62,245 research outputs found
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
A spectral scheme for Kohn-Sham density functional theory of clusters
Starting from the observation that one of the most successful methods for
solving the Kohn-Sham equations for periodic systems -- the plane-wave method
-- is a spectral method based on eigenfunction expansion, we formulate a
spectral method designed towards solving the Kohn-Sham equations for clusters.
This allows for efficient calculation of the electronic structure of clusters
(and molecules) with high accuracy and systematic convergence properties
without the need for any artificial periodicity. The basis functions in this
method form a complete orthonormal set and are expressible in terms of
spherical harmonics and spherical Bessel functions. Computation of the occupied
eigenstates of the discretized Kohn-Sham Hamiltonian is carried out using a
combination of preconditioned block eigensolvers and Chebyshev polynomial
filter accelerated subspace iterations. Several algorithmic and computational
aspects of the method, including computation of the electrostatics terms and
parallelization are discussed. We have implemented these methods and algorithms
into an efficient and reliable package called ClusterES (Cluster Electronic
Structure). A variety of benchmark calculations employing local and non-local
pseudopotentials are carried out using our package and the results are compared
to the literature. Convergence properties of the basis set are discussed
through numerical examples. Computations involving large systems that contain
thousands of electrons are demonstrated to highlight the efficacy of our
methodology. The use of our method to study clusters with arbitrary point group
symmetries is briefly discussed.Comment: Manuscript submitted (with revisions) to Journal of Computational
Physic
ELSI: A Unified Software Interface for Kohn-Sham Electronic Structure Solvers
Solving the electronic structure from a generalized or standard eigenproblem
is often the bottleneck in large scale calculations based on Kohn-Sham
density-functional theory. This problem must be addressed by essentially all
current electronic structure codes, based on similar matrix expressions, and by
high-performance computation. We here present a unified software interface,
ELSI, to access different strategies that address the Kohn-Sham eigenvalue
problem. Currently supported algorithms include the dense generalized
eigensolver library ELPA, the orbital minimization method implemented in
libOMM, and the pole expansion and selected inversion (PEXSI) approach with
lower computational complexity for semilocal density functionals. The ELSI
interface aims to simplify the implementation and optimal use of the different
strategies, by offering (a) a unified software framework designed for the
electronic structure solvers in Kohn-Sham density-functional theory; (b)
reasonable default parameters for a chosen solver; (c) automatic conversion
between input and internal working matrix formats, and in the future (d)
recommendation of the optimal solver depending on the specific problem.
Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800
basis functions) on distributed memory supercomputing architectures.Comment: 55 pages, 14 figures, 2 table
Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials
Quantum ESPRESSO is an integrated suite of computer codes for
electronic-structure calculations and materials modeling, based on
density-functional theory, plane waves, and pseudopotentials (norm-conserving,
ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn
Source Package for Research in Electronic Structure, Simulation, and
Optimization". It is freely available to researchers around the world under the
terms of the GNU General Public License. Quantum ESPRESSO builds upon
newly-restructured electronic-structure codes that have been developed and
tested by some of the original authors of novel electronic-structure algorithms
and applied in the last twenty years by some of the leading materials modeling
groups worldwide. Innovation and efficiency are still its main focus, with
special attention paid to massively-parallel architectures, and a great effort
being devoted to user friendliness. Quantum ESPRESSO is evolving towards a
distribution of independent and inter-operable codes in the spirit of an
open-source project, where researchers active in the field of
electronic-structure calculations are encouraged to participate in the project
by contributing their own codes or by implementing their own ideas into
existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte
Status and Future Perspectives for Lattice Gauge Theory Calculations to the Exascale and Beyond
In this and a set of companion whitepapers, the USQCD Collaboration lays out
a program of science and computing for lattice gauge theory. These whitepapers
describe how calculation using lattice QCD (and other gauge theories) can aid
the interpretation of ongoing and upcoming experiments in particle and nuclear
physics, as well as inspire new ones.Comment: 44 pages. 1 of USQCD whitepapers
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
Hierarchical Parallelisation of Functional Renormalisation Group Calculations -- hp-fRG
The functional renormalisation group (fRG) has evolved into a versatile tool
in condensed matter theory for studying important aspects of correlated
electron systems. Practical applications of the method often involve a high
numerical effort, motivating the question in how far High Performance Computing
(HPC) can leverage the approach. In this work we report on a multi-level
parallelisation of the underlying computational machinery and show that this
can speed up the code by several orders of magnitude. This in turn can extend
the applicability of the method to otherwise inaccessible cases. We exploit
three levels of parallelisation: Distributed computing by means of Message
Passing (MPI), shared-memory computing using OpenMP, and vectorisation by means
of SIMD units (single-instruction-multiple-data). Results are provided for two
distinct High Performance Computing (HPC) platforms, namely the IBM-based
BlueGene/Q system JUQUEEN and an Intel Sandy-Bridge-based development cluster.
We discuss how certain issues and obstacles were overcome in the course of
adapting the code. Most importantly, we conclude that this vast improvement can
actually be accomplished by introducing only moderate changes to the code, such
that this strategy may serve as a guideline for other researcher to likewise
improve the efficiency of their codes
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
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