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Course: Scientific computing in R, 27 May 2020

Scientific computing in R

There is interest among R users to get started in High Performance Computing (HPC) as they need more CPU power, memory or both. Because most of the Machine Learning (ML) models in R are computationally demanding, they are a good starting point to introduce HPC concepts. In the present course, you will learn how to improve your code so that it could run more efficiently on a Desktop and also on a HPC environment. As realistic ML models are computationally expensive when running on a Desktop, we will also teach you how to run these models on Kebnekaise, a HPC cluster at our center. The focus of the course will not be about ML though.

This one-day, online course will have lectures interspersed with some hands-on sessions where you get to try out what you have just learned.

This HPC2N course is part of the PRACE Training courses.

NOTE This is an old course and some of the scripts specific for Kebnekaise are no longer valid and have thus been removed. You may find some similar examples for that part in the material from the newer course "Using R in an HPC environment". 

Recordings from the newer course can be found on HPC2N's YouTube channel.

Preliminary Schedule

  • 08:00-09:00 Optional: Testing your setup: audio/video, R installation, connection to HPC2N
  • 09:00-09:20 Profiling code
  • 09:20-09:30 break
  • 09:30-09:50 hands-on
  • 09:50-10:00 break
  • 10:00-10:20 Optimizing code
  • 10:20-10:30 break
  • 10:30-10:50 hands-on
  • 10:50-11:00 break
  • 11:00-11:20 Large Arrays
  • 11:20-11:30 break
  • 11:30-11:50 hands-on
  • 11:50-12:00 Summary
  • 12:00-13:00 Lunch
  • 13:00-13:20 Using HPC2N
  • 13:20-13:30 break
  • 13:30-13:50 hands-on
  • 13:50-14:00 break
  • 14:00-14:30 Using R at HPC2N
  • 14:30-14:40 break
  • 14:40-16:00 hands-on and summary

Requirements:  Basic knowledge of R, Linux. 

Part of the course will be done on your own computer and part will be done on HPC2N's cluster Kebnekaise. Because of this, you will need accounts at SUPR/HPC2N. If you do not already have those, we will contact you about creating such accounts.

Installations and setup before the course: https://www.hpc2n.umu.se/events/courses/scientific-r-2020/setup

Slides from the course: R_for_HPC.pdf | slides-R-course-2020.pdf

The materials for the R course can be found here: https://github.com/pojeda/R_in_HPC.git

Date: 2020-05-27
Time: 8:00-17:00
Location: ONLINE. Zoom: connection information will be sent to participants before the course
Instructor: Pedro Ojeda-May
Helpers: Mirko Myllykoski, Birgitte Brydsö, Lars Viklund
Deadline for registration: 2020-05-20

Contact Person: bbrydsoe@hpc2n.umu.se


Please fill in the below form to sign up. All fields marked with * are required. ALL SEATS TAKEN! REGISTRATION FORM CLOSED!

We will have a waiting list. In case someone cancels, the people on the waiting list will be given the seat on a first-come first-serve basis. If you want to be put on this waiting list, then please email bbrydsoe@hpc2n.umu.se with the following information:

1) Yes, I want to be put on a a waiting list for the course "Scientific computing in R"
2) Name
3) Organization
4) Email
5) Do you have an account at SUPR? Yes/no
6) Do you have an account at HPC2N? Yes/no
7) What is the operating system on the computer you would use for the course?

Updated: 2021-09-09, 15:12