arXiv subjects

Adrian Jackson

Publications and source records attributed to Adrian Jackson.

25 records · Page 2Linked to original sources

arXiv2018

Architectures for High Performance Computing and Data Systems using Byte-Addressable Persistent Memory

Non-volatile, byte addressable, memory technology with performance close to main memory promises to revolutionise computing systems in the near future. Such memory technology provides the potential for extremely large memory regions (i.e. > 3TB per server), very high performance I/O, and new ways of storing and sharing data for applications and workflows. This paper outlines an architecture that has been designed to exploit such memory for High Performance Computing and High Performance Data Analytics systems, along with descriptions of how applications could benefit from such hardware.

cs.DC↗

arXiv2017

BeatBox - HPC Simulation Environment for Biophysically and Anatomically Realistic Cardiac Electrophysiology

The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell excitation, tissue/anatomy models, stimulation protocols may be included into a BeatBox script, and simulation run either sequentially or in parallel (MPI) without re-compilation. BeatBox is a free software written in C language to be run on a Unix-based platform. It provides the whole spectrum of multi scale tissue modelling from 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations, with run time measurements including cardiac re-entry tip/filament tracing, ECG, local/global samples of any variables, etc. BeatBox solvers, cell, and tissue/anatomy models repositories are extended via robust and flexible interfaces, thus providing an open framework for new developments in the field. In this paper we give an overview of the BeatBox current state, together with a description of the main computational methods and MPI parallelisation approaches.

cs.CE↗

arXiv2016

Efficient Large Eddy Simulation for the Discontinuous Galerkin Method

In this paper we present a new technique for efficiently implementing Large Eddy Simulation with the Discontin- uous Galerkin method on unstructured meshes. In particular, we will focus upon the approach to overcome the computational complexity that the additional degrees of freedom in Discontinuous Galerkin methods entail. The turbulence algorithms have been implemented within Fluidity, an open-source computational fluid dynamics solver. The model is tested with the well known backward-facing step problem, and is shown to concur with published results.

physics.flu-dyn↗

arXiv2013

MDMP: Managed Data Message Passing

MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based parallel programs to be optimised and extended without requiring the whole code to be re-written from scratch. MDMP utilises a directives based approach to enable users to specify what communications should take place in the code, and then implements those communications for the user in an optimal manner using both the information provided by the user and data collected from instrumenting the code and gathering information on the data to be communicated. This work will present the basic concepts and functionality of MDMP and discuss the performance that can be achieved using our prototype implementation of MDMP on some model scientific simulation applications.

cs.DC↗

arXiv2013

Optimised hybrid parallelisation of a CFD code on Many Core architectures

COSA is a novel CFD system based on the compressible Navier-Stokes model for unsteady aerodynamics and aeroelasticity of fixed structures, rotary wings and turbomachinery blades. It includes a steady, time domain, and harmonic balance flow solver. COSA has primarily been parallelised using MPI, but there is also a hybrid parallelisation that adds OpenMP functionality to the MPI parallelisation to enable larger number of cores to be utilised for a given simulation as the MPI parallelisation is limited to the number of geometric partitions (or blocks) in the simulation, or to exploit multi-threaded hardware where appropriate. This paper outlines the work undertaken to optimise these two parallelisation strategies, improving the efficiency of both and therefore reducing the computational time required to compute simulations. We also analyse the power consumption of the code on a range of leading HPC systems to further understand the performance of the code.

cs.DC↗

arXiv2012

Optimising Performance Through Unbalanced Decompositions

GS2 is an initial value gyrokinetic simulation code developed to study low-frequency turbulence in magnetized plasma. It is parallelised using MPI with the simulation domain decomposed across tasks. The optimal domain decomposition is non-trivial, and complicated by the different requirements of the linear and non-linear parts of the calculations. GS2 users currently choose a data layout, and are guided towards processor count that are efficient for linear calculations. These choices can, however, lead to data decompositions that are relatively inefficient for the non-linear calculations. We have analysed the performance impact of the data decompositions on the non-linear calculation and associated communications. This has helped us to optimise the decomposition algorithm by using unbalanced data layouts for the non-linear calculations whilst maintaining the existing decompositions for the linear calculations, which has completely eliminated communications for parts of the non-linear simulation and improved performance by up to 15% for a representative simulation.

cs.DC↗

arXiv2012

Dynamic Loop Parallelisation

Regions of nested loops are a common feature of High Performance Computing (HPC) codes. In shared memory programming models, such as OpenMP, these structure are the most common source of parallelism. Parallelising these structures requires the programmers to make a static decision on how parallelism should be applied. However, depending on the parameters of the problem and the nature of the code, static decisions on which loop to parallelise may not be optimial, especially as they do not enable the exploitation of any runtime characteristics of the execution including changes to the iterations of the loops to be parallelised. We have developed a system that allows a code to make a dynamic choice, at runtime, of what parallelism is applied to nested loops. Our method for providing dynamic decisions on which loop to parallelise significantly outperforms the standard methods for acheiving this through OpenMP (using if clauses).

cs.PL↗