2013 Volume 12 Issue 3 Pages 172-180
With the rapid expansion of multi-core computing, the parallel processing platform such as MPI and OpenMP becomes popular as a way to improve the efficiency of computation. These techniques can increase the speed of calculation of software after compiled source codes, with revision using parallel programming rules, through parallel libraries. However, parallel programming is generally difficult for effective speeding-up in the search of finding all solution, because parallel processing is usually repeated each time in the calculation of the energy and structure optimization. To solve these problems, we developed a system based on the distributed processing method, which consists of the procedures of the pretreatment of the division of input-file and distribution of divided processes to many slave machines. This system can divide the input-file into appropriate size of jobs and execute them without having to optimize the source code with parallel processing. It is expected to improve computing speed, reliability of result and data accessibility. To show the efficiency of this system, we applied it to make a conformational energy map of cellulose triacetate using the charmm molecular dynamics simulation program.