Application of parallel hybrid algorithm in massively parallel GPGPU-the improved effective and efficient method for calculating coulombic interactions in simulations of many ions with SIMION

摘要

In our previous study, we introduced a new hybrid approach to effectively approximate the total force on each ion during a trajectory calculation in mass spectrometry device simulations, and the algorithm worked successfully with SIMION. We took one step further and applied the method in massively parallel general-purpose computing with GPU (GPGPU) to test its performance in simulations with thousands to over a million ions. We took extra care to minimize the barrier synchronization and data transfer between the host (CPU) and the device (GPU) memory, and took full advantage of the latency hiding. Parallel codes were written in CUDA C++ and implemented to SIMION via the user-defined Lua program. In this study, we tested the parallel hybrid algorithm with a couple of basic models and analyzed the performance by comparing it to that of the original, fully-explicit method written in serial code. The Coulomb explosion simulation with 128,000 ions was completed in 309 s, over 700 times faster than the 63 h taken by the original explicit method in which we evaluated two-body Coulomb interactions explicitly on one ion with each of all the other ions. The simulation of 1,024,000 ions was completed in 2650 s. In another example, we applied the hybrid method on a simulation of ions in a simple quadrupole ion storage model with 100,000 ions, and it only took less than 10 d. Based on our estimate, the same simulation is expected to take 5-7 y by the explicit method in serial code.