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

In an ideal world, scientific applications are computationally efficient, maintainable and composable and allow scientists to work very productively. We argue that these goals are achievable for a specific application field by choosing suitable domain-specific abstractions that encapsulate domain knowledge with a high degree of expressiveness. This thesis demonstrates the design and composition of domain-specific […]

February 1, 2015 by hgpu

The finite element method (FEM) has several computational steps to numerically solve a particular problem, to which many efforts have been directed to accelerate the solution stage of the linear system of equations. However, the finite element matrix construction, which is also time-consuming for unstructured meshes, has been less investigated. The generation of the global […]

January 21, 2015 by fjramireg

In recent years clock speeds and memory bandwidths of Graphics Processing Units (GPUs) increased dramatically compared to CPUs. Also GPU vendors developed and freely released new programming tools to make scientific computing on GPUs easier. With these recent developments the use of GPUs for general purpose computing becomes a popular research field. Researchers previously demonstrated […]

January 16, 2015 by hgpu

In the finite element method simulation we often deal with large sparse matrices. Sparse matrix-vector multiplication (SpMV) is of high importance for iterative solvers. During the solver stage, most of the time is in fact spent in the SpMV routine. The SpMV routine is highly memory-bound; the processor spends much time waiting for the needed […]

August 15, 2014 by hgpu

The last decade saw the long tradition of frequency scaling of processing units grind to a halt, and efforts were re-focused on maintaining computational growth by other means; such as increased parallelism, deep memory hierarchies and complex execution logic. After a long period of "boring productivity", a host of new architectures, accelerators, programming languages and […]

July 24, 2014 by hgpu

The numerical solution of partial differential equations using the finite element method is one of the key applications of high performance computing. Local assembly is its characteristic operation. This entails the execution of a problem-specific kernel to numerically evaluate an integral for each element in the discretized problem domain. Since the domain size can be […]

July 10, 2014 by hgpu

We have developed a graphics processor unit (GPU-) based high-speed fully 3D system for diffuse optical tomography (DOT). The reduction in execution time of 3D DOT algorithm, a severely ill-posed problem, is made possible through the use of (1) an algorithmic improvement that uses Broyden approach for updating the Jacobian matrix and thereby updating the […]

June 6, 2014 by hgpu

Power and energy consumption are becoming an increasing concern in high performance computing. Compared to multi-core CPUs, GPUs have a much better performance per watt. In this paper we discuss efforts to redesign the most computation intensive parts of BLAST, an application that solves the equations for compressible hydrodynamics with high order finite elements, using […]

May 20, 2014 by hgpu

By consulting the state-of-the-art methods on massive linear equations solving and parallel computing, the main issue of calculation have been extracted from finite element method. The author test some solving routines on the CPU based as well as design and implement on GPU by using CUDA. The coalesced access result on GPU shows a ten […]

May 7, 2014 by hgpu

Computer-based surgical simulation and non-rigid medical image registration in image-guided interventions are examples of applications that would benefit from real-time deformation simulation of soft tissues. The physics of deformation for biological soft-tissue is best described by nonlinear continuum mechanics-based models which then can be discretized by the Finite Element Method (FEM) for a numerical solution. […]

May 5, 2014 by hgpu

In this paper we present computational cost estimates for parallel shared memory isogeometric multi-frontal solver. The estimates show that the ideal isogeometric shared memory parallel direct solver scales as O(p^2 log(N/p)) for one dimensional problems, O(Np^2) for two dimensional problems, and O(N^(4/3)p^2) for three dimensional problems, where N is the number of degrees of freedom, […]

April 21, 2014 by hgpu