WG – Alba Cristina Magalhaes Alves de Melo: Parallel Sequence Alignment of Whole Chromosomes with Hundreds of GPUs and Pruning


Title: Parallel Sequence Alignment of Whole Chromosomes with Hundreds of
GPUs and Pruning

Speaker: Alba Cristina Magalhaes Alves de Melo

Abstract: Biological Sequence Alignment is a very basic operation in Bioinformatics used routinely worldwide. Smith-Waterman is the exact algorithm used to compare two sequences, obtaining the optimal alignment in quadratic time and space. In order to accelerate Smith-Waterman, many GPU-based strategies were proposed in the literature. However, aligning DNA sequences of millions of characters, or Base Pairs (MBP), is still a very challenging task. In this talk, we discuss related work in the area of parallel biological sequence alignment and present our multi-GPU strategy to align DNA sequences with up to 249 millions of characters in 384 GPUs. In order to achieve this, we propose an innovative speculation technique, which is able to parallelize a phase of the Smith-Waterman algorithm that is inherently sequential. We combined our speculation technique with sophisticated buffer management and fine-grain linear space matrix processing strategies to obtain our parallel algorithm. As far as we know, this is the first implementation of Smith-Waterman able to retrieve the optimal alignment between sequences with more than 50
millions of characters. We will also present a pruning technique for one GPU that is able to prune more than 50% of the Smith-Waterman matrix and still retrieve the optimal alignment. We will show the results obtained in the Keeneland cluster (USA), where we compared all the human x chimpanzee homologous chromosomes (ranging from 26 MBP to 249 MBP). The human_chimpanzee chromosome 5 comparison (180 MBP x 183 MBP) attained 10.35 TCUPS (Trillions of Cells Updated per Second) using 384 GPUs. In this case, we processed 45 petacells, being able to produce the optimal alignment in 53 minutes and 7 seconds, with a speculation hit ratio of 98.2%.

Speaker Bio:  Alba Cristina Magalhaes Alves de Melo obtained her PhD degree in Computer Science from the Institut National Polytechnique de Grenoble (INPG), France, in 1996. In 2008, she did a postdoc at the University of Ottawa, Canada; in 2011, she was invited as Guest Scientist at Université Paris-Sud, France; and in 2013 she did a sabbatical at the Universitat Polytecnica de Catalunya, Spain. Since 1997, she works at the Department of Computer Science at the University of Brasilia (UnB), Brazil, where she is now a Full Professor. She is also a CNPq Research Fellow level 1D in Brazil. She was the Coordinator of the Graduate Program in Informatics at UnB for several years (2000-2002, 2004-2006, 2008, 2010, 2014) and she coordinated international collaboration projects with the Universitat Politecnica de Catalunya, Spain (2012, 2014-2016) and with the University of Ottawa, Canada (2012-2015). In 2016, she received the Brazilian Capes Award on “Advisor of the Best PhD Thesis in Computer Science”. Her research interests are High Performance Computing, Bioinformatics and Cloud Computing. She advised 2 postdocs, 4 PhD Thesis and 22 MsC Dissertations. Currently, she advises 4 PhD students and 2 MsC students. She is Senior Member of the IEEE Society and Member of the Brazilian Computer Society. She gave invited talks at Universitat Karlshure, Germany, Université Paris-Sud, France, Universitat Polytecnica de Catalunya, Spain, University of Ottawa, Canada and at Universidad del Chile, Chile. She has currently 91 papers
listed at  DBLP (www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Melo:Alba_Cristina_Magalhaes_Alves_de.html).

WG – Prof. Rajkumar Buyya: New Frontiers in Cloud Computing for Big Data and Internet-of-Things (IoT) Applications


Title: New Frontiers in Cloud Computing for Big Data and Internet-of-Things (IoT) Applications

Speaker: Prof. Rajkumar Buyya
Director, Cloud Computing and Distributed Systems (CLOUDS) Lab,
The University of Melbourne, Australia

CEO, Manjrasoft Pvt Ltd, Melbourne, Australia

Abstract: Computing is being transformed to a model consisting of services that are commoditised and delivered in a manner similar to utilities such as water, electricity, gas, and telephony. Several computing paradigms have promised to deliver this utility computing vision. Cloud computing has emerged as one of the buzzwords in the IT industry and turned the vision of “computing utilities” into a reality.  Clouds deliver infrastructure, platform, and software (application) as services, which are made available as subscription-based services in a pay-as-you-go model to consumers. Cloud application platforms need to offer (1) APIs and tools for rapid creation of elastic applications and (2) a runtime system for deployment of applications on geographically distributed computing infrastructure in a seamless manner.
The Internet of Things (IoT) paradigm enables seamless integration of cyber-and-physical worlds and opening up opportunities for creating a new class of applications for domains such as smart cities. The emerging Fog computing is extending Cloud computing paradigm to edge resources for latency-sensitive IoT applications.
This keynote presentation will cover (a) 21st century vision of computing and identifies various IT paradigms promising to deliver the vision of computing utilities; (b) opportunities and challenges for utility and market-oriented Cloud computing, (c) innovative architecture for creating market-oriented and elastic Clouds by harnessing virtualisation technologies; (d) Aneka, a Cloud Application Platform, for rapid development of Cloud/Big Data applications and their deployment on private/public Clouds with resource provisioning driven by SLAs; (e) experimental results on deploying Cloud and Big Data/Internet-of-Things (IoT) applications in engineering, and health care, satellite image processing, and smart cities on elastic Clouds;and (f) directions for delivering our 21st century vision along with pathways for future research in Cloud and Fog computing.

Speaker Bio:  Dr. Rajkumar Buyya is a Redmond Barry Distinguished Professor and Director of the Cloud Computing and Distributed Systems (CLOUDS) Laboratory at the University of Melbourne, Australia. He is also serving as the founding CEO of Manjrasoft, a spin-off company of the University, commercializing its innovations in Cloud Computing. He served as a Future Fellow of the Australian Research Council during 2012-2016. He has authored over 625 publications and seven textbooks including “Mastering Cloud Computing” published by McGraw Hill, China Machine Press, and Morgan Kaufmann for Indian, Chinese and international markets respectively. He also edited several books including “Cloud Computing: Principles and Paradigms” (Wiley Press, USA, Feb 2011). He is one of the highly cited authors in computer science and software engineering worldwide (h-index=114, g-index=245, 67,600+ citations).  Dr. Buyya is recognized as a “Web of Science Highly Cited Researcher” in 2016 and 2017 by Thomson Reuters, a Fellow of IEEE, and Scopus Researcher of the Year 2017 with Excellence in Innovative Research Award by Elsevier for his outstanding contributions to Cloud computing.
Software technologies for Grid and Cloud computing developed under Dr. Buyya’s leadership have gained rapid acceptance and are in use at several academic institutions and commercial enterprises in 40 countries around the world. Dr.  Buyya has led the establishment and development of key community activities, including serving as foundation Chair of the IEEE Technical Committee on Scalable Computing and five IEEE/ACM conferences. These contributions and international research leadership of Dr. Buyya are recognized through the award of “2009 IEEE Medal for Excellence in Scalable Computing” from the IEEE Computer Society TCSC.
Manjrasoft’s Aneka Cloud technology developed under his leadership has received “2010 Frost & Sullivan New Product Innovation Award”. Recently, Dr. Buyya received “Mahatma Gandhi Award” along with Gold Medals for his outstanding and extraordinary achievements in Information Technology field and services rendered to promote greater friendship and India-International cooperation. He served as the founding Editor-in-Chief of the IEEE Transactions on Cloud Computing. He is currently serving as Co-Editor-in-Chief of Journal of Software: Practice and Experience, which was established over 45 years ago. For further information on Dr.Buyya, please visit his cyber home: www.buyya.com