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 256 PUs).

(1) Hirosaki University (2) Information and Mathematical Science Laboratory, Inc. (3) Arrow Co. (4) Real World Computing Partnership