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Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
TLDR
We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. Expand
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Accelerating Viola-Jones Face Detection to FPGA-Level Using GPUs
TLDR
We present a multi-GPU implementation of the Viola-Jones face detection algorithm that meets the performance of the fastest known FPGA implementation. Expand
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Mint: realizing CUDA performance in 3D stencil methods with annotated C
TLDR
We present Mint, a programming model that enables the non-expert to enjoy the performance benefits of hand coded CUDA without becoming entangled in the details. Expand
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Dynamic Partitioning of Non-Uniform Structured Workloads with Spacefilling Curves
TLDR
We discuss inverse spacefilling partitioning (ISP), a partitioning strategy for non-uniform scientific computations running on distributed memory MIMD parallel computers, and compare ISP against orthogonal recursive bisection (ORE) and a median of medians variant of ORE. Expand
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Analysis of the numerical effects of parallelism on a parallel genetic algorithm
TLDR
We examine the effects of relaxed synchronization on both the numerical and parallel efficiency of parallel genetic algorithms (GAs). Expand
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A local corrections algorithm for solving Poisson’s equation in three dimensions
We present a second-order accurate algorithm for solving the free-space Poisson's equation on a locally-refined nested grid hierarchy in three dimensions. Our approach is based on linearExpand
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Redefining the Role of the CPU in the Era of CPU-GPU Integration
TLDR
We've seen the quick adoption of GPUs as general purpose computing engines in recent years, fueled by high computational throughput and energy efficiency. Expand
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Accelerating a 3D Finite-Difference Earthquake Simulation with a C-to-CUDA Translator
TLDR
An annotation-based programming model, called Mint, and its accompanying source-to-source translator are used to automatically generate CUDA source code and simplify the exploration of performance tradeoffs. Expand
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An Efficient Implementation of a Local Binning Algorithm for Digital Elevation Model Generation of LiDAR/ALSM Dataset
H. S. Kim, J R. Arrowsmith, C. J. Crosby, E. Jaeger-Frank, V. Nandigam, A. Memon, J. Conner, S. B. Baden, C. Baru Department of Computer Science and Engineering, University of California, San DiegoExpand
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Efficient Run-Time Support for Irregular Block-Structured Applications
TLDR
We describe a set of intuitive geometric programming abstractions that simplify coordination of irregular block-structured scientific calculations without sacrificing performance. Expand
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