Java 32-bit vs 64-bit compatibility

Yes, Java bytecode (and source code) is platform independent, assuming you use platform independent libraries. 32 vs. 64 bit shouldn't matter.

I accidentally ran our (largeish) application on a 64bit VM rather than a 32bit VM and didn't notice until some external libraries (called by JNI) started failing.

Data serialized on a 32bit platform was read in on the 64bit platform with no issues at all.

What sort of issues are you getting? Do some things work and not others? Have you tried attaching JConsole etc and have a peak around?

If you have a very big VM you may find that GC issues in 64 bit can affect you.

Yes to the first question and no to the second question; it's a virtual machine. Your problems are probably related to unspecified changes in library implementation between versions. Although it could be, say, a race condition.

There are some hoops the VM has to go through. Notably references are treated in class files as if they took the same space as ints on the stack. double and long take up two reference slots. For instance fields, there's some rearrangement the VM usually goes through anyway. This is all done (relatively) transparently.

Also some 64-bit JVMs use "compressed oops". Because data is aligned to around every 8 or 16 bytes, three or four bits of the address are useless (although a "mark" bit may be stolen for some algorithms). This allows 32-bit address data (therefore using half as much bandwidth, and therefore faster) to use heap sizes of 35- or 36-bits on a 64-bit platform.