Message from the Chair of the Board

Benchmarking SHARCNET clusters

Containing Bio-Threats

Executive Director's Message

Severely limited without SHARCNET

Swimming with SHARCS: New HPTC Consultant

A meeting of the minds: HP and SHARCNET foster innovation through Collaboration and Competency Network

Great discoveries and innovations most often come through the efforts of people working together. Theorists – in a variety of disciplines from astrophysics to earth sciences to genomics – need to be able to share their knowledge to advance their ideas. They also need to be able to see horizontally across boundary disciplines and build on the work of others.

Multi-disciplinary, inter-institutional and academic-industrial collaboration are the principles upon which SHARCNET was founded. Upon this foundation, SHARCNET has built a network of industrial relationships, including a significant strategic partnership with its primary vendor partner, HP.

“As a global leader within high-performance technical computing (HPTC) technologies, HP is pleased to include SHARCNET as one of its key Canadian partners,” confirms Greg Chappell, VP Business Critical Systems at HP Canada.

SHARCNET and HP leverage their strategic relationship in a variety of ways, including collaborative initiatives like pre-market product pilots, which are ultimately of benefit to a variety of academic and industrial applications.

Hewlett-Packard’s Collaboration and Competency Network (HP CCN) was conceived with this same ideal – advancement through collaboration. HP CCN is an open forum to facilitate communication and collaboration among members, partners and customers so they can more effectively adopt and apply high-performance technical computing (HPTC) technologies in their diverse research and development initiatives.

Members of HP CCN include more than 30 prestigious institutions around the world, including SHARCNET, CERN, the National Centre for Supercomputing Applications, the Bioinformatics Institute of Singapore and the High Performance Computing Centre in Stuttgart.

HP CCN is currently focused on five major initiatives: Scientific Visualization, Computational & Data Grids, Linux SMP Scaling, Global File System for Linux and Linux on Itanium.

Under the HP CCN program, Hugh Couchman, McMaster University Professor of Astrophysics and Fellow of the CIAR Cosmology Programme, and Patricia Monger, Technical Director of McMaster’s Research and High-Performance Computing Support Department, are working with HP to test the HP Sepia Parallel Visualization system, a scalable system for high-performance computing, scientific research and engineering applications. Their ground-breaking research in astrophysics, which involves the simulation and visualization of the formation of galaxies and the universe, has intensive data and transactional requirements. Through this pilot, SHARCNET is able to provide immediate feedback to HP to shape the evolution and customization of its visualization systems.

“Our ability to generate data from massively parallel simulations has far outstripped our ability to visualize it. The Sepia parallel visualization system once again allows us to interactively manipulate these massive datasets,” states Couchman. “The ability to shape the direction of parallel scientific visualization is of central importance to our HPC efforts, and SHARCNET’s partnership with HP is making this happen.”

HP CCN provides members with a clear collaboration and engagement model that features HP-sponsored services to enable communications and information-sharing, and an annual conference to facilitate networking and sharing of research experiences related to emerging HPTC technologies.

HP and SHARCNET are proud to lead the way as HPTC technology becomes more accessible to a larger community of commercial and academic applications. New opportunities and possibilities for progress and achievement in science and business will surely be generated with the meeting of imagination, ambition and minds from every corner of the planet and every field of endeavor.

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SHARCNET's unique model pays high dividends

Giuseppe Campolieti firmly believes that in the research process, people are as important as processors.

Campolieti, a SHARCNET Chair in Financial Mathematics and an associate Professor of Mathematics at Wilfrid Laurier University, was attracted to Laurier from the University of Toronto because of SHARCNET’s unique combination of state-of-the-art equipment and research support programs.

“The SHARCNET Chairs program offered a very attractive and unique opportunity for my academic career,” confirms Campolieti. “The marriage of computing power with research personnel support will have a great impact on the success of my research.”

Campolieti was the fourth of 12 renowned national and international researchers attracted to SHARCNET institutions through the Chairs program. His research focuses on computational and analytical problems in modeling and pricing of complex derivative instruments.

Derivatives are essentially option contracts which have a present value determined by an expectation of random future payoffs. The modeling and pricing of derivative contracts play a key role in the daily risk management and trading strategies used by leading financial institutions. The use of more complex derivatives has generated a great demand for sophisticated mathematical tools, algorithms and models, such as those made possible by high performance computing.

“Due to the numerically intensive nature of many of these projects, the implementation of parallel algorithms on the SHARCNET clusters is vital to this research, and could ultimately expand the options for risk management in the financial industry” Campolieti confirms.

The commercial applications of Campolieti’s research are numerous, including new and more efficient software applications for banks, insurance companies, hedge funds, and other entities that have to efficiently manage and assess large risks on a daily basis. He believes that HPC will play an increasing role in the creation and development of new financial management applications, and confirms the importance of SHARCNET resources and programs in this evolution.

“The use and importance of HPC in mathematical finance will continue to escalate well into the next decade,” he predicts. “Given its resources and this kind of funding support, SHARCNET continues to place itself in a strategic leadership position.”

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SHARCNET researcher bridges worlds to produce stronger, lighter alums

Nikolas Provatas’ use of high performance computing to “bridge the disparity in length scales between the microscopic and mesoscopic worlds”, will likely one day affect the car you drive.

Provatas, an associate Professor of Materials Science and Engineering at McMaster University, is investigating microstructure in metal alloys, and how material properties can be modeled and simulated to ultimately predict novel material properties. His current collaborations include projects with Alcan International and the Centre for Automotive Materials Manufacturing (CAMM), to investigate precisely this.

Provatas completed his Ph.D in Physics at McGill University and post-doctoral work as a NASA-funded research associate (the micro-gravity research program) at the Department of Materials Science and Mechanical Engineering at the University of Illinois at Urbana-Champaign (UIUC). At UIUC, he developed a new computational algorithm to simulate crystal growth using a technique known as the phase-field method, a method which had previously been too impractical to simulate numerically with any experimental relevance.

Provatas also held a postoctoral position at the University of Helsinki, where he studied the percolation properties of random fibre networks and paper structure. Provatas applied this experience to industrial work at the Pulp and Paper Research Institute of Canada, and is currently also collaborating with Xerox to examine the role of paper microstructure on electrostatics of Xerographic printing.

Today, Provatas’ research continues to focus on solidification structures but within the context of what is often termed “multi-scale modeling”. He studies dentritic solidification using adaptive-mesh refinement (AMR) methods to predict material microstructure formation from the scale of about one hundredth of millimetre to billionths of a metre.

“Examples of dentrites are seen everywhere in nature, such as when looking at a frozen window on cold winter's day. The needle-like crystals that run across the window are just special kinds of dendrites,” explains Provatas. “Similar structures emerge when casting a huge piece of metal in an industrial plant”.

The challenge for Provatas and perhaps, he estimates, the greatest challenge to modern science, is the disparity or difference in the multiple scales that make up any material. There is a need to understand and fabricate materials on the everyday scale of centimetres and meters, while simultaneously probing the physics of their micro and nano-scale structure.

To tackle this enormous challenge, Provatas uses SHARCNET’s high performance computing infrastructure and his AMR technique to create a “virtual multi-scale world”.
This research has the potential for future applications to the aluminum, automotive, and aerospace industries, which are putting ever-increasing demands on metal manufacturers to produce stronger and lighter metal alloys.

“Many industrial sectors are moving toward the use of computational modeling to help guide costly and time-consuming hit-or-miss approaches often used to optimize material properties,” he expands. “Some important examples for Canada include biotechnology, electronics, automotive manufacturing, digital printing and pulp and paper science and engineering.

According to Provatas, organizations like Alcan and Xerox, which currently employ HPC, are positioned to be future leaders.

“In my experience, the industrial leaders of tomorrow are already beginning to take a lead role in the area of HPC, and in this process, SHARCNET will be instrumental.”

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SHARCNET forms North American High Performance Computing Strategic Council

SHARCNET is pleased to announce the constitution of the SHARCNET High Performance Computing Strategic Council.

The Council, which held its inaugural meeting on November 22, is tasked with providing guidance and advice to the SHARCNET Board of Directors on the North American environment for HPC and strategic issues facing SHARCNET as the organization moves forward.

The Council is comprised of subject matter experts in a variety of fields related to high performance computing, including SHARCNET vendor partners, prominent HPC users, and the directors of pre-eminent North American HPC centers.

Council members include:

Phil Baker, President and CEO Optical Regional Advanced Network of Ontario (ORANO)

Andrew Bjerring, President and CEO, CANARIE

Linda Gowman, Vice-President, Research and Development, Trojan Technologies

Gregory Frank, Director, Market Risk Modeling, Bank of Montreal

George Loo, Telecom Engineer Specialist, Ontario Ministry of Economic Development and Trade

William R. Martin, Director, Laboratory for Scientific Computation, University of Michigan

Russ Miller, Director, Center for Computational Research, University of Buffalo (UB)

Steve Munro, General Manager, ISIT Enterprise Solutions, Networks and Technology, Bell Canada

C.C. (Cliff) Pedersen, Manager, Operational Support Systems, Suncor Energy Products

Richard (Dick) Peltier, Professor of Physics, University of Toronto

Andrew Pollard, President, C3.ca

Winston Prather, Vice President and General Manager, High Performance Technical Computing, Enterprise Storage and Servers, Hewlett Packard

Ralph Roskies, Co-Scientific Director, Pittsburgh Supercomputing Center (PSC)

Hala Saab, Business Development Manager, Intel Corporation

Gian Vascotto, Director of Research, Systems Simulation and Control Research, NRC’s Integrated Manufacturing Technologies Institute (IMTI)

Jingwen Wang, Vice President, Research and Development, Platform Computing Inc.

Scott Misage, Director, Strategic Customer Management, HPTC Division, Hewlett Packard,
and Ted Mao, R&D Manager, Trojan Technologies attended the inaugural meeting as delegates.

ORANO President Phil Baker described the Council as an ideal vehicle to foster synergy and success in the Canadian HPC community.

“Canada’s HPC resources can be second to none in the world. The Council is an ideal vehicle to start looking at how we can achieve a broader, more effective integration of all these resources, including funding sources and criteria for research involving distributed and high performance computing.”

SHARCNET is pleased to welcome these academic, business and industry leaders to its community.

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Containing Bio-Threats: SHARCNET researchers help decipher the spread of infectious animal diseases

The foot-and-mouth (FMD) crisis in the UK highlighted to the world the impact that animal disease can have on society. One important aspect of disease control is the computational modelling of disease spread. At the University of Guelph, Deborah Stacey an Associate Professor, Computing and Information Science, along with research associate Neil Harvey, is being funded by the Canadian Food Inspection Agency (CFIA), the Ontario Ministry of Agriculture and Food (OMAF) and the CBRN Research and Technology Initiative (CRTI) to develop a high performance disease spread model for FMD.

To accomplish this, Stacey and Harvey are using the high performance computing (HPC) capabilities of SHARCNET. They are developing a software tool to not only model FMD outbreaks, but to allow easy adaptation to model other animal diseases, providing epidemiologists with the ability to generate many disease-spread scenarios using various parameters and hypotheses.

“Understanding how disease spread models work and how they relate to biological reality is crucial if these models are to play a part in helping animal health professionals design outbreak containment strategies,” explains Stacey. “Researchers will be able test out increasingly more complex models, with improved speed and larger capacities.”

The area of infectious disease spread models is also extremely important to the public health community, for both policy formulation and epidemic control.

“Validated models of infectious disease spread provide crucial insight into the factors that determine disease spread, which is essential for agricultural and public health policy development and for analyzing and planning strategies to monitor and combat bioterrorism,” she confirms.

Use of SHARCNET systems will not only enable a novel approach to disease spread problems, but will also expose researchers throughout North America to an innovative application of HPC.

“SHARCNET’s facilities were crucial in attracting this project to Guelph”, says Stacey. “High performance computing has not been applied to this problem before and this opportunity to work with animal health researchers from Canada and the United States and to expose them to the potential of cluster computing is extremely exciting.”

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Benchmarking SHARCNET clusters
by Baolai Ge, HPC Consultant

Finding an appropriate metric to measure the power of SHARCNET systems has been a rewarding challenge for our high performance technical computing support team. Computer systems are evaluated using benchmark programs. A benchmark is a suite of programs that tests the performance of hardware and/or software under certain conditions. Perhaps the most popular benchmark in the HPC community is the linear algebra package or LINPACK. Since 1993, the results of LINPACK have been used as the de-facto measurement by Top500 (http://www.top500.org/) for ranking the most powerful computers in the world. The results of LINPACK benchmark tests are given in terms of the number of floating point operations per second (“flops”), hence, the higher the better.

In the recent November 2003 release, 131 supercomputer sites around world had achieved the LINPACK speed of over 1 Tflops. The entry score for the Top 500 list, now approximately 403 Gflops, has almost doubled every year since 2000 and will likely double again by 2004. A single cluster on the SHARCNET grid no longer has the power to achieve this minimum threshold (in 2001, SHARCNET systems at Western, McMaster and Guelph ranked 183rd, 280th and 315th.) The entire grid, however, will! With all systems combined, the SHARCNET grid can achieve a theoretical peak of up to 1.49 Teraflops (1,490,000,000,000 flops)! Our dedicated high speed 1 Gbit/s connection over the Ontario Research Innovation Optical Network (ORION), could enable us to potentially achieve a LINPACK benchmark performance close to 1 Tflops. If this can be done, SHARCNET will be the first in the world to achieve a Top500 score on a geographically distributed cluster of clusters. However, given SHARCNET’s unique distributed model – clusters of heterogeneous clusters – we need to devise an innovative, new benchmark to evaluate it.

Already a distinguished computational resource and recognized test bed for new technologies in grid computing, SHARCNET will continue, with this project and others, its role as a pioneer in distributed HPC environments.

Baolai Ge joined SHARCNET in 2002 from Liberate Technologies Canada, Inc., where he was a system programmer for large distributed systems.

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SHARCNET Administrative Officer ensures transparency, efficiency, synergy

Cindy Munro is a central member of the SHARCNET administration, but because she keeps the organization running so smoothly, you rarely see her.

As SHARCNET’s Administrative Officer, it is Munro’s job to ensure organizational efficiency and transparency, from the administration of SHARCNET programs and budgets to human resource management.

A key part of her role is to ensure that SHARCNET continues to be financially viable and accountable – with over 100 budgets in total. Each and every cash and in-kind transaction at SHARCNET has to be meticulously reported, as, in the case of ORDCF, in-kind contributions translate into matching dollars.

“Cindy’s role is not only reactive and but also very strategic,” confirms Carmen Gicante, SHARCNET Executive Director. “She performs contingency planning to ensure our future sustainability and is always concentrating on what needs to be done to prepare for the next evolution of SHARCNET”

Munro also manages both the SHARCNET Chairs and Fellowships programs. In the case of the Fellowships program, she manages all of the administrative processes that underlie the initiative, so the Fellow Selection Committee can focus exclusively on the individual applicants and the merit of their proposed research.

“It is more than managing paperwork,” she admits. “It is about creating a system that is efficient, streamlined, and as with the Fellowships program, web-enabled and scalable, because we intend to award many more Fellowships in the future.”

Since SHARCNET has been the recipient of substantial funding awards, proper fiscal policies are critical to additional funding opportunities. Munro’s meticulous management of financial affairs reinforces SHARCNET’s credibility among partner institutions, funding agencies and the research community in general. SHARCNET is audited annually by CFI and ORDCF to ensure all expenditures and processes are correct, transparent, and reconciled. Munro must ensure the policies and accounting processes of SHARCNET’s seven original partner institutions, and soon all eleven partners, are respected and followed, and that these processes are in turn compliant with those of funding agencies. This is no easy task, particularly when SHARCNET represents an entirely unique organizational model.

“The scope of the SHARCNET project is enormous; there is really nothing comparable,” she confirms. “SHARCNET is setting precedents and to some degree, we are establishing a new model for future institutional consortia with multiple partners and substantial operating budgets.”

Though Munro’s efforts make her role largely transparent, the synergistic effects do not go unnoticed by the SHARCNET executive.

“Cindy has been critical to our success,” confirms Nils Petersen, Chair of the SHARCNET Board of Governors. “I often think that one of my most important contributions to SHARCNET in the early days was to participate in the selection of Cindy Munro as the Administrative Officer for the organization.”

Cindy Munro has extensive experience in academic and information technology environments. From 1984-2001, she was employed with Information Technology Services (ITS) at Western, most recently as their Administrative Officer. She also was and continues to be involved in the establishment and ongoing operation of LARG*net.

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Severely limited without SHARCNET:
Five minutes with Nick Mosey, Ph.D. candidate, Western Department of Chemistry

On his research…
“ The application-based aspect of my research focuses on the study of engine anti-wear additives, called zinc dialkyldithiophosphates (ZDDPs), which are commonly used in conventional motor oils. Despite the use of ZDDPs in engine oil formulations for over sixty years, very little is known about how these compounds actually protect the engine from wear. Recently there has been substantial interest in the replacement of these compounds due to environmental concerns associated with ZDDPs, and the development of automobile engines made of materials which significantly diminish the capabilities of ZDDP-based anti-wear additives. We are applying a battery of chemical simulation techniques to examine the structure, behaviour and chemical reactivity of ZDDPs in an effort to obtain insight into the origins of their anti-wear properties and aid in the development of other anti-wear additives.”

On SHARCNET…
“ Quantum chemical simulations are computationally intensive. The use of large systems is necessary to obtain relevant information regarding the atomic level behaviour of ZDDPs. Our particular simulations are ideally suited to the high-performance parallel computing facilities at SHARCNET, effectively increasing the amount of useful information that can be obtained. Without SHARCNET the types of simulations that we could perform, and the relevance of these simulations, would be severely limited.”

Nicholas is currently working towards a Ph.D. in theoretical chemistry in the Western-based research group of Dr. Tom Woo. Their research involves collaboration with Dr. Martin Müser, SHARCNET Chair in Computational Materials, from Western’s Department of Applied Mathematics, Dr. Peter Norton’s experimental group in Western’s Department of Chemistry and experimental and theoretical researchers at General Motor’s Research and Development Labs in Warren, Michigan.

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© 2003 The Shared Hierarchical Academic Research Computing Network.
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