Compute Ontario Research Day 2014

Conference Date: 
Wednesday, May 7, 2014 (All day)
Pirsa Collection: 
Scientific Areas: 
Other

 

Formerly known as SHARCNET's Research Day, this event has been expanded for 2014 and is expected to be the premier annual event where Ontario researchers meet to learn about each other's High Performance Computing (HPC) related research. This includes both research performed via HPC as a science tool, as well as research regarding HPC itself. Research Day welcomes everybody, not just participants from Ontario.

Compute Ontario Research Day will be held on May 7, 2014, at the Perimeter Institute for Theoretical Physics in Waterloo, Ontario, Canada. We anticipate oral presentations of 20 minutes, with select presentations of 30 minutes. There will be a poster session as well.  Saul Teukolsky (Cornell University) has graciously agreed to deliver a keynote presentation.

As a geographically local meeting, Research Day is an excellent opportunity for students to advertise their projects. We anticipate offering a prize for best student presentation and/or best student poster. 

To register for this event, click here

Sponsorship for this conference has been provided by:

 

  • Nasser Mohieddin Abukhdeir, University of Waterloo
  • Adrian Adamescu, University of Waterloo
  • Alena Antipova, University of Western Ontario
  • Bill Appelbe, Orion
  • Sadegh Babaii Kochekseraii, Sheridan College
  • Shyam Badu, Wilfrid Laurier University
  • Michael Bauer, University of Western Ontario
  • Eric Bembenek, University of Waterloo
  • James Bergstra, University of Waterloo
  • Wilson Brenna, University of Waterloo
  • Alan Campopiano, Brock University
  • Charles Davis, Brock University
  • Hendrick de Haan, University of Ontario Institute of Technology
  • James Desjardins, Brock University
  • Antoine Dumont, York University
  • Dalibor Dvorski, Wilfrid Laurier University
  • Ahmed Elshamli, University of Guelph
  • Lawrence Folland, University of Waterloo
  • Simon Forest, Institute of Quantum Computing
  • Fred Fu, University of Waterloo
  • Marcial Garbanzo-Salas, University of Western Ontario
  • Abbas Ghasemi, University of Waterloo
  • Ali Ghasemi, McMaster University
  • Abby Goodrum, Wilfrid Laurier University
  • Stephen Green, University of Guelph
  • Daniel Gruner, University of Toronto
  • Greg Gulyas, Compute Ontario / MRI
  • Thad Harroun, Brock University
  • Lauren Hayward, University of Waterloo
  • Harold Hodgins, Wilfrid Laurier University
  • Jemmy Hu, Sharcnet
  • Heqing Huang, Wilfrid Laurier University
  • Michael Hudson, Universtiy of Waterloo
  • Lucian Ivan, University of Waterloo
  • Craig Jeffrey, CMC Microsystems
  • Mohamed Khalil, University of Guelph
  • Ilias Kotsireas, Wilfrid Laurier University
  • Apichart Linhananta, Lakehead University
  • Chris Loken, University of Toronto
  • Pendar Mahmoudi, University of Waterloo
  • Hugh Merz, Sharcnet
  • Jonah Miller, University of Guelph
  • Pawel Pomorski, Sharcnet
  • Marcelo Ponce, University of Guelph
  • Sanjay Prbahakar, Wilfrid Laurier University
  • Michelle Przedborski, Brock University
  • Doug Roberts, Wilfrid Laurier University
  • Mina Rohanizadegan, University of Waterloo
  • Yasser Ruiz Blanco, Carleton University
  • Vincent Russo, University of Waterloo
  • Kaushik Saha, University of Waterloo
  • Erik Schnetter, Perimeter Institute
  • Hurmiz Shamana, McMaster University
  • An-Chang Shi, McMaster University
  • Affan Shoukat, York University
  • Dan Sinai, University of Western Ontario
  • Silviga Smith, Wilfrid Laurier University
  • Sebastian Steinhaus, Perimeter Institute
  • Avital Sternin, Brock University
  • Edward Sternin, Brock University
  • Ed Sykes, Sheridan College
  • Pawel Tecmer, McMaster University
  • Saul Teukolsky, Cornell University
  • Lennaert van Veen, University of Ontario Institute of Technology
  • Coby Viner, University of Western Ontario
  • Mark Wachowiak, Nipissing University
  • Renata Wachowiak-Smolikova, Nipissing University
  • Jingyi Wang, University of Waterloo
  • Xingyu Wang, University of Waterloo
  • Ryan Westernacher-Schneider, University of Guelph
  • Benjamin Wilk, University of Ontario Institute of Technology
  • Rory Woods, McMaster University
  • Thomas Wolf, Brock University
  • Serene Wong, York University
  • Li Xi, McMaster University
  • Lixan Zhan, Grand River Regional Cancer Centre
  • Xiaozhou Zhang, McMaster University

Time

Event

Location

9:00-9:30am

Registration, Coffee and Poster Setup

Atrium

9:30-9:45am

Welcome 

Theatre

9:45-10:10am

Ilias Kotsireas, Wilfred Laurier University

Recent advances in the search for complementary sequences

Theatre

10:10-10:35am

Hendrick De Haan, University of Ontario Institute of Technology

Simulating the Capture and Translocation of

Rigid fd Viruses though a Nanopore

Theatre

10:35-11:00am

Li Xi, McMaster University

New insights into polymer-induced drag

reduction in turbulent flows

Theatre

11:00-11:25am

Coffee Break

Bistro

 

Parallel Sessions I

(Each talk is scheduled for 12+3 or 15+5 minutes)

 

Track A

L. Van Veen, S. Wong, J. Desjardins, J. Miller

 

Track B

A. Ghasemi, E. Bembenek, L. Ivan, B. Wilk

 

 

 

Bob Room

 

 

Space Room

 

Track A Talks

 

11:25-11:55am

Lennaert Van Veen, University of Ontario Institute of Technology

Solving initial-boundary value problems without

numerical differentiation

Bob Room

11:55-12:10pm

Serene Wong, York University

Biological graph dissimilarity characterization using graph theory

Bob Room

12:10-12:25pm

James Desjardins, Brock University

Designing Electroencephalographic (EEG) analysis software with HPC in mind: Focus on a modular submission interface and flexible data annotation

Bob Room

12:25-12:40pm

Jonah Miller, University of Guelph

Testing Discontinuous Galerkin Methods in the Einstein Toolkit for Numerical Relativity

Bob Room

 

Track B Talks

 

11:25-11:55am

Abbas Ghasemi, University of Waterloo

HPC Application in Large Eddy Simulation of

Fuel Spray / Air Jet interaction

Space Room

11:55-12:10pm

Erik Bembenek, University of Waterloo

Modelling Surface Driven Flows in the Ocean

Space Room

12:10-12:25pm

Lucian Ivan, University of Toronto

A Fourth-Order Solution-Adaptive CENO Scheme for Space-Physics Flows on Three-Dimensional Multi-Block Cubed-Sphere Grids

Space Room

12:25-12:40pm

Benjamin Wilk, University of Ontario Institute of Technology

Predicting New Graphene - Boron Nitride 2D Nano-Materials: Structure Electron Bands Optical Response and Vibrations

Space Room

12:40-1:50pm

Lunch, Followed by the Poster Session

Bistro

1:50-2:00pm

Conference Photo

Atrium

2:00-3:00pm

Keynote Presentation

 

Saul Teukolsky

Simulations of Black Holes and Neutron Stars

Theatre

3:00-3:30pm

Coffee Break and Poster Session II

Atrium

 

 

Parallel Sessions II

(Each talk is scheduled for 12+3 or 15+5 minutes)

 

Track A

S. Kocheskeraii, S. Steinhaus, R. Woods, S. Green,

M. Ponce, R. Westernacher-Schneider

 

Track B

N.M. Abukhdeir, M. Garbanzo-Salas, A. Antipova, S. Badu, C. Viner,

M. Przedborski

 

 

 

 

Bob Room

 

 

Space Room

 

Track A Talks

 

3:30-3:50pm

Sadegh Babaii Kochekseraii, Sheridan College

Fast calculation of electro thermo static and elasticity fields in 3D-medium with isolated inclusions using application of Gaussian approximating functions

Bob Room

3:50-4:05pm

Sebastian Steinhaus, Perimeter Institute

HPC in Quantum Gravity

Bob Room

4:05-4:20pm

Rory Woods, McMaster University

Tree-Based Cosmological Radiative Transfer

Bob Room

4:20-4:35pm

Stephen Green, University of Guelph

Holographic Path to the Turbulent Side of Gravity

Bob Room

4:35-4:50pm

Marcelo Ponce, University of Guelph

Simulations of Binary Neutron Star Mergers

Bob Room

4:50-5:05pm

Ryan Westernacher-Schneider, University of Guelph

Towards Scaling Relations in Relativistic

Hydrodynamics and Gravity

Bob Room

 

Track B Talks

 

3:30-3:50pm

N.M. Abukhdeir, University of Waterloo

Polycrystalline On-Lattice Kinetic Monte Carlo

Simulations of Electrodeposition

Space Room

3:50-4:05pm

Marcial Garbanzo-Salas, University of Western Ontario

Uses of HPC in radar data processing and analysis

Space Room

4:05-4:20pm

Alena Antipova, University of Western Ontario

Motion of disc-shaped colloids and pairs of colloidal

discs in a nematic liquid crystal

Space Room

4:20-4:35pm

Shyam Badu, Wilfred Laurier University

Modeling of RNA Nanotube using Molecular Dynamics Simulation

Space Room

4:35-4:50pm

Coby Viner, University of Western Ontario

Validation of predicted mRNA splicing mutations using high-throughput transcriptome data

Space Room

4:50-5:05pm

Michelle Przedborski, Brock University

Critical Behavior of the Classical XY-model on Fractal Structures

Space Room

 

 

Wednesday May 07, 2014

There has been considerable interest in determining whether the universality hypothesis extends to systems which are of non-integer dimension or to systems which are scale invariant (fractals). Specifically research into these types of systems is concerned with determining the relevance of topological properties to their critical phenomena. We have performed Monte Carlo simulations for the XY model on three fractal lattices with different topological properties: the Sierpinski pyramid Menger sponge and Sierpinski carpet.

Collection/Series: 

 

Wednesday May 07, 2014

Turbulence is ubiquitous in hydrodynamics and its study is dominated by statistical methods and dimensional arguments. Even so analytic results tend to rely heavily on statistical symmetries. I will discuss some such results in non-relativistic turbulence and possible extensions to the relativistic case. The 2+1 dimensionality of our numerical setup allows for gaining insight about 3+1 gravity through the fluid/gravity duality. This work aims to further our understanding of the fluid side in its own right.

Collection/Series: 

 

Wednesday May 07, 2014
Speaker(s): 

By numerically solving Einstein equations we are able to study the strong regime of gravity. In many astrophysical scenarios strong gravity plays a fundamental role such as compact binary systems: e.g. Black Hole binaries binary Neutron Stars and Black Hole-Neutron Star systems. In this talk I will discuss the simulations our group has been conducting in binary Neutron Star system where we can study the dynamics and gravitational radiation of the systems but also establish important connections with electromagnetic counterparts and even testing alternatives theories of gravity (i.e.

Collection/Series: 

 

Wednesday May 07, 2014

This work has been published:Viner C Dorman SN Shirley BC and Rogan PK (2014)Validation of predicted mRNA splicing mutations using high-throughput transcriptome data [v1; ref status: indexedhttp://f1000r.es/2no]F1000Research20143:8 (doi:10.12688/f1000research.3-8.v1)Additionally this work has been accepted for a highlights presentation at the upcoming Great Lakes Bioinformatics Conference (GLBIO) in Cincinnati Ohio and it was recently presented as a poster at London Health Research Day (LHRD).Abstract:Interpretation of variants present in complete genomes or exomes reveals numerous s

Collection/Series: 

 

Wednesday May 07, 2014
Speaker(s): 

We study the dynamics of a 2 1-dimensional relativistic viscous conformal fluid in Minkowski spacetime. Such fluid solutions arise as duals under the gravity/fluid correspondence to 3 1-dimensional asymptotically antide Sitter (AAdS) black-brane solutions to the Einstein equation. We examine stability properties of shear flows which correspond to hydrodynamic quasinormal modes of the black brane. We find that for sufficiently high Reynolds number the solution undergoes an inverse turbulent cascade to long-wavelength modes.

Collection/Series: 

 

Wednesday May 07, 2014
Speaker(s): 

We construct the novel RNA nanpclusters- the RNAnanotubes made of several nanorings. We study the struc-tural properties (i.e. the Root Mean Square Deviation (RMSD)the radius of gyration and radial distribution function) ofRNA nanotube up to the size of about 20nm in physilogicalsolution that can be used for drug delivery into human body.We model RNA nanotube by utilizing molecular dynamicssimulation method implemented in NAMD and VMD. Thepatterns of energy and temperature variations of the systemsare also discussed.

Collection/Series: 

 

Wednesday May 07, 2014
Speaker(s): 

In the present work the motion of disc-shaped particles in a nematic liquid crystal was simulated via a Lattice Boltzmann algorithm. Under the action of a rotating magnetic field the colloidal disc with perpendicular surface anchoring immersed in a nematic liquid crystal experiences a torque and continues turning following the field. However when the disc reaches some critical position when the director field around it is highly distorted the disc suddenly flips to minimize the free energy.

Collection/Series: 

 

Wednesday May 07, 2014

One of the most challenging problems in computational galaxy formation is modeling distant heating and ionization by locally produced radiation. Most Radiative Transfer (RT) techniques are very computationally expensive and limit users to poor resolution or post-processing thus decoupling the radiation from the dynamics of the simulation. We present a new efficient method for RT implemented in the SPH code GASOLINE aimed at full cosmological simulations.

Collection/Series: 

 

Wednesday May 07, 2014

Accurate efficient and scalable computational methods are highly desirable for large-scale scientific computing applications especially for problems exhibiting spatial and temporal multi-resolution scales non-trivial geometries and complex boundary conditions (BSc). For global magnetohydrodynamics (MHD) modelling of space-physics problemshigh-performance approaches could significantly reduce the grid requirements to achieve targeted solution accuracies thereby enabling more affordable yet accurate predictions of space-plasma flows.

Collection/Series: 

 

Wednesday May 07, 2014

A low troposphere MST type radar located in Costa Rica was used to gather information up to 6 km. With the digital radar technique used thousands of sweeps can be recorded every second. Challenges in processing spectral analysis and radar imaging were addressed with tools provided by HPC.

Collection/Series: 

Pages

Scientific Organizers:

Nasser Mohieddin Abukhdeir, University of Waterloo
Erik Schnetter, Perimeter Institute