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Convolutional neural network (CNN) extracts features from big data by using the multilayer network structure. Due to the high effectiveness, CNN has achieved great successes in many fields such as computer vision and speech analysis. However, CNN training is quite challenging because computing the gradients through multiple layers is time consuming. In this paper, we propose to accelerate the computation...
Molecular dynamics (MD) is a computer simulation method of studying physical movements of atoms and molecules that provide detailed microscopic sampling on molecular scale. With the continuous efforts and improvements, MD simulation gained popularity in materials science, biochemistry and biophysics with various application areas and expanding data scale. Assisted Model Building with Energy Refinement...
Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules, which is a very important research technique for the study of biological and chemical systems at micro-scale. Assisted Model Building with Energy Refinement (AMBER) is one of the most commonly used software for MD. However, the microsecond MD simulation of large-scale atom system requires a lot of computation...
MD5 Crypt is a cryptographic algorithm used commonly in UNIX system for authentication. By using the additional randomization of the salt and complexity of the scheme, it makes the traditional password cracking techniques invalid on common computing systems and the security of the system is guaranteed. Benefited from the thriving of petaflops heterogeneous supercomputer system recently, such as Tianhe-1A,...
We discuss an implementation and optimization of GPU-accelerated Molecular Dynamics (MD) simulation of high-speed collision molecular model in NVIDIA CUDA language. A series of optimization methods are presented: spatial decomposition, use of shared memory and use of blockcell-link structure. These optimization methods effectively improve the performance by reducing data transfer time between CPU...
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