scholarly journals А Gpu-based Orthogonal Matrix Factorization Algorithm that Produces a Two-Diagonal Shape

2021 ◽  
Vol 4 ◽  
pp. 10-15
Author(s):  
Gennadii Malaschonok ◽  
Serhii Sukharskyi

With the development of the Big Data sphere, as well as those fields of study that we can relate to artificial intelligence, the need for fast and efficient computing has become one of the most important tasks nowadays. That is why in the recent decade, graphics processing unit computations have been actively developing to provide an ability for scientists and developers to use thousands of cores GPUs have in order to perform intensive computations. The goal of this research is to implement orthogonal decomposition of a matrix by applying a series of Householder transformations in Java language using JCuda library to conduct a research on its benefits. Several related papers were examined. Malaschonok and Savchenko in their work have introduced an improved version of QR algorithm for this purpose [4] and achieved better results, however Householder algorithm is more promising for GPUs according to another team of researchers – Lahabar and Narayanan [6]. However, they were using Float numbers, while we are using Double, and apart from that we are working on a new BigDecimal type for CUDA. Apart from that, there is still no solution for handling huge matrices where errors in calculations might occur. The algorithm of orthogonal matrix decomposition, which is the first part of SVD algorithm, is researched and implemented in this work. The implementation of matrix bidiagonalization and calculation of orthogonal factors by the Hausholder method in the jCUDA environment on a graphics processor is presented, and the algorithm for the central processor for comparisons is also implemented. Research of the received results where we experimentally measured acceleration of calculations with the use of the graphic processor in comparison with the implementation on the central processor are carried out. We show a speedup up to 53 times compared to CPU implementation on a big matrix size, specifically 2048, and even better results when using more advanced GPUs. At the same time, we still experience bigger errors in calculations while using graphic processing units due to synchronization problems. We compared execution on different platforms (Windows 10 and Arch Linux) and discovered that they are almost the same, taking the computation speed into account. The results have shown that on GPU we can achieve better performance, however there are more implementation difficulties with this approach.

2007 ◽  
Author(s):  
Fredrick H. Rothganger ◽  
Kurt W. Larson ◽  
Antonio Ignacio Gonzales ◽  
Daniel S. Myers

2021 ◽  
Vol 22 (10) ◽  
pp. 5212
Author(s):  
Andrzej Bak

A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.


2021 ◽  
Vol 20 (3) ◽  
pp. 1-22
Author(s):  
David Langerman ◽  
Alan George

High-resolution, low-latency apps in computer vision are ubiquitous in today’s world of mixed-reality devices. These innovations provide a platform that can leverage the improving technology of depth sensors and embedded accelerators to enable higher-resolution, lower-latency processing for 3D scenes using depth-upsampling algorithms. This research demonstrates that filter-based upsampling algorithms are feasible for mixed-reality apps using low-power hardware accelerators. The authors parallelized and evaluated a depth-upsampling algorithm on two different devices: a reconfigurable-logic FPGA embedded within a low-power SoC; and a fixed-logic embedded graphics processing unit. We demonstrate that both accelerators can meet the real-time requirements of 11 ms latency for mixed-reality apps. 1


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