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382 results on '"Nakajima, Kengo"'

101. Examination of the Effect of the Combined Use of Nd: YAG Laser Irradiation and Mechanical Force Loading on Bone Metabolism Using Cultured Human Osteoblasts

Author

Tsuka, Yuji, primary, Kunimatsu, Ryo, additional, Gunji, Hidemi, additional, Abe, Takaharu, additional, Medina, Cynthia Concepción, additional, Nakajima, Kengo, additional, Kimura, Aya, additional, Hiraki, Tomoka, additional, Nakatani, Ayaka, additional, and Tanimoto, Kotaro, additional

Published
2020
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106. Equipping Sparse Solvers for Exascale

Author

Basermann, Achim, Wellein, Gerhard, Lang, Bruno, Fehske, Holger, Hager, Georg, Sakurai, Tetsuya, and Nakajima, Kengo

Subjects
Exascale computing, quantum physics, performance engineering, High Performance Computing, hybrid programming, software frameworks, sparse eigensolvers, GPU parallelization, extreme scalability, resilience, multicoloring, Many-Core parallelization
Abstract

The ESSEX project is funded by the German DFG priority programme 1648 Software for Exascale Computing (SPPEXA). In 2016 it has entered its second funding phase, ESSEX-II. ESSEX investigated programming concepts and numerical algorithms for scalable, efficient and robust iterative sparse matrix applications on exascale systems. Starting with successful blueprints and prototype solutions identified in ESSEX-I, the second phase project ESSEX-II developed a collection of broadly usable and scalable sparse eigenvalue solvers with high hardware efficiency for the computer architectures to come. Project activities were organized along the traditional software layers of low-level parallel building blocks (kernels), algorithm implementations, and applications. The classic abstraction boundaries separating these layers were broken in ESSEX by strongly integrating objectives: scalability, numerical reliability, fault tolerance, and holistic performance and power engineering. The basic building block library supports an elaborate MPI+X approach that is able to fully exploit hardware heterogeneity while exposing functional parallelism and data parallelism to all other software layers in a flexible way. In addition, facilities for fully asynchronous checkpointing, silent data corruption detection and correction, performance assessment, performance model validation, and energy measurements are provided transparently.

Published
2018

107. Equipping Sparse Solvers for Exascale (ESSEX / ESSEX II)

Author

Basermann, Achim, Wellein, Gerhard, Lang, Bruno, Fehske, Holger, Hager, Georg, Sakurai, Tetsuya, and Nakajima, Kengo

Subjects
many-core parallelization, Exascale computing, quantum physics, performance engineering, High Performance Computing, sparse eigensolvers, GPU parallelization, resilience, multicoloring, extreme scalability, software repository
Abstract

The ESSEX project is funded by the German DFG priority programme 1648 "Software for Exascale Computing" (SPPEXA). In 2016 it has entered its second funding phase, ESSEX-II. ESSEX investigated programming concepts and numerical algorithms for scalable, efficient and robust iterative sparse matrix applications on exascale systems. Starting with successful blueprints and prototype solutions identified in ESSEX-I, the second phase project ESSEX-II developed a collection of broadly usable and scalable sparse eigenvalue solvers with high hardware efficiency for the computer architectures to come. Project activities were organized along the traditional software layers of low-level parallel building blocks (kernels), algorithm implementations, and applications. The classic abstraction boundaries separating these layers were broken in ESSEX by strongly integrating objectives: scalability, numerical reliability, fault tolerance, and holistic performance and power engineering. The basic building block library supports an elaborate MPI+X approach that is able to fully exploit hardware heterogeneity while exposing functional parallelism and data parallelism to all other software layers in a flexible way. In addition, facilities for fully asynchronous checkpointing, silent data corruption detection and correction, performance assessment, performance model validation, and energy measurements are provided transparently. The advanced building blocks were defined and employed by the developments at the algorithms layer. Here, ESSEX-II provides state-of-the-art library implementations of classic linear sparse eigenvalue solvers including block Jacobi-Davidson, Kernel Polynomial Method (KPM), and Chebyshev filter diagonalization (ChebFD) that are ready to use for production on modern heterogeneous compute nodes with best performance and numerical accuracy. Research in this direction included the development of appropriate parallel adaptive AMG software for the block Jacobi-Davidson method. Contour integral-based approaches were also covered in ESSEX-II and were extended in two directions: The FEAST method was further developed for improved scalability, and the Sakurai-Sugiura method (SSM) method was extended to nonlinear sparse eigenvalue problems. These developments were strongly supported by additional Japanese project partners from University of Tokyo, Computer Science, and University of Tsukuba, Applied Mathematics. The applications layer delivers scalable solutions for conservative (Hermitian) and dissipative (non- Hermitian) quantum systems with strong links to optics and biology and to novel materials such as graphene and topological insulators. This talk gives a survey on latest results of the ESSEX-II project.

Published
2018

113. Baicalin Promotes Osteogenic Differentiation of Human Cementoblast Lineage Cells Via the Wnt/β Catenin Signaling Pathway

Author

Kimura, Aya, primary, Kunimatsu, Ryo, additional, Yoshimi, Yuki, additional, Tsuka, Yuji, additional, Awada, Tetsuya, additional, Horie, Kayo, additional, Gunji, Hidemi, additional, Abe, Takaharu, additional, Nakajima, Kengo, additional, Kitagawa, Masae, additional, Miyauchi, Mutsumi, additional, Takata, Takashi, additional, and Tanimoto, Kotaro, additional

Published
2019
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118. A Fast Scalable Implicit Solver for Nonlinear Time-Evolution Earthquake City Problem on Low-Ordered Unstructured Finite Elements with Artificial Intelligence and Transprecision Computing

Author

Ichimura, Tsuyoshi, primary, Fujita, Kohei, additional, Yamaguchi, Takuma, additional, Naruse, Akira, additional, Wells, Jack C., additional, Schulthess, Thomas C., additional, Straatsma, Tjerk P., additional, Zimmer, Christopher J., additional, Martinasso, Maxime, additional, Nakajima, Kengo, additional, Hori, Muneo, additional, and Maddegedara, Lalith, additional

Published
2018
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125. A Fast Scalable Implicit Solver with Concentrated Computation for Nonlinear Time-Evolution Problems on Low-Order Unstructured Finite Elements

Author

Ichimura, Tsuyoshi, primary, Fujita, Kohei, additional, Horikoshi, Masashi, additional, Meadows, Larry, additional, Nakajima, Kengo, additional, Yamaguchi, Takuma, additional, Koyama, Kentaro, additional, Inoue, Hikaru, additional, Naruse, Akira, additional, Katsushima, Keisuke, additional, Hori, Muneo, additional, and Maddegedara, Lalith, additional

Published
2018
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127. Effect of high-frequency near-infrared diode laser irradiation on periodontal tissues during experimental tooth movement in rats

Author

Gunji, Hidemi, primary, Kunimatsu, Ryo, additional, Tsuka, Yuji, additional, Yoshimi, Yuki, additional, Sumi, Keisuke, additional, Awada, Tetsuya, additional, Nakajima, Kengo, additional, Kimura, Aya, additional, Hiraki, Tomoka, additional, Hirose, Naoto, additional, Yanoshita, Makoto, additional, and Tanimoto, Kotaro, additional

Published
2018
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134. Bone Regeneration in a Canine Model of Artificial Jaw Cleft Using Bone Marrow–Derived Mesenchymal Stem Cells and Carbonate Hydroxyapatite Carrier.

Author

Abe, Takaharu, Sumi, Keisuke, Kunimatsu, Ryo, Oki, Nanae, Tsuka, Yuji, Awada, Tetsuya, Nakajima, Kengo, Sugiyama, Masaru, and Tanimoto, Kotaro

Subjects
STEM cell transplantation, ANIMAL experimentation, BIOLOGICAL models, BONE marrow transplantation, BONE regeneration, BONE substitutes, CARBONATES, CELL transplantation, CLEFT palate, DOGS, HISTOLOGICAL techniques, HYDROXYAPATITE, NANOPARTICLES, SILICA, SURVIVAL analysis (Biometry), CELL survival, DESCRIPTIVE statistics
Abstract

Objective: Cleft lip and palate (CLP) is a common anomaly of the orofacial region. Mesenchymal stem cell (MSC) transplantation has been a focus of regenerative medicine, and its application to the repair of bone defects in patients with CLP is highly anticipated. This study investigated the potential for using MSCs to regenerate bone in a jaw cleft as well as the survival of transplanted MSCs using a canine model of CLP. Design: Mesenchymal stem cells collected from the bone marrow of beagle dogs were transplanted along with carbonate hydroxyapatite into jaw clefts in beagle dogs. Mesenchymal stem cells labeled with fluorescent silica nanoparticles were also transplanted, and a histological analysis was performed 3 months later to evaluate MSC survival. Results: Carbonate hydroxyapatite regeneration into bone was enhanced by cotransplantation of MSCs. The survival rate of MSCs transplanted after 3 months was 5.7%. Conclusions: Transplanted MSCs promote bone regeneration, although their survival rate is low. [ABSTRACT FROM AUTHOR]

Published
2020
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135. Using MUMPS as a preconditioner solver for a Hetero3D elasticity problem (poster)

Author

Daydé, Michel, Guivarch, Ronan, Joslin, Guillaume, Nakajima, Kengo, Algorithmes Parallèles et Optimisation (IRIT-APO), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Centre Européen de Recherche et de Formation Avancée en Calcul Scientifique (CERFACS), CERFACS, Computer Science Department (CST), and The University of Tokyo (UTokyo)

Subjects
[INFO]Computer Science [cs]
Abstract

International audience; This poster will present a hybrid parallel approach to solvethe Hetero3D elasticity problem using direct solver MUMPS as a pre-conditioner.

Published
2014

138. From FLOPS to BYTES

Author

Matsuoka, Satoshi, primary, Amano, Hideharu, additional, Nakajima, Kengo, additional, Inoue, Koji, additional, Kudoh, Tomohiro, additional, Maruyama, Naoya, additional, Taura, Kenjiro, additional, Iwashita, Takeshi, additional, Katagiri, Takahiro, additional, Hanawa, Toshihiro, additional, and Endo, Toshio, additional

Published
2016
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140. Towards exascale with the ANR-JST japanese-french project FP3C (Framework and Programming for Post- Petascale Computing)

Author

Antoniu, Gabriel, Boku, Taisuke, Calvin, Christophe, Codognet, Philippe, Daydé, Michel, Emad, Nahid, Ishikawa, Yuyaka, Matsuoka, Satoshi, Nakajima, Kengo, Nakashima, Hiroshi, Namyst, Raymond, Petiton, Serge, Sakurai, Tetsuya, Sato, Mitsuhisa, Scalable Storage for Clouds and Beyond (KerData), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SYSTÈMES LARGE ÉCHELLE (IRISA-D1), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Department of Computer Science [Tsukuba], Graduate School of Systems and Information Engineering [Tsukuba], Université de Tsukuba = University of Tsukuba -Université de Tsukuba = University of Tsukuba, Laboratoire de Logiciels pour la Physique des Réacteurs (LLPR), Service des Réacteurs et de Mathématiques Appliquées (SERMA), Département de Modélisation des Systèmes et Structures (DM2S), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Département de Modélisation des Systèmes et Structures (DM2S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Japanese French Laboratory for Informatics (JFLI), Centre National de la Recherche Scientifique (CNRS)-The University of Tokyo (UTokyo)-Université Pierre et Marie Curie - Paris 6 (UPMC)-National Institute of Informatics (NII), Algorithmes Parallèles et Optimisation (IRIT-APO), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Institut National Polytechnique (Toulouse) (Toulouse INP), Parallélisme, Réseaux, Systèmes, Modélisation (PRISM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Computer Science Department (CST), The University of Tokyo (UTokyo), Department of Mathematical and Computing Sciences, Tokyo Institute of Technology [Tokyo] (TITECH), Kyoto University [Kyoto], Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Efficient runtime systems for parallel architectures (RUNTIME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Center for Computational Sciences [Tsukuba] (CCS), Université de Tsukuba = University of Tsukuba, ANR-10-JTIC-0003,FP3C(2010), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Service d’Études des Réacteurs et de Mathématiques Appliquées (SERMA), National Institute of Informatics (NII)-Université Pierre et Marie Curie - Paris 6 (UPMC)-The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Kyoto University, and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
high-performance computing, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract

International audience; The Japanese-french project FP3C targets the post-petascale and the next generation of exascale systems. Its goal is to study the software technologies, languages and programming models to achieve the performance promised by post-petascale computing. The project consortium regroups some of the HPC key players in Japan and in France: * Universities of Kyoto, Tokyo and Tsukuba, Tokyo Institute of Technology, Japanese- French Laboratory on Informatics * CEA Saclay, CNRS (IRIT and PRISM), INRIA (Bordeaux, Rennes and Saclay), with a strong connection with RIKEN AICS at Kobe in Japan. The ability to efficiently program and exploit these future high performance systems is considered as a strategical issue by all research national agencies worldwide. The exascale computers are expected to a large-scale highly hierarchical architecture with many-core processsors possibly mixed with accelerators with up to millions of cores and threads. As a consequence, existing operating and runtime systems, languages, programming paradigms and parallel algorithms would have, at best, to be adapted, and may become often obsolete. Exploiting these ultra large-scale parallelsystems will require runtime systems allowing the management of huge amount of distributed data, minimizing the energy consumption, and exhibiting fault resilient properties. In addition to these features, accelerating technology, based on GPGPU and many-core processors, are also crucial issues for post-petascale computing systems. Efficient exploitation (programing, execution) of large scale systems is an important challenge. The hierarchical nature of these architecture and the scalability issues (parallelization at different level: intra / inter computational nodes composed of many core processors and/or accelerators) complexifies the algorithm design. Existing programming framework and runtime systems together with new approaches should be examined, experimented andevaluated. Benchmarks and libraries adapted to the post-petascale systems will have to be proposed. The FP3C project aims at defining a framework for high performance computing on the road to exascale. We cover most of the issues related to the emergence of post- petascale computing: from high level languages to efficient exploitation of the underlying architecture at the runtime level or using specific extensions for accelerators. Our approach is illustrated with experiments on a set of numerical codes (including numerical libraries) that can be seen as a benchmark. One of the goal of the project is to proceed to experiments on some of the most recent computers available in Europe (e.g. CURIE Computer at TGCC/France) and in Japan (e.g. K Computer at Kobe).

Published
2013

141. Implementation of FEM Application on GPU with StarPU

Author

Ohshima, Satoshi, Katagiri, Satoshi, Nakajima, Kengo, Thibault, Samuel, Namyst, Raymond, The University of Tokyo (UTokyo), Computer Science Department (CST), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Efficient runtime systems for parallel architectures (RUNTIME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), SIAM, and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)

Subjects
[INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], GeneralLiterature_MISCELLANEOUS, ComputingMethodologies_COMPUTERGRAPHICS
Abstract

International audience; We are aiming at accelerating FEM application on multicore CPUs with GPU. While it isn't easy to obtain very good performance because FEM application requires many non-sequential memory accesses, our GPU implementation has obtained better performance than multicore CPUs. We are now trying to accelerate FEM with StarPU runtime system. In this talk, we talk about the implementation and performance of it.

Published
2013

142. High Performance Computing for Computational Science -- VECPAR 2014 : 11th International Conference, Eugene, OR, USA, June 30 -- July 3, 2014, Revised Selected Papers / edited by Michel Dayd , Osni Marques, Kengo Nakajima.

Author

Dayd , Michel. editor., Marques, Osni. editor., Nakajima, Kengo. editor., SpringerLink (Online service), Dayd , Michel. editor., Marques, Osni. editor., Nakajima, Kengo. editor., and SpringerLink (Online service)

Abstract

This book constitutes the thoroughly refereed post-conference proceedings of the 11th International Conference on High Performance Computing for Computational Science, VECPAR 2014, held in Eugene, OR, USA, in June/July 2014. The 25 papers presented were carefully reviewed and selected of numerous submissions. The papers are organized in topical sections on algorithms for GPU and manycores, large-scale applications, numerical algorithms, direct/hybrid methods for solving sparse matrices, performance tuning. The volume also contains the papers presented at the 9th International Workshop on Automatic Performance Tuning.

Published
2015

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