10,239 research outputs found
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
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Computational Strategies for Scalable Genomics Analysis.
The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications
Automatic Machine Learning by Pipeline Synthesis using Model-Based Reinforcement Learning and a Grammar
Automatic machine learning is an important problem in the forefront of
machine learning. The strongest AutoML systems are based on neural networks,
evolutionary algorithms, and Bayesian optimization. Recently AlphaD3M reached
state-of-the-art results with an order of magnitude speedup using reinforcement
learning with self-play. In this work we extend AlphaD3M by using a pipeline
grammar and a pre-trained model which generalizes from many different datasets
and similar tasks. Our results demonstrate improved performance compared with
our earlier work and existing methods on AutoML benchmark datasets for
classification and regression tasks. In the spirit of reproducible research we
make our data, models, and code publicly available.Comment: ICML Workshop on Automated Machine Learnin
Towards the Evolution of Novel Vertical-Axis Wind Turbines
Renewable and sustainable energy is one of the most important challenges
currently facing mankind. Wind has made an increasing contribution to the
world's energy supply mix, but still remains a long way from reaching its full
potential. In this paper, we investigate the use of artificial evolution to
design vertical-axis wind turbine prototypes that are physically instantiated
and evaluated under approximated wind tunnel conditions. An artificial neural
network is used as a surrogate model to assist learning and found to reduce the
number of fabrications required to reach a higher aerodynamic efficiency,
resulting in an important cost reduction. Unlike in other approaches, such as
computational fluid dynamics simulations, no mathematical formulations are used
and no model assumptions are made.Comment: 14 pages, 11 figure
From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation
Starting from a high-level problem description in terms of partial
differential equations using abstract tensor notation, the Chemora framework
discretizes, optimizes, and generates complete high performance codes for a
wide range of compute architectures. Chemora extends the capabilities of
Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient
manner for complex applications, without low-level code tuning. Chemora
achieves parallelism through MPI and multi-threading, combining OpenMP and
CUDA. Optimizations include high-level code transformations, efficient loop
traversal strategies, dynamically selected data and instruction cache usage
strategies, and JIT compilation of GPU code tailored to the problem
characteristics. The discretization is based on higher-order finite differences
on multi-block domains. Chemora's capabilities are demonstrated by simulations
of black hole collisions. This problem provides an acid test of the framework,
as the Einstein equations contain hundreds of variables and thousands of terms.Comment: 18 pages, 4 figures, accepted for publication in Scientific
Programmin
21st Century Simulation: Exploiting High Performance Computing and Data Analysis
This paper identifies, defines, and analyzes the limitations imposed on Modeling and Simulation by outmoded
paradigms in computer utilization and data analysis. The authors then discuss two emerging capabilities to
overcome these limitations: High Performance Parallel Computing and Advanced Data Analysis. First, parallel
computing, in supercomputers and Linux clusters, has proven effective by providing users an advantage in
computing power. This has been characterized as a ten-year lead over the use of single-processor computers.
Second, advanced data analysis techniques are both necessitated and enabled by this leap in computing power.
JFCOM's JESPP project is one of the few simulation initiatives to effectively embrace these concepts. The
challenges facing the defense analyst today have grown to include the need to consider operations among non-combatant
populations, to focus on impacts to civilian infrastructure, to differentiate combatants from non-combatants,
and to understand non-linear, asymmetric warfare. These requirements stretch both current
computational techniques and data analysis methodologies. In this paper, documented examples and potential
solutions will be advanced. The authors discuss the paths to successful implementation based on their experience.
Reviewed technologies include parallel computing, cluster computing, grid computing, data logging, OpsResearch,
database advances, data mining, evolutionary computing, genetic algorithms, and Monte Carlo sensitivity analyses.
The modeling and simulation community has significant potential to provide more opportunities for training and
analysis. Simulations must include increasingly sophisticated environments, better emulations of foes, and more
realistic civilian populations. Overcoming the implementation challenges will produce dramatically better insights,
for trainees and analysts. High Performance Parallel Computing and Advanced Data Analysis promise increased
understanding of future vulnerabilities to help avoid unneeded mission failures and unacceptable personnel losses.
The authors set forth road maps for rapid prototyping and adoption of advanced capabilities. They discuss the
beneficial impact of embracing these technologies, as well as risk mitigation required to ensure success
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