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In this paper, we use multithreaded fast Fourier transforms provided in three highly optimized packages, FFTW-2.1.5, FFTW-3.3.7, and Intel MKL FFT, to present a novel model-based parallel computing technique as a very effective and portable…

The paper demonstrates the optimization of the execution environment of a hybrid OpenMP+MPI computational fluid dynamics code (shallow water equation solver) on a cluster enabled with Intel Xeon Phi coprocessors. The discussion includes:…

B-spline based orbital representations are widely used in Quantum Monte Carlo (QMC) simulations of solids, historically taking as much as 50% of the total run time. Random accesses to a large four-dimensional array make it challenging to…

In the push for exascale computing, energy efficiency is of utmost concern. System architectures often adopt accelerators to hasten application execution at the cost of power. The Intel Xeon Phi co-processor is unique accelerator that…

The paper presents investigations on the implementation and performance of the finite element numerical integration algorithm for first order approximations and three processor architectures, popular in scientific computing, classical CPU,…

Co-expression network is a critical technique for the identification of inter-gene interactions, which usually relies on all-pairs correlation (or similar measure) computation between gene expression profiles across multiple samples.…

Supervised learning of Convolutional Neural Networks (CNNs), also known as supervised Deep Learning, is a computationally demanding process. To find the most suitable parameters of a network for a given application, numerous training…

Chebyshev filter diagonalization is well established in quantum chemistry and quantum physics to compute bulks of eigenvalues of large sparse matrices. Choosing a block vector implementation, we investigate optimization opportunities on the…

Faced with physical and energy density limitations on clock speed, contemporary microprocessor designers have increasingly turned to on-chip parallelism for performance gains. Algorithms should accordingly be designed with ample amounts of…

K Nearest Neighbor (KNN) joins are used in scientific domains for data analysis, and are building blocks of several well-known algorithms. KNN-joins find the KNN of all points in a dataset. This paper focuses on a hybrid CPU/GPU approach…

Limits on power dissipation have pushed CPUs to grow in parallel processing capabilities rather than clock rate, leading to the rise of "manycore" or GPU-like processors. In order to achieve the best performance, applications must be able…

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is widely used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. Although many SpGEMM algorithms have…

In recent years, Field-Programmable Gate Arrays (FPGA) have evolved rapidly paving the way for a whole new range of computing paradigms. On the other hand, computer applications are evolving. There is a rising demand for a system that is…

The speed of deep neural networks training has become a big bottleneck of deep learning research and development. For example, training GoogleNet by ImageNet dataset on one Nvidia K20 GPU needs 21 days. To speed up the training process, the…

In this paper we explore the performance of Intel Xeon MAX CPU Series, representing the most significant new variation upon the classical CPU architecture since the Intel Xeon Phi Processor. Given the availability of a large on-package…

Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures…

Results of porting parts of the Lattice Quantum Chromodynamics code to modern FPGA devices are presented. A single-node, double precision implementation of the Conjugate Gradient algorithm is used to invert numerically the Dirac-Wilson…

This article presents an automatic approach to quickly derive a good solution for hardware resource partition and task granularity for task-based parallel applications on heterogeneous many-core architectures. Our approach employs a…

Pairwise association measure is an important operation in data analytics. Kendall's tau coefficient is one widely used correlation coefficient identifying non-linear relationships between ordinal variables. In this paper, we investigated a…