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The 188th R-CCS Cafe -partⅠ
Date and Time: Tue. Jan. 14, 2020, 13:00 - 13:40
Place: Lecture Hall (6th floor) at R-CCS

Title: Traffic simulation and models
Speaker: Nobuyasu Ito (Team Leader, Discrete Event Simulation Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

Simple model is expected to make reliable simulations, but it is not always available for social phenomena and complicated adhoc models are often used. Traffic simulation is an example. Various models are proposed and used for traffic phenomena, In this talk, traffic phenomena and their models are briefly reviewed.

The 188th R-CCS Cafe -partⅡ
Date and Time: Tue. Jan. 14, 2020, 13:40 - 14:20
Place: Lecture Hall (6th floor) at R-CCS

Title: Performance Improvement by Domain Specific Architectures: A Case Study in Graph Processing
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 ways to improve performance of computer systems in the post-Moore era is utilizing domain specific architectures. In this talk, we briefly introduce our recent research efforts on a domain specific architecture for graph processing. In this research, we focus on the edge-centric graph processing model and propose a dedicated cache architecture for exploiting data locality. We have evaluated our cache architecture by a light weight cache simulation and the results showed that it can reduce the number of LLC cache misses by up to 89.9%.

The 187th R-CCS Cafe -partⅠ
Date and Time: Mon. Dec. 16, 2019, 15:30 - 16:10
Place: Lecture Hall (6th floor) at R-CCS

Title: Scalable fixed-mesh method for simulations of multi-material vehicle structures
Speaker: Koji Nishiguchi (Complex Phenomena Unified Simulation Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

In recent years, in the automotive industry, weight reductions are indispensable for complying with carbon dioxide emission regulations. Although automotive companies have been mainly using steel sheets, they want to employ multi-material structures including extrusions, castings, or 3D printings of aluminum alloy or resin to achieve weight reductions. However, the structural design will be more complex because multi-material structures have a higher degree of geometric freedom than sheet metal structures. Therefore, numerical simulations need to play a more critical role in designing optimal vehicle structures.
For the last several decades, a Lagrangian finite element method (FEM) using mainly shell formulation has been the de facto standard in the automotive industry. However, shell formulation cannot numerically model the multi-material structures mentioned above because they do not have a constant thickness. Thus, the continuum formulation has to be applied, but this approach poses two computational problems.
The first problem is that an enormous number of finite elements using continuum formulation is required to discretize the multi-material structures spatially. A scalable method in a massively parallel environment is indispensable for this simulation. Secondly, we need to spend more than a month to generate the finite element mesh of a car body. Therefore, it is challenging to investigate many patterns of vehicle structures.
Considering the background as mentioned above, we focus on a Eulerian finite volume method (FVM) [1] based on continuum formulation [2] using a scalable hierarchical Cartesian mesh method [1]. This Eulerian FVM [1] has the following three advantages. The first one is good scalability [1] in a massively parallel computing environment. Secondly, we can easily generate the computational mesh of a car body only within 10 minutes. We will demonstrate the stiffness analysis of a body-in-white structure, which is spatially discretized by approximately 200 million cells and was computed using 104,520 cores on the K computer. Thirdly, the proposed Eulerian method is easy to couple a conventional finite volume fluid solver.
In future work, we plan to conduct car crash simulations using many patterns of multi-material vehicle structures to study ultralight vehicle structures.
[1] K. Nishiguchi 2019 https://doi.org/10.1002/nme.5954 [2] K. Nishiguchi 2018 https://doi.org/10.1002/nme.5790

The 187th R-CCS Cafe -partⅡ
Date and Time: Mon. Dec. 16, 2019, 16:10 - 16:50
Place: Lecture Hall (6th floor) at R-CCS

Title: System Software for Emerging Hardware Technologies in Computing Systems
Speaker: Atsushi Koshiba (Processor Research Team)

Presentation Language: English
Presentation Material: English

Abstract:Detail

In this talk, I will introduce some of my previous work including my Ph.D. thesis, new OS features and middleware to make use of emerging hardware technologies. Emerging hardware devices/features (e.g., FPGA/ASICs, non-volatile memories, Intel SGX) have been widely studied due to strong demands on performance improvement, energy efficiency, and data protection of computer systems. However, due to a lack of system software support, existing computer systems cannot fully utilize these new devices. I have proposed new operating system functions and middleware, which are useful to improve the performance/usability of the devices or analyze an application behavior with them.

The 186th R-CCS Cafe
Date and Time: Tue. Dec. 10, 2019, 10:00 - 11:00
Place: Seminar Room (1st floor) at R-CCS

Title: Next generation optics/photonics broadens system architecture aperture
Speaker: Dube, Nicolas (Dr. / Chief Strategist for High-Performance Computing at Hewlett Packard Enterprise)

Presentation Language: English
Presentation Material: English

Abstract:Detail

This presentation will introduce new optical devices that enable HPC and AI system architectures to free up from cost-prohibitive active optical cables and scale-limiting copper cables. Developed by parallel teams at HPE, VCSEL based and silicon photonics ring resonator technologies both enable passive optics at scale, and can integrate as mid-board, co-packaged or even 3D-stacked optical devices. These technologies set the course for much more capable interconnects, thanks to a significantly reduced cost structure and an energy profile tracking to sub 10 pJ/bit. Application at the system level will then be outlined, including the enablement of the Hyper-X and other multi-dimensional all to all topologies thanks to new components like fiber-shuffles.

The 185th R-CCS Cafe -partⅠ
Date and Time: Mon. Dec. 2, 2019, 13:00 - 13:40
Place: Lecture Hall (6th floor) at R-CCS

Title: Parallel Multigrid Methods on Manycore Clusters with IHK/McKernel
Speaker: Kengo Nakajima (Deputy Director, RIKEN Center for Computational Science)
*Online seminar on BlueJeans

Presentation Language: English
Presentation Material: English

Abstract:Detail

The parallel multigrid method is expected to play an important role in large-scale scientific computing on exa-scale supercomputer systems. Previously we proposed Hierarchical Coarse Grid Aggregation (hCGA), which dramatically improved the performance of the parallel multigrid solver when the number of MPI processes was O(10^4) or more. Because hCGA can handle only two layers of parallel hierarchical levels, the computation overhead due to coarse grid solver may become significant when the number of MPI processes reaches O(10^5)- O(10^6) or more. In the present work, we propose AM-hCGA (Adaptive Multilevel hCGA) that can take into account multiple layers of three or more levels, and show preliminary results using the Oakforest-PACS (OFP) system by JCAHPC. Additionally, we also examine the impact of a lightweight multi-kernel operating system, called IHK/McKernel, for parallel multigrid solvers running on OFP.

This is a joint work with Balazs Gerofi (RIKEN R-CCS), Yutaka Ishikawa (RIKEN R-CCS), and Masashi Horikoshi (Intel).

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.