
  at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
  at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:135)
  at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.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$2.call(DefaultThreadService.java:181)
  at java.util.concurrent.FutureTask.run(FutureTask.java:262)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
Information about your version of Java:
  os.arch => amd64
  os.name => Linux
  os.version => 3.13.11-031311ckt16-generic
  java.version => 1.7.0_67
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.7.0_67-b01
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 24.65-b04
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/albert/Programming/fiji-linux64-20091014/Fiji.app/java/linux-amd64/jdk1.7.0_67//jre
  imagej.dir => /home/albert/Programming/fiji-linux64-20091014/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150522062918)
Fiji: http://fiji.sc/update/ (last check:20150528120151)
ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20150527195605)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606112449)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20150227140151)

Files not up-to-date:
  1581bc4d (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-macosx
  75db148f (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-tiger
  1ad3be0d (LOCAL_ONLY) 20090930112722 jars/jpedalSTD.jar
  32a5cb57 (LOCAL_ONLY) 20090910082726 macros/StartupMacros.txt
  dc7fce6b (LOCAL_ONLY) 20111014094119 plugins/Motion_Deblur.jar
  32738eb1 (LOCAL_ONLY) 20120511160900 plugins/SAT-lib-Drosophila-3rd-instar.clj
  3335decb (LOCAL_ONLY) 20101016092738 plugins/T2-NIT.jar
  063de9b3 (LOCAL_ONLY) 20150526100515 plugins/dynamic_vision_sensor-like.py
  7c95e931 (LOCAL_ONLY) 20140420121925 plugins/test_haskell_splitAt.py
  7f241f66 (LOCAL_ONLY) 20100603001850 plugins/tests/Example_Cursors.class
  a47f6af3 (LOCAL_ONLY) 20130425143259 plugins/tests/crop-file.py
  d3260180 (LOCAL_ONLY) 20090910082729 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20090910082729 scripts/Record_Window.py

The original bug report is Fiji BugZilla #1076.

mabruce commented 9 years ago

I'm getting the same segfault, OpenJDK 7 or Oracle JDK 8 on Ubuntu 14.04, 64 bit.

royerloic commented 9 years ago

@mabruce : can you paste the exception and/or hs_err_pidXXXXX.log file contents please? What is your graphics card? which drivers do you have installed? what does glxinfo return? You need at least OpenGL 3.3 and OpenCL 1.1

mabruce commented 9 years ago

Last message spit to System.out/err is "com.apple.eawt.Application".

Main graphics card is NVIDIA Quadro K2200 running 346.46 drivers. Card/drivers fully support OpenGL 4.5. OpenCL 1.1 has been supported in NVIDIA drivers for several years.

hs_err is below.

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f80f9b3ed80, pid=7501, tid=140153879516928
#
# JRE version: Java(TM) SE Runtime Environment (8.0_45-b14) (build 1.8.0_45-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode linux-amd64 )
# Problematic frame:
# C  [ld-linux-x86-64.so.2+0x9d80]
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  T H R E A D  ---------------

Current thread (0x0000000002492800):  JavaThread "SciJava-3d484181-Thread-1" [_thread_in_native, id=7541, stack(0x00007f781e23d000,0x00007f781e33e000)]

siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000000564

Registers:
RAX=0x0000000000000057, RBX=0x00007f781e3385f0, RCX=0x000000003c887d4c, RDX=0x00007f77c96aa26c
RSP=0x00007f781e338580, RBP=0x0000000000000560, RSI=0x00000000000002a8, RDI=0x0000000000000560
R8 =0x0000000000f221f5, R9 =0x00007f781e3385f0, R10=0x00007f781e3385f0, R11=0x00007f781e3386f0
R12=0x0000000000000003, R13=0x00007f78001984a0, R14=0x0000000000000000, R15=0x000000000000000d
RIP=0x00007f80f9b3ed80, EFLAGS=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007f781e338580)
0x00007f781e338580:   00007f781e338d60 000000003c887d4d
0x00007f781e338590:   0000000000000000 0000000000000003
0x00007f781e3385a0:   00007f78001984a0 00007f80f9b3f816
0x00007f781e3385b0:   00007f781e338640 00007f781e3385f0
0x00007f781e3385c0:   00000000000002a8 00007f781e338700
0x00007f781e3385d0:   00007f77c96aa26c 0000000000f221f5
0x00007f781e3385e0:   00007f781e3386f0 00007f781e3387e0
0x00007f781e3385f0:   0000000000000000 0000000000000000
0x00007f781e338600:   00007f78001a5de0 00007f780035af00
0x00007f781e338610:   00000000000006c8 0000000000000000
0x00007f781e338620:   0000000200000000 000000000000001d
0x00007f781e338630:   00007f77c98bc080 00007f781e3387e0
0x00007f781e338640:   00007f781e338790 0000000000000000
0x00007f781e338650:   0000000000000000 00007f78001a6168
0x00007f781e338660:   00007f78001a5de0 00007f80f9b3f991
0x00007f781e338670:   0000000000000000 0000000000000000
0x00007f781e338680:   0000000000000002 0000000000000000
0x00007f781e338690:   0000000000000000 00007f78001a5de0
0x00007f781e3386a0:   0000000000000558 00007f781e338ae0
0x00007f781e3386b0:   00007f78001f8a30 00007f780035ad70
0x00007f781e3386c0:   0000000000000000 00007f78001a6168
0x00007f781e3386d0:   00007f781e338700 00007f781e3386f0
0x00007f781e3386e0:   000000003c887d4d 00007f780035af00
0x00007f781e3386f0:   00000000ffffffff 00007f781e338ae0
0x00007f781e338700:   0000000000000000 0000000000000000
0x00007f781e338710:   00007f781e3387b0 00007f77c8e1bfc0
0x00007f781e338720:   00007f80f9b54500 00007f780035af00
0x00007f781e338730:   00007f80f9b513c7 00007f80f9b513c7
0x00007f781e338740:   00007f781e3387b0 00007f80f67fefe9
0x00007f781e338750:   0000000002492800 0000000002a243e0
0x00007f781e338760:   00007f782c5d63d0 0000000000e71790
0x00007f781e338770:   00007f80f9d57cc0 00007f780035af00 

Instructions: (pc=0x00007f80f9b3ed80)
0x00007f80f9b3ed60:   77 fd ff ff 66 2e 0f 1f 84 00 00 00 00 00 66 90
0x00007f80f9b3ed70:   41 55 41 54 55 48 89 fd 53 4c 89 d3 48 83 ec 08
0x00007f80f9b3ed80:   0f b6 47 04 83 e0 0f 48 83 7f 08 00 0f 84 13 01
0x00007f80f9b3ed90:   00 00 31 d2 66 83 7d 06 00 0f 94 c2 85 53 3c 0f 

Register to memory mapping:

RAX=0x0000000000000057 is an unknown value
RBX=0x00007f781e3385f0 is pointing into the stack for thread: 0x0000000002492800
RCX=0x000000003c887d4c is an unknown value
RDX=
[error occurred during error reporting (printing register info), id 0xb]

Stack: [0x00007f781e23d000,0x00007f781e33e000],  sp=0x00007f781e338580,  free space=1005k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [ld-linux-x86-64.so.2+0x9d80]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
J 2310  java.lang.ClassLoader$NativeLibrary.find(Ljava/lang/String;)J (0 bytes) @ 0x00007f80e120010c [0x00007f80e12000c0+0x4c]
j  java.lang.ClassLoader.findNative(Ljava/lang/ClassLoader;Ljava/lang/String;)J+49
v  ~StubRoutines::call_stub
j  jogamp.common.os.UnixDynamicLinkerImpl.dlopen(Ljava/lang/String;I)J+0
j  jogamp.common.os.PosixDynamicLinkerImpl.openLibraryGlobalImpl(Ljava/lang/String;)J+4
j  jogamp.common.os.DynamicLinkerImpl.openLibraryGlobal(Ljava/lang/String;Z)J+7
j  com.jogamp.common.os.NativeLibrary.open(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;ZLjava/lang/ClassLoader;Z)Lcom/jogamp/common/os/NativeLibrary;+206
j  com.jogamp.common.os.NativeLibrary.open(Ljava/lang/String;Ljava/lang/ClassLoader;Z)Lcom/jogamp/common/os/NativeLibrary;+6
j  com.jogamp.common.os.DynamicLibraryBundle.loadFirstAvailable(Ljava/util/List;Ljava/lang/ClassLoader;Z)Lcom/jogamp/common/os/NativeLibrary;+24
j  com.jogamp.common.os.DynamicLibraryBundle.loadLibraries()Lcom/jogamp/common/os/DynamicLinker;+81
j  com.jogamp.common.os.DynamicLibraryBundle$1.run()V+9
j  com.jogamp.common.util.RunnableExecutor$CurrentThreadExecutor.invoke(ZLjava/lang/Runnable;)V+1
j  com.jogamp.common.os.DynamicLibraryBundle.<init>(Lcom/jogamp/common/os/DynamicLibraryBundleInfo;)V+260
j  jogamp.opengl.GLDynamicLookupHelper.<init>(Ljogamp/opengl/GLDynamicLibraryBundleInfo;)V+2
j  jogamp.opengl.DesktopGLDynamicLookupHelper.<init>(Ljogamp/opengl/DesktopGLDynamicLibraryBundleInfo;)V+2
j  jogamp.opengl.x11.glx.X11GLXDrawableFactory$1.run()Ljogamp/opengl/DesktopGLDynamicLookupHelper;+11
j  jogamp.opengl.x11.glx.X11GLXDrawableFactory$1.run()Ljava/lang/Object;+1
v  ~StubRoutines::call_stub
J 1838  java.security.AccessController.doPrivileged(Ljava/security/PrivilegedAction;)Ljava/lang/Object; (0 bytes) @ 0x00007f80e1696fcf [0x00007f80e1696f80+0x4f]
j  jogamp.opengl.x11.glx.X11GLXDrawableFactory.<init>()V+24
v  ~StubRoutines::call_stub
J 2549  sun.reflect.NativeConstructorAccessorImpl.newInstance0(Ljava/lang/reflect/Constructor;[Ljava/lang/Object;)Ljava/lang/Object; (0 bytes) @ 0x00007f80e14c6ea3 [0x00007f80e14c6e40+0x63]
J 2548 C1 sun.reflect.NativeConstructorAccessorImpl.newInstance([Ljava/lang/Object;)Ljava/lang/Object; (89 bytes) @ 0x00007f80e1501f84 [0x00007f80e1500f80+0x1004]
J 767 C1 sun.reflect.DelegatingConstructorAccessorImpl.newInstance([Ljava/lang/Object;)Ljava/lang/Object; (9 bytes) @ 0x00007f80e12ff904 [0x00007f80e12ff800+0x104]
J 764 C1 java.lang.reflect.Constructor.newInstance([Ljava/lang/Object;)Ljava/lang/Object; (87 bytes) @ 0x00007f80e1300184 [0x00007f80e12ffcc0+0x4c4]
j  com.jogamp.common.util.ReflectionUtil.createInstance(Ljava/lang/reflect/Constructor;[Ljava/lang/Object;)Ljava/lang/Object;+2
j  com.jogamp.common.util.ReflectionUtil.createInstance(Ljava/lang/Class;[Ljava/lang/Class;[Ljava/lang/Object;)Ljava/lang/Object;+6
j  com.jogamp.common.util.ReflectionUtil.createInstance(Ljava/lang/String;[Ljava/lang/Class;[Ljava/lang/Object;Ljava/lang/ClassLoader;)Ljava/lang/Object;+8
j  com.jogamp.common.util.ReflectionUtil.createInstance(Ljava/lang/String;Ljava/lang/ClassLoader;)Ljava/lang/Object;+4
j  com.jogamp.opengl.GLDrawableFactory.initSingletonImpl()V+179
j  com.jogamp.opengl.GLDrawableFactory.initSingleton()V+21
j  com.jogamp.opengl.GLProfile.initProfilesForDefaultDevices()V+109
j  com.jogamp.opengl.GLProfile.access$000()V+0
j  com.jogamp.opengl.GLProfile$1.run()Ljava/lang/Object;+58
v  ~StubRoutines::call_stub
J 1838  java.security.AccessController.doPrivileged(Ljava/security/PrivilegedAction;)Ljava/lang/Object; (0 bytes) @ 0x00007f80e1696fcf [0x00007f80e1696f80+0x4f]
j  com.jogamp.opengl.GLProfile.initSingleton()V+78
j  com.jogamp.opengl.GLProfile.getProfileMap(Lcom/jogamp/nativewindow/AbstractGraphicsDevice;Z)Ljava/util/HashMap;+0
j  com.jogamp.opengl.GLProfile.get(Lcom/jogamp/nativewindow/AbstractGraphicsDevice;Ljava/lang/String;)Lcom/jogamp/opengl/GLProfile;+16
j  com.jogamp.opengl.GLProfile.get(Ljava/lang/String;)Lcom/jogamp/opengl/GLProfile;+4
j  clearvolume.renderer.cleargl.ClearGLVolumeRenderer.<clinit>()V+19
v  ~StubRoutines::call_stub
j  clearvolume.renderer.factory.ClearVolumeRendererFactory.newOpenCLRenderer(Ljava/lang/String;IILcoremem/types/NativeTypeEnum;IIIZ)Lclearvolume/renderer/ClearVolumeRendererInterface;+25
j  de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(Ljava/util/List;Ljava/lang/String;IIIIZZ)Lclearvolume/renderer/ClearVolumeRendererInterface;+52
j  de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(Ljava/util/List;Ljava/lang/String;IIIIZ[D[DZ)Lclearvolume/renderer/ClearVolumeRendererInterface;+19
j  de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run()V+36
j  de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager()V+220
j  de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(Lnet/imagej/ImgPlus;IZ)V+47
j  de.mpicbg.jug.plugins.ClearVolumePlugin.run()V+158
j  org.scijava.command.CommandModule.run()V+4
j  org.scijava.module.ModuleRunner.run()V+144
j  org.scijava.module.ModuleRunner.call()Lorg/scijava/module/Module;+1
j  org.scijava.module.ModuleRunner.call()Ljava/lang/Object;+1
j  org.scijava.thread.DefaultThreadService$2.call()Ljava/lang/Object;+28
j  java.util.concurrent.FutureTask.run()V+42
j  java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j  java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j  java.lang.Thread.run()V+11
v  ~StubRoutines::call_stub

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x00007f7800197800 JavaThread "process reaper" daemon [_thread_blocked, id=7641, stack(0x00007f781d40d000,0x00007f781d446000)]
  0x00007f7804098800 JavaThread "TimerQueue" daemon [_thread_blocked, id=7629, stack(0x00007f781c72a000,0x00007f781c82b000)]
  0x00007f780003a800 JavaThread "Thread-3" daemon [_thread_blocked, id=7628, stack(0x00007f781c82b000,0x00007f781c92c000)]
  0x00007f7800027800 JavaThread "SciJava-3d484181-Thread-11" [_thread_blocked, id=7627, stack(0x00007f781c326000,0x00007f781c427000)]
  0x00007f77e8001000 JavaThread "SciJava-3d484181-Thread-10" [_thread_blocked, id=7626, stack(0x00007f781c124000,0x00007f781c225000)]
  0x00007f7804093800 JavaThread "Open in ClearVolume" [_thread_blocked, id=7617, stack(0x00007f781d7ab000,0x00007f781d8ac000)]
  0x00007f80f004f000 JavaThread "zSelector" [_thread_blocked, id=7589, stack(0x00007f781d4aa000,0x00007f781d5ab000)]
  0x0000000000e74800 JavaThread "DestroyJavaVM" [_thread_blocked, id=7501, stack(0x00007fffdecb1000,0x00007fffdedb1000)]
  0x0000000002510800 JavaThread "Image Fetcher 0" daemon [_thread_blocked, id=7542, stack(0x00007f781df3c000,0x00007f781e03d000)]
=>0x0000000002492800 JavaThread "SciJava-3d484181-Thread-1" [_thread_in_native, id=7541, stack(0x00007f781e23d000,0x00007f781e33e000)]
  0x0000000002479800 JavaThread "Timer-0" daemon [_thread_blocked, id=7540, stack(0x00007f781e53e000,0x00007f781e63f000)]
  0x0000000002981000 JavaThread "SciJava-3d484181-Thread-0" [_thread_blocked, id=7539, stack(0x00007f781ee56000,0x00007f781ef57000)]
  0x0000000002908800 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=7537, stack(0x00007f781ef57000,0x00007f781f058000)]
  0x0000000002907800 JavaThread "AWT-Shutdown" [_thread_blocked, id=7536, stack(0x00007f781f058000,0x00007f781f159000)]
  0x0000000002451800 JavaThread "AWT-XAWT" daemon [_thread_in_native, id=7535, stack(0x00007f781f359000,0x00007f781f45a000)]
  0x000000000243d000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=7534, stack(0x00007f781f45a000,0x00007f781f55b000)]
  0x0000000000fd1800 JavaThread "Service Thread" daemon [_thread_blocked, id=7523, stack(0x00007f80c036b000,0x00007f80c046c000)]
  0x0000000000fc4800 JavaThread "C1 CompilerThread3" daemon [_thread_blocked, id=7522, stack(0x00007f80c046c000,0x00007f80c056d000)]
  0x0000000000fc2800 JavaThread "C2 CompilerThread2" daemon [_thread_blocked, id=7521, stack(0x00007f80c056d000,0x00007f80c066e000)]
  0x0000000000fc0000 JavaThread "C2 CompilerThread1" daemon [_thread_in_native, id=7520, stack(0x00007f80c066e000,0x00007f80c076f000)]
  0x0000000000fbe000 JavaThread "C2 CompilerThread0" daemon [_thread_in_native, id=7519, stack(0x00007f80c076f000,0x00007f80c0870000)]
  0x0000000000fbc000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=7518, stack(0x00007f80c0870000,0x00007f80c0971000)]
  0x0000000000fba800 JavaThread "Surrogate Locker Thread (Concurrent GC)" daemon [_thread_blocked, id=7517, stack(0x00007f80c0971000,0x00007f80c0a72000)]
  0x0000000000f83800 JavaThread "Finalizer" daemon [_thread_blocked, id=7516, stack(0x00007f80c0a72000,0x00007f80c0b73000)]
  0x0000000000f81800 JavaThread "Reference Handler" daemon [_thread_blocked, id=7515, stack(0x00007f80c0b73000,0x00007f80c0c74000)]

Other Threads:
  0x0000000000f7c800 VMThread [stack: 0x00007f80c0c74000,0x00007f80c0d75000] [id=7514]
  0x0000000000fd4800 WatcherThread [stack: 0x00007f80c026a000,0x00007f80c036b000] [id=7524]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap:
 par new generation   total 231616K, used 134908K [0x00007f787da00000, 0x00007f788d550000, 0x00007f78a7390000)
  eden space 205888K,  53% used [0x00007f787da00000, 0x00007f788449f3b8, 0x00007f788a310000)
  from space 25728K, 100% used [0x00007f788a310000, 0x00007f788bc30000, 0x00007f788bc30000)
  to   space 25728K,   0% used [0x00007f788bc30000, 0x00007f788bc30000, 0x00007f788d550000)
 concurrent mark-sweep generation total 514752K, used 39672K [0x00007f78a7390000, 0x00007f78c6a40000, 0x00007f80bc000000)
 Metaspace       used 43511K, capacity 43903K, committed 44260K, reserved 45056K

Card table byte_map: [0x00007f787980c000,0x00007f787da00000] byte_map_base: 0x00007f38bd41f000

Marking Bits: (CMSBitMap*) 0x0000000000efd978
 Bits: [0x00007f7855233000, 0x00007f7875764c00)

Mod Union Table: (CMSBitMap*) 0x0000000000efda38
 Bits: [0x00007f80e05e9000, 0x00007f80e0dfdc70)

Polling page: 0x00007f80f9d4c000

CodeCache: size=245760Kb used=10714Kb max_used=10714Kb free=235045Kb
 bounds [0x00007f80e1000000, 0x00007f80e1a90000, 0x00007f80f0000000]
 total_blobs=4145 nmethods=3159 adapters=898
 compilation: enabled

Compilation events (10 events):
Event: 9.471 Thread 0x0000000000fc4800 nmethod 3674 0x00007f80e1a5b150 code [0x00007f80e1a5b2c0, 0x00007f80e1a5b490]
Event: 9.471 Thread 0x0000000000fc4800 3675       3       sun.java2d.xr.XRRenderer$XRDrawHandler::drawScanline (19 bytes)
Event: 9.471 Thread 0x0000000000fc4800 nmethod 3675 0x00007f80e1a5acd0 code [0x00007f80e1a5ae40, 0x00007f80e1a5b068]
Event: 9.479 Thread 0x0000000000fc2800 nmethod 3614 0x00007f80e1a62bd0 code [0x00007f80e1a63060, 0x00007f80e1a68030]
Event: 9.480 Thread 0x0000000000fc2800 3672       4       sun.java2d.SunGraphics2D::invalidatePipe (41 bytes)
Event: 9.480 Thread 0x0000000000fc2800 nmethod 3672 0x00007f80e1a4f4d0 code [0x00007f80e1a4f620, 0x00007f80e1a4f6b8]
Event: 9.563 Thread 0x0000000000fc4800 3676       3       java.awt.Component$1::isDisplayable (13 bytes)
Event: 9.563 Thread 0x0000000000fc4800 nmethod 3676 0x00007f80e1a82f50 code [0x00007f80e1a830c0, 0x00007f80e1a83270]
Event: 9.570 Thread 0x0000000000fc4800 3677       3       java.awt.Component::repaint (16 bytes)
Event: 9.571 Thread 0x0000000000fc4800 nmethod 3677 0x00007f80e1a83c90 code [0x00007f80e1a83e00, 0x00007f80e1a84028]

GC Heap History (4 events):
Event: 1.546 GC heap before
{Heap before GC invocations=0 (full 0):
 par new generation   total 231616K, used 205888K [0x00007f787da00000, 0x00007f788d550000, 0x00007f78a7390000)
  eden space 205888K, 100% used [0x00007f787da00000, 0x00007f788a310000, 0x00007f788a310000)
  from space 25728K,   0% used [0x00007f788a310000, 0x00007f788a310000, 0x00007f788bc30000)
  to   space 25728K,   0% used [0x00007f788bc30000, 0x00007f788bc30000, 0x00007f788d550000)
 concurrent mark-sweep generation total 514752K, used 0K [0x00007f78a7390000, 0x00007f78c6a40000, 0x00007f80bc000000)
 Metaspace       used 19994K, capacity 20315K, committed 20480K, reserved 20480K
Event: 1.570 GC heap after
Heap after GC invocations=1 (full 0):
 par new generation   total 231616K, used 20969K [0x00007f787da00000, 0x00007f788d550000, 0x00007f78a7390000)
  eden space 205888K,   0% used [0x00007f787da00000, 0x00007f787da00000, 0x00007f788a310000)
  from space 25728K,  81% used [0x00007f788bc30000, 0x00007f788d0aa7e8, 0x00007f788d550000)
  to   space 25728K,   0% used [0x00007f788a310000, 0x00007f788a310000, 0x00007f788bc30000)
 concurrent mark-sweep generation total 514752K, used 0K [0x00007f78a7390000, 0x00007f78c6a40000, 0x00007f80bc000000)
 Metaspace       used 19994K, capacity 20315K, committed 20480K, reserved 20480K
}
Event: 8.418 GC heap before
{Heap before GC invocations=1 (full 1):
 par new generation   total 231616K, used 226858K [0x00007f787da00000, 0x00007f788d550000, 0x00007f78a7390000)
  eden space 205888K, 100% used [0x00007f787da00000, 0x00007f788a310000, 0x00007f788a310000)
  from space 25728K,  81% used [0x00007f788bc30000, 0x00007f788d0aa828, 0x00007f788d550000)
  to   space 25728K,   0% used [0x00007f788a310000, 0x00007f788a310000, 0x00007f788bc30000)
 concurrent mark-sweep generation total 514752K, used 0K [0x00007f78a7390000, 0x00007f78c6a40000, 0x00007f80bc000000)
 Metaspace       used 37211K, capacity 37566K, committed 37820K, reserved 38912K
Event: 8.483 GC heap after
Heap after GC invocations=2 (full 1):
 par new generation   total 231616K, used 25728K [0x00007f787da00000, 0x00007f788d550000, 0x00007f78a7390000)
  eden space 205888K,   0% used [0x00007f787da00000, 0x00007f787da00000, 0x00007f788a310000)
  from space 25728K, 100% used [0x00007f788a310000, 0x00007f788bc30000, 0x00007f788bc30000)
  to   space 25728K,   0% used [0x00007f788bc30000, 0x00007f788bc30000, 0x00007f788d550000)
 concurrent mark-sweep generation total 514752K, used 39672K [0x00007f78a7390000, 0x00007f78c6a40000, 0x00007f80bc000000)
 Metaspace       used 37211K, capacity 37566K, committed 37820K, reserved 38912K
}

Deoptimization events (10 events):
Event: 8.820 Thread 0x0000000002492800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00007f80e19524f8 method=net.imglib2.img.array.AbstractArrayLocalizingCursor.fwd()V @ 4
Event: 8.820 Thread 0x0000000002492800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00007f80e19524f8 method=net.imglib2.img.array.AbstractArrayLocalizingCursor.fwd()V @ 4
Event: 8.820 Thread 0x0000000002492800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00007f80e19524f8 method=net.imglib2.img.array.AbstractArrayLocalizingCursor.fwd()V @ 4
Event: 8.845 Thread 0x0000000002492800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f80e153fbb8 method=net.imglib2.img.planar.PlanarRandomAccess.setPosition(Lnet/imglib2/Localizable;)V @ 78
Event: 8.866 Thread 0x0000000002492800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f80e19bafc4 method=net.imglib2.img.planar.PlanarRandomAccess.setPosition(Lnet/imglib2/Localizable;)V @ 78
Event: 8.977 Thread 0x0000000002492800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f80e19bd6d8 method=java.lang.Math.max(DD)D @ 17
Event: 9.131 Thread 0x0000000002492800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f80e19c18bc method=de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.copy(Lnet/imglib2/RandomAccessible;Lnet/imglib2/IterableInterval;Lnet/imglib2/converter/Converter;)V @ 63
Event: 9.140 Thread 0x0000000002492800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f80e1784e9c method=java.io.File.getName()Ljava/lang/String; @ 16
Event: 9.170 Thread 0x0000000002492800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f80e14b36ec method=sun.reflect.annotation.AnnotationParser.parseArray(Ljava/lang/Class;Ljava/nio/ByteBuffer;Lsun/reflect/ConstantPool;Ljava/lang/Class;)Ljava/lang/Object; @ 179
Event: 9.223 Thread 0x0000000002492800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f80e123a6bc method=java.lang.ThreadLocal$ThreadLocalMap.getEntry(Ljava/lang/ThreadLocal;)Ljava/lang/ThreadLocal$ThreadLocalMap$Entry; @ 29

Internal exceptions (10 events):
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clEnqueueWaitForEvents> (0x00007f7882407fb0) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clEnqueueBarrier> (0x00007f7882408298) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clGetExtensionFunctionAddress> (0x00007f78824085a0) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clCreateFromGLTexture> (0x00007f7882408898) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clGetGLObjectInfo> (0x00007f7882408b88) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clGetGLTextureInfo> (0x00007f7882408e78) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clEnqueueAcquireGLObjects> (0x00007f7882409178) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.249 Thread 0x0000000002492800 Exception <a 'java/lang/NoSuchMethodError': clEnqueueReleaseGLObjects> (0x00007f7882409478) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 1598]
Event: 9.251 Thread 0x0000000002492800 Exception <a 'java/lang/UnsatisfiedLinkError': com.nativelibs4java.opencl.library.OpenCLLibrary.clIcdGetPlatformIDsKHR(IJJ)I> (0x00007f78824b50a0) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/nativeLookup.cpp
Event: 9.312 Thread 0x0000000002492800 Exception <a 'java/io/FileNotFoundException'> (0x00007f7882c43fa0) thrown at [/RE-WORK/workspace/8-2-build-linux-amd64/jdk8u45/3457/hotspot/src/share/vm/prims/jni.cpp, line 709]

Events (10 events):
Event: 9.581 loading class com/jogamp/common/os/NativeLibrary$1
Event: 9.581 loading class com/jogamp/common/os/NativeLibrary$1 done
Event: 9.581 loading class com/jogamp/common/os/NativeLibrary$2
Event: 9.581 loading class com/jogamp/common/os/NativeLibrary$2 done
Event: 9.581 loading class jogamp/common/os/PosixDynamicLinkerImpl
Event: 9.581 loading class jogamp/common/os/PosixDynamicLinkerImpl done
Event: 9.581 loading class jogamp/common/os/UnixDynamicLinkerImpl
Event: 9.581 loading class jogamp/common/os/UnixDynamicLinkerImpl done
Event: 9.582 loading class jogamp/common/os/DynamicLinkerImpl
Event: 9.582 loading class jogamp/common/os/DynamicLinkerImpl done

Dynamic libraries:
00400000-00411000 r-xp 00000000 08:06 4240925                            /home/marc/bin/Fiji.app/ImageJ-linux64
00610000-00611000 r--p 00010000 08:06 4240925                            /home/marc/bin/Fiji.app/ImageJ-linux64
00611000-00612000 rw-p 00011000 08:06 4240925                            /home/marc/bin/Fiji.app/ImageJ-linux64
00612000-00614000 rw-p 00000000 00:00 0 
00e56000-02d0a000 rw-p 00000000 00:00 0                                  [heap]
200000000-1f00000000 ---p 00000000 00:00 0 
7f77bc000000-7f77bc021000 rw-p 00000000 00:00 0 
7f77bc021000-7f77c0000000 ---p 00000000 00:00 0 
7f77c4000000-7f77c4021000 rw-p 00000000 00:00 0 
7f77c4021000-7f77c8000000 ---p 00000000 00:00 0 
7f77c8c9a000-7f77c8e5a000 rw-p 00000000 00:00 0 
7f77c8e5a000-7f77c8e9a000 ---p 00000000 00:00 0 
7f77c8e9a000-7f77c8ea1000 r-xp 00000000 08:05 528218                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libnativewindow_x11.so
7f77c8ea1000-7f77c90a0000 ---p 00007000 08:05 528218                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libnativewindow_x11.so
7f77c90a0000-7f77c90a1000 rw-p 00006000 08:05 528218                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libnativewindow_x11.so
7f77c90a1000-7f77c90a5000 r-xp 00000000 08:05 1189940                    /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f77c90a5000-7f77c92a5000 ---p 00004000 08:05 1189940                    /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f77c92a5000-7f77c92a6000 r--p 00004000 08:05 1189940                    /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f77c92a6000-7f77c92a7000 rw-p 00005000 08:05 1189940                    /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f77c92a7000-7f77c92a9000 r-xp 00000000 08:05 528217                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libnativewindow_awt.so
7f77c92a9000-7f77c94a8000 ---p 00002000 08:05 528217                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libnativewindow_awt.so
7f77c94a8000-7f77c94a9000 rw-p 00001000 08:05 528217                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libnativewindow_awt.so
7f77c94a9000-7f77c94aa000 r-xp 00000000 08:05 103394                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjawt.so
7f77c94aa000-7f77c96a9000 ---p 00001000 08:05 103394                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjawt.so
7f77c96a9000-7f77c96aa000 rw-p 00000000 08:05 103394                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjawt.so
7f77c96aa000-7f77c96ac000 r-xp 00000000 08:05 528214                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libgluegen-rt.so
7f77c96ac000-7f77c98ab000 ---p 00002000 08:05 528214                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libgluegen-rt.so
7f77c98ab000-7f77c98ac000 rw-p 00001000 08:05 528214                     /tmp/jogamp_0000/file_cache/jln7766078208988453423/jln8169961639362185005/libgluegen-rt.so
7f77c98ac000-7f77c9a9e000 rw-p 00000000 00:00 0 
7f77c9a9e000-7f77c9aac000 ---p 00000000 00:00 0 
7f77c9aac000-7f77ca570000 r-xp 00000000 08:05 1182527                    /usr/lib/x86_64-linux-gnu/libcuda.so.346.46
7f77ca570000-7f77ca76f000 ---p 00ac4000 08:05 1182527                    /usr/lib/x86_64-linux-gnu/libcuda.so.346.46
7f77ca76f000-7f77ca921000 rw-p 00ac3000 08:05 1182527                    /usr/lib/x86_64-linux-gnu/libcuda.so.346.46
7f77ca921000-7f77ca936000 rw-p 00000000 00:00 0 
7f77ca936000-7f77cb411000 r-xp 00000000 08:05 1185944                    /usr/lib/x86_64-linux-gnu/libnvidia-opencl.so.346.46
7f77cb411000-7f77cb611000 ---p 00adb000 08:05 1185944                    /usr/lib/x86_64-linux-gnu/libnvidia-opencl.so.346.46
7f77cb611000-7f77cb7c6000 rw-p 00adb000 08:05 1185944                    /usr/lib/x86_64-linux-gnu/libnvidia-opencl.so.346.46
7f77cb7c6000-7f77cb7dc000 rw-p 00000000 00:00 0 
7f77cb7dc000-7f77cb7e1000 r-xp 00000000 08:05 1201569                    /usr/local/cuda-7.0/targets/x86_64-linux/lib/libOpenCL.so
7f77cb7e1000-7f77cb9e1000 ---p 00005000 08:05 1201569                    /usr/local/cuda-7.0/targets/x86_64-linux/lib/libOpenCL.so
7f77cb9e1000-7f77cb9e2000 rw-p 00005000 08:05 1201569                    /usr/local/cuda-7.0/targets/x86_64-linux/lib/libOpenCL.so
7f77cb9e2000-7f77cb9fd000 r-xp 00000000 08:05 527817                     /tmp/BridJExtractedLibraries5314595325653826016/libbridj.so
7f77cb9fd000-7f77cbbfc000 ---p 0001b000 08:05 527817                     /tmp/BridJExtractedLibraries5314595325653826016/libbridj.so
7f77cbbfc000-7f77cbbfd000 r--p 0001a000 08:05 527817                     /tmp/BridJExtractedLibraries5314595325653826016/libbridj.so
7f77cbbfd000-7f77cbbfe000 rw-p 0001b000 08:05 527817                     /tmp/BridJExtractedLibraries5314595325653826016/libbridj.so
7f77cbbfe000-7f77cbdf0000 rw-p 00000000 00:00 0 
7f77cbdf0000-7f77cbdfe000 ---p 00000000 00:00 0 
7f77cbdfe000-7f77cbe01000 rwxp 00000000 00:00 0 
7f77cbe01000-7f77cbeff000 rwxp 00000000 00:00 0 
7f77cbeff000-7f77cbf02000 rwxp 00000000 00:00 0 
7f77cbf02000-7f77cc000000 rwxp 00000000 00:00 0 
7f77cc000000-7f77cc021000 rw-p 00000000 00:00 0 
7f77cc021000-7f77d0000000 ---p 00000000 00:00 0 
7f77d0000000-7f77d0021000 rw-p 00000000 00:00 0 
7f77d0021000-7f77d4000000 ---p 00000000 00:00 0 
7f77d4000000-7f77d4021000 rw-p 00000000 00:00 0 
7f77d4021000-7f77d8000000 ---p 00000000 00:00 0 
7f77d8000000-7f77d8021000 rw-p 00000000 00:00 0 
7f77d8021000-7f77dc000000 ---p 00000000 00:00 0 
7f77dc000000-7f77dc021000 rw-p 00000000 00:00 0 
7f77dc021000-7f77e0000000 ---p 00000000 00:00 0 
7f77e0000000-7f77e0021000 rw-p 00000000 00:00 0 
7f77e0021000-7f77e4000000 ---p 00000000 00:00 0 
7f77e4000000-7f77e4021000 rw-p 00000000 00:00 0 
7f77e4021000-7f77e8000000 ---p 00000000 00:00 0 
7f77e8000000-7f77e8021000 rw-p 00000000 00:00 0 
7f77e8021000-7f77ec000000 ---p 00000000 00:00 0 
7f77ec000000-7f77ec021000 rw-p 00000000 00:00 0 
7f77ec021000-7f77f0000000 ---p 00000000 00:00 0 
7f77f0000000-7f77f0021000 rw-p 00000000 00:00 0 
7f77f0021000-7f77f4000000 ---p 00000000 00:00 0 
7f77f4000000-7f77f403c000 rw-p 00000000 00:00 0 
7f77f403c000-7f77f8000000 ---p 00000000 00:00 0 
7f77f8000000-7f77f8021000 rw-p 00000000 00:00 0 
7f77f8021000-7f77fc000000 ---p 00000000 00:00 0 
7f77fc000000-7f77fc021000 rw-p 00000000 00:00 0 
7f77fc021000-7f7800000000 ---p 00000000 00:00 0 
7f7800000000-7f78004d3000 rw-p 00000000 00:00 0 
7f78004d3000-7f7804000000 ---p 00000000 00:00 0 
7f7804000000-7f7804136000 rw-p 00000000 00:00 0 
7f7804136000-7f7808000000 ---p 00000000 00:00 0 
7f7808000000-7f78082f1000 rw-p 00000000 00:00 0 
7f78082f1000-7f780c000000 ---p 00000000 00:00 0 
7f780c000000-7f780c02c000 rw-p 00000000 00:00 0 
7f780c02c000-7f7810000000 ---p 00000000 00:00 0 
7f7810000000-7f7810021000 rw-p 00000000 00:00 0 
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7f80f00e0000-7f80f4000000 ---p 00000000 00:00 0 
7f80f4000000-7f80f4002000 r--s 00001000 08:06 4241260                    /home/marc/bin/Fiji.app/jars/swing-checkbox-tree-1.0.0.jar
7f80f4002000-7f80f4005000 r--s 00035000 08:06 4241208                    /home/marc/bin/Fiji.app/jars/jsch-0.1.49.jar
7f80f4005000-7f80f4007000 r--s 0001d000 08:06 4241262                    /home/marc/bin/Fiji.app/jars/udunits-4.3.18.jar
7f80f4007000-7f80f4009000 r--s 00004000 08:06 4241153                    /home/marc/bin/Fiji.app/jars/imagej-plugins-uploader-ssh-0.2.0.jar
7f80f4009000-7f80f4016000 r--s 000d8000 08:06 4463736                    /home/marc/bin/Fiji.app/jars/bio-formats/ome-poi-5.1.2.jar
7f80f4016000-7f80f4667000 rw-p 00000000 00:00 0 
7f80f4667000-7f80f4668000 ---p 00000000 00:00 0 
7f80f4668000-7f80f4768000 rwxp 00000000 00:00 0                          [stack:7510]
7f80f4768000-7f80f4769000 ---p 00000000 00:00 0 
7f80f4769000-7f80f4869000 rwxp 00000000 00:00 0                          [stack:7509]
7f80f4869000-7f80f486a000 ---p 00000000 00:00 0 
7f80f486a000-7f80f496a000 rwxp 00000000 00:00 0                          [stack:7508]
7f80f496a000-7f80f496b000 ---p 00000000 00:00 0 
7f80f496b000-7f80f4a6b000 rwxp 00000000 00:00 0                          [stack:7507]
7f80f4a6b000-7f80f4a6c000 ---p 00000000 00:00 0 
7f80f4a6c000-7f80f4b6c000 rwxp 00000000 00:00 0                          [stack:7506]
7f80f4b6c000-7f80f4b6d000 ---p 00000000 00:00 0 
7f80f4b6d000-7f80f4c6d000 rwxp 00000000 00:00 0                          [stack:7505]
7f80f4c6d000-7f80f4c6e000 ---p 00000000 00:00 0 
7f80f4c6e000-7f80f4d6e000 rwxp 00000000 00:00 0                          [stack:7504]
7f80f4d6e000-7f80f4d99000 rw-p 00000000 00:00 0 
7f80f4d99000-7f80f512e000 ---p 00000000 00:00 0 
7f80f512e000-7f80f5148000 r-xp 00000000 08:05 103395                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libzip.so
7f80f5148000-7f80f5348000 ---p 0001a000 08:05 103395                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libzip.so
7f80f5348000-7f80f5349000 rw-p 0001a000 08:05 103395                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libzip.so
7f80f5349000-7f80f5354000 r-xp 00000000 08:05 264516                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f80f5354000-7f80f5553000 ---p 0000b000 08:05 264516                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f80f5553000-7f80f5554000 r--p 0000a000 08:05 264516                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f80f5554000-7f80f5555000 rw-p 0000b000 08:05 264516                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f80f5555000-7f80f5560000 r-xp 00000000 08:05 274668                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f80f5560000-7f80f575f000 ---p 0000b000 08:05 274668                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f80f575f000-7f80f5760000 r--p 0000a000 08:05 274668                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f80f5760000-7f80f5761000 rw-p 0000b000 08:05 274668                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f80f5761000-7f80f5778000 r-xp 00000000 08:05 274645                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f80f5778000-7f80f5977000 ---p 00017000 08:05 274645                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f80f5977000-7f80f5978000 r--p 00016000 08:05 274645                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f80f5978000-7f80f5979000 rw-p 00017000 08:05 274645                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f80f5979000-7f80f597b000 rw-p 00000000 00:00 0 
7f80f597b000-7f80f5984000 r-xp 00000000 08:05 274644                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f80f5984000-7f80f5b83000 ---p 00009000 08:05 274644                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f80f5b83000-7f80f5b84000 r--p 00008000 08:05 274644                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f80f5b84000-7f80f5b85000 rw-p 00009000 08:05 274644                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f80f5b85000-7f80f5baf000 r-xp 00000000 08:05 103349                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjava.so
7f80f5baf000-7f80f5daf000 ---p 0002a000 08:05 103349                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjava.so
7f80f5daf000-7f80f5db1000 rw-p 0002a000 08:05 103349                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjava.so
7f80f5db1000-7f80f5dbe000 r-xp 00000000 08:05 103368                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libverify.so
7f80f5dbe000-7f80f5fbe000 ---p 0000d000 08:05 103368                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libverify.so
7f80f5fbe000-7f80f5fc0000 rw-p 0000d000 08:05 103368                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libverify.so
7f80f5fc0000-7f80f5fc7000 r-xp 00000000 08:05 274662                     /lib/x86_64-linux-gnu/librt-2.19.so
7f80f5fc7000-7f80f61c6000 ---p 00007000 08:05 274662                     /lib/x86_64-linux-gnu/librt-2.19.so
7f80f61c6000-7f80f61c7000 r--p 00006000 08:05 274662                     /lib/x86_64-linux-gnu/librt-2.19.so
7f80f61c7000-7f80f61c8000 rw-p 00007000 08:05 274662                     /lib/x86_64-linux-gnu/librt-2.19.so
7f80f61c8000-7f80f6e76000 r-xp 00000000 08:05 103386                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so
7f80f6e76000-7f80f7075000 ---p 00cae000 08:05 103386                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so
7f80f7075000-7f80f714c000 rw-p 00cad000 08:05 103386                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so
7f80f714c000-7f80f7190000 rw-p 00000000 00:00 0 
7f80f7190000-7f80f7195000 r-xp 00000000 08:05 1187084                    /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f80f7195000-7f80f7394000 ---p 00005000 08:05 1187084                    /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f80f7394000-7f80f7395000 r--p 00004000 08:05 1187084                    /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f80f7395000-7f80f7396000 rw-p 00005000 08:05 1187084                    /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f80f7396000-7f80f739f000 r-xp 00000000 08:05 1187710                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f80f739f000-7f80f759e000 ---p 00009000 08:05 1187710                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f80f759e000-7f80f759f000 r--p 00008000 08:05 1187710                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f80f759f000-7f80f75a0000 rw-p 00009000 08:05 1187710                    /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f80f75a0000-7f80f75a9000 r-xp 00000000 08:05 1186477                    /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
7f80f75a9000-7f80f77a8000 ---p 00009000 08:05 1186477                    /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
7f80f77a8000-7f80f77a9000 r--p 00008000 08:05 1186477                    /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
7f80f77a9000-7f80f77aa000 rw-p 00009000 08:05 1186477                    /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
7f80f77aa000-7f80f7a73000 r--p 00000000 08:05 1203425                    /usr/lib/locale/locale-archive
7f80f7a73000-7f80f7a74000 ---p 00000000 00:00 0 
7f80f7a74000-7f80f8274000 rwxp 00000000 00:00 0 
7f80f8274000-7f80f8279000 r-xp 00000000 08:05 1191407                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f80f8279000-7f80f8478000 ---p 00005000 08:05 1191407                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f80f8478000-7f80f8479000 r--p 00004000 08:05 1191407                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f80f8479000-7f80f847a000 rw-p 00005000 08:05 1191407                    /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f80f847a000-7f80f847c000 r-xp 00000000 08:05 1187280                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f80f847c000-7f80f867c000 ---p 00002000 08:05 1187280                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f80f867c000-7f80f867d000 r--p 00002000 08:05 1187280                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f80f867d000-7f80f867e000 rw-p 00003000 08:05 1187280                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f80f867e000-7f80f869b000 r-xp 00000000 08:05 1187535                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f80f869b000-7f80f889b000 ---p 0001d000 08:05 1187535                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f80f889b000-7f80f889c000 r--p 0001d000 08:05 1187535                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f80f889c000-7f80f889d000 rw-p 0001e000 08:05 1187535                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f80f889d000-7f80f89a2000 r-xp 00000000 08:05 264452                     /lib/x86_64-linux-gnu/libm-2.19.so
7f80f89a2000-7f80f8ba1000 ---p 00105000 08:05 264452                     /lib/x86_64-linux-gnu/libm-2.19.so
7f80f8ba1000-7f80f8ba2000 r--p 00104000 08:05 264452                     /lib/x86_64-linux-gnu/libm-2.19.so
7f80f8ba2000-7f80f8ba3000 rw-p 00105000 08:05 264452                     /lib/x86_64-linux-gnu/libm-2.19.so
7f80f8ba3000-7f80f8bb4000 r-xp 00000000 08:05 1184595                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f80f8bb4000-7f80f8db3000 ---p 00011000 08:05 1184595                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f80f8db3000-7f80f8db4000 r--p 00010000 08:05 1184595                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f80f8db4000-7f80f8db5000 rw-p 00011000 08:05 1184595                    /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f80f8db5000-7f80f8ee5000 r-xp 00000000 08:05 1187633                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f80f8ee5000-7f80f90e5000 ---p 00130000 08:05 1187633                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f80f90e5000-7f80f90e6000 r--p 00130000 08:05 1187633                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f80f90e6000-7f80f90ea000 rw-p 00131000 08:05 1187633                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f80f90ea000-7f80f914b000 r-xp 00000000 08:05 103370                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libsplashscreen.so
7f80f914b000-7f80f934a000 ---p 00061000 08:05 103370                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libsplashscreen.so
7f80f934a000-7f80f934b000 rw-p 00060000 08:05 103370                     /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libsplashscreen.so
7f80f934b000-7f80f934e000 rw-p 00000000 00:00 0 
7f80f934e000-7f80f9509000 r-xp 00000000 08:05 274656                     /lib/x86_64-linux-gnu/libc-2.19.so
7f80f9509000-7f80f9708000 ---p 001bb000 08:05 274656                     /lib/x86_64-linux-gnu/libc-2.19.so
7f80f9708000-7f80f970c000 r--p 001ba000 08:05 274656                     /lib/x86_64-linux-gnu/libc-2.19.so
7f80f970c000-7f80f970e000 rw-p 001be000 08:05 274656                     /lib/x86_64-linux-gnu/libc-2.19.so
7f80f970e000-7f80f9713000 rw-p 00000000 00:00 0 
7f80f9713000-7f80f972c000 r-xp 00000000 08:05 274658                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f80f972c000-7f80f992b000 ---p 00019000 08:05 274658                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f80f992b000-7f80f992c000 r--p 00018000 08:05 274658                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f80f992c000-7f80f992d000 rw-p 00019000 08:05 274658                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f80f992d000-7f80f9931000 rw-p 00000000 00:00 0 
7f80f9931000-7f80f9934000 r-xp 00000000 08:05 274638                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f80f9934000-7f80f9b33000 ---p 00003000 08:05 274638                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f80f9b33000-7f80f9b34000 r--p 00002000 08:05 274638                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f80f9b34000-7f80f9b35000 rw-p 00003000 08:05 274638                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f80f9b35000-7f80f9b58000 r-xp 00000000 08:05 274650                     /lib/x86_64-linux-gnu/ld-2.19.so
7f80f9b58000-7f80f9b59000 r--s 00001000 08:06 5119807                    /home/marc/bin/Fiji.app/jars/T2-TreelineGraph-1.1.0.jar
7f80f9b59000-7f80f9b5c000 r--s 00013000 08:06 4463734                    /home/marc/bin/Fiji.app/jars/bio-formats/mdbtools-java-5.1.2.jar
7f80f9b5c000-7f80f9b9e000 rw-p 00000000 00:00 0 
7f80f9b9e000-7f80f9b9f000 ---p 00000000 00:00 0 
7f80f9b9f000-7f80f9ca0000 rwxp 00000000 00:00 0                          [stack:7503]
7f80f9ca0000-7f80f9ca7000 rwxp 00000000 00:00 0 
7f80f9ca7000-7f80f9cae000 r--s 00000000 08:05 1201569                    /usr/local/cuda-7.0/targets/x86_64-linux/lib/libOpenCL.so
7f80f9cae000-7f80f9ce0000 rw-s 00000000 00:04 5144596                    /SYSV00000000 (deleted)
7f80f9ce0000-7f80f9ce7000 r--s 00122000 08:06 4463732                    /home/marc/bin/Fiji.app/jars/bio-formats/formats-gpl-5.1.2.jar
7f80f9ce7000-7f80f9ce9000 r--s 0013b000 08:06 4463739                    /home/marc/bin/Fiji.app/jars/bio-formats/turbojpeg-5.1.2.jar
7f80f9ce9000-7f80f9cee000 r--s 00091000 08:06 4463738                    /home/marc/bin/Fiji.app/jars/bio-formats/specification-5.1.2.jar
7f80f9cee000-7f80f9cfd000 r--s 000ed000 08:06 4463733                    /home/marc/bin/Fiji.app/jars/bio-formats/jai_imageio-5.1.2.jar
7f80f9cfd000-7f80f9d03000 r--s 0008f000 08:06 4463737                    /home/marc/bin/Fiji.app/jars/bio-formats/ome-xml-5.1.2.jar
7f80f9d03000-7f80f9d05000 r--s 0001b000 08:06 4463731                    /home/marc/bin/Fiji.app/jars/bio-formats/formats-common-5.1.2.jar
7f80f9d05000-7f80f9d07000 r--s 00022000 08:06 4463729                    /home/marc/bin/Fiji.app/jars/bio-formats/formats-api-5.1.2.jar
7f80f9d07000-7f80f9d0c000 r--s 000a2000 08:06 4463730                    /home/marc/bin/Fiji.app/jars/bio-formats/formats-bsd-5.1.2.jar
7f80f9d0c000-7f80f9d0e000 r--s 0000a000 08:06 4241109                    /home/marc/bin/Fiji.app/jars/asm-4.0.jar
7f80f9d0e000-7f80f9d11000 r--s 0002b000 08:06 4241203                    /home/marc/bin/Fiji.app/jars/joni-2.1.1.jar
7f80f9d11000-7f80f9d21000 r--s 000e2000 08:06 4241238                    /home/marc/bin/Fiji.app/jars/scifio-jai-imageio-1.1.0.jar
7f80f9d21000-7f80f9d25000 rw-p 00000000 00:00 0 
7f80f9d25000-7f80f9d26000 r--s 00002000 08:06 4463735                    /home/marc/bin/Fiji.app/jars/bio-formats/metakit-5.1.2.jar
7f80f9d26000-7f80f9d2c000 r--s 0004b000 08:06 4241179                    /home/marc/bin/Fiji.app/jars/jcommon-1.0.23.jar
7f80f9d2c000-7f80f9d2f000 r--s 00012000 08:06 4241136                    /home/marc/bin/Fiji.app/jars/eventbus-1.4.jar
7f80f9d2f000-7f80f9d31000 r--s 00003000 08:06 4241141                    /home/marc/bin/Fiji.app/jars/gentyref-1.1.0.jar
7f80f9d31000-7f80f9d32000 r--s 00003000 08:06 4241252                    /home/marc/bin/Fiji.app/jars/scripting-groovy-0.2.0.jar
7f80f9d32000-7f80f9d34000 r--s 00011000 08:06 4241218                    /home/marc/bin/Fiji.app/jars/miglayout-3.7.4-swing.jar
7f80f9d34000-7f80f9d37000 r--s 00014000 08:06 4196006                    /home/marc/bin/Fiji.app/jars/CoreMem-0.1.0.jar
7f80f9d37000-7f80f9d38000 r--s 00003000 08:06 5119817                    /home/marc/bin/Fiji.app/jars/opencsv-2.0.jar
7f80f9d38000-7f80f9d3a000 r--s 00008000 08:06 4241174                    /home/marc/bin/Fiji.app/jars/jama-1.0.3.jar
7f80f9d3a000-7f80f9d43000 r--s 0007f000 08:06 4241184                    /home/marc/bin/Fiji.app/jars/jep-2.4.2.jar
7f80f9d43000-7f80f9d4b000 rw-s 00000000 08:05 529500                     /tmp/hsperfdata_marc/7501
7f80f9d4b000-7f80f9d4c000 rw-p 00000000 00:00 0 
7f80f9d4c000-7f80f9d4d000 r--p 00000000 00:00 0 
7f80f9d4d000-7f80f9d4e000 r--s 00004000 08:06 4241148                    /home/marc/bin/Fiji.app/jars/imagej-launcher-3.1.6.jar
7f80f9d4e000-7f80f9d55000 r--s 00000000 08:05 204874                     /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f80f9d55000-7f80f9d57000 rw-p 00000000 00:00 0 
7f80f9d57000-7f80f9d58000 r--p 00022000 08:05 274650                     /lib/x86_64-linux-gnu/ld-2.19.so
7f80f9d58000-7f80f9d59000 rw-p 00023000 08:05 274650                     /lib/x86_64-linux-gnu/ld-2.19.so
7f80f9d59000-7f80f9d5a000 rw-p 00000000 00:00 0 
7fffdecb1000-7fffdecb4000 ---p 00000000 00:00 0 
7fffdecb5000-7fffdedae000 rwxp 00000000 00:00 0                          [stack]
7fffdedae000-7fffdedb1000 rw-p 00000000 00:00 0 
7fffdedcf000-7fffdedd1000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

VM Arguments:
jvm_args: -Dpython.cachedir.skip=true -Dplugins.dir=/home/marc/bin/Fiji.app -Xmx33765m -Xincgc -XX:PermSize=128m 
java_command: <unknown>
java_class_path (initial): /home/marc/bin/Fiji.app/jars/imagej-launcher-3.1.6.jar
Launcher Type: generic

Environment Variables:
JAVA_HOME=/usr/lib/jvm/java-8-oracle/jre
PATH=/home/marc/google-cloud-sdk/bin:/home/marc/texlive/2014/bin/x86_64-linux:/home/marc/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
LD_LIBRARY_PATH=.:/home/marc/lib:/usr/local/cuda/lib64:/usr/local/cuda/nvvm/lib64::/home/marc/bin/Fiji.app/lib/linux64:/home/marc/bin/Fiji.app/mm/linux64
SHELL=/bin/bash
DISPLAY=:0

Signal Handlers:
SIGSEGV: [libjvm.so+0xaad1e0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGBUS: [libjvm.so+0xaad1e0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGFPE: [libjvm.so+0x90b450], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGPIPE: [libjvm.so+0x90b450], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGXFSZ: [libjvm.so+0x90b450], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGILL: [libjvm.so+0x90b450], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGUSR2: [libjvm.so+0x90ca90], sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
SIGHUP: [libjvm.so+0x90dde0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGINT: [libjvm.so+0x90dde0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGTERM: [libjvm.so+0x90dde0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGQUIT: [libjvm.so+0x90dde0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO

---------------  S Y S T E M  ---------------

OS:DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=14.04
DISTRIB_CODENAME=trusty
DISTRIB_DESCRIPTION="Ubuntu 14.04.2 LTS"

uname:Linux 3.13.0-53-generic #89-Ubuntu SMP Wed May 20 10:34:39 UTC 2015 x86_64
libc:glibc 2.19 NPTL 2.19 
rlimit: STACK 8192k, CORE 0k, NPROC 384033, NOFILE 4096, AS infinity
load average:1.06 0.65 0.52

/proc/meminfo:
MemTotal:       49401832 kB
MemFree:        36075148 kB
Buffers:          944860 kB
Cached:          7788800 kB
SwapCached:            0 kB
Active:          7357600 kB
Inactive:        4999292 kB
Active(anon):    3624916 kB
Inactive(anon):    13200 kB
Active(file):    3732684 kB
Inactive(file):  4986092 kB
Unevictable:        2512 kB
Mlocked:            2512 kB
SwapTotal:       2109436 kB
SwapFree:        2109436 kB
Dirty:              9432 kB
Writeback:             0 kB
AnonPages:       3626232 kB
Mapped:           315320 kB
Shmem:             14580 kB
Slab:             493416 kB
SReclaimable:     366128 kB
SUnreclaim:       127288 kB
KernelStack:        6208 kB
PageTables:        44128 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    26810352 kB
Committed_AS:    8185988 kB
VmallocTotal:   34359738367 kB
VmallocUsed:      496600 kB
VmallocChunk:   34359237628 kB
HardwareCorrupted:     0 kB
AnonHugePages:   1722368 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
DirectMap4k:      472304 kB
DirectMap2M:     9951232 kB
DirectMap1G:    41943040 kB

CPU:total 8 (4 cores per cpu, 2 threads per core) family 6 model 62 stepping 4, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, aes, clmul, erms, ht, tsc, tscinvbit

/proc/cpuinfo:
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 3701.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 0
cpu cores   : 4
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 1
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 3701.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 1
cpu cores   : 4
apicid      : 2
initial apicid  : 2
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 2
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 1200.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 2
cpu cores   : 4
apicid      : 4
initial apicid  : 4
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 3
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 3701.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 3
cpu cores   : 4
apicid      : 6
initial apicid  : 6
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 4
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 3701.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 0
cpu cores   : 4
apicid      : 1
initial apicid  : 1
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 5
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 1200.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 1
cpu cores   : 4
apicid      : 3
initial apicid  : 3
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 6
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 3701.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 2
cpu cores   : 4
apicid      : 5
initial apicid  : 5
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 7
vendor_id   : GenuineIntel
cpu family  : 6
model       : 62
model name  : Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
stepping    : 4
microcode   : 0x416
cpu MHz     : 3701.000
cache size  : 10240 KB
physical id : 0
siblings    : 8
core id     : 3
cpu cores   : 4
apicid      : 7
initial apicid  : 7
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
bogomips    : 7400.38
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

Memory: 4k page, physical 49401832k(36075148k free), swap 2109436k(2109436k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (25.45-b02) for linux-amd64 JRE (1.8.0_45-b14), built on Apr 10 2015 10:07:45 by "java_re" with gcc 4.3.0 20080428 (Red Hat 4.3.0-8)

time: Fri May 29 11:42:32 2015
elapsed time: 9 seconds (0d 0h 0m 9s)
royerloic commented 9 years ago

Ok, this seems to be a problem with JOGL . Could you test this executable JAR: https://github.com/ClearVolume/ClearGL/releases/download/1.0.0/TestProg.jar (or if you prefer compile and run the corresponding code in ClearGL cleargl.testprog.JOGLTestProgram.java) It is a simple test JOGL program. If that fails we have to fill up a bug report upstream to the JOGL Team...

mabruce commented 9 years ago

The jar's trying to load 32 bit libraries: Exception in thread "main" java.lang.UnsatisfiedLinkError: /tmp/jogamp_0000/file_cache/jln5968353291559684597/jln8154034231802500972/libnativewindow_awt.so: /tmp/jogamp_0000/file_cache/jln5968353291559684597/jln8154034231802500972/libnativewindow_awt.so: wrong ELF class: ELFCLASS32 (Possible cause: architecture word width mismatch)

royerloic commented 9 years ago

Ok thanks! I think we are getting closer. It could be that we are packaging the wrong linux binaries - which makes no sense since we don't even ship the 32bit libs only the 64bit ones. Could you check if there is any JOGL jars installed somewhere in you JDK/JRE like in the ext folder? We are going to do more testing under linux to figure out what's going on. Now we have a good lead on the cause. Thanks!

skalarproduktraum commented 9 years ago

@mabruce: I just saw in your crashlog that you are using CUDA 7.0. Unfortunately, JCuda is currently stuck at 6.5... would you mind trying it with 6.5? OpenCL unfortunately is also affected by that as CUDA includes a significant part of the OpenCL libs...

mabruce commented 9 years ago

It's the driver that supports CUDA 7.0, the drivers are backwards compatible with older runtimes, JCuda is bundled with its own run runtime, and JCuda was updated to 7.0 on April 10.

fjug commented 9 years ago

I've tried to open an RGB image and did not get an exception. (Weather or not current behavior makes sense or not is a different discussion... it gets converted to a monochrome image and then displayed.)

Also I tried to open without open image which results in a sensible error message in an dialog window.

Should we close this issue or is some stuff with @mabruce still unresolved?

elimirks commented 8 years ago

I am also having it crash when I try to open an image stack:

% uname -a

Linux yellowarmadillo 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt11-1+deb8u3 (2015-08-04) x86_64 GNU/Linux

( I tried on an integrated Intel GPU so maybe that is what is causing this )

[ERROR] Cannot create module: de.mpicbg.jug.plugins.ClearVolumePlugin
org.scijava.module.ModuleException: org.scijava.InstantiableException: Class not found: de.mpicbg.jug.plugins.ClearVolumePlugin
    at org.scijava.command.CommandInfo.createModule(CommandInfo.java:320)
    at org.scijava.module.DefaultModuleService.createModule(DefaultModuleService.java:156)
    at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:195)
    at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:186)
    at org.scijava.module.DefaultModuleService.run(DefaultModuleService.java:171)
    at org.scijava.command.DefaultCommandService.run(DefaultCommandService.java:185)
    at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:270)
    at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:161)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:136)
    at ij.Executer.run(Executer.java:65)
    at java.lang.Thread.run(Thread.java:662)
Caused by: org.scijava.InstantiableException: Class not found: de.mpicbg.jug.plugins.ClearVolumePlugin
    at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:285)
    at org.scijava.command.CommandInfo.loadClass(CommandInfo.java:245)
    at org.scijava.command.CommandInfo.createModule(CommandInfo.java:314)
    ... 11 more

In the exception window:

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.6.0_24 [64-bit]; Linux 3.16.0-4-amd64; 41MB of 2391MB (1%)

java.lang.NullPointerException
    at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:270)
    at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:161)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:136)
    at ij.Executer.run(Executer.java:65)
    at java.lang.Thread.run(Thread.java:662)
ctrueden commented 8 years ago 
Caused by: org.scijava.InstantiableException: Class not found: de.mpicbg.jug.plugins.ClearVolumePlugin
    at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:285)

FYI, this same problem sprang up during the recent hackathon in Konstanz. By which I mean: the error regarding why a class cannot be loaded is currently incomplete, due to SciJava Common eating the cause rather than chaining it. I need to fix this in SJC; see scijava/scijava-common#219 for details.

skalarproduktraum commented 8 years ago

@elimirks: You are using Java 1.6, with which ClearVolume is not compatible (you need at least 1.8).

You can either:

Btw, what kind of Intel Integrated Graphics you have? With 3000, you are out of luck, but 4000 and upwards work without problems.

skalarproduktraum commented 8 years ago

@elimirks: We have just updated the plugin, so if you get a fresh Fiji from http://fiji.sc and activate the ClearVolume update site, it should work without problems. Please let us know if it works for you as well.

elimirks commented 8 years ago

@skalarproduktraum I downloaded the latest version of Fiji and the issue is fixed, but it is complaining about OpenCL now - I have an i5 2520M, so as you said, I guess I am out of luck with this computer.

skalarproduktraum commented 8 years ago

@elimirks: Yes, that processor has only the 3000, which we currently do not support due to only a weird set of datatypes being supported (see #41). Sorry!