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High throughput parallel implementation of aho-corasick algorithm on a GPU

High throughput parallel implementation of aho-corasick algo...

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2013 IEEE 37th Annual computer Software and Applications conference, COMPSAC 2013

作者： Tran, Nhat-Phuong Lee, Myungho Hong, Sugwon Choi, Jaeyoung Department of Computer Science and Engineering Myongji University 38-2 San Namdong Cheo-In GuYong In Kyung Ki Do 449-728 Korea Republic of School of Computer Science and Engineering Soongsil University 369 Sangdo Ro Dongjak gu Seoul 156-743 Korea Republic of

ISBN: (纸本)9780769549798

Pattern matching is an important operation in various applications such as computer and network security, bioinformatics, image processing, among many others. Aho-Corasick (AC) algorithm is a multiple patterns matching algorithm commonly used for such applications. In order to meet the highly demanding performance requirements imposed on these applications, achieving high performance for AC algorithm is crucial. In this paper, we present a high performance parallel implementation of AC algorithm on a Graphic Processing Unit (GPU) which efficiently utilizes the high degree of on-chip parallelism and the memory hierarchy of the GPU so that the aggregate performance (or throughput) of the GPU can be maximized. For this purpose our approach carefully places and caches the input text data and the reference pattern data used for pattern matching in the on-chip shared memories and the texture caches of the GPU. Furthermore, it efficiently schedules the off-chip global memory loads and the shared memory stores in order to minimize the overheads in loading the input data to the shared memories and also to minimize the shared memory bank conflicts. the proposed approach leads to a significant cut-down of the effective memory access latencies and leads to impressive performance improvements. Experimental results on Nvidia GeForce GTX 285 GPU show that our approach delivers up to 127Gbps throughput performance and up to 222-times speedup compared with a serial version running on 2.2Ghz Core2Duo Intel processor. © 2013 IEEE.

关键词： graphics processing unit

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Impact of shape on apparent translucency differences 27

Impact of shape on apparent translucency differences

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27th Color and Imaging conference: Color Science and Engineering Systems, Technologies, and Applications, CIC 2019

作者： Gigilashvili, Davit Urban, Philipp thomas, Jean-Baptiste Hardeberg, Jon Yngve Pedersen, Marius Department of Computer Science Norwegian University of Science and Technology Gjøvik Norway Fraunhofer Institute for Computer Graphics Research IGD Darmstadt Germany

ISBN: (纸本)9780892083435

Translucency is one of the major appearance attributes. Apparent translucency is impacted by various factors including object shape and geometry. Despite general proposals that object shape and geometry have a significant effect on apparent translucency, no quantification has been made so far. Quantifying and modeling the impact of geometry, as well as comprehensive understanding of the translucency perception process, are a point of not only academic, but also industrial interest with 3D printing as an example among many. We hypothesize that a presence of thin areas in the object facilitates material translucency estimation and changes in material properties have larger impact on apparent translucency of the objects with thin areas. computergenerated images of objects with various geometry and thickness have been used for a psychophysical experiment in order to quantify apparent translucency difference between objects while varying material absorption and scattering properties. Finally, absorption and scattering difference thresholds where the human visual system starts perceiving translucency difference need to be identified and its consistency needs to be analyzed across different shapes and geometries. © 2019 Society for Imaging Science and Technology.

关键词： Geometry

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GPU-Accelerated protein family identification for metagenomics

GPU-Accelerated protein family identification for metagenomi...

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2013 IEEE 37th Annual computer Software and Applications conference, COMPSAC 2013

作者： Wu, Changjun Kalyanaraman, Ananth Xerox Innovation Group Xerox Research Center Webster NY United States School of Electrical Engineering and Computer Science Washington State University Pullman WA United States

ISBN: (纸本)9780769549798

the clustering of putative protein/Open Reading Frame (ORF) sequences available from large-scale metagenomics survey projects is a core analytical function that has led to the identification and characterization of novel protein families of environmental microbial communities. the implementation of this function, however, is currently challenged not only by data size but also by data complexity. In this paper, we present a CPU-GPU implementation of a randomized graph clustering heuristic called Shingling, which was originally developed by Gibson et al. Our implementation uses the CPU and GPU for different stages of computation, using GPUs for the most time-consuming steps. Experimental results of a 2M ocean metagenomics data set obtained from the Sorcerer II Global Ocean Sampling project show that our new implementation is able to achieve a ~7X speedup over our serial implementation without using asynchronous CPU-GPU communication, with the GPU part alone contributing to over ~374X speedup in the accelerated part. Qualitative evaluation of the 2M data set shows that our method is able to improve sensitivity of clustering over existing methods, and is more successful in recruiting more sequences into the clustering without impacting the overall specificity. As a demonstration of a large scale run, we were able to cluster a real world homology graph, containing 11M vertices and 640M edges, and constructed from sequences of an ongoing Pacific Ocean metagenomics survey project, in about 94 minutes. © 2013 IEEE.

关键词： graphics processing unit

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GPU peer-to-peer techniques applied to a cluster interconnect

GPU peer-to-peer techniques applied to a cluster interconnec...

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2013 IEEE 37th Annual computer Software and Applications conference, COMPSAC 2013

作者： Ammendola, Roberto Bernaschi, Massimo Biagioni, Andrea Bisson, Mauro Fatica, Massimiliano Frezza, Ottorino Lo Cicero, Francesca Lonardo, Alessandro Mastrostefano, Enrico Paolucci, Pier Stanislao Rossetti, Davide Simula, Francesco Tosoratto, Laura Vicini, Piero Istituto Nazionale di Fisica Nucleare Sezione Roma Tor Vergata Rome Italy Istituto Applicazioni Calcolo Consiglio Nazionale Delle Ricerche Rome Italy Istituto Nazionale di Fisica Nucleare Sezione Roma Piazzale Aldo Moro 2 I-00186 Rome Italy NVIDIA Corp. CA United States Sapienza University Department of Computer Science Via Salaria 113 Rome Italy

ISBN: (纸本)9780769549798

Modern GPUs support special protocols to exchange data directly across the PCI Express bus. While these protocols could be used to reduce GPU data transmission times, basically by avoiding staging to host memory, they require specific hardware features which are not available on current generation network adapters. In this paper we describe the architectural modifications required to implement peer-to-peer access to NVIDIA Fermi-And Kepler-class GPUs on an FPGA-based cluster interconnect. Besides, the current software implementation, which integrates this feature by minimally extending the RDMA programming model, is discussed, as well as some issues raised while employing it in a higher level API like MPI. Finally, the current limits of the technique are studied by analyzing the performance improvements on low-level benchmarks and on two GPU-Accelerated applications, showing when and how they seem to benefit from the GPU peer-to-peer method. © 2013 IEEE.

关键词： graphics processing unit

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Status of spring-8 photocathode RF gun for future light sources

Status of spring-8 photocathode RF gun for future light sour...

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27th International Free Electron Laser conference, FEL 2005

作者： Tomizawa, H. Dewa, H. Taniuchi, T. Mizuno, A. Asaka, T. Yanagida, K. Suzuki, S. Kobayashi, T. Hanaki, H. Matsui, F. Kouto Mikazuki-cho Sayo-gun Hyogo 679-5198 Japan Creative and Advanced Research Department Industrial Technology Center of Fukui Prefecture 61 Kawaiwashitsuka-cho Fukui City 910-0102 Japan

Since 1996, we have been researching a photocathode single-cell pillbox rf gun for future light sources, and to date have achieved a maximum field gradient of 187 MV/m with a chemical etching processed cavity. For the last three years, we have been focusing on the development of a stable and highly qualified UV laser source for the rf gun. the UV laser pulse (10 Hz) energy is 80 μJ/pulse at the entrance window. the energy stability (rms) of the laser has been reduced to 0.2∼0.3% at the fundamental and 0.7∼1.3% at the third harmonic generations. this stability can be held continuously for two months, 24 hours a day. the improvement is the result of the stabilization of the laser system in a humidity-controlled cleanroom. In addition, the ideal spatial and temporal profiles of a shot-by-shot single laser pulse are essential to suppress the emittance growth of the electron beam from the rf gun. We prepared a deformable mirror for spatial shaping and a spatial light modulator based on fused silica plates for temporal shaping. With a computer-aided deformable mirror, we obtained a minimum horizontal normalized emittance of 1.74 mm mrad with a beam energy of 28.8 MeV, holding its net charge to 0.09 nC/bunch. We applied the variable quadrupole method to evaluate the emittance. the 3D shape of the laser was spatially flattop with a 1 mm diameter on the cathode and temporally a function of sech(t) with a pulse duration of 5 ps (FWHM). this laser pulse was illuminated on the copper cathode with normal incidence. We are currently preparing both adaptive optics to automatically optimize the electron beam parameters for lower emittance with a feedback routine.

关键词： Adaptive optics

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Acceleration of a high order finite-difference WENO scheme for large-scale cosmological simulations on GPU

Acceleration of a high order finite-difference WENO scheme f...

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2013 IEEE 37th Annual computer Software and Applications conference, COMPSAC 2013

作者： Meng, Chen Wang, Long Cao, Zongyan Ye, Xianfeng Feng, Long-Long Supercomputing Center Computer Network Information Center Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China National Astronomical Observatories Chinese Academy of Sciences Beijing China Purple Mountain Observatory Chinese Academy of Sciences Beijing China Center for Astrophysics University of Science and Technology of China Anhui China

ISBN: (纸本)9780769549798

In this work, we present our implementation of a three-dimensional 5th order finite-difference weighted essentially non-oscillatory (WENO) scheme in double precision on CPU/GPU clusters, which targets on large-scale cosmological hydrodynamic flow simulations involving both shocks and complicated smooth solution structures. In the level of MPI parallelization, we subdivided the domain along each of three axial directions. then on each process, we ported the WENO computation to GPU. this method is memory-bound derived from the calculations of the weights and it becomes a greater challenge for a 3D high order problem in double precision. To make full use of impressive computing power of GPU and avoid its memory limitation, we performed a series of optimizations that are focused on memory accessing mode at all levels. We subjected this code to a number of typical tests for the evaluation of effectiveness and efficiency. Our tests indicate that, in a mono-thread Fortran code reference, the GPU version achieves a 12~19 speed-up and about 19~36 in the computation part. We analyzed the results on both Fermi and Kepler GPUs. We also outlined what is needed to further increase the speed by reducing the time spent on the communications part and other future work. © 2013 IEEE.

关键词： graphics processing unit

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A graph grammar approach to software architecture verification and transformation

A graph grammar approach to software architecture verificati...

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IEEE Annual International computer Software and Applications conference (COMPSAC)

作者： Jun Kong Kang Zhang Jing Dong Guanglei Song Department of Computer Science University of Texas Dallas Richardson TX USA

ISBN: (纸本)0769520200

Software architecture and design are usually modeled and represented by informal diagrams, such as architecture diagrams and UML diagrams. While these graphic notations are easy to understand and are convenient to use, they are not amendable to automated verification and transformation. this paper provides graph grammars for architecture and UML class diagrams. these grammars enable a high level of abstraction for the general organization of a class of software architectures, and form a basis for various analysis and transformations. In this approach, software verification is performed through a syntax analyzer. Architecture transformation is achieved by applying predefined transformation rules.

关键词： Software architecture Software design computer architecture Unified modeling language Object oriented modeling computer science computer graphics Software performance Performance analysis Writing

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CHARLIE: a computer-managed homework, assignment and response, learning and instruction environment

CHARLIE: a computer-managed homework, assignment and respons...

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Frontiers in Education (FIE) conference

作者： D.S. Barker Technology Department Electrical Engineering Technology Option State University of New York College Buffalo Buffalo NY USA

CHARLIE is a new asynchronous learning system which was developed for engineering technology students at Buffalo State College. CHARLIE contains many fully-electronic and fully-automated features including: individualized homework with graphics, course agenda, course syllabus, tutorials, lecture summaries, student bulletin board, laboratory descriptions, grades, and access to the Internet. In this paper, CHARLIE is compared to other asynchronous learning systems. the distinguishing features of CHARLIE are ease of creation and administration by the instructor who has a knowledge of the DEC VMS operating system and C, simple exercise development concurrent with its use, and implementation on text-only terminals which are networked to a central computer. the goals of CHARLIE include: improved student learning, reduced homework grading, alternative teaching and learning opportunities, and efficient delivery of course information.

关键词： Home computing Learning systems Educational institutions computer graphics Laboratories Internet Voice mail Operating systems computer networks Concurrent computing

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spring Buddy: A Self-Adaptive Elastic Memory Management Scheme for Efficient Concurrent Allocation/Deallocation in Cloud Computing Systems 27

Spring Buddy: A Self-Adaptive Elastic Memory Management Sche...

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27th IEEE International conference on Parallel and Distributed Systems, ICPADS 2021

作者： Lu, Yihui Liu, Weidong Wu, Chentao Wang, Jia Gao, Xiaoming Li, Jie Guo, Minyi Shanghai Jiao Tong University Department of Computer Science and Engineering Shanghai China Sichuan Research Institute Shanghai Jiao Tong University Sichuan China Tencent Inc. Cloud Architecture and Platform TEG Beijing Shenzhen China

ISBN: (纸本)9781665408783

Within the cloud computing scenario, each server usually carries multiple service processes, which intensifies the concurrency pressure of the system. As a result, the process of memory management during page allocation and deallocation becomes a significant bottleneck. Although several methods such as Buddy System and Inverse Buddy System (iBuddy) have been proposed to improve the performance of memory management, they cannot adapt to the highly concurrent environment of cloud computing, because they either force the memory allocation/deallocation requests to be serialized or bring extra fragmentation. To address the above problem, we propose spring Buddy, which improves the concurrency of both memory allocation and deallocation and avoids unnecessary fragmentation. It can detect the changes of system- and process-level memory request patterns and dynamically adjust the organization of page frames. Inventively, spring Buddy uses the spring core layer to provide both concurrent response and resource aggregation capability which is adapted to the system's concurrency pressure, and also uses the spring lazy layer to further mitigate the system resource contention through process behavior prediction. To demonstrate the effectiveness of spring Buddy, we implement it in the Linux kernel. the results demonstrate that spring Buddy can reduce memory allocation latency by 71.47 % and deallocation latency by 93.20% on average compared to the existing methods. © 2021 IEEE.

关键词： Inverse problems

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AMF-CSR: Adaptive Multi-Row Folding of CSR for SpMV on GPU 27

AMF-CSR: Adaptive Multi-Row Folding of CSR for SpMV on GPU

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27th IEEE International conference on Parallel and Distributed Systems, ICPADS 2021

作者： Gao, Jianhua Ji, Weixing Liu, Jie Shao, Senhao Wang, Yizhuo Shi, Feng School of Computer Science and Technology Beijing Institute of Technology China

ISBN: (纸本)9781665408783

SpMV is a cost-dominant operation used in many iterative methods for solving large-scale sparse linear systems. However, irregular memory access of SpMV to the multiplied vector leads to low data locality and then harms the performance. this paper presents an adaptive multi-row folding of CSR (AMF-CSR) format for SpMV calculation on GPU. this new storage format supports the folding of the variable number of rows in order to achieve better load balancing in computation. AMF-CSR not only increases the density of non-zero elements in a folded row, thereby improving the access locality of the multiplied vector, but also merges an approximately equal number of nonzero elements in a folded row, hence achieving load balancing. the performance evaluation using 28 sparse matrices shows that the proposed SpMV algorithm based on AMF-CSR achieves the highest speedup of 4.11x and 3.62x on GTX 1080 Ti and Tesla V100 respectively against a fixed multi-row folding-based SpMV algorithm. Evaluation results using 450 regular sparse matrices and 450 irregular sparse matrices also show that AMF-CSR is superior to other SpMV implementations. © 2021 IEEE.

关键词： graphics processing unit

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