'Contour Plot' produces Exception

Question

'Contour Plot' produces Exception

cbroker1 opened this issue 2 years ago · comments

Carl Broker commented 2 years ago

Describe the bug
Attempt to run Contour Plot, fails, with Terminal output of error.

To Reproduce
Steps to reproduce the behavior:

Unzip `VERDI_2.1.4_win64_20220526.zip'
Load model data "CCTM46_P16.base02a.36k.O3Max" to VERDI
Add 'NO[1]' to Formulas tab
See error below

Expected behavior
A contour plot.

Screenshots
Windows 11

Linux

Desktop (please complete the following information):

OS: Windows 11 Home (10.0.22000 Build 22000)
OS: Ubuntu (20.04)

Yadong Xu · Answer 1 · Tue Jun 07 2022 03:50:40 GMT+0800 (China Standard Time)

Retested with VERDI_2.1.4_linux64_20220526.tar.gz on Atmos, got similar error messages as @cbroker1 reported on Windows build.

Liz Adams · Answer 2 · Thu Jun 09 2022 03:44:22 GMT+0800 (China Standard Time)

I tested using MacOS, and was able to create the contour plot, but I obtained alot of error messages at the console.
The file used for testing must have vertical layers.

./verdi.sh

Selected CCTM46_P16.baseO2a.36k.O3MAX

Selected NO

Clicked on Contour Plot

The contour plot takes a bit of time to display.

Console error messages:

Java HotSpot(TM) 64-Bit Server VM warning: Ignoring option --illegal-access=permit; support was removed in 17.0
Caught AppContextInfo(Bug 1004) InaccessibleObjectException: Unable to make public static sun.awt.AppContext sun.awt.AppContext.getAppContext() accessible: module java.desktop does not "exports sun.awt" to unnamed module @6a472554 on thread J3D-Renderer-1
    [0]: java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
    [1]: java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
    [2]: java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199)
    [3]: java.base/java.lang.reflect.Method.setAccessible(Method.java:193)
    [4]: com.jogamp.nativewindow.awt.AppContextInfo$1$1.run(AppContextInfo.java:40)
    [5]: com.jogamp.common.util.UnsafeUtil.doWithoutIllegalAccessLogger(UnsafeUtil.java:219)
    [6]: com.jogamp.nativewindow.awt.AppContextInfo$1.run(AppContextInfo.java:34)
    [7]: java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
    [8]: com.jogamp.nativewindow.awt.AppContextInfo.<clinit>(AppContextInfo.java:31)
    [9]: com.jogamp.nativewindow.awt.JAWTWindow.<init>(JAWTWindow.java:128)
    [10]: jogamp.nativewindow.jawt.macosx.MacOSXJAWTWindow.<init>(MacOSXJAWTWindow.java:79)
    [11]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    [12]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    [13]: java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    [14]: java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    [15]: java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
    [16]: jogamp.nativewindow.NativeWindowFactoryImpl.getAWTNativeWindow(NativeWindowFactoryImpl.java:105)
    [17]: jogamp.nativewindow.NativeWindowFactoryImpl.getNativeWindowImpl(NativeWindowFactoryImpl.java:66)
    [18]: com.jogamp.nativewindow.NativeWindowFactory.getNativeWindow(NativeWindowFactory.java:654)
    [19]: org.jogamp.java3d.JoglPipeline$QueryCanvas.addNotify(JoglPipeline.java:8665)
    [20]: java.desktop/java.awt.Container.addNotify(Container.java:2804)
    [21]: java.desktop/java.awt.Window.addNotify(Window.java:791)
    [22]: java.desktop/java.awt.Dialog.addNotify(Dialog.java:770)
    [23]: java.desktop/java.awt.Dialog.conditionalShow(Dialog.java:917)
    [24]: java.desktop/java.awt.Dialog.show(Dialog.java:1048)
    [25]: java.desktop/java.awt.Component.show(Component.java:1728)
    [26]: java.desktop/java.awt.Component.setVisible(Component.java:1675)
    [27]: java.desktop/java.awt.Window.setVisible(Window.java:1036)
    [28]: java.desktop/java.awt.Dialog.setVisible(Dialog.java:1016)
    [29]: org.jogamp.java3d.JoglPipeline.getBestConfiguration(JoglPipeline.java:8439)
    [30]: org.jogamp.java3d.Renderer.doWork(Renderer.java:497)
    [31]: org.jogamp.java3d.J3dThread.run(J3dThread.java:271)
Caught AppContextInfo(Bug 1004) IllegalAccessException: class com.jogamp.nativewindow.awt.AppContextInfo cannot access class sun.awt.AppContext (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @6a472554 on thread J3D-Renderer-1
    [0]: java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
    [1]: java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
    [2]: java.base/java.lang.reflect.Method.invoke(Method.java:560)
    [3]: com.jogamp.nativewindow.awt.AppContextInfo.fetchAppContext(AppContextInfo.java:191)
    [4]: com.jogamp.nativewindow.awt.AppContextInfo.update(AppContextInfo.java:135)
    [5]: com.jogamp.nativewindow.awt.AppContextInfo.<init>(AppContextInfo.java:50)
    [6]: com.jogamp.nativewindow.awt.JAWTWindow.<init>(JAWTWindow.java:128)
    [7]: jogamp.nativewindow.jawt.macosx.MacOSXJAWTWindow.<init>(MacOSXJAWTWindow.java:79)
    [8]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    [9]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    [10]: java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    [11]: java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    [12]: java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
    [13]: jogamp.nativewindow.NativeWindowFactoryImpl.getAWTNativeWindow(NativeWindowFactoryImpl.java:105)
    [14]: jogamp.nativewindow.NativeWindowFactoryImpl.getNativeWindowImpl(NativeWindowFactoryImpl.java:66)
    [15]: com.jogamp.nativewindow.NativeWindowFactory.getNativeWindow(NativeWindowFactory.java:654)
    [16]: org.jogamp.java3d.JoglPipeline$QueryCanvas.addNotify(JoglPipeline.java:8665)
    [17]: java.desktop/java.awt.Container.addNotify(Container.java:2804)
    [18]: java.desktop/java.awt.Window.addNotify(Window.java:791)
    [19]: java.desktop/java.awt.Dialog.addNotify(Dialog.java:770)
    [20]: java.desktop/java.awt.Dialog.conditionalShow(Dialog.java:917)
    [21]: java.desktop/java.awt.Dialog.show(Dialog.java:1048)
    [22]: java.desktop/java.awt.Component.show(Component.java:1728)
    [23]: java.desktop/java.awt.Component.setVisible(Component.java:1675)
    [24]: java.desktop/java.awt.Window.setVisible(Window.java:1036)
    [25]: java.desktop/java.awt.Dialog.setVisible(Dialog.java:1016)
    [26]: org.jogamp.java3d.JoglPipeline.getBestConfiguration(JoglPipeline.java:8439)
    [27]: org.jogamp.java3d.Renderer.doWork(Renderer.java:497)
    [28]: org.jogamp.java3d.J3dThread.run(J3dThread.java:271)
Caught AppContextInfo(Bug 1004) IllegalAccessException: class com.jogamp.nativewindow.awt.AppContextInfo cannot access class sun.awt.AppContext (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @6a472554 on thread AppKit Thread
    [0]: java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
    [1]: java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
    [2]: java.base/java.lang.reflect.Method.invoke(Method.java:560)
    [3]: com.jogamp.nativewindow.awt.AppContextInfo.fetchAppContext(AppContextInfo.java:191)
    [4]: com.jogamp.nativewindow.awt.AppContextInfo.update(AppContextInfo.java:135)
    [5]: com.jogamp.nativewindow.awt.AppContextInfo.invokeOnAppContextThread(AppContextInfo.java:107)
    [6]: com.jogamp.nativewindow.awt.JAWTWindow.attachSurfaceLayer(JAWTWindow.java:492)
    [7]: jogamp.opengl.macosx.cgl.MacOSXCGLContext$NSOpenGLImpl$AttachGLLayerCmd.run(MacOSXCGLContext.java:821)
    [8]: com.jogamp.common.util.RunnableTask.run(RunnableTask.java:125)
Caught AppContextInfo(Bug 1004) IllegalAccessException: class com.jogamp.nativewindow.awt.AppContextInfo cannot access class sun.awt.AppContext (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @6a472554 on thread J3D-Renderer-1
    [0]: java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
    [1]: java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
    [2]: java.base/java.lang.reflect.Method.invoke(Method.java:560)
    [3]: com.jogamp.nativewindow.awt.AppContextInfo.fetchAppContext(AppContextInfo.java:191)
    [4]: com.jogamp.nativewindow.awt.AppContextInfo.update(AppContextInfo.java:135)
    [5]: com.jogamp.nativewindow.awt.AppContextInfo.<init>(AppContextInfo.java:50)
    [6]: com.jogamp.nativewindow.awt.JAWTWindow.<init>(JAWTWindow.java:128)
    [7]: jogamp.nativewindow.jawt.macosx.MacOSXJAWTWindow.<init>(MacOSXJAWTWindow.java:79)
    [8]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    [9]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    [10]: java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    [11]: java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    [12]: java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
    [13]: jogamp.nativewindow.NativeWindowFactoryImpl.getAWTNativeWindow(NativeWindowFactoryImpl.java:105)
    [14]: jogamp.nativewindow.NativeWindowFactoryImpl.getNativeWindowImpl(NativeWindowFactoryImpl.java:66)
    [15]: com.jogamp.nativewindow.NativeWindowFactory.getNativeWindow(NativeWindowFactory.java:654)
    [16]: org.jogamp.java3d.JoglPipeline$QueryCanvas.addNotify(JoglPipeline.java:8665)
    [17]: java.desktop/java.awt.Container.addNotify(Container.java:2804)
    [18]: java.desktop/java.awt.Window.addNotify(Window.java:791)
    [19]: java.desktop/java.awt.Dialog.addNotify(Dialog.java:770)
    [20]: java.desktop/java.awt.Dialog.conditionalShow(Dialog.java:917)
    [21]: java.desktop/java.awt.Dialog.show(Dialog.java:1048)
    [22]: java.desktop/java.awt.Component.show(Component.java:1728)
    [23]: java.desktop/java.awt.Component.setVisible(Component.java:1675)
    [24]: java.desktop/java.awt.Window.setVisible(Window.java:1036)
    [25]: java.desktop/java.awt.Dialog.setVisible(Dialog.java:1016)
    [26]: org.jogamp.java3d.JoglPipeline.createQueryContext(JoglPipeline.java:6572)
    [27]: org.jogamp.java3d.Canvas3D.createQueryContext(Canvas3D.java:4650)
    [28]: org.jogamp.java3d.Canvas3D.createQueryContext(Canvas3D.java:3643)
    [29]: org.jogamp.java3d.Renderer.doWork(Renderer.java:462)
    [30]: org.jogamp.java3d.J3dThread.run(J3dThread.java:271)
Caught AppContextInfo(Bug 1004) IllegalAccessException: class com.jogamp.nativewindow.awt.AppContextInfo cannot access class sun.awt.AppContext (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @6a472554 on thread AppKit Thread
    [0]: java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
    [1]: java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
    [2]: java.base/java.lang.reflect.Method.invoke(Method.java:560)
    [3]: com.jogamp.nativewindow.awt.AppContextInfo.fetchAppContext(AppContextInfo.java:191)
    [4]: com.jogamp.nativewindow.awt.AppContextInfo.update(AppContextInfo.java:135)
    [5]: com.jogamp.nativewindow.awt.AppContextInfo.invokeOnAppContextThread(AppContextInfo.java:107)
    [6]: com.jogamp.nativewindow.awt.JAWTWindow.attachSurfaceLayer(JAWTWindow.java:492)
    [7]: jogamp.opengl.macosx.cgl.MacOSXCGLContext$NSOpenGLImpl$AttachGLLayerCmd.run(MacOSXCGLContext.java:821)
    [8]: com.jogamp.common.util.RunnableTask.run(RunnableTask.java:125)
Caught AppContextInfo(Bug 1004) IllegalAccessException: class com.jogamp.nativewindow.awt.AppContextInfo cannot access class sun.awt.AppContext (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @6a472554 on thread J3D-Renderer-1
    [0]: java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
    [1]: java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
    [2]: java.base/java.lang.reflect.Method.invoke(Method.java:560)
    [3]: com.jogamp.nativewindow.awt.AppContextInfo.fetchAppContext(AppContextInfo.java:191)
    [4]: com.jogamp.nativewindow.awt.AppContextInfo.update(AppContextInfo.java:135)
    [5]: com.jogamp.nativewindow.awt.AppContextInfo.<init>(AppContextInfo.java:50)
    [6]: com.jogamp.nativewindow.awt.JAWTWindow.<init>(JAWTWindow.java:128)
    [7]: jogamp.nativewindow.jawt.macosx.MacOSXJAWTWindow.<init>(MacOSXJAWTWindow.java:79)
    [8]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    [9]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    [10]: java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    [11]: java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    [12]: java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
    [13]: jogamp.nativewindow.NativeWindowFactoryImpl.getAWTNativeWindow(NativeWindowFactoryImpl.java:105)
    [14]: jogamp.nativewindow.NativeWindowFactoryImpl.getNativeWindowImpl(NativeWindowFactoryImpl.java:66)
    [15]: com.jogamp.nativewindow.NativeWindowFactory.getNativeWindow(NativeWindowFactory.java:654)
    [16]: org.jogamp.java3d.JoglPipeline.createNewContext(JoglPipeline.java:6397)
    [17]: org.jogamp.java3d.Canvas3D.createNewContext(Canvas3D.java:4643)
    [18]: org.jogamp.java3d.Canvas3D.createNewContext(Canvas3D.java:2389)
    [19]: org.jogamp.java3d.Renderer.doWork(Renderer.java:938)
    [20]: org.jogamp.java3d.J3dThread.run(J3dThread.java:271)
Caught AppContextInfo(Bug 1004) IllegalAccessException: class com.jogamp.nativewindow.awt.AppContextInfo cannot access class sun.awt.AppContext (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @6a472554 on thread AppKit Thread
    [0]: java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
    [1]: java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
    [2]: java.base/java.lang.reflect.Method.invoke(Method.java:560)
    [3]: com.jogamp.nativewindow.awt.AppContextInfo.fetchAppContext(AppContextInfo.java:191)
    [4]: com.jogamp.nativewindow.awt.AppContextInfo.update(AppContextInfo.java:135)
    [5]: com.jogamp.nativewindow.awt.AppContextInfo.invokeOnAppContextThread(AppContextInfo.java:107)
    [6]: com.jogamp.nativewindow.awt.JAWTWindow.attachSurfaceLayer(JAWTWindow.java:492)
    [7]: jogamp.opengl.macosx.cgl.MacOSXCGLContext$NSOpenGLImpl$AttachGLLayerCmd.run(MacOSXCGLContext.java:821)
    [8]: com.jogamp.common.util.RunnableTask.run(RunnableTask.java:125)

Yadong Xu · Answer 3 · Fri Jul 08 2022 04:49:41 GMT+0800 (China Standard Time)

Retested with VERDI_2.1.4_linux64_20220706.tar.gz on Atmos, found that this issue has not resolved.
No scatter plot was displayed, lots of error messages showed up in the command window (see descriptions for issue #184).

Yadong Xu · Answer 4 · Sat Jul 09 2022 01:43:11 GMT+0800 (China Standard Time)

Retested with VERDI_2.1.4_win64_20220706.zip on a Windows 10 PC, was able to create the contour plot and no error messages showed up in the command window.

dkang2 · Answer 5 · Mon Jul 11 2022 22:29:32 GMT+0800 (China Standard Time)

The Contour plot doesn't work on Linux (tested on Atmos) either for the July 7th build. When I click the Contour Plot button, it generated the following exceptions and no plot shown.
Java HotSpot(TM) 64-Bit Server VM warning: Ignoring option --illegal-access=permit; support was removed in 17.0
Caught AppContextInfo(Bug 1004) InaccessibleObjectException: Unable to make public static sun.awt.AppContext sun.awt.AppContext.getAppContext() accessible: module java.desktop does not "exports sun.awt" to unnamed module @3d36e4cd on thread J3D-Renderer-1
[0]: java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
[1]: java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
[2]: java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199)
[3]: java.base/java.lang.reflect.Method.setAccessible(Method.java:193)
[4]: com.jogamp.nativewindow.awt.AppContextInfo$1$1.run(AppContextInfo.java:40)
[5]: com.jogamp.common.util.UnsafeUtil.doWithoutIllegalAccessLogger(UnsafeUtil.java:219)
[6]: com.jogamp.nativewindow.awt.AppContextInfo$1.run(AppContextInfo.java:34)
[7]: java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
[8]: com.jogamp.nativewindow.awt.AppContextInfo.(AppContextInfo.java:31)
[9]: com.jogamp.nativewindow.awt.JAWTWindow.(JAWTWindow.java:128)
[10]: jogamp.nativewindow.jawt.x11.X11JAWTWindow.(X11JAWTWindow.java:60)
[11]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[12]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
[13]: java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[14]: java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
[15]: java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
[16]: jogamp.nativewindow.NativeWindowFactoryImpl.getAWTNativeWindow(NativeWindowFactoryImpl.java:105)
[17]: jogamp.nativewindow.NativeWindowFactoryImpl.getNativeWindowImpl(NativeWindowFactoryImpl.java:66)
[18]: com.jogamp.nativewindow.NativeWindowFactory.getNativeWindow(NativeWindowFactory.java:654)
[19]: org.jogamp.java3d.JoglPipeline$QueryCanvas.addNotify(JoglPipeline.java:8665)
[20]: java.desktop/java.awt.Container.addNotify(Container.java:2804)
[21]: java.desktop/java.awt.Window.addNotify(Window.java:791)
[22]: java.desktop/java.awt.Dialog.addNotify(Dialog.java:770)
[23]: java.desktop/java.awt.Dialog.conditionalShow(Dialog.java:917)
[24]: java.desktop/java.awt.Dialog.show(Dialog.java:1048)
[25]: java.desktop/java.awt.Component.show(Component.java:1728)
[26]: java.desktop/java.awt.Component.setVisible(Component.java:1675)
[27]: java.desktop/java.awt.Window.setVisible(Window.java:1036)
[28]: java.desktop/java.awt.Dialog.setVisible(Dialog.java:1016)
[29]: org.jogamp.java3d.JoglPipeline.getBestConfiguration(JoglPipeline.java:8439)
[30]: org.jogamp.java3d.Renderer.doWork(Renderer.java:497)
[31]: org.jogamp.java3d.J3dThread.run(J3dThread.java:271)
Caught AppContextInfo(Bug 1004) IllegalAccessException: class com.jogamp.nativewindow.awt.AppContextInfo cannot access class sun.awt.AppContext (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @3d36e4cd on thread J3D-Renderer-1
[0]: java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
[1]: java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
[2]: java.base/java.lang.reflect.Method.invoke(Method.java:560)
[3]: com.jogamp.nativewindow.awt.AppContextInfo.fetchAppContext(AppContextInfo.java:191)
[4]: com.jogamp.nativewindow.awt.AppContextInfo.update(AppContextInfo.java:135)
[5]: com.jogamp.nativewindow.awt.AppContextInfo.(AppContextInfo.java:50)
[6]: com.jogamp.nativewindow.awt.JAWTWindow.(JAWTWindow.java:128)
[7]: jogamp.nativewindow.jawt.x11.X11JAWTWindow.(X11JAWTWindow.java:60)
[8]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[9]: java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
[10]: java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[11]: java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
[12]: java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
[13]: jogamp.nativewindow.NativeWindowFactoryImpl.getAWTNativeWindow(NativeWindowFactoryImpl.java:105)
[14]: jogamp.nativewindow.NativeWindowFactoryImpl.getNativeWindowImpl(NativeWindowFactoryImpl.java:66)
[15]: com.jogamp.nativewindow.NativeWindowFactory.getNativeWindow(NativeWindowFactory.java:654)
[16]: org.jogamp.java3d.JoglPipeline$QueryCanvas.addNotify(JoglPipeline.java:8665)
[17]: java.desktop/java.awt.Container.addNotify(Container.java:2804)
[18]: java.desktop/java.awt.Window.addNotify(Window.java:791)
[19]: java.desktop/java.awt.Dialog.addNotify(Dialog.java:770)
[20]: java.desktop/java.awt.Dialog.conditionalShow(Dialog.java:917)
[21]: java.desktop/java.awt.Dialog.show(Dialog.java:1048)
[22]: java.desktop/java.awt.Component.show(Component.java:1728)
[23]: java.desktop/java.awt.Component.setVisible(Component.java:1675)
[24]: java.desktop/java.awt.Window.setVisible(Window.java:1036)
[25]: java.desktop/java.awt.Dialog.setVisible(Dialog.java:1016)
[26]: org.jogamp.java3d.JoglPipeline.getBestConfiguration(JoglPipeline.java:8439)
[27]: org.jogamp.java3d.Renderer.doWork(Renderer.java:497)
[28]: org.jogamp.java3d.J3dThread.run(J3dThread.java:271)
Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: java.lang.IllegalAccessException: class org.jogamp.java3d.JoglPipeline cannot access class sun.awt.X11GraphicsDevice (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @3d36e4cd
at org.jogamp.java3d.JoglPipeline.getScreen(JoglPipeline.java:8614)
at org.jogamp.java3d.Screen3D.(Screen3D.java:354)
at org.jogamp.java3d.Canvas3D.(Canvas3D.java:1123)
at org.jogamp.java3d.Canvas3D.(Canvas3D.java:1025)
at org.jogamp.java3d.Canvas3D.(Canvas3D.java:989)
at visad.java3d.VisADCanvasJ3D.(VisADCanvasJ3D.java:214)
at anl.verdi.plot.util.VerdiCanvas3D.(VerdiCanvas3D.java:35)
at anl.verdi.plot.types.Contour3D.(Contour3D.java:281)
at anl.verdi.plot.gui.PlotFactory.getPlot(PlotFactory.java:119)
at anl.verdi.plot.gui.PlotFactory.getPlot(PlotFactory.java:82)
at anl.verdi.plot.gui.DefaultPlotCreator.doCreatePlot(DefaultPlotCreator.java:48)
at anl.verdi.plot.gui.AbstractPlotCreator.createPlot(AbstractPlotCreator.java:39)
at anl.verdi.plot.gui.action.Contour3DPlot.actionPerformed(Contour3DPlot.java:22)
at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2313)
at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279)
at java.desktop/java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:297)
at java.desktop/java.awt.Component.processMouseEvent(Component.java:6626)
at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3389)
at java.desktop/java.awt.Component.processEvent(Component.java:6391)
at java.desktop/java.awt.Container.processEvent(Container.java:2266)
at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5001)
at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833)
at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:97)
at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:746)
at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:744)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:743)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Caused by: java.lang.IllegalAccessException: class org.jogamp.java3d.JoglPipeline cannot access class sun.awt.X11GraphicsDevice (in module java.desktop) because module java.desktop does not export sun.awt to unnamed module @3d36e4cd
at java.base/jdk.internal.reflect.Reflection.newIllegalAccessException(Reflection.java:392)
at java.base/java.lang.reflect.AccessibleObject.checkAccess(AccessibleObject.java:674)
at java.base/java.lang.reflect.Method.invoke(Method.java:560)
at org.jogamp.java3d.JoglPipeline.getScreen(JoglPipeline.java:8612)

systemsgo · Answer 6 · Tue Jul 19 2022 02:08:22 GMT+0800 (China Standard Time)

This is fixed in the most recent build.

dkang2 · Answer 7 · Tue Jul 19 2022 03:36:56 GMT+0800 (China Standard Time)

I tested on Atmos. Yes, the problem has been fixed. But I found another issue that doesn't directly relate to the current issue.
The issue is: after the contour plot was produced, I tried to configure the scale for the contour plot by clicking on the "Configure" then "Configure Plot", at the pop-up window, I clicked "Color Map", and tried to rebuild the color scales, it failed (no response). For other options, such as "Titles", "Labels", it worked well. Don't know if this should be open as a separate issue or continue this one?

Yadong Xu · Answer 8 · Wed Jul 20 2022 02:10:06 GMT+0800 (China Standard Time)

I tested on Atmos. Yes, the problem has been fixed. But I found another issue that doesn't directly relate to the current issue. The issue is: after the contour plot was produced, I tried to configure the scale for the contour plot by clicking on the "Configure" then "Configure Plot", at the pop-up window, I clicked "Color Map", and tried to rebuild the color scales, it failed (no response). For other options, such as "Titles", "Labels", it worked well. Don't know if this should be open as a separate issue or continue this one?

Hi Daiwen,
I tested VERDI_2.1.4_linux64_20220718.tar.gz on Atmos, found that the contour plot worked properly and could not re-produce the new issue of using "Configure Plot" to rebuild the color scales. I was able to change the color scale to a customized one shown as below:

the automatic color scale
the customized color scale

dkang2 · Answer 9 · Wed Jul 20 2022 02:19:26 GMT+0800 (China Standard Time)

Hi Yadong, It seemed that the customized scale was changed in the configure window, but the color plot didn't seem to have changed. See the legend bar and the Z-axis. The situation that I found this problem is when I try to make a plot over 3-D field, in that some layers have higher values, but some layers have very small values. When I try to visualize the small value by changing the scales, but it didn't show up. Thanks. From: Yadong Xu ***@***.***> Sent: Tuesday, July 19, 2022 2:10 PM To: CEMPD/VERDI ***@***.***> Cc: Kang, Daiwen ***@***.***>; Comment ***@***.***> Subject: Re: [CEMPD/VERDI] 'Contour Plot' produces Exception (Issue #299) I tested on Atmos. Yes, the problem has been fixed. But I found another issue that doesn't directly relate to the current issue. The issue is: after the contour plot was produced, I tried to configure the scale for the contour plot by clicking on the "Configure" then "Configure Plot", at the pop-up window, I clicked "Color Map", and tried to rebuild the color scales, it failed (no response). For other options, such as "Titles", "Labels", it worked well. Don't know if this should be open as a separate issue or continue this one? Hi Daiwen, I tested VERDI_2.1.4_linux64_20220718.tar.gz on Atmos, found that the contour plot worked properly and could not re-produce the new issue of using "Configure Plot" to rebuild the color scales. I was able to change the color scale to a customized one shown as below: 1. the automatic color scale [VERDI_testing_issue_299_1]<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F73186639%2F179819469-e238f6b4-ec56-44c3-bf64-b64c5abf6e54.png&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327518972%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nBmY7fFI2Z6jwGh5vM%2FCT4lBPmasL0e3t84mI%2BFTqtg%3D&reserved=0> 2. the customized color scale [VERDI_testing_issue_299_2]<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F73186639%2F179819520-9929fefd-eb88-4f41-8042-dbcaa125fff2.png&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327518972%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rBRu%2FHKPyXhxgaOkPRbCK6Yv2ta78lQrEp5Hfg0o5tM%3D&reserved=0> - Reply to this email directly, view it on GitHub<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCEMPD%2FVERDI%2Fissues%2F299%23issuecomment-1189400928&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327675759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=evfUGwYio4yu5vkxm6As9HIxgbVpndd8Ib0qef9qtmw%3D&reserved=0>, or unsubscribe<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADTIXN3QPWWGJDLKFUJWWPTVU3VQTANCNFSM5XU62DEA&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327675759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Se9E25q2yJZ6AwGEC8br4%2B%2FzpuR58ouc%2FL8NUNSl3Q8%3D&reserved=0>. You are receiving this because you commented.Message ID: ***@***.******@***.***>>

Yadong Xu · Answer 10 · Wed Jul 20 2022 02:23:04 GMT+0800 (China Standard Time)

Hi Yadong, It seemed that the customized scale was changed in the configure window, but the color plot didn't seem to have changed. See the legend bar and the Z-axis. The situation that I found this problem is when I try to make a plot over 3-D field, in that some layers have higher values, but some layers have very small values. When I try to visualize the small value by changing the scales, but it didn't show up. Thanks. From: Yadong Xu @.> Sent: Tuesday, July 19, 2022 2:10 PM To: CEMPD/VERDI @.> Cc: Kang, Daiwen @.>; Comment @.> Subject: Re: [CEMPD/VERDI] 'Contour Plot' produces Exception (Issue #299) I tested on Atmos. Yes, the problem has been fixed. But I found another issue that doesn't directly relate to the current issue. The issue is: after the contour plot was produced, I tried to configure the scale for the contour plot by clicking on the "Configure" then "Configure Plot", at the pop-up window, I clicked "Color Map", and tried to rebuild the color scales, it failed (no response). For other options, such as "Titles", "Labels", it worked well. Don't know if this should be open as a separate issue or continue this one? Hi Daiwen, I tested VERDI_2.1.4_linux64_20220718.tar.gz on Atmos, found that the contour plot worked properly and could not re-produce the new issue of using "Configure Plot" to rebuild the color scales. I was able to change the color scale to a customized one shown as below: 1. the automatic color scale [VERDI_testing_issue_299_1]https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F73186639%2F179819469-e238f6b4-ec56-44c3-bf64-b64c5abf6e54.png&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327518972%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nBmY7fFI2Z6jwGh5vM%2FCT4lBPmasL0e3t84mI%2BFTqtg%3D&reserved=0 2. the customized color scale [VERDI_testing_issue_299_2]https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F73186639%2F179819520-9929fefd-eb88-4f41-8042-dbcaa125fff2.png&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327518972%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rBRu%2FHKPyXhxgaOkPRbCK6Yv2ta78lQrEp5Hfg0o5tM%3D&reserved=0 - Reply to this email directly, view it on GitHubhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCEMPD%2FVERDI%2Fissues%2F299%23issuecomment-1189400928&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327675759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=evfUGwYio4yu5vkxm6As9HIxgbVpndd8Ib0qef9qtmw%3D&reserved=0, or unsubscribehttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADTIXN3QPWWGJDLKFUJWWPTVU3VQTANCNFSM5XU62DEA&data=05%7C01%7CKang.Daiwen%40epa.gov%7C923987ed4c33417ab1a808da69b1f75e%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637938510327675759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Se9E25q2yJZ6AwGEC8br4%2B%2FzpuR58ouc%2FL8NUNSl3Q8%3D&reserved=0. You are receiving this because you commented.Message ID: @.@.>>

Hi Daiwen,

Now I see what you meant. Can you please share the link of the data file you used for testing on Atmos?
Thanks,
Yadong

dkang2 · Answer 11 · Wed Jul 20 2022 02:44:09 GMT+0800 (China Standard Time)

/work/MOD3EVAL/dkj/LTNG/OAQPS/WWLLNs_36US3/CCTM_LTNGEMIS3D_WWLLNs_20160701.nc

The large numbers are often in Layers 20-30. The surface values are quite small, but they are there. You can try to change the max value to 5 or 1 to visualize it.

Yadong Xu · Answer 12 · Wed Jul 20 2022 05:02:03 GMT+0800 (China Standard Time)

/work/MOD3EVAL/dkj/LTNG/OAQPS/WWLLNs_36US3/CCTM_LTNGEMIS3D_WWLLNs_20160701.nc

The large numbers are often in Layers 20-30. The surface values are quite small, but they are there. You can try to change the max value to 5 or 1 to visualize it.

Thanks for sharing the data file, Daiwen.
I just opened a new Github issue #304 under /CEMPD/VERDI.