For an RNA sequence of length 400, this leads, depending on the threshold, to a 10 138 fold speed-up compared with the previous complete method.
The advance, enabling a 100-fold speed gain over wired connectors, will be crucial to future Sun supercomputers.
The box method employing 213 boxes achieves 30-fold speed ups in the case involving 20,000 segments.
A total of 128 threads per block can lead to the best performance with nearly an 18-fold speed increase.
Dr. John Von Neumann, mathematician and newly appointed Atomic Energy Commissioner, listed three other jobs only the Naval Ordnance Research Computer NORCcoulduldodo because of its ten-fold speed advantage over any other electronic brain now in existence.
The results show that the proposed approach significantly outperforms the traditional ones (up to a 15-fold speed increase on a 200 node machine).
Performance test on IBM p690 architecture shows that the parallel scheme adds up 20-fold speed ups when using 36 processors.
Precise comparisons are difficult, says Vijay Pande, Folding@home's director, but "a ten-fold speed increase is easy, a 50-fold one is possible, and you might even reach 100 if your application was particularly suitable".That is because GPUs are well suited to the types of calculations involved when simulating protein folding.
These results provide a compelling demonstration of the potential utility of very long molecular dynamics simulations in redesigning proteins well beyond their evolved stability and folding speed.
"GPU" achieved only a 6.6-fold speed up compared with "1CPU" in this case.
