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We carry out a comparative performance study of multi-core CPUs, GPUs and Intel Xeon Phi (Many Integrated Core - MIC) with a microscopy image analysis application. We experimentally evaluate the performance of computing devices on core…

Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has…

In this paper, we describe the performance of an $N$-body simulation of star cluster with 64k stars on a Cray XD1 system with 400 dual-core Opteron processors. A number of astrophysical $N$-body simulations were reported in SCxy…

This paper concerns development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors. We discuss suitability of the method for Xeon Phi architecture and present our…

A finite-difference Micromagnetic simulation code written in MATLAB is presented with Graphics Processing Unit (GPU) acceleration. The high performance of Graphics Processing Unit (GPU) is demonstrated compared to a typical Central…

eGPU, a recently-reported soft GPGPU for FPGAs, has demonstrated very high clock frequencies (more than 750 MHz) and small footprint. This means that for the first time, commercial soft processors may be competitive for the kind of heavy…

Tensor cores are specialized processing units within GPUs that have demonstrated significant efficiency gains in compute-bound applications such as Deep Learning Training by accelerating dense matrix operations. Given their success,…

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…

We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…

Although modern FPGAs have a performance potential of a 1 GHz clock frequency - with both clock networks and embedded blocks such as memories and DSP Blocks capable of these clock rates - user implementations approaching this speed are…

This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…

As the need for more computing power grows, traditional methods are hitting limits. To boost performance, we're expanding Central Processing Unit (CPU) capabilities and using specialized hardware accelerators. For example, mobile devices…

The state vector-based simulation offers a convenient approach to developing and validating quantum algorithms with noise-free results. However, limited by the absence of cache-aware implementations and unpolished circuit optimizations, the…

A myriad of applications ranging from engineering and scientific simulations, image and signal processing as well as high-sensitive data retrieval demand high processing power reaching up to teraflops for their efficient execution. While a…

With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…

Many architects believe that major improvements in cost-energy-performance must now come from domain-specific hardware. This paper evaluates a custom ASIC---called a Tensor Processing Unit (TPU)---deployed in datacenters since 2015 that…

In this paper I describe some results on the use of virtual processors technology for parallelize some SPMD computational programs in a cluster environment. The tested technology is the INTEL Hyper Threading on real processors, and the…

In this paper, we describe the algorithms we implemented in FDPS to make efficient use of accelerator hardware such as GPGPUs. We have developed FDPS to make it possible for many researchers to develop their own high-performance parallel…

In this article we study the suitability of dierent computational accelerators for the task of real-time data processing. The algorithm used for comparison is the polyphase filter, a standard tool in signal processing and a well established…

Quantum processes have been confirmed for various biological phenomena. Here we model a quantum process in cells based on coherent waves of established ultrafast energy transfers in water. We compute wave speed, ~156 km/s, and wavelength,…