Profile

Kento Aoyama (M.Sc.) is a Ph.D. Student at Department of Computer Science, School of Computing, Tokyo Institute of Technology. Research interests include High Performance Computing, Parallel/Distributed/Cloud Computing, Container Virtualization, and Bioinformatics.

Work Experience and Education

Ph.D. student

Tokyo Institute of Technology
2016 - Present

Research & development of Linux containers for High-Performance Computing applications, and implementation of the parallel/distributed system for bioinformatics software on clouds and supercomputers. (e.g. TSUBAME, ABCI, MS Azure)

Achievements:

The research results were presented at academic conferences and tech-reports.

  • The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC19).
  • The 25th International Conference on Parallel and Distributed Processing Techniques and Application (PDPTA'19).
  • High Performance Computing Symposium 2017 (HPCS 2017).
  • Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL) Annual Meeting 2019.
  • IPSJ SIG Technical Report (SIGBIO49, 54).

Technology keywords:

  • Linux containers
  • Docker
  • Singularity
  • Shifter/Sarus
  • OCI container
  • OCI image
  • OCI registry
  • MPI/OpenMP
  • CUDA
  • Cloud Computing
  • Supercomputers
  • Bioinformatics
  • HPC Engineering

Research Internship

Swiss National Supercomputing Centre (CSCS), ETH Zurich
2017.9 - 2017.12

Research collaboration with HPC System Integration Group at CSCS. Designing and developing the software architecture of "Shifter", an open source Linux container for HPC environments. The internal designs were inherited to new container "Sarus".

Achievements:

The research results are used in the production environment of HPC system in CSCS.

  • HPC System at Swiss National Supercomputing Centre.
  • HPC-AI Advisory Council 2018, 2019.

Technology keywords:

  • Python
  • C/C++
  • Docker
  • Shifter/Sarus
  • OCI image
  • OCI registry

Fujitsu Ltd.

Software Developper
2015 - 2016

R&D for a cloud-integrated application platform service. Development of an Android version of the mobile platform which manages multi-media contents and web-based applications interacting with BaaS (Backend-as-a-Service).

Technology keywords:

  • Java
  • C/C++
  • Android
  • CI/CD
  • Agile Programming
  • DevOps Engineering

M.Sc in Computer Science

Tokyo Institute of Technology
2013 - 2015

Development of a Pipeline for Genome/Exome Analysis on the K computer. The pipeline can perform on over thousands of computing-nodes on the K computer and provides massively parallelized genome/exome sequencing analysis.

Achievements:

The research results were presented at academic journal and tech-report.

  • IPSJ Transactions on Advanced Computing System (ACS), 2016.
  • IPSJ SIG Technical Report (SIGBIO38).

Technology keywords:

  • C/C++
  • Python
  • Java
  • MPI/OpenMP
  • Job Scheduling
  • Pipeline Development
  • The K computer
  • Bioinformatics
  • HPC Engineering

B.Sc in Computer Science

The University of Electro-Communications
2011 - 2013

Publications

Peer-reviewed Journal Paper

  • Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, "Development of Exome Analysis Pipeline on the K Computer", IPSJ Transactions on Advanced Computing System(ACS), No.9, Vol.2, pp.15-33, 2016. [IPSJ]

Peer-reviewed Conference Paper

  • Kento Aoyama, Yuki Yamamoto, Ohue Masahito, Yutaka Akiyama, "Performance evaluation of MEGADOCK protein–protein interaction prediction system implemented with distributed containers on a cloud computing environment", The 25th International Conference on Parallel and Distributed Processing Techniques and Application (PDPTA'19), 175-181, Las Vegas, NV, USA, July 29, 2019.

Conference Paper (without peer-review)

  • Kento Aoyama, Masahito Ohue, Yutaka Akiyama, "Survey and Performance Comparison of Container Technologies in Bioinformatics Field, IPSJ SIG Technical Report, 2017-BIO-54(47), pp.1–7. 2018.
  • Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama, "Evaluation of Container Virtualized MEGADOCK System in Distributed Computing Environment", IPSJ SIG Technical Report, 2017-BIO-49(3), pp.1–8. 2017. [Slide]
  • Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, "Large-scale Parallelization of Exome Analysis Pipeline on K-computer", IPSJ SIG Technical Report, 2014-BIO-38(33), pp.1–7. 2014.
  • Kento Aoyama, Kyouhei Akai, Junichi Akita, Akira Tsukada, "Improvements of the GPU accelerated Simulation for Mach Bands Generation Mechanism in Human Visual System Model", IEEJ Hokuriku Branch, B-5, 2010.

Poster Presentation

  • Kento Aoyama, Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama, "Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application", The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC19), Nov. 2019. (accepted)
  • Kento Aoyama, Masahito Ohue, Yutaka Akiyama, "Comparison of the HPC Container Technologies for Bioinformatics Application", Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL) 1st Workshop, May. 2018.
  • Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama, "Large-Scale Parallelization of Cloud Native PPI-System using Container Virtualization", ACLS International Summer School 2017, Sep. 2017.
  • Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama, "High-Performance Protein-Protein Interaction Predictions on Distributed Containerized Environment", High Performance Computing Symposium 2017 (HPCS 2017), Jun. 2017.
  • Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, "Large-scale Parallelization of Exome Analysis Pipeline on K-computer", ACLS International Summer School 2014, Aug. 2014.

Presentation (without paper)

  • Kento Aoyama, Masahito Ohue, Yutaka Akiyama, "Container virtualizations for computational science on HPC environments, Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL) Annual Meeting 2019, Mar. 2019.

Graduation Thesis

  • Large-scale Parallelization of Exome Analysis Pipeline on K-computer
    Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, M.Sc.
  • Large-scale Parallelization of Matrix-matrix Product in Double-double Precision using Fox Algorithm on GPU Cluster
    Department of Computer Science, The University of Electro-Communications, B.Sc.
  • Improvements of the GPU accelerated Simulation for Mach Bands Generation Mechanism in Human Visual System Model
    National Institute of Technology, Toyama College, A.Sc.

Skills & Tools

HPC engineering

  • Linux containers for HPC
  • MPI/OpenMP
  • CUDA
  • Performance Optimization

DevOps, Backend engineering

  • Docker/Swarm
  • CI/CD
  • C/C++
  • Python

Others

  • Git
  • Java
  • R
  • MATLAB
  • Machine learning
  • Computing simulation
  • Linux system administration

Education

  • M.Sc. in Computer Science
    Tokyo Institute of Technology
    2013 - 2015
  • B.Sc. in Computer Science
    The University of Electro-Communications
    2011 - 2013
  • A.Sc. in Computer Science
    National Institute of Technology, Toyama College
    2006 - 2011

Awards

  • Runner-Up Award
    ACLS International Summer School 2017.
  • Outstanding Student Award
    IPSJ Hokuriku Branch, 2010.

Language

  • Japanese (Native)
  • English

Interests

  • High Performance Computing
  • Parallel/Distributed Computing
  • Bioinformatics
  • DevOps Engineering