Towards a Mini-App for Smoothed Particle Hydrodynamics at Exascale

The smoothed particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations with detailed physics represent computationally-demanding calculations. The parallelization of SPH codes is not trivial due to the absence of a structured grid. Additionally, the performance of the SPH codes can be, in general, adversely impacted by several factors, such as multiple time-stepping, long-range interactions, and/or boundary conditions. This work presents insights into the current performance and functionalities of three SPH codes: SPHYNX, ChaNGa, and SPH-flow. These codes are the starting point of an interdisciplinary co-design project, SPH-EXA, for the development of an Exascale-ready SPH mini-app. To gain such insights, a rotating square patch test was implemented as a common test simulation for the three SPH codes and analyzed on two modern HPC systems. Furthermore, to stress the differences with the codes stemming from the astrophysics community (SPHYNX and ChaNGa), an additional test case, the Evrard collapse, has also been carried out. This work extrapolates the common basic SPH features in the three codes for the purpose of consolidating them into a pure-SPH, Exascale-ready, optimized, mini-app. Moreover, the outcome of this serves as direct feedback to the parent codes, to improve their performance and overall scalability.Comment: 18 pages, 4 figures, 5 tables, 2018 IEEE International Conference on Cluster Computing proceedings for WRAp1

On the Performance Of the Thread-Multiple Support Level In Thread-Based MPI

Proceedings of: First International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2014). Porto (Portugal), August 27-28, 2014.Exascale systems are likely to have orders of magnitude less memory per core than current systems (though still large amounts of memory). As the amount of memory per core is dropping, going to thread-based models might be an unavoidable step towards the exascale milestone. AzequiaMPI is a thread-based open source full conformant implementation of MPI-1.3 for shared memory. We expose the techniques introduced in AzequiaMPI that, first, simplify the implementation and second, make the thread-based model to significantly improve the bandwidth of process-based implementations. Current version is also compliant with the MPI_THREAD_MULTIPLE thread-safety level, a feature of MPI-2.0 standard. The well known Thakur and Gropp MPI_THREAD_MULTIPLE tests show that both latency and bandwidth figures of AzequiaMPI significantly improve that of MPC-MPI, MPICH and Open MPI in an eight cores Intel Xeon E5620 Nehalem machine.The work presented in this paper has been partially supported by EU under the COST programme Action IC1305, ’Network for Sustainable Ultrascale Computing (NESUS)’

Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Prioritized Data Compression using Wavelets

The volume of data and the velocity with which it is being generated by com- putational experiments on high performance computing (HPC) systems is quickly outpacing our ability to effectively store this information in its full fidelity. There- fore, it is critically important to identify and study compression methodologies that retain as much information as possible, particularly in the most salient regions of the simulation space. In this paper, we cast this in terms of a general decision-theoretic problem and discuss a wavelet-based compression strategy for its solution. We pro- vide a heuristic argument as justification and illustrate our methodology on several examples. Finally, we will discuss how our proposed methodology may be utilized in an HPC environment on large-scale computational experiments

Load-Varying LINPACK: A Benchmark for Evaluating Energy Efficiency in High-End Computing

For decades, performance has driven the high-end computing (HEC) community. However, as highlighted in recent exascale studies that chart a path from petascale to exascale computing, power consumption is fast becoming the major design constraint in HEC. Consequently, the HEC community needs to address this issue in future petascale and exascale computing systems. Current scientific benchmarks, such as LINPACK and SPEChpc, only evaluate HEC systems when running at full throttle, i.e., 100% workload, resulting in a focus on performance and ignoring the issues of power and energy consumption. In contrast, efforts like SPECpower evaluate the energy efficiency of a compute server at varying workloads. This is analogous to evaluating the energy efficiency (i.e., fuel efficiency) of an automobile at varying speeds (e.g., miles per gallon highway versus city). SPECpower, however, only evaluates the energy efficiency of a single compute server rather than a HEC system; furthermore, it is based on SPEC's Java Business Benchmarks (SPECjbb) rather than a scientific benchmark. Given the absence of a load-varying scientific benchmark to evaluate the energy efficiency of HEC systems at different workloads, we propose the load-varying LINPACK (LV-LINPACK) benchmark. In this paper, we identify application parameters that affect performance and provide a methodology to vary the workload of LINPACK, thus enabling a more rigorous study of energy efficiency in supercomputers, or more generally, HEC