CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Appendix A. Faculty Members of CCS
Director:

Mitsuhisa Sato

Deputy Director: Masayuki Umemura
Taisuke Boku
Division of Particle Physics and Astrophysics (Division Manager: Masayuki Umemura)

Particle Physics Group (Group Leader: Sinya Aoki)
Faculty Members

Tomoteru Yoshie, Associate Professor
Graduate School:
Physics , Graduate School of Pure and Applied Sciences
Research topics:
Elementary Particle Physics
Naruhito Ishizuka, Associate Professor
Graduate School:
Physics , Graduate School of Pure and Applied Sciences
Research topics:Computational studies on strong interactions
using lattice field theories
Yoshinobu Kuramashi, Assoicate Professor
Graduate School
Physics , Graduate School of Pure and Applied Sciences
Research topics:
Theoretical and computational studies
on strong interact ions using lattice field theories
Yusuke Taniguchi, Assistant Professor
Graduate School:
Physics , Graduate School of Pure and Applied Sciences
Research topics:
Lattice gauge theory- 33 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Akira Ukawa, Professor, Executive Advisor to the President
Graduate School
Physics , Graduate School of Pure and Applied Sciences ,Research topics
Computational particle physics, in particular lattice QCD,
and development of computers for such studies

Collaborative researchers
Sinya Aoki, Professor
Graduate School:
Physics, Graduate School of Pure and Applied Sciences
Research topics:
Elementary Particle Physics Theory, Lattice Field Theory
Kazuyuki Kanaya, Professor
Graduate School:
Physics, Graduate School of Pure and Applied Sciences
Research topics:
lattice field theory, parallel computers

Research staff••••

Kiyoshi SASAKI
Noriyoshi Ishii
Naoya Ukita
Daisuke Kadoh- 34 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Astrophysics Group (Group Leader: Masayuki Umemura)
Faculty Members

Masayuki Umemura, Professor
Graduate School:
Physics , Graduate School of Pure and Applied Sciences
Research topics:
Theoretical Astrophysics.
In particular, the study with radiation hydrodynamics
on the formation of first generation objects and galaxies
Hiroyuki Hirashita, Assistant Professor
Graduate School:
Physics , Graduate School of Pure and Applied Sciences
Research topics:
Theoretical study of element production history
in galaxy formation and evolution
Kohji Yoshikawa, Assistant Professor
Graduate School:
Physics , Graduate School of Pure and Applied Sciences ,Research topics
Astrophysics.
Theoretical studies on observational cosmology,
the formation of galaxies and galaxy clusters, and intergalactic medium
Junichiro Makino, Visiting Associate Professor
Graduate School:
Graduate School of Science, University of Tokyo
Research topics:
Computational Astrophysics,
Development of dedicated computers for computational science

Research Staff•••

Yoshiaki KatoTamon Suwa

Takuya Akahori- 35 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

 Division of Material and Life Sciences (Division Manager: Atsushi Oshiyama)
Material Science Group (Group Leader: Atsushi Oshiyma)
Faculty Members

Atsushi Oshiyama, Professor
Graduate School:
Frontier Science, Graduate School of Pure and Applied Sciences
Research topics:
Nanoscience and Theoretical Condensed Matter Physics
Kenji Shiraishi, Professor
Graduate School:
Frontier Science , Graduate School of Pure and Applied Sciences
Research topics:
Nanoscience and Theoretical Condensed Matter Physics
Susumu Okada, Associate Professor
Graduate School:
Frontier Science , Graduate School of Pure and Applied Sciences
Research topics:
Nanoscience and Theoretical Condensed Matter Physics

Susumu Saito, Visiting Professor
Graduate School:
Department of Physics, Tokyo Institute of Technology
Research topics:
Nanoscience and Theoretical Condensed Matter Physics

Research Staff•

Jun'ichi Iwata- 36 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Life Science Group (Group Leader: Masaru Tateno)
Faculty Members

Masaru Tateno, Associate Professor
Graduate School
Physics , Graduate School of Pure and Applied Sciences ,Research topics:
Computational analysesof functional controle mechanisms of biological macromolecules
Yasuteru Shigeta, Assistant Professor
Graduate School
Physics , Graduate School of Pure and Applied Sciences ,Research topics:
Theoretical studies on electronand proton transfer reactions in biological systems

Collaborative researchers
Mauro Boero, Associate Professor
Graduate School:Physics, Graduate School of Pure and Applied Sciences
Research topics:
First principles molecular dynamics simulations :checmical and biochemical reactions of organic and inorganic materials
in liquid and solid phases

Research Staff••

Kamiya Katsumasa
Yoshitaka Fujimoto- 37 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Quantum Many-Body Systems Group (Group Leader: Kazuhiro Yabana)Faculty Members

Kazuhiro Yabana, ProfessorGraduate School
Physics , Graduate School of Pure and Applied Sciences ,Research topics:
Nuclear physics, computational sciences on atomic,
molecular,and optical sciences
Yukio Hashimoto, Assistant Professor
Graduate School
Physics , Graduate School of Pure and Applied Sciences ,Research topics:
Microscopic theory of nuclear collective motions
Hiroyasu Koizumi, Associate Professor
Graduate School:
Materials Science, Graduate School of Pure and Applied Science
Research topics:

Tong Xiao-Min, Associate Professor
Graduate School:
Materials Science, Graduate School of Pure and Applied Science
Research topics:
Atoms, molecules interaction with intense laser fieldand time-dependent density functional theory

Collaborative researchers
Kenichi Hino, Professor
Materials Science, Graduate School of Pure and Applied Science- 38 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

 Division of Global Environment and Biological Science (Division Manager: HiroshiTanaka)
Global Environmental Science Group (Group Leader: Hiroshi Tanaka)
Faculty Members

Hiroshi L. Tanaka, Professor
Graduate School:Geoenvironmental Sciences,
Graduate School of Life and Environmental Sciences
Research topics:
General circulation, dynamics and energetics of the atmosphere
Kusaka Hiroyuki, Assistant Professor
Graduate School:
Geoenvironmental Sciences,
Graduate School of Life and Environmental Sciences
Research topics:
Urban climate, Applied Meteorology,
Numerical simulationof mesoscale weather using the WRF model

Collaborative researchers
Fujio Kimura, Professor
Graduate School:
Geoenvironmental Sciences
Graduate School of Life and Environmental Sciences
Research topics：- 39 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Global Environmental Science Group (Group Leader: Tetsuo Hashimoto)
Faculty Members

Yuji Inagaki, Associate Professor
Graduate School:
Biological Sciences, Graduate School of Life and Environmental Sciences ,Research topics
Molecular phylogeny of eukaryotes Investigation of lateral genetransfers
Estimation of protein functions by combining structuraland evolutionary parameters Artifacts in molecular dataanalyses

Collaborative researchers
Tetsuo Hashimoto, Professor
Graduate School:
Biological Sciences, Graduate School of Life and Environmental Sciences ,Research topics
Molecular evolutionary studies
on the origin and early evolution of eukaryotes
Hideko Urushihara, Professor
Graduate School:
Functional Biosciences, Graduate School of Life and Environmental Science
Research topics
Studies on developmental programs described in the genome- 40 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

 Division of High Performance Computing SystemsBoku)(Division Manager: Taisuke

System Architecture Group (Group Leader: Taisuke Boku)
Faculty Members

Boku Taisuke, Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
High performance parallel computing,cluster computing, hybrid parallel processing system,
grid computing
Daisuke Takahashi, Assoicate Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
High performance parallel computing,High-performance numerical algorithms on parallel computersand performance evaluation
Hiroshi NAKAMURA, Visiting Assoicate Professor
Graduate School:
Graduate School of Information Science and Technology, University of Toky
Research topics:
High-Performance and Low-Power Processor Architecture,
High-Performance Computing, Dependable Computer System- 41 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Collaborative researchers
Moritoshi Yasunaga, Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
VLSI Engineering, Evolvable Hardware, Dependable Systems

Kouichi Wada, Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
Numerical algorithms and simulation,
Mathematical software for GRID computing

Research Staff•

Toshihiro Hanawa- 42 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Grid Computing Group (Group Leader: Mitsuhisa Sato)
Faculty Members

Mitsuhisa Sato, Professor, Director
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
High performance parallel computing,compilers and performance evaluation, grid computing
Osamu Tatebe, Associate Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
High performance parallel computing,
Grid Computing, Distributed File System- 43 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

 Division of Computational Informatics(Division Manager: Yuichi Ohta)

Computational Intelligence Group (Group Leader: Hiroyuki Kitagawa)
Faculty Members

Hiroyuki Kitagawa, Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
Database systems, Data engineering Information integration,
WWW and databases, Knowledge discovery, XML databases,
Multimedia information retrieval, and DBMS architecture
Toshiyuki Amagasa, Assistant Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
Database Systems, Data Engineering.
XML Databases, Web Information Systems, Bioinformatics
Hideyuki Kawashima, Assistant Professor
Graduate School:
Computer Science, Graduate School of Systems and Information Engineerin
Research topics:
Database Systems and Data Engineering:
DBMS Architecture, Sensor Networks- 44 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Computational Media Group (Group Leader: Yuichi Ohta)
Faculty Members

Yuichi Ohta, Professor
Graduate School:
Advanced Engineering Systems,
Graduate School of Systems and Information Engineering
Research topics:

Yoshinari Kameda, Assoicate Professor
Graduate School:
Research topics:
Massive Sensing, Intelligent Video Making based on Scene Understanding,Model Based Vision,Coorperative Distributed Vision, Lecture Archiving andDistance Learning, Visual Surveillance, Human Interface to Virtual Reality
Itaru Kitahara, Assistant Professor
Graduate School:
Advanced Engineering Systems,
Graduate School of Systems and Information Engineering
Research topics:
Image media with ubiquitous sensor networks

Collaborative researchers

Tomonori Shirakawa, Professor
Graduate School:
Advanced Engineering Systems,
Graduate School of Systems and Information Engineering
Research topics:- 45 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

Appendix B. Facilities of CCS
1. Computer Systems Overview
The computational facilities of the center mainly consist of a massively parallel cluster
system PACS-CS and its front-end computer system, and the new generation ofastrophysics simulator FIRST.
The front-end computer system consists of the system controlling servers to manage thePACS-CS cluster and the small-sized mini-PACS-CS for program development, Magellan(Hitachi SR11000J) for post-processing and analysis on generated data by PACS-CS, 100
TByte of large capacity file server to hold all data of these machines. There are additional
medium to small size clusters for data analysis and general networking services. Beside ofthese main facilities in Computer Building, there are a number of graphic workstations andPCs to support daily research of researchers and students in Research Building. A central
switch in Computer Building connects all computational facilities by Gigabit Ethernet for
high-speed data exchange. It is also connected another central switch in Research Building
via 10 Gigabit Ethernet to support high-speed data access among all resources in the center.
Main computational facilities in the center are shifting from vector machines to large scale
high-end clusters including PACS-CS and FIRST to support various fields of computational
sciences and computer science in all research divisions in the center.
Since the PACS-CS system is the main central facility in the center, the operation, job
status and detailed system temperature such as CPU, chassis and network interfaces of eachcomputational node are monitored in real-time. The status of the machine and air
conditioners in Computer Building are remotely monitored to detect any failure.

- 46 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007- 47 -CCS Report: PART I, Overview of Center for Computational Sciences
Summary of Activities 2004-2007

2. Network Environment
University of Tsukuba has been connected 10 Gbps of nation-wide network for researchand education named SINET3 under MEXT since April 2007. In addition, the university isalso connected to major research institutes in Tsukuba City by a high-speed WAN with 20
Gbps bandwidth named TSUKUBA-WAN. Our center is connected to SINET3 with 2 Gbpsof general purpose network and three of 1 Gbps special purpose research network.
Moreover, we are also connected to the nation-wide research network JGN2 with 10Gbps
link to stimulate various research activities in the center. In such network environment, weshare the valuable data computed by PACS-CS and other center facilities as well as
high-performance Grid computing research toward new generation of computationalsciences.

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