scholarly journals A Framework for Simulating and Estimating the State and Functional Topology of Complex Dynamic Geometric Networks

2011 ◽  
Vol 23 (1) ◽  
pp. 183-214 ◽  
Author(s):  
Marius Buibas ◽  
Gabriel A. Silva
Keyword(s):  
Neural Networks ◽  
High Performance ◽  
Graphics Processing Unit ◽  
Signal Propagation ◽  
Cellular Neural Networks ◽  
Standard Test ◽  
The State ◽  
Processing Unit ◽  
Complex Dynamic ◽  
Functional Topology

We introduce a framework for simulating signal propagation in geometric networks (networks that can be mapped to geometric graphs in some space) and developing algorithms that estimate (i.e., map) the state and functional topology of complex dynamic geometric networks. Within the framework, we define the key features typically present in such networks and of particular relevance to biological cellular neural networks: dynamics, signaling, observation, and control. The framework is particularly well suited for estimating functional connectivity in cellular neural networks from experimentally observable data and has been implemented using graphics processing unit high-performance computing. Computationally, the framework can simulate cellular network signaling close to or faster than real time. We further propose a standard test set of networks to measure performance and compare different mapping algorithms.

SWIRL: High-performance many-core CPU code generation for deep neural networks

2019 ◽  
Vol 33 (6) ◽  
pp. 1275-1289 ◽  
Author(s):  
Anand Venkat ◽  
Tharindu Rusira ◽  
Raj Barik ◽  
Mary Hall ◽  
Leonard Truong
Keyword(s):  
Neural Networks ◽  
Language Processing ◽  
Code Generation ◽  
High Performance ◽  
Deep Neural Networks ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Data Movement ◽  
Central Processing ◽  
The Status

Deep neural networks (DNNs) have demonstrated effectiveness in many domains including object recognition, speech recognition, natural language processing, and health care. Typically, the computations involved in DNN training and inferencing are time consuming and require efficient implementations. Existing frameworks such as TensorFlow, Theano, Torch, Cognitive Tool Kit (CNTK), and Caffe enable Graphics Processing Unit (GPUs) as the status quo devices for DNN execution, leaving Central Processing Unit (CPUs) behind. Moreover, existing frameworks forgo or limit cross layer optimization opportunities that have the potential to improve performance by significantly reducing data movement through the memory hierarchy. In this article, we describe an alternative approach called SWIRL, a compiler that provides high-performance CPU implementations for DNNs. SWIRL is built on top of the existing domain-specific language (DSL) for DNNs called LATTE. SWIRL separates DNN specification and its schedule using predefined transformation recipes for tensors and layers commonly found in DNN layers. These recipes synergize with DSL constructs to generate high-quality fused, vectorized, and parallelized code for CPUs. On an Intel Xeon Platinum 8180M CPU, SWIRL achieves performance comparable with Tensorflow integrated with MKL-DNN; on average 1.00× of Tensorflow inference and 0.99× of Tensorflow training. It also outperforms the original LATTE compiler on average by 1.22× and 1.30× on inference and training, respectively.

scholarly journals Deep Learning Framework for Vehicle and Pedestrian Detection in Rural Roads on an Embedded GPU

Electronics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 589 ◽  
Author(s):  
Luis Barba-Guaman ◽  
José Eugenio Naranjo ◽  
Anthony Ortiz
Keyword(s):  
Neural Networks ◽  
Computer Vision ◽  
Deep Learning ◽  
Embedded System ◽  
Rural Areas ◽  
High Performance ◽  
Processing Time ◽  
Graphics Processing Unit ◽  
Pedestrian Detection ◽  
Processing Unit

Object detection, one of the most fundamental and challenging problems in computer vision. Nowadays some dedicated embedded systems have emerged as a powerful strategy for deliver high processing capabilities including the NVIDIA Jetson family. The aim of the present work is the recognition of objects in complex rural areas through an embedded system, as well as the verification of accuracy and processing time. For this purpose, a low power embedded Graphics Processing Unit (Jetson Nano) has been selected, which allows multiple neural networks to be run in simultaneous and a computer vision algorithm to be applied for image recognition. As well, the performance of these deep learning neural networks such as ssd-mobilenet v1 and v2, pednet, multiped and ssd-inception v2 has been tested. Moreover, it was found that the accuracy and processing time were in some cases improved when all the models suggested in the research were applied. The pednet network model provides a high performance in pedestrian recognition, however, the sdd-mobilenet v2 and ssd-inception v2 models are better at detecting other objects such as vehicles in complex scenarios.

scholarly journals A lightweight approach to performance portability with targetDP

2016 ◽  
Vol 32 (2) ◽  
pp. 288-301
Author(s):  
Alan Gray ◽  
Kevin Stratford
Keyword(s):  
Particle Physics ◽  
Message Passing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Message Passing Interface ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Performance Portability ◽  
Graphics Processing

Leading high performance computing systems achieve their status through use of highly parallel devices such as NVIDIA graphics processing units or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital for the application programmer. In this paper we describe targetDP, a lightweight abstraction layer which allows grid-based applications to target data parallel hardware in a platform agnostic manner. We demonstrate the effectiveness of our pragmatic approach by presenting performance results for a complex fluid application (with which the model was co-designed), plus separate lattice quantum chromodynamics particle physics code. For each application, a single source code base is seen to achieve portable performance, as assessed within the context of the Roofline model. TargetDP can be combined with Message Passing Interface (MPI) to allow use on systems containing multiple nodes: we demonstrate this through provision of scaling results on traditional and graphics processing unit-accelerated large scale supercomputers.

scholarly journals Embedded GPU Implementation for High-Performance Ultrasound Imaging

Electronics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 884
Author(s):  
Stefano Rossi ◽  
Enrico Boni
Keyword(s):  
High Performance ◽  
Graphics Processing Unit ◽  
Digital Signal ◽  
Processing Unit ◽  
Embedded Computing ◽  
Field Programmable ◽  
Peripheral Component Interconnect ◽  
Programmable Gate Arrays ◽  
Graphics Processing ◽  
Signal Processors

Methods of increasing complexity are currently being proposed for ultrasound (US) echographic signal processing. Graphics Processing Unit (GPU) resources allowing massive exploitation of parallel computing are ideal candidates for these tasks. Many high-performance US instruments, including open scanners like ULA-OP 256, have an architecture based only on Field-Programmable Gate Arrays (FPGAs) and/or Digital Signal Processors (DSPs). This paper proposes the implementation of the embedded NVIDIA Jetson Xavier AGX module on board ULA-OP 256. The system architecture was revised to allow the introduction of a new Peripheral Component Interconnect Express (PCIe) communication channel, while maintaining backward compatibility with all other embedded computing resources already on board. Moreover, the Input/Output (I/O) peripherals of the module make the ultrasound system independent, freeing the user from the need to use an external controlling PC.

scholarly journals Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes

2017 ◽  
Vol 25 (1) ◽  
pp. 93-98 ◽  
Author(s):  
Yuan Luo ◽  
Yu Cheng ◽  
Özlem Uzuner ◽  
Peter Szolovits ◽  
Justin Starren
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Graphics Processing Unit ◽  
Medical Problem ◽  
Feature Engineering ◽  
Processing Unit ◽  
Clinical Notes ◽  
Overall Evaluation ◽  
Relation Classification

Abstract We propose Segment Convolutional Neural Networks (Seg-CNNs) for classifying relations from clinical notes. Seg-CNNs use only word-embedding features without manual feature engineering. Unlike typical CNN models, relations between 2 concepts are identified by simultaneously learning separate representations for text segments in a sentence: preceding, concept1, middle, concept2, and succeeding. We evaluate Seg-CNN on the i2b2/VA relation classification challenge dataset. We show that Seg-CNN achieves a state-of-the-art micro-average F-measure of 0.742 for overall evaluation, 0.686 for classifying medical problem–treatment relations, 0.820 for medical problem–test relations, and 0.702 for medical problem–medical problem relations. We demonstrate the benefits of learning segment-level representations. We show that medical domain word embeddings help improve relation classification. Seg-CNNs can be trained quickly for the i2b2/VA dataset on a graphics processing unit (GPU) platform. These results support the use of CNNs computed over segments of text for classifying medical relations, as they show state-of-the-art performance while requiring no manual feature engineering.

scholarly journals Prediction of Residual Stresses in a Multipass Pipe Weld by a Novel 3D Finite Element Approach

2018 ◽  
Author(s):  
Hui Huang ◽  
Jian Chen ◽  
Blair Carlson ◽  
Hui-Ping Wang ◽  
Paul Crooker ◽  
...  
Keyword(s):  
Finite Element ◽  
Residual Stresses ◽  
High Performance ◽  
Large Scale ◽  
Graphics Processing Unit ◽  
Computational Cost ◽  
Three Dimensional ◽  
Processing Unit ◽  
Girth Welds ◽  
Welding Processes

Due to enormous computation cost, current residual stress simulation of multipass girth welds are mostly performed using two-dimensional (2D) axisymmetric models. The 2D model can only provide limited estimation on the residual stresses by assuming its axisymmetric distribution. In this study, a highly efficient thermal-mechanical finite element code for three dimensional (3D) model has been developed based on high performance Graphics Processing Unit (GPU) computers. Our code is further accelerated by considering the unique physics associated with welding processes that are characterized by steep temperature gradient and a moving arc heat source. It is capable of modeling large-scale welding problems that cannot be easily handled by the existing commercial simulation tools. To demonstrate the accuracy and efficiency, our code was compared with a commercial software by simulating a 3D multi-pass girth weld model with over 1 million elements. Our code achieved comparable solution accuracy with respect to the commercial one but with over 100 times saving on computational cost. Moreover, the three-dimensional analysis demonstrated more realistic stress distribution that is not axisymmetric in hoop direction.

High-Performance, Graphics Processing Unit-Accelerated Fock Build Algorithm

2020 ◽  
Vol 16 (12) ◽  
pp. 7232-7238
Author(s):  
Giuseppe M. J. Barca ◽  
Jorge L. Galvez-Vallejo ◽  
David L. Poole ◽  
Alistair P. Rendell ◽  
Mark S. Gordon
Keyword(s):  
High Performance ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Graphics Processing

scholarly journals Ballooning Graphics Memory Space in Full GPU Virtualization Environments

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Younghun Park ◽  
Minwoo Gu ◽  
Sungyong Park
Keyword(s):  
High Performance ◽  
Virtual Machines ◽  
Graphics Processing Unit ◽  
Performance Degradation ◽  
Processing Unit ◽  
Memory Space ◽  
Memory Size ◽  
Memory Sharing ◽  
Gpu Virtualization ◽  
Graphics Processing

Advances in virtualization technology have enabled multiple virtual machines (VMs) to share resources in a physical machine (PM). With the widespread use of graphics-intensive applications, such as two-dimensional (2D) or 3D rendering, many graphics processing unit (GPU) virtualization solutions have been proposed to provide high-performance GPU services in a virtualized environment. Although elasticity is one of the major benefits in this environment, the allocation of GPU memory is still static in the sense that after the GPU memory is allocated to a VM, it is not possible to change the memory size at runtime. This causes underutilization of GPU memory or performance degradation of a GPU application due to the lack of GPU memory when an application requires a large amount of GPU memory. In this paper, we propose a GPU memory ballooning solution called gBalloon that dynamically adjusts the GPU memory size at runtime according to the GPU memory requirement of each VM and the GPU memory sharing overhead. The gBalloon extends the GPU memory size of a VM by detecting performance degradation due to the lack of GPU memory. The gBalloon also reduces the GPU memory size when the overcommitted or underutilized GPU memory of a VM creates additional overhead for the GPU context switch or the CPU load due to GPU memory sharing among the VMs. We implemented the gBalloon by modifying the gVirt, a full GPU virtualization solution for Intel’s integrated GPUs. Benchmarking results show that the gBalloon dynamically adjusts the GPU memory size at runtime, which improves the performance by up to 8% against the gVirt with 384 MB of high global graphics memory and 32% against the gVirt with 1024 MB of high global graphics memory.

scholarly journals GPU empowered pipelines for calculating genome-wide kinship matrices with ultra-high dimensional genetic variants and facilitating 1D and 2D GWAS

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Wenchao Zhang ◽  
Xinbin Dai ◽  
Shizhong Xu ◽  
Patrick X Zhao
Keyword(s):  
Genetic Variants ◽  
High Performance ◽  
Genome Wide Association Study ◽  
Graphics Processing Unit ◽  
High Dimensional ◽  
Processing Unit ◽  
Kinship Matrix ◽  
Matrix Operations ◽  
Genome Wide ◽  
Matrix Calculation

Abstract Genome-wide association study (GWAS) is a powerful approach that has revolutionized the field of quantitative genetics. Two-dimensional GWAS that accounts for epistatic genetic effects needs to consider the effects of marker pairs, thus quadratic genetic variants, compared to one-dimensional GWAS that accounts for individual genetic variants. Calculating genome-wide kinship matrices in GWAS that account for relationships among individuals represented by ultra-high dimensional genetic variants is computationally challenging. Fortunately, kinship matrix calculation involves pure matrix operations and the algorithms can be parallelized, particular on graphics processing unit (GPU)-empowered high-performance computing (HPC) architectures. We have devised a new method and two pipelines: KMC1D and KMC2D for kinship matrix calculation with high-dimensional genetic variants, respectively, facilitating 1D and 2D GWAS analyses. We first divide the ultra-high-dimensional markers and marker pairs into successive blocks. We then calculate the kinship matrix for each block and merge together the block-wise kinship matrices to form the genome-wide kinship matrix. All the matrix operations have been parallelized using GPU kernels on our NVIDIA GPU-accelerated server platform. The performance analyses show that the calculation speed of KMC1D and KMC2D can be accelerated by 100–400 times over the conventional CPU-based computing.

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