It’s now very common for modern computers to contain multiple CPU cores, which allow the computer to process multiple sets of information in parallel. Most computers contain dual- or quad-core CPUs, and we expect to see more and more CPU cores as time goes on. In FAH, we use these multiple CPU cores together to speed up our simulations. For example, a quad-core CPU can complete Work Units nearly four times faster than a single-core CPU. Now that these are common, a project that would have taken a year to complete now takes us only a few months. Initially, it was a challenge to scale the GROMACS core — the highly optimized software that performs the actual protein folding simulations behind the scenes — to fully utilize multiple CPU cores, but our methods are now quite efficient at using them.
We’re very excited about what the multi-core processors has been able to do so far. One of our papers (#53 in our Papers page) would have been impossible without the multi-core processors and represents a landmark calculation in the simulation of protein folding. We’re looking forward to more exciting results like that in the years to come! Please see the SMP FAQ for more information.