17,734 research outputs found
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
ASCR/HEP Exascale Requirements Review Report
This draft report summarizes and details the findings, results, and
recommendations derived from the ASCR/HEP Exascale Requirements Review meeting
held in June, 2015. The main conclusions are as follows. 1) Larger, more
capable computing and data facilities are needed to support HEP science goals
in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of
the demand at the 2025 timescale is at least two orders of magnitude -- and in
some cases greater -- than that available currently. 2) The growth rate of data
produced by simulations is overwhelming the current ability, of both facilities
and researchers, to store and analyze it. Additional resources and new
techniques for data analysis are urgently needed. 3) Data rates and volumes
from HEP experimental facilities are also straining the ability to store and
analyze large and complex data volumes. Appropriately configured
leadership-class facilities can play a transformational role in enabling
scientific discovery from these datasets. 4) A close integration of HPC
simulation and data analysis will aid greatly in interpreting results from HEP
experiments. Such an integration will minimize data movement and facilitate
interdependent workflows. 5) Long-range planning between HEP and ASCR will be
required to meet HEP's research needs. To best use ASCR HPC resources the
experimental HEP program needs a) an established long-term plan for access to
ASCR computational and data resources, b) an ability to map workflows onto HPC
resources, c) the ability for ASCR facilities to accommodate workflows run by
collaborations that can have thousands of individual members, d) to transition
codes to the next-generation HPC platforms that will be available at ASCR
facilities, e) to build up and train a workforce capable of developing and
using simulations and analysis to support HEP scientific research on
next-generation systems.Comment: 77 pages, 13 Figures; draft report, subject to further revisio
Sniper: scalable and accurate parallel multi-core simulation
Sniper is a next generation parallel, high-speed and accurate x86 simulator. This multi-core simulator is based on the interval core model and the Graphite simulation infrastructure, allowing for fast and accurate simulation and for trading off simulation speed for accuracy to allow a range of flexible simulation options when exploring different homogeneous and heterogeneous multi-core architectures. The Sniper simulator allows one to perform timing simulations for both multi-programmed workloads and multi-threaded, shared-memory applications running on 10s to 100+ cores, at a high speed when compared to existing simulators. The main feature of the simulator is its core model which is based on interval simulation, a fast mechanistic core model. Interval simulation raises the level of abstraction in architectural simulation which allows for faster simulator development and evaluation times; it does so by ’jumping’ between miss events, called intervals. Sniper has been validated against multi-socket Intel Core2 and Nehalem systems and provides average performance prediction errors within 25% at a simulation speed of up to several MIPS. This simulator, and the interval core model, is useful for uncore and system-level studies that require more detail than the typical one-IPC models, but for which cycle-accurate simulators are too slow to allow workloads of meaningful sizes to be simulated. As an added benefit, the interval core model allows the generation of CPI stacks, which show the number of cycles lost due to different characteristics of the system, like the cache hierarchy or branch predictor, and lead to a better understanding of each component’s effect on total system performance. This extends the use for Sniper to application characterization and hardware/software co-design. The Sniper simulator is available for download at http://snipersim.org and can be used freely for academic research
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
Architecture for Analysis of Streaming Data
While several attempts have been made to construct a scalable and flexible
architecture for analysis of streaming data, no general model to tackle this
task exists. Thus, our goal is to build a scalable and maintainable
architecture for performing analytics on streaming data.
To reach this goal, we introduce a 7-layered architecture consisting of
microservices and publish-subscribe software. Our study shows that this
architecture yields a good balance between scalability and maintainability due
to high cohesion and low coupling of the solution, as well as asynchronous
communication between the layers.
This architecture can help practitioners to improve their analytic solutions.
It is also of interest to academics, as it is a building block for a general
architecture for processing streaming data
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