Course: Using R in an HPC environment (25-26 February 2021)

Using R in an HPC environment

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 in an 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 course will be two half-days. It will have lectures interspersed with some hands-on sessions where you get to try out what you have just learned.

NOTE: The course will be online!

Preliminary Schedule

DAY 1

• 08:00-09:00 Optional: Testing your setup: audio/video, R installation, connection to HPC2N
• 09:00-09:25 Profiling code
• 09:25-09:30 break
• 09:30-10:00 hands-on
• 10:00-10:05 break
• 10:05-10:25 Optimizing code
• 10:25-10:30 break
• 10:30-10:55 hands-on
• 10:55-11:00 break
• 11:00-11:20 Dealing with memory
• 11:20-11:25 break
• 11:25-11:55 hands-on
• 11:55-12:00 Summary

DAY 2

• 09:00-09:15 Motivation for using HPC
• 09:15-09:35 Using HPC2N
• 09:35-09:40 break
• 09:40-10:00 hands-on
• 10:00-10:05 break
• 10:05-10:25 Using R at HPC2N
• 10:25-10:30 break
• 10:30-12:00 hands-on and summary

Requirements:  Basic knowledge of R, a comprehensive material can be found in the Software Carpentry lesson on R. Linux, we have a recorded video on our Youtube channel (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/r-in-hpc-spring-2021/setup

Slides from the course: https://hpc2n.github.io/R_for_HPC/

All the materials for the R course can be found here: GitHub | Zip-file

Recordings of the lectures can be found on HPC2N's Youtube channel.

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 uses 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.

Date: 2021-02-(25-26)
Time: 8:00-12:00 (Thursday), 09:00-12:00 (Friday)
Location: ONLINE. Zoom: connection information will be sent to participants before the course
Instructor: Pedro Ojeda-May
Helpers: Mirko Myllykoski, Birgitte Brydsö
Deadline for registration: 2021-02-18

Contact Person: bbrydsoe@hpc2n.umu.se

Registration

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