کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
6935335 868794 2014 14 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر نرم افزارهای علوم کامپیوتر
پیش نمایش صفحه اول مقاله
Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations
چکیده انگلیسی
Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel efficiency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Parallel Computing - Volume 40, Issues 5–6, May 2014, Pages 86-99
نویسندگان
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