2,019 research outputs found
Memory and Parallelism Analysis Using a Platform-Independent Approach
Emerging computing architectures such as near-memory computing (NMC) promise
improved performance for applications by reducing the data movement between CPU
and memory. However, detecting such applications is not a trivial task. In this
ongoing work, we extend the state-of-the-art platform-independent software
analysis tool with NMC related metrics such as memory entropy, spatial
locality, data-level, and basic-block-level parallelism. These metrics help to
identify the applications more suitable for NMC architectures.Comment: 22nd ACM International Workshop on Software and Compilers for
Embedded Systems (SCOPES '19), May 201
Design and optimization of a portable LQCD Monte Carlo code using OpenACC
The present panorama of HPC architectures is extremely heterogeneous, ranging
from traditional multi-core CPU processors, supporting a wide class of
applications but delivering moderate computing performance, to many-core GPUs,
exploiting aggressive data-parallelism and delivering higher performances for
streaming computing applications. In this scenario, code portability (and
performance portability) become necessary for easy maintainability of
applications; this is very relevant in scientific computing where code changes
are very frequent, making it tedious and prone to error to keep different code
versions aligned. In this work we present the design and optimization of a
state-of-the-art production-level LQCD Monte Carlo application, using the
directive-based OpenACC programming model. OpenACC abstracts parallel
programming to a descriptive level, relieving programmers from specifying how
codes should be mapped onto the target architecture. We describe the
implementation of a code fully written in OpenACC, and show that we are able to
target several different architectures, including state-of-the-art traditional
CPUs and GPUs, with the same code. We also measure performance, evaluating the
computing efficiency of our OpenACC code on several architectures, comparing
with GPU-specific implementations and showing that a good level of
performance-portability can be reached.Comment: 26 pages, 2 png figures, preprint of an article submitted for
consideration in International Journal of Modern Physics
The Glasgow Parallel Reduction Machine: Programming Shared-memory Many-core Systems using Parallel Task Composition
We present the Glasgow Parallel Reduction Machine (GPRM), a novel, flexible
framework for parallel task-composition based many-core programming. We allow
the programmer to structure programs into task code, written as C++ classes,
and communication code, written in a restricted subset of C++ with functional
semantics and parallel evaluation. In this paper we discuss the GPRM, the
virtual machine framework that enables the parallel task composition approach.
We focus the discussion on GPIR, the functional language used as the
intermediate representation of the bytecode running on the GPRM. Using examples
in this language we show the flexibility and power of our task composition
framework. We demonstrate the potential using an implementation of a merge sort
algorithm on a 64-core Tilera processor, as well as on a conventional Intel
quad-core processor and an AMD 48-core processor system. We also compare our
framework with OpenMP tasks in a parallel pointer chasing algorithm running on
the Tilera processor. Our results show that the GPRM programs outperform the
corresponding OpenMP codes on all test platforms, and can greatly facilitate
writing of parallel programs, in particular non-data parallel algorithms such
as reductions.Comment: In Proceedings PLACES 2013, arXiv:1312.221
Characterizing traits of coordination
How can one recognize coordination languages and technologies? As this report
shows, the common approach that contrasts coordination with computation is
intellectually unsound: depending on the selected understanding of the word
"computation", it either captures too many or too few programming languages.
Instead, we argue for objective criteria that can be used to evaluate how well
programming technologies offer coordination services. Of the various criteria
commonly used in this community, we are able to isolate three that are strongly
characterizing: black-box componentization, which we had identified previously,
but also interface extensibility and customizability of run-time optimization
goals. These criteria are well matched by Intel's Concurrent Collections and
AstraKahn, and also by OpenCL, POSIX and VMWare ESX.Comment: 11 pages, 3 table
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
A Parallel Iterative Method for Computing Molecular Absorption Spectra
We describe a fast parallel iterative method for computing molecular
absorption spectra within TDDFT linear response and using the LCAO method. We
use a local basis of "dominant products" to parametrize the space of orbital
products that occur in the LCAO approach. In this basis, the dynamical
polarizability is computed iteratively within an appropriate Krylov subspace.
The iterative procedure uses a a matrix-free GMRES method to determine the
(interacting) density response. The resulting code is about one order of
magnitude faster than our previous full-matrix method. This acceleration makes
the speed of our TDDFT code comparable with codes based on Casida's equation.
The implementation of our method uses hybrid MPI and OpenMP parallelization in
which load balancing and memory access are optimized. To validate our approach
and to establish benchmarks, we compute spectra of large molecules on various
types of parallel machines.
The methods developed here are fairly general and we believe they will find
useful applications in molecular physics/chemistry, even for problems that are
beyond TDDFT, such as organic semiconductors, particularly in photovoltaics.Comment: 20 pages, 17 figures, 3 table
Master of Science
thesisTo address the need of understanding and optimizing the performance of complex applications and achieving sustained application performance across different architectures, we need performance models and tools that could quantify the theoretical performance and the resultant gap between theoretical and observed performance. This thesis proposes a benchmark-driven Roofline Model Toolkit to provide theoretical and achievable performance, and their resultant gap for multicore, manycore, and accelerated architectures. Roofline micro benchmarks are specialized to quantify the behavior of different architectural features. Compared to previous work on performance characterization, these micro benchmarks focus on capturing the performance of each level of the memory hierarchy, along with thread-level parallelism(TLP), instruction-level parallelism(ILP), and explicit Single Instruction, Multiple Data(SIMD) parallelism, measured in the context of the compilers and runtime environment on the target architecture. We also developed benchmarks to explore detailed memory subsystems behaviors and evaluate parallelization overhead. Beyond on-chip performance, we measure sustained Peripheral Component Interconnect Express(PCIe) throughput with four Graphics Processing Unit(GPU) memory managed mechanisms. By combining results from the architecture characterization with the Roofline Model based solely on architectural specification, this work offers insights for performance prediction of current and future architectures and their software systems. To that end, we instrument three applications and plot their resultant performance on the corresponding Roofline Model when run on a Blue Gene/Q architecture
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