SC Conference - Activity Details

Massively Parallel Variational Transition State Theory Calculations for Association Reactions with POLYRATE

Shuxia Zhang  (University of Minnesota)
Jingjing Zheng  (University of Minnesota)
Donald G. Truhlar  (University of Minnesota)
Posters Session
Tuesday,  05:15PM - 07:00PM
Room Rotunda Lobby
We have parallelized the POLYRATE computer program to predict chemical reaction rate constants of barrierless association reactions based on Monte Carlo evaluations of the critical multidimensional variational transition state configuration space integrals. We will discus how, even with a task-parallel Monte Carlo algorithm, the load balance can still be poor. We will also discuss how scalability can disappear at a certain number of processors due the bottleneck of bandwidth and latency in a parallel I/O system that cannot efficiently handle hundreds of simultaneous input/output operations, and we will discuss the strategies we employed to circumvent these problems and achieve good performance on a Linux cluster with a relatively low-end I/O system. Test runs have shown that the calculations are linearly scalable up to 320 processors (the largest number we employed) and efficient in disk usage. The new POLYRATE will be made available to the scientific community on our Web server.
   IEEE Computer Society  /  ACM     2 0   Y E A R S   -   U N L E A S H I N G   T H E   P O W E R   O F   H P C