High performance Python for direct numerical simulations of turbulent flows

Direct Numerical Simulations (DNS) of the Navier Stokes equations is an invaluable research tool in fluid dynamics. Still, there are few publicly available research codes and, due to the heavy number crunching implied, available codes are usually written in low-level languages such as C/C++ or Fortran. In this paper we describe a pure scientific Python pseudo-spectral DNS code that nearly matches the performance of C++ for thousands of processors and billions of unknowns. We also describe a version optimized through Cython, that is found to match the speed of C++. The solvers are written from scratch in Python, both the mesh, the MPI domain decomposition, and the temporal integrators. The solvers have been verified and benchmarked on the Shaheen supercomputer at the KAUST supercomputing laboratory, and we are able to show very good scaling up to several thousand cores. A very important part of the implementation is the mesh decomposition (we implement both slab and pencil decompositions) and 3D parallel Fast Fourier Transforms (FFT). The mesh decomposition and FFT routines have been implemented in Python using serial FFT routines (either NumPy, pyFFTW or any other serial FFT module), NumPy array manipulations and with MPI communications handled by MPI for Python (mpi4py). We show how we are able to execute a 3D parallel FFT in Python for a slab mesh decomposition using 4 lines of compact Python code, for which the parallel performance on Shaheen is found to be slightly better than similar routines provided through the FFTW library. For a pencil mesh decomposition 7 lines of code is required to execute a transform

Finite Difference Computing with Exponential Decay Models

Computational Science and Engineering; software Engineering; Programming Technique

Pulse-induced acoustoelectric vibrations in surface-gated GaAs-based quantum devices

We present the results of a numerical investigation which show the excitation of acoustoelectric modes of vibration in GaAs-based heterostructures due to sharp nano-second electric-field pulses applied across surface gates. In particular, we show that the pulses applied in quantum information processing applications are capable of exciting acoustoelectric modes of vibration including surface acoustic modes which propagate for distances greater than conventional device dimensions. We show that the pulse-induced acoustoelectric vibrations are capable of inducing significant undesired perturbations to the evolution of quantum systems.Comment: To be published in Phys. Rev.

Unified Framework for Finite Element Assembly

At the heart of any finite element simulation is the assembly of matrices and vectors from discrete variational forms. We propose a general interface between problem-specific and general-purpose components of finite element programs. This interface is called Unified Form-assembly Code (UFC). A wide range of finite element problems is covered, including mixed finite elements and discontinuous Galerkin methods. We discuss how the UFC interface enables implementations of variational form evaluation to be independent of mesh and linear algebra components. UFC does not depend on any external libraries, and is released into the public domain

Programming for Computations - Python: A Gentle Introduction to Numerical Simulations with Python

Numerical simulations; programming; Pytho

Solving PDEs in Python

This book offers a concise and gentle introduction to finite element programming in Python based on the popular FEniCS software library. Using a series of examples, including the Poisson equation, the equations of linear elasticity, the incompressible Navier–Stokes equations, and systems of nonlinear advection–diffusion–reaction equations, it guides readers through the essential steps to quickly solving a PDE in FEniCS, such as how to define a finite variational problem, how to set boundary conditions, how to solve linear and nonlinear systems, and how to visualize solutions and structure finite element Python programs. This book is open access under a CC BY license