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Book Overview & Buying
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Table Of Contents
GPU-Accelerated Computing with Python 3 and CUDA
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In this chapter, we explored the practical aspects of implementing GPU-accelerated molecular dynamics simulations. We began by understanding the basics of MD simulations. We then implemented a system of particles, specifically utilizing Numba-CUDA to parallelize force calculation and time integration.
Additionally, we discussed how to effectively use device functions and when to inline them for optimal performance. This allowed us to develop an MD simulator capable of simulating thousands of atoms.
Next, we compared our implementation to both a serial and multithreaded version, demonstrating simulation speeds up to two orders of magnitude faster. We covered essential profiling techniques to measure kernel execution and global memory access, identifying a compute-bound problem as the bottleneck in our simulation. Finally, we provided a few hints on how to address this issue.
Having successfully applied our knowledge of CUDA to parallelize a real-world MD simulation, we will now...