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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 185th R-CCS Cafe -partⅡ
Date and Time: Mon. Dec. 2, 2019, 13:40 - 14:20
Place: Lecture Hall (6th floor) at R-CCS

Title: Task-Parallelism and Dataflow: Programming models for FPGA accelerated HPC
Speaker: Mitsuhisa Sato (Deputy Director, RIKEN Center for Computational Science / Team Leader, Programming Environment Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

Recently, FPGA has been attracting attention as an alternative device to accelerate HPC applications. Data flow computing model is a popular abstraction of computing in both fine-grain and coarse-grain from decades, and this model is used as a programming model for FPGA such as Maxler DFE and SPGen (Stream Processor Generator). While it is a kind of “static” data flow model, it might be interesting to extend models by using “dynamic” data flow models as old dataflow architecture to handle the dynamic behavior of systems. On other hands, global programming models to integrate FPGA computing into parallel computing of host processors are also important. OpenMP task and target directives, which are recently introduced in OpenMP 4.5, can be extended to specify the interface to offloaded computation done by FPGA. And, the optimization for FGPA needs different metric such as hardware resources, which are very different from the optimization of CPU and GPU. In this talk, issues on programming models for FPGA accelerated HPC are presented.

The 185th R-CCS Cafe -partⅢ
Date and Time: Mon. Dec. 2, 2019, 14:20 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Operation improvement towards new service on Fugaku
Speaker: Fumiyoshi Shoji (Division Director, Operations and Computer Technologies Division)

Presentation Language: English
Presentation Material: English

Abstract:Detail

The K computer shut down in August with many achievements. We are now working on the installation and preparation of the operation of the Fugaku supercomputer. In the spring of next year, an early access program that uses a part of Fugaku installed in R-CCS will start. To improve user services, we are now considering "cloud service," which includes collaboration with commercial service providers. The "cloud service" is expected to contribute to improve the usability of Fugaku and increase the number of users and application areas drastically. To achieve highly energy-efficient, we optimize the Fugaku system and its facility operation based on operation data analysis and have to motivate users to increase energy efficiency by using Power API. To steadily advance these new activities, it is more critical to collaborate with research teams and operation division tightly. In this talk, I give a vision of the operation improvement towards new service on Fugaku.

The 184th R-CCS Cafe -partⅠ
Date and Time: Mon. Nov. 25, 2019, 15:30 - 16:10
Place: Lecture Hall (6th floor) at R-CCS

Title: Linear solvers in LQCD application
Speaker: Issaku Kanamori (Field Theory Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

Every proton and neutron are made of elementary particles called quark. The dynamics of quarks is described by Quantum Chromo Dynamics (QCD) and it can be formulated on a structure lattice (Lattice QCD or simply LQCD). The bottle neck of LQCD simulation, which a Markov Chain Monte Carlo (MCMC), is solving large sparse linear equation. It appears in both generating configurations and calculating physical observables using configurations. In this talk, I will discuss linear solvers for LQCD application. I will mainly focus on our recent implementation of multigrid type solvers. I will also discuss usage of simd variables in LQCD.

The 184th R-CCS Cafe -partⅡ
Date and Time: Mon. Nov. 25, 2019, 16:10 - 16:40
Place: Lecture Hall (6th floor) at R-CCS

Title: Atomistic modeling of the alternating access mechanism of the mitochondrial ADP/ATP carrier with molecular simulations
Speaker: Koichi Tamura (Computational Biophysics Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

ADP/ATP Carrier (AAC) is a membrane transport protein embedded in the inner mitochondrial membrane and mediates a 1:1 exchange of ADP and ATP. The transporter is known to alternate between the so-called c-state and the m-state in the course of the transport cycle. The crystallographic structure of the c-state has been known since 2003, while that of the m-state is not known until 2019. In 2015, we developed a molecular dynamics (MD) technique to simulate global conformational changes of protein. The method, linear response path following (LRPF), enables us to sample large conformational changes of protein without the prior knowledge of the target conformation. The method is suitable for the study of AAC, as no structural knowledge of the m-state is available when the project is started. Using LRPF simulations, we successfully predicted a model structure for the m-state structure (Tamura and Hayashi, 2017, PLOS ONE). The predicted structure was later validated by the experimentally determined m-state structure.

The 183rd R-CCS Cafe -partⅠ
Date and Time: Mon. Nov. 11, 2019, 13:00 - 13:40
Place: Lecture Hall (6th floor) at R-CCS

Title: Convergence of AI/Big Data and HPC
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 at RIKEN Center for Computational Science (RIKEN R-CCS) has been researching and developing system software to facilitate extreme-scale big data processing, machine learning and deep learning for high performance computing (HPC) systems, i.e., convergence of AI/Big Data and HPC. In this talk, Kento Sato introduce several R&D activities for accelerating AI/Big data applications on HPC systems (HPC for AI/Big data) as well as ones for resolving HPC challenges by using these AI/Big data techniques (AI/Big data for HPC).

The 183rd R-CCS Cafe -partⅡ
Date and Time: Mon. Nov. 11, 2019, 13:40 - 14:20
Place: Lecture Hall (6th floor) at R-CCS

Title: Structure and dynamics of protein biological functions via X-ray crystallography and molecular dynamics simulations
Speaker: Florence Tama (Team Leader, Computational Structural Biology Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

High resolution structures of biological molecules provide insights into their functions. Such structures are often derived from X-ray crystallographic experiments, but the information is not complete. Crystals are first cryo-cooled before collecting X-ray data. It has been suggested that, while backbone structures are usually very similar between room-temperature and cryo-temperature, cryo-cooling may hamper biologically relevant dynamics. In addition, X-ray crystallography requires crystals, which might lead to some artifacts as biomolecules might interact which each other, stabilizing specific conformations which might be different than in solution.
Furthermore, to fully understand function of biomolecules, dynamics need also to be considered. However, such X-ray crystallographic structure only represent one specific snapshot of the overall conformational space that biomolecules can cover. Therefore, to complement experimental data, Molecular Dynamics (MD) simulations can be utilized to connect structure, dynamics and function. We will be illustrating those points with studies we have been conducting on different biological systems.

The 183rd R-CCS Cafe -partⅢ
Date and Time: Mon. Nov. 11, 2019, 14:20 - 15:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Toward a human-scale whole-brain simulation on the Fugaku
Speaker: Jun Igarashi (Head Office for Information Systems and Cybersecurity, Computational Engineering Applications Unit)

Presentation Language: English
Presentation Material: English

Abstract:Detail

The human brain is estimated to include about 100 billion neurons and 100 trillion connections. A whole-brain simulation helps us to investigate all interactions between neurons for elucidating brain function and disease. However, a human-scale whole-brain simulation has not been realized due to the lack of sufficient computational resources in the current supercomputers and experimental data for modeling.
In the project of Exploratory Challenge on post-K computer #4-1, to realize human-scale whole-brain simulation on the Fugaku computer, we have been constructing a mammalian whole-brain model consisting of the cerebral cortex, thalamus, cerebellum, and basal ganglia using NEST simulator, and developing an in-house simulator specialized for the whole brain-simulation on the next-generation supercomputers.
In the first part of the presentation, we are going to introduce simulation studies on modulation of a network state by a hierarchical inhibitory circuitry in the primary motor cortex, and neural responses to different spatial size signals in the primary somatosensory cortex. In the second part, we are going to present studies on one-third of human-scale cortical simulation and a full of human-scale cerebellar simulation on the K computer. Finally, we are going to present our future perspective of large-scale brain simulations on Fugaku computer based on the current result in our project.

The 182nd R-CCS Cafe -part Ⅰ
Date and Time: Mon. Oct. 7, 2019, 13:00 - 13:55
Place: Lecture Hall (6th floor) at R-CCS

Title: Data Processing for Digital Ensemble and Topographical Aspect of Simulation of Disaster
Speaker: Satoru Oishi (Team Leader, Computational Disaster Mitigation and Reduction Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

Simulation of disaster on HPC requires well scaled program and urban structure data. A very small number of people make well scaled program as an academic achievement, whereas a very large number of people are necessary for applying it into real world through making urban structure data. Urban structure data consists of variety of sources like government, commercial and satellite data. It means that urban structure model is ill-structured. And due to its frequent changes, it is necessary for us to make a sophisticated way of data processing for introducing urban structure alive in numerical simulation. The first part of the talk will deal with the data processing and its applications.
On the other hand, people are anxious about the predictability of disaster simulation because cities are devastated by disasters every year. In the second part of the talk, we will discuss about the predictability of damage of disasters. We are living in concave system, then, a highly accurate simulation result can be obtained when we deal with disaster damage.

The 182nd R-CCS Cafe -partⅡ
Date and Time: Mon. Oct. 7, 2019, 13:55 - 14:50
Place: Lecture Hall (6th floor) at R-CCS

Title: Toward Fugaku: Symmetry to be Unfolded
Speaker: Yasumichi AOKI (Team Leader, Field Theory Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

Symmetry is one of the most important notions to understand the fundamental lows of nature. Using a finite degree of freedom, which is unavoidable for numerical simulations, leaves many symmetry broken. In the main application of the field theory research team, which is QCD (Quantum Chromo Dynamics), chiral symmetry is the most important one. This symmetry is not only crucial to understand the QCD dynamics and then the history of the universe, but also important to control the systematic error associated with the discretization. Using a chiral symmetric formulation, which is made possible even with the finite degree of freedom, some important, unsolved problems are expected to be solved on Fugaku. It is especially so for the study of the high temperature phase transition of QCD, for which the chiral symmetric analysis has not been done in complete manner. I will explain the current status and the future plan of the team toward such large scale simulation on Fugaku and discuss what it would bring to us.

The 182nd R-CCS Cafe -partⅢ
Date and Time: Mon. Oct. 7, 2019, 15:05 - 16:00
Place: Lecture Hall (6th floor) at R-CCS

Title: Earth & Planetary Materials (to be) Explored by K and Fugaku Computers & Quantum Beamlines
Speaker: Toshiaki Iitaka (Head Office for Information Systems and Cybersecurity, Computational Engineering Applications Unit)

Presentation Language: English
Presentation Material: English