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Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements […]
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Fiona Reid, Iain Bethune
CP2K, a popular open-source European atomistic simulation package has been ported to the Intel Xeon Phi architecture, requiring no code modifications except minor bug fixes. Benchmarking of a small molecular dynamics simulation has been carried out using CP2K’s existing MPI, OpenMP and mixed-mode MPI/OpenMP implementations to achieve full utilisation of the Xeon Phi’s 240 virtual […]
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Mariusz Uchronski, Agnieszka Kwiecien, Marcin Gebarowski
CP2K is an application for atomistic and molecular simulation and, with its excellent scalability, is particularly important with regards to use on future exascale systems. The code is well parallelized using MPI and hybrid MPI/OpenMP, typically scaling well to ~1 core per atom in the system. The research on CP2K done within PRACE-1IP stated that […]
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Istvan Lagzi, Robert Meszaros, Gyorgyi Gelybo, Adam Leelossy
Atmospheric chemistry is a multidisciplinary research field with respect to emissions, interactions and physical and chemical transformation of chemical compounds in the atmosphere. It also investigates the key physical processes occurring in the atmosphere. This eBook provides a comprehensive review of this topic showing recent advances in this field e.g., parallelization of mathematical models with […]
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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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