论文标题

使用PETSC和SLEPC对地球机器的地球磁环境建模

Modelling the earth's geomagnetic environment on Cray machines using PETSc and SLEPc

论文作者

Brown, Nick, Bainbridge, Brian, Beggan, Ciarán, Macmillan, Susan, Brown, William, Hamilton, Brian

论文摘要

英国地质调查局的全球地磁模型,地球磁性环境的模型(MEME)是计算地球磁场的重要工具,该工具不断地发生。尽管从基于地面的观察站点和卫星中收集数据的能力已经增长,但该代码的记忆界限已证明是在现代科学所需的建模问题大小的建模方面的限制。在本文中,我们描述了用SLEPC包装的定制,顺序的,特征 - 溶剂代替定制,顺序的,特征溶剂的工作,用于求解正常方程的系统。这项工作具有双重目的,可以突破代码的内存限制,从而通过支持分布式计算机上的执行并提高性能来支持更大系统的建模。但是,当采用SLEPC时,它不仅是解决正常方程式的求解,而且从根本上讲,我们如何构建和分发数据结构。我们描述了一种构建对称矩阵的方法,该方法可以提供良好的负载平衡,并避免在过程之间进行密切协调或复制工作。我们还研究了代码的内存结合性质,并将详细的分析与软件缓存预取相结合以显着优化。在Cray XC30的Archer上探索了性能和缩放,通过用SLEPC替换模型的定制方法,我们可以为求解器实现294次的速度。这项工作还提供了建模更大的系统尺寸(最多100,000个模型系数)的能力。探索了该大规模建模系统的一些挑战,还考虑了包括混合MPI+OpenMP在内的缓解以及使用迭代求解器的使用。这项工作的结果是一种现代模因模型,它不仅能够模拟由最先进的地磁规范所需的问题大小,而且还可以作为SLEPC性欲效用的进一步证据。

The British Geological Survey's global geomagnetic model, Model of the Earth's Magnetic Environment (MEME), is an important tool for calculating the earth's magnetic field, which is continually in flux. Whilst the ability to collect data from ground based observation sites and satellites has grown, the memory bound nature of the code has proved a limitation in modelling problem sizes required by modern science. In this paper we describe work replacing the bespoke, sequential, eigen-solver with that of the SLEPc package for solving the system of normal equations. This work had a dual purpose, to break through the memory limit of the code, and thus support the modelling of much larger systems, by supporting execution on distributed machines, and to improve performance. But when adopting SLEPc it was not just the solving of the normal equations, but also fundamentally how we build and distribute the data structures. We describe an approach for building symmetric matrices in a way that provides good load balance and avoids the need for close co-ordination between processes or replication of work. We also study the memory bound nature of the code and combine detailed profiling with software cache prefetching to significantly optimise. Performance and scaling are explored on ARCHER, a Cray XC30, where we achieve a speed up for the solver of 294 times by replacing the model's bespoke approach with SLEPc. This work also provided the ability to model much larger system sizes, up to 100,000 model coefficients. Some of the challenges of modelling systems of this large scale are explored, and mitigations including hybrid MPI+OpenMP along with the use of iterative solvers are also considered. The result of this work is a modern MEME model that is not only capable of simulating problem sizes demanded by state of the art geomagnetism but also acts as further evidence to the utility of the SLEPc libary.

扫码加入交流群

加入微信交流群

微信交流群二维码

扫码加入学术交流群,获取更多资源