Westgrid – High Performance Computing at the University of Alberta

A look inside of high performance computing at the University of Alberta.

As part of Research Data Management week (May 4-8 2015), several sessions on High Performance Computing are bundled into the Compute Canada and WestGrid User Training Seminar.  I was lucky enough to attend a session on High Performance Computing that concluded with a tour of the Westgrid High Performance Computing center on campus at the University of Alberta.

Hidden away in the depths of General Services Building (I knew this building housed some critical facilities) is the server center. It holds two of the most powerful systems in Canada, and perhaps the world: Jasper (4160 cores, 8 TB RAM, 356 TB file system) and Hungabee (2048 cores, 16 TB RAM, 53 TB file system).

Westgrid is connected by high-performance networks, so users can connect to the system which best fits their needs regardless of physical location.

Rumors were confirmed, namely that there is a small section of the North Saskatchewan River that does not freeze due to the water exchange (ice cold water in to cool the systems and hot  water out) to keep these behemoths running smooth.

Find the photo here: http://www.urbanrail.net/am/edmo/Edmonton-Dudley_B_%20Menzies_LRT_Bridge_winter.JPG
Photo by XuanZhang

The workshop also did a great job at breaking down jargon terms like the ‘cloud’, the ‘grid’, and ‘big data’ into meaningful, technical, understandable concepts.

Computer Science Projects

Computer Science projects in Artificial Intelligence, Machine Learning, Computer Vision and Reinforcement Learning.

In September 2014 I started a graduate program in Computer Science at the University of Alberta, in beautiful Edmonton, Alberta, Canada.

Since I started the program, I have been able to work on some awesome projects. While I do host some code publicly, lots of the projects do not have public repositories.

Feature Selection and Classification in EEG Motor Imagery

CMPUT 551: Machine Learning with Dr. Russ Greiner and Dr. Patrick Pilarski

Comparing Contemporary Trackers on Benchmark Datasets

CMPUT 615: Multiple View Geometry with Dr. Martin Jagersand

Perceptive Prosthetics

Dr. Patrick Pilarski

Big Data, Large Scale Psychology Studies using Amazon Turk

Dr. Kyle Mathewson

Projects in development:

  • CleanMyStreet.ca – Find out when your neighborhood will be cleaned.
  • ThisIsLikeThat – Find your favorite restaurant in a new city.
  • Optimal Pub Crawling in Edmonton
  • Eigenfaces in Photobooth Photos
  • Heart Rate from Video

Thesis, First First Author and Convocation

Academic news nearing the end of 2014.

First, my thesis publication embargo has finally been lifted and my Master’s thesis, Simultaneous Measurement of Blood Flow and Oxygen Consumption Immediately Post-Exercise with Magnetic Resonance Imaging, is now posted and you can access it on the Education & Research Archive, or download it directly.

I have just recently been informed that the second chapter of the thesis, Feasibility and reproducibility of measurement of whole muscle blood flow, oxygen extraction, and VO2 with dynamic exercise using MRI, will be published in Magnetic Resonance in Medicine in the coming weeks. That marks my very first first author publication.

November 19 2014 marked convocation day for my degree, Master of Science in Biomedical Engineering, to be conferred at the Jubilee Auditorium.

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I was asked to join the Platform Party as a past Governor on the Board of Governors of the University of Alberta.

63431_10152389644960404_5829216227945298672_nAs part of each convocation celebration the University likes to celebrate the mentorship of several graduands. Here is a great write up on the motivation behind my research in Biomedical Engineering: Ingenuity helps engineering grad succeed in strong field.

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Here are a few behind the scenes photos from the article’s photoshoot in the Peter S. Allen MR Research Centre along side my two wonderful mentors, Mark Haykowsky and Rich Thompson.

Neonatal Resuscitation Simulation Walkthough

Neonatal Resuscitation Training Simulation Training in Photos

I am currently a Teaching Assistant for CMPUT250: Computers and Games, and one of the groups is working with the Community Service Learning office at the University of Alberta as well as the Northern Alberta Neonatal Program at the Royal Alexandra Hospital Neonatal Intensive Care Unit.

In CMPUT250, each team applies class concepts to create a short narrative-based game using the Neverwinter Nights™ game engine from BioWare, for one group the proposal is to design a serious game that could be used as a supplementary tool for Neonatal resuscitation training/ re-training.

A major component in the design and build of this game is to research how neonatal resuscitation training occurs now in the hospital. I was lucky enough to be invited along to see the simulator.

Looking forward to updating this as the team progresses. In the mean time, this was an invaluable experience which I very much appreciated being a part of.

Thesis Defense Live Blog

Minute by minute live blog of my thesis defense. TL;DR I passed.

6:38 am – Wake up 7 minutes before the alarm clock. First success of the day. Disabled alarms for 7:00 am and 7:15 am. Will not be needing them.
7:02 am – Bike to the University of Alberta. Be sure to note the beautiful green and gold foliage. Arrive at the conference room.
7:30 am – Set up the projector and the Mac Book Air in the conference room. Test the slides. Rehearse the timing. Items needed for the defense include: MacBook Air, 1 black pen, 2 sheets of blank paper, 750 mL water.

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8:00 am – Walk to the Tim Hortons. Purchase: 20 assorted Tim Bits, 4 ginger snap cookies, 1 bacon snack wrap and a single espresso. Consume bacon grilled breakfast wrap and espresso.

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8:30 am – Start the coffee maker in the  conference room.  Ensure that the room smells like coffee and fresh gingerbread cookies.
9:00 am – Call to order by the thesis committee chair
9:05 am – Excuse myself from the room to allow preliminary discussion.
9:10 am – Commence 20 minute thesis defense presentation.
9:16 am – Consume 250mL of room temperature water
9:30 am – Conclude the 20 minute presentation in 20:38s … Chair makes joke that he turned off his ears for the last 38 s. Quick retort that in that time all I did was thank him.
9:31 am – Questions commence. 4 committee members, 15 minutes of questioning each, from most external to the research to most internal. Questions range from general to specific and easy to hard. Some writing on a CHALK BOARD (noted for posterity’s sake).

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10:30 am – Questions conclude almost exactly on time. Motion to recess.
10:34 am – Some brief discussion with lab mate during the recess. Consume 200 mL water.
10:43 am – Motion to reconvene. 2nd round of questions, following the same order.
10:46 am – Break to deliberate and discuss. Excused myself from the room.
10:48 am – Inviting to rejoin the meeting. Pass subject to the revisions outlined in the committee’s notes. Feeling of satisfaction, and humble pride emanating from my body. Awkward handshakes ensure.
10:49 am – Motion to adjourn.
10:53 am – Fire alarm goes off in the building. Everyone evacuates. This is a great opportunity to inform everyone of the results of the defense.

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11:05 am – Review committee’s notes on revisions, and start to work through the edits.
12 noon – Enjoy lunch with the committee. Talk about success.

Thank you to my committee for asking the hard questions and not letting me off easy.
Thank you to my friends and family who volunteered their time and effort in my pursuit of scientific knowledge.

I have performed in front of thousands of people with no idea what I was going to say, and yet, I was more nervous performing to a group of four extremely supportive individuals with a well rehearsed talk I had been preparing for three years.

Master of Science in Biomedical Engineering

CaptureUpdate September 5, 2014: Thesis defense date has been scheduled, see the attached PDF announcement:

I have been honoured to work with the incredibly inspirational Dr. Richard Thompson and Dr. Mark Haykowsky at the University of Alberta on a Master’s in Biomedical Engineering.

As I move towards completion and defense of my thesis, and publication of the results from our major pilot study, I thought it would be nice to post some video of the content I have been studying and presenting at several conferences. The first is a video of the Research Elevator Pitch Competition (or the Thesis in Three Minutes) at the Faculty of Engineering Graduate Research Symposium 2014. I was honoured to be awarded 2nd place in the competition; the winner, Katherin Evans, had an incredible pitch on “Optimizing a Tactor System to Provide Sensory Feedback for Upper Limb Amputees”.

Added a few reactions to make the video a little more dynamic and enjoyable. Here is the video of the full 12 minute that I was honoured to give at the Faculty of Engineering Graduate Research Symposium 2014. This is very similar to the talk that I gave at the International Society for Magnetic Resonance in Medicine Annual Meeting in Milan, Italy May 10-18 2014.