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WestGrid - Spring 2013




Date: January 16, 2013
Roman Baranowski, Site Lead, University of British Columbia

A video archive for this particular session is not available. To view an archive of a similar session on this topic, presented on October 17, 2012 by WestGrid's University of Manitoba Site Lead, Jonatan Aronsson, please click here.

How to Use WestGrid Tutorial
This session will provide attendees with a step-by-step tutorial on using WestGrid machines, including demonstrations of how to log in, submit jobs, move data, troubleshoot, etc. This will be an introductory-level session, covering the basics of getting started and providing tips for efficient and effective use of the machines. WestGrid Support Personnel will be on-hand at each site to answer more advanced questions attendees may have.


Date: February 6, 2013
Speaker: Brian Corrie, Visualization Coordinator, WestGrid

To view the archived video, click here.

Visualization Tutorial
This session provides attendees with a step-by-step tutorial on using WestGrid resources for the visualization of scientific data. The talk will discuss the visualization software that is available for use on WestGrid computational resources and how to use this software remotely from your desktop. In particular, the presentation will cover the use of the Graphics Processing Units (GPUs) on for remote visualization of large data sets.


Date: March 6, 2013 
Andriy Kovalenko, Adjunct Professor, University of Alberta, and Senior Research Officer at the National Institute for Nanotechnology.

To view the archived video, click here.

A Closer Look at the HPC Behind Multiscale Theory and Modeling

Andriy Kovalenko is an Adjunct Professor in the Department of Mechanical Engineering at the University of Alberta and a Senior Research Officer at the National Institute for Nanotechnology. His research focuses on (i) developing fundamental methodology of multiscale theory, modeling and simulation, capable of predicting the behaviour of complex nanomaterials and nanosystems, and (ii) applying this predictive methodology to provide understanding and rational design of realistic systems and processes of crucial importance in nanoscience and nanotechnology. An essential part of this multiscale methodology is statistical-mechanical, integral equation theory of molecular liquids, in particular, the three-dimensional (3D) molecular theory of solvation, also known as the three-dimensional reference interaction site model with the Kovalenko-Hirata closure relation (3D-RISM-KH). The multiscale methods he developed include the self-consistent field coupling of quantum chemistry methods (ab initio CASSCF, Kohn-Sham DFT, and Orbital-Free Embedded DFT) with 3D-RISM-KH for nanochemistry, photochemistry, electrochemistry, and nanocatalysis in solution, at solid-liquid interfaces, and in nanoporous materials; 3D-RISM-KH based protein-ligand docking algorithms; milti-time-step molecular dynamics (MTS-MD) of biomolecules steered by solvation forces obtained from 3D-RISM-KH for function-related solvation, folding, misfolding, aggregation, interaction, and bioadsorption of proteins and other biomolecular and hybrid nanosystems in solution. In this talk, Dr. Kovalenko will discuss how WestGrid and Compute Canada - Calcul Canada resources support and advance those investigations.


Date: March 20, 2013 
Doug Phillips, Senior Computational Science Consultant, University of Calgary

To view the archived video, click here.

Using MATLAB on WestGrid systems
MATLAB is a general-purpose high-level programming package that is available for use on WestGrid. It is typically used for numerical work such as linear algebra, but, has many add-on toolboxes to extend its capabilities into discipline-specific areas. Although MATLAB is probably used most often on researchers' desktops as an interactive program through its desktop graphical user interface, that is not the primary way it is used in the batch-oriented WestGrid environment.

This talk will cover the various ways in which MATLAB can be run on WestGrid systems, as determined by the restrictions imposed by licensing considerations. In particular, the use of the MATLAB compiler to create standalone applications will be illustrated. The compiled applications can then be run in normal WestGrid batch jobs.

Note that the talk will not cover MATLAB programming. Instead, it is intended for researchers who would like to run their own MATLAB code on WestGrid, but, are unsure of how to get started with doing so. Most of the material for the talk is drawn from the MATLAB pages on the WestGrid web site at