On Thursday 18 September 2008, Andrzej Lyskowski wrote: > I was just testing CUDA enabled version of VMD and saw an increase of > calculation speed just like promised - more or less 70 times! > > Makes me wonder is anybody writing crystallographic software plans to > implement GPU support for the calculations? It would be nice to use all > the resources of our computers.
During the many years I have been using computers for crystallography, I have seen repeated cycles of a leap-frog race between specialized hardware and faster general-purpose CPUs. As you point out, we are currently in a cycle where customizing your code to offload certain computations to a GPU can increase the overall throughput. At least for crystallographic software, previous iterations of this leap-frogging have shown that such code customization is quite expensive in development time while yielding only a short-lived advantage over general-purpose code run on general-purpose hardware. For instance, there was a period in the late 1980s when you could improve your refinement time by buying machines with separate vector array processors (Convex, FPS, probably others I have forgotten). But it was only a few years before cheaper general-purpose machines leap-frogged back into the lead. I am dubious that averaged over a 5-year period the investment in specialized code development and expensive specialized hardware was a net win. And indeed, here is a recent harbinger that the era of GPU-based computation may be very short-lived: http://arstechnica.com/articles/paedia/gpu-sweeney-interview.ars A similar alternation has been seen historically in the tradeoff between self-contained platforms and external computational resources accessed by relatively dumb terminals. For some years now computer use has favored self-contained laptops or graphics workstations. But now the pendulum is swinging back again. Yeah, it's a bit different this time. This time around the external resource is distributed ("cloud computing") rather than centralized, but in essence it's "déjà vu all over again". Whether the cloud computing fad will extend to crystallography remains to be seen. Note that distributed ("cloud") data storage has been seriously proposed as a possible solution to the problem of archiving raw diffraction images. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
