Multiple kernels in a single OpenCL file

You're very welcome. I guess most applications that I have seen with FPGAs target a very specific application. So in terms of simulation, it would be targeted to a specific simulation that you want to be accelerated and now the questions are where is the bottleneck in the simulation, can an FPGA be a good fit as to accelerated it, and if so, how to best deconstruct the problem such that it can take advantage of the properties and power of an FPGA. So you would essentially choose the functions that are required in the current simulation, optimize and tune it, and target it that way.

Of course if you start scaling up to larger HPCs, now you're talking about hundreds of FPGAs and so you can have specific FPGAs loaded with certain kernels and etc. The thing to also keep in mind is that with a lot of these kernels that implement physics functions, i'm not sure how complicated each kernel is, but something to keep in mind is the data movement from one kernel to the other which can become an issue. The best practice guide recommends combining small kernels into a larger one.

Yes you are correct, FPGA's are usually targeted toward a set application or rather, have a set logic. There are cases where you can do partial reconfiguration where there is a region on the FPGA that can reconfigure the logic to what you need on the fly or to rapidly assemble the bitstream with the required function. But to my knowledge, Altera doesn't support partial reconfiguration with OpenCL.