Introduction to HPC2N and Kebnekaise

Introduction to HPC2N and Kebnekaise, 2017-02-21

Introduction to HPC2N's systems with a focus on the new Kebnekaise cluster.

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. See the schedule.

We then continue with a walkthrough of the system, including the GPUs. After lunch, 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. For those who are interested, there will be a guided tour of the machine rooms.

Some examples we will use for the course will be found in ~bbrydsoe/pfs/kebnekaise-intro. Take a look at the file README.txt for information about the files there and how to run them. The examples can also be downloaded in a tarball. IF USING AFTER THE COURSE, REMEMBER TO CHANGE THE PROJECT ID!

The slides used in the course: Introduction to Linux | HPC2N presentation | Using Abisko and Kebnekaise/modules/file system | Running Gromacs etc.

THIS IS AN OLD COURSE AND EXAMPLE JOB SCRIPTS ARE NO LONGER VALID.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

Please see the course website for newer courses which may have updated material linked.

Preliminary schedule

• 09:00
  • Introduction to Linux for beginners
• 10:45 COFFEE BREAK
• 11:00
  • Short presentation of HPC2N
  • HPC – What is that?
  • HPC2N – Abisko and Kebnekaise
  • HPC Programming models
  • OpenMP, OpenAcc, CUDA
• 12:00 LUNCH
• 13:00
  • Kebnekaise – How to use it
  • 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
  • More examples
    • Compiling/linking with libraries
    • Software packages (GROMACS)
    • GPU
• 17:00 TOUR OF THE MACHINE ROOMS / END OF COURSE

Participation is free. Lunch and coffee/tea will be provided.

Please bring a laptop, and make sure you have an account at HPC2N if you want to participate in the hands-on part of the training.

Prerequisites: nothing particular

Instructors: Jerry Eriksson, Birgitte Brydsö, Pedro Ojeda May

Time and date: 21. February 2017, 09:00 - 17:00.

Location: MIT-Huset, Umeå University. Room MA136 (Directions to MIT huset here).

Deadline for registration: 14. February 2017. Please register using this form. All fields are mandatory. REGISTRATION CLOSED! Contact bbrydsoe@hpc2n.umu.se to check if it is still possible to participate!