RCS Summer School 2024

Research Computing Services' 3rd annual summer school offers a handful of courses with a wide range of topics to help empower your research. We will cover topics including Linux/Slurm, ARC/HPC, Research Data Management (RDM) and Data Management Plan (DMP), working with research software and workflows, plus much more. The sessions and workshops is available from introductory to intermediate levels and is suitable for everyone interested in research in HPC.

The summer school will run from Monday, June 10 through to Wednesday, June 12, 2024 from 9AM to 5PM. This 3 day event is completely free to all University of Calgary members.

Registration

Registration is required to attend the RCS Summer School sessions. Registration is free to all members of the University of Calgary only.

Register now

There will be a limit of approximately 100 seats. If you are unable to attend after registering, please cancel/modify your registration or notify us via email.

Topics

• Introduction to RCS services and HPC resources
• Introduction to Linux & Bash command line
• Using Linux utilities for large datasets
• Hands on with Linux & Slurm: Workshop
• Using Open OnDemand on ARC
• Develop a research data management plan
• Reproducible data management with Datalad
• Digital File Management
• Using containers in HPC with Apptainer
• Managing scientific software with Conda
• Research workflow development with Prefect
• AWS: ML in the Cloud, a walkthrough followed by a workshop
• NVIDIA: Workflow optimization using NVIDIA GPUs
• Dell & AMD: Machine learning with Dell and AMD

Schedule

The summer school sessions will be held in ICT 102 and ICT 114. Refreshments will be available in ICT 114 on all 3 days.

Time	June 10		June 11		June 12
	Track 1	Track 2	Track 1	Track 2	Track 1	Track 2
8:30 AM	Registration & check-in ICT 102		Registration & check-in ICT 102		Registration & check-in ICT 102
9:00 AM	Introduction to RCS ICT 102, 9:00 AM - 9:20 AM Jill Kowalchuk	Refreshments ICT 114	The Alliance: Introduction ICT 102 Brock Kahanyshyn	Refreshments ICT 114	TBD ICT 102	Refreshments ICT 114
9:30 AM	Introduction to Linux, Bash, and the command line ICT 102, 9:30 AM - 10:30 AM Robert Fridman	Data in Motion: Navigating Storage Solutions for Active Research Data ICT 114, 9:30 AM - 11:20 AM Ian Percel	Introduction to HPC resources ICT 102, 9:30 AM - 10:20 AM Robert Fridman, Dave Schulz	Reproducible Data Management with Datalad: Part II ICT 114, 9:30 AM - 10:20 AM David Deepwell, Pedro Martinez	NVIDIA: Workflow Optimization with NVIDIA GPUs ICT 102, 9:30 AM - 12:00 PM Jonathan Dursi
10:00 AM				Refreshments ICT 114
10:30 AM	Workshop: Hands on with Linux & Slurm ICT 102, 10:30 AM - 11:50 AM Robert Fridman		Linux tools & utilities for working with large data sets ICT 102, 10:30 AM - 11:20 AM Leo Leung, Dave Schulz
11:00 AM
11:30 AM		Reproducible Data Management with Datalad: Part I ICT 114, 11:30 AM - 12:20 AM David Deepwell, Pedro Martinez	RCS Q&A period: Ask RCS anything ICT 102, 11:30 AM - 12:00 PM RCS Team
12:00 PM	Open OnDemand on ARC ICT 102, 12:00 AM - 12:20 AM Leo Leung		Lunch break 12:00 PM - 1:00 PM		Lunch break 12:00 PM - 1:00 PM
12:30 PM	Lunch break 12:30 PM - 1:30 PM
1:00 PM			Research Data Management and Data File Management ICT 102, 1:00 PM - 2:20 PM Jennifer Abel, Alex Thistlewood, Ingrid Reiche	Refreshments ICT 114	Dell & AMD: Machine learning with Dell & AMD ICT 102, 1:00 PM - 1:50 PM Rob Lucas
1:30 PM	AWS: Inspiring the art of the possible ICT 102, 1:30 PM - 1:50 PM AWS	Refreshments ICT 114
2:00 PM	AWS: How AWS works with Researchers ICT 102, 2:00 PM - 2:20 PM AWS
2:30 PM	AWS: Machine Learning with low-code workshop ICT 102, 2:30 PM - 4:50 PM AWS		Introduction to containers with Apptainer ICT 102, 2:30 PM - 3:20 PM Tannistha Nandi		Prefect for Research Workflow Development ICT 102, 2:30 PM - 3:50 PM David Deepwell, Pedro Martinez
3:00 PM
3:30 PM			Managing scientific software with Conda ICT 102, 3:30 PM - 4:20 PM Dmitri Rozmanov
4:00 PM					End of day: 4:00 PM
4:30 PM			End of day: 4:30 PM
5:00 PM	End of day: 5:00 PM

Sessions

Session	Time and Location	Synopsis
Introduction to RCS	June 10, 9:00AM - 9:20AM ICT 102	We will begin the RCS summer school with a quick introduction by Jill Kowalchuk, the Interim director of Research Computing Services. We will introduce the RCS team, provide a high level overview of our services, and how to get help and support from our analysts. Speaker: Jill Kowalchuk Format: Lecture Level: Introductory Prerequisites: None
Introduction to Linux, Bash, and the command line	June 10, 9:30AM - 10:30AM ICT 102	This course provides you with essential skills to effectively use the Linux command line. We will go over from ground up how to log-in and interact with our HPC cluster, traverse the filesystem, execute programs, and manage files. This beginner friendly session requires no prior experience to Linux. We recommend bringing your own device to follow along. By the end of the course, you should be familiar with what is possible with the Linux command line. Speaker: Robert Fridman Format: Lecture + Follow along Level: Introductory Prerequisites: None
Workshop: Hands on with Linux & Slurm	June 10, 10:30AM - 11:50 AM ICT 102	This follow-up workshop comes immediately after the Introduction to Linux session. We will build on what we learned in the previous session and go into details on how to use the HPC cluster using the Slurm scheduler. This workshop will provide you with the skills necessary to write a simple Slurm batch script, submit jobs to Slurm, view and manage your jobs. By the end of the course, you will be familiar with what Slurm is, how it fits in in a HPC environment, and how to start using Slurm on our HPC clusters for your research. This is a beginner friendly workshop. You should be familiar with the Linux command line. We recommend bringing your own device to follow along. Speaker: Robert Fridman Format: Workshop + Hands on Level: Introductory Prerequisites: None
Open OnDemand on ARC	June 10, 12:00 AM - 12:20 AM ICT 102	Did you know you can run a Linux desktop and graphical tools on ARC? This session will cover what ARC Open OnDemand is and how it may help with your research. We will show you how to: Connect to Open OnDemand through your browser Start a graphical desktop environment in our ARC HPC cluster environment View and mange files in your home directory via Open OnDemand Connect to ARC through your web browser View the status of your submitted jobs By the end of this session, you will be familiar with the options available on Open OnDemand and be able to start graphical sessions through this service. This is a beginner friendly workshop and no prior experience is necessary. We recommend bringing your own device to follow along. Speaker: Leo Leung Format: Lecture + Follow along Level: Introductory Prerequisites: None
Data in Motion: Navigating Storage Solutions for Active Research Data	June 10, 9:30AM - 11:20AM ICT 114, Track 2	Planning for and requesting specialized storage for large research projects can be a daunting proposition. The variety of storage options and the expected justifications for allocations locally to UCalgary, at national supercomputing sites, and in the public cloud can quickly become overwhelming. This talk aims to provide an introduction to the cost/benefit tradeoff in using different storage systems, when to reach out to different support services around the university for help in making critical decisions, and basic techniques for providing a quantitative justification for a storage request. By the end of the session, you will be familiar with the types of storage related questions that should be answered when tackling large research projects and the different types of solutions that the University offers our researchers. Speaker: Ian Percel Format: Lecture Level: Introductory Prerequisites: None
Reproducible Data Management with Datalad	June 10, 10:30AM - 11:20AM June 11, 9:30AM - 10:20AM ICT 114, Track 2	Data management and research data is critical to research. This is a two part workshop that introduces you to DataLad, a digital data management system based on the Git version control system. Content to be covered in the two-part session includes: Dataset basics, Capturing data-provenance, and Collaborative data analysis. Background content will be covered before conducting the primary hands-on training where attendees will create a small demonstrative research project containing data provenance. Although no git knowledge is required, familiarity with git is strongly advised. Command line experience is required. Speaker: David Deepwell and Pedro Martinez Format: Lecture + Hands on Level: Introductory Prerequisites: Command line experience, Familiarity with Git
Introduction to HPC resources	June 11, 9:30AM - 10:20AM ICT 102	This session is a primer for those new to high performance computing (HPC) or computing on remote resources. We will build on the foundations built from our previous Linux and Slurm introductory sessions and expand on the larger picture, including: Motivation for using HPC Finding available resources on HPC resources Issues and pitfalls to avoid (such as incorrect job resource requests) Troubleshooting job failures High level overview of parallel programming with Slurm How to transfer data to/from other institutionsThis is a beginner friendly workshop. You should be familiar with the Linux command line. We recommend bringing your own device to follow along. Speaker: Robert Fridman, Dave Schulz Format: Lecture Level: Introductory Prerequisites: Linux command line, Slurm
Linux tools & utilities for working with large data sets	June 11, 10:30AM - 11:20AM ICT 102	This session introduces more intermediate to advanced uses of the Linux environment for handling large data sets. The course will demonstrate the power of shell pipes and how you can work with large datasets with just standard Linux tools and utilities that is built-in to the system. We will cover some common use cases including: How to download large datasets from the Internet How to parsing text-based data using tools such as sed, awk, grep How to build powerful text mining, conversion, and visualization with just the command line This is an intermediate course. You should be familiar with the Linux command line and some common Linux utilities prior to the course. Some understanding of regular expressions may be useful. Speaker: Leo Leung, Dave Schulz Format: Lecture Level: Introductory to Intermediate Prerequisites: Command line experience
RCS Q&A period: Ask RCS anything	June 11, 11:30AM - 12:00PM ICT 102	This is a general question and answers period where you may ask the Research Computing Services team questions related to RCS and HPC. You may ask both technical and non-technical questions. Speaker: The RCS team Format: Question & Answer period Level: Introductory Prerequisites: None
Research Data Management and Data File Management	June 11, 1:00PM - 2:20PM ICT 102	Managing your digital files and research materials is critical for keeping yourself organized, collaborating, and communicating with colleagues. In this session, we will cover Research Data Management (RDM) and Data Management Plan (DMP). We will also go over best practices in digital file management depending on your individual and organizational needs. This presentation will also discuss best practices, versioning, and how to document and share your file and folder convention using a README file. By the end of this session, you should be familiar with RDM and DMP concepts to help keep your research materials organized. Speaker: Jennifer Abel, Alex Thistlewood, and Ingrid Reiche (from The University of Calgary Libraries and Cultural Resources) Format: Lecture Level: Introductory Prerequisites: None
Introduction to containers with Apptainer	June 11, 2:30PM - 3:20PM ICT 102	Reproducible research workflows is essential for repeatability. This session will cover the basics of using containers with Apptainer, a secure container technology designed to be used on for high performance compute clusters. We will cover: How to use Apptainer to run a containerized environment How to build Apptainer containers How to deploy software inside Apptainer containers How to use Apptainer containers with your Slurm job submissions. The instructor for this session will be remote and will be streamed in ICT 102. We will provide a zoom link for those who wishes to attend virtually. Speaker: Tannistha Nandi Format: Lecture + Hands on Level: Introductory Prerequisites: None
Managing scientific software with Conda	June 11, 3:30PM - 4:20PM ICT 102	Running customized scientific software on a shared HPC environment may be challenging. This session, we will go over how to set up customized software environments using Conda. Speaker: Dmitri Rozmanov Level: Introductory Prerequisites: None
Prefect for Research Workflow Development	June 12, 2:30PM - 3:50PM ICT 102	Modernize your research workflows using Prefect, an open source workflow orchestration tool. In this session we will cover some of the fundamentals of building workflows with Prefect, with examples on how to deploy Prefect on local and distributed computing infrastructure. Speaker: David Deepwell and Pedro Martinez Format: Lecture + Hands on Level: Introductory Prerequisites: None
AWS: Inspiring the art of the possible ‎‎	June 11, 1:30PM - 1:50PM ICT 102	Learn what is possible on AWS Cloud for research. Speaker: AWS Format: Lecture Level: Introductory Prerequisites: None
AWS: How AWS works with Researchers	June 11, 1:30PM - 1:50PM ICT 102	AWS has many programs to support researchers such as credits, letter of supports, immersion days, working on proof of concepts. In this session, we will cover how we engage with researchers and what programs are out there to help accelerate your research with the AWS Cloud. Speaker: AWS Format: Lecture Level: Introductory Prerequisites: None
AWS: Machine learning with low-code workshop	June 11, 1:30 PM - 4:45 PM ICT 102	The Machine Learning (ML) journey requires continuous experimentation and rapid prototyping to be successful. In order to create highly accurate and performant models, data scientists have to first experiment with feature engineering, model selection and  optimization techniques. These processes are traditionally time consuming and expensive. In this workshop attendees will learn the following: How the Low-Code ML capabilities found in Amazon SageMaker Data Wrangler, Autopilot and Jumpstart, make it easier to experiment faster and bring highly accurate models to production more quickly and efficiently How to simplify the process of data preparation and feature engineering, and complete each step of the data preparation workflow Understand how to automatically build, train, and tune the best machine learning models based on your data, while allowing you to maintain full control and visibility. Get started with ML easily and quickly using pre-built solutions for common financial use cases and open source models from popular model zoos. Speaker: AWS Format: Workshop + Hands on Level: Introductory Prerequisites: None
Workflow Optimization with NVIDIA GPUs ‎‎	June 12, 9:30AM - 12:20AM ICT 102	TBD Speaker: Jonathan Dursi from NVIDIA Format: Lecture Level: Introductory Prerequisites: None
Dell Presentation: TBD ‎‎	June 12, 1:00 PM - 1:50 PM ICT 102	TBD Speaker: Rob Lucas from Dell Format: Lecture Level: Introductory Prerequisites: None