Running Scala on command line error

[Jean-Rassaire Fouefack]

Hi

due to the memory issue, I am trying to use the university server to run my code on the command line with Linux.

I  connected to the server properly and run SBT project. After running it gives option number as following to run each method.

When I select a number I got the error below as you can see below I selected number 20.

Please look at the error below and let me know what could be the problem.

login as: ffcjea001

Multiple main classes detected, select one to run:

 [1] PCA.PCScore

 [2] Plugins.FittingwithModel

 [3] StatisticalAnalysis.MANOVA

 [4] PCA.Eigenvalues

 [5] Plugins.SurfaceToSurfaceDifference

 [6] NormalisedPCA.NormalisedDataMatrix

 [7] TangentSpace.TransformMeshToMatrix

 [8] PCACrossdata.CrossDataEigDecomp

 [9] VerticesSelection.MeshToSignificantVector

 [10] Plugins.MeasureDrift

 [11] Plugins.DataMatrixWithtreshold

 [12] Plugins.SSMPcaWithflexibility

 [13] ScalismoPCA.NormalisedPCAWithTreshold

 [14] VerticesSelection.EllipsoidVolumCsvfile

 [15] Plugins.ReflectionObject

 [16] ScalismoPCA.NormalisedPCA

 [17] Plugins.CentroidSizeOfMesh

 [18] MarginalPCA.MarginalAreaOfshape

 [19] NormalisedVerticeSelection.NormalisedEllipsoidVolumeOfVertex

 [20] ScalismoPCA.pca

 [21] VerticesSelection.EllipsoidVolumeOfVertex

 [22] StatisticalAnalysis.DiscriminantAnalysis

 [23] Plugins.LandmarkError

 [24] TangentSpace.ProjectionToTangentSpace

 [25] VerticesSelection.getcorrespendpointOfId

 [26] PCA.DataMatrix

 [27] NormalisedVerticeSelection.NormalisedEllipsoidVolumCsvfile

 [28] NormalisedPCA.NormalisedDataMatrixWithtreshold

 [29] Plugins.MeshToVector

 [30] Plugins.meshTomatrix

 [31] ScalismoPCA.PCAWithTreshold

 [32] Plugins.FemurDataRigidAligned

 [33] Plugins.Hausdorff

 [34] NormalisedPCA.NormalisedPCScore

 [35] Plugins.SSMPca

 [36] VerticesSelection.testsinglecode

 [37] Plugins.ExampleApp

 [38] Plugins.MeshWithcolorvariation

 [39] MarginalPCA.MarginalDataMatrix

 [40] PCA.NaitivePCs

Enter number: 20

[info] Running ScalismoPCA.pca 3

It seems like there's an exception while loading the JOGL libraries.

The reason might be that the program is running on a headless system.

If that is the case, try enabling the "java.awt.headless" property,

e.g. java -Djava.awt.headless=true -jar program.jar

scalismo.support.nativelibs.NativeLibraryException: javax.media.nativewindow.NativeWindowException: X11Util.Display: Unable to create a display(nil) connection. Thread run-main-0

        at scalismo.support.nativelibs.NativeLibraryException.wrap(NativeLibraryException.java:45)

        at scalismo.support.nativelibs.jogl.JoglLibraryBundle.onInitializeEnd(JoglLibraryBundle.java:105)

        at scalismo.support.nativelibs.impl.NativeLibraryBundle.initialize(NativeLibraryBundle.java:192)

        at scalismo.support.nativelibs.NativeLibraryBundlesImplementation.initialize(NativeLibraryBundlesImplementation.java:131)

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:483)

        at scalismo.support.nativelibs.NativeLibraryBundles.delegateInitializeCall(NativeLibraryBundles.java:166)

        at scalismo.support.nativelibs.NativeLibraryBundles.initialize(NativeLibraryBundles.java:56)

        at scalismo.package$.initialize(package.scala:30)

        at ScalismoPCA.pca$.main(pca.scala:34)

        at ScalismoPCA.pca.main(pca.scala)

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:483)

        at sbt.Run.invokeMain(Run.scala:67)

        at sbt.Run.run0(Run.scala:61)

        at sbt.Run.sbt$Run$$execute$1(Run.scala:51)

        at sbt.Run$$anonfun$run$1.apply$mcV$sp(Run.scala:55)

        at sbt.Run$$anonfun$run$1.apply(Run.scala:55)

        at sbt.Run$$anonfun$run$1.apply(Run.scala:55)

        at sbt.Logger$$anon$4.apply(Logger.scala:85)

        at sbt.TrapExit$App.run(TrapExit.scala:248)

        at java.lang.Thread.run(Thread.java:745)

Caused by: javax.media.nativewindow.NativeWindowException: X11Util.Display: Unable to create a display(nil) connection. Thread run-main-0

        at jogamp.nativewindow.x11.X11Util.openDisplay(X11Util.java:452)

        at jogamp.opengl.x11.glx.X11GLXDrawableFactory$SharedResourceImplementation.isDeviceSupported(X11GLXDrawableFactory.java:246)

        at jogamp.opengl.SharedResourceRunner.getOrCreateShared(SharedResourceRunner.java:187)

        at jogamp.opengl.x11.glx.X11GLXDrawableFactory.getOrCreateSharedResourceImpl(X11GLXDrawableFactory.java:379)

        at jogamp.opengl.x11.glx.X11GLXDrawableFactory.getOrCreateSharedResourceImpl(X11GLXDrawableFactory.java:81)

        at jogamp.opengl.GLDrawableFactoryImpl.getOrCreateSharedResource(GLDrawableFactoryImpl.java:100)

        at jogamp.opengl.GLDrawableFactoryImpl.createSharedResourceImpl(GLDrawableFactoryImpl.java:129)

        at javax.media.opengl.GLDrawableFactory.createSharedResource(GLDrawableFactory.java:375)

        at javax.media.opengl.GLProfile.initProfilesForDeviceCritical(GLProfile.java:1877)

        at javax.media.opengl.GLProfile.initProfilesForDevice(GLProfile.java:1838)

        at javax.media.opengl.GLProfile.initProfilesForDefaultDevices(GLProfile.java:1807)

        at javax.media.opengl.GLProfile.access$000(GLProfile.java:77)

        at javax.media.opengl.GLProfile$1.run(GLProfile.java:201)

        at java.security.AccessController.doPrivileged(Native Method)

        at javax.media.opengl.GLProfile.initSingleton(GLProfile.java:187)

        at scalismo.support.nativelibs.jogl.JoglLibraryBundle$1.run(JoglLibraryBundle.java:124)

        at scalismo.support.nativelibs.jogl.JoglLibraryBundle.onInitializeEnd(JoglLibraryBundle.java:95)

        ... 24 more

Exception: sbt.TrapExitSecurityException thrown from the UncaughtExceptionHandler in thread "run-main-0"

java.lang.RuntimeException: Nonzero exit code: 1

        at scala.sys.package$.error(package.scala:27)

[trace] Stack trace suppressed: run last compile:run for the full output.

[error] (compile:run) Nonzero exit code: 1

[error] Total time: 35 s, completed Nov 28, 2017 11:06:04 AM

ffcjea001@srvslshpc001:~/project-code-10-07-2017>

Please, what could be the issue?

[Marcel Luethi]

Hi Jean-Raissaire,

You need to run the jvm in headless mode like this:
sbt -Djava.awt.headless=true run

Best regards,

Marcel

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