I needed to limit how much cpu a certain process uses to about 50%. I tried cpulimit but it is not working for me on a quad-core system (it says to use values over 100% for multicores but when you enter any value above 100% it doesn't limit at all). Is there any other way to limit a cpu by percentage, or to fix cpulimit so it will work?

Limiting cpu time will not work for me because this particular process im using (tophat) slows down to one core at one point and if I limit cpu time this part will take twice as long which will add an extra few hours...or days..on to my computing time

I am assuming you are doing this sort of thing in order to make your system usable while doing some heavy duty computation. If this is the case then instead of limiting processing power you could use the nice system. It gives priority to certain tasks and if tasks with higher priority need more power then it is taken from tasks with lower priority. By default most tasks have a nice of 0, but it ranges forom -19 (very important) to 19 (not important). To use this system just use "nice <priority> <command>". I would recommend doing something like this instead of limiting processing power.

Have a look a cgroups. You can define a cpuset that limits the CPUS (cores) processes can use. You could limit it to 2 CPUs, and it will never use more. If it only needs one, other tasks can use the CPU (depending on if you declare it as "exclusive" or not).
I do similar for benchmarks - limit them to all except one CPU. I use that other CPU to monitor how things are going without getting locked out.

Thanks for the replies. The goal is more to just reduce heat than making cpu available for other programs. Niceing might work if I had a dummy program running but I dont know much programming. The program will let me limit number of CPUs, which is best solution now. But after awhile the temps get a little too hot for my liking. Id much rather run four cores at 50% than two at 100%