Data Exchange Engine for Parallel Computing and Its Application to 3D Chromosome Modelling

Data Exchange Engine for Parallel Computing (abbreviated as DEEPC) is a universal parallel programming interface for scientific computing environments such as MATLAB, Octave, R and Python. It is a software developed by us to support Bulk Synchronous Parallel (BSP) computing for these mainstream script-driven scientific computing environments. BSP is one of the most dominant parallel program models, and it affects the design of parallel algorithms profoundly. However, most of these scientific computing environments have been lack of the software support of BSP for a long time until the birth of DEEPC. The main features of our DEEPC is its ease of use and high performance, especially that without much modification to the sequential-computing programs, one can combine these programs to a high performance parallel program with a short script. To demonstrate these features, we put DEEPC in use to a MATLAB program for the 3D modelling of chromosomes. It has been observed that DEEPC performs very well even without much modification to the corresponding program for sequential computing.