I am in the process of running Java 3d applets on my machine, which has linux. The problem is that after I install jdk(1.6 as specified on the official site), jre and icedtea plugin (needed on browser) softwares, normal applets work fine but java 3d application does not work. Also it gives no error. Could someone please give a solution on how to install java 3d on linux or point me to some useful documentation for the procedure.
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Please follow these instructions to install the very latest version of Java3D: http://jogamp.org/wiki/index.php/Downloading_and_installing_Java3D
The applets are quite broken whatever the plugin you use, with Oracle Java and with OpenJDK + Icedtea-web plugin, especially since the latest security changes. Maybe your problem has nothing to do with Java3D itself.
Moreover, you don't have to install Java3D on your system to use applets based on it. You can use third party libraries with Java Web Start and applets without installing them on your system. When you install a library as an extension, it can cause conflicts with the applets and the applications that could rely on a different version. Moreover, the extension mechanism has been removed from Java 1.9, just look at its early access versions.