High-Performance Computing Courses at RCS: Difference between revisions

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# Inform us about the Linux background of the researchers; this information aids us in designing the course effectively.
# Inform us about the Linux background of the researchers; this information aids us in designing the course effectively.


Past courses offered by the Research Computing Services Team:
== Past courses offered by the Research Computing Services Team ==


=== Year 2023 ===
=== Year 2023 ===


* May 01, 2023- Grad Success Week (GSW) 2023 (invited by: Paul Pappin)
* Nov 07, Nov 09, 2023 - course BMEN 619.42 (invited by: Singe Bray)
: ''HPC training for BMEN619.42''
* Oct 31, 2023- course ENSF 619.02 (invited by: Ethan MacDonald).
: ''Parallel Models''
* May 01, 2023 - Grad Success Week (GSW) 2023 (invited by: Paul Pappin)
:  ''Data Analysis in R and Accessing Advanced Research Computing''  
:  ''Data Analysis in R and Accessing Advanced Research Computing''  
* Jan 04, 2023 - Session for undergraduate bioinformatics students (invited by: David Anderson)
* Jan 04, 2023 - Session for undergraduate bioinformatics students (invited by: David Anderson)
:  ''Introduction to High-Performance Computing Infrastructure at the University of Calgary''
:  ''Introduction to High-Performance Computing Infrastructure for Bioinformatics''
* Oct 10, 2023 - ENSF 619


=== Year 2022 ===
=== Year 2022 ===
* Nov 01, 2022 - course ENSF 619.02 (invited by: Ethan MacDonald).
: ''Parallel Models''
* May 05, 2022- Grad Success Week (GSW) 2022 (invited by: Paul Pappin)
* May 05, 2022- Grad Success Week (GSW) 2022 (invited by: Paul Pappin)
:  ''Data Analysis in R and Accessing Advanced Research Computing''
:  ''Data Analysis in R and Accessing Advanced Research Computing''
* Jan 04, 2022- Block week 2022 by David Anderson (invited by: David Anderson)
* Jan 04, 2022- Block week 2022 by David Anderson (invited by: David Anderson)
:  ''Introduction to High-Performance Computing Infrastructure at the University of Calgary''
:  ''Introduction to High-Performance Computing Infrastructure at the University of Calgary''
*Oct 11, 2022 - ENSF 619


=== Year 2021 ===
=== Year 2021 ===
* Nov 02.2022 - course ENSF 619.02 (invited by: Ethan MacDonald).
: ''Parallel Models''
* May 06, 2022 (invited by: Svetlana Yanushkevich),
: ''HPC training for Summer research students''.
* May 05, 2021- Grad Success Week (GSW) 2021 (invited by: Paul Pappin)
* May 05, 2021- Grad Success Week (GSW) 2021 (invited by: Paul Pappin)
:  ''Data Analysis in R and Accessing Advanced Research Computing''  
:  ''Data Analysis in R and Accessing Advanced Research Computing''  
* Apr 22, 2021 - Centre for Health Informatics  
* Apr 22, 2021 - Centre for Health Informatics  
:  ''Secure Computing on the MARC cluster''
:  ''Secure Computing on the MARC cluster''
*Oct 21, 2021 - ENSF 619


=== Year 2020 ===
=== Year 2020 ===
* Dec 08, 2020 (invited by Samira’s Siahrostami)
: ''HPC training for Siahrostami research group''.
* Aug 04, EBG Group
: ''ARC intro trainning''.
* Jun 22, Hamidreza Zareipour's group and Michael Kallos group
: ''HPC intro training''.
* May 11. Dr. Whalley’s group
: ''HPC intro training''.
* May 05, 2020- Grad Success Week (GSW) 2020 (invited by: Paul Pappin)
* May 05, 2020- Grad Success Week (GSW) 2020 (invited by: Paul Pappin)
:    ''Data Analysis in R and Accessing Advanced Research Computing''
:    ''Data Analysis in R and Accessing Advanced Research Computing''
Line 35: Line 63:


**********************************************************************************************************************************************
**********************************************************************************************************************************************
== Overview of the courses we offer ==
== Overview of the courses we offer ==


=== 1. Introduction to Bash and Linux - Basic ===
=== Introduction to Bash and Linux - Basic ===


:    ''I. Understanding the Command Line Interface (CLI)''
:    ''I. Understanding the Command Line Interface (CLI)''
Line 46: Line 75:
:*          Opening the Terminal
:*          Opening the Terminal
:*          Basic Shell Commands
:*          Basic Shell Commands
:                  1. ls: Listing files and directories
:                  2. cd: Changing directories
:                  3. pwd: Present working directory


:    ''III. File and Directory Manipulation''
:    ''III. File and Directory Manipulation''
Line 58: Line 84:
:*          cat, head, and tail commands
:*          cat, head, and tail commands
:*          grep for pattern matching
:*          grep for pattern matching
:*.          Redirection and Pipelines
:*           Redirection and Pipelines


:      ''V. Basic Scripting''
:      ''V. Basic Scripting''
Line 64: Line 90:
:*          Variables and Basic Control Structures
:*          Variables and Basic Control Structures
:*          Introduction to Functions
:*          Introduction to Functions
=== Introduction to Bash and Linux - Advanced ===
:      ''I. Advanced Text Processing''
:*          Regular Expressions
:*          Text Manipulation
:      ''II. Shell Scripting Best Practices
:*          Error Handling and Logging
:*          Command-Line Arguments
:*          Debugging Techniques
.
.
.
.
.
=== Introduction to Python on ARC ===
=== Introduction to R on ARC ===
=== How to Speed Up R Codes? ===
=== Introduction to Singularity/Apptainer - Basic ===
=== Introduction to Singularity/Apptainer - Advanced ===

Latest revision as of 23:17, 2 January 2024

For University of Calgary researchers intending to leverage the HPC infrastructure for their research work and seeking customized sessions, please contact us at support@hpc.ucalgary.ca for further discussion.

To customize our courses according to your requirements, please furnish the following details at least four weeks in advance:

  1. Specify the number of researchers to undergo training (minimum of 5 or more).
  2. Share the domain of your research.
  3. Let us know if you have a particular workflow or application in mind.
  4. Inform us about the Linux background of the researchers; this information aids us in designing the course effectively.

Past courses offered by the Research Computing Services Team

Year 2023

  • Nov 07, Nov 09, 2023 - course BMEN 619.42 (invited by: Singe Bray)
HPC training for BMEN619.42
  • Oct 31, 2023- course ENSF 619.02 (invited by: Ethan MacDonald).
Parallel Models
  • May 01, 2023 - Grad Success Week (GSW) 2023 (invited by: Paul Pappin)
Data Analysis in R and Accessing Advanced Research Computing
  • Jan 04, 2023 - Session for undergraduate bioinformatics students (invited by: David Anderson)
Introduction to High-Performance Computing Infrastructure for Bioinformatics
  • Oct 10, 2023 - ENSF 619

Year 2022

  • Nov 01, 2022 - course ENSF 619.02 (invited by: Ethan MacDonald).
Parallel Models
  • May 05, 2022- Grad Success Week (GSW) 2022 (invited by: Paul Pappin)
Data Analysis in R and Accessing Advanced Research Computing
  • Jan 04, 2022- Block week 2022 by David Anderson (invited by: David Anderson)
Introduction to High-Performance Computing Infrastructure at the University of Calgary
  • Oct 11, 2022 - ENSF 619

Year 2021

  • Nov 02.2022 - course ENSF 619.02 (invited by: Ethan MacDonald).
Parallel Models
  • May 06, 2022 (invited by: Svetlana Yanushkevich),
HPC training for Summer research students.
  • May 05, 2021- Grad Success Week (GSW) 2021 (invited by: Paul Pappin)
Data Analysis in R and Accessing Advanced Research Computing
  • Apr 22, 2021 - Centre for Health Informatics
Secure Computing on the MARC cluster
  • Oct 21, 2021 - ENSF 619

Year 2020

  • Dec 08, 2020 (invited by Samira’s Siahrostami)
HPC training for Siahrostami research group.
  • Aug 04, EBG Group
ARC intro trainning.
  • Jun 22, Hamidreza Zareipour's group and Michael Kallos group
HPC intro training.
  • May 11. Dr. Whalley’s group
HPC intro training.
  • May 05, 2020- Grad Success Week (GSW) 2020 (invited by: Paul Pappin)
Data Analysis in R and Accessing Advanced Research Computing


Overview of the courses we offer

Introduction to Bash and Linux - Basic

I. Understanding the Command Line Interface (CLI)
  • Overview of CLI vs. Graphical User Interface (GUI)
  • Importance of CLI in Bioinformatics and Data Science
II. Getting Started with Bash
  • Opening the Terminal
  • Basic Shell Commands
III. File and Directory Manipulation
  • Creating and Deleting Files/Directories
  • Copying and Moving Files/Directories
  • Understanding Permissions (chmod)
IV. Text Processing with Bash
  • cat, head, and tail commands
  • grep for pattern matching
  • Redirection and Pipelines
V. Basic Scripting
  • Creating and Executing Bash Scripts
  • Variables and Basic Control Structures
  • Introduction to Functions

Introduction to Bash and Linux - Advanced

I. Advanced Text Processing
  • Regular Expressions
  • Text Manipulation
II. Shell Scripting Best Practices
  • Error Handling and Logging
  • Command-Line Arguments
  • Debugging Techniques

. . . . .

Introduction to Python on ARC

Introduction to R on ARC

How to Speed Up R Codes?

Introduction to Singularity/Apptainer - Basic

Introduction to Singularity/Apptainer - Advanced