Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower computational overheads and longer timescales with respect to atom- istic level models. However, their acceleration on parallel architectures such as Graphic Processing Units (GPU) presents original challenges that must be carefully evaluated. The objective of this work is to characterize the impact of CG model features on parallel simulation performance. To achieve this, we implemented a GPU-accelerated version of a CG molecular dynamics simulator, to which we applied specic optimizations for CG models, such as dedicated data structures to handle dierent bead type interac- tions, obtaining a maximum speed-up of 14 on the NVIDIA GTX480 GPU with Fermi architecture. We provide a complete characterization and evaluation of algorithmic and simulated system features of CG models impacting the achievable speed-up and accuracy of results, using three dierent GPU architectures as case studie

TEAPOT: a toolset for evaluating performance, power and image quality on mobile graphics systems

In this paper we present TEAPOT, a full system GPU simulator, whose goal is to allow the evaluation of the GPUs that reside in mobile phones and tablets. To this extent, it has a cycle accurate GPU model for evaluating performance, power models for the GPU, the memory subsystem and for OLED screens, and image quality metrics. Unlike prior GPU simulators, TEAPOT supports the OpenGL ES 1.1/2.0 API, so that it can simulate all commercial graphical applications available for Android systems. To illustrate potential uses of this simulating infrastructure, we perform two case studies. We first turn our attention to evaluating the impact of the OS when simulating graphical applications. We show that the overall GPU power/performance is greatly aff ected by common OS tasks, such as image composition, and argue that application level simulation is not sufficient to understand the overall GPU behavior. We then utilize the capabilities of TEAPOT to perform studies that trade image quality for energy. We demonstrate that by allowing for small distortions in the overall image quality, a signifi cant amount of energy can be saved.Postprint (author’s final draft

GPGPU-Enabled Physics Based Deformed Model Simulation

Computer simulation techniques are widely adopted nowadays in many areas like manufacturing, engineering, graphics, animation, virtual reality and so on. However, the standard finite element based simulation is notorious for its expensive computation. To address this challenge, I present a GPU-based parallel implementation for simulating large elastic deformation. Classic modal analysis provides a set of orthonormal bases vectors, which span a spectral space encoding the dynamics of the elastic body. As each basis vector is orthogonal to each other, the computation is completely decoupled and can be well-fit into the modern GPGPU platform. We further explore the latest feature of NVIDIA CUDA so that the result of GPU computation can be directly used for upcoming rendering/visualization and a significant amount of overheads for transmitting data from client GPU and host CPU via the PCI-Express bus are avoided. Real-time simulation is made possible with this technique for many cases that otherwise is not possible

Performance Analysis of a Novel GPU Computation-to-core Mapping Scheme for Robust Facet Image Modeling

Though the GPGPU concept is well-known in image processing, much more work remains to be done to fully exploit GPUs as an alternative computation engine. This paper investigates the computation-to-core mapping strategies to probe the efficiency and scalability of the robust facet image modeling algorithm on GPUs. Our fine-grained computation-to-core mapping scheme shows a significant performance gain over the standard pixel-wise mapping scheme. With in-depth performance comparisons across the two different mapping schemes, we analyze the impact of the level of parallelism on the GPU computation and suggest two principles for optimizing future image processing applications on the GPU platform