Winter 2003, Vol. 1, Issue 1
in this issue:
But, more than an acronym, SHARCNET embodies what we want to do and how we do it. Our purpose is:
To Share High Performance Computing (HPC) resources between academic institutions, optimizing access, utilization and sustainability of precious and necessary resources.
Establishing a Hierarchical structure of computing clusters to provide the best fit for a wide range of computational challenges.
Supporting the Academic Research mission by providing leading edge research programs in science, social science, engineering, business and medicine, with access to the necessary computing tools and systems.
Creating a Computing Network that allows for transparent sharing and optimal placement of resources, leading to a model for grid computing.
We are very fortunate to have partners who support our
vision. The academic partners – Guelph, McMaster, Western, Wilfrid Laurier and Windsor
Universities, and Fanshawe and Sheridan Colleges – provide researchers
and support. Private sector partners – HP, Bell, Nortel,
Collectively, we demonstrated to government funding agencies: the Canada Foundation for Innovation, Ontario Innovation Trust, and the Ontario Research and Development Challenge Fund, that we have outstanding researchers with innovative ideas that will lead to great benefits. Our vision is becoming reality.
Our 15 SHARCNET Research Chairs will bring the best and brightest faculty members and researchers to Southwestern Ontario, using HPC to solve problems in bioinformatics, materials research, financial mathematics, and developing computational tools.
The SHARCNET research fellowships create the opportunity to recruit visiting scholars, post-doctoral fellows, and graduate and undergraduate students to support the academic computing-based research programs.
The fact that more than half our resources are dedicated to support the human infrastructure, that we have a dedicated research community driving the projects, that we have recruited outstanding faculty, staff and students to join SHARCNET, and that our partners have provided their support from the outset, has enabled us to get this project up to speed in an incredibly short period of time – from the first CFI Award in February 2000, to full implementation of all programs in 2002.
On behalf of SHARCNET’s Board of Governors, I thank
all of you who have contributed to these efforts. I look forward to
you to make this an enduring vision.
Nils O. Petersen, Chair
|Executive Director's Message|
|Message from the Chair of the Board|
|A Hewlett Packard partnership|
|SHARCNET Chairs program attracts world-renowned experts|
SHARCNET has achieved a great deal in a surprisingly short period of time. This is because we have been guided by a set of principles and a simple, clear, fundamental vision:
To establish a world-leading, multi-university and college, interdisciplinary institute with an active academic-industry partnership enabling forefront computational research in criticalareas of science, engineering, and business.
These words were chosen with great care. They convey the principles that will allow SHARCNET to succeed and grow. The concept of partnership – sharing resources as equals and enabling world-class research – has allowed SHARCNET to rapidly reach a point where we can document many successes.
In our vision we talk about developing an “active academic-industry partnership.” This is rooted in the belief that no one partner needs to sacrifice its principles. An initial goal to find a win-win arrangement for both the academic and the industrial partners will endure.
The successes we have enjoyed will stand as proof that industry, academia and government can work together to further individual goals, as well as those of SHARCNET. I am very proud of the faith our industrial partners have shown in the future viability o SHARCNET, as evidenced by their continued investment and involvement in the program – in particular HP Canada.
Our vision also talks about our fundamental goal of “enabling
forefront computational research”. From the onset, we knew that
SHARCNET would need to provide a human infrastructure to complement our
High Performance Computing (HPC) infrastructure. While our facilities
are second to none in Canada, I truly believe it is the HPC consultants
and systems administrators, and the work they do daily with faculty and
students, that sets SHARCNET apart. It is their work that will build
the community of well-trained HPC researchers. All of this will lead
to long-term benefits for our academic and industrial partners and, ultimately,
for the economies of Ontario and Canada.
HP Canada is pleased to be SHARCNET’s principal supplier of computing infrastructure.
The organization’s focus, based on distributed clusters of powerful SMP systems, is consistent with HP’s strategy and in keeping with designs that today power many of the most powerful research computing facilities in the world. This focus has resulted in one of the most successful shared computing infrastructures in Canada, which is serving as a model for proposed developments all across Canada.
Furthermore, SHARCNET’s people understand the value of genuine partnership within the IT realm. HP Canada values the feedback provided by SHARCNET’s researchers and support staff, and uses this feedback in designing next-generation product and service offerings. The success of this partnership has resulted in the selection of SHARCNET as a development partner on future products in High Performance Visualization, powering fully immersive simulation environments to allow deeper understanding of areas as diverse as protein folding, high energy physics and geology.
On behalf of HP Canada, I salute the staff and researchers who have made SHARCNET such a success, and look forward to years of further and deeper collaboration.
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:
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:
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.
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,
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
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.
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.
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.
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.
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.
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.
channel their energies with SHARCNET
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.
Health and economic resources are the two key factors in retirement, but they’ve never been linked very well… until now.
Todd Stinebrickner, a University of Western Ontario economics professor, is conducting research on factors that influence people to retire – and providing policy makers with new, pertinent information for making decisions about social security.
Collaborating with Prof. John Bound of the University of Michigan and Dr. Tim Waidmann of the Urban Institute in Washington, D.C., Stinebrickner is developing a comprehensive model that identifies reasons why people retire. It draws relationships between these reasons and provides a new understanding of how these combined circumstances can determine decisions about retirement.
SHARCNET is providing a conduit for the researchers to implement the model, and accurately predict the outcomes of social and economic policy changes.
“The model we’ve been working on is complex, and it would not be possible to estimate parameters in this model on other machines,” says Stinebrickner. “SHARCNET is providing the computing power that enables us to estimate models and conduct important policy simulations that weren’t possible before.”
Stinebrickner says past modelling efforts have typically focused on either the effect of health or of financial resources on retirement.
“The two factors are related, so combining them into a single cohesive model is important in understanding how they interact to influence retirement decisions and the effects of new policies – such as changing the age of eligibility for social security,” he says.
However, the estimation of such models is extremely time-sensitive and has constrained researchers working with economic models in the past. SHARCNET addresses this problem directly.
“With SHARCNET, we can model how much one factor picks up the effects of the other, and we can create a much more cohesive, more realistic model for retirement decisions than would otherwise be possible,” says Stinebrickner.
This research is sponsored by the Canada Foundation for Innovation, the U.S. National Institutes of Health and the Ontario Research and Development Challenge Fund.
The Shared Hierarchical Academic Research Computing