I recently overhauled a simulation model I have been working. I cleaned up a lot of clutter and redundant code. However, prior my ODE was taking advantage of my dual CPU with nearly 80% utilization. However, now that I am using a few functions (I think might be the issue) it seems like my code has actually slowed down. I'm now only using around 6-8% I was hoping for a drastic reduction of memory usage (check) and speed (nope).
Without seeing the code it is impossible to know the reason of the slowdown. But 6-8% is really small. Do you have a machine with 16 cores? Then this number might mean, that only one core is active. But it is more likely that your RAM is exhausted and the CPU is waiting for the very slow virtual memory store on the disk. Please check this.
You can get a more specific answer, if you use the profiler to find the bottleneck of your code and post it here. This will be more successful than guessing, where the bottleneck might be.