To see if I can really take any benefit of native code (written C) by using JNI (instead of writing complete java application), I want to measure overhead of calling through JNI. What is the best way to measure this overhead?
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I wouldn’t use a profiler to do quantitative performance testing. Profiling tends to introduce distortions into the actual timing numbers.
I’d create a benchmark that performed one of the actual calculations that you are considering doing in C and compare the C + JNI + Java version against a pure Java version. Be sure that you are comparing apples and apples; i.e. profile and optimize both versions before you benchmark them.
To do the actual benchmarking, I’d construct a loop that performed the calculation a large number of times, record the timings over a large number of iterations and compare. Make sure that you take account of JVM warmup effects; e.g. class loading, JIT compilation and heap warmup.
Like Thihara, I doubt that using C + JNI will help much. And even if it does, you need to take account of the downsides of JNI; e.g. C code portability, platform specific build issues … and possible JVM hard crashes if your native code has bugs.