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Research computing workshops coming to the University of Saskatchewan - January 15-18, 2019

WestGrid and the University of Saskatchewan (USask) are co-hosting a series of free Research Computing Workshops on the USask campus during January 15-18, 2019. Researchers in all disciplines are invited to participate (you don't need to be based at the USask). No prior experience is required for any of the topics being covered.

You can attend single sessions or the entire series. There is no cost to attend but you must register online in advance.

Registration Instructions

** IF YOU ARE BASED AT USASK **

Please follow the links below to register via the USask website:

** IF YOU ARE A NON-USASK ATTENDEE **

Daily Schedule

Each topic is a full-day session. Each day will follow the same schedule:

  • Morning: 9:00 am - 12:00 pm (noon)
  • Lunch Break: 12:00 - 1:00 pm (attendees responsible for their own lunch) 
  • Afternoon: 1:00 - 4:00 pm

All sessions are held at the University of Saskatchewan. Check the session descriptions below for the room locations on campus.

Session Descriptions

Day 1 - Tueday, JAN-15
Room 175, Physics Building, USasak 

Moving your research from Windows-based desktops to Linux and command line in remote servers

This workshop will be a hands-on introduction to Linux command line and the interaction with a remote server. We will review basic Linux commands, file management (edit, copy, remove and remote-transfer files), directories and the file system, remote access, basic version control (git, github), bash scripts and basic bash programming.

Presenter:

  • Dr. Alex Razoumov, Westgrid Training and Visualization Coordinator, Compute Canada

Pre-requisites/requirements:

  • This is an introductory course, no previous experience is required.
  • We will provide guest accounts to one of our Linux systems.
  • All attendees will need to bring their laptops with wireless access and with a remote SSH client installed (on Windows laptops we recommend the free edition of https://mobaxterm.mobatek.net/download.html; on Mac and Linux laptops no need to install anything).

Day 2 - Wednesday, JAN-16
Room 175, Physics Building, USask

Introduction to HPC: using clusters to speed up your research

We will start with an overview of the hardware of common HPC clusters, and quick description of the resources available on National systems (Cedar and Graham), and locally at the UofS (local cluster Plato, DataStore and Globus). We will then continue learning the basic tools and techniques to work on a cluster: software environment and modules, overview of installed programming languages and compilers, working with Make files and installing new software locally. Finally, we will take a look at Slurm job scheduler: why use it, fairshare and priority, submitting serial jobs and job arrays, submitting OpenMP / MPI / hybrid / GPU jobs, working inside interactive jobs, and tracking your job's memory usage. We will also take a quick look at working with common packages such as R, Python and Matlab on the clusters, as well as best practices in cluster workflows.

Presenters:

  • Dr. Alex Razoumov, Westgrid Training and Visualization Coordinator, Compute Canada
  • Sergiy Stepanenko, Advanced Computing Coordinator, University of Saskatchewan
  • Dr. Juan Zuniga, University of Saskatchewan

Pre-requisites/requirements: I

  • n this workshop we assume all attendees have a working knowledge of the Linux command line (this material will be covered in Day 1 of our workshop series, Moving your research from Windows-based desktops to Linux and command line in remote servers).
  • All attendees will need to bring their laptops with wireless access and with a remote SSH client installed (on Windows laptops we recommend the free edition of https://mobaxterm.mobatek.net/download.html; on Mac and Linux no need to install anything).

Day 3 - Thursday, JAN-17
B16, Law Building, USask

Introduction to scientific visualization: plotting, interactive 3D, scripting, animation, large datasets

We will start with simple 1D/2D/3D plotting using plot.ly. The rest of the day we will study 3D scientific visualization with ParaView, an open source, multi-platform data analysis and visualization tool designed to run on a variety of hardware from an individual laptop to large supercomputers. With ParaView users can interactively visualize 2D and 3D data sets defined on structured, adaptive and unstructured meshes or particles, animate these datasets in time, and manipulate them with a variety of filters. ParaView supports both interactive (GUI) and scripted (including offscreen) visualization, and is an easy and fun tool to learn.

Presenter:

  • Dr. Alex Razoumov, Westgrid Training and Visualization Coordinator, Compute Canada

Pre-requisites/requirements:

  • This is an introductory course, no prior visualization experience is required.
  • This workshop will feature many interactive hands-on exercises, so attendees need to bring a laptop (and perhaps a power cord for use throughout the day) and should have ParaView installed from https://www.paraview.org/download before the workshop (we recommend version 5.6).
  • We will provide all sample data and codes for the exercises, and you can bring your dataset if you want to visualize it with ParaView.
  • No need to install plot.ly on your laptop — we will have it installed on a remote cluster.

Day 4 - Friday, JAN-18
Room 144, Edwards School of Business, USask

Foundations of parallel programming and the Chapel programming language

This course is a general introduction to the main concepts of Parallel programming and the Chapel programming language. Chapel is a relatively new language for both shared and distributed-memory programming, with easy-to-use, high-level abstractions for both task and data parallelism that make it ideal for learning parallel programming for a novice HPC user. Chapel is incredibly intuitive, striving to merge the ease-of-use of Python and the performance of traditional compiled languages such as C and Fortran. Parallel constructs that typically take tens of lines of MPI code can be expressed in only a few lines of Chapel code. Chapel is open source and can run on any Unix-like operating system, with hardware support from laptops to large HPC systems.

Presenters:

  • Dr. Alex Razoumov, Westgrid Training and Visualization Coordinator, Compute Canada
  • Dr. Juan Zuniga, University of Saskatchewan.

Pre-requisites/requirements:

  • This is an introductory course so no prior parallel programming experience is required, however, having some programming background will allow the attendees to get the most out of this workshop. Also, we strongly recommend that all attendees know the material covered on days 1 and 2 of our workshop series, Moving your research from Windows-based desktops to Linux and command line in remote servers, and Introduction to HPC: using clusters to speed up your research.
  • All attendees will need to bring their laptops with wireless access and with a remote SSH client installed (on Windows laptops we recommend the free edition of https://mobaxterm.mobatek.net/download.html; on Mac and Linux no need to install anything).
  • We will be using Chapel on a remote cluster, but it can also be installed on laptops from https://chapel-lang.org.

More Information

Contact us if you have any questions about these sessions.