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General Purpose Computation on the GPU (GPGPU)

GPUPC GPU GPUCPU GPU

Middleware for GPU-accelerated grid systems

GPU GPU CPU

A Fine Grained Cycle Sharing System with Cooperative Multitasking on GPUs
Fumihiko Ino, Yosuke Oka, and Kenichi Hagihara
International Journal of Networking and Computing, Vol.4, No.2, pp.236-250, (2014-07). - [PDF]

The original publication is available at http://dx.doi.org/10.15803/ijnc.4.2_236

The Past, Present, and Future of GPU-Accelerated Grid Computing
Fumihiko Ino
In Proceedings of the 1st International Symposium on Computing and Networking (CANDAR 2013), pp.17-21, (2013-12). - [PDF]

Copyright©2013 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The original publication is available at http://dx.doi.org/10.1109/CANDAR.2013.10
Sequence Homology Search Using Fine Grained Cycle Sharing of Idle GPUs
Fumihiko Ino, Yuma Munekawa, and Kenichi Hagihara
IEEE Transactions on Parallel and Distributed Systems, Vol.23, No.4, pp.751-759, (2012-04). - [PDF] - [Supplemental Material (PDF)]

Copyright©2012 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The original publication is available at http://dx.doi.org/10.1109/TPDS.2011.239
Cooperative Multitasking for GPU-Accelerated Grid Systems
Fumihiko Ino, Akihiro Ogita, Kentaro Oita, and Kenichi Hagihara
Concurrency and Computation: Practice and Experience, Vol.24, No.1, pp.96-107, (2012-01). - [PDF]

This is the pre-peer reviewed version of the following article: Concurrency and Computation: Practice and Experience, Copyright©2012 John Wiley and Sons, Inc., which has been published in final form at http://dx.doi.org/10.1002/cpe.1722

Cooperative Multitasking for GPU-Accelerated Grid Systems
Fumihiko Ino, Akihiro Ogita, Kentaro Oita, and Kenichi Hagihara
In Proceedings of the 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2010), pp.774-779, Melbourne, Australia, (2010-05). Presented at the 1st Frontiers of GPU, Multi and Many-Core System Workshop (FGMMS 2010). - [PDF]

Copyright©2010 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/CCGRID.2010.18
Harnessing the Power of Idle GPUs for Acceleration of Biological Sequence Alignment
Fumihiko Ino, Yuki Kotani, Yuma Munekawa, and Kenichi Hagihara
Parallel Processing Letters, Vol.19, No.4, pp.513-533, (2009-12). 20. - [PDF]

Copyright©2009 World Scientific Publishing Company. The original publication is available at http://dx.doi.org/10.1142/S0129626409000390
A Resource Selection System for Cycle Stealing in GPU Grids
Yuki Kotani, Fumihiko Ino, and Kenichi Hagihara
Journal of Grid Computing, Vol.6, No.4, pp.399-416, (2008-12). - [PDF]

Copyright©2008 Springer Science + Business Media B.V. The original publication is available at www.springerlink.com. http://dx.doi.org/10.1007/s10723-008-9099-7

A Resource Selection Method for Cycle Stealing in the GPU Grid
Yuki Kotani, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 4th International Symposium on Parallel and Distributed Processing and Applications Workshops (ISPA 2006 Workshops), Lecture Notes in Computer Science 4331, Springer-Verlag, pp.939-950, Sorrento, Italy, (2006-12). - [PDF]

Copyright©2006 Springer-Verlag. The original publication is available at www.springerlink.com. http://dx.doi.org/10.1007/11942634_79

GPU accelerated applications

2/3 GPUGPU 1GPUPC128PC GPU LU

An Out-of-Core Branch and Bound for Solving the 0-1 Knapsack Problem on a GPU
Jingcheng Shen, Kentaro Shigeoka, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 17th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2017), Lecture Notes in Computer Science 10393, Springer-Verlag, pp.254-267, Helsinki, Finland, (2017-08). - [PDF]

Copyright©2017 Springer-Verlag. The original publication is available at www.springerlink.com. https://doi.org/10.1007/978-3-319-65482-9_17
Parallelizing Exact and Approximate String Matching via Inclusive Scan on a GPU
Yasuaki Mitani, Fumihiko Ino, and Kenichi Hagihara
IEEE Transactions on Parallel and Distributed Systems, Vol.xx, No.xx, pp.xx-xx, (201x-xx). IEEE Transactions on Parallel and Distributed Systems, Vol.28, No.7, pp.1989-2002, (2017-07). - [Supplemental Material (PDF)]

Copyright©2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The original publication is available at http://dx.doi.org/10.1109/TPDS.2016.2645222
Cache-Aware GPU Optimization for Out-of-Core Cone Beam CT Reconstruction of High-Resolution Volumes
Yuechao Lu, Fumihiko Ino, and Kenichi Hagihara
IEICE Transactions on Information and Systems, Vol.E99-D, No.12, pp.3060-3071, (2016-12). - [PDF]

Copyright©2016 IEICE. This is the original publication available at IEICE Transactions Online http://dx.doi.org/10.1587/transinf.2016EDP7174
Reducing Memory Usage by the Lifting-based Discrete Wavelet Transform with a Unified Buffer on a GPU
Takuya Ikuzawa, Fumihiko Ino, and Kenichi Hagihara
Journal of Parallel and Distributed Computing, Vol.93/94, pp.44-55, (2016-07). - [PDF]

Copyright©2016 Elsevier B.V. This is the authorfs version of a work that was accepted for publication. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published at http://dx.doi.org/10.1016/j.jpdc.2016.03.010
Accelerating the Smith-Waterman Algorithm with an Interpair Pruning Method for All-Pairs Comparison of Base Sequences
Daiki Okada, Fumihiko Ino, and Kenichi Hagihara
BMC Bioinformatics, Vol.16, No.321, 15 pages, (2015-10). - [PDF]

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver applies to the data made available in this article, unless otherwise stated. The original version is available at http://dx.doi.org/10.1186/s12859-015-0744-4
A Bit-Parallel Algorithm for Searching Multiple Patterns with Various Lengths
Ko Kusudo, Fumihiko Ino, and Kenichi Hagihara
Journal of Parallel and Distributed Computing, Vol.76, pp.49-57, (2015-02). - [PDF]

Copyright©2015 Elsevier B.V. This is the authors version of a work that was accepted for publication. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published at http://dx.doi.org/10.1016/j.jpdc.2014.11.003
Enumerating Joint Weight of a Binary Linear Code Using Parallel Architectures: multi-core CPUs and GPUs
Shohei Ando, Fumihiko Ino, Toru Fujiwara, and Kenichi Hagihara
International Journal of Networking and Computing, Vol.5, No.2, pp.290-303, (2015-07). - [PDF]

The original publication is available at http://dx.doi.org/10.15803/ijnc.5.2_290

A Parallel Algorithm for Enumerating Joint Weight of a Binary Linear Code in Network Coding
Shohei Ando, Fumihiko Ino, Toru Fujiwara, and Kenichi Hagihara
In Proceedings of the 2nd International Symposium on Networking and Computing (CANDAR 2014), pp. 137-143, Shizuoka, Japan, (2014-12). - [PDF]

Copyright©2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Efficient Acceleration of Mutual Information Computation for Nonrigid Registration Using CUDA
Kei Ikeda, Fumihiko Ino, and Kenichi Hagihara. IEEE Journal of Biomedical and Health Informatics, Vol.18, No.3, pp.956-968, (2014-05). - [PDF]

Copyright©2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The original publication is available at http://dx.doi.org/10.1109/JBHI.2014.2310745
Acceleration of Variance of Color Differences-Based Demosaicing Using CUDA
Muhammad Ismail Faruqi, Fumihiko Ino, and Kenichi Hagihara. In Proceedings of the 10th International Conference on High Performance Computing and Simulation (HPCS 2012), pp.503-510, Madrid, Spain, (2012-07). Nominated for the Outstanding Paper Award. - [PDF]

Copyright©2012 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The original publication is available at http://dx.doi.org/10.1109/HPCSim.2012.6266965
A Multi-GPU Spectrometer System for Real-time Wide Bandwidth Radio Signal Analysis
Hirofumi Kondo, Eric Heien, Masao Okita, Dan Werthimer, and Kenichi Hagihara. In Proceedings of the 8th International Symposium on Parallel and Distributed Processing with Applications (ISPA 2010), pp.594-604, Taipei, Taiwan, (2010-09). - [PDF]

Copyright©2010 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/ISPA.2010.53
Out-of-Core Cone Beam Reconstruction Using Multiple GPUs
Fumihiko Ino, Yusuke Okitsu, Taketo Kishi, Syuhei Ohnishi, and Kenichi Hagihara. In Proceedings of the 7th IEEE International Symposium on Biomedical Imaging (ISBI 2010), pp.792-795, Rotterdam, The Netherlands, (2010-04). - [PDF]

Copyright©2010 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/ISBI.2010.5490055
High-Performance Cone Beam Reconstruction Using CUDA Compatible GPUs
Yusuke Okitsu, Fumihiko Ino, and Kenichi Hagihara
Parallel Computing, Vol.36, No.2/3, pp.129-141, (2010-02). - [PDF]

Copyright©2010 Elsevier B.V. This is the authors version of a work that was accepted for publication. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published at http://dx.doi.org/10.1016/j.parco.2010.01.004

Fast Cone Beam Reconstruction Using the CUDA-enabled GPU
Yusuke Okitsu, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of 15th International Conference on High Performance Computing (HiPC 2008), Lecture Notes in Computer Science 5374, Springer-Verlag, pp.108-119, Bangalore, India, (2008-12). - [PDF]

Copyright©2008 Springer-Verlag. The original publication is available at www.springerlink.com. http://dx.doi.org/10.1007/978-3-540-89894-8_13
RGBA Packing for Fast Cone Beam Reconstruction on the GPU
Fumihiko Ino, Seiji Yoshida, and Kenichi Hagihara
In Proceedings of the SPIE Medical Imaging (MI 2009), Vol. 7258, Orlando, FL, USA, (2009-02). 8 pages (CD-ROM). - [PDF]

Copyright©2009 Society of Photo-Optical Instrumentation Engineers. This paper was published in Proceedings of the SPIE Medical Imaging and is made available as an electronic reprint with permission of SPIE. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited. http://dx.doi.org/10.1117/12.811149
A Task Parallel Algorithm for Finding All-Pairs Shortest Paths Using the GPU
Tomohiro Okuyama, Fumihiko Ino, and Kenichi Hagihara
International Journal of High Performance Computing and Networking, Vol.7, No.2, pp.87-98, (2012-04). - [PDF]

Copyright©2012 Inderscience Enterprises Ltd. The original publication is available at http://dx.doi.org/10.1504/IJHPCN.2012.046384

A Task Parallel Algorithm for Computing the Costs of All-Pairs Shortest Paths on the CUDA-compatible GPU
Tomohiro Okuyama, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 6th International Symposium on Parallel and Distributed Processing with Applications (ISPA 2008), pp.284-291, (2008-12). Selected as one of the best papers. - [PDF]

Copyright©2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/ISPA.2008.40
Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs
Yuma Munekawa, Fumihiko Ino, and Kenichi Hagihara
IEICE Transactions on Information and Systems, Vol.E93-D, No.6, pp.1479-1488, (2010-06). - [PDF]

Copyright©2010 IEICE. This is the original publication available at IEICE Transactions Online

Design and Implementation of the Smith-Waterman Algorithm on the CUDA-Compatible GPU
Yuma Munekawa, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2008), BI-8-1-3, Athens, Greece, (2008-10). 6 pages (CD-ROM). - [PDF]

Copyright©2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/BIBE.2008.4696721
A GPGPU Approach for Accelerating 2-D/3-D Rigid Registration of Medical Images
Fumihiko Ino, Jun Gomita, Yasuhiro Kawasaki, and Kenichi Hagihara
In Proceedings of the 4th International Symposium on Parallel and Distributed Processing and Applications (ISPA 2006), Lecture Notes in Computer Science 4330, Springer-Verlag, pp.769-780, Sorrento, Italy, (2006-12). - [PDF]

Copyright©2006 Springer-Verlag. The original publication is available at www.springerlink.com. http://dx.doi.org/10.1007/11946441_84
Performance Study of LU Decomposition on the Programmable GPU
Fumihiko Ino, Manabu Matsui, Keigo Goda, and Kenichi Hagihara
In Proceedings of the 12th International Conference on High Performance Computing (HiPC 2005), Lecture Notes in Computer Science 3769, Springer-Verlag, pp.83-94, Goa, India, (2005-12). - [PDF]

Copyright©2005 Springer-Verlag. The original publication is available at www.springerlink.com. http://dx.doi.org/10.1007/11602569_13

Tools for Accelerating GPU Appplications

GPUGPU 1810 40% IPDPS

Towards Automating Multi-dimensional Data Decomposition for Executing a Single-GPU Code on a Multi-GPU System
Ryotaro Sakai, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 4th International Symposium on Networking and Computing (CANDAR 2016), pp.xx-xx, Hiroshima, Japan, (2016-11). Presented at the 4th International Workshop on Computer Systems and Architectures (CSA 2016) - [PDF]

Copyright©2016 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/xx.2016.xx
An Extension of OpenACC Directives for Out-of-Core Stencil Computation with Temporal Blocking
Nobuhiro Miki, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 3rd Workshop on Accelerator Programming Using Directives (WACCPD 2016), pp.36-45, Salt Lake City, UT, USA, (2016-11). - [PDF]

Copyright©2016 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/WACCPD.2016.10
An OpenACC Optimizer for Accelerating Histogram Computation on a GPU
Kei Ikeda, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 24th Euromicro International Conference on Parallel, Distributed and Network-Based Computing (PDP 2016), pp.466-477, Heraklion, Greece, (2016-02). - [PDF]

Copyright©2016 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/PDP.2016.14
GPU-Chariot: A Programming Framework for Stream Applications Running on Multi-GPU Systems
Fumihiko Ino, Shinta Nakagawa, and Kenichi Hagihara
IEICE Transactions on Information and Systems, Vol.E96-D, No.12, pp.2604-2616, (2013-12). - [PDF]

Copyright©2013 IEICE. This is the original publication available at IEICE Transactions Online
A Parallel Scheme for Accelerating Parameter Sweep Applications on a GPU
Fumihiko Ino, Kentaro Shigeoka, Tomohiro Okuyama, Masaya Motokubota, and Kenichi Hagihara
Concurrency and Computation: Practice and Experience, Vol.26, No.2, pp.516-531, (2014-02). - [PDF]

This is the pre-peer reviewed version of the following article: Concurrency and Computation: Practice and Experience, Copyright©2014 John Wiley and Sons, Inc., which has been published in final form at http://dx.doi.org/10.1002/cpe.3016

Accelerating Parameter-Sweep Applications Using CUDA
Masaya Motokubota, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 19th Euromicro International Conference on Parallel, Distributed and Network-Based Computing (PDP 2011), pp.111-118, Ayia Napa, Cyprus, (2011-02). - [PDF]

Copyright©2011 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/PDP.2011.19
A Middleware for Efficient Stream Processing in CUDA
Shinta Nakagawa, Fumihiko Ino, and Kenichi Hagihara
Computer Science - Research and Development, Vol.25, No.1/2, pp.41-49, (2010-05). - [PDF]

Copyright©2010 Springer-Verlag. The original publication is available at www.springerlink.com. http://dx.doi.org/10.1007/s00450-010-0107-3
GPGPU
, ,
, Vol.48, No. SIG 13(ACS 19), pp.235-246, (2007-08). - [PDF]

Notice for the use of this material The copyright of this material is retained by the Information Processing Society of Japan (IPSJ). This material is published on this web site with the agreement of the author (s) and the IPSJ. Please be complied with Copyright Law of Japan and the Code of Ethics of the IPSJ if any users wish to reproduce, make derivative work, distribute or make available to the public any part or whole thereof.
A Code Motion Technique for Accelerating General-Purpose Computation on the GPU
Takatoshi Ikeda, Fumihiko Ino, and Kenichi Hagihara
In Proceedings of the 20th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2006), Rhodes Island, Greece, (2006-04). 10 pages (CD-ROM). - [PDF]

Copyright©2006 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. http://dx.doi.org/10.1109/IPDPS.2006.1639323