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Christos G Xanthis, Ioannis E Venetis, Anthony H Aletras
BACKGROUND: MRI physics simulators have been developed in the past for optimizing imaging protocols and for training purposes. However, these simulators have only addressed motion within a limited scope. The purpose of this study was the incorporation of realistic motion, such as cardiac motion, respiratory motion and flow, within MRI simulations in a high performance […]
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Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements […]
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Arne Vansteenkiste, Jonathan Leliaert, Mykola Dvornik, Felipe Garcia-Sanchez, Bartel Van Waeyenberge
We report on the design, verification and performance of mumax3, an open-source GPU-accelerated micromagnetic simulation program. This software solves the time- and space dependent magnetization evolution in nano- to micro scale magnets using a finite-difference discretization. Its high performance and low memory requirements allow for large-scale simulations to be performed in limited time and on […]
M. Rieke, T. Trost, R. Grauer
We present a way to combine Vlasov and two-fluid codes for the simulation of a collisionless plasma in large domains while keeping full information of the velocity distribution in localized areas of interest. This is made possible by solving the full Vlasov equation in one region while the remaining area is treated by a 5-moment […]
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Jie Liu, Chunye Gong, Weimin Bao, Guojian Tang, Yuewen Jiang
We present a parallel GPU solution of the Caputo fractional reaction-diffusion equation in one spatial dimension with explicit finite difference approximation. The parallel solution, which is implemented with CUDA programming model, consists of three procedures: preprocessing, parallel solver, and postprocessing. The parallel solver involves the parallel tridiagonal matrix vector multiplication, vector-vector addition, and constant vector […]
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C.-G. Jia, L.-X. Guo, J. Li
In this paper, the graphic processor unit (GPU) implementation of the finite-difference time domain (FDTD) algorithm is presented to investigate the electromagnetic (EM) scattering from one dimensional (1-D) Gaussian rough soil surface. The FDTD lattices are truncated by uniaxial perfectly matched layer (UPML), in which the finite-difference equations are carried out for the total computation […]
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D. Funke, T. Hauth, V. Innocente, G. Quast, P. Sanders, D. Schieferdecker
The Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) is a general-purpose particle detector and comprises the largest silicon-based tracking system built to date with 75 million individual readout channels. The precise reconstruction of particle tracks from this tremendous amount of input channels is a compute-intensive task. The foreseen LHC beam parameters […]
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Michelle Perry, Harrison B. Prosper, Anke Meyer-Baese
We describe a graphical processing unit (GPU) implementation of the Hybrid Markov Chain Monte Carlo (HMC) method for training Bayesian Neural Networks (BNN). Our implementation uses NVIDIA’s parallel computing architecture, CUDA. We briefly review BNNs and the HMC method and we describe our implementations and give preliminary results.
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Q. Lu, J. Amundson
Synergia is a parallel, 3-dimensional space-charge particle-in-cell accelerator modeling code. We present our work porting the purely MPI-based version of the code to a hybrid of CPU and GPU computing kernels. The hybrid code uses the CUDA platform in the same framework as the pure MPI solution. We have implemented a lock-free collaborative charge-deposition algorithm […]
A. Lonardo, F. Ameli, R. Ammendola, A. Biagioni, O. Frezza, G. Lamanna, F. Lo Cicero, M. Martinelli, P. S. Paolucci, E. Pastorelli, L. Pontisso, D. Rossetti, F. Simeone, F. Simula, M. Sozzi, L. Tosoratto, P. Vicini
While the GPGPU paradigm is widely recognized as an effective approach to high performance computing, its adoption in low-latency, real-time systems is still in its early stages. Although GPUs typically show deterministic behaviour in terms of latency in executing computational kernels as soon as data is available in their internal memories, assessment of real-time features […]
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Alexey Badalov, Daniel Campora, Gianmaria Collazuol, Marco Corvo, Stefano Gallorini, Alessio Gianelle, Elisabet Golobardes, Donatella Lucchesi, Anna Lupato, Niko Neufeld, Lorenzo Sestini, Rainer Schwemmer, Xavier Vilasis-Cardona
This note describes arguments to study the use general purpose graphic processing units to improve the performance of the LHCb trigger, presents the current developments in the integration into the Gaudi framework and the implementation of algorithms and points towards possible R and D directions.
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Huda Ibeid, Rio Yokota, David Keyes
Exascale systems are predicted to have approximately one billion cores, assuming Gigahertz cores. Limitations on affordable network topologies for distributed memory systems of such massive scale bring new challenges to the current parallel programing model. Currently, there are many efforts to evaluate the hardware and software bottlenecks of exascale designs. There is therefore an urgent […]
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