Macs in Chemistry

Insanely Great Science


I was at the Cresset UGM last week and had a chance to hear more about BlazeGPU. The original CPU application Blaze uses the shape and electrostatic character of known ligands to rapidly search large chemical collections for molecules with similar properties. The latest version BlazeGPU runs at 40 times the speed of the CPU version of Blaze but loses nothing in accuracy. At a fraction of the hardware cost, BlazeGPU delivers the same effective, ligand based virtual screening as Blaze, based on the shape and electrostatic nature of molecules.

BlazeGPU is written in OpenCL and OpenCL libraries are available from NVidia and AMD for their graphics cards, but also from Intel for the CPU and for their new Xeon Phi coprocessor cards. BlazeGPU is currently designed only to run on the GPU - for CPU-only clusters the original code is just as fast, and on a machine with a reasonably fast GPU or two the CPU tends to run flat out just feeding data to the graphics card, so there's not that much gain running on the CPU as well as the GPU.

Currently the conformer generation still runs on the CPU, but they are looking at the possibility of porting that to OpenCL as well in the future.

The relative performance is shown in the plot below, it is worth noting that these are relatively inexpensive graphics cards that you can pick up on Amazon or ebay for a few hundred pounds. Also note for a $2.10/hour GPU instance on AmazonEC2 you can process 2m conformations.


There are more examples of GPU science here.