Nicolo' Savioli
The aim of my thesis is to parallelize the Weighting Histogram Analysis Method (WHAM), which is a popular algorithm used to calculate the Free Energy of a molecular system in Molecular Dynamics simulations. WHAM works in post processing in cooperation with another algorithm called Umbrella Sampling. Umbrella Sampling has the purpose to add a biasing […]
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Xiao Zhang, Wan Guo, Xiao Qin, Xiaonan Zhao
Molecular dynamics (MD) was widely used in chemistry and bio molecules. Numerous attempts have been made to accelerate MD simulations. CUDA enabled NVIDIA Graphics processing units (GPUs) use as a general purpose parallel computer chips as CPU. But it is not easy to port a program to GPU. We present a highly extensible framework for […]
Sudhir B Kylasa, Hasan Metin Aktulga, Ananth Grama
We present a parallel/GPU implementation of our open-source reactive molecular dynamics code, PG-PuReMD (Parallel GPU-Purdue Reactive Molecular Dynamics). Using a variety of innovative algorithms and optimizations, PGPuReMD achieves over 350x speedup compared to a single CPU implementation on a cluster of 36 state of the art GPUs. This is a significant development, since it enables […]
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Samuel Schlachter, Stephen Herbein, Michela Taufer, Shuching Ou, Sandeep Patel, Jeremy S. Logan
Efficiently studying Sodium Dodecyl Sulfate (SDS) molecules’ formations in the presence of different molar concentrations on high-end GPU clusters whose nodes share accelerators exposes us to several challenges, including the need to dynamically adapt the job lengths. Neither virtualization nor lightweight OS solutions can easily support generality, portability, and maintainability in concert. Our solution complements […]
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W. Michael Brown, Masako Yamada
The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), […]
S. Mulla, S. Ivekovic, J.M. Reese
The aim of the project described in this report was to integrate the Molecular Fluid Dynamics simulation package OpenFOAM with the molecular-modelling library OpenMM, in order to enable the execution of Molecular Fluid Dynamics simulations on Graphics Processing Units (GPUs). The reason for this integration, rather than a straightforward substitution of OpenFOAM with OpenMM, was […]
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Julian Hornich
Molecular dynamics simulations are a very useful tool to study the behavior and interaction of atoms and molecules in chemical and bio-molecular systems. With the fast rising complexity of such simulations hybrid systems with both, multi-core processors (CPUs) and multiple graphics processing units (GPUs), become more and more popular. To obtain an optimal performance this […]
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Andrey Asadchev
This document covers the basics of computational chemistry and how using the modern programming techniques the theory can be efficiently implemented on digital computers. The computer implementations are developed from the core two-electron integrals to many-body and coupled cluster algorithms. A particular attention is paid to the physical constraints of he computer resources and the […]
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Robin M. Betz, Ross C. Walker
Continuous integration is the software engineering principle of rapid and automated development and testing. We identify several key points of continuous integration and demonstrate how they relate to the needs of computational science projects by discussing the implementation and relevance of these principles to AMBER, a large and widely used molecular dynamics software package. The […]
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Anuj Varghese Prakash
The use of Population Balance Models (PBM) for simulating dynamics of particulate systems are inevitably limited at some point by the demands they place on computational resources. PBMs are widely used to describe the time evolutions and distributions of many industrial particulate processes, and its efficient and quick simulation would certainly be beneficial for process […]
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Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu
This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynamics systems developed by the Molecular Dynamics Group, University of Groningen, the Netherlands. One should note that molecular dynamics simulations are time-consuming simulations of systems, running time ranging from days to weeks and months. Therefore parallelization is a key issue […]
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Vlad Slavici
The clock speed of current CPUs and RAM has stopped scaling with Moore’s Law. Yet the scale of applications in science and engineering continues to increase. In order to address this scaling of applications, newer NUMA architectures are emerging. These include parallel disks, hybrid CPU-GPU, and many-core CPUs. Existing CPU-based algorithms, as well as legacy […]
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