Booth Talk Schedule | [GSIC] Tokyo Institute of Technology | Global Scientific Information and Computing Center

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Booth Talk Schedule

Booth Talk Schedule

Tuesday, November 18th

10:30–11:00	GPU-acceleration of Biosupercomputing: Protein-Protein Interaction and Metagenome Analysis
	Takashi Ishida - Graduate School of Information Science and Engineering, Tokyo Institute of Technology

15:30–16:00	Review of Large-scale GPU Applications on TSUBAME2.5
	Takayuki Aoki - GSIC, Tokyo Institute of Technology

16:30–17:00	Porting Towards Graph Computing with Extreme-scale Infrastructures
	Hitoshi Sato - GSIC, Tokyo Institute of Technology

Wednesday, November 19th

11:00–11:30	Towards TSUBAME3.0 and Beyond to 4.0
	Satoshi Matsuoka - GSIC, Tokyo Institute of Technology

11:45–12:15	Piz Daint and Piz Dora: A Productive, Heterogeneous Supercomputing Infrastructure for Science
	Thomas C. Schulthess - Swiss National Supercomputing Center (CSCS)

14:00–14:30	Design and Implementation of High Density JETSON TK1 Cluster
	Shin'ichi Miura - GSIC, Tokyo Institute of Technology

Thursday, November 20th (Schedule is updated at 12:40 11/20)

14:15–14:45	TSUBAME-KFC: an Ultra Green Supercomputer with Liquid Submersion Cooling
	Akira Nukada & Toshio Endo - GSIC, Tokyo Institute of Technology

Talk Abstracts and Speaker Biographies

Title	GPU-acceleration of biosupercomputing: Protein-Protein Interaction and Metagenome Analysis
Abstract	Currently, the size of biological data has been rapidly increased because of the improvement of technology, such as DNA sequencers and so on. Therefore, for analyzing such huge amounts of data, the acceleration of bioinformatics software is highly demanded. In this talk, we introduce our two bioinformatics applications accelerated by using general purpose GPU computing techniques and large-scale distributed parallel processing. First application is protein-protein interaction prediction based on docking calculation. We mapped our software MEGADOCK onto GPUs and implemented almost all processes including “FFT calculation", “modulation" and “ligand voxelization". We also implemented the system for utilizing all CPU cores and GPUs in a computation node. As results, MEGADOCK-GPU on 12 CPU cores and 3 GPUs achieved a calculation speed that was 37.0 times faster than MEGADOCK CPU version on 1 CPU core. Second application is sequence homology search. We developed a new efficient homology search algorithm suitable for GPU calculations. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated indexes and then calculates local alignments around the candidate positions before calculating alignment scores. We implemented both of these processes on GPUs. The system achieved calculation speeds that were 130 times faster than BLAST with 1 GPU.
Speaker	Takashi Ishida
Affiliation	Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology
Biography	Takashi Ishida is an Associate Professor in Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Japan. He received BA degree in environmental information from Keio University, Japan, and his MA and Ph.D degrees in agriculture from University of Tokyo, Japan. His research interests include bioinformatics, machine learning, and high-performance computing.

Title	Review of Large-scale GPU Applications on TSUBAME2.5
Abstract	The TSUBAME2.5 system is equipped with 4,224 GPUs and 5.7 PFLOPS of the peak performance. We show several large-scale stencil-based PDE and Lattice-Boltzmann applications well suited for GPU computing, including turbulent air flows over a 10 km x 10 km central part of metropolitan Tokyo with 1m resolution and a phase-field simulation for the dendritic solidification of a binary alloy with 0.3 trillion cells. We also demonstrate granular Discrete Element Method (DEM) and fluid Smoothed Particle Hydrodynamics (SPH) simulations based on short-range particle interactions, in which a dynamic load balance has to be introduced. For most of the applications, the performance scalabilities based on the "roofline model" are shown.
Speaker	Takayuki Aoki
Affiliation	GSIC, Tokyo Institute of Technology
Biography	Takayuki Aoki received a BS in Applied Physics (1983), an MSc in Energy Science and Dr. Sci. (1989) from Tokyo Institute of Technology, has been a professor in Tokyo Institute of Technology since 2001 and the deputy director of the Global Scientific Information and Computing Center since 2009. He received the Minister Award of the Ministry of Education, Culture, Sports, Science & Technology, the Computational Mechanics Achievement Award from Japan Society of Mechanical Engineers, the Achievement Award of the Japan Society for Industrial and Applied Mathematics and many awards and honors in GPU computing, scientific visualization, and others. His team got the Gordon Bell Prize in 2011. He was also recognized as a CUDA fellow by NVIDIA in 2012.

Title	Towards Graph Computing with Extreme-scale Infrastructures
Abstract	Recent emergence of extremely large-scale graphs in various application fields, such as health care, system biology, social networks, business intelligence, and electric power grid, etc., requires fast and scalable analysis. Rapidly increasing numbers of these large-scale graphs and their applications cause significant attractions to the existing HPC communities. For instance, the Graph500 list has been established for benchmarking supercomputers by executing large-scale graph problems as an instance of data-intensive supercomputing applications. This talk will give an overview of various projects and efforts on large-scale graph processing using commodity-based modern HPC techniques, such as GPU accelerators and Flash-based NVM devices, on TSUBAME2 towards graph computing with extreme-scale infrastructures.
Speaker	Hitoshi Sato
Affiliation	GSIC, Tokyo Institute of Technology
Biography	Hitoshi Sato is a project assistant professor at the Global Scientific Information and Computing Center (GSIC) of Tokyo Institute of Technology. He joined GSIC in 2009 and has been involved with several HPC projects including a series of TSUBAME supercomputers especially in storage systems. His research interests include high-performance data-intensive computing for future extreme-scale supercomputers and cloud datacenters. He is currently working for many big data projects such as JST Graph CREST project and Extreme Big Data (EBD) CREST project.

Title	Towards TSUBAME3.0 and Beyond to 4.0
Abstract	Rapid growth in the use cases and demands for extreme computing and huge data processing is eading to convergence of the two infrastructures. Tokyo Tech.’s TSUBAME3.0, a 2016 successor to the highly successful TSUBAME2/2.5, will aim to deploy a series of innovative technologies, including ultra-efficient liquid cooling and power control, petabytes of non-volatile memory, as well as low cost Petabit-class interconnect. To address the challenges of such technology adoption, proper system architecture, software stack, and algorithm must be desgined and developed; these are being addressed by several of our ongoing research projects as well as prototypes, such as the TSUBAME-KFC prototype which became #1 in the world in power efficiency on the Green500 twice in a row, the Billion-way Resiliency project that is investigating effective methods for future resilient supercomputers, as well as the Extreme Big Data (EBD) project which is looking at co-design development of convergent system stack given future data and computing workloads.
Speaker	Satoshi Matsuoka
Affiliation	GSIC, Tokyo Institute of Technology
Biography	Satoshi Matsuoka has been a Full Professor at the Global Scientific Information and Computing Center (GSIC), a Japanese national supercomputing center hosted by the Tokyo Institute of Technology, since 2001. He received his Ph. D. from the University of Tokyo in 1993. He is the leader of the TSUBAME series of supercomputers, including TSUBAME2.0 which was the first supercomputer in Japan to exceed Petaflop performance and became the 4th fastest in the world on the Top500 in Nov. 2010, as well as the recent TSUBAME-KFC becoming #1 in the world for power efficiency for both the Green 500 and Green Graph 500 lists in Nov. 2013. He is also currently leading several major supercomputing research projects, such as the MEXT Green Supercomputing, JSPS Billion-Scale Supercomputer Resilience, as well as the JST-CREST Extreme Big Data. He has written over 500 articles according to Google Scholar, and chaired numerous ACM/IEEE conferences, most recently the overall Technical Program Chair at the ACM/IEEE Supercomputing Conference (SC13) in 2013. He is a fellow of the ACM and European ISC, and has won many awards, including the JSPS Prize from the Japan Society for Promotion of Science in 2006, awarded by his Highness Prince Akishino, the ACM Gordon Bell Prize in 2011, the Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology in 2012, and recently the 2014 IEEE-CS Sidney Fernbach Memorial Award, the highest prestige in the field of HPC.

Title	Piz Daint and Piz Dora: A Productive, Heterogeneous Supercomputing Infrastructure for Science
Abstract	The Cray XC30 system at CSCS, which includes "Piz Daint", the most energy efficient peta-scale supercomputer in operation today, has been extended with additional multi-core CPU cabinets (aka "Piz Dora"). In this heterogeneous system we unify a variety for high-end computing services - extreme scale compute, data analytics, pre- and post processing, as well as visualization - that are all important parts for the scientific workflow. Besides reviewing the successes for "Piz Daint" I will discuss how integration of multiple services into one platform shows promise to enhance productivity of our users.
Speaker	Thomas C. Schulthess
Affiliation	Swiss National Supercomputing Centre (CSCS)
Biography	Thomas Schulthess received his PhD in physics from ETH Zurich in 1994. He is a professor for computational physics at ETH Zurich and Director of the Swiss National Supercomputing Center in Lugano, Switzerland. Thomas holds a visiting distinguished professor appointment at ORNL, where he was group leader and researcher in computational materials science before moving to ETH Zurich in 2008. His current research interests are in development of efficient and scalable algorithms for the study of strongly correlated quantum systems, as well as electronic structure methods in general. He is also engaged in the development of efficient tools and simulations systems for other domain areas, such as meteorology/climate and geophysics.

Title	Design and Implementation of High Density JETSON Cluster
Abstract	In recent years, a mobile processor used in smartphones have a big performance enhancement. In particular, "NVIDIA TEGRA K1" mobile processor is an attractive processor for future HPC systems. We constructed a TEGRA K1 based high density cluster, named "TSUBAME-GB". TSUBAM-GB is also used oil cooling technology for power saving. In this talk, we introduce design and implementation of TSUBAME-GB. We also demonstrate the TSUBAME-GB systems in our booth.
Speaker	Shinichi Miura
Affiliation	GSIC, Tokyo Institute of Technology
Biography	Shin'ichi MIURA is an assistant professor at the Global Scientific Information and Computing Center of Tokyo Institute of Technology. His research interests include interconnect and wide area network for HPC. He received a Ph.D. in engineering from University of Tsukuba (2008).

Title	TSUBAME-KFC: an Ultra Green Supercomputer with Liquid Submersion Cooling
Abstract	The TSUBAME-KFC supercomputer testbed is designed to achieve high power efficiency both in compute nodes and cooling system. Each 1U compute node equips two CPUs and four Kepler GPUs, and the 40+ high heat density nodes are cooled by liquied submersion cooling technology. The system was installed in 2013, and became No.1 in Green500 List twice (Nov. 2013 and Jun. 2014). In this talk, we will report details of the system, measurement, and latest results.
Speaker	Akira Nukada & Toshio Endo
Affiliation	GSIC, Tokyo Institute of Technology
Biography	Akira Nukada: Associate Professor at Global Scientific Information and Computing Center, Tokyo Institute of Technology. His research interest includes high performance computing, especially using many-core accelerators. Toshio Endo: Toshio Endo is an associate professor at the Global Scientific Information and Computing Center (GSIC) of Tokyo Institute of Technology. He is also a leader of JST (Japan Science and Technology Agency) CREST project, "Software Technology that Deals with Deeper Memory Hierarchy in Post-petascale Era" (2012-2017). His research interests include high performance and low power computing. He has a Ph.D. in science from the University of Tokyo (2001).