Parallelization and Performance Evaluation of MD Program
AMBER and Barnes-Hut Tree Code

Minoru Saito(1), Kiyotaka Misoo(2), Yoshihisa Shizawa(2), Kazushi Marukawa(3),
Yutaka Akiyama(4), Tamotsu Noguchi(4), Kentaro Onizuka(4),

We parallelized molecular dynamics (MD) simulation program AMBER and Barnes-Hut tree code using the MPI library and evaluated those performance on SR2201. The speed of AMBER was remarkably increased by our improvements compared with the performance data of AMBER home page. On the other hand, the speed of Barnes-Hut tree code was also accelerated by our parallelization approach on SR2201 (189 times faster for 256PUs). We demonstrated that Coulomb interactions of a protein in water were efficiently calculated by the parallelized Barnes-Hut tree code. In addition, the parallelized AMBER and Barnes-Hut tree code showed the good acceleration on our PC cluster (Pentium Pro 200MHz, 64PUs, netBSD) (16 and 30 times faster than 1PU for 64PUs, respectively).

(1) Real World Computing Partnership, presently with Hirosaki University (2) Information and Mathematical Science Laboratory, Inc. (3) Arrow Co., presently with University of Illinois at Chicago (4) Real World Computing Partnership