10,649 research outputs found
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
BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations
Objective: The advent of High-Performance Computing (HPC) in recent years has
led to its increasing use in brain study through computational models. The
scale and complexity of such models are constantly increasing, leading to
challenging computational requirements. Even though modern HPC platforms can
often deal with such challenges, the vast diversity of the modeling field does
not permit for a single acceleration (or homogeneous) platform to effectively
address the complete array of modeling requirements. Approach: In this paper we
propose and build BrainFrame, a heterogeneous acceleration platform,
incorporating three distinct acceleration technologies, a Dataflow Engine, a
Xeon Phi and a GP-GPU. The PyNN framework is also integrated into the platform.
As a challenging proof of concept, we analyze the performance of BrainFrame on
different instances of a state-of-the-art neuron model, modeling the Inferior-
Olivary Nucleus using a biophysically-meaningful, extended Hodgkin-Huxley
representation. The model instances take into account not only the neuronal-
network dimensions but also different network-connectivity circumstances that
can drastically change application workload characteristics. Main results: The
synthetic approach of three HPC technologies demonstrated that BrainFrame is
better able to cope with the modeling diversity encountered. Our performance
analysis shows clearly that the model directly affect performance and all three
technologies are required to cope with all the model use cases.Comment: 16 pages, 18 figures, 5 table
COLAB:A Collaborative Multi-factor Scheduler for Asymmetric Multicore Processors
Funding: Partially funded by the UK EPSRC grants Discovery: Pattern Discovery and Program Shaping for Many-core Systems (EP/P020631/1) and ABC: Adaptive Brokerage for Cloud (EP/R010528/1); Royal Academy of Engineering under the Research Fellowship scheme.Increasingly prevalent asymmetric multicore processors (AMP) are necessary for delivering performance in the era of limited power budget and dark silicon. However, the software fails to use them efficiently. OS schedulers, in particular, handle asymmetry only under restricted scenarios. We have efficient symmetric schedulers, efficient asymmetric schedulers for single-threaded workloads, and efficient asymmetric schedulers for single program workloads. What we do not have is a scheduler that can handle all runtime factors affecting AMP for multi-threaded multi-programmed workloads. This paper introduces the first general purpose asymmetry-aware scheduler for multi-threaded multi-programmed workloads. It estimates the performance of each thread on each type of core and identifies communication patterns and bottleneck threads. The scheduler then makes coordinated core assignment and thread selection decisions that still provide each application its fair share of the processor's time. We evaluate our approach using the GEM5 simulator on four distinct big.LITTLE configurations and 26 mixed workloads composed of PARSEC and SPLASH2 benchmarks. Compared to the state-of-the art Linux CFS and AMP-aware schedulers, we demonstrate performance gains of up to 25% and 5% to 15% on average depending on the hardware setup.Postprin
GAMER: a GPU-Accelerated Adaptive Mesh Refinement Code for Astrophysics
We present the newly developed code, GAMER (GPU-accelerated Adaptive MEsh
Refinement code), which has adopted a novel approach to improve the performance
of adaptive mesh refinement (AMR) astrophysical simulations by a large factor
with the use of the graphic processing unit (GPU). The AMR implementation is
based on a hierarchy of grid patches with an oct-tree data structure. We adopt
a three-dimensional relaxing TVD scheme for the hydrodynamic solver, and a
multi-level relaxation scheme for the Poisson solver. Both solvers have been
implemented in GPU, by which hundreds of patches can be advanced in parallel.
The computational overhead associated with the data transfer between CPU and
GPU is carefully reduced by utilizing the capability of asynchronous memory
copies in GPU, and the computing time of the ghost-zone values for each patch
is made to diminish by overlapping it with the GPU computations. We demonstrate
the accuracy of the code by performing several standard test problems in
astrophysics. GAMER is a parallel code that can be run in a multi-GPU cluster
system. We measure the performance of the code by performing purely-baryonic
cosmological simulations in different hardware implementations, in which
detailed timing analyses provide comparison between the computations with and
without GPU(s) acceleration. Maximum speed-up factors of 12.19 and 10.47 are
demonstrated using 1 GPU with 4096^3 effective resolution and 16 GPUs with
8192^3 effective resolution, respectively.Comment: 60 pages, 22 figures, 3 tables. More accuracy tests are included.
Accepted for publication in ApJ
A GPU-accelerated Branch-and-Bound Algorithm for the Flow-Shop Scheduling Problem
Branch-and-Bound (B&B) algorithms are time intensive tree-based exploration
methods for solving to optimality combinatorial optimization problems. In this
paper, we investigate the use of GPU computing as a major complementary way to
speed up those methods. The focus is put on the bounding mechanism of B&B
algorithms, which is the most time consuming part of their exploration process.
We propose a parallel B&B algorithm based on a GPU-accelerated bounding model.
The proposed approach concentrate on optimizing data access management to
further improve the performance of the bounding mechanism which uses large and
intermediate data sets that do not completely fit in GPU memory. Extensive
experiments of the contribution have been carried out on well known FSP
benchmarks using an Nvidia Tesla C2050 GPU card. We compared the obtained
performances to a single and a multithreaded CPU-based execution. Accelerations
up to x100 are achieved for large problem instances
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