HPCS2010

Data Intensive Computing: Cross Disciplines, Cross Canada

HPCS is made possible through generous sponsor support

Thank you to
Our Platinum sponsors: Dell, IBM, Intel, Microsoft
Our Gold sponsors: GridCentric, ORION
Our Silver sponsors: Adaptive Computing, Cray,
DataDirect Networks, Force10, Mellanox, NVidia, QLogic,
SGI/Scalar, SpectraLogic, TotalView, Voltaire
And our Bronze sponsors: CANARIE, NAG
Letters
Welcome to HPCS2010

Welcome from Deputy Minister,

Ministry of Research and Innovation, George Ross
On behalf of the Ministry of Research and Innovation, I would like to extend my warmest regards and best wishes for the
success of the 24th annual High Performance Computing (HPC) Symposium. I am sorry my schedule did not permit me
to attend.
At the Ministry of Research and Innovation, we know that robust research is the foundation that will drive innovation in
Ontario and ensure our province remains healthy and prosperous. We are committed to helping Ontario’s top research-
ers and innovators get the support they need to develop cutting-edge ideas and bring them to the marketplace.
That is why the ministry awarded SciNet funding through the Ontario Research Fund - Research Excellence program.
HPC platforms like SciNet, SHARCNET and HPCVL are encouraging collaboration between leading-edge institutions and
industry and fostering a true culture of innovation and partnership.
As you know, this kind of collaboration is central to attracting and retaining the brightest minds from around the world
and to driving innovation in Ontario. And you’re doing just that - everyday.
I look forward to hearing about the groundbreaking research that that the Ontario consortia will, no doubt, support in
areas like bioinformatics, medical imaging and aerospace - just to name a few.
Once again, please accept my apologies for being unable to attend the conference and my sincere thanks to SciNet for
its ongoing contributions to Ontario’s knowledge-based economy.
Sincerely,

George Ross
Deputy Minister

SciNet Compute Canada

SciNet is Canada’s largest supercomputer Compute Canada is leading the creation
centre, providing researchers with the of a powerful national HPC platform for
computational resources and expertise research. This national platform integrates
necessary to perform their work on scales HPC resources at seven partner consortia
not previously possible in fields from across the country to create a dynamic
the biomedical sciences and aerospace computational resource. These integrated
engineering to astrophysics and climate resources represent close to a petaflop
science. It is one of seven Compute of computing capability and online &
Canada consortia spanning the country. long term storage with rapid access and
www.scinet.utoronto.ca retrieval over Canada’s HP networks.
 Schedule
Sat. June 5th & Sun. June 6th

Workshops * Datacentre Tour * Welcome Reception

Time Description Room
Saturday June 5th
9:00am- 12:30 Jonathan Dursi; Practical Parallel Programming: SciNet 109
Concepts, Open MP, MPI
9:00am- 12:30 James Fung; CUDA and GPGPU Programming SciNet 108
9:00am- 12:30 TotalView; Debugging Parallel Programs SciNet 235
10:30- 10:45 Break served in SciNet Reception Area, 2nd Floor
Jonathan Dursi
12:30pm- 1:30 Lunch
1:30pm- 5:00 Practical Parallel Programming: Concepts cont’d SciNet 109
1:30pm- 5:00 Bill Gardner; Pilot: A Fresh Alternative to MPI SciNet 108

1:30pm- 5:00 Ettore Tiotto; Introduction to Partitioned Global SciNet 235

Address Space Programming: UPC
3:30pm- 3:45 Break served in SciNet Reception Area, 2nd Floor
Sunday June 6th
9:00am- 12:30 Practical Parallel Programming: Concepts cont’d SciNet 109
James Fung
9:00am- 12:30 Hartmut Schmider & Gang Liu; Introduction to Posix SciNet 108
Multithreading
9:00am- 12:30 Ian Bush & Jon Gibson; Parallel I/O Workshop: MPI- SciNet 235
IO, HDF5, NetCDF
10:30- 10:45 Break served in SciNet Reception Area, 2nd Floor
12:30pm- 1:30 Lunch
1:30pm- 5:00 Practical Parallel Programming: Concepts cont’d SciNet 109
1:30pm- 5:00 Introduction to Posix Multithreading cont’d SciNet 108
1:30pm- 5:00 Parallel I/O Workshop: MPI-IO, HDF5, NetCDF cont’d SciNet 235
Bill Gardner
3:30pm- 3:45 Break served in SciNet Reception Area, 2nd Floor
4:00pm Datacentre Tour: departs from SciNet @ 256 McCaul SciNet
7:15pm Datacentre Tour: arrives at Welcome Reception Brewery
Welcome Reception
7:00pm- 9:30 HPCS2010 Welcome Reception will take place Brewery
at Steam Whistle Brewery. Brewery tours will be
available during the reception.

Harmut Schmider
& Gang Liu

Ian Bush &

John Gibson
Schedule
Monday June 7th

Physical Sciences & Industry; HPC Tools; Poster Session; Pub Night
Time Description Room
8:00am- 9:00 Continental Breakfast (on 1st and 2nd floor) Old Vic
9:00am- 9:15 R. Paul Young- Welcome Address NF 003
HPC in Physical Sciences & Industry
9:15am- 10:00 John Chen, University of Calgary; the use of HPC for NF 003
the energy exploration industry
John Chen 10:00am-10:45 Bryan Caron, Triumf and the University of Alberta; Data NF 003
Intensive Computing for Particle Physics at the LHC
10:45am- 11:20 Break (on 1st and 2nd floor) Old Vic
11:20am- 12:40 Contributed talks NF 003
• Jeremie Farret, Parallel Geometry Inc; “High performance geometric computing
for mobile robotics simulation”
• Meghdad Saffaripour, University of Toronto; “Distributed-Memory Parallel
Computation of a Laminar Sooting Coflow Jet-A1 Diffusion Flame”
• Sabine McConnell, Trent University; “Self-Organizing Maps on the Cell Broadband
Engine Architecture”
Bryan Caron • Catalin Patulea and Robert Peace, Carleton University; “CUDA-accelerated Genetic
Feedforward-ANN Training for Data Mining”
12:40pm- 1:30 Lunch hosted by Microsoft Burwash
1:30pm- 2:15 Venkatramani Balaji, Geophysical Fluid Dynamics NF 003
Laboratory at NOAA and Princeton; the crucial role of
HPC in climate science
2:15pm- 3:00 Zheng Yang, GlaxoSmithKline; the pharmaceutical NF 003
industry, and the Cross-Pharma HPC Forum
3:00pm- 3:15 Break (on 1st and 2nd floor) Old Vic
3:15pm- 4:45 Contributed talks NF 003
V. Balaji • Guido Vettoretti, University of Toronto; “Visualization in Climate Change Science”
• Chris Neale, University of Toronto; “High-throughput computing of protein
function for rational drug design”
• Sarah Rauscher, Hospital for Sick Children; “Large scale molecular dynamics
simulations of elastin”
• Dhundy Bastola, University of Nebraska at Omaha; “A Parallel Non-Alignment
Based Approach to Efficient Sequence Comparison using Longest Common
Subsequences”
HPC Tools: an opportunity to learn about some of the tools and technologies
available when using or designing new HPC systems.
3:30pm - 4:15 Jim McKinley, SpectraLogic; Managing Exabytes of VIC 212
Zheng Yang Data in Exascale Computing
3:30pm - 4:15 Don Gunning, Intel; TBD VIC 206
3:30pm - 4:15 Tim Smith, GridCentric; GridCentric Copper: High- VIC 215
performance Cloud Computing
4:15pm - 5:00 Dr. Jeff Layton, Dell; IO Profiling of HPC Applications – VIC 212
What you Don’t Know Can Hurt You
4:15pm - 5:00 Ed Hinkel, TotalView Technologies; New Ways to Debug VIC 206
on HPC Systems
5:00pm- 5:30 John Hickson and Rob Burton, Starz Animation; NF 003
John Hickson & Making movies with HPC
Rob Burton 5:30pm - 6:30 Wine & Cheese Poster Reception (2nd Floor) Old Vic
7:00pm-9:30 Pub Night hosted by IBM at Charlotte Room
 Schedule
Tuesday June 8th

Bio, Life & Medicine; Humanities; Grid/Cloud Computing; GPGPU

Time Description Room
8:00am- 9:00 Full Breakfast hosted by DELL: Dr. Glen Otero on HPC Burwash
Bioinformatics – Configurations and Concepts for
Now and Next-Gen Sequencing
9:00am- 9:20 Suzanne Fortier, President, NSERC NF 003
HPC in the Biological, Life & Medical Sciences
9:20am- 10:05 Andrew McLellan, Einstein School of Medicine at NF 003
Yeshiva University; Computational Epigenomics Andrew McLellan
10:05am-10:50 Lincoln Stein, Ontario Institute for Cancer Research; NF 003
HPC and high througput gene sequencing
10:50am- 11:30 Break (on 1st and 2nd floor) Old Vic
11:30pm- 12:15 Chad Peck, Columbia University/IBM; the Role of HPC NF 003
for Understanding the Brain
12:15pm- 1:00 Marc Rousseau, McGill University; development of NF 003
a Canadian, then Global, grid for brain imaging and
neuroscience
1:00pm- 2:00 Lunch Hosted By IBM Burwash
HPC in the Humanities Lincoln Stein
2:00pm- 2:45 J. Stephen Downie, University of Illinois at Urbana- NF 003
Champaign; High Performance Cultural Computing:
The Case of Large-Scale Music Informatics Research
3:35pm- 4:00 The parallel sessions below will have a break at Old Vic
3:35pm
2:50pm- 5:15 GPGPU/Multicore Methods: Contributed talks VIC 212
• Michael Kinsner, McMaster University; “A modular CUDA-based framework for
scale-space feature detection in video streams”
• Anthony Brown, McMaster University;“GPU-accelerated 3D model-based tracking”
• Wei Pan, University of Western Ontario; “Fast polynomial arithmetic on a GPU” Chad Peck
• Steven Solomon, University of Manitoba; “Mapping the MPM Maximum Flow
Algorithm on GPUs”
• Abdul Mroue, University of Toronto; “Binary black holes simulations using CUDA”
• Bijia Pang, University of Toronto; “Magnetohydrodynamics simulation on GPU
cluster”
• Peter Colberg, University of Toronto; “Accelerating Glassy Dynamics using
Graphics Processing Units”
• Jinhui Qin, University of Western Ontario; “Accelerated synchrotron X-ray
diffraction data analysis on a Heterogeneous HPC System”
2:50pm- 4:30 Grid/Cloud Computing: Contributed talks VIC 215
Marc Rousseau
• Mario Dantas, Federal University of Santa Catarina; “An Ontological-Fuzzy
Approach to Advance Reservation in Multi-Cluster Grids”
• Mohammad Shorfuzzaman, University of Manitoba; “Adaptive Placement of
Replicas in Hierarchical Data Grids”
• Adel Ben Mnaouer, University of Trinidad and Tobago; “An Adaptive Priority Tuning
System for Optimized Local CPU”
• Violeta Holmes, University of Huddersfield ; “Huddersfield University Campus Grid:
Grid of OSCAR clusters”
• Kyle Fransham, University of Victoria; “Research computing in a distributed cloud
environment”
7:00pm- 9:00 Cocktails at Panorama: Poster and Paper Awards J. Stephen Downie
Schedule
Wednesday June 9th

Exascale Forum * Datacentre Tour

Time Description Room
8:00am- 9:00 Continental Breakfast Old Vic
9:00am- 9:20 Chad Gaffield, President, SSHRC NF 003
Exascale Forum
9:20am- 11:00 • Don Rudish, Sandia; what we can learn from Botnets NF 003
• Alan Gara , Chief Architect, IBM BlueGene
Supercomputer; IBM’s vision
• Eng Lim Goh, CTO, Silicon Graphics Inc.; SGI’s vision
11:00 am- 11:20 Break Old Vic
11:20am- 12:50 • George Almasi, IBM Watson Labs; Programming NF 003
languages to enable massively parallel computing
• Jeff Denworth, DDN; storage challenges and
opportunities in the exascale age
• David Rich, Microsoft; Microsoft’s vision
12:50pm- 1:50 Lunch hosted by Intel Burwash
Richard Dracott on Exascale; Intel’s vision
2:00pm Datacentre Tour: departs from SciNet @ 256 McCaul SciNet
1:50pm- 2:30 Introduction of remaining panelists: NF 003
• Hugh Couchman, SHARCNET, on the HPC funding
environment in Canada
• Greg Wilson, Software Carpentry, on programmer
productivity at the exascale
• Nicolas Dubé, Oracle/Sun, on datacentres for the
exascale
Panel discussion / moderated Q&A amongst panelists.
2:30pm- 3:15 Questions from the floor Old Vic
4:30pm Datacentre Tour returns to SciNet SciNet
 Venues
Pubs, Breweries and Patios

HPCS2010 has planned some amazing events!

We hope you’ll attend all of them.
Information on the venues, rooms and other details can be found
below. The registration/information desk is in Old Vic if you can’t find
what you need here.

SciNet Victoria College Steam Whistle Charlotte Room Panorama

256 McCaul Street 91 Charles Street 255 Bremner Blvd 19 Charlotte Street 55 Bloor Street West
McCaul & College University & Bloor Spadina & Lakeshore Spadina & King Bay & Bloor

• WORKSHOPS: The • ROOM LOCATIONS: • The welcome reception • Sponsored by IBM! • The 51st floor of the
SciNet offices will host NF 003, is on the lower is June 6 (6-8:30PM). Bar food, pints and pool! Manulife Centre is the
the workshops taking level of Northrop Frye Brewery tours will be home of Panorama
• The Charlotte Room
place June 5th & 6th Hall available during the Lounge. The lounge has
is located in Toronto’s
reception~ as will Steam 2 outdoor patios with
• 256 McCaul is a secure exciting entertainment
VIC 206, 212, 215 are all Whistle’s own pilsner! amazing views of the
building; someone will district. It has been
located on the 2nd floor city. Cocktails and light
be present to open the • Steamwhistle Brewery voted one of the top
of Old Vic fare will be served
front door for attendees, located in the historic billiards rooms in North
Must be 19+ to attend
so please be prompt • MEAL LOCATIONS: John St. Roundhouse, America. The evening
Burwash Hall will serve which functioned as a will include buffet • Poster & Paper Awards
• Workshop coffee
all conference lunches, Canadian Pacific Rail dinner, bar service and will be presented during
breaks will be served in
as well as the full steam locomotive repair use of all 7 pool tables. the evening
the SciNet Reception
breakfast on Tuesday facility when built in Must be 19+ to attend
area on the 2nd floor • The Manulife Centre
morning. 1929. It serviced steam
• From St. Andrew is a short walk from
• DATACENTRE TOURS: locomotives that helped
station, head west Victoria College (see
The Sunday tour to Continental Breakfast, pioneer this nation
on King Street to map). It is on the south-
the datacentre will and coffee breaks will Must be 19+ to attend
Charlotte Street (either east corner of Bay &
leave from the front be served on BOTH the
• From Union Station, on the streetcar or by Bloor. Go to the Varsity
of the building. Tour first and second floor of
follow signage to the foot). Turn north onto movie theatres located
participants will be Old Vic
Skywalk. Take Skywalk Charlotte. The bar is on at the south end of the
dropped off directly at
• INFO DESK: to final exit and head the east side. centre. The elevators
the Welcome Reception
The Registration & down the path towards to Panorama are next
• Closest TTC stop is St.
• The Wednesday tour to Information desk is the CN Tower. The the the theatre. A
Andrew
the datacentre will leave located on the main Brewery is located across hostess will check in all
and return to the front of floor of Old Vic the street from the tower attendees on arrival
the building
• Closest TTC stop is • Closest TTC stop is • Closest TTC stop is Bay
• Closest TTC stop is Museum Union
Queen’s Park
Posters
Old Vic- 2nd Floor

Posters!
Take a look at the submissions for 2010
Awards will be presented on Tuesday evening at Panorama Lounge.

Algorithms
A01- Tetrahedral Elements in Finite Element Models with Continuous Pressure Approximation; Kehinde O. Ladipo University of
Ontario Institute of Technology
A02- Domain Decomposition of Stochastic PDEs: A Two-Level Scalable Preconditioner; Waad Subber and Abhijit Sarkhar
Carleton University
A03- Preconditioned Iterative Linear Solver for Ill-Conditioned Power System Matricies using Graphics Processing Units; A.
Asgari Kamiabad and Joseph Euzebe Tate University of Toronto
A04- Parallel Branch and Bound Algorithm - A Comparision Between Serial, OpenMP, and MPI Implementations; Lucio S.
Barreto and Michael Bauer The University of Western Ontario
A05- A Pipelining Implementation for Parsing X-ray Diffraction Source Data and Removing the Background Noise; Michael
Bauer, N. Sterwart McIntyre, and Yuzhen Xie The University of Western Ontario
Biology
B01- Elucidation of Protein Primary and Secondary Structure from the Optical Second Harmonic Gneration Response using ab
initio Calculations; Danielle Tokarz, Richard Cisek, Adam Tuer, and Virginijus Barzda, University of Toronto
B02- Optimizing refinement of 3D protein maps from single particle electron cryomicroscopy; Lindsay Baker and John
Rubinstein, The Hospital for Sick Children Research Institute
B03- Towards a Cure for Alzheimer’s Disease: Molecular Mechanism of Amyloid Inhibition by Inositol; Grace Li, Réges Pomès,
The Hospital for Sick Children
B04- Monte Carlo simulations to asses the impact of model parameter uncertanties on mrophological and ecological
descriptors in a nonlinear diffusion-reaction model of a dual species biofilm; Nasim Muhammad, Hermann J. Eberl, University
of Guelph
B05- Development of the coarse-grained model for RNA nanostructures using all-atom Molecular Dynamics Data; Maxim
Paliy, Roderick Melnick, and Bruce Shapiro, Wilfred Laurier University
B06- Relaxed complex scheme virtual screening predicts novel inhibitors for the lyase activity of DNA polymerase beta;
Khaled H. Barakat and Jack A. Tuszynski
Computer Centers/Security
C01- When to Renew Software Licenses at HPC Centres? A Mathematical Analysis; Ge Baolai, Henning Rasmussen, and Allan B.
MacIsaac, University of Western Ontario
C02- MPI Enhancements in John the Ripper; Edward R. Sykes, Michael Lin, and Wesley Skoczen
C03- Optimization Research on Processes’ I/O Performance in Container-level Virtualization; Yi Zhao, Chinese Academy of
Sciences
C04- Backfilling with Fairness and Slack for Parallel Job Scheduling; Angela C. Sodan and Wei Jin
Geophysics and Astrophysics
G01- A parallel computational framework for integrated surface-subsurface flow and transport simulation; Hyoun-Tae Hwang,
Young-Jin Park, Edward A. Sudicky, University of Waterloo
G02- A Global Model of Rapidly Rotating Spherical Convection as a Test-bed for Novel Numerical Technologies; C. Nenkov and
W. R. Peltier, University of Toronto
G03- A Physically-based approach to assess the impact of climate change on Canadian water resources; Jianming Chen,
Edward A. Sudicky, W. R. Peltier, Young-Jin Park, University of Waterloo
G04- Protostellar Outflow-driven turbulence: A Numerical Look; Michael Gorelick and Christopher Matzner, University of
Toronto
G05- Analyzing the ACT cosmology telescope data; J. Sievers and M. Nolta, University of Toronto
Multicore/GPU
M01- A Parallel Algorithm for Connected Component Labelling of Gray-Scale Images on Homogeneous Multicore
Architectures; Mehdi Niknam, Parimala Thulasiraman and Sergio Camorlinga, University of Manitoba
M02- Polymer Dynamic Field Theory on Graphical Processing Units; I. Wright and R. A Wickham, Perimeter Institute and
University of Guelph
M03- The CellPilot Library: Seamless end-to-end communication for heterogeneous clusters; Natalie Girard, J. Carter, W.
Gardner, and G. Grewal, University of Guelph
 Awards & Map
TBD

Awards & Prizes

Best Paper Student Paper Awesome award Prizes for YOU!
NVidia Best Paper Intel Best Student Sandia Awesome Attendees of HPCS
Prize Paper Prize awards can win stuff too!
Submissions for Student submissions Submissions for • SpectraLogic is entering all of its HPC Tool
oral or poster for oral or poster oral or poster session attendees in a draw for an iPad gift card
presentations will be presentations will be presentations are
• Photo contest: Take photos at HPCS2010,
eligible for the NVIDIA eligible for the Intel eligible for one
upload them to our Flickr page, and possibly win
Best Paper Prize, an Best Student Paper of three Sandia
one of 10 best photo prizes!
NVIDIA Quadro FX Prize, a gift card worth Awesome awards,
5800. $500 CDN each gift card worth • Naming contest: GPC? TCS? Not great names
$300. for SciNet’s amazing supercomputers. Stop by
the registration desk and fill out a ballot. Top 3
naming entries will win iPods.

Conference
The core symposium
will take place in three
buildings on the Victoria
College campus.
• Burwash Dining Hall
• Old Vic (VIC)
• Northrop Frye Hall (NF)

Tours
Both tours will depart from
the SciNet building.
The Sunday tour will
return to Toronto and drop
participants off directly at
the Welcome reception at
the Brewery.
The Wednesday tour will
return to SciNet.
Maps
Part 2

Event Maps
Directions are from the nearest subway station
Panorama is noted on previous page map of Victoria College.
 Notes

Notes:
Session Chairs
HPC in Physical Sciences & Industry: Daniel Gruner (morning sessions)
Chris Loken (afternoon sessions)
HPC in the Biological, Life and Medical Sciences: Shoshana Wodak
HPC in the Humanities: Jonathan Dursi
Grid/Cloud Computing: Leslie Groer
GPGPU/Multicore Methods: Scott Northrup
Exascale Forum: Daniel Gruner
Poster Session: Jonathan Dursi

www.hpcs.ca