Java performance tips

Question

I have a program I ported from C to Java. Both apps use quicksort to order some partitioned data (genomic coordinates).

The Java version runs fast, but I'd like to get it closer to the C version. I am using the Sun JDK v6u14.

Obviously I can't get parity with the C application, but I'd like to learn what I can do to eke out as much performance as reasonably possible (within the limits of the environment).

What sorts of things can I do to test performance of different parts of the application, memory usage, etc.? What would I do, specifically?

Also, what tricks can I implement (in general) to change the properties and organization of my classes and variables, reducing memory usage and improving speed?

EDIT : I am using Eclipse and would obviously prefer free options for any third-party tools. Thanks!

Answer 1

If your algorithm is CPU-heavy, you may want to consider taking advantage of parallelisation. You may be able to sort in multiple threads and merge the results back later.

This is however not a decision to be taken lightly, as writing concurrent code is hard.

Answer 2

First caveat - make sure you have done appropriate profiling or benchmarking before embarking on any optimisation work. The results will often enlighten you, and nearly always save you a lot of wasted effort in optimising something that doesn't matter.

Assuming that you do need it, then you can get performance comparable to C in Java, but it takes some effort. You need to know where the JVM is doing "extra work" and avoid these.

In particular:

• Avoid unnecessary object creation. While the JVM heap and GC is extremely fast and efficient (probably the best in the world, and almost certainly better than anything you could roll yourself in C), it is still heap allocation and that will be beaten by avoiding the heap in the first place (stack or register allocation)
• Avoid boxed primitives. You want to be using double and not Double.
• Use primitive arrays for any big chunks of data. Java primitive arrays are basically as fast as C/C++ arrays (they do have an additional bounds check but that is usually insignificant)
• Avoid anything synchronized - Java threading is pretty decent but it is still overhead that you may not need. Give each thread it's own data to work on.
• Exploit concurrency - Java's concurrency support is very good. You might as well use all your cores! This is a big topic but there are plenty of good books / tutorials available.
• Use specialised collection classes for certain types of data if you have some very specific requirements, e.g. supporting some specialised sorting/search algorithms. You may need to roll your own, but there are also some good libraries with high performance collection classes available that may fit your needs - see e.g. Javoltion
• Avoid big class heirarchies - this is a design smell in performance code. Every layer of abstraction is costing you overhead. Very fast Java code will often end up looking rather like C....
• Use static methods - the JIT can optimise these extremely well. It will usually inline them.
• Use final concrete classes - again, the JIT can optimise these very well by avoiding virtual function calls.
• Generate your own bytecode - if all else fails, this can be a viable option if you want the absolute maximum performance out of the JVM. Particularly useful if you need to compile your own DSL. Use something like ASM.