GOTPM: a parallel hybrid particle-mesh treecode

Dubinski, John; Kim, Juhan; Park, Changbom; Humble, Robin

doi:10.1016/j.newast.2003.08.002

Cited by 93 publications

(100 citation statements)

References 25 publications

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“…If double precision values require 8 bytes and integers require 4, then a threedimensional simulation on one processor, with either entirely N-body or entirely SPH particles will require 474 or 584 bytes of memory per particle when the leapfrog integrator is used (292 or 368 bytes in single precision), and 522 or 706 bytes per particle when the Runge-Kutta integrator is used (318 or 410 bytes in single precision). In comparison, VINE requires 30%-50% more total memory per particle than the Gadget and GOTPM codes (Springel 2005;Dubinski et al 2003), when they are used in double precision mode. Approximately half of the extra cost is due to fact that VINE includes the quadrupole in the multipole summation of gravity, which requires 96 bytes/ particle to store the quadrupole moments for all nodes.…”

Section: Overview Of the Codementioning

confidence: 99%

Vine—a Numerical Code for Simulating Astrophysical Systems Using Particles. Ii. Implementation and Performance Characteristics

Nelson

Wetzstein

Naab

2009

ApJS

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We continue our presentation of VINE. In this paper, we begin with a description of relevant architectural properties of the serial and shared memory parallel computers on which VINE is intended to run, and describe their influences on the design of the code itself. We continue with a detailed description of a number of optimizations made to the layout of the particle data in memory and to our implementation of a binary tree used to access that data for use in gravitational force calculations and searches for smoothed particle hydrodynamics (SPH) neighbor particles. We describe the modifications to the code necessary to obtain forces efficiently from special purpose "GRAPE" hardware, the interfaces required to allow transparent substitution of those forces in the code instead of those obtained from the tree, and the modifications necessary to use both tree and GRAPE together as a fused GRAPE/ tree combination. We conclude with an extensive series of performance tests, which demonstrate that the code can be run efficiently and without modification in serial on small workstations or in parallel using the OpenMP compiler directives on large-scale, shared memory parallel machines. We analyze the effects of the code optimizations and estimate that they improve its overall performance by more than an order of magnitude over that obtained by many other tree codes. Scaled parallel performance of the gravity and SPH calculations, together the most costly components of most simulations, is nearly linear up to at least 120 processors on moderate sized test problems using the Origin 3000 architecture, and to the maximum machine sizes available to us on several other architectures. At similar accuracy, performance of VINE, used in GRAPE-tree mode, is approximately a factor 2 slower than that of VINE, used in host-only mode. Further optimizations of the GRAPE/host communications could improve the speed by as much as a factor of 3, but have not yet been implemented in VINE. Finally, we find that although parallel performance on small problems may reach a plateau beyond which more processors bring no additional speedup, performance never decreases, a factor important for running large simulations on many processors with individual time steps, where only a small fraction of the total particles require updates at any given moment.

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Section: Overview Of the Codementioning

confidence: 99%

Vine—a Numerical Code for Simulating Astrophysical Systems Using Particles. Ii. Implementation and Performance Characteristics

Nelson

Wetzstein

Naab

2009

ApJS

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“…The simulation starts at z i = 27 and is evolved to the present epoch with 600 global time steps. The code used for the run is an improved version of the GOTPM code ("Grid-of-OctTrees-Particle-Mesh") originally devised by Dubinski et al (2004); a new procedure has been implemented in order to more accurately describe the particle positions using single precision.…”

Section: The Horizon Run 3 N-body Simulationmentioning

confidence: 99%

Topology of Luminous Red Galaxies From the Sloan Digital Sky Survey

Choi¹,

Kim²,

Rossi³

et al. 2013

ApJS

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We present measurements of the genus topology of luminous red galaxies (LRGs) from the Sloan Digital Sky Survey (SDSS) Data Release 7 catalog, with unprecedented statistical significance. To estimate the uncertainties in the measured genus, we construct 81 mock SDSS LRG surveys along the past light cone from Horizon Run 3, one of the largest N-body simulations to date, which evolved 7210 3 particles in a 10,815 h −1 Mpc box. After carefully modeling and removing all known systematic effects due to finite pixel size, survey boundary, radial and angular selection functions, shot noise, and galaxy biasing, we find that the observed genus amplitude reaches 272 at a 22 h −1 Mpc smoothing scale, with an uncertainty of 4.2%; the estimated error fully incorporates cosmic variance. This is the most accurate constraint on the genus amplitude to date and significantly improves on our previous results. In particular, the shape of the genus curve agrees very well with the mean topology of the SDSS LRG mock surveys in a Λ cold dark matter universe. However, comparison with simulations also shows small deviations of the observed genus curve from the theoretical expectation for Gaussian initial conditions. While these discrepancies are mainly driven by known systematic effects such as shot noise and redshift-space distortions, they do contain important cosmological information on the physical effects connected with galaxy formation, gravitational evolution, and primordial non-Gaussianity. We address the key role played by systematics on the genus curve and show how to accurately correct for their effects to recover the topology of the underlying matter. A future work will provide an interpretation of these deviations in the context of the local model of non-Gaussianity.

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“…The simulation is run by a PM+Tree N-body code (Dubinski et al 2004) and has a force resolution of 0.24 h −1 Mpc.…”

Section: N-body Simulationmentioning

confidence: 99%

Three-Dimensional Genus Topology of Luminous Red Galaxies

Gott

Choi

Park

et al. 2009

ApJ

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We measure the three-dimensional genus topology of large-scale structure using luminous red galaxies (LRGs) in the Sloan Digital Sky Survey and find it consistent with the Gaussian random phase initial conditions expected from the simplest scenarios of inflation. This studies three-dimensional topology on the largest scales ever obtained. The topology is spongelike. We measure topology in two volume-limited samples: a dense shallow sample studied with smoothing length of 21 h −1 Mpc, and a sparse deep sample studied with a smoothing length of 34 h −1 Mpc. The amplitude of the genus curve is measured with 4% uncertainty. Small distortions in the genus curve expected from nonlinear biasing and gravitational effects are well explained (to about 1σ accuracy) by N-body simulations using a subhalo-finding technique to locate LRGs. This suggests that the formation of LRGs is a clean problem that can be modeled well without any free-fitting parameters. This bodes well for using LRGs to measure the characteristic scales such as the baryon oscillation scale in future deep redshift surveys.

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GOTPM: a parallel hybrid particle-mesh treecode

Cited by 93 publications

References 25 publications

Vine—a Numerical Code for Simulating Astrophysical Systems Using Particles. Ii. Implementation and Performance Characteristics

Vine—a Numerical Code for Simulating Astrophysical Systems Using Particles. Ii. Implementation and Performance Characteristics

Topology of Luminous Red Galaxies From the Sloan Digital Sky Survey

Three-Dimensional Genus Topology of Luminous Red Galaxies

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