GreeM : Massively Parallel TreePM Code for Large Cosmological N-body Simulations

In this paper, we describe the implementation and performance of GreeM, a massively parallel TreePM code for large-scale cosmological N-body simulations. GreeM uses a recursive multi-section algorithm for domain decomposition. The size of the domains are adjusted so that the total calculation time of the force becomes the same for all processes. The loss of performance due to non-optimal load balancing is around 4%, even for more than 10^3 CPU cores. GreeM runs efficiently on PC clusters and massively-parallel computers such as a Cray XT4. The measured calculation speed on Cray XT4 is 5 \times 10^4 particles per second per CPU core, for the case of an opening angle of \theta=0.5, if the number of particles per CPU core is larger than 10^6.Comment: 13 pages, 11 figures, accepted by PAS

A hybrid MPI-OpenMP scheme for scalable parallel pseudospectral computations for fluid turbulence

A hybrid scheme that utilizes MPI for distributed memory parallelism and OpenMP for shared memory parallelism is presented. The work is motivated by the desire to achieve exceptionally high Reynolds numbers in pseudospectral computations of fluid turbulence on emerging petascale, high core-count, massively parallel processing systems. The hybrid implementation derives from and augments a well-tested scalable MPI-parallelized pseudospectral code. The hybrid paradigm leads to a new picture for the domain decomposition of the pseudospectral grids, which is helpful in understanding, among other things, the 3D transpose of the global data that is necessary for the parallel fast Fourier transforms that are the central component of the numerical discretizations. Details of the hybrid implementation are provided, and performance tests illustrate the utility of the method. It is shown that the hybrid scheme achieves near ideal scalability up to ~20000 compute cores with a maximum mean efficiency of 83%. Data are presented that demonstrate how to choose the optimal number of MPI processes and OpenMP threads in order to optimize code performance on two different platforms.Comment: Submitted to Parallel Computin

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Solving the Klein-Gordon equation using Fourier spectral methods: A benchmark test for computer performance

The cubic Klein-Gordon equation is a simple but non-trivial partial differential equation whose numerical solution has the main building blocks required for the solution of many other partial differential equations. In this study, the library 2DECOMP&FFT is used in a Fourier spectral scheme to solve the Klein-Gordon equation and strong scaling of the code is examined on thirteen different machines for a problem size of 512^3. The results are useful in assessing likely performance of other parallel fast Fourier transform based programs for solving partial differential equations. The problem is chosen to be large enough to solve on a workstation, yet also of interest to solve quickly on a supercomputer, in particular for parametric studies. Unlike other high performance computing benchmarks, for this problem size, the time to solution will not be improved by simply building a bigger supercomputer.Comment: 10 page

An efficient parallel immersed boundary algorithm using a pseudo-compressible fluid solver

We propose an efficient algorithm for the immersed boundary method on distributed-memory architectures, with the computational complexity of a completely explicit method and excellent parallel scaling. The algorithm utilizes the pseudo-compressibility method recently proposed by Guermond and Minev [Comptes Rendus Mathematique, 348:581-585, 2010] that uses a directional splitting strategy to discretize the incompressible Navier-Stokes equations, thereby reducing the linear systems to a series of one-dimensional tridiagonal systems. We perform numerical simulations of several fluid-structure interaction problems in two and three dimensions and study the accuracy and convergence rates of the proposed algorithm. For these problems, we compare the proposed algorithm against other second-order projection-based fluid solvers. Lastly, the strong and weak scaling properties of the proposed algorithm are investigated