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R-CCS Cafe

R-CCS Cafe is a place where R-CCS researchers can informally discuss their research beyond the boundary of their discipline to facilitate integration of different disciplines. R-CCS Cafe is held twice a month. All who are interested are welcome to attend.

  • Purpose: To provide a forum for researchers to exchange ideas and information, with the goal to facilitate interdisciplinary collaboration and develop new research fields.
  • Place: Lecture Hall (6th floor) or Seminar Room (1st floor) at R-CCS
  • Language: Presentations will be in Japanese or English. Slides will be in English.

Please make your presentation understandable to researchers in other fields. Questions and active discussion are encouraged.

The 176th R-CCS Cafe -part I
Date and Time: Fri. July 26, 2019, 10:15 - 11:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Composability and Scalability in Large-Scale Supercomputing through Modularity
Speaker: Thomas Lippert(Prof. Dr. Dr./Director of the Institute for Advanced Simulation, Head of Jülich Supercomputing Centre)

Presentation Language: English
Presentation Material: English

Abstract:

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.

The 176th R-CCS Cafe -part Ⅱ
Date and Time: Fri. July 26, 2019, 11:00 - 11:45
Place: Lecture Hall (6th floor) at R-CCS

Title: Supercomputing and Service Oriented Architectures
Speaker: Thomas Schulthess(Prof. Dr./Director of the Swiss National Supercomputing Centre)

Presentation Language: English
Presentation Material: English

Abstract:

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.

The 175th R-CCS Cafe -part I
Date and Time: Mon. July 22, 2019, 15:30 - 16:10
Place: Lecture Hall (6th floor) at R-CCS

Title: Building an FPGA cluster for application acceleration
Speaker: Takaaki Miyajima (Processor Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

TBA

The 175th R-CCS Cafe -partⅡ
Date and Time: Mon. July 22, 2019, 16:10 - 16:50
Place: Lecture Hall (6th floor) at R-CCS

Title: The Assimilation of Dual Phased Array Weather Radar Observations to Short-range Convective Forecasts
Speaker: James Taylor (Data Assimilation Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

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.

The 174th R-CCS Cafe
Date and Time: Thu. July 18, 2019, 14:00 - 14:45
Place: Lecture Hall (6th floor) at R-CCS

Title: Introducing Arm and Arm Research: enabling innovation across all compute continuum.
Speaker: Filippo Spiga, (SLSS, Arm Research (UK))

Presentation Language: English
Presentation Material: English

Abstract:

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.

The 173rd R-CCS Cafe -part I
Date and Time: Mon. July 1, 2019, 13:00 - 13:55
Place: Lecture Hall (6th floor) at R-CCS

Title: Molecular Mechanisms for Protein-Ligand Binding in a Living Cell
Speaker: Yuji Sugita (Team Leader, Computational Biophysics Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

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.

The 173rd R-CCS Cafe -part Ⅱ
Date and Time: Mon. July 1, 2019, 13:55 - 14:50
Place: Lecture Hall (6th floor) at R-CCS

Title: High-performance numerical library and numerical reproducibility
Speaker: Toshiyuki Imamura (Team Leader, Large-scale Parallel Numerical Computing Technology Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

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.

The 173rd R-CCS Cafe -part Ⅲ
Date and Time: Mon. July 1, 2019, 15:05 - 16:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Development of a Unified Continuum Mechanics Simulation Framework for Industrial Applications
Speaker: Makoto Tsubokura (Team Leader, Complex Phenomena Unified Simulation Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

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

The 172nd R-CCS Cafe -part I
Date and Time: Mon. June 24, 2019, 15:30 - 16:10
Place: Lecture Hall (6th floor) at R-CCS

Title: Examination of efficient calculation method of relativistic molecular orbital method
Speaker: Nobuki Inoue (Computational Molecular Science Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

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.

The 172nd R-CCS Cafe -part Ⅱ
Date and Time: Mon. June 24, 2019, 16:10 - 16:50
Place: Lecture Hall (6th floor) at R-CCS

Title: An Introduction to Chemical Evolution of Galaxies
Speaker: Yutaka Hirai (Particle Simulator Research Team)

Presentation Language: English
Presentation Material: English

Abstract:

Galactic chemical evolution studies the enrichment histories of elements in the Universe. At the time of the Big Bang, the Universe consists of hydrogen, helium, and lithium. However, we are now living in the Universe with various kinds of elements. Most of the elements are synthesized in stars and distributed to space when a star ends its life.
These elements are inherited to the next generation stars. Elemental abundances of stars, therefore, reflect the nucleosynthetic histories in the galaxy. In the first part of this talk, I will show how the observed elemental abundances of stars in the Milky Way and satellite dwarf galaxies preserve information about their enrichment histories. In the Milky Way, the distribution of elements is different among old and new stars. The second part of this presentation focuses on the modeling of galaxy evolution. Hydrodynamic simulations of galaxies are presently a powerful tool to study galactic chemical evolution. It can self-consistently follow the formation of galaxies and the enrichment histories of elements. The last part discusses the enrichment of elements heavier than iron. The origin of elements synthesized by a rapid neutron-capture process such as europium, platinum, and gold is a long-standing problem in astronomy. Recently, binary neutron star mergers have been detected by the gravitational wave observations. I will show that they can be the source of such elements in galaxies. I will also present the future prospects of the studies of galactic chemical evolution.