Message from the Chair of the Board

What is SHARCNET?

The computational Infrastructure

SHARCNET Chairs and Fellowships programs

SHARCNET events well-attended

Researchers channel their energies with SHARCNET

Health, wealth and SHARCNET

Executive Director's Message

What is SHARCNET?

SHARCNET was formally established in June 2001, in Southwestern Ontario, to develop a network of High Performance Computing (HPC) clusters. Funded by the Ontario Research and Development Challenge Fund (ORDCF), Ontario Innovation Trust (OIT) and Canada Foundation for Innovation (CFI), SHARCNET is a unique partnership between leading universities and colleges and industry partners.

SHARCNET’s primary clusters are located at the University of Guelph, McMaster University, and The University of Western Ontario. Smaller clusters, at the University of Windsor and at Wilfrid Laurier University, enable researchers to develop and test software before moving their research to one of the larger clusters. Fanshawe College and Sheridan College provide parallel computer systems and training programs for students who will learn how to support the HPC technology.

SHARCNET’s vision is:
To establish a world-leading, multi-university and college, interdisciplinary institute with an active academic-industry partnership, enabling forefront computational research in critical areas of science, engineering and businessBy providing world-class HPC resources, we will:

• accelerate the production of research results to meet the needs of researchers and industry partners in today’s competitive and fast-paced academic and business environments,
• attract and retain the best students, researchers and companies by providing cutting-edge hardware and computational expertise,
• link academic researchers and business partners, in search of new opportunities, to create new companies that will continue to develop Canada’s knowledge-based society.

SHARCNET is more than hardware. To ensure we achieve our goals, we have a number of programs and services available to both researchers and business partners including:

• full-time system administrators and HPC consultants at the larger sites who optimize system availability and assist researchers in utilizing the full potential of HPC resources,
• the SHARCNET Chairs Program, to enable strategic faculty recruitment,
• matching funds to support research and training, and
• seminars, workshops, and conferences.

Through this infrastructure, and with all these resources, SHARCNET will enable world-class computational research over a broad and interrelated spectrum of scientific, engineering and business fields.

Currently, in excess of 340 researchers utilize SHARCNET resources.

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The Computational Infrastructure

SHARCNET’s strategy is to provide scalable computational resources to drive internationally competitive science through a hierarchy of processing capability of over 400 HP/Compaq Alpha processors and large symmetric multiprocessor computers.

There are three large clusters at Guelph, McMaster and Western.

The McMaster cluster consists of a 32 4-processor Alpha multiprocessor system (128 processors), each with 4Gb of shared memory connected via a Quadrics interconnect and a 100Mb Ethernet. This cluster runs Tru64.

At Guelph, there is a 108 processor cluster (27 4-processor Alpha multiprocessor systems) each with 4Gb of memory connected by both a Quadrics interconnect and a 1 Gb Ethernet. This system runs RedHat Linux.

The clusters at Western are built with the same 4-processor Alpha systems, also using
Quadrics interconnect and a 1 Gb Ethernet. One cluster is a 37 4-processor system (148 processors). A second smaller cluster consists of 48 processors (12 4-processor Alpha systems). They both run RedHat Linux.

Smaller 8-processor clusters, comprised of the 4-processor Alpha systems, are at Windsor and at Wilfrid Laurier Universities, and are used for processing and program development.

In addition, 4-processor systems have been installed at Sheridan College and Fanshawe College, to enable applied research and training for students.

SHARCNET also has two large symmetric multiprocessor clusters: one at Guelph, and one at McMaster. The system at Guelph is an HP v2500 with 16 processors and 16Gb of memory. An HP/Compaq GS160 with 32 processors and 16GB of memory is at McMaster. In the near future, there will be a 128 processor serial farm located at Western, and another 96 processors unit at McMaster.

A key element of SHARCNET’s strategy is to develop, deploy and use a High Performance Computing grid. The next step is to connect these systems together through high-speed networking and to develop and deploy software to enable computational processes to operate across multiple nodes.

A key element of this networking will be provided by ORION (Ontario Research and
Innovation Optical Network) being developed and deployed by Optical Regional Advanced Network of Ontario (ORANO).

A prototype of such an High Performance Computing (HPC) grid has been operating at Western for several months. The network connects the large Alpha cluster (148 processors) to the smaller one (48 processors) approximately a kilometer away. The interconnection is provided by a Nortel Optera 5200 optical switch using Dense Wave Division Multiplexing (DWDM) across three wave lengths with a throughput of about 8Gbs.

Software is another element of the SHARCNET infrastructure. Parallel programs are typically written using the Message Passing Interface (MPI) library. Scheduling and load sharing are provided by LSF from Platform Computing. SHARCNET was a key player in the initial beta tests of LSF 5. As part of the prototype test of a high performance grid at Western, LSF 5 was successfully utilized to share processors between the two clusters over the optical connection. By extending this concept across the ORION network researchers will have access to the full complement of 432 Alpha processors.

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SHARCNET Chairs and Fellowships Program

High Performance Computing (HPC) has become an essential component for both the academic and business communities. In order to carry out this work, highly skilled people are required.
SHARCNET’s founding philosophy has been to foster Ontario’s HPC knowledge base. We exist, not only to provide the hardware, but also to support programs to bring and train the brightest to carry out the scientific computations, research and support for this technology for decades to come. SHARCNET funds a range of research personnel in support of these objectives. Here are some of these programs:

Chairs Program

A fundamental component, which represents a long-term, strategic investment in HPC, is the chairs program. This program with a $2.9M budget provides bridge funding for new faculty in four key areas: computational materials, computational finance, bio-computing and HPC tools. To date fifteen chairs have been approved.

Fellowships Program

Our fellowships program supports research personnel, visitors, and faculty teaching relief. These fellowships are administered by SHARCNET, through grant competition, and provide various levels of funding matched by local sources. Applications are considered on the basis of research excellence in fields that will further SHARCNET’s HPC goals. The application process is very simple – three pages filled out electronically. Results from the semi-annual competition are announced within six weeks. Over the five-year grant period, approximately $3.2 million will be allocated towards fellowships.

Research fellowships provide teaching relief for up to two courses, allowing a faculty member to devote time to a specific SHARCNET HPC project.

Visiting fellowships allow researchers to bring outstanding computational scientists to SHARCNET. Other fellowships are undergraduate fellows, graduate fellows and post-doctoral fellows. These form the most important component of the program. The graduate fellowships and post-doctoral fellowships create the next generation of computational scientists and faculty.

SHARCNET provides a generous 63% of the salary costs for these fellows.

Undergraduate fellowships frequently fund, but aren’t limited to, summer students. In many cases, these awards provide opportunities for students that would not otherwise be available.

We are very confident that the training offered through these fellowships will provide people with outstanding HPC skills for the Ontario and Canadian economies. To date SHARCNET has awarded 74 fellowships with $1.7 million in financial support.

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SHARCNET Chairs program attracts world-renowned experts

SHARCNET is excited about the success of our chairs program and the high credentials of the incumbents who have joined us. The chairs program is designed to attract world-renowned experts in a variety of fields who will utilize SHARCNET’s resources to enable leading research.

To date, 15 chairs have been approved for the chairs program and five have already joined us. They are:

Dr. Eric Sorensen is working in the computational materials area in the Physics & Astronomy Department, at McMaster University. He joins us from the Universite Paul Sabatier in Toulouse, France.

Dr. Mark Reesor is located at Western, working in the area of computational finance in the Applied Mathematics Department. Dr. Reesor was recruited from the Financial Markets Department at the Bank of Canada in Ottawa.

Dr. Giuseppe Campolieti comes to SHARCNET from the Department of Mathematical Finance at the University of Toronto. He has an appointment at Wilfrid Laurier University in the Financial Mathematics program.

Dr. Martin Müser was recruited to Canada from Johannes Gutenberg- Universität, Germany and is working in the filed of computational condensed matter physics and materials science in the Applied Mathematics Department at The University of Western Ontario.

Dr. Jonathon Stone, with the Biology Department at McMaster University, is working in the emerging field of computational biology and bioinformatics. Dr. Stone was recruited from the Biology Department at Dalhousie University in Halifax, N.S.

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SHARCNET events well-attended

lSHARCNET recently hosted several events to provide training on High Performance Computing and the application of computational methods to research.

The first SHARCNET fall workshop was held this year from October 22-25, 2002 at McMaster University with supporting sponsorship from C3.ca and Hewlett-Packard. The theme of the workshop was parallel and High Performance Computing with an additional session on grid computing. Nearly 50 researchers from throughout Ontario attended these workshops and rated them highly in both content and importance to their research. On the first day the topics of Parallel Programming, Open MP and MPI were covered by Kenneth Tan, James Wadsley and Baolai Ge, the SHARCNET HPC Consultants. These served as introduction for the in-depth Hewlett-Packard programming course that followed for the next two days-presented by William Smith of Hewlett-Packard. The workshop concluded with “Grid day“, sessions and demonstrations on grid computing concepts presented by Ian Lumb (Platform Computing), Darcy Quesnel (Grid Canada) and Gabriel Mateescu (NRC).

The co-sponsored SHARCNET-Fields Institute Conference on Monte Carlo Methods in Quantitative Finance was held on Saturday, November 9, 2002 at The University of Western Ontario. More than 70 people participated in the day, with equal representation from both the private sector and professors and graduate students from various Canadian and American universities. Nils Petersen, the Chair of the Board of SHARCNET and V.P. (Research) at UWO presented an overview of SHARCNET and its successes. The scientific part of the conference opened with an inspiring keynote address by the father of Monte Carlo in finance, Phelim Boyle from the University of Waterloo. This was followed by presentations from Alexander Kreinin (Algorithmics), David Bolder (Bank of Canada),

George Jiang (University of Arizona), Marcel Rindisbacher (University of Toronto), Ken Seng Tan (University of Waterloo), and Duncan Murdoch (The University of Western Ontario). We are most pleased with the attendance, in particular the strong representation from Canada’s leading banking, insurance and investment institutions and the quality of the presentations.

SHARCNET is committed to sponsoring continuing educational events. Over 700 researchers and students have received training on HPC programming through SHARCNET workshops. Please refer to the SHARCNET website www.sharcnet.ca for notices on upcoming events.

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Researchers channel their energies with SHARCNET
by Murray Tong

Ion channels are small and elusive, but they’re worth watching – they’re important doorways to the cell, and University of Guelph researchers will use computer models to explore their structure and increase the understanding of them.

Ion channels are small, heavily regulated passages found in the membranes of all cells, from bacteria to humans. They shuttle electrically charged atoms and molecules in and out of the cell with high specificity. Researchers have identified a variety of ion channels, and determined their roles in some physiological processes such as hormone signaling, nerve impulses and muscular movement.

But ion channel protein structures remain mostly unknown. And attempts to understand them using classical laboratory methods have been unsuccessful.

That’s where Profs. Saul Goldman, Department of Chemistry and Biochemistry, Chris Gray, Department of Physics, and Robert Guy of the National Institutes of Health (Bethesda, Maryland) come in. They believe that an accurate computer model could explain the structure and physiology of ion channel… and the newest SHARCNET computers are allowing them to assemble these complex models, and simulate the mechanism by which ion channels select for and transport their ions of choice.

“We’re developing models of the ion channel proteins and the way they transport ions,” says Gray. “Then we can compare the properties of the model to the actual proteins, and see how well they correlate.”

Currently, the researchers are studying a potassium-specific ion channel found in human heart tissue designated IRK1, which is believed to control blood flow to the brain. Gray says discovering the structures of ion channels can help scientists develop new therapies for many diseases caused by ion channel defects, including hypothyroidism, epilepsy and cystic fibrosis.

This isn’t the first time computers have been used to model the structures and mechanisms of different proteins, including ion channels, but low computing power has limited researchers to simpler, less accurate models and shorter simulation times. Now, Gray and his colleagues have modeled the movement of a single potassium ion through an ion channel down to one-femtosecond frames – equivalent to about one million billion frames per second – which would have been impossible without state-of-the-art computing connections such as SHARCNET. The researchers can then follow the movement of a single potassium ion across the cell membrane, which takes from two to 100 nanoseconds, or up to 100 million individual frames.

“We may be the first group in the world to simulate the mechanism of an ion channel in this much detail,” says Gray. And by elucidating the conduction structure of ion channels and the mechanism by which they transport ions, the researchers hope to gain new insight into how ion channels work… and pave the road to better human health through technology.

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© 2003 The Shared Hierarchical Academic Research Computing Network.
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