Hi all,
Two problems are outlined here:
1) JVM: We reocmmand to use the embeded JVM (in ThirdPart). Most of the Linux systems use th OpenJDK by default and this one will not work with the JNI wrapping of VTK. You must use a SUN based JVAM (at least a version 1.6).
2) After some testings, apparently the binary version of Gmsh provided on the Web site (and embeded in SPIS) is not fully 64bits. This is whyt the meshsing phase does not work properly on some Linux systems.
Its works on my Suse only if I install in add of the 64 bits, the 32bits version of Fltk, Glu, glic.... A recommend to recompile Gmsh for you own system if this one is full 64bits.
Actually, contributions are welcome…

Best,
Julien Forest
(Artenum's crew)