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R-CCS Cafe

R-CCS Cafe は、異分野融合のための足掛かりとして、計算科学研究センター(R-CCS)に集う研究者が井戸端会議的にざっくばらんに議論する場として、毎月2回程度予定しております。興味をお持ちの方は原則どなたでも参加可能です。

  • 目 的: 異分野間の壁を超えた研究協力を促進し、新しい学問分野の開拓を目指すため、 研究者間の情報交換・相互理解の場を提供し、研究協力のきっかけを作る。
  • 会 場:R-CCS 6階講堂もしくは1階セミナー室
  • 言 語:講演は日本語/英語、スライドは英語
  • その他:講演者は他分野の方にも理解できる発表を心掛け、参加者は積極的に質問しましょう。

第177回
日時: 2019年7月31日(水)、14:00 - 15:30
場所: R-CCS 1階セミナー室

・講演題目: Global Collaboration to Improve HPC Energy Efficiency
・講演者: Natalie Bates(Energy Efficient HPC Working Group)
※発表・スライド共に英語

講演要旨: 詳細を見る

The purpose of the Energy Efficient HPC Working Group (EE HPC WG) is to promote energy efficiency in HPC. The EE HPC WG develops best practices for maximizing energy efficiency in HPC facilities and systems. It provides a venue for sharing of information (peer-to-peer exchange) and collective action. The EE HPC WG is cross-disciplinary and encourages interaction between facilities, operations and computational science organizations.
The EE HPC WG has a strong presence in the United States and Europe, with a growing presence in Japan. The Japanese HPC centers have a lot of innovative technologies and approaches that work towards improving HPC energy efficiency. The United States and European HPC centers would like to learn more about their Japanese counterparts.
The purpose of this seminar is to promote further collaboration between the United States, Europe and Japan within the EE HPC WG. This seminar will describe the EE HPC WG. It will describe areas where Japanese HPC centers have already contributed to the EE HPC WG. The seminar will be informational, but will also allow for discussion and exploration of further collaborative opportunities.
Below are some of the EE HPC WG Teams that will be discussed in this seminar. Some of the Teams focus more on HPC systems and others more on HPC facilities, but none of them are exclusively one or the other..
• _Energy and Power Aware Job Scheduling and Resource Management:_ This team did a global survey of sites deploying the emerging EPA JSRM technologies to evaluate what they are doing and trying to accomplish. Three papers were published. The team is currently investigating site policies for EPAJSRM with a view towards optimization techniques.
• _Operational Data Analytics:_ This team has published 3 case studies and is doing a global survey to evaluate the benefits and challenges of instrumentation, data collection and analytics for facility operations, including data from HPC systems.
• _System Power Measurement Methodology:_ The Green500 and Top500 power measurement methodology has been made more rigorous, consistent and higher quality as a result of this Team. The team is still working on promoting the use of the highest quality measurements.
• _Grid Integration:_ Demand Response for the electric grid was the initial focus of this team and two papers were published describing how sites were reacting to demand response opportunities from their electricity service providers. The Team is now focused on rapid and extreme voltage fluctuations from HPC systems and the impact that might have on the electric grid. It has done a limited site survey and published a short paper on this topic. Further investigation is underway.

第176回 第1部
日時: 2019年7月26日(金)、10:15 - 11:00
場所: R-CCS 6階講堂

・講演題目: Composability and Scalability in Large-Scale Supercomputing through Modularity
・講演者: Thomas Lippert(Prof. Dr./Director of the Institute for Advanced Simulation, Head of Jülich Supercomputing Centre)
※発表・スライド共に英語

講演要旨: 詳細を見る

The leading supercomputers in the Top 500 list are based on a traditional, monolithic architectural approach. They all use complex nodes consisting of different elements such as CPUs and GPUs or FPGAs with common I/O interfaces. It is a well-known difficulty with such systems that one often encounters underutilization, because the more complex the node, the more prone the overall system becomes to inefficiencies. A second problem is the cost of scalability, because a node must be able to perform very complex calculations for problems that are often not scalable, and the same node must perform scalable calculations for problems that would not require such complex nodes. This make the system extremely costly. A third difficulty is the composability of resources, as for instance future computing systems like quantum computers. In order to try solving these problems, we propose a disaggregation of resources and their dynamic recomposition by a programming paradigm called modular supercomputing. We motivate the approach by relying on computer-theoretical considerations for a generalization of Amdahl's law. We present arguments for for the usefulness of modularity for important applications such as Earth System simulations, continuous learning and data analysis problems. FInally, we are presenting first results of test problems.

第176回 第2部
日時: 2019年7月26日(金)、11:00 - 11:45
場所: R-CCS 6階講堂

・講演題目: Supercomputing and Service Oriented Architectures
・講演者: Thomas Schulthess(Prof. Dr./Director of the Swiss National Supercomputing Centre)
※発表・スライド共に英語

講演要旨: 詳細を見る

In modern science there is a need for developing extreme-scale computing infrastructures towards support for workflows with complex computing and data requirements. In order to simplify the experience of scientists using the infrastructure and minimizing the need for large movements of data, a combination of capability, throughput as well as interactive computing services have to be offered in a transparent way. In this talk, I will show how CSCS is improving its service portfolio, which is rooted in traditional supercomputing operations, towards a service-oriented architecture (SOA) that use many of the virtues of native cloud computing. Key technologies such as interactive notebooks, containers for software deployment and their orchestration, as well as web-accessible supercomputing infrastructure will be discussed. I will review recent experiences of CSCS in covering needs of the User Lab (traditional supercomputing operations), the Swiss Institute of Particle Physics (CHIPP, the Swiss part of the World LHC Computing Grid), as well the Materials Cloud platform and the HBP Collaboratory (a platform of the Human Brain Project). Looking at this from a SOA point of view is allowing us to evolve our supercomputing systems to meet the needs of modern science.

第175回 第1部
日時: 2019年7月22日(月)、15:30 - 16:10
場所: R-CCS 6階講堂

・講演題目: Building an FPGA cluster for application acceleration
・講演者: 宮島 敬明 (プロセッサ研究チーム 特別研究員)
※発表・スライド共に英語

講演要旨: 詳細を見る

In this talk, I will give you an research topic about network subsystem for FPGA cluster. A heterogeneous system with Field Programmable Gate Array (FPGA) is gathering attention in High-Performance Computing (HPC) area. When FPGA is used as an accelerator attached to the host CPU, there can be many configurations such as network topology to construct FPGA cluster. Sustained data transfer bandwidth between FPGA memory and CPU memory on a distant node is one of the most important factors to decide a topology of FPGA cluster. In order to explore the best topology, a quantitative evaluation of bandwidth is required. We conducted bandwidth measurement on two host nodes both nodes are connected via 100Gbps InfiniBand cable and one host node has PCIe Gen3 x8-based FPGA accelerator card. We implemented a Direct Memory Access (DMA) function on an FPGA-attached node and a software bridged data transfer function to transfer data between two nodes. The result shows that DMA function and software bridged data transfer function achieve 82.2% and 69.6% of the theoretical bandwidth of PCIe Gen3 x8, a bottleneck of data transfer path, respectively.

第175回 第2部
日時: 2019年7月22日(月)、16:10 - 16:50
場所: R-CCS 6階講堂

・講演題目: The Assimilation of Dual Phased Array Weather Radar Observations to Short-range Convective Forecasts
・講演者: James Taylor (データ同化研究チーム 特別研究員)
※発表・スライド共に英語

講演要旨: 詳細を見る

The assimilation of Doppler radial velocity and reflectivity observations from phased array weather radar (PAWR) have been widely studied for the use of short-range numerical weather prediction (NWP) and have shown to have positive impact to analyses and forecasts of convective weather systems (e.g. Maejima 2017). However, these studies only assimilated observations from a single PAWR and the use of multiple PAWR observations for NWP has not yet been explored. In this talk we present an overview into the assimilation of PAWR observations within the SCALE-LETKF modelling system (Lien et al 2017), including research into dual PAWR assimilation and the development of a new quality control method that aids the removal of false echoes from radar datasets. This talk will also introduce research currently being undertaken for a proposed Precipitation Radar onboard a satellite in geostationary orbit that could in future provide continuous global observation of the three-dimensional precipitation structure.

第174回
日時: 2019年7月18日(木)、14:00 - 14:45
場所: R-CCS 6階講堂

・講演題目: Introducing Arm and Arm Research: enabling innovation across all compute continuum.
・講演者: Filippo Spiga, (SLSS, Arm Research (UK))
※発表・スライド共に英語

講演要旨: 詳細を見る

Arm vision is develop technology that invisibly enables opportunities for a globally connected population. Nowadays Arm IP is at the foundation of billions of devices across all compute continuum (from Cloud to Edge to mobile and IoT). The aim of this talk is to provide an overview of Arm, in particular how we operate and how we pursue innovation via our Research group in partnership with academic and industrial institutions worldwide. The talk will also highlight some the latest technology announcements and some key Arm Research activities in various areas, including High Performance Computing.

第173回 第1部
日時: 2019年7月1日(月)、13:00 - 13:55
場所: R-CCS 6階講堂

・講演題目: Molecular Mechanisms for Protein-Ligand Binding in a Living Cell
・講演者: 杉田 有治(粒子系生物物理研究チーム、チームリーダー)
※発表・スライド共に英語

講演要旨: 詳細を見る

The inside of cell is highly crowded with proteins, nucleic acids, ribosomes, metabolites, ions and water. In the macromolecular crowding environments, protein behaviors can be altered compared to those in dilute solution. The effect of macromolecular crowding was mainly explained via the excluded volume effect. However, recent in-cell NMR spectroscopy and atomistic molecular dynamics (MD) simulations in explicit solvent (R. Harada eta al. JACS (2012, 2013)) have shown the importance of weak protein-protein interactions on protein stability and dynamics. In the talk, we discuss the effect of macromolecular crowding on protein-ligand interactions. In the simulations of the all-atom model of Mycoplasma Genitalium (I. Yu et al. eLife (2016)), we observed that not only hydrophobic but also hydrophilic metabolites also stay on the surfaces of proteins longer than in the bulk solution. Non-specific and weak protein-metabolite interaction is likely important for the metabolite distributions. We also investigated kinase-inhibitor binding processes in dilute solution and crowded protein solution by all-atom MD simulations.

第173回 第2部
日時: 2019年7月1日(月)、13:55 - 14:50
場所: R-CCS 6階講堂

・講演題目: High-performance numerical library and numerical reproducibility
・講演者: 今村 俊幸(大規模並列数値計算技術研究チーム、チームリーダー)
※発表・スライド共に英語

講演要旨: 詳細を見る

As it is the second round on the PI progress report on R-CCS Café, two research topics are selected from the recent outstanding results and the future project. First, the most outstanding result of my team activities was that Dr. Kudo won the best paper award in HPC Asia 2019, Guangzhou, China. The main contribution of his paper was dedicated to accelerating a very compact and scalable eigenvalue solver on several types of manycore processors. His main idea was to reconstruct carefully but boldly any part of the implementation by introducing a systematic code generator to achieve performance portability and future extensibility. What is more, another idea to incorporate the “BLAS+X” approach improved the TRD algorithm (Householder tridiagonalization) and extended the functionality of TRD beyond the batch operations. The second topic is that new research pillar of “numerical reproducibility”. This is a new concept and approach to guarantee numerical precision on any software and hardware configurations. This project is based on several mathematical theories and hardware/software/algorithmic supports of higher precision arithmetic. In this project, we intend to guarantee input/output numerical reproducibility. Internally, we secure the numerical accuracy fully 64bit or necessary precision (bit fields) by a stochastic approach with CADNA and PROMISE developed by the LIPS6 group, France. Naturally, as the rounding error contaminates any floating calculations, we must extend the internal data format with a much wider one, for example, IEEE754 real128 or other individual floating point formats. We are going to overcome this difficulty by incorporating the arithmetic engine of the FPGA. Furthermore, we need to investigate software emulation of a wider precision floating point format and higher precision algorithms. I would like to introduce these topics at the next R-CCS Café briefly.

第173回 第3部
日時: 2019年7月1日(月)、15:05 - 16:00
場所: R-CCS 6階講堂

・講演題目: Development of a Unified Continuum Mechanics Simulation Framework for Industrial Applications
・講演者: 坪倉 誠(複雑現象統一的解法研究チーム、チームリーダー)
※発表・スライド共に英語

講演要旨: 詳細を見る

A High-Performance Computing(HPC) framework for the fluid-structure interaction problems with complicated geometry have been developed, considering its application to industrial matters. To overcome the difficulty of mesh generation and treatment of moving boundary, hierarchically structured finite volume method was adopted as its data structure in which both the fluid motion and structure deformation are solved in unified Eulerian manner. To achieve higher computational efficiency of parallelization and scaling on the massively parallel environment, Building Cube Method (BCM) proposed by Nakahashi was adopted. In the method, numerical domain is first decomposed into cubic sub-domains based on the octree method. Then the same number of numerical grids is allocated to each cubic subdomain. The solid surface with complicated geometry is represented by the immersed boundary method (IBM). In the fluid-structure interaction problems with structure surface in motion, accurate representation of the immersed body is indispensable. Thus Lagrangian description for tracking the moving solid body surface is adopted in the Eulerian framework of solving fluid and structure motions. So far, the framework can handle maximum of tens of billions of numerical meshes using hundreds of thousands of CPU cores on the K-computer. Applications of the method to vehicle aerodynamics, aero-acoustics, combustion systems, and structure analysis are introduced.

Keywords: unified simulation, HPC, immersed boundary, hierarchically structured grid, industrial application

第172回 第1部
日時: 2019年6月24日(月)、15:30 - 16:10
場所: R-CCS 6階講堂

・講演題目: Examination of efficient calculation method of relativistic molecular orbital method
・講演者: 井上 頌基(量子系分子科学研究チーム、特別研究員)
※発表・スライド共に英語

講演要旨: 詳細を見る

Molecular orbital method is a powerful tool to theoretically clarify the properties of molecular systems. The calculation accuracy of the molecular orbital method depends on the number of basis functions expanding the molecular orbital, which is a one-particle wave function of electrons, the treating of electron correlation, and the treating of relativistic effects. Relativistic effects are important mainly for heavy and superheavy elements, sometimes at a qualitative level.
However, relativistic molecular orbital calculation has large computational cost than non-relativistic one. This is a obstacle to clarifying the chemistry of heavy element systems theoretically. The cost of relativistic calculations comes from the facts that the Fock matrix is larger than that of non-relativistic ones, and that integrals of high angular momentum must be calculated.
So, in this talk, I will introduce the research that has been performed as an approach to these problems.