Here is a paper (tech report) by Brian Amedro et al. of INRIA that discusses the current state of Java for High Performance Computing (HPC).
“About ten years after the Java Grande effort, this paper aims at providing a snapshot of the current status of Java for High Performance Computing. Multi-core chips are becoming mainstream, offering many ways for a Java Virtual Machine (JVM) to take advantage of such systems for critical tasks such as Just-In-Time compilation or Garbage Collection. We first perform some micro benchmarks for various JVMs, showing the overall good performance for basic arithmetic operations. Then we study a Java implementation of the Nas Parallel Benchmarks, using the ProActive middleware for distribution. Comparing this implementation with a Fortran/MPI one, we show that they have similar performance on computation intensive benchmarks, but still have scalability issues when performing intensive communications. Using experiments on clusters and multi-core machines, we show that the performance varies greatly, depending on the Java Virtual Machine used (version and vendor) and the kind of computation performed.”