Course: Introduction to HPC2N, 2020-09-09

Introduction to HPC2N

We begin with a short introduction to Linux, which is what is used on HPC2N's compute clusters. This part is only meant for complete beginners to the Linux operating system, and can be omitted if you are proficient already. See the schedule.

We then continue with a walkthrough of the Kebnekaise system, including the GPUs and KNLs. In the afternoon we go through the module system and take a brief look at how to submit jobs. During the hands-on you will get the opportunity to try loading modules, compile a program, and submit a job to the Kebnekaise cluster.

Remote/online participation: The course will be streamed. We will use Zoom. The participants who have expressed a wish to participate remotely will receive an email the day before the course, containing the connection info.

NOTE: due to the situation with COVID-19, the course will be done online. You will get an email shortly before the course with information on how to connect, using Zoom.

THIS IS AN OLD COURSE AND EXAMPLE JOB SCRIPTS ARE NO LONGER VALID. THUS, THE ORIGINAL MATERIAL IS NO LONGER AVAILABLE FOR DOWNLOAD!

Updated material from a similar course given later can be found on the HPC2N Github page. There you will also find a link to the newest recordings of the course.

Preliminary Schedule

• 09:00
  • Introduction to Linux for beginners
• 10:45 COFFEE BREAK
• 11:00 Introduction to HPC2N, Kebnekaise and High Performance Computing
• 11:50 LUNCH (on your own)
• 12:45
  • Guided tour of the machine room for those participating onsite (meet inside the entrance to MIT huset)
• 13:00
  • Kebnekaise – How to use our systems
    • File Systems
    • The Module System
    • Compiler Tool Chains
    • The Batch System (SLURM)
• 14:00
  • Simple example (Hands-on/walk-through)
• 14:30 COFFEE BREAK
• 14:45
  • Application examples
    • Software packages - various examples
    • GPUs
• 17:00 END OF COURSE

Materials (links will follow closer to the course):

• Linux introduction - presentation [PDF]
• Kebnekaise - How to use our systems [PDF]
• Introduction to HPC2N, Kebnekaise and HPC [PDF]
• Application examples - presentation [PPTX]
• The simple examples can be downloaded from here: [tar.gz]
• The simple examples can ALSO be found on the HPC2N clusters, at this path: /pfs/nobackup/home/b/bbrydsoe/hpc2n-intro-fall2020.tar.gz
• The Linux examples and the application examples can be found here: [tar.gz]
• You can also copy the Linux examples and application examples from this path on the HPC2N clusters: /pfs/nobackup/home/b/bbrydsoe/app-examples

Participation is free. Coffee/tea will be provided.

Please make sure have an account at SUPR as well as at HPC2N if you want to participate in the hands-on part of the training. There will be a course project that can be used to run the examples in during the hands-on. If you don't have an account at SUPR and/or HPC2N, you will be contacted with further instructions for how to sign up.

Course project: As part of the HPC2N hands-on, you will be given temporary access to a course project, which will be used for running the hands-on examples. There are some policies regarding this, that we ask that you follow:

• You may be given access to the project before the course; please do not use the allocation for running your own codes in. Usage of the project before the course means the priority of jobs submitted to it goes down, diminishing the opportunity for you and your fellow participants to run the examples during the course. You can read more detailed information about the job policies at HPC2N here.
• The course project will be open 1-2 weeks after the course, giving the participants the opportunity to test run examples and shorter codes related to the course. During this time, we ask that you only use it for running course related jobs. Use your own discretion, but it could be: (modified) examples from the hands-on, short personal codes that have been modified to test things learned at the course, etc.
• Anyone found to be misusing the course project, using up large amounts of the allocation for their own production runs, will be removed from the course project.

The course used computing resources provided by the Swedish National Infrastructure for Computing (SNIC) at HPC2N partially funded by the Swedish Research Council through grant agreement no. 2018-05973.

Note: Participants are kindly asked to limit the use of fragrances due to perfume intolerance issues.  Thank you.

Prerequisites: nothing particular

Instructors: Birgitte Brydsö, Pedro Ojeda May, Mirko Myllykoski

Time and date: 9. September, 2020, 09:00-17:00

Location: ONLINE. Zoom link will be sent to participants.

Deadline for registration: 2. September 2020.

Please register by filling in the below form. Fields marked with a * are mandatory. REGISTRATION CLOSED! Contact bbrydsoe@hpc2n.umu.se to hear if it is still possible to sign up. Remember to include the following information:

1) Name
2) Organization
3) Email
4) Do you have an account at SUPR? Yes/no
5) Do you have an account at HPC2N? Yes/no
6) What is the operating system on the computer you would use for the course?