HPC and NIRD toolkit course fall 2020

In the fall 2020, the Scientific Computing group at the IT department (UiB) is offering a basic hands-on course for current and future users of national HPC systems (Saga, Fram, Betzy) and the NIRD Toolkit. The course is aimed at those with no or little experience on these systems. For those who have never worked on the command line of a terminal or little experience with UNIX-like operating systems such as Linux, we will offer an optional hands-on pre-course about UNIX a week before the HPC & NIRD Toolkit lectures.

On each course day, we will start at 09:00 and conclude at 12:30. Each morning will include presentations and hands-on time on one of the actual HPC systems or the NIRD Toolkit. We recommend that participants use the afternoon on each day to repeat examples from the morning to get more experience on the systems.

Participants require access to a computer (not provided by the course organisers) with Internet connectivity and pre-installed programs to participate in the video meeting of the course (zoom, might work from a browser), to access the HPC systems (ssh or Putty) or the NIRD Toolkit (web browser).

Registrations will close a few days before the course dates, but we ask participants to register as soon as possible such that we can arrange access to one of the HPC systems or the NIRD Toolkit well in advance (arranging access during the course won't be very practical as we need to focus on the course itself).

The courses are free of charge.

UNIX pre-course

Dates: October 19 and 20, 2020
Time: each day 09:00-12:30 with ~ 3 short breaks
Location: video meeting (information will be send to registered participants)

Participants may choose the lectures which they are interested in.

Registration

The course is free of charge and is organised by the Scientific Computing group at UiB IT department.

Registration https://skjemaker.app.uib.no/view.php?id=9042605
Registration closes on October 14th for those attending the pre-course (and the HPC & NIRD Toolkit part). We need a bit time to ensure that everyone has an account on the HPC systems and the NIRD Toolkit in case a participant does not already have one.

Agenda

Day 1 - Hello UNIX - 19.10.2020

Get introduced to UNIX and make your first steps on the command line.

• We will start by outlining the course goals and how we want to conduct the course via the video meeting.
• Then we plan to cover the following topics on day 1 (Note, exact details and order may still be changed.):
  1. logging into a remote machine using ssh or Putty
  2. exploring the $HOME folder (commands: ls, cd; brief excursion into program arguments)
  3. creating a directory (command: mkdir)
  4. creating a file (command: touch, echo; brief excursion into redirecting program output)
  5. copying a file (command: cp)
  6. showing the contents of a file (commands: cat, more, less; brief excursion into file/directory permissions)
  7. editing the contents of a file (commands: nano)
  8. Deleting files and directories (commands: rm, rmdir)
  9. Moving files and directories (command: mv; brief excursion into file names)
  10. Showing and using commands you have run before (command: history)
• A few exercises for the afternoon to practise the tools discussed on day 1.

Day 2 - Getting around - 20.10.2020

Learn & practise more commands to do your work more efficiently. Get to know what you should practise before the HPC and NIRD Toolkit course starts about a week later.

• We start with a quick recap of what was covered on day 1.
• Then we plan to cover the following topics on day 2 (Note, exact details and order may still be changed.):
  1. Showing and changing file/directory ownership and permissions (commands: chown, chmod)
  2. Finding data in files (command: grep; brief excursion into pipes)
  3. Inspecting parts of files (commands: head, tail)
  4. Un-/packing and compressing files and directories (commands: tar, gzip, zip)
  5. Writing shell scripts (understanding shebang, variables, comments, redirection)
• We conclude the pre-course with recommendations on how participants prepare themselves for the HPC and NIRD Toolkit course.

HPC and NIRD Toolkit course

Dates: October 27, 28 and 29, 2020
Time: each day 09:00-12:30 with ~ 3 short breaks
Location: video meeting (information will be send to registered participants)

Participants may choose the lectures which they are interested in.

Registration

The course is free of charge and is organised by the Scientific Computing group at UiB IT department.

Registration (same as for the UNIX pre-course, only needs to be filled once) https://skjemaker.app.uib.no/view.php?id=9042605
Registration closes on October 21st for those attending the HPC and NIRD Toolkit lectures only. We need a bit time to ensure that everyone has an account on the HPC systems and the NIRD Toolkit in case a participant does not already have one.

Agenda

Day 1 - Your first job on an HPC system - 27.10.2020

Get introduced to HPC and submit your job from the command line. (Note, exact details and order may still be changed.)

09:00-09:10 Welcome and overview of HPC resources and services available to students and researchers

09:10-09:20 Overview of the course and its goals, logistics, how to use zoom, chat, etc

09:20-09:30 What is HPC? Why may I need it?

09:30-09:40 Demo (login & first job)

09:40-09:50 break

09:50-10:20 Logging into an HPC system (presentation and hands-on; we use ssh (Linux & macOS) and Putty (Windows))

10:20-10:50 Using software modules (presentation and hands-on; we use the commands module avail, module load and module list)

10:50-11:00 break

11:00-11:20 Creating a directory for the job and copying some files (presentation and hands-on; we use the commands cd, mkdir and cp)

11:20-11:50 Submitting the first job (presentation and hands-on; we use the commands sbatch, squeue, ls and cat)

11:50-12:00 break

12:00-12:10 Recap and take aways from day 1; recommendations for practising during the afternoon

12:00-12:30 Q&A

Day 2 - How to organise your work on an HPC system - 28.10.2020

Learn & practise more commands to use an HPC system more efficiently. (Note, exact details and order may still be changed.)

09:00-09:40 Queues, Quality-of-Service and resource requirements (presentation and hands-on: we look at the documentation, use the commands squeue and time, look at job outputs and adjust the job script)

09:40-09:50 break

09:50-10:30 More about managing jobs (presentation and hands-on; we use commands scancel, srun/salloc and the slurmbrowser)

10:30-10:40 break

10:40-11:20 File systems, data transfers and disk usage (presentation and hands-on: we look at the documentation, use the command scp and the program winscp as well as dusage)

11:20-11:30 break

11:30-12:00 Best practices on HPC systems (presentation + discussion: topics may include login nodes, module environment, python environments)

12:00-12:10 How to start using an HPC system? (presentation: recap & take aways from day 1 and day 2)

12:10-12:30 Q&A

Day 3 - Hello NIRD Toolkit and How to get help - 29.10.2020

Get introduced to the NIRD Toolkit and learn about how to get help when you got stuck. (Note, exact details and order may still be changed.)

09:00-09:50 Introduction to the NIRD Toolkit part 1

09:50-10:00 break

10:00-10:50 Introduction to the NIRD Toolkit part 2

10:50-11:00 break

11:00-11:50 How to get help if you get stuck (presentation and hands-on: where to find documentation, how does the support team work, how to write effective support requests)

11:50-12:00 break

12:00-12:10 Recap and take aways from day 3

12:10-12:20 Outlook to future courses

12:20-12:30 Q&A