Make sure you're compiling with optimization flags appropriate for the
hardware you're planning to run on. For instance, if you spec -msse3 or
newer on a pre-Prescott P4, you'll generate instructions the CPU can't
execute. I'm pretty sure GCC won't generate these instructions unless
you specify it using these flags so make sure your automake/cmake setup
isn't doing so.
Another issue is if you compile on a 32-bit compiler it'll barf on a
64-bit system, and this might generate an illegal instruction error.
This is the reason package maintainers keep a 32-bit and 64-bit version
of their packages. If you want to make code that runs on a 64-bit system
from your 32-bit system, you'll have to use a 64-bit GCC installation (I
think GCC is the same for either, but you need 64-bit libc) and use -m64
as a compile flag.