71 research outputs found
Harvesting graphics power for MD simulations
We discuss an implementation of molecular dynamics (MD) simulations on a
graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code
on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms
suitable for short-ranged and long-ranged interactions, and a congruential
shift random number generator are presented. The performance of the GPU's is
compared to their main processor counterpart. We achieve speedups of up to 80,
40 and 150 fold, respectively. With newest generation of GPU's one can run
standard MD simulations at 10^7 flops/$.Comment: 12 pages, 5 figures. Submitted to Mol. Si
Analysing Astronomy Algorithms for GPUs and Beyond
Astronomy depends on ever increasing computing power. Processor clock-rates
have plateaued, and increased performance is now appearing in the form of
additional processor cores on a single chip. This poses significant challenges
to the astronomy software community. Graphics Processing Units (GPUs), now
capable of general-purpose computation, exemplify both the difficult
learning-curve and the significant speedups exhibited by massively-parallel
hardware architectures. We present a generalised approach to tackling this
paradigm shift, based on the analysis of algorithms. We describe a small
collection of foundation algorithms relevant to astronomy and explain how they
may be used to ease the transition to massively-parallel computing
architectures. We demonstrate the effectiveness of our approach by applying it
to four well-known astronomy problems: Hogbom CLEAN, inverse ray-shooting for
gravitational lensing, pulsar dedispersion and volume rendering. Algorithms
with well-defined memory access patterns and high arithmetic intensity stand to
receive the greatest performance boost from massively-parallel architectures,
while those that involve a significant amount of decision-making may struggle
to take advantage of the available processing power.Comment: 10 pages, 3 figures, accepted for publication in MNRA
NBSymple, a double parallel, symplectic N-body code running on Graphic Processing Units
We present and discuss the characteristics and performances, both in term of
computational speed and precision, of a numerical code which numerically
integrates the equation of motions of N 'particles' interacting via Newtonian
gravitation and move in an external galactic smooth field. The force evaluation
on every particle is done by mean of direct summation of the contribution of
all the other system's particle, avoiding truncation error. The time
integration is done with second-order and sixth-order symplectic schemes. The
code, NBSymple, has been parallelized twice, by mean of the Computer Unified
Device Architecture to make the all-pair force evaluation as fast as possible
on high-performance Graphic Processing Units NVIDIA TESLA C 1060, while the
O(N) computations are distributed on various CPUs by mean of OpenMP Application
Program. The code works both in single precision floating point arithmetics or
in double precision. The use of single precision allows the use at best of the
GPU performances but, of course, limits the precision of simulation in some
critical situations. We find a good compromise in using a software
reconstruction of double precision for those variables that are most critical
for the overall precision of the code. The code is available on the web site
astrowww.phys.uniroma1.it/dolcetta/nbsymple.htmlComment: Paper composed by 29 pages, including 9 figures. Submitted to New
Astronomy
A pilgrimage to gravity on GPUs
In this short review we present the developments over the last 5 decades that
have led to the use of Graphics Processing Units (GPUs) for astrophysical
simulations. Since the introduction of NVIDIA's Compute Unified Device
Architecture (CUDA) in 2007 the GPU has become a valuable tool for N-body
simulations and is so popular these days that almost all papers about high
precision N-body simulations use methods that are accelerated by GPUs. With the
GPU hardware becoming more advanced and being used for more advanced algorithms
like gravitational tree-codes we see a bright future for GPU like hardware in
computational astrophysics.Comment: To appear in: European Physical Journal "Special Topics" : "Computer
Simulations on Graphics Processing Units" . 18 pages, 8 figure
Computational Physics on Graphics Processing Units
The use of graphics processing units for scientific computations is an
emerging strategy that can significantly speed up various different algorithms.
In this review, we discuss advances made in the field of computational physics,
focusing on classical molecular dynamics, and on quantum simulations for
electronic structure calculations using the density functional theory, wave
function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012,
Helsinki, Finland, June 10-13, 201
Dynamical Processes in Globular Clusters
Globular clusters are among the most congested stellar systems in the
Universe. Internal dynamical evolution drives them toward states of high
central density, while simultaneously concentrating the most massive stars and
binary systems in their cores. As a result, these clusters are expected to be
sites of frequent close encounters and physical collisions between stars and
binaries, making them efficient factories for the production of interesting and
observable astrophysical exotica. I describe some elements of the competition
among stellar dynamics, stellar evolution, and other processes that control
globular cluster dynamics, with particular emphasis on pathways that may lead
to the formation of blue stragglers.Comment: Chapter 10, in Ecology of Blue Straggler Stars, H.M.J. Boffin, G.
Carraro & G. Beccari (Eds), Astrophysics and Space Science Library, Springe
A Problem Solving Environment for Modelling Stony Coral Morphogenesis
Apart from experimental and theoretical approaches, computer simulation is an important tool in testing hypotheses about stony coral growth. However, the construction and use of such simulation tools needs extensive computational skills and knowledge that is not available to most research biologists. Problem solving environments (PSEs) aim to provide a framework that hides implementation details and allows the user to formulate and analyse a problem in the language of the subject area. We have developed a prototypical PSE to study the morphogenesis of corals using a multi-model approach. In this paper we describe the design and implementation of this PSE, in which simulations of the coral's shape and its environment have been combined. We will discuss the relevance of our results for the future development of PSEs for studying biological growth and morphogenesis
Gravitational Dynamics of Large Stellar Systems
Internal dynamical evolution can drive stellar systems into states of high
central density. For many star clusters and galactic nuclei, the time scale on
which this occurs is significantly less than the age of the universe. As a
result, such systems are expected to be sites of frequent interactions among
stars, binary systems, and stellar remnants, making them efficient factories
for the production of compact binaries, intermediate-mass black holes, and
other interesting and eminently observable astrophysical exotica. We describe
some elements of the competition among stellar dynamics, stellar evolution, and
other mechanisms to control the dynamics of stellar systems, and discuss
briefly the techniques by which these systems are modeled and studied.
Particular emphasis is placed on pathways leading to massive black holes in
present-day globular clusters and other potentially detectable sources of
gravitational radiation.Comment: 21 pages, invited talk presented at the 18th International Conference
on General Relativity and Gravitation (GRG18), Sydney, July 2007. To appear
in Classical and Quantum Gravit
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