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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

Error message preventing the 3D viewer to work #67

Open hadim opened 7 years ago

hadim commented 7 years ago

I am using a Fiji updated installation with the ClearVolume update site checked.

I am running Ubuntu 18.10 with kernel 4.13.0-16-generic on an Asus notebook laptop with the following graphic card: Intel(R) HD Graphics Haswell Ultrabook GT3 reserved

Here is the output of clinfo:

$ clinfo
X server found. dri2 connection failed! 
Number of platforms                               1
  Platform Name                                   Intel Gen OCL Driver
  Platform Vendor                                 Intel
  Platform Version                                OpenCL 2.0 beignet 1.3
  Platform Profile                                FULL_PROFILE
  Platform Extensions                             cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_byte_addressable_store cl_khr_3d_image_writes cl_khr_image2d_from_buffer cl_khr_depth_images cl_khr_spir cl_khr_icd cl_intel_accelerator cl_intel_subgroups cl_intel_subgroups_short cl_khr_gl_sharing
  Platform Extensions function suffix             Intel
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 

  Platform Name                                   Intel Gen OCL Driver
Number of devices                                 1
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
  Device Name                                     Intel(R) HD Graphics Haswell Ultrabook GT3 reserved
  Device Vendor                                   Intel
  Device Vendor ID                                0x8086
  Device Version                                  OpenCL 1.2 beignet 1.3
  Driver Version                                  1.3
  Device OpenCL C Version                         OpenCL C 1.2 beignet 1.3
  Device Type                                     GPU
  Device Profile                                  FULL_PROFILE
  Max compute units                               40
  Max clock frequency                             1000MHz
  Device Partition                                (core)
    Max number of sub-devices                     1
    Supported partition types                     None, None, None
  Max work item dimensions                        3
  Max work item sizes                             512x512x512
  Max work group size                             512
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
  Preferred work group size multiple              16
  Preferred / native vector sizes                 
    char                                                16 / 8       
    short                                                8 / 8       
    int                                                  4 / 4       
    long                                                 2 / 2       
    half                                                 0 / 8        (n/a)
    float                                                4 / 4       
    double                                               0 / 2        (n/a)
  Half-precision Floating-point support           (n/a)
  Single-precision Floating-point support         (core)
    Denormals                                     No
    Infinity and NANs                             Yes
    Round to nearest                              Yes
    Round to zero                                 No
    Round to infinity                             No
    IEEE754-2008 fused multiply-add               No
    Support is emulated in software               No
    Correctly-rounded divide and sqrt operations  No
  Double-precision Floating-point support         (n/a)
  Address bits                                    32, Little-Endian
  Global memory size                              2147483648 (2GiB)
  Error Correction support                        No
  Max memory allocation                           1610612736 (1.5GiB)
  Unified memory for Host and Device              Yes
  Minimum alignment for any data type             128 bytes
  Alignment of base address                       1024 bits (128 bytes)
  Global Memory cache type                        Read/Write
  Global Memory cache size                        8192
  Global Memory cache line                        64 bytes
  Image support                                   Yes
    Max number of samplers per kernel             16
    Max size for 1D images from buffer            65536 pixels
    Max 1D or 2D image array size                 2048 images
    Base address alignment for 2D image buffers   4096 bytes
    Pitch alignment for 2D image buffers          1 bytes
    Max 2D image size                             8192x8192 pixels
    Max 3D image size                             8192x8192x2048 pixels
    Max number of read image args                 128
    Max number of write image args                8
  Local memory type                               Local
  Local memory size                               65536 (64KiB)
  Max constant buffer size                        134217728 (128MiB)
  Max number of constant args                     8
  Max size of kernel argument                     1024
  Queue properties                                
    Out-of-order execution                        No
    Profiling                                     Yes
  Prefer user sync for interop                    Yes
  Profiling timer resolution                      80ns
  Execution capabilities                          
    Run OpenCL kernels                            Yes
    Run native kernels                            Yes
    SPIR versions                                 1.2
  printf() buffer size                            1048576 (1024KiB)
  Built-in kernels                                __cl_copy_region_align4;__cl_copy_region_align16;__cl_cpy_region_unalign_same_offset;__cl_copy_region_unalign_dst_offset;__cl_copy_region_unalign_src_offset;__cl_copy_buffer_rect;__cl_copy_image_1d_to_1d;__cl_copy_image_2d_to_2d;__cl_copy_image_3d_to_2d;__cl_copy_image_2d_to_3d;__cl_copy_image_3d_to_3d;__cl_copy_image_2d_to_buffer;__cl_copy_image_3d_to_buffer;__cl_copy_buffer_to_image_2d;__cl_copy_buffer_to_image_3d;__cl_fill_region_unalign;__cl_fill_region_align2;__cl_fill_region_align4;__cl_fill_region_align8_2;__cl_fill_region_align8_4;__cl_fill_region_align8_8;__cl_fill_region_align8_16;__cl_fill_region_align128;__cl_fill_image_1d;__cl_fill_image_1d_array;__cl_fill_image_2d;__cl_fill_image_2d_array;__cl_fill_image_3d;
  Device Available                                Yes
  Compiler Available                              Yes
  Linker Available                                Yes
  Device Extensions                               cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_byte_addressable_store cl_khr_3d_image_writes cl_khr_image2d_from_buffer cl_khr_depth_images cl_khr_spir cl_khr_icd cl_intel_accelerator cl_intel_subgroups cl_intel_subgroups_short cl_khr_gl_sharing

NULL platform behavior
  clGetPlatformInfo(NULL, CL_PLATFORM_NAME, ...)  Intel Gen OCL Driver
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
  clGetDeviceIDs(NULL, CL_DEVICE_TYPE_ALL, ...)   Success [Intel]
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
  clCreateContext(NULL, ...) [default]            Success [Intel]
X server found. dri2 connection failed! 
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_CPU)  No devices found in platform
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_GPU)  Success (1)
    Platform Name                                 Intel Gen OCL Driver
    Device Name                                   Intel(R) HD Graphics Haswell Ultrabook GT3 reserved
X server found. dri2 connection failed! 
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_ACCELERATOR)  No devices found in platform
X server found. dri2 connection failed! 
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_CUSTOM)  No devices found in platform
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
X server found. dri2 connection failed! 
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_ALL)  Success (1)
    Platform Name                                 Intel Gen OCL Driver
    Device Name                                   Intel(R) HD Graphics Haswell Ultrabook GT3 reserved

ICD loader properties
  ICD loader Name                                 OpenCL ICD Loader
  ICD loader Vendor                               OCL Icd free software
  ICD loader Version                              2.2.11
  ICD loader Profile                              OpenCL 2.1

And the error message trying to open ClearVolume on a Z stack:

ClearGLWindow: GLProfile[GL4/GL4.hw]
1.0
1.0
1.0
Linuxjava.lang.NullPointerException
    at badtrack.email.GmailBadTrackNotifier.getUniqueId(GmailBadTrackNotifier.java:73)
    at badtrack.email.GmailBadTrackNotifier.notify(GmailBadTrackNotifier.java:51)
    at badtrack.BadTrack$1.uncaughtException(BadTrack.java:198)
    at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1057)
    at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1052)
    at java.lang.Thread.dispatchUncaughtException(Thread.java:1952)
java.lang.NullPointerException
    at cleargl.GLTexture.<init>(GLTexture.java:141)
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.ensureTextureAllocated(ClearGLVolumeRenderer.java:630)
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.displayInternal(ClearGLVolumeRenderer.java:508)
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.display(ClearGLVolumeRenderer.java:490)
    at jogamp.opengl.GLDrawableHelper.displayImpl(GLDrawableHelper.java:692)
    at jogamp.opengl.GLDrawableHelper.display(GLDrawableHelper.java:674)
    at jogamp.opengl.GLAutoDrawableBase$2.run(GLAutoDrawableBase.java:443)
    at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1293)
    at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
    at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
    at jogamp.opengl.GLAutoDrawableBase.defaultWindowResizedOp(GLAutoDrawableBase.java:260)
    at com.jogamp.newt.opengl.GLWindow.access$200(GLWindow.java:119)
    at com.jogamp.newt.opengl.GLWindow$2.windowResized(GLWindow.java:141)
    at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4383)
    at jogamp.newt.WindowImpl.sendWindowEvent(WindowImpl.java:4317)
    at jogamp.newt.WindowImpl.sizeChanged(WindowImpl.java:4520)
    at jogamp.newt.WindowImpl.sizePosMaxInsetsVisibleChanged(WindowImpl.java:4864)
    at jogamp.newt.driver.x11.DisplayDriver.DispatchMessages0(Native Method)
    at jogamp.newt.driver.x11.DisplayDriver.dispatchMessagesNative(DisplayDriver.java:112)
    at jogamp.newt.DisplayImpl.dispatchMessages(DisplayImpl.java:753)
    at jogamp.newt.DisplayImpl$7.run(DisplayImpl.java:672)
    at jogamp.newt.DefaultEDTUtil$NEDT.run(DefaultEDTUtil.java:347)
java.lang.NullPointerException
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.displayInternal(ClearGLVolumeRenderer.java:571)
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.display(ClearGLVolumeRenderer.java:490)
    at jogamp.opengl.GLDrawableHelper.displayImpl(GLDrawableHelper.java:692)
    at jogamp.opengl.GLDrawableHelper.display(GLDrawableHelper.java:674)
    at jogamp.opengl.GLAutoDrawableBase$2.run(GLAutoDrawableBase.java:443)
    at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1293)
    at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
    at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
    at jogamp.opengl.GLAutoDrawableBase.defaultWindowRepaintOp(GLAutoDrawableBase.java:215)
    at com.jogamp.newt.opengl.GLWindow.access$100(GLWindow.java:119)
    at com.jogamp.newt.opengl.GLWindow$2.windowRepaint(GLWindow.java:136)
    at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4401)
    at jogamp.newt.WindowImpl.consumeEvent(WindowImpl.java:3372)
    at jogamp.newt.WindowImpl.doEvent(WindowImpl.java:3318)
    at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4715)
    at jogamp.newt.driver.x11.DisplayDriver.DispatchMessages0(Native Method)
    at jogamp.newt.driver.x11.DisplayDriver.dispatchMessagesNative(DisplayDriver.java:112)
    at jogamp.newt.DisplayImpl.dispatchMessages(DisplayImpl.java:753)
    at jogamp.newt.DisplayImpl$7.run(DisplayImpl.java:672)
    at jogamp.newt.DefaultEDTUtil$NEDT.run(DefaultEDTUtil.java:347)
java.lang.NullPointerException
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.displayInternal(ClearGLVolumeRenderer.java:571)
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.display(ClearGLVolumeRenderer.java:490)
    at jogamp.opengl.GLDrawableHelper.displayImpl(GLDrawableHelper.java:692)
    at jogamp.opengl.GLDrawableHelper.display(GLDrawableHelper.java:674)
    at jogamp.opengl.GLAutoDrawableBase$2.run(GLAutoDrawableBase.java:443)
    at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1293)
    at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
    at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
    at jogamp.opengl.GLAutoDrawableBase.defaultWindowRepaintOp(GLAutoDrawableBase.java:215)
    at com.jogamp.newt.opengl.GLWindow.access$100(GLWindow.java:119)
    at com.jogamp.newt.opengl.GLWindow$2.windowRepaint(GLWindow.java:136)
    at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4401)
    at jogamp.newt.WindowImpl.consumeEvent(WindowImpl.java:3372)
    at jogamp.newt.WindowImpl.doEvent(WindowImpl.java:3318)
    at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4715)
    at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4694)
    at com.jogamp.newt.opengl.GLWindow.windowRepaint(GLWindow.java:810)
    at com.jogamp.newt.awt.NewtCanvasAWT.paint(NewtCanvasAWT.java:732)
    at sun.awt.RepaintArea.paintComponent(RepaintArea.java:264)
    at sun.awt.X11.XRepaintArea.paintComponent(XRepaintArea.java:64)
    at sun.awt.RepaintArea.paint(RepaintArea.java:240)
    at sun.awt.X11.XComponentPeer.handleEvent(XComponentPeer.java:584)
    at java.awt.Component.dispatchEventImpl(Component.java:4967)
    at java.awt.Component.dispatchEvent(Component.java:4713)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
    at java.awt.EventQueue$4.run(EventQueue.java:731)
    at java.awt.EventQueue$4.run(EventQueue.java:729)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
javax.mail.AuthenticationFailedException: 534-5.7.14 <https://accounts.google.com/signin/continue?sarp=1&scc=1&plt=AKgnsbvs
534-5.7.14 jQsLXOP5FOWNL4F-8TgTN9-nT-uc_RZM2d5FvLV5x34RQ6-lYSMiSahqGeYY1-ue2M5Skj
534-5.7.14 hC7K22Yn0FxNKx5pdvgO8q4BEGt6KNFNfh6v7HHfiHxKcknZuzxacTnhxEJ07KN8rOHmdr
534-5.7.14 WgGt9nhqc-eZq-1pqRCLvi8DlFCh31WyTMbeZG8eJifciBwvR_2GlQTu_-CYhB74RTQseG
534-5.7.14 HbZqe9-hGPKLQMUkflsXfaX0O76V8> Please log in via your web browser and
534-5.7.14 then try again.
534-5.7.14  Learn more at
534 5.7.14  https://support.google.com/mail/answer/78754 k43sm8577251qtc.75 - gsmtp

    at com.sun.mail.smtp.SMTPTransport$Authenticator.authenticate(SMTPTransport.java:826)
    at com.sun.mail.smtp.SMTPTransport.authenticate(SMTPTransport.java:761)
    at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:685)
    at javax.mail.Service.connect(Service.java:317)
    at javax.mail.Service.connect(Service.java:176)
    at javax.mail.Service.connect(Service.java:125)
    at javax.mail.Transport.send0(Transport.java:253)
    at javax.mail.Transport.send(Transport.java:124)
    at badtrack.email.GmailClient.sendMessage(GmailClient.java:83)
    at badtrack.email.GmailBadTrackNotifier.notify(GmailBadTrackNotifier.java:65)
    at badtrack.BadTrack$1.uncaughtException(BadTrack.java:198)
    at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1057)
    at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1052)
    at java.lang.Thread.dispatchUncaughtException(Thread.java:1952)
com.jogamp.opengl.util.AnimatorBase$UncaughtAnimatorException: com.jogamp.opengl.GLException: Caught UnsatisfiedLinkError: Could not initialize native OpenCL library. Implementation library could not be loaded on thread SciJava-3a23140e-Thread-0-FPSAWTAnimator#00-Timer0
    at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:92)
    at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
    at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
    at java.util.TimerThread.mainLoop(Timer.java:555)
    at java.util.TimerThread.run(Timer.java:505)
Caused by: com.jogamp.opengl.GLException: Caught UnsatisfiedLinkError: Could not initialize native OpenCL library. Implementation library could not be loaded on thread SciJava-3a23140e-Thread-0-FPSAWTAnimator#00-Timer0
    at com.jogamp.opengl.GLException.newGLException(GLException.java:76)
    at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1327)
    at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
    at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
    at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
    ... 4 more
Caused by: java.lang.UnsatisfiedLinkError: Could not initialize native OpenCL library. Implementation library could not be loaded
    at org.jocl.LibInitializer.initNativeLibrary(LibInitializer.java:74)
    at org.jocl.CL.loadNativeLibrary(CL.java:66)
    at org.jocl.CL.<clinit>(CL.java:51)
    at clearcl.backend.jocl.ClearCLBackendJOCL.<clinit>(ClearCLBackendJOCL.java:61)
    at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30)
    at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65)
    at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91)
    at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
    at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
    at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
    at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
    at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
    at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
    at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
    ... 7 more

By the way what the status of the project? How does it compare to the still in development SciView.

Thank you.

HaaPut commented 6 years ago

@fjug @royerloic I get a similar error and some more...

ClearGLWindow: GLProfile[GL4bc/GL4bc.hw] 1.0 1.0 1.0 Linuxjava.lang.NullPointerException at badtrack.email.GmailBadTrackNotifier.getUniqueId(GmailBadTrackNotifier.java:73) at badtrack.email.GmailBadTrackNotifier.notify(GmailBadTrackNotifier.java:51) at badtrack.BadTrack$1.uncaughtException(BadTrack.java:198) at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1057) at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1052) at java.lang.Thread.dispatchUncaughtException(Thread.java:1952) java.lang.NullPointerException at cleargl.GLTexture.(GLTexture.java:141) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.ensureTextureAllocated(ClearGLVolumeRenderer.java:630) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.displayInternal(ClearGLVolumeRenderer.java:508) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.display(ClearGLVolumeRenderer.java:490) at jogamp.opengl.GLDrawableHelper.displayImpl(GLDrawableHelper.java:692) at jogamp.opengl.GLDrawableHelper.display(GLDrawableHelper.java:674) at jogamp.opengl.GLAutoDrawableBase$2.run(GLAutoDrawableBase.java:443) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1293) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at jogamp.opengl.GLAutoDrawableBase.defaultWindowResizedOp(GLAutoDrawableBase.java:260) at com.jogamp.newt.opengl.GLWindow.access$200(GLWindow.java:119) at com.jogamp.newt.opengl.GLWindow$2.windowResized(GLWindow.java:141) at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4383) at jogamp.newt.WindowImpl.sendWindowEvent(WindowImpl.java:4317) at jogamp.newt.WindowImpl.sizeChanged(WindowImpl.java:4520) at jogamp.newt.WindowImpl.sizePosMaxInsetsVisibleChanged(WindowImpl.java:4864) at jogamp.newt.driver.x11.DisplayDriver.DispatchMessages0(Native Method) at jogamp.newt.driver.x11.DisplayDriver.dispatchMessagesNative(DisplayDriver.java:112) at jogamp.newt.WindowImpl.waitForSize(WindowImpl.java:4534) at jogamp.newt.WindowImpl.access$600(WindowImpl.java:96) at jogamp.newt.WindowImpl$SetSizeAction.run(WindowImpl.java:1369) at jogamp.newt.DisplayImpl.runOnEDTIfAvail(DisplayImpl.java:450) at jogamp.newt.WindowImpl.runOnEDTIfAvail(WindowImpl.java:2782) at jogamp.newt.WindowImpl.setSize(WindowImpl.java:1394) at com.jogamp.newt.opengl.GLWindow.setSize(GLWindow.java:588) at jogamp.newt.awt.event.AWTParentWindowAdapter$1.run(AWTParentWindowAdapter.java:128) at com.jogamp.common.util.RunnableTask.run(RunnableTask.java:127) at jogamp.newt.DefaultEDTUtil$NEDT.run(DefaultEDTUtil.java:375) java.lang.NullPointerException at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.displayInternal(ClearGLVolumeRenderer.java:571) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.display(ClearGLVolumeRenderer.java:490) at jogamp.opengl.GLDrawableHelper.displayImpl(GLDrawableHelper.java:692) at jogamp.opengl.GLDrawableHelper.display(GLDrawableHelper.java:674) at jogamp.opengl.GLAutoDrawableBase$2.run(GLAutoDrawableBase.java:443) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1293) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at jogamp.opengl.GLAutoDrawableBase.defaultWindowRepaintOp(GLAutoDrawableBase.java:215) at com.jogamp.newt.opengl.GLWindow.access$100(GLWindow.java:119) at com.jogamp.newt.opengl.GLWindow$2.windowRepaint(GLWindow.java:136) at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4401) at jogamp.newt.WindowImpl.consumeEvent(WindowImpl.java:3372) at jogamp.newt.WindowImpl.doEvent(WindowImpl.java:3318) at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4715) at jogamp.newt.driver.x11.DisplayDriver.DispatchMessages0(Native Method) at jogamp.newt.driver.x11.DisplayDriver.dispatchMessagesNative(DisplayDriver.java:112) at jogamp.newt.WindowImpl.waitForSize(WindowImpl.java:4534) at jogamp.newt.WindowImpl.access$600(WindowImpl.java:96) at jogamp.newt.WindowImpl$SetSizeAction.run(WindowImpl.java:1369) at jogamp.newt.DisplayImpl.runOnEDTIfAvail(DisplayImpl.java:450) at jogamp.newt.WindowImpl.runOnEDTIfAvail(WindowImpl.java:2782) at jogamp.newt.WindowImpl.setSize(WindowImpl.java:1394) at com.jogamp.newt.opengl.GLWindow.setSize(GLWindow.java:588) at jogamp.newt.awt.event.AWTParentWindowAdapter$1.run(AWTParentWindowAdapter.java:128) at com.jogamp.common.util.RunnableTask.run(RunnableTask.java:127) at jogamp.newt.DefaultEDTUtil$NEDT.run(DefaultEDTUtil.java:375) java.lang.NullPointerException at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.displayInternal(ClearGLVolumeRenderer.java:571) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.display(ClearGLVolumeRenderer.java:490) at jogamp.opengl.GLDrawableHelper.displayImpl(GLDrawableHelper.java:692) at jogamp.opengl.GLDrawableHelper.display(GLDrawableHelper.java:674) at jogamp.opengl.GLAutoDrawableBase$2.run(GLAutoDrawableBase.java:443) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1293) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at jogamp.opengl.GLAutoDrawableBase.defaultWindowRepaintOp(GLAutoDrawableBase.java:215) at com.jogamp.newt.opengl.GLWindow.access$100(GLWindow.java:119) at com.jogamp.newt.opengl.GLWindow$2.windowRepaint(GLWindow.java:136) at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4401) at jogamp.newt.WindowImpl.consumeEvent(WindowImpl.java:3372) at jogamp.newt.WindowImpl.doEvent(WindowImpl.java:3318) at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4715) at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4694) at com.jogamp.newt.opengl.GLWindow.windowRepaint(GLWindow.java:810) at com.jogamp.newt.awt.NewtCanvasAWT.paint(NewtCanvasAWT.java:732) at sun.awt.RepaintArea.paintComponent(RepaintArea.java:264) at sun.awt.X11.XRepaintArea.paintComponent(XRepaintArea.java:64) at sun.awt.RepaintArea.paint(RepaintArea.java:240) at sun.awt.X11.XComponentPeer.handleEvent(XComponentPeer.java:584) at java.awt.Component.dispatchEventImpl(Component.java:4967) at java.awt.Component.dispatchEvent(Component.java:4713) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) java.lang.NullPointerException at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.displayInternal(ClearGLVolumeRenderer.java:571) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.display(ClearGLVolumeRenderer.java:490) at jogamp.opengl.GLDrawableHelper.displayImpl(GLDrawableHelper.java:692) at jogamp.opengl.GLDrawableHelper.display(GLDrawableHelper.java:674) at jogamp.opengl.GLAutoDrawableBase$2.run(GLAutoDrawableBase.java:443) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1293) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at jogamp.opengl.GLAutoDrawableBase.defaultWindowRepaintOp(GLAutoDrawableBase.java:215) at com.jogamp.newt.opengl.GLWindow.access$100(GLWindow.java:119) at com.jogamp.newt.opengl.GLWindow$2.windowRepaint(GLWindow.java:136) at jogamp.newt.WindowImpl.consumeWindowEvent(WindowImpl.java:4401) at jogamp.newt.WindowImpl.consumeEvent(WindowImpl.java:3372) at jogamp.newt.WindowImpl.doEvent(WindowImpl.java:3318) at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4715) at jogamp.newt.WindowImpl.windowRepaint(WindowImpl.java:4694) at com.jogamp.newt.opengl.GLWindow.windowRepaint(GLWindow.java:810) at com.jogamp.newt.awt.NewtCanvasAWT.paint(NewtCanvasAWT.java:732) at sun.awt.RepaintArea.paintComponent(RepaintArea.java:264) at sun.awt.X11.XRepaintArea.paintComponent(XRepaintArea.java:64) at sun.awt.RepaintArea.paint(RepaintArea.java:240) at sun.awt.X11.XComponentPeer.handleEvent(XComponentPeer.java:584) at java.awt.Component.dispatchEventImpl(Component.java:4967) at java.awt.Component.dispatchEvent(Component.java:4713) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) javax.mail.AuthenticationFailedException: 534-5.7.14 <https://accounts.google.com/signin/continue?sarp=1&scc=1&plt=AKgnsbvG 534-5.7.14 qXhC1VWQWzl86nSHyBx2qeHOA59XJjWI2U7ZV_WO2NZIaKi63suRGoVPHF70as0r9DaCNC 534-5.7.14 i9S3AuGzLTjKmXTgc6iQFjk3kEchYwtUuUREqGMHKaxxpi5T0lQ7V8tv11zciqTHYoCO8m 534-5.7.14 z8PWnAEv0Jdro8-1djmmQARkWTUIhmRvgWYhdGMILXwSoPsEy0OcU2_ZpmGvnyoCsMF1Yd 534-5.7.14 cKRH1mEoOUdiUt78dejsr_XaWvXN0> Please log in via your web browser and 534-5.7.14 then try again. 534-5.7.14 Learn more at 534 5.7.14 https://support.google.com/mail/answer/78754 k127-v6sm26374529qke.20 - gsmtp

at com.sun.mail.smtp.SMTPTransport$Authenticator.authenticate(SMTPTransport.java:826)
at com.sun.mail.smtp.SMTPTransport.authenticate(SMTPTransport.java:761)
at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:685)
at javax.mail.Service.connect(Service.java:317)
at javax.mail.Service.connect(Service.java:176)
at javax.mail.Service.connect(Service.java:125)
at javax.mail.Transport.send0(Transport.java:253)
at javax.mail.Transport.send(Transport.java:124)
at badtrack.email.GmailClient.sendMessage(GmailClient.java:83)
at badtrack.email.GmailBadTrackNotifier.notify(GmailBadTrackNotifier.java:65)
at badtrack.BadTrack$1.uncaughtException(BadTrack.java:198)
at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1057)
at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1052)
at java.lang.Thread.dispatchUncaughtException(Thread.java:1952)

com.jogamp.opengl.util.AnimatorBase$UncaughtAnimatorException: com.jogamp.opengl.GLException: Caught UnsatisfiedLinkError: Error while loading native library "JOCL_2_0_0-linux-x86_64" Operating system name: Linux Architecture : amd64 Architecture bit size: 64 ---(start of nested stack traces)--- Stack trace from the attempt to load the library as a file: java.lang.UnsatisfiedLinkError: no JOCL_2_0_0-linux-x86_64 in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at org.jocl.LibUtils.loadLibrary(LibUtils.java:136) at org.jocl.CL.loadNativeLibrary(CL.java:65) at org.jocl.CL.(CL.java:51) at clearcl.backend.jocl.ClearCLBackendJOCL.(ClearCLBackendJOCL.java:61) at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30) at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65) at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91) at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48) at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667) at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81) at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452) at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505) Stack trace from the attempt to load the library as a resource: java.lang.UnsatisfiedLinkError: /tmp/libJOCL_2_0_0-linux-x86_64.so: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version CXXABI_1.3.8' not found (required by /tmp/libJOCL_2_0_0-linux-x86_64.so) at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1938) at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1821) at java.lang.Runtime.load0(Runtime.java:809) at java.lang.System.load(System.java:1086) at org.jocl.LibUtils.loadLibraryResource(LibUtils.java:269) at org.jocl.LibUtils.loadLibrary(LibUtils.java:151) at org.jocl.CL.loadNativeLibrary(CL.java:65) at org.jocl.CL.<clinit>(CL.java:51) at clearcl.backend.jocl.ClearCLBackendJOCL.<clinit>(ClearCLBackendJOCL.java:61) at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30) at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65) at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91) at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48) at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667) at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81) at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452) at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505) ---(end of nested stack traces)--- on thread SciJava-2e1c3e0f-Thread-1-FPSAWTAnimator#00-Timer0 at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:92) at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452) at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505) Caused by: com.jogamp.opengl.GLException: Caught UnsatisfiedLinkError: Error while loading native library "JOCL_2_0_0-linux-x86_64" Operating system name: Linux Architecture : amd64 Architecture bit size: 64 ---(start of nested stack traces)--- Stack trace from the attempt to load the library as a file: java.lang.UnsatisfiedLinkError: no JOCL_2_0_0-linux-x86_64 in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at org.jocl.LibUtils.loadLibrary(LibUtils.java:136) at org.jocl.CL.loadNativeLibrary(CL.java:65) at org.jocl.CL.<clinit>(CL.java:51) at clearcl.backend.jocl.ClearCLBackendJOCL.<clinit>(ClearCLBackendJOCL.java:61) at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30) at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65) at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91) at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48) at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667) at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81) at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452) at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505) Stack trace from the attempt to load the library as a resource: java.lang.UnsatisfiedLinkError: /tmp/libJOCL_2_0_0-linux-x86_64.so: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: versionCXXABI_1.3.8' not found (required by /tmp/libJOCL_2_0_0-linux-x86_64.so) at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1938) at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1821) at java.lang.Runtime.load0(Runtime.java:809) at java.lang.System.load(System.java:1086) at org.jocl.LibUtils.loadLibraryResource(LibUtils.java:269) at org.jocl.LibUtils.loadLibrary(LibUtils.java:151) at org.jocl.CL.loadNativeLibrary(CL.java:65) at org.jocl.CL.(CL.java:51) at clearcl.backend.jocl.ClearCLBackendJOCL.(ClearCLBackendJOCL.java:61) at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30) at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65) at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91) at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48) at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667) at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81) at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452) at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505) ---(end of nested stack traces)--- on thread SciJava-2e1c3e0f-Thread-1-FPSAWTAnimator#00-Timer0 at com.jogamp.opengl.GLException.newGLException(GLException.java:76) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1327) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81) ... 4 more Caused by: java.lang.UnsatisfiedLinkError: Error while loading native library "JOCL_2_0_0-linux-x86_64" Operating system name: Linux Architecture : amd64 Architecture bit size: 64 ---(start of nested stack traces)--- Stack trace from the attempt to load the library as a file: java.lang.UnsatisfiedLinkError: no JOCL_2_0_0-linux-x86_64 in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at org.jocl.LibUtils.loadLibrary(LibUtils.java:136) at org.jocl.CL.loadNativeLibrary(CL.java:65) at org.jocl.CL.(CL.java:51) at clearcl.backend.jocl.ClearCLBackendJOCL.(ClearCLBackendJOCL.java:61) at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30) at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65) at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91) at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48) at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667) at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81) at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452) at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505) Stack trace from the attempt to load the library as a resource: java.lang.UnsatisfiedLinkError: /tmp/libJOCL_2_0_0-linux-x86_64.so: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /tmp/libJOCL_2_0_0-linux-x86_64.so) at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1938) at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1821) at java.lang.Runtime.load0(Runtime.java:809) at java.lang.System.load(System.java:1086) at org.jocl.LibUtils.loadLibraryResource(LibUtils.java:269) at org.jocl.LibUtils.loadLibrary(LibUtils.java:151) at org.jocl.CL.loadNativeLibrary(CL.java:65) at org.jocl.CL.(CL.java:51) at clearcl.backend.jocl.ClearCLBackendJOCL.(ClearCLBackendJOCL.java:61) at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30) at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65) at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91) at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48) at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130) at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644) at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667) at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431) at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291) at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147) at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759) at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81) at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452) at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505) ---(end of nested stack traces)---

at org.jocl.LibUtils.loadLibrary(LibUtils.java:185)
at org.jocl.CL.loadNativeLibrary(CL.java:65)
at org.jocl.CL.<clinit>(CL.java:51)
at clearcl.backend.jocl.ClearCLBackendJOCL.<clinit>(ClearCLBackendJOCL.java:61)
at clearcl.backend.ClearCLBackends.getBackendList(ClearCLBackends.java:30)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:65)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:91)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
... 7 more
fjug commented 6 years ago

@royerloic Is this the bug tracker???

royerloic commented 6 years ago

The bug tracker is not present fro some time already, must be an old version of CV in the wilde…

On 7. Jun 2018, at 09:30, Florian Jug notifications@github.com wrote:

@royerloic https://github.com/royerloic Is this the bug tracker???

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ClearVolume/ClearVolume/issues/67#issuecomment-395484191, or mute the thread https://github.com/notifications/unsubscribe-auth/AByMkoeMReSztUr_mbIuKNweBRCGyacJks5t6VVDgaJpZM4QamSL.

HaaPut commented 6 years ago

So..... is there no way to report an issue? If I have an old-wild version how can I get the latest-tame one? (I installed following instruction here ).

fjug commented 6 years ago

Our discussion referred to an old bug submission module we once have used. When did you install ClearVolume? If either the entire Fiji or only ClearVolume is ‘ancient’ you might try to download the latest Fiji and install ClearVolume as described on the page you pointed at. What happened?!?

HaaPut commented 6 years ago

My Fiji install is a few months old and ClearVolume is 1 day old.. I don't think that counts as ancient :P.. The install works fine but when I try to load a ( 3D ome-tiff image) volume it spits out the above error on the console. The GUI is displayed but the region for displaying volume is a dark void! ............................................................................................................ ClearVolume Version : 1.3.20 Fiji Properties... java.version: 1.8.0_66 java.vendor: Oracle Corporation os.name: Linux os.version: 4.4.0-124-generic os.arch: amd64 file.separator: / path.separator: : line.separator: user.name: . user.home: HOME user.dir: HOME user.country: file.encoding: UTF-8 java.home: HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre java.class.path: HOME/opt/Fiji.app/jars/imagej-launcher-4.0.5.jar java.ext.dirs: HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/ext:/usr/java/packages/lib/ext java.io.tmpdir: /tmp

IJ.getVersion: 2.0.0-rc-67/1.52c IJ.getFullVersion: 1.52c99 IJ.javaVersion: 8 IJ.isLinux: true IJ.isMacintosh: false IJ.isMacOSX: false IJ.isWindows: false IJ.is64Bit: true

All Java Properties ij.dir: HOME/opt/Fiji.app java.runtime.name: Java(TM) SE Runtime Environment fiji.dir: HOME/opt/Fiji.app imagej.dir: HOME/opt/Fiji.app sun.boot.library.path: HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/amd64 java.vm.version: 25.66-b17 fiji.defaultLibPath: lib/amd64/server/libjvm.so java.vm.vendor: Oracle Corporation java.vendor.url: http://java.oracle.com/ path.separator: : java.vm.name: Java HotSpot(TM) 64-Bit Server VM file.encoding.pkg: sun.io user.country: sun.os.patch.level: unknown java.vm.specification.name: Java Virtual Machine Specification user.dir: HOME java.runtime.version: 1.8.0_66-b17 java.awt.graphicsenv: sun.awt.X11GraphicsEnvironment java.endorsed.dirs: HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/endorsed os.arch: amd64 java.io.tmpdir: /tmp line.separator:

java.vm.specification.vendor: Oracle Corporation os.name: Linux sun.jnu.encoding: UTF-8 java.library.path: HOME/torch/install/lib:/usr/local/cuda/lib64::HOME/opt/Fiji.app/lib/linux64:HOME/opt/Fiji.app/mm/linux64 sun.awt.enableExtraMouseButtons: true java.specification.name: Java Platform API Specification java.class.version: 52.0 sun.management.compiler: HotSpot 64-Bit Tiered Compilers os.version: 4.4.0-124-generic user.home: HOME user.timezone: java.awt.printerjob: sun.print.PSPrinterJob file.encoding: UTF-8 java.specification.version: 1.8 plugins.dir: HOME/opt/Fiji.app java.class.path: HOME/opt/Fiji.app/jars/imagej-launcher-4.0.5.jar user.name: java.vm.specification.version: 1.8 java.home:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre sun.arch.data.model: 64 user.language: en java.specification.vendor: Oracle Corporation awt.toolkit: sun.awt.X11.XToolkit java.vm.info: mixed mode java.version: 1.8.0_66 java.ext.dirs: HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/ext:/usr/java/packages/lib/ext sun.boot.class.path: HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/resources.jar:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/rt.jar:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/sunrsasign.jar:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/jsse.jar:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/jce.jar:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/charsets.jar:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/jfr.jar:HOME/opt/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/classes java.vendor: Oracle Corporation ij.executable: HOME/opt/Fiji.app/ImageJ-linux64 python.cachedir.skip: true file.separator: / java.vendor.url.bug: http://bugreport.sun.com/bugreport/ sun.font.fontmanager: sun.awt.X11FontManager sun.io.unicode.encoding: UnicodeLittle sun.cpu.endian: little sun.desktop: gnome fiji.executable: HOME/opt/Fiji.app/ImageJ-linux64 sun.cpu.isalist:

.................................................................................... If you need more details please let me know.

skalarproduktraum commented 6 years ago

@fjug @royerloic,

could it be that the latest change to the update site ate some dependencies? @HaaPut's error is looking as if a dependency JAR for JOCL is missing. Plus, there's also BadTrack there, which should have been gone since quite a bit.

fjug commented 6 years ago

@skalarproduktraum On the update site I've only placed the new (and fixed) clearvolume-imglib2 bridge. Maybe while uploading I removed some dependencies within the updater, but why do you think it might cause this problem? @HaaPut I would love if you could download a fresh Fiji and then activate the ClearVolume update site. It would save us a lot of digging time if it would turn out that it simply worked then. (Ideally you'd not even turn on any other update site before testing, only ClearVolume...)

Thanks to both of you, Florian

skalarproduktraum commented 6 years ago

@fjug Because the bottom-most error in the stack trace is a UnsatisfiedLinkError bringing me to ... @HaaPut, I've just seen a piece that I had missed in the stack trace before, namely `

java.lang.UnsatisfiedLinkError: /tmp/libJOCL_2_0_0-linux-x86_64.so: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /tmp/libJOCL_2_0_0-linux-x86_64.so)

Apparently, the JOCL .so it's shipping is slightly old, that ABI version is from GCC 4.9... I guess there's two options here:

HaaPut commented 6 years ago

@skalarproduktraum updating GCC is not a feasible option for me. I can try a fresh install of fiji if you think that may help @fjug . Note: I have been regularly updating my fiji install.. my current version is: IJ.getVersion: 2.0.0-rc-67/1.52c IJ.getFullVersion: 1.52c99 ClearVolume Version : 1.3.20