RIKEN Center for Computational Science

Menu
Menu
Events/Documents イベント・広報

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 164th R-CCS Cafe (Special Edition 2)
Date and Time: Fri. Mar. 15, 2019, 13:15 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Can computer simulations be regarded as science?: a perspective from philosophy of science
Speaker: Tetsuji Iseda (Associate Professor, Kyoto University)

Presentation Language: English
Presentation Material: English

Abstract: Detail

What distinguishes scientific research from other types of activities? One answer to this question is that empirical science construct theory based on experiments and observations. Then, what about 'experiments' through computer simulations, according to such a view? Can we regard simulation-based research as scientific? Computer simulations also attract attention of philosophy of science, and some of the considerations in that field are relevant to the above question. This lecture try to locate computer simulation within science properly through introducing such recent trends in philosophy of science.

The 163rd R-CCS Cafe -part I
Date and Time: Fri. Mar. 1, 2019, 13:00 - 14:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Novel features of a familiar theory --- QCD near phase boundary analyzed through large scale numerical simulations
Speaker: Yasumichi Aoki(Team Leader, Field theory Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

Understanding the chiral symmetry and its spontaneous breakdown is essential to theoretically reveal the nature of QCD (Quantum Chromo Dynamics) in the Standard Model of particle physics. To this end non-perturbative approaches to QCD dynamics are indispensable and numerical computation based on lattice QCD is only one available method to pursue this for targeted precision in the state-of-the-art application. Ever since the first trial in this approach started in 1980, tremendous effort to improve the algorithms has been made. With that and the increased computer capability we (lattice community) now achieved percent level precision computation for not all, but, some important physical quantities. On the other hand, if one's focus is at the boundary of chiral symmetric - broken "phases", then a delicate treatment of the chiral symmetry is required to even predict the qualitative nature of the system. Such a treatment has become possible only recently in large-scale numerical simulations, which have led to some hints of novel features of QCD. Taking the latter examples, this talk describes such features of QCD, which appears in two different contexts: 1) when the numbers of quarks are increased and 2) in the finite temperature phase transition of two-flavor QCD. The implication to the physics beyond the Standard Model 1); and also the impact to the real world 2) are discussed with the results obtained from large scale numerical simulations. Finally problems which needs to be solved in the next generation supercomputers are also discussed.

The 163rd R-CCS Cafe -part Ⅱ
Date and Time: Fri. Mar. 1, 2019, 14:00 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Next Generation System Software for High Performance Big Data
Speaker: Kento Sato (Team Leader, High Performance Big Data Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

The High Performance Big Data Research Team is investigating and developing system software to facilitate extreme-scale big data processing, machine learning and deep learning for the K computer, post-K computer and beyond. The computational power in high performance computing (HPC) systems has been dramatically increasing, driven in particular by advanced multi/many-core architectures and new memory technologies such as high bandwidth memory and hybrid memory cubes. Although these HPC systems are keeping pace with required computational and memory performance for running scientific applications, they are inadequate with respect to I/O performance required by data-intensive applications. In this talk, we briefly introduce various approaches to resolve these I/O issues and future research directions for the next generation HPC systems.

The 163rd R-CCS Cafe -part Ⅲ
Date and Time: Fri. Mar. 1, 2019, 15:15 - 16:15
Place: Lecture Hall (6th floor) at R-CCS

Title: Towards Next Generation HPC Architecture and its Power Management
Speaker: Masaaki Kondo (Team Leader, Next Generation High Performance Architecture Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

The continuous improvement in processing speed in high-performance computer systems has been enabled by transistor scaling known as Moore's law. However, this trend is predicted to end in the near future. It is vital to research and develop new, more efficient high performance architectures to continue realizing high performance computing systems. One of the missions of our team is to research and develop a next-generation high-performance computer architecture together with strategies to improve the power efficiency of exascale supercomputer systems. Our research focus includes non-von Neumann architectures, integrating next generation non-volatile memories and/or various types of accelerators into a general-purpose processor, acceleration of machine learning computations, and hybrid computing architectures that combine new and classical computing models. In this talk, we briefly introduce our recent research efforts on next generation high-performance architectures. We also present a power-aware resource management framework which have been developed by our JST CREST project. The developed framework controls power allocation among co-scheduled jobs to optimize total system throughput and power-efficiency within a given power constraint. We have tested this framework on a large-scale HPC cluster system with about 1000 compute-nodes and showed that it can successfully manage the system's power consumption.

The 162nd R-CCS Cafe(Special Edition 1)
Date and Time: Fri. Feb. 22, 2019, 10:40 - 11:40
Place: Lecture Hall (6th floor) at R-CCS

Title: An Introduction to Quantum Computing and Its Application, Probably
Speaker: Bo Ewald(President, D-WAVE INTERNATIONAL)

Presentation Language: English
Presentation Material: English

Abstract: Detail

This presentation will briefly introduce the ideas behind quantum mechanics and its possible application in quantum sensing, communication and computing. We’ll then discuss the ideas and principles that have enabled the world’s first quantum computers. We’ll briefly review the technologies and architectures, then dive a little more deeply into how the D-Wave quantum annealing computer works. We’ll survey the “proto-applications” that customers have been developing in areas of optimization, machine learning and material science that point the way to production use of quantum computers in the next few years. Finally, we’ll discuss some of the future directions of quantum computing.

The 161st R-CCS Cafe
Date and Time: Fri. Feb. 15, 2019, 15:30 - 16:30
Place: Lecture Hall (6th floor) at R-CCS

Title: Recent advances in MXenes: From fundamentals to applications
Speaker: Mohammad Khazaei (Computational Materials Science Research Team)

Presentation Language: English
Presentation Material: English

Abstract: Detail

The family of MAX phases — with chemical formula of Mn+1AXn, where n = 1, 2, or 3, “M” is an early transition metal (Sc, Ti, Zr, Hf, V, Nb, Ta, Cr, Mo), "A" is A group elements (Al, Si, P, S, Ga, Ge, As, In, Sn) and "X" is carbon and/or nitrogen — are a large family of layered ceramics with structural applications. Recently, MAX phases have been exfoliated into 2D single and/or multi Mn+1Xn layers by using appropriate acid solutions. The resulting 2D-Mn+1Xn transitional metal carbides and nitrides have been named as MXenes. Considering a large number of compositional possibilities of MAX phase compounds, a large number of MXenes with unprecedented properties could also be obtained in the future. Owing to their large surface area, hydrophilicity, adsorption ability, and high surface reactivity, 2D MXenes have experimentally attracted attention for many potential applications, e.g., catalysts, ion batteries, gas storage media, and sensors. Given the fast progress of MXene-based science and technology, in this presentation, I would like to update your knowledge of electronic properties and some of the possible applications of MXenes.

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.