National Cheng Kung University, Taiwan: Three Lectures mini-series
31 Mar 2014 - 01 Apr 2014

The Supercomputing Research Center at National Cheng Kung University (NCKU-SRC) Taiwan aims to boost the research energy by collaborating with domestic and foreign high performance computing institutes. The vision of SRC is to facilitate the research institutes in Taiwan, including the fields of hazard and disaster mitigation, renewable energy innovation, biomedical, photo-electronics technology and so forth, to achieve world-class research excellence. The SRC also plan to provide learning and training opportunities for the domestic professionals in supercomputer hardware and software development. NCKU-SRC had developed world’s first switchless cluster supercomputer at Nov. 2014, in the long run, NCKU-SRC expects to play a role as a mediator in the collaboration among the domestic high-tech firms and the oversea HPC teams to design and develop the next-generation supercomputers. Finally, NCKU-SRC currently pays special attention to HPC applications on genetic/genomic medicine and other related issues in computer aided drug design. 

Title Date Time
Lecture 1 Market Trend, Market of Supercomputer Based Gene Sequencing & Genetic Testing 31 March 2014, Monday 2.00 pm
Lecture 2 Liberal Communications, Democracy Topologies, Fraternity Software Engineering: Approach to the Exascale Supercomputer 1 April 2014, Tuesday 10.00 am
Lecture 3 Core Technologies of Genetic Testing & Disease Diagnostic Services 1 April 2014, Tuesday 2.00 pm

Venue
: Level 17, Charles Babbage Room, 1 Fusionopolis Way,Connexis South, Singapore 138632
Speaker: Prof Huang Chi Chuan, Frank Yeh, Dr Chen Yu Tin, Dr Liang Chi Hsiu

ABSTRACT
Lecture 1: Market Trend, Market of Supercomputer Based Gene Sequencing & Genetic Testing
Based on NCKU SRC new invention of HPC, we have some evaluation about the potential marketing value and the influence. With the new invention, we have implemented it on some specific application of Gene sequencing. We find the advantages of supercomputing implementing on gene sequencing, will also bring some change in the market of gene testing. More than gene sequencing, the NCKU SRC invention of HPC will bring the end users more efficiency in computing and energy which make the application more effective as well. 

Lecture 2: Liberal Communications, Democracy Topologies, Fraternity Software Engineering: Approach to the Exascale Supercomputer
Switchless cluster, CK-STAR, are established in NCKU, which has been the only so far in world. Performance data of the "CK-STAR" proves the achievement. Eight 2 way-server reached 98.41%, MPI applications like LAMMPS (molecular dynamics), WRF (Weather Research and Forecasting) and ABySS (de novo assembler) were well perform at this architecture. Furthermore, the system adopt eight pieces of Xeon Phi, It reached, 80.2% and 77.5% of the four nodes and eight nodes. Switchless resolve bottleneck while numbers of nodes were getting too much. The CK-STAR, solves such dilemma and enlarges the model of cluster computers. 

Democracy topologies established achievement in competitive average hop distances. Construct with 10 interconnections from each node, and 1024 nodes has short average hop distance as 3.63, which break IBM 5D torus' achievement. Furthermore, with 16 and 8 interconnections from each node, large supercomputer has 100 K nodes reach average hop distance as 5.365 and 8.665, respectively. 

Fraternity software engineering are challenging tasks, it is necessary for using accelerators in HPC. Practical course for Intel coprocessors, and parallel software engineering task were in progressing in SRC, NCKU. We purpose software engineering workflow for porting application to accelerator. 

In conclusion, this is a prototype design, in which, Smart-post office protocol (liberal communication), quasi-optimal interconnection network (Democracy topology), parallel software application porting in heterogeneous environment (fraternity software engineering) are three practice methods approach to resolve exascale challenge. 

Lecture 3: Core Technologies of Genetic Testing & Disease Diagnostic Services
This presentation covers recent developments in genetic risk assessment core technologies and our proposal of utilising qualitative information in nucleotide polymorphism. Fairly introductory information about gene assessment and disease diagnostic will be given in this talk together with our strategies. The data collected and analysed with our developing expert system eventually will be used to uncover the missing links in the current healthcare services. In all, the genetic assessment as a tool can be used to improve the rational drug and early treatment suggestions after disease prognosis; furthermore, it can also be considered as a part of the routine tasks to increase the facets in healthcare services.

Biography
Prof. Huang Chi Chuan
Prof Huang Chi-Chuan is Chair professor of Department of Engineering Science, NCKU. He was also previous Dean of Academic Affairs of NCKU. Prof Hwang is specialised in non-linear chaotic theory, microscopic mechanics, semiconductor engineering, quantum information, quantum system control theory, bioinformatics, and neurosciences.

Frank Yeh
Frank Yeh was working for Cray Inc. in the past 4 years. At Cray, he was in charge of the business development crossing Taiwan, Hong Kong and Philippines. He is currently recruited as the Chief Consultant of Supercomputing Research Center, NCKU. At same time, Frank is also the representative of a pre-opening office of "Taiji Gene and Life Company". This start-up company will work very closely with NCKU SRC to get technical support in gene and disease analysis. Before Cray, Frank also worked with different responsibility as the role of management and senior sales marketing for other MNC, including EMC, SGI, McAfee and HP. 

Dr Chen Yu Tin
Dr. Chen Yu-Tin received his PhD in Computer Science from National Tsing Hua University, Hsin-Chu in 2012. He is currently a post-doctoral fellow of Supercomputing Research Center, NCKU (2013-Now), Tainan, his research fields are in comparative genomics and evolution biology, and he was a postdoctoral follow of Life Science, NCKU (2012-2013). Four years of professional career in bioinformatics and pharmacogenomics (2000-2004), and was a research assistant, a research associate at National Yang Ming University, Vita Genomics, Inc., respectively. 

Dr Liang Chi Hsiu
Dr Liang Chi-Hsiu is specialized in biology and physical sciences. He received his PhD in University of Manchester, UK. In his first position he contributed to MESMER, an object-oriented code describing statistical aspects of gas phase chemitry. He is now working on genetic risk assessment of diseases and several other projects related to high-performance computing.

No of Participants: 15, 16, 11

<Back