High performance molecular dynamics simulations with fpga. Despite its widespread use, there exists a many orderofmagnitude gap between the demand and the performance currently achieved. In this paper, we propose a system that can implement the computation on fpga for lennard. Quantum monte carlo methods enable us to determine the groundstate properties of atomic or molecular clusters. Architectures, tools and applications third international workshop, arc 2007, mangaratiba, brazil, march 2729, 2007.
Hoe, carnegie mellon university to date, the most common form of simulators of computer systems are software based running on standard computers. Both designs are synthesized using xilinx ise and implemented on the xilinx virtexii pro fpga development kit field programmable gate array fpga, an fpga system is now capable of accelerating molecular dynamics simulations in a costeffective way. The implementation of molecular dynamics md on fpgas has. Anton is a massively parallel specialpurpose supercomputer designed to accelerate molecular dynamics md simulations by several orders of magnitude, making possible for the first time the atomiclevel simulation of many biologically important phenomena that take place over microsecond to. Their hardware and software architectures, programming tools and performance on scientific applications are discussed. Mar 11, 2009 in life sciences, there are many molecular mechanical codes used for visualizing molecular docking and solving atomtoatom interactions for drug discovery. Fpgaaccelerated hpc in paderborn plans lessons learned conclusions and call to action outline.
Fpgaaccelerated simulation of computer systems hari angepat, the university of texas and microsoft derek chiou, microsoft and the university of texas eric s. Flex units are able to switch between tasks required by a molecular dynamics algorithm as often as needed in order to cater to the nature of the input parameters. Explicit design of fpgabased coprocessors for shortrange. Molecular dynamics simulations on high performance reconfigurable computing systems. In this paper we report on progress and challenges in advancing. Prasanna, a hardware software approach to molecular dynamics on reconfigurable computers, in. To date, the most common form of simulators of computer systems are software based running on standard computers. Molecular dynamics a next frontier for fpga acceleration. The software quantum monte carlo application runs on the host processor. Fpgaaccelerated highperformance computing close to. Accelerating life science and bioinformatics applicationsas. While molecular dynamics simulation md uses a large fraction of the worlds high performance compute cycles, the modeling of many physical phenomena remains far out of reach. Herbordt abstract molecular dynamics simulation md is one of the most important applications in computational science and engineering.
Each simulation cycle, in the brut force approach, consists. Fully integrated fpga molecular dynamics simulations. Molecular dynamics simulation md is one of the most important applications in computational science and engineering. Molecular dynamics md simulation, supported by parallel software and special hardware, is widely used in materials, computational chemistry and biology science. A hardware software approach to molecular dynamics on reconfigurable computers. Highperformance computing using fpgas wim vanderbauwhede. In life sciences, there are many molecular mechanical codes used for visualizing molecular docking and solving atomtoatom interactions for drug discovery. Fpgas offer very high io bandwidth and finegrained, custom and. Abstract molecular dynamics simulation md is one of the most important ap. Explicit design of fpgabased coprocessors for shortrange force computations in molecular dynamics simulations. Fpgabased acceleration of molecular dynamics simulations md has been the subject of several recent studies. Api for software and hardware components has been successfully used by saldana et al.
To this end, we develop a methodology by which critical algorithms in existing software projects can be quickly identified and accelerated using fpgas. Explicit design of fpgabased coprocessors for shortrange force. On the feasibility of fpga acceleration of molecular dynamics simulations technical report v0. Scalable molecular dynamics simulation using fpgas and. Towards production fpgaaccelerated molecular dynamics ncsa. Fpgabased acceleration of molecular dynamics simulations md has been the. Timelogics fpga accelerated biocomputing solutions for. Exploring accelerating science applications with fpgas.
Molecular dynamics md simulations, supported by parallel software and special hardware, are widely used in materials, computational chemistry and biology science. Towards production fpgaaccelerated molecular dynamics. Hardware software codesign for embedded implementation of neural networks. Fpga implementation thesishow to write a good essay for a. Ive been looking for some topic related to fpga design for my masters thesis. Computer science paderborn university, germany 24 january 2018 2. Molecular dynamics md is a technique of atomistic simulation which has facilitated scientific discovery of interactions among particles since its advent in the late 1950s. Pdf molecular dynamics on fpga based accelerated processing. The shortrange force computation, which dominates the execution time, is the primary focus. On the feasibility of fpga acceleration of molecular. It has successfully demonstrated a common communication model for the simulation of molecular dynamics.
Fpgaaccelerated simulation of computer systems, morgan. With advances in fpga capability and inclusion of embedded multipliers, lots of studies steer to focus on fpgaaccelerated md simulations. Herbordt computer architecture and automated design laboratory department of electrical and computer engineering boston university. Our xilinx alveo powered workstations and servers perform up. Your print orders will be fulfilled, even in these challenging times. Fpgaaccelerated molecular dynamics simulations system ieee. Long, fpgaaccelerated molecular dynamics simulations system, 8th int. Fpgabased hprc for bioinformatics applications yoshiki yamaguchi, yasunori osana, masato yoshimi, hideharu amano. Towards production fpga accelerated molecular dynamics. Highperformance computing using fpga covers the area of high performance reconfigurable computing hprc. Furthermore, we show that in an application with tightly coupled datapath and latency constraints, having a large amount of computing resources can actually reduce performance. Highperformance computing for neuroinformatics using fpga. We demonstrate that correct parameter sizing, based on the application, can reduce latency by 20% on average.
Cesar torreshuitzil, bernard girau, adrien gauffriau. Molecular dynamics a next frontier for fpga acceleration january 10, 2017 nicole hemsoth code, compute 3 molecular dynamics codes have a wide range of uses across scientific research and represent a target base for a variety of accelerators and approaches, from gpus to custom asics. Extension of the amber molecular dynamics software to intels many integrated core mic architecture. Molecular dynamics on fpga based accelerated processing units. An intel experiment that moved the simplescalar simoutorder l1 data cache into a. Boston, ma 02215 abstractrecent work in the fpga acceleration of molecular dynamics simulation has shown that. Fpga based acceleration of molecular dynamics simulations md has been the subject of several recent studies. However, to date none of the leading md simulation packages fully support fpga acceleration and a direct comparison of gpu versus fpga.
Request pdf fpgaaccelerated molecular dynamics simulations system molecular dynamics md simulations, supported by parallel software and special hardware, are widely used in materials. Jan 25, 2018 fpgaaccelerated highperformance computing close to breakthrough or pipedream. Herbordt fpgabased hprc for bioinformatics applications. However, the inherent scalability problem of particleparticle interactions and the sequential dependency of subsequent time steps render md computationally intensive and difficult to scale. This book is concerned with the emerging field of high performance reconfigurable computing hprc, which aims to harness the high performance and relative low power of reconfigurable hardwarein the form field programmable gate arrays fpgasin high performance computing hpc applications. Searching the web for gpu life sciences will highlight the types of applications gpu cards are most commonly used for, namely smithwaterman based alignment algorithms or computational chemistry molecular dynamics algorithms. It presents the latest developments in this field from applications, architecture, and tools and. Highperformance computing using fpgas springer for. Montecarlo simulationbased financial computing on the maxwell fpga parallel machine xiang tian, khaled benkrid bioinformatics applications on the fpga based highperformance computer rivyera lars wienbrandt fpga accelerated molecular dynamics m. One promising approach to improve simulation performance is to apply hardware, specifically reconfigurable hardware in the form of field programmable gate arrays fpgas. A heterogeneous gasnet implementation for fpgaaccelerated computing ruediger willenberg and paul chow october 9, 2014. Thirteen application chapters which present the most important application areas tackled by high performance reconfigurable computers, namely.
Fast and accurate molecular dynamics simulation of a protein using a specialpurpose computer. An fpga accelerator for molecular dynamics simulation using. The potential energy pe and wave function wf kernels are implemented on. Tmdmpi is a library that implements a subset of the mpi standard to enable message passing between fpga and cpu components. Very different thinking than software programming established hardware description languages verilog hdl, vhdl are very lowlevel. Fpgaaccelerated molecular dynamics simulations system. However, the inherent scalability problem of particleparticle interactions and the sequential dependency of subsequent time steps render md computationally intensive. Fpgaaccelerated highperformance computing close to breakthrough or pipedream.
If you dont want to wait have a look at our ebook offers and start reading immediately. Accelerating life science and bioinformatics applications. Opencl for fpga, molecular dynamics simulation, hardware acceleration, sci entific computing. Herbordt fpga based hprc for bioinformatics applications.
Gpgpus have shown proof to accelerated codes like namd nanoscale molecular dynamics, vmd visual molecular dynamics, and charmm chemistry at harvard macromolecular mechanics. Here, we present a reconfigurable computing architecture using field programmable gate arrays fpgas to accelerate two computationally intensive kernels of a quantum monte carlo qmc application applied to nbody systems. Montecarlo simulationbased financial computing on the maxwell fpga parallel machine xiang tian, khaled benkrid bioinformatics applications on the fpgabased highperformance computer rivyera lars wienbrandt fpgaaccelerated molecular dynamics m. Fpgaaccelerated molecular dynamics boston university. With advancing of fpga capability and inclusion of embedded multipliers, lots of studies steer to focus on fpga accelerated md simulations. While molecular dynamics simulation md uses a large fraction of the worlds high performance compute cycles, the modeling of many physical phenomena remains far out of. With sensors becoming increasingly fast, frameworks such as deep neural networks are required to perform. Realtime analysis of patient data during medical procedures can provide vital diagnostic feedback that significantly improves chances of success. This book provides an overview of architectures, tools and applications for highperformance reconfigurable computing hprc. On the feasibility of fpga acceleration of molecular dynamics.
As it stands now, all of the major molecular dynamics software packages have been ported to cuda for use on gpu for acceleration, which. Timelogics fpgaaccelerated systems provide superior priceperformance for bioinformatics sequence comparison tools such as blast. Classical molecular dynamics md simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. This process is both timeconsuming and limits the flexibility of both the software and the hardware. What high performance computing solutions can do for you with custom datapaths and memory hierarchies, and a rich developer toolset, xilinx fpga accelerated applications can enable optimized hardware and software implementations with the flexibility to adapt to changing requirements without sacrificing performance and energy efficiency. Load balancing is primarily achieved through the use of specialized processing units, referred to as flex units. A heterogeneous gasnet implementation for fpgaaccelerated computing. Gpuaccelerated computing enabling a high degree of parallelism each.
981 1254 595 1107 900 837 413 883 286 1174 98 1356 144 28 687 1051 1299 122 1086 220 188 417 463 230 1470 931 1193 97 1187 75 587 292 1340 1102 123 1404 216 1042 283 1252 581 830 1040 1167 248