Welcome to the Celsius Linné e Science Day February 15, 2013
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1 Welcome to the Celsius Linné e Science Day February 15, 2013 Science at the Edge of Computing A multi disciplinary symposium on new avenues for high performance computing and data handling in research Professor Ingela Nyström Head of Centre for Image Analysis Coordinator of essence Dept. of Information Technology Uppsala University Ingela.Nystrom@it.uu.se
2 Agenda Friday February 15, William Dally: Impact of computer architecture on bioinformatics Coffee break Gene Myers: Big problems in computational biology David van der Spoel: Prediction of viral genome structure using HPC Jan Komorovski: Discovering weak associations with rule networks Lunch Erland Källén: Supercomputer use for weather prediction and climate Dan Henningson: Numerical experiments of turbulent flows on super Anders Bergman: Simulation of magnetization dynamics in materials Coffee break Anders Lansner: Supercomputer simulations of detailed and abstract Sverker Holmgren: Scientific computing and the Swedish computing Concluding discussion
3 Where is Uppsala University? Everywhere!
4 Uppsala University founded in 1477 Oldest University in the Nordic countries Traditions of culture and research Nine faculties 6,000 staff 40,000 students Eight Nobel Prizes Professor Anders Celsius Professor Carl Linnaeus
5 Strategic Research Area: e Science e Science is one of 20 strategic research areas funded by the Swedish government during KTH LiU SU KI, 30 MSEK/year UU Umeå Lund, 26 MSEK/year Infrastructure funded separately by SNIC HPC centra PDC and NSC part of SeRC UPPMAX, HPC2N, and Lunarc part of essence C3SE part of CheSC
6 e Science has emerged as the third pillar underlying research, complementing theory and experiments builds on developing, implementing and using computerbased tools in research where traditional experimental and theoretical approaches are not sufficient provides new opportunities for collaboration in academia and industry, within the same and different disciplines, and over short and long geographical distances is connected to the development of computational tools and methods, as well as to the readiness of application areas to novel paradigms and to meet challenges from new directions
7 Components Illustration: Gustaf Kylberg
8 Enabling Science:
9 Vision Provide excellence and scientific solutions at all stages of the e Science process e Science for disciplinary progress in distributed research collaborations Multi disciplinary collaboration for progress in methods and tools for e Science applications Advancing science through leading computation, information and communication technologies Ingela.Nystrom@it.uu.se
10 Swedish e Science builds on Swedish e Infrastructure Swedish National Infrastructure for Computing (SNIC), Swedish University Computer Network (SUNET), SNIC and SUNET are bodies of the Swedish Research Council (Vetenskapsrådet, VR),
11 Research Areas & Programs with collaboration between Universities Materials Science Materials physics Chemistry of complex materials Nano materials Human Function and Environment Linguistics and visual information Pattern recognition in the living brain Economic demography Ecosystems and climate change Life Science Computational biology Bioinformatics Generic e Science Methods and Tools Distributed computing services and grid Computational algorithms, implementation also for GPU:s High performance parallel computing Database technology
12 Programme Council 3 university, 1 external representatives Management Group Programme Coordinator 6 university representatives Local Reference Groups PI:s and other stakeholders Focus Area Materials Science Research groups Focus Area Human Function and Environment Research groups Focus Area Generic e Science Methods and Tools Research groups Focus Area Life Science Research groups Additional e Science Initiatives Research groups
13 Current Status A set of focus areas was selected for funding of essence programs with recruitments Several PostDoc projects launched after application rounds A group of application experts supports researchers in usage of HPC Workshops Seminars Host of 35 th CERN School of Computing
14 Materials Science: Chemistry of complex materials PI: Professor Kersti Hermansson, Dept. of Chemistry Ångström Laboratory, Uppsala University Our vision: is to develop efficient multi scale and hybrid methods that will enable large scale and accurate simulations to help solve important chemical problems. One project: Heterogeneous catalysis (i.e., the surfaces of some materials speed up chemical reactions) This is extremely important industrially. We want to know: How does it happen? and Can we improve the functionality of the catalyst? Our approach: Multiscale modelling Real world Our developments * New hierarchical models (communication between layers) * New force fields methods * Dynamics simulations * New method to improve convergence of closely degenerate electronic states * UU & UmU collaboration on new Grid/Cloud middleware from UmU
15 Human Function and Environment Project examples Information service for historical demographic information and geographic information PIs: Prof. Tommy Bengtsson Centre for Economic Demography and Dept. of Economic History Assoc. Prof. Lars Harrie Dept. of Physical Geography and Ecosystem Sciences Lund University Aims Develop methods for storing and visualizing (e.g. in animations) geographic information with different time representations. This tool is crucial to a wide range of applications within social science and medicine in particular. A specific aim is to develop methods for making historic demographic information more accessible and easier to analyse (e.g. visually).
16 e Science methods for distributed pharmacology predictions Aims Life Science Project examples PIs:Ola Spjuth and Jarl Wikberg Dept. of Pharmaceutical Biosciences Uppsala University Develop methods for modeling pharmaceutical problems with Big Data and high computational demands and for distributed data and predictive modeling in computational toxicology. Allow researchers to take advantage of the offerings of escience by adapting the Bioclipse workbench ( to deliver e Science technologies to scientists with low computational expertise. The project is propelled by industrial use cases and will be carried out in close collaboration with AstraZeneca R&D.
17 Cloud and Grid Computing Generic e Science Methods & Tools Project examples PI: Prof. Erik Elmroth Dept. of Computing Science Umeå University Aims Develop algorithms and software for a range of grid and cloud resource management problems, including: a system for decentralized fairsharescheduling a system for autonomous job management in virtual computing environments scheduling of virtual machines within and between clouds cloud elasticity integration of job management tools with bioinformatics applications
18 Ingela s messages e Science will become the Science I challenge you to bring new research problems into e Science I encourage you to bring out the research problems that you put away in the drawer years ago. They may be solvable now!
19 Agenda Friday February 15, William Dally: Impact of computer architecture on bioinformatics Coffee break Gene Myers: Big problems in computational biology David van der Spoel: Prediction of viral genome structure using HPC Jan Komorovski: Discovering weak associations with rule networks Lunch Erland Källén: Supercomputer use for weather prediction and climate Dan Henningson: Numerical experiments of turbulent flows on super Anders Bergman: Simulation of magnetization dynamics in materials Coffee break Anders Lansner: Supercomputer simulations of detailed and abstract Sverker Holmgren: Scientific computing and the Swedish computing Concluding discussion
20 Welcome to the Celsius Linné e Science Day February 15, 2013 Science at the Edge of Computing A multi disciplinary symposium on new avenues for high performance computing and data handling in research Professor Ingela Nyström Head of Centre for Image Analysis Coordinator of essence Dept. of Information Technology Ingela.Nystrom@it.uu.se
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