SPH-EXA: Enhancing the Scalability of SPH codes Via an Exascale-Ready SPH Mini-App

Numerical simulations of fluids in astrophysics and computational fluid dynamics (CFD) are among the most computationally-demanding calculations, in terms of sustained floating-point operations per second, or FLOP/s. It is expected that these numerical simulations will significantly benefit from the future Exascale computing infrastructures, that will perform 10^18 FLOP/s. The performance of the SPH codes is, in general, adversely impacted by several factors, such as multiple time-stepping, long-range interactions, and/or boundary conditions. In this work an extensive study of three SPH implementations SPHYNX, ChaNGa, and XXX is performed, to gain insights and to expose any limitations and characteristics of the codes. These codes are the starting point of an interdisciplinary co-design project, SPH-EXA, for the development of an Exascale-ready SPH mini-app. We implemented a rotating square patch as a joint test simulation for the three SPH codes and analyzed their performance on a modern HPC system, Piz Daint. The performance profiling and scalability analysis conducted on the three parent codes allowed to expose their performance issues, such as load imbalance, both in MPI and OpenMP. Two-level load balancing has been successfully applied to SPHYNX to overcome its load imbalance. The performance analysis shapes and drives the design of the SPH-EXA mini-app towards the use of efficient parallelization methods, fault-tolerance mechanisms, and load balancing approaches.Comment: arXiv admin note: substantial text overlap with arXiv:1809.0801

An Application Perspective on High-Performance Computing and Communications

We review possible and probable industrial applications of HPCC focusing on the software and hardware issues. Thirty-three separate categories are illustrated by detailed descriptions of five areas -- computational chemistry; Monte Carlo methods from physics to economics; manufacturing; and computational fluid dynamics; command and control; or crisis management; and multimedia services to client computers and settop boxes. The hardware varies from tightly-coupled parallel supercomputers to heterogeneous distributed systems. The software models span HPF and data parallelism, to distributed information systems and object/data flow parallelism on the Web. We find that in each case, it is reasonably clear that HPCC works in principle, and postulate that this knowledge can be used in a new generation of software infrastructure based on the WebWindows approach, and discussed in an accompanying paper

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Improving the scalability of parallel N-body applications with an event driven constraint based execution model

The scalability and efficiency of graph applications are significantly constrained by conventional systems and their supporting programming models. Technology trends like multicore, manycore, and heterogeneous system architectures are introducing further challenges and possibilities for emerging application domains such as graph applications. This paper explores the space of effective parallel execution of ephemeral graphs that are dynamically generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The workloads are expressed using the semantics of an Exascale computing execution model called ParalleX. For comparison, results using conventional execution model semantics are also presented. We find improved load balancing during runtime and automatic parallelism discovery improving efficiency using the advanced semantics for Exascale computing.Comment: 11 figure