Accelerating Molecular Dynamics Simulations With High Performance Reconfigurable Systems
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Accelerating Molecular Dynamics Simulations With High Performance Reconfigurable Systems
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Author : Shihchin Chiu
language : en
Publisher:
Release Date : 2011
Accelerating Molecular Dynamics Simulations With High Performance Reconfigurable Systems written by Shihchin Chiu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Abstract: Molecular Dynamics (MD) simulation plays an important role in understanding functionally important phenomena of biological processes. Many of such events, however, occur on time scales beyond the capabilities of modern computers. Hence, accelerating MD simulations becomes one of critical challenges in the current study of Computational Biology and Chemistry. For the past several years, various implementations and efficient algorithms have been developed toward this goal. Of these, accelerating MD with Field Programmable Gate Arrays (FPGAs) has been shown to be a viable candidate for improved MD cost/performance. Given the intense competition from multi-core and GPUs, there is now a question whether MD on High Performance Reconfigurable Computing (HPRC) can be competitive. The goal of this research is to create an FPGA-based MD system to achieve substantial speedup over production MD software without compromising simulation quality. In one part of the study, we systematically explore and evaluate the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, equation complexity, and various other optimizations. We find that the FPGAs' Block RAM (BRAM) architecture makes them well suited to support unusually fine-grained intervals. This leads to a reduction in other logic and a proportional increase in performance. In the other part, we present the first FPGA study of the filtering of particle pairs having nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA's resources. Overall, we find that, for an Altera Stratix-III EP3ES260, six force pipelines running at nearly 200 MHz can fit on the FPGA. This results in a 26x per core speedup for the nonbonded short-range force. The resulting integrated system is likely to make FPGAs highly competitive for MD.
High Performance Computing Using Fpgas
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Author : Wim Vanderbauwhede
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-08-23
High Performance Computing Using Fpgas written by Wim Vanderbauwhede and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-08-23 with Technology & Engineering categories.
High-Performance Computing using FPGA covers the area of high performance reconfigurable computing (HPRC). This book provides an overview of architectures, tools and applications for High-Performance Reconfigurable Computing (HPRC). FPGAs offer very high I/O bandwidth and fine-grained, custom and flexible parallelism and with the ever-increasing computational needs coupled with the frequency/power wall, the increasing maturity and capabilities of FPGAs, and the advent of multicore processors which has caused the acceptance of parallel computational models. The Part on architectures will introduce different FPGA-based HPC platforms: attached co-processor HPRC architectures such as the CHREC’s Novo-G and EPCC’s Maxwell systems; tightly coupled HRPC architectures, e.g. the Convey hybrid-core computer; reconfigurably networked HPRC architectures, e.g. the QPACE system, and standalone HPRC architectures such as EPFL’s CONFETTI system. The Part on Tools will focus on high-level programming approaches for HPRC, with chapters on C-to-Gate tools (such as Impulse-C, AutoESL, Handel-C, MORA-C++); Graphical tools (MATLAB-Simulink, NI LabVIEW); Domain-specific languages, languages for heterogeneous computing(for example OpenCL, Microsoft’s Kiwi and Alchemy projects). The part on Applications will present case from several application domains where HPRC has been used successfully, such as Bioinformatics and Computational Biology; Financial Computing; Stencil computations; Information retrieval; Lattice QCD; Astrophysics simulations; Weather and climate modeling.
Scalable Molecular Dynamics Simulation Using Fpgas And Multicore Processors
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Author : Md. Ashfaquzzaman Khan
language : en
Publisher:
Release Date : 2013
Scalable Molecular Dynamics Simulation Using Fpgas And Multicore Processors written by Md. Ashfaquzzaman Khan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with categories.
Abstract: While Molecular Dynamics Simulation (MD) uses a large fraction of the world's High Performance Compute cycles, the modeling of many physical phenomena remains far out of reach. Improving the cost-effectiveness of MD has therefore received much attention, especially in using accelerators or modifying the computation itself. While both approaches have demonstrated great potential, scalability has emerged as a critical common challenge. The goal of this research is to study this issue and develop MD solutions that not only achieve substantial acceleration but also remain scalable. In the first part of this research, we focus on Discrete Molecular Dynamics Simulation (DMD), which achieves high performance by simplifying the underlying computation by converting it into a Discrete Event Simulation (DES). In addition to the inherent serial nature of DES, causality issues make DMD a notorious target for parallelization. We propose a parallel version of DMD that, unlike any previous work, uses task decomposition and efficient synchronization and achieves more than 8.5x speed-up for 3D physical systems on a 12 core processor, with potential for further strong scaling. The second part of this research focuses on FPGA acceleration of timestep-driven MD. We first enhance an existing FPGA kernel to take advantage of the Block RAM architecture of FPGAs. This results in a 50% improvement in speed-up, without sacrificing simulation quality. We then parallelize the design targeting multiple on-board FPGA cores. We combine this with software pipelining and careful load distribution at the application level to achieve a 3.37x speedup over its CPU counterpart. In the third part we create a framework that integrates the FPGA accelerator into a prominent MD package called NAMD. This framework allows users to switch between the actual accelerator and a simulated version, and provides a means to study different characteristics, such as the communication pattern, of such an accelerated system. Using this framework, we identify the drawbacks of the current FPGA kernel and provide guidelines for future designs. In addition, the integrated design achieves 2.22x speed-up over a quad-core CPU, making it the first ever FPGA-accelerated full-parallel MD package to achieve a positive end-to-end speed-up.
Enhancing Molecular Dynamics Simulations With Machine Learning And Advanced Cyberinfrastructure
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Author : Jayanath Chamindu Sandanuwan Kadupitiya Kadupitige
language : en
Publisher:
Release Date : 2022
Enhancing Molecular Dynamics Simulations With Machine Learning And Advanced Cyberinfrastructure written by Jayanath Chamindu Sandanuwan Kadupitiya Kadupitige and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with Bioinformatics categories.
Molecular dynamics simulations accelerated by high-performance computing methods are powerful tools for investigating and extracting the microscopic mechanisms characterizing the properties of a wide range of materials, including soft matter. Generally, the runtimes for these simulations range from hours to days to furnish accurate information using optimal parallelization techniques. These simulations produce enormous amounts of data that can guide the design and engineering of materials and devices. However, these large datasets can be very high-dimensional and thus challenging to be analyzed by conventional processing approaches. There is a critical need for new approaches to accelerate simulations, leverage past simulations to generate accurate predictions, and expedite the analysis of simulation data to investigate and understand material properties. This dissertation contributes to addressing this need. We discuss broad and effective deep learning approaches for training machine learning surrogates and demonstrate their success in molecular dynamics simulations of soft-matter systems. We introduce artificial neural networks based timestep auto-tuners for molecular dynamics simulations and develop recurrent neural networks based integrators that accurately solve Newton's equations utilizing sequences of past trajectory data using timesteps that are orders of magnitude larger than the Verlet timestep. We illustrate how machine learning techniques can perform feature investigation of high-dimensional datasets generated in nonequilibrium molecular dynamics simulations of polymeric liquids. Finally, we demonstrate the use of advanced cyberinfrastructure such as transient cloud servers to reduce the computational costs of molecular dynamics simulations of soft matter.
Applied Reconfigurable Computing Architectures Tools And Applications
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Author : Lin Gan
language : en
Publisher: Springer Nature
Release Date : 2022-10-27
Applied Reconfigurable Computing Architectures Tools And Applications written by Lin Gan and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-10-27 with Computers categories.
This book constitutes the proceedings of the 18th International Symposium on Applied Reconfigurable Computing, ARC 2022, held as a virtual event, in September 2022. The 13 full papers presented in this volume were reviewed and selected from 16 submissions. The papers cover a broad spectrum of applications of reconfigurable computing, from driving assistance, data and graph processing acceleration, computer security to the societal relevant topic of supporting early diagnosis of Covid infectious conditions.
A Preliminary Study Of Molecular Dynamics On Reconfigurable Computers
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Author :
language : en
Publisher:
Release Date : 2003
A Preliminary Study Of Molecular Dynamics On Reconfigurable Computers written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003 with categories.
In this paper we investigate the performance of platform FPGAs on a compute-intensive, floating-point-intensive supercomputing application, Molecular Dynamics (MD). MD is a popular simulation technique to track interacting particles through time by integrating their equations of motion. One part of the MD algorithm was implemented using the Fabric Generator (FG)[l I] and mapped onto several reconfigurable logic arrays. FG is a Java-based toolset that greatly accelerates construction of the fabrics from an abstract technology independent representation. Our experiments used technology-independent IEEE 32-bit floating point operators so that the design could be easily re-targeted. Experiments were performed using both non-pipelined and pipelined floating point modules. We present results for the Altera Excalibur ARM System on a Programmable Chip (SoPC), the Altera Strath EPlS80, and the Xilinx Virtex-N Pro 2VP. 50. The best results obtained were 5.69 GFlops at 8OMHz(Altera Strath EPlS80), and 4.47 GFlops at 82 MHz (Xilinx Virtex-II Pro 2VF50). Assuming a lOWpower budget, these results compare very favorably to a 4Gjlop/40Wprocessing/power rate for a modern Pentium, suggesting that reconfigurable logic can achieve high performance at low power on jloating-point-intensivea pplications.
Encyclopedia Of Bioinformatics And Computational Biology
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Author :
language : en
Publisher: Elsevier
Release Date : 2018-08-21
Encyclopedia Of Bioinformatics And Computational Biology written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-21 with Medical categories.
Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Molecular Simulation Studies In Material And Biological Sciences
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Author : Kholmirzo Kholmurodov
language : en
Publisher: Nova Publishers
Release Date : 2007
Molecular Simulation Studies In Material And Biological Sciences written by Kholmirzo Kholmurodov and has been published by Nova Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Science categories.
Book & CD. Computer molecular simulations of complex multi-particle systems play a fascinating role in fundamental physics, biochemical and life sciences. Having an increasingly significant impact on many applied industries, especially in modern biophysical and nanotechnological areas, molecular simulation provides a set of tools for predicting many functional properties of molecular systems. The chemical, pharmaceutical, materials and related industries -- all share the computer molecular simulation methods. The molecular simulation studies cover different fields of either biological processes -- protein folding and electron densities of DNA and proteins, or thin film formations and surface-cluster phenomena in nanoelectronics, synthetic copolymers and biopolymer design in biochemistry, so on. Practically all of the world's present supercomputers and many specially developed high performance computing clusters over the world are performing molecular simulations or are aimed on these needs. This book presents leading international research in this dynamic field.
Design Of Fpga Based Computing Systems With Opencl
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Author : Hasitha Muthumala Waidyasooriya
language : en
Publisher: Springer
Release Date : 2017-10-24
Design Of Fpga Based Computing Systems With Opencl written by Hasitha Muthumala Waidyasooriya and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-24 with Technology & Engineering categories.
This book provides wide knowledge about designing FPGA-based heterogeneous computing systems, using a high-level design environment based on OpenCL (Open Computing language), which is called OpenCL for FPGA. The OpenCL-based design methodology will be the key technology to exploit the potential of FPGAs in various applications such as low-power embedded applications and high-performance computing. By understanding the OpenCL-based design methodology, readers can design an entire FPGA-based computing system more easily compared to the conventional HDL-based design, because OpenCL for FPGA takes care of computation on a host, data transfer between a host and an FPGA, computation on an FPGA with a capable of accessing external DDR memories. In the step-by-step way, readers can understand followings: how to set up the design environment how to write better codes systematically considering architectural constraints how to design practical applications
Reconfigurable Computing Architectures Tools And Applications
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Author : Pedro C. Diniz
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-03-19
Reconfigurable Computing Architectures Tools And Applications written by Pedro C. Diniz and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-03-19 with Computers categories.
This book constitutes the refereed proceedings of the Third International Workshop on Applied Reconfigurable Computing, ARC 2007, held in Mangaratiba, Brazil, in March 2007. The 27 full papers and 10 short papers presented together with a late-comer contribution from ARC 2006 are organized in topical sections on architectures, mapping techniques and tools, arithmetic, and applications.