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Almgren, Ann S.

Publications and source records attributed to Almgren, Ann S..

The Pele Simulation Suite for Reacting Flows at Exascale

In this work, we present the Pele suite of software tools for compressible and incompressible reacting flows. The Pele suite leverages several different libraries, notably AMReX and SUNDIALS, to achieve performance portability on heterogeneous computing architectures across the supercomputing landscape. The Pele suite is comprised of PeleC, a compressible reacting flow block-structured adaptive mesh refinement solver, PeleLMeX, a low-Mach number reacting flow block-structured adaptive mesh refinement solver, Pele-Physics, a library for transport, thermodynamics, finite rate chemistry, soot, spray and radiation physics. The objective of this paper is (i) to present the code development efforts necessary to achieve highly effective and scalable applications for exascale machines and (ii) to detail the performance results of the Combustion-Pele project applications on Oak Ridge National Laboratory's Frontier. We show good weak and strong scaling results for both PeleC and PeleLMeX up to more than 50 billion cells on more than 4096 Frontier graphics processing unit nodes. We also present a capability demonstration simulation of a dual-fuel pulse compression ignition engine (six adaptive mesh refinement levels, and 60 billion cells or 2.1 trillion degrees of freedom) on Frontier, to date one of the largest simulations performed on the first exascale-class supercomputer.

adaptive mesh refinement↗

BMX: Biological modelling and interface exchange

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

97 MATHEMATICS AND COMPUTING↗