MATLAB R2014b Patch Released

MathWorks has informed us that they have found and resolved a number of problems in MATLAB R2014b that could lead to files being removed.

Information about the bugs and patch is available in bug report #1184018 on MathWorks’ website. In short, the most serious one is removal of files in the current directory when MATLAB exits. The others are crashes when using Simulink. The fixes are ZIP files that must be extracted in the MATLAB R2041b install directory, by a privileged user.

The main distribution from MathWorks has been patched, and installs from the ditto distribution site after the morning of January 16 will have these patches in place.

If you have any questions about these MATLAB patches, please contact Research Computing for answers. Remember to backup your files (such as the .m files) to prevent loss of data or work.

ESRI Canada Scholarship, 2015

ESRI Canada has given a scholarship to University of Saskatchewan students for the past several years. You can see previous winners on The Spatial Initiative (TSI) web site. They are offering this scholarship again this year. Details of the scholarship are available at the ESRI Canada website. (PDF file) Applications for the scholarship are to be sent via email to The deadline for application is January 24, 2015.

Applicants must have a “B+” average in their classes (i.e. a  minimum 75% average), and must include a CV and a transcript. They should also note how they have used ESRI software in the past. Other information required follows below: Continue reading

Introductory Course on High Performance Computing and Scientific Computing

High performance computing (HPC) is taking a fundamental role in scientific research around the world. Here at the University of Saskatchewan, the research computing group is making efforts to provide access to these new resources and technology to our researchers.  As part of these efforts, we designed an delivered an introductory course intended for those graduate students, PDFs and researchers who want to start using HPC resources to speed up their researches.

The first offering of our course ran on September 18 and 19.  During 12 hours, the 25 attendees (mostly graduate students and some staff members) reviewed the basic commands and concepts of a Linux system, and the characteristics of the different HPC systems that we have at the University (Plato, Zeno and Meton). They learned how to use efficiently these systems and which kind of problems fit better to each one: shared memory, distributed memory, GPU clusters, and large memory systems. Finally, they analyzed and solved practical examples using the systems (for more details see the course outline below).

Originally we designed the course with an aim to bring new users with no experience or little experience with Linux systems and HPC servers, to a point where they must be able to deploy HPC applications on the most suitable system depending on the problem at hand. The contents of the course could be customized, however, for future offerings according to the attendees backgrounds and interests. We are willing to offer the course again soon, with next offering potentially in January, as long as there are people interested. So, please do not hesitate to contact us at with your questions and comments if you are interested in attending.

Original course outline:

1. Introduction to scientific computing
2. Linux basics
3. Compiled and interpreted languages
4. High performance computers
5. Running serial codes in a server
6. Running parallel code in distributed memory systems
7. Running parallel code in shared memory systems
8. Running code with GPU acceleration

Coast2Coast Fall Seminar Series in WestGrid Collaboration Facility: Antibody Sequencing

The University has been participating in the Coast2Coast Seminar series for a number of years.  Organized out of IRMACS at Simon Fraser University, two themed seminar series are delivered per year, Fall and Spring.  This term’s C2C Seminar is on Antibody Sequencing, organized by Dr. Felix Breden from SFU.

 The University of Saskatchewan local connection to this seminar series will be held in the WestGrid Visualization and Collaboration Facility (Agriculture 2D71).  The first seminar of the series is Tuesday, September 30 at 12:30 CST Saskatoon time.

Space is limited, so please RSVP to for each attendee.

Felix Breden describes the Seminar Series beneath the cut:

Continue reading

REDCap Service Launch Announcement

As pre-announced in an earlier post in this blog, REDCap hosting is being launched as a service from ICT today.

REDCap is a data collection and management tool written by a group at Vanderbilt University, and adopted by over 1100 institutions world-wide from Dunedin to Reykjavik, who form the REDCap Consortium. Researchers on campus have been requesting this tool for their research.

The University of Saskatchewan implementation is described on this service page in ICT’s website. There are some restrictions on the use of the service, many having to do with the terms of our agreement signed to allow us to join the REDCap Consortium. Researchers wishing to use the service will complete a form and send that to the service support team.

We will respond with information on how to access the REDCap service and other information on its use. There is currently no charge for the service, and none are anticipated in the future.

For the REDCap service only, please contact with any questions or support requests.

ESRI User Conference to be held in Saskatoon

ESRI, the makers of the ArcGIS software, is holding their user conference in Saskatoon on the 16th of September. There are early bird rates available until September 5. Details are available on the conference web site.

Attendees normally pay ~$150. However, the fee for educators/students is $35, which includes a hot lunch and reception. Please note that a valid U of S ID is required to qualify for the reduced rate.

If you are available to present your work (e.g., posters) to the GIS community, please contact André Piasta at

After you click “Register Now” on the conference site, on the registration page you can select Educator/Student as “attendee type” which should trigger the reduced rate.

Should you have any questions, please contact André Piasta at