This system runs all OpenGL applications such as Stellarium or Celestia etc fine:

Linux host.domain 2.6.35.14-96.PhenomX4.fc14.x86_64 #6 SMP PREEMPT Mon Jan 16 14:47:34 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

$ /s/jdk1.8.0/bin/java -version
java version "1.8.0-ea"
Java(TM) SE Runtime Environment (build 1.8.0-ea-b114)
Java HotSpot(TM) 64-Bit Server VM (build 25.0-b56, mixed mode)

Nothing is drawn in the scene except grey background and the below is thrown:

ant -f /home/user/NetBeansProjects/MoleculeSampleApp jfxsa-run
init:
deps-clean:
Updating property file: /home/user/NetBeansProjects/MoleculeSampleApp/build/built-clean.properties
Deleting directory /home/user/NetBeansProjects/MoleculeSampleApp/build
clean:
init:
deps-jar:
Created dir: /home/user/NetBeansProjects/MoleculeSampleApp/build
Updating property file: /home/user/NetBeansProjects/MoleculeSampleApp/build/built-jar.properties
Created dir: /home/user/NetBeansProjects/MoleculeSampleApp/build/classes
Created dir: /home/user/NetBeansProjects/MoleculeSampleApp/build/empty
Created dir: /home/user/NetBeansProjects/MoleculeSampleApp/build/generated-sources/ap-source-output
Compiling 2 source files to /home/user/NetBeansProjects/MoleculeSampleApp/build/classes
compile:
Created dir: /home/user/NetBeansProjects/MoleculeSampleApp/dist
Detected JavaFX Ant API version 1.3
Launching <fx:jar> task from /FileDump.1TB/jdk1.8.0/lib/ant-javafx.jar
Warning: From JDK7u25 the Codebase manifest attribute should be used to restrict JAR repurposing.
         Please set manifest.custom.codebase property to override the current default non-secure value '*'.
Launching <fx:deploy> task from /s/jdk1.8.0/lib/ant-javafx.jar
jfx-deployment-script:
jfx-deployment:
jar:
Copying 12 files to /home/user/NetBeansProjects/MoleculeSampleApp/dist/run1081385062
jfx-project-run:
Executing /home/user/NetBeansProjects/MoleculeSampleApp/dist/run1081385062/MoleculeSampleApp.jar using platform /s/jdk1.8.0/bin/java
Nov 08, 2013 7:54:40 PM javafx.scene.PerspectiveCamera <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.paint.Material <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.paint.Material <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.paint.Material <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.paint.Material <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.paint.Material <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.paint.Material <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.paint.Material <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Shape3D <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.Scene <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.Scene$7 invalidated
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Mesh <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Mesh <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Mesh <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Mesh <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Mesh <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Nov 08, 2013 7:54:40 PM javafx.scene.shape.Mesh <init>
WARNING: System can't support ConditionalFeature.SCENE3D
Deleting directory /home/user/NetBeansProjects/MoleculeSampleApp/dist/run1081385062
jfxsa-run:
BUILD SUCCESSFUL (total time: 10 seconds)