We present the FARGO3D code, recently publicly released. It is a magnetohydrodynamics code developed with special emphasis on protoplanetary disks physics and planet-disk interactions, and parallelized with MPI. The hydrodynamics algorithms are based on finite difference upwind, dimensionally split methods. The magnetohydrodynamics algorithms consist of the constrained transport method to preserve the divergence-free property of […]

February 10, 2016 by hgpu

Compact finite difference schemes are widely used in the direct numerical simulation of fluid flows for their ability to better resolve the small scales of turbulence. However, they can be expensive to evaluate and difficult to parallelize. In this work, we present an approach for the computation of compact finite differences and similar tridiagonal schemes […]

February 3, 2016 by hgpu

High-order numerical methods for unstructured grids combine the superior accuracy of high-order spectral or finite difference methods with the geometric flexibility of low-order finite volume or finite element schemes. The Flux Reconstruction (FR) approach unifies various high-order schemes for unstructured grids within a single framework. Additionally, the FR approach exhibits a significant degree of element […]

December 23, 2015 by hgpu

This thesis documents the analysis and optimization of a high-order finite difference computational fluid dynamics (CFD) application (PlasComCM). Performance bottlenecks were identified using performance tools and hardware counters. The performance analysis of PlasComCM showed that the quantity of memory accesses and the lack of vectorization inhibited optimal serial performance on a x86-based CPU. Optimizing techniques […]

October 18, 2015 by hgpu

The paper presents a comparison of central processing unit (CPU) and graphics processing unit (GPU) performance in sound synthesis based on physical modeling. The goal was to achieve real-time performance with two- and three-dimensional finite difference (FD) instrument models. Two abstract instruments, a membrane and a block, were modeled and tested using a CPU and […]

July 29, 2015 by hgpu

This thesis, entitled "High Performance Computing for solving large sparse systems. Optical Diffraction Tomography as a case of study" investigates the computational issues related to the resolution of linear systems of equations which come from the discretization of physical models described by means of Partial Differential Equations (PDEs). These physical models are conceived for the […]

March 30, 2015 by hgpu

High performance computing of Meshless Time Domain Method (MTDM) on multi-GPU using the supercomputer HA-PACS (Highly Accelerated Parallel Advanced system for Computational Sciences) at University of Tsukuba is investigated. Generally, the finite difference time domain (FDTD) method is adopted for the numerical simulation of the electromagnetic wave propagation phenomena. However, the numerical domain must be […]

February 23, 2015 by hgpu

Today, heterogeneous computing has truly reshaped the way scientists think and approach high-performance computing (HPC). Hardware accelerators such as general-purpose graphics processing units (GPUs) and Intel Many Integrated Core (MIC) architecture continue to make in-roads in accelerating large-scale scientific applications. These advancements, however, introduce new sets of challenges to the scientific community such as: selection […]

October 29, 2014 by hgpu

By projecting observed microseismic data backward in time to when fracturing occurred, it is possible to locate the fracture events in space, assuming a correct velocity model. In order to achieve this task in near real-time, a robust computational system to handle backward propagation, or Reverse Time Migration (RTM), is required. We can then test […]

September 13, 2014 by hgpu

In recent years, the finite difference time domain (FDTD) method has been prevailed in the simulation of metamaterials widely. As the FDTD method can be suitable for the parallel computing, we apply this method to the Fermi-architecture Graphic Process Units (GPUs) to calculate the electromagnetic simulation of double negative materials in this paper. Finally, both […]

September 5, 2014 by hgpu

This paper describes a hybrid multicore/GPU solver for the incompressible Navier-Stokes equations with constant coefficients, discretized by the finite difference method. By applying the prediction-projection method, the Navier-Stokes equations are transformed into a combination of Helmholtzlike and Poisson equations for which we describe efficient solvers. As an extension of our previous paper [1], this paper […]

September 4, 2014 by hgpu

A model of a multilayer device with non-trivial geometrical and material structure and its working process is suggested. The thermal behavior of the device as one principle characteristic is simulated. The algorithm for solving the non-stationary heat conduction problem with a time-dependent periodical heating source is suggested. The algorithm is based on finite difference explicit–implicit […]

August 27, 2014 by hgpu