Compiled hardware acceleration of Molecular Dynamics code (original) (raw)
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2007
Recent widespread interest in the use of configurable hardware accelerators has brought to light the need for a portable application programmer interface (API) to achieve widespread adoption. Recent activities defining a candidate common generic API for field programmable gate arrays have facilitated the definition of an application specific API for accelerating molecular dynamics programs. Using the LAMMPS application as a prototype implementation platform, both the general FPGA API and application specific molecular dynamics API are presented with preliminary results confirming the viability of the portability of both a general and functionally specific API across reconfigurable hardware and development environments.
2007
Recent widespread interest in the use of configurable hardware accelerators has brought to light the need for a portable application programmer interface (API) to achieve widespread adoption. Recent activities defining a candidate common generic API for field programmable gate arrays have facilitated the definition of an application specific API for accelerating molecular dynamics programs. Using the LAMMPS application as a prototype implementation platform, both the general FPGA API and application specific molecular dynamics API are presented with preliminary results confirming the viability of the portability of both a general and functionally specific API across reconfigurable hardware and development environments.
A Heterogeneous, Purpose Built Computer Architecture for Accelerating Biomolecular Simulation
Biophysical Journal, 2011
Molecular dynamics (MD) is a powerful computer simulation technique providing atomistic resolution across a broad range of time scales. In the past four decades, researchers have harnessed the exponential growth in computer power and applied it to the simulation of diverse molecular systems. Although MD simulations are playing an increasingly important role in biomedical research, sampling limitations imposed by both hardware and software constraints establish a de facto upper bound on the size and length of MD trajectories. While simulations are currently approaching the hundred-thousand-atom, millisecond-timescale mark using large-scale computing centres To all the lifelong friends who have provided a great number of diversions over the years, thanks.
Accelerating molecular modeling applications with graphics processors
Journal of Computational Chemistry, 2007
Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. Stateof-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed.
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Journal of Computational Chemistry, 2009
We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.
On the performance of molecular dynamics applications on current high-end systems
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2005
The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's national HPC resources, an IBM p690C cluster and an SGI Altix 3700.
Accelerating molecular dynamic simulation on the cell processor and Playstation 3
2009
Abstract Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3).
Porting the GROMACS Molecular Dynamics Code to the Cell Processor
2007 IEEE International Parallel and Distributed Processing Symposium, 2007
The Cell processor offers substantial computational power which can be effectively utilized only if application design and implementation are tuned to the Cell architecture. In this paper, we examine application characteristics which facilitate efficient use of the Cell processor, and those which present obstacles to it. Moreover, we consider possible solutions designed to mitigate inefficiencies. The target application in our study is the GROMACS molecular dynamics package. We have accelerated the most-often used compute-intensive kernel while maintaining the constraints imposed by the structure of the surrounding program. The significant contribution of this paper is the consideration of the kernel in the context of a complex end-to-end application, with irregular data and code patterns, rather than an isolated kernel code. For this challenging scenario, our results show a 2X speedup versus hand-tuned VMX/SSE code running on high-end PowerPC and x86 uniprocessor machines.
Scalable molecular dynamics on CPU and GPU architectures with NAMD
The Journal of Chemical Physics, 2020
NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, p...