CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

CCS Report: PART III

Vision and Strategies of Center for Computational Sciences

October 2007

Center for Computational Sciences
University of Tsukuba-1-

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CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

Table of Contents
1. Introduction ......................................................................................................................... 4
2. Mission and Role of CCS .................................................................................................. 5
3. “Interdisciplinary Computational Science” and Vision of the Center for
Computational Sciences ................................................................................................. 6
4. Strategies and Plan ........................................................................................................... 8
4.1 Research and Development ....................................................................................... 9
4.2 Educational Activities ............................................................................................... 10
4.3 Acquisition and Operation of the Next Supercomputer and T2K Project . 11
4.4 Contribution to the Next-generation Supercomputer Project ...................... 12
4.5 Collaboration and Alliance ...................................................................................... 13-3-

CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

1. Introduction
This document, CCS report: PART III, presents the vision and strategies of the Center for
Computational Sciences, University of Tsukuba. The vision focuses on the time frame of
2007-2011.
The report has been prepared for review of the Center scheduled from 30 October to 1
November 2007.
The purpose of the review is to receive an outside examination on the research activities
and their outcomes of the Center in view of the founding objectives, and to incorporate therecommendations from the review for future developments of the Center.
Since details of the research results are prepared as a separate report, this report puts more
focuses on the vision, strategies and plans of the Center. An overview, chronology and theorganizational aspects of CCS are described in CCS Report: PART I, and details of theresearch plans of each division and group are described in CCS Report: PART II.

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2. Mission and Role of CCS
The mission of the Center of Computational Sciences is to promote scientificdiscovery by computational science through the application of advanced computing
technologies, and to support research of computational science in Japanese
universities and institutes by operating leading-edge computing systems.
The center carries out research in material, life and environmental sciences usinglarge-scale numerical simulations and data analyses. To advance these studies, the center
carries out research and development in high-performance computing and networking
systems, and applications of novel information technologies. The center is aninter-university facility open to researchers throughout Japan.
From the nationwide viewpoint of the development of scientific research, the CCS is aunique research “inter-university” organization which jointly carries out “interdisciplinary”
research in the computational sciences, including development of cutting-edgehigh-performance computer systems. While the computational science activities in each ofthese disciplines is conducted by university labs and institutes specific to that discipline, we
conduct computational science in each discipline, as well as “interdisciplinary” in an
attempt to integrate many research fields. In contrast to institutes that are organized with afocus on computer sciences, our center is concerned with both computer sciences andcomputational sciences. For example, the National Institute of Informatics (NII) focuses on
information science, but not on computational science or the development ofhigh-performance computer systems. In Japan, there are supercomputer centers in major
universities that only focus on the operation and service of their computing facilities, andnot on computational science research.
From the viewpoint of the development of scientific research within our university, ourcenter is the topmost research center, and it actively supports budgets, faculty positions, andfacilities. The CCS faculty is a graduate school and contributes to the education ofcomputational science.

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CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

3. “Interdisciplinary Computational Science” and Vision of the Center for
Computational Sciences
Computational science, which enables us to explore uncharted fields of science throughapplications of high-performance computing, is a third paradigm of scientific research thathas become indispensable for the development of science and technology in the 21st century.
The methods of large-scale numerical analyses that form the pillar of computational science
are common over a wide range of scientific disciplines, from fundamental science tomaterial, life and geo-environmental sciences. This common foundation promotes thedevelopment of mutual and intimate connections among the various scientific disciplines
and allows us to approach science holistically from a global perspective. This in turn leads
to a global approach to nature, life and the environment, which is indispensable for the
harmonious advance of science and technology, and consequently, of mankind.
Furthermore, progress in computational science will help produce the next generation ofscientists that will conduct research from a global perspective.
Development of computational science cannot be satisfactorily achieved solely by thescientists who use computers, and close collaboration and synergy is required withcomputer scientists with expertise in computer hardware, software, algorithms andprogramming, and information scientists with expertise in data and media engineering andtechnologies. Therefore, in order to establish a solid basis for the development ofcomputational science, it is necessary to build a system that integrates the activities at theforefront of scientific research with those of computer science and information science.
Computational science is thus a multi-disciplinary area: each discipline X may have a“computational X” where X is an established discipline such as mathematics, biology,
finance, physics, chemistry, or social science. For example, physics has “computational
physics”. To date, most researchers of “computational X” make use of an existingsupercomputing center to execute their tasks. Often these activities are short-term projects
that have nothing to do with other computational sciences, such as “computational Y.”
However, some knowledge, models and algorithms, can sometimes be shared among thedifferent computational sciences. In view of solutions to problems, extensive knowledge
and integration of computational sciences from different disciplines are necessary.

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CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

Computational science is a cutting-edge, indispensable multidisciplinary andinterdisciplinary area for the development of science and technology in the 21st century.
We define “Interdisciplinary Computational Science” using the following two aspects:• Integration and collaboration of computational science and computer science:− High-performance computing systems (HPC) will be increasing in size andbecome more complex in configuration. HPC technologies are indispensablefor optimizing the possible benefits associated with these advances.
− Continuous development and investment are required to facilitate the next
generation of computational science.
• The common base of computational science brings mutual intimate connections
among various science disciplines and allows us to approach science as a whole froma global perspective.
University of Tsukuba and the Center for Computational Sciences have undertaken along-standing effort to establish an international and national research center for theadvancement of computational science by taking advantage of the top-level researchachievements produced and accumulated at the Center.
The CCS’s vision is as follows:
The CCS aims to be a worldwide COE that develops “InterdisciplinaryComputational Science” as a new area essential to 21st century advances in scienceand technology, and support it continuously from global and long-term perspectives.
The vision of CCS is to further enhance and develop the close collaboration among
various science disciplines by applying the activities undertaken in the computer andinformation sciences pursued at the Center, which is quite unique in the world. In doing so
the Center hopes to establish a system that advances computational science from a global
perspective and simultaneously produces the next generation of scientists who will pushscience forward within a global context.
We aim to establish an organization for computational science research at the world’s
highest level through a close integration of science and computer and information
sciences. On this basis, we aim to meet the grand challenges associated with various
scientific disciplines such as fundamental, material, life and geo-environmental sciences.
Simultaneously, the organization should function as an advanced educational system foreducating the next generation of computational scientists.
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CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

4. Strategies and Plan
To realize our vision and accomplish our mission, we will implement the following
strategies and plans. The vision and this plan focus on the time frame of 2007-2011.
[Research & Development] Integrate advances of scientific research with those ofcomputer science and information science, and thereby establish and promote newinterdisciplinary computational science.
− Execute “Interdisciplinary Computational Science Promotion Program” or theoperation of inter-university facilities such as PACS-CS for promotion andacceleration of interdisciplinary computational science.
− Integrate computational science with grid/network computing, sensing
technologies, data engineering and informatics to explore “new” concepts ofcomputational science.
[Education & Public Relations] Educate and produce the next generation of scientists
who push forward new interdisciplinary computational science from global viewpoints.
− Dual-degree (double major) program− Campus-wide courses on “computational science” for graduate students− HPC seminar series− Workshops and symposiums[Infrastructure & Service] Support research by operating a leading-edge, advanced,
large-scale computing facility for inter-university computing resources, and by
development of an advanced computing infrastructure.
− Acquire & operate the next supercomputer as a part of the inter-university
computing resources, making an “open supercomputer” alliance with the
University of Tokyo and Kyoto University (T2K).
− Contribute to the “national” next-generation supercomputer project, and takeleadership of the nationwide computing infrastructure, and explore thenext-generation high-performance platform.
[Collaboration & Alliance] Promote alliances and collaboration, and establish
international/national networks of researches on computational science.
− Ally the Center with “supercomputer” centers at other universities, thenext-generation supercomputer center of RIKEN, and research laboratories in
Tsukuba− Promote international collaborations by “Computational Science Researchers
Invitation Program,” and support virtual organization using Grid technologies.
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CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

4.1 Research and Development
The Interdisciplinary Computational Science Promotion Program will be one of the main
activities for promotion and acceleration of interdisciplinary computational science. The
purpose of this program is to encourage research activities of computational sciences. The
computational power of the PACS-CS is provided to researchers throughout Japan throughthis program.
The Interdisciplinary Computational Science Promotion Program has two categories:••

The “Interdisciplinary Collaboration Program” will promote the interdisciplinary
research activities of different disciplines. We will support the establishment of a
network of interdisciplinary research projects and encourage all challenges ofinterdisciplinary computational science. For this program, we will organize an“Interdisciplinary Collaboration Program Support Committee” to help match researchgroups from different fields. We will follow up the research activity produced by theinterdisciplinary collaboration.
A large-scale scientific simulation program will push forward the challenges ofseveral fields in computational sciences by providing the computational power of the
PACS-CS. We will review proposals and concentrate our computational power tomake new scientific discoveries and to follow up the scientific results.

We already started the program in October 2007 for the PACS-CS. The detail is describedin CCS Report: PART I. Also, opening the FIRST simulator that was previously dedicatedto computational astrophysics at University of Tsukuba is under consideration for the next
academic year.
Computational science has made rapid and considerable progress. The computational
capability of supercomputers is now on the verge of surpassing a petaflops (1015 floating
operations per second), which is roughly a millions times faster than today’s PCs. Thisadvance allows us to explore a wide range of phenomena through computer simulations,which was impossible in the past, e.g., the creation and evolution of the universe, thequantum properties of nano- and biomaterials and their contribution to life, and global
climate changes.
At the same time, the development of intelligent information processing technologies isbeginning to enable the management and analysis of enormous amounts of data in thepetabyte ranges, and this development is accelerating discoveries in many science
disciplines, such as genome analyses, high-energy accelerator experiments, astronomical-9-

CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

observations and satellite observation of geo-environments. Furthermore, the recent growthof high-speed Internet is creating a communication environment that has enabled scientificresearch and education to be carried out on a global scale.
Data, data analysis, and visualization are vital for progress in the increasingly
data-intensive realm of science and engineering research and education. Any cogent planaddressing cyberinfrastructure must address the phenomenal growth of data in all its forms.
Scientists and engineers are producing, accessing, analyzing, integrating, storing andretrieving massive amounts of data daily. Furthermore, this is a trend that is expected to see
significant growth in the very near future as advances in sensors and sensor networks,
high-throughput technologies and instrumentation, automated data acquisition,
computational modeling and simulation, and other methods and technologies materialize.
In short, computational science is rapidly developing into a unified framework, or a “new”
concept of computational science, in which large-scale modeling and simulation,
large-scale data analysis, and experiments and observations are integrated to solve
challenging issues in various branches of science. As such, computational science has now
become an indispensable tool to better understand 21st century sciences.
Several challenges have already begun. The Computational Media Group and the Grid
Computing Group have started the project, “Sensing Web,” in collaboration with Kyoto
University and other universities for new integration of sensing technology, the Internet andgrids. Also, the Computational Informatics Division and High-performance Computing
System Division, Global Environment and Biological Sciences Division have proposed an
idea to integrate sensing, databases and computation to capture and observe phenomena of
humans and nature in the real world; this would be called “Real-world Computational
Informatics.”
4.2 Educational Activities
The Computational Science Dual-Degree (double major) Program will enable a graduate
student in a doctoral program to simultaneously belong to a masters program of a different
graduate school, and receive both a doctoral degree in science and a master’s degree incomputer science, or vice versa, upon graduation. The program is intended to educate
researchers who can advance new interdisciplinary computational science from global
viewpoints. We will design curriculum and courses for advanced computational science andbegin this program in 2008. The first expected combination of majors is a Ph. D in Physics
and a master’s degree in Computer Sciences.
Campus-wide courses on computational sciences for graduate students are other planned- 10 -CCS Report: PART III, Vision and Strategies of Center for Computational Sciences

educational activities. Currently, we propose two courses:••

Computational Science Literacy
High-performance Parallel Computing Technology for Computational Sciences(overlapped with the HPC Seminar)

The lectures will be given by faculty members of CCS and will be worth one unit ofgraduate credit. These courses will start in the summer of 2008.
The HPC Seminar presents knowledge, methods and techniques for programming modern
high-performance computer systems, including recent microprocessors and theirperformance, and parallel programming. This is an inter-university activity open forresearchers outside the Center, even researchers in companies not related to the university.
The seminar is held during 2 or 3 days in the summer. The number of participants in the lastseminar in 2007 was more than 80. It is also was broadcasted via the Internet.
We will organize workshops and symposiums. We have a plan for a “Long-term
Computational Science Workshop,” in which an advanced subject encompassing multiple
disciplines of science and computer science will be chosen, and participants who can stayfrom a few weeks to a few months are encouraged to carry out interdisciplinary researchcollaborations. In addition to this, we plan to have an annual international symposium,
which will be part of an existing symposia series covering various areas of computational
science that is held every year in Tsukuba (there have been 10 symposia over the past five
years).
4.3 Acquisition and Operation of the Next Supercomputer and T2K Project
In University of Tsukuba, we had a supercomputer system (VPP5500) which was operated
by the Academic Computing and Communications Center until 2006. The university
decided that the Center of Computational Sciences should acquire and operate the next
supercomputer. This next supercomputer may be used as part of the inter-university
computing resources, like PACS-CS.
For acquisition of the system, we, University of Tsukuba, have made an alliance with
University of Tokyo and Kyoto University, since the three universities were planning toprocure their next supercomputers in the same time frame to replace their current ones. We
agree to cooperate and make an alliance to share the main system architecture on threemachines. The alliance should take the following topics into account:•

Common Architecture - Nodes and interconnections- 11 -CCS Report: PART III, Vision and Strategies of Center for Computational Sciences•••

Use of Open System/Software – based on a Linux cluster
Source code level compatibility – easy code porting & grids
Grid computing – resource sharing both CPU and data

We call this conceptual design “Open Supercomputer,” and our alliance “T2K Open
Supercomputer Alliance.” We define “Open Supercomputer” as follows:•

Openness of basic architecture− Use of a high-performance commodity processor− Use of the leading processor in the market facilitates the high-performance,high-density and low-power characteristics computing facility in the
supercomputer center•

Openness of system software− Use of open source software based operating system and libraries− Provide a seamless environment for both multi-scale and multi-sites to enable
users to develop various fields and sizes of applications•

Openness of users’ needs− Support much wider area of users than traditional supercomputer centers− Explore new application fields

We expect that this architecture will be useful for bridging the gap between/connecting
small laboratories and supercomputing centers.
We expect a performance of more than 80 TFLOPS performance for our site. According to
the schedule, the bid will be done at the end of December 2007, and installation will becompleted by the end of May. The operation will be started in the beginning of June 2008.
We will continue the alliance with University of Tokyo and Kyoto University also for
operation and research on computational science.
4.4 Contribution to the Next-generation Supercomputer ProjectIn 2006, the Japanese government launched the National Project (The Next-Generation
Supercomputer Project) to develop a peta-scale computer system (called the “Keisoku”
computer), which has the performance of more than 10 PFLOPS. The Project spans sevenyears, from 2006 to 2012, and RIKEN (Research Institute for Science and Chemistry) has
been selected to conduct the project.

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In September 2006, RIKEN and University of Tsukuba signed a collaboration agreementon the Next-Generation Supercomputer Project. Based on this agreement, several membersof the Center for Computational Sciences have been appointed as visiting fellows of
RIKEN, and have been involved in the project. More information about related projects aredescribed in CCS Report: PART I.
CCS will contribute not only to the design of the system but also to the evaluation andperformance improvement of real target application codes. The Center and RIKEN are
setting up a research collaboration program under the General Agreement for tuning
performance of QCD, RS-DFT and FFT codes for the Next-Generation Supercomputer as
peta-scale applications. Such a contribution is made possible by the unique environment of
CCS, where researchers of computer science and computational science are working
together.
In 2012, the peta-scale system is scheduled to become operational. The system will have agreat impact on the communities of computational science, because the performance of thissystem will be huge in the nationwide computing infrastructure. As a leading researchorganization, it is a very important issue for us to take leadership regarding the operation of
the peta-scale system in the nationwide computing infrastructure.
Besides the contribution to the next-generation supercomputer project, we have to explore
the next-generation high-performance computing platforms, including arithmetic
accelerators such as GRAPE-DR, Clear-speed, GPU and many-core architectures, which
integrate many functions on one chip. These architectures are promising for somespecial-purpose applications. Since our center has a long history of collaboration withcomputational science and computer science, this approach is possible just in our center.
The FIRST project is a very good example of what we have achieved so far in thisapproach.
4.5 Collaboration and Alliance
Finally, collaborations and alliance on the research of computational science are importantfactors for promoting and accelerating interdisciplinary computational science.
For nationwide alliance, we are going to strengthen the T2K alliance with Tokyo andKyoto, as well as the connection to the coming peta-scale system, not just for computing
facilities, but also for research on computational science.
Our university is located in Tsukuba Science City, which has many government researchorganizations. We already have connections to the major research institutions in Tsukuba- 13 -CCS Report: PART III, Vision and Strategies of Center for Computational Sciences(e.g., High Energy Accelerator Research Organization (KEK), Advanced Institute for
Science and Technology (AIST), National Institute for Materials Science (NIMS),
Meteorological Research Institute (MRI), and National Institute for Environmental
Studies (NIES)). The strategy is to strengthen research connections among the institutionsin Tsukuba for the research of computational science.
National Institute of Informatics has been carrying out the “Cyber Science Infrastructure
Project,” which is building a grid infrastructure for academic research between theuniversities and research institutions. Because of its well-known research achievement
record, the Center for Computational Sciences, which forms one of the centers, has beenrequested to participate in the project, and have been playing an active role. We will hostthe virtual organization (VO) of several disciplines by grid technology. We already host thelattice QCD communities’ VO through the JLDG activities.
We will strengthen and expand the wide spectrum of international and domestic
collaborations already underway, and use these connections as bridges to send and invite
researchers and students for research collaborations. We have a plan to run the“Computational Science Researchers Invitation Program,” which will invite researchers
who are at the forefront of research in science and computational science.
The list of international collaborations are as follows:i)International Lattice Data Grid in particle physics (Edinburgh University(UK), DESY (Germany), Univ. di Roma (Italy), FNAL/BNL/JLAB (USA))ii)
Astronomical Radiation Hydrodynamics Research (National Astronomical
Observatory (Japan), SISSA (Italy))iii) Nano-Bio Science Collaboration (ETH (Switzerland), Princeton University andVanderbilt University (USA), Advanced Institute for Science and Technology(AIST), National Institute for Materials Science (NIMS))iv) Quantum Structural Biological Science Collaboration (AIST, Hyogo
Prefectural University (Japan), ETH and IBM Zurich (Switzerland))v)
Quantum Dynamics Collaboration (RIKEN (Japan), Washington University(USA))vi) Warming of Arctic Research (IARC of Alaska University/Hawaii University(USA), Pusan University (Korea), Academia Sinica (China))vii) France-Japan Grid Computing (National Institute of Informatics (Japan),
INRIA (France), Pennsylvania State University (USA))viii) Information Integration/Knowledge Discovery Research (Carnegie-Mellon
University and Georgia Institute of Technology (USA), Chubun University(Hong-Kong)).
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Within the Center, we will continue collaborations between different divisions and groups
to bring synergy. The following collaborations are possible and some of them have alreadybegun:
i)

ii)
iii)

iv)
v)

Particle Physics and Astrophysics division collaborates with High-performance
Computing Systems and Computational Informatics divisions on thedevelopment of peta-scale computing systems, algorithms, and a global-scale data
grid formation
Astrophysics group and Geo-environment group collaborate on thedevelopment of physical modeling which relies principally on radiation transport
Materials and Life Science division and High-performance Computing
Systems division collaborate to develop, implement and optimize quantum
mechanical first-principle methods for multi-atom systems such as the real-spaceand real-time density functional methods which are scalable to petaflops range
Life Science group and Biological Science group collaborate on the inter-relation
at the molecular level between biological functions and the evolution tree
Computational Informatics division and Global environment groupcollaborate on the development and operation of the climate/weather database anduse it as a testbed for innovations in knowledge discovery from large-scale
databases.

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