So I started searching for a profiler for Java, and I found the YourKit Java Profiler, and it seemed to be what I was searching for. I briefly tried it and, thanks to the "HotSpot" feature, I immediately found a bottleneck (formatting the log messages even when they are discarded), so I asked them if they would provide free licenses for open source developers; i then discovered that YourKit is kindly supporting open source projects with free licenses of its full-featured Java Profiler.
Yourkit profilers are produced by YourKit, LLc: they produce both a Java and a .NET profiler. Of course I only briefly tried the Java profiler, and I can tell you that it was really easy to spot that obvious bottleneck. I'm going to spend some time to profile EduMIPS64 and remove the most prominent bottlenecks.