Omar Valerio Minero
Over the last few decades, computer modelling and computer simulation have become an invaluable tool for computational chemists interested in advancing their research and experiment in a more efficient, cost effective way with new molecules. As computer capabilities increase the demand for more accurate models and faster simulations has also grown. Some of these models […]
Istvan Lorentz, Razvan Andonie, Levente Fabry-Asztalos
We focus on the following computational chemistry problem: Given a subset of the exact distances between atoms, reconstruct the three-dimensional position of each atom in the given molecule. The distance matrix is generally sparse. This problem is both important and challenging. Our contribution is a novel combination of two known techniques (parallel breadth-first search and […]
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Levente Fabry-Asztalos, Istvan Lorentz, Razvan Andonie
We present a combination of methods addressing the molecular distance problem, implemented on a graphic processing unit. First, we use geometric build-up and depth-first graph traversal. Next, we refine the solution by simulated annealing. For an exact but sparse distance matrix, the buildup method reconstructs the 3D structures with a root-meansquare error (RMSE) in the […]
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Mayank Daga, Wu-chun Feng
BACKGROUND: Calculating the electrostatic surface potential (ESP) of a biomolecule is critical towards understanding biomolecular function. Because of its quadratic computational complexity (as a function of the number of atoms in a molecule), there have been continual efforts to reduce its complexity either by improving the algorithm or the underlying hardware on which the calculations […]
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Mayank Daga, Thomas Scogland, Wu-chun Feng
The graphics processing unit (GPU) continues to make in-roads as a computational accelerator for highperformance computing (HPC). However, despite its increasing popularity, mapping and optimizing GPU code remains a difficult task; it is a multi-dimensional problem that requires deep technical knowledge of GPU architecture. Although substantial literature exists on how to map and optimize GPU […]
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Yuki Furukawa, Ryota Koga, Koji Yasuda
Computational quantum chemistry mehods such as the Hartree-Fock (HF), the density functional theory (DFT) or the fragment molecular orbital (FMO) require heavy computational resources. In this study they are accelerated by using graphics processing units (GPUs) and the vector instruction set (AVX) of latest CPU. PRISM algorithm to evaluate the electron repulsion integrals was vectorized […]
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A. Eugene DePrince III, Jeff R. Hammond, Stephen K. Gray
Heterogeneous nodes composed of a multicore CPU and at least one graphics processing unit (GPU) are increasingly common in high-performance scientific computing, and significant programming effort is currently being undertaken to port existing scientific algorithms to these unique architectures. We present implementations for two many-body quantum chemistry methods on heterogeneous nodes: the coupled-cluster with single […]
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Bharat Sukhwani
Computational accelerators such as Field Programmable Gate Arrays (FPGAs) and Graphics Processing Units (GPUs) possess tremendous compute capabilities and are rapidly becoming viable options for effective high performance computing (HPC). In addition to their huge computational power, these architectures provide further benefits of reduced size and power dissipation. Despite their immense raw capabilities, achieving overall […]
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Leonid Uroshlev, Sergei Rahmanov, Ivan Kulakovskiy, Vsevolod Makeev
Prediction of binding sites for different types of ions in protein 3D structure context is a complex challenge for biophysical computational methods. One possible approach involves using empirical, also called as knowledge-based, potentials. In the current study, we present a new GPGPU program complex, PIONCA (Protein-ION CAlculator) for efficient generation of empirical potentials for protein-ion […]
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Mayank Daga, Thomas R.W. Scogland, Wu-chun Feng
The graphics processing unit (GPU) continues to make significant strides as an accelerator in commodity cluster computing for high-performance computing (HPC). For example, three of the top five fastest supercomputers in the world, as ranked by the TOP500, employ GPUs as accelerators. Despite this increasing interest in GPUs, however, optimizing the performance of a GPU-accelerated […]
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Mayank Daga
The emergence of scientific applications embedded with multiple modes of parallelism has made heterogeneous computing systems indispensable in high performance computing. The popularity of such systems is evident from the fact that three out of the top five fastest supercomputers in the world employ heterogeneous computing, i.e., they use dissimilar computational units. A closer look […]
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Simon McIntosh-Smith, Terry Wilson, Jon Crisp, Amaurys Avila Ibarra, Richard B. Sessions
With the advent of heterogeneous computing systems consisting of multi-core CPUs and many-core GPUs, robust methods are needed to facilitate fair benchmark comparisons between different systems. In this paper we present a benchmarking methodology for measuring a number of performance metrics for heterogeneous systems. Methods for comparing performance and energy efficiency are included. Consideration is […]
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