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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 160th R-CCS Cafe -part I
Date and Time: Fri. Feb. 1, 2019, 13:00 - 14:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Regional-scale data assimilation with Himawari-8 satellite radiances
Speaker: Takumi Honda (Data Assimilation Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

In this talk, we review our achievement in regional-scale data assimilation with Himawari-8 satellite radiances. In July 2015, the Japan Meteorological Agency (JMA) started full operations of their new geostationary satellite “Himawari-8”, the first of a series of the third-generation geostationary meteorological satellites. Himawari-8 can produce high-resolution observations with 16 frequency bands every 10 minutes for full disk. To assimilate Himawari-8 radiances, we implemented a radiative transfer model into a regional-scale data assimilation system known as SCALE-LETKF, consists of the Scalable Computing for Advanced Library and Environment-Regional Model (SCALE-RM) and the Local Ensemble Transform Kalman Filter (LETKF). We assimilated all-sky every-10-minute infrared (IR) radiances from Himawari-8. The results showed that assimilating the every-10-minute Himawari-8 IR radiances improves the analyzed tropical cyclone (TC) structure and intensity forecasts. In another case in September 2015, the heavy precipitation forecasts are greatly improved by assimilating the Himawari-8 IR observations. We ran a rainfall-runoff model using the improved precipitation forecasts and found that assimilating the Himawari-8 observations frequently may give longer lead times in terms of the flood risk. We also show other case studies on a different TC case and the extremely-heavy precipitation event in July 2018.

The 160th R-CCS Cafe -part II
Date and Time: Fri. Feb. 1, 2019, 14:00 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Explorations in Protein Structures and Dynamics using Computational Studies ‒ beyond X-ray Crystallography ‒
Speaker: Miki Nakano (Computational Structural Biology Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

X-ray crystallography has been the most important experimental method to obtain the structural information of biomolecules. However, there are some limitations on it. For example, using X-ray crystallography, it is difficult to capture the conformational dynamics of bio-macromolecules in solution, which is closely related with their functions. In addition, this technique requires molecules to be crystallized. So it is difficult to apply to insoluble molecules or intrinsically disordered proteins. Limitations of crystallography are being complemented by alternative methods in both experimental and computational methods. In this presentation, I will show two kind of computational studies to capture biological molecular structures and dynamics.
First topic is "Thermodynamic properties of water molecules around DNA". DNA strands can adopt many structures in addition to Watson-Crick duplex, which depend on the solvent conditions. To understand how cosolute molecules such as ethylene glycol affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around the different DNA structures using grid inhomogeneous solvation theory (GIST). I will discuss free energy of water molecules dependence on DNA structures in the presence of cosolutes.
Second topic is "Three-dimensional reconstruction from diffraction images obtained by X-ray free electron laser experiment". Single particle analysis using X-ray free electron laser (XFEL) enables us to observe hard-to-crystallize biomolecules in a state close to nature. In order to restore 3D structures of the molecule from the diffraction images obtained by XFEL experiments, estimation of laser beam incidence angles to the molecule for each image and phase retrieval are required. For this purpose, we are developing an algorithm, “slice matching”. I will show the results of simulation study of slice matching for large biomolecule, ribosome, and the trials for applying our slice matching protocol for two experimental data. Also, I will discuss the requirements for the experimental conditions to obtain the diffraction images to restore the molecular structure at certain resolution.

The 159th R-CCS Cafe
Date and Time: Fri. Jan. 18, 2019, 15:30 - 16:30
Place: Lecture Hall (6th floor) at R-CCS

Title: Nonadiabatic electron dynamics in intense laser field
Speaker: Takahide Matsuoka (Computational Molecular Science Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

Recent advances in laser technology have provided methods to track the dynamics of the electrons in molecular systems. The molecular systems in intense laser-field involves repetitive re-collision of the ionizing electron and parent ion and intense emission of radiation, thus resulting in high-order harmonic generation (HHG) and above-threshold ionization (ATI) processes. Moreover, the availability of intense X-ray laser pulse allows further investigations involving auto-ionization and the Auger effect. The theoretical studies of HHG processes and ATI processes have succeeded in giving reasonably accurate results for a single atomic system or very small molecules. In this talk, I would introduce my theoretical studies on nonadiabatic electron dynamics of molecules in intense laser field. Time-dependent configuration interaction method has been applied to single water molecule system with nuclear nonadiabatic effect. The electron wavefunction is represented by complex natural orbitals, thus allowing evaluation of electron flux, which is an one-particle operator, for each natural orbitals. Within this treatment, we can determine how the nuclear nonadiabatic force induce the electron flux and clarify the validity of adiabatic approximation. Ionization process has been included in the calculations by means of continuity equations of electron fluxes for each complex natural orbital, which allows us to target molecular system in intense laser field. The nuclear nonadiabatic effect introduces isotope effect in ATI process and HHG process for systems in intense laser field. The path-branching method has also been implemented, thereby the symmetry-breaking force induced by nuclear nonadiabatic effect introduces spontaneous symmetry-breaking to the electronic state. System of single water molecule in intense laser field undergoes electronic excitation to continuum state. The symmetry-breaking induced by nuclear nonadiabatic effect for such system can be attributed to pseudo-Jahn-Teller effect. The numerical calculation allows a simple evaluation of complex nuclear nonadiabatic effect among quasi-degenerate electronic states.

The 158th R-CCS Cafe-part I
Date and Time: Fri. Jan. 11, 2019, 13:00 - 14:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Beyond Post-K and Moore’s Law --- Imminent Failure of FLOPS-centric HPC leading to a Bright Future towards Post-Moore
Speaker: Satoshi Matsuoka (Director, R-CCS)

Presentation Language: English
Presentation Material: English

Abstract: Detail

No one can now deny the inevitability that Moore’s Law, which has sustained performance growth in computing terms of FLOPS, is approaching its end; already the number of fabs that sustain continued shrinkage of lithography is less than a handful, as technical difficulties result in soaring costs, with little hope for economic gains. Architectural one-time techniques to circumvent the limitations, such as many-core architectures as well as reduced precision computing, have already been applied as today’s techniques, and thus cannot be “used again” to attain speedups. As such we might consider ourselves to be in crisis --- as transistor power improvement saturate over time, our next machines will no longer be significantly faster in terms of “catalog FLOPS” compared to the machines in the early 2020s as all the techniques to improve FLOPS in a straightforward way will be used up, be it for HPC or for other apps such as AI. However, the situation in reality is welcome, as we can finally break away from the classical, FLOPS-centric thinking (as per represented by outdated metrics such as Linpack/Top500), and move onto the real of new computing paradigms to improve the time-to-solutions of real applications. Already such “Post-Moore” research has arisen recently in a global fashion, and it is essential that, Riken R-CCS as the leadership center in High Performance Computing in Japan, to break away from FLOPS mindset and assume leadership in alternative devices and architectural parameters leading to new programing, new algorithms and new applications, Already some of us are at the task with new research agenda, from Data or BYTES-centric computing, use of ML to augment/replace first-principle simulations, as well as new computing models such as neuromorphic as well as quantum computing. We will discuss our future research roadmaps and activities for research on machines beyond Post-K in the late 2020s, as well as into the 2030s.

The 158th R-CCS Cafe-part II
Date and Time: Fri. Jan. 11, 2019, 14:00 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: An Innovative Method for Integration of Simulation/Data/Learning in the Exascale/Post-Moore Era
Speaker: Kengo Nakajima (Deputy Director, R-CCS)

Presentation Language: English
Presentation Material: English

Abstract: Detail

"ppOpen-HPC" is an open source infrastructure for development and execution of optimized and reliable simulation code on post-peta-scale (pp) parallel computers based on many-core architectures, and it consists of various types of libraries, which cover general procedures for scientific computation. Source code developed on a PC with a single processor is linked with these libraries, and the parallel code generated is optimized for post-peta-scale systems with manycore architectures, such as the Oakforest-PACS system of Joint Center for Advanced High Performance Computing (JCAHPC). "ppOpen-HPC" is part of a five-year project (FY.2011-2015) spawned by the "Development of System Software Technologies for Post-Peta Scale High Performance Computing" funded by JST-CREST. The framework covers various types of procedures for scientific computations, such as parallel I/O of data-sets, matrix-assembly, linear- solvers with practical and scalable preconditioners, visualization, adaptive mesh refinement and dynamic load-balancing, in various types of computational models, such as FEM, FDM, FVM, BEM and DEM. Automatic tuning (AT) technology enables automatic generation of optimized libraries and applications under various types of environments. We release the most updated version of ppOpen-HPC as open source software every year in November (2012-2015), which is available at http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/ . In 2016, the team of ppOpen-HPC joined ESSEX-II (Equipping Sparse Solvers for Exascale) project (Leading P.I. Professor Gerhard Wellein (University of Erlangen-Nuremberg)), which is funded by JST-CREST and the German DFG priority programme 1648 "Software for Exascale Computing" (SPPEXA) under Japan (JST)-Germany (DFG) collaboration until FY.2018. In ESSEX-II, we develop pK-Open-HPC (extended version of ppOpen-HPC, framework for exa-feasible applications), preconditioned iterative solvers for quantum sciences, and a framework for automatic tuning (AT) with performance model. In the presentation, various types of achievements of ppOpen-HPC, ESSEX-II, and pK-OpenHPC project, such as applications using HACApK library for H-matrix computation, coupling simulations by ppOpen-MATH/MP, and parallel preconditioned iterative solvers will be shown. Supercomputing in the Exa-scale and the Post-Moore Era is inherently different from that in the Peta- scale Era and before. Although supercomputers have been the essential tool for computational science in recent 30 years, they are now used for other purposes, such as data analytics, and machine learning. Architecture of the next generation supercomputing system is essentially heterogeneous for these multiple purposes (simulations + data + learning). We propose a new innovative method for integration of computational and data science (Big Data & Extreme Computing, BDEC) for sustainable promotion of new scientific discovery by supercomputers in the Exa-Scale/Post-Moore Era with heterogeneous architecture. "h3-Open-BDEC (h3: hierarchical, hybrid, heterogeneous,)" is an open source infrastructure for development and execution of optimized and reliable codes for BDEC on such supercomputers, which is the extended version of ppOpen-HPC. In this presentation, we will overview the h3-Open-BDEC, and the target supercomputer system, which will start operation in April 2021.

The 157th R-CCS Cafe-part I
Date and Time: Thu. Jan. 10, 2019, 14:00 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Multigrid for structured grids on large-scale parallel computers
Speaker: Prof. Dr. Matthias Bolten(University of Wuppertal, High performance computing / software engineering)

Presentation Language: English
Presentation Material: English

Abstract: Detail

In many simulations in computational science and engineering a partial differential equation has to be solved. Multigrid methods are among the fastest methods for accomplishing this task, in many cases with optimal, i.e., O(N), complexity. As a consequence, in simulations of huge problems on large-scale supercomputers often a multigrid method is used. If the underlying problem is formulated on a structured grid, this structure can be exploited in the multigrid method to build up the grid hierarchyd. Additionally, the presence of structure allows for a relatively straightforward efficient implementation on modern computer architectures, like modern CPUs or GPUs. Further, structure allows for a rigorous analysis of the problem and the multigrid method used for solving it. Still, the used multigrid components, i.e., grid transfer operators and smoothers, have to be carefully chosen to be able to treat the underlying problem. Besides the adaption to the problem the chosen component can have a huge influence on the serial efficiency and the parallel scalability of the whole method. In this talk multigrid methods for structured grids, their analysis and the specific choice of algorithmic components for parallel computers will be discussed.

The 157th R-CCS Cafe-part II
Date and Time: Thu. Jan. 10, 2019, 15:20 - 15:50
Place: Lecture Hall (6th floor) at R-CCS

Title: Multiplicative Schwartz type block multi-color Gauss-Seidel smoother for AMG/GMG method
Speaker: Masatoshi Kawai (HPC Usability Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

In this talk, we will focus on a multigrid method. A convergence and performance of the multigrid method strongly depend on a smoother. We proposed a multiplicative Schwartz type block multi-color Gauss-Seidel(MS-BMC-GS) smoother. This smoother has better convergence, higher cache-hit ratio, and fewer communications compared with existing methods. In this talk, we introduce the MS-BMC-GS smoother and show the numerical evaluations with a geometric and algebraic multigrid method.

The 156th R-CCS Cafe
Date and Time: Fri. Dec. 21, 2018, 15:15 - 16:15
Place: Lecture Hall (6th floor) at R-CCS

Title: Designing Communication Platform for an FPGA Cluster
Speaker: Tomohiro Ueno (Processor Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

A Field programmable gate array (FPGA) is a reconfigurable device on which we can implement arbitrary circuits repeatedly. By optimal implementation and stream processing, FPGA-based computing achieves both high computing performance and high power efficiency. To further improve the performance, it is necessary to realize an FPGA cluster with multiple nodes. We have developed a directly connected FPGA cluster and communication platform for the cluster. In this talk, I introduce the design and structure of the FPGA cluster and how to communicate in the cluster. I also explain the communication modules and actual data movement on the FPGA cluster. Finally, I shows that the proposed platform achieves fast and flexible communication for various application on FPGAs.

The 155th R-CCS Cafe-part I
Date and Time: Fri. Dec. 7, 2018, 13:00 - 14:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Applying HPC to mitigate disaster damage by developing and integrating advanced computational science
Speaker: Satoru Oishi (Team Leader, Computational Disaster Mitigation and Reduction Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

Computational Disaster Mitigation and Reduction Research Team is aimed at developing advanced large-scale numerical simulation of natural disasters such as earthquake, tsunami, flood and inundation, for Kobe City and other urban areas in Hyogo Prefecture. Oishi team integrates geo hazards, water hazards and related hazards. Demand for natural disaster simulations became increasing because disasters frequently take place. Therefore, we are developing appropriate sets of computer programs which meet the demand of calculations. Computational Disaster Mitigation and Reduction Research Team is dealing with the following three kinds of research topics. Urban model development: Research for urban hazards requires urban models which represent structure and shape of cities in numerical form. However, it takes very long time to develop urban models consisting of buildings, foundations and infrastructures like bridges, ports and roads. Therefore, it is indispensable to invent methods which automatically construct urban models from exiting data that is basically ill-structured. Oishi team developed Data Processing Platform (DPP) for such purpose. By using DPP, construction of a national-wide urban model and 3D model construction from engineering drawings are achieved. Recently, Oishi team has a couple of big collaborative researches with Hanshin Expressway Co. Ltd. and National Institute for Land and Infrastructure Management (MLIT). Three dimensional bridge model for programming code will be generated automatically from paper-based engineering drawings or 2D CAD so that Oishi team can simulate the seismic response of the entire network with high fidelity models. Since paper-based engineering drawings include errors and lack of information, it is hopeless to perform a robust model construction by merely extracting information from engineering drawings. To tackle with this problem, Oishi team have developed a template-based methodology. Developing particle methods for landslide simulation using FDPS: Conventional mesh-based numerical methods, such as finite element method (FEM) and finite difference method (FDM) have difficulty to simulate the large deformations, the evolution and break-down of the traction-free-surfaces during a landslide process. On the other hand, meshfree methods, such as smoothed particle hydrodynamics (SPH), and moving particle semi-implicit method (MPS), are regarded as promising candidates for landslide simulations. Using a framework of developing parallel particle simulation code (FDPS), we try to develop a large-scale simulation code for landslide simulation. Since FDPS provides those common routines needed for parallelizing a general particle method, we can focus on the numerical schemes and the mechanisms of landslides. In this talk, we present an improvement of a mathematical reformulation of MPS (iMRMPS). This iMRMPS shows no deterioration of accuracy and convergence for randomly distributed particles, outperforming most conventional particles methods. Water related disaster: Frequency of water disaster has increased. Not only water itself but also sediment cause damage to residents and their assets. Understanding possible hazards is necessary for a measure of precaution and making less damage. Therefore, Oishi team started to deal with water and sediment related disasters by making numerical simulation model for river basins in Kobe city and Hyogo prefecture. Estimation of a damage of sediment-related disaster accompanied with flood, inundation, and sediment supply due to landslides is important to establish a prevention plan. Oishi team has developed a 2D Distributed Rainfall and Sediment Runoff/Inundation Simulator (DRSRIS) with coupling the 2D rainfall runoff model, inundation flow model , and sediment transport model on the staggered grid which performs on the supercomputer.

The 155th R-CCS Cafe-part Ⅱ
Date and Time: Fri. Dec. 7, 2018, 14:00 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Predictability of the July 2018 Record-breaking Rainfall in Western Japan
Speaker: Takemasa Miyoshi (Team Leader, Data Assimilation Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

Data assimilation combines the computer model simulation and real-world data based on dynamical systems theory and statistical mathematics. Data assimilation addresses predictability of dynamical systems and has long been playing a crucial role in numerical weather prediction. Data Assimilation Research Team (DA Team) has been working on various problems of data assimilation, mainly focusing on weather prediction. In July 2018, a broad area in western Japan was damaged severely due to record-breaking heavy rainfall. DA Team developed real-time regional and global weather forecasting systems and investigated the historic rainfall event using these systems. Also, DA Team took the lead in organizing a rapid-response conference for meteorologist in August, about a month later of the event, in collaboration with the Computational Climate Science Research Team. In this presentation, we will report recent research progress of DA Team mainly focusing on the investigation related to the July 2018 rainfall event.