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

Simplifying Parallelization of Scientific Codes by a Function-Centric Approach in Python

The purpose of this paper is to show how existing scientific software can be parallelized using a separate thin layer of Python code where all parallel communication is implemented. We provide specific examples on such layers of code, and these examples may act as templates for parallelizing a wide set of serial scientific codes. The use of Python for parallelization is motivated by the fact that the language is well suited for reusing existing serial codes programmed in other languages. The extreme flexibility of Python with regard to handling functions makes it very easy to wrap up decomposed computational tasks of a serial scientific application as Python functions. Many parallelization-specific components can be implemented as generic Python functions, which may take as input those functions that perform concrete computational tasks. The overall programming effort needed by this parallelization approach is rather limited, and the resulting parallel Python scripts have a compact and clean structure. The usefulness of the parallelization approach is exemplified by three different classes of applications in natural and social sciences.Comment: 29 pages, submitted to Computational Science and Discover

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

A finite element analysis of a silicon based double quantum dot structure

We present the results of a finite-element solution of the Laplace equation for the silicon-based trench-isolated double quantum-dot and the capacitively-coupled single-electron transistor device architecture. This system is a candidate for charge and spin-based quantum computation in the solid state, as demonstrated by recent coherent-charge oscillation experiments. Our key findings demonstrate control of the electric potential and electric field in the vicinity of the double quantum-dot by the electric potential applied to the in-plane gates. This constitutes a useful theoretical analysis of the silicon-based architecture for quantum information processing applications

A numerical investigation of a piezoelectric surface acoustic wave interaction with a one-dimensional channel

We investigate the propagation of a piezoelectric surface acoustic wave (SAW) across a GaAs/Al$_X$Ga$_{1-X}$As heterostructure surface, on which there is fixed a metallic split-gate. Our method is based on a finite element formulation of the underlying equations of motion, and is performed in three-dimensions fully incorporating the geometry and material composition of the substrate and gates. We demonstrate attenuation of the SAW amplitude as a result of the presence of both mechanical and electrical gates on the surface. We show that the incorporation of a simple model for the screening by the two-dimensional electron gas (2DEG), results in a total electric potential modulation that suggests a mechanism for the capture and release of electrons by the SAW. Our simulations suggest the absence of any significant turbulence in the SAW motion which could hamper the operation of SAW based quantum devices of a more complex geometry.Comment: 8 pages, 8 figure

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.