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

Abstract

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.

DYNAMICS OF CIRCUMSTELLAR DISKS III: THE CASE OF GG Tau A

“…We use the Smoothed Particle Hydrodynamics (SPH) code "VINE" Nelson et al 2009), to evolve our simulations forward in time. SPH is a particle based, Lagrangian method for solving the hydrodynamic equations, and so is very well suited to the complex geometry present in the multi-component systems we study.…”

Consistent SPH Simulations of Protostellar Collapse and Fragmentation

“…It is well known that this form of the artificial viscosity introduces excessive dissipation in shear flows, leading to spurious angular momentum transport in the presence of vorticity. Therefore, it is desirable to suppress this excessive dissipation in regions where the vorticity dominates over the velocity divergence (Nelson et al 2009). In particular, Morris & Monaghan (1997) proposed individual viscosity coefficients that adapt their values according to velocity-based source terms.…”

Decoupling of a giant planet from its disk in an inclined binary system

“…We used two different SPH codes to model the evolution of a Jupiter-sized planet that is embedded in the disk that surrounds the primary star of an inclined binary system: -VINE Nelson et al 2009), which is a hybrid N-body/SPH code and has been updated to improve momentum and energy conservation, as described in Picogna & Marzari (2013); -PHANTOM (Price & Federrath 2010;Lodato & Price 2010), a modern SPH code that models the massive bodies as sink particles (Bate et al 1995).…”