Abstract:
Octree-based mesh adaptation has enabled simulations of complex physical phenomena. Existing meshing algorithms were proposed with the assumption that computer memory is ...Show MoreMetadata
Abstract:
Octree-based mesh adaptation has enabled simulations of complex physical phenomena. Existing meshing algorithms were proposed with the assumption that computer memory is volatile. Consequently, for failure recovery, the in-core algorithms need to save memory states as snapshots with slow file I/Os. The out-of-core algorithms store octants on disks for persistence. However, neither of them was designed to leverage unique characteristics of non-volatile byte-addressable memory (NVBM). In this paper, we propose a novel data structure P ersistent M erged octree (PM-octree) for both meshing and in-memory storage of persistent octrees using NVBM. It is a multi-version data structure and can recover from failures using its earlier persistent version stored in NVBM. In addition, we design a feature-directed sampling approach to help dynamically transform the PM-octree layout for reducing NVBM-induced memory write latency. PM-octree has been successfully integrated with Gerris software for simulation of fluid dynamics. Our experimental results with real-world scientific workloads show that PM-octree scales up to 1.1 billion mesh elements with 1000 processors on the Titan supercomputer. CCS CONCEPTS • Software and its engineering \rightarrow Memory management; • Mathematics of computing \rightarrow Mesh generation;
Published in: SC17: International Conference for High Performance Computing, Networking, Storage and Analysis
Date of Conference: 12-17 November 2017
Date Added to IEEE Xplore: 27 October 2022
Electronic ISBN:978-1-4503-5114-0
ISSN Information:
Conference Location: Denver, CO, USA