1,642 research outputs found
Partition Around Medoids Clustering on the Intel Xeon Phi Many-Core Coprocessor
Abstract. The paper touches upon the problem of implementation Partition Around Medoids (PAM) clustering algorithm for the Intel Many Integrated Core architecture. PAM is a form of well-known k-Medoids clustering algorithm and is applied in various subject domains, e.g. bioinformatics, text analysis, intelligent transportation systems, etc. An optimized version of PAM for the Intel Xeon Phi coprocessor is introduced where OpenMP parallelizing technology, loop vectorization, tiling technique and efficient distance matrix computation for Euclidean metric are used. Experimental results for different data sets confirm the efficiency of the proposed algorithm
GeantV: Results from the prototype of concurrent vector particle transport simulation in HEP
Full detector simulation was among the largest CPU consumer in all CERN
experiment software stacks for the first two runs of the Large Hadron Collider
(LHC). In the early 2010's, the projections were that simulation demands would
scale linearly with luminosity increase, compensated only partially by an
increase of computing resources. The extension of fast simulation approaches to
more use cases, covering a larger fraction of the simulation budget, is only
part of the solution due to intrinsic precision limitations. The remainder
corresponds to speeding-up the simulation software by several factors, which is
out of reach using simple optimizations on the current code base. In this
context, the GeantV R&D project was launched, aiming to redesign the legacy
particle transport codes in order to make them benefit from fine-grained
parallelism features such as vectorization, but also from increased code and
data locality. This paper presents extensively the results and achievements of
this R&D, as well as the conclusions and lessons learnt from the beta
prototype.Comment: 34 pages, 26 figures, 24 table
Breadth First Search Vectorization on the Intel Xeon Phi
Breadth First Search (BFS) is a building block for graph algorithms and has
recently been used for large scale analysis of information in a variety of
applications including social networks, graph databases and web searching. Due
to its importance, a number of different parallel programming models and
architectures have been exploited to optimize the BFS. However, due to the
irregular memory access patterns and the unstructured nature of the large
graphs, its efficient parallelization is a challenge. The Xeon Phi is a
massively parallel architecture available as an off-the-shelf accelerator,
which includes a powerful 512 bit vector unit with optimized scatter and gather
functions. Given its potential benefits, work related to graph traversing on
this architecture is an active area of research.
We present a set of experiments in which we explore architectural features of
the Xeon Phi and how best to exploit them in a top-down BFS algorithm but the
techniques can be applied to the current state-of-the-art hybrid, top-down plus
bottom-up, algorithms.
We focus on the exploitation of the vector unit by developing an improved
highly vectorized OpenMP parallel algorithm, using vector intrinsics, and
understanding the use of data alignment and prefetching. In addition, we
investigate the impact of hyperthreading and thread affinity on performance, a
topic that appears under researched in the literature. As a result, we achieve
what we believe is the fastest published top-down BFS algorithm on the version
of Xeon Phi used in our experiments. The vectorized BFS top-down source code
presented in this paper can be available on request as free-to-use software
Evaluating kernels on Xeon Phi to accelerate Gysela application
This work describes the challenges presented by porting parts ofthe Gysela
code to the Intel Xeon Phi coprocessor, as well as techniques used for
optimization, vectorization and tuning that can be applied to other
applications. We evaluate the performance of somegeneric micro-benchmark on Phi
versus Intel Sandy Bridge. Several interpolation kernels useful for the Gysela
application are analyzed and the performance are shown. Some memory-bound and
compute-bound kernels are accelerated by a factor 2 on the Phi device compared
to Sandy architecture. Nevertheless, it is hard, if not impossible, to reach a
large fraction of the peek performance on the Phi device,especially for
real-life applications as Gysela. A collateral benefit of this optimization and
tuning work is that the execution time of Gysela (using 4D advections) has
decreased on a standard architecture such as Intel Sandy Bridge.Comment: submitted to ESAIM proceedings for CEMRACS 2014 summer school version
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A Novel Hybrid Quicksort Algorithm Vectorized using AVX-512 on Intel Skylake
The modern CPU's design, which is composed of hierarchical memory and
SIMD/vectorization capability, governs the potential for algorithms to be
transformed into efficient implementations. The release of the AVX-512 changed
things radically, and motivated us to search for an efficient sorting algorithm
that can take advantage of it. In this paper, we describe the best strategy we
have found, which is a novel two parts hybrid sort, based on the well-known
Quicksort algorithm. The central partitioning operation is performed by a new
algorithm, and small partitions/arrays are sorted using a branch-free
Bitonic-based sort. This study is also an illustration of how classical
algorithms can be adapted and enhanced by the AVX-512 extension. We evaluate
the performance of our approach on a modern Intel Xeon Skylake and assess the
different layers of our implementation by sorting/partitioning integers, double
floating-point numbers, and key/value pairs of integers. Our results
demonstrate that our approach is faster than two libraries of reference: the
GNU \emph{C++} sort algorithm by a speedup factor of 4, and the Intel IPP
library by a speedup factor of 1.4.Comment: 8 pages, research pape
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