I\'ve seen this question and this article on how to debug a native Java crash. The article is with respect to Windows. What are the equivalent debugging aids on Linux?
Unless your JNI library has corrupted a random area of memory (which is extreamly difficult to debug), the most likely cause of a crash in the libjvm is a bug in the JVM. Given the current release is Java 6 update 23 and you have Java 6 update 3, upgrading is the first thing I would try.
BTW: Also you appear to have a 64-bit OS, you might like to try the 64-bit Java.
BTW2: You can write -Xmx2000000k as -mx2g. The default maximum on a 8 GB machine should be about 2 GB anyway.