We investigate the relative performance of a second-order Adams-Bashforth scheme and second- and fourth-order Runge-Kutta schemes when time-stepping a 2D linear advection problem discretised using a spectral/hp element technique for a range of different mesh sizes and polynomial orders. Numerical experiments explore the effects of short (2 wavelengths) and long (32 wavelengths) time integration for […]
Simplifying the Development, Use and Sustainability of HPC Software
Developing software to undertake complex, compute-intensive scientific processes requires a challenging combination of both specialist domain knowledge and software development skills to convert this knowledge into efficient code. As computational platforms become increasingly heterogeneous and newer types of platform such as Infrastructure-as-a-Service (IaaS) cloud computing become more widely accepted for HPC computations, scientists require more […]
High-order spectral/hp element discretisation for reaction-diffusion problems on surfaces: Application to cardiac electrophysiology
We present a numerical discretisation of an embedded two-dimensional manifold using high-order continuous Galerkin spectral/hp elements, which provide exponential convergence of the solution with increasing polynomial order, while retaining geometric flexibility in the representation of the domain. Our work is motivated by applications in cardiac electrophysiology where sharp gradients in the solution benefit from the […]
Nekkloud: A software environment for high-order finite element analysis on clusters and clouds
As the capabilities and diversity of computational platforms continue to grow, scientific software is becoming ever more complex in order to target resources effectively. In the libhpc project we are developing a suite of tools and services to simplify job description and execution on heterogeneous infrastructures.
Severe gap junctional uncoupling causes electrogram fractionation in a novel 1D numerical model of discrete myocytes
Determining the resolution of data required for tracking rotors in a downsampled computational model of atrial fibrillation
Finite element assembly strategies on multi-core and many-core architectures
We demonstrate that radically differing implementations of finite element methods (FEMs) are needed on multi-core (CPU) and many-core (GPU) architectures, if their respective performance potential is to be realised. Our numerical investigations using a finite element advection–diffusion solver show that increased performance on each architecture can only be achieved by committing to specific and diverse […]
libHPC: Software sustainability and reuse through metadata preservation
Software development, particularly of complex scientific applications, requires a detailed understanding of the problem(s) to be solved and an ability to translate this understanding into the generic constructs of a programming language. We believe that such knowledge – information about a code’s “building blocks”, especially the low-level functions and procedures in which domain-specific tasks are […]
From h to p efficiently: strategy selection for operator evaluation on hexahedral and tetrahedral elements
A spectral/hp element discretisation permits both geometric flexibility and beneficial convergence properties to be attained simultaneously. The choice of elemental polynomial order has a profound effect on the efficiency of different implementation strategies with their performance varying substantially for low and high order spectral/hp discretisations. We examine how careful selection of the strategy minimises computational […]
From h to p efficiently: selecting the optimal spectral/hp discretisation in three dimensions
There is a growing interest in high-order finite and spectral/hp element methods using continuous and discontinuous Galerkin formulations. In this paper we investigate the effect of h– and p-type refinement on the relationship between runtime performance and solution accuracy. The broad spectrum of possible domain discretisations makes establishing a performance-optimal selection non-trivial. Through comparing the […]