"normally" you include gluegen-rt.jar and jocl.jar on the classpath
gluegen-rt will then look for its natives inside the jar gluegen-rt-natives-linux-amd64.jar next to the gluegen-rt.jar and jocl.jar will look for its natives inside jocl-natives-linux-amd64.jar next to the jocl.jar
if that fail then it will try load the natives from the natives/linux-amd64 inside the main jar
and if that also fail then it will try load the natives from the natives/linux-amd64/ folder on the filesystem.
example 1 if you have built gluegen jocl and jocl-demos manually then the following command line will launch HelloJOCL
java -cp jocl-demos/build/jar/jocl-demos.jar:gluegen/build/gluegen-rt.jar:jocl/build/jar/jocl.jar com/jogamp/opencl/demos/hellojocl/HelloJOCL
example 2 if you use the pre-build jogamp release then the following command lines will launch HelloJOCL. This example uses the "slim" jar layout.
wget
http://jogamp.org/deployment/archive/master/gluegen_896-joal_622-jogl_1451-jocl_1094-signed/archive/jogamp-all-platforms.7zwget
http://jogamp.org/deployment/archive/master/gluegen_896-joal_622-jogl_1451-jocl_1094-signed/archive/jocl-demos.7z7z x jogamp-all-platforms.7z
7z x jocl-demos.7z
java -cp jocl-demos/jar/jocl-demos.jar:jogamp-all-platforms/jar/gluegen-rt.jar:jogamp-all-platforms/jar/jocl.jar com/jogamp/opencl/demos/hellojocl/HelloJOCL
example 3 if you use the pre-build jogamp release then the following command lines will launch HelloJOCL. This example uses the "fat" jar layout. The jogamp-fat.jar contains all the natives for all jogamp modules and platforms we support.
wget
http://jogamp.org/deployment/archive/master/gluegen_896-joal_622-jogl_1451-jocl_1094-signed/fat/jogamp-fat.jarwget
http://jogamp.org/deployment/archive/master/gluegen_896-joal_622-jogl_1451-jocl_1094-signed/archive/jocl-demos.7z7z x jocl-demos.7z
java -cp jocl-demos/jar/jocl-demos.jar:jogamp-fat.jar com/jogamp/opencl/demos/hellojocl/HelloJOCL