R in an HPC environment, 14-15 December 2022

R in an HPC environment

In the present course you will learn several strategies to write faster and more efficient code in R. This will be done in several steps starting from a serial code and then using existing packages to parallelize code so that it can take advantage of the many core architecture of Kebnekaise. An HPC cluster such as Kebnekaise is useful for R users because it can provide both more CPU power and memory than what a personal computer can offer, but one needs to make the code aware of these resources. We will explore ways to achieve the latter and when parallel algorithms are suitable and possible. 

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! We will use Zoom. A link to the Zoom room will be distributed to the participants shortly before the course.

The course is a cooperation between HPC2N and PDC and is also part of the PRACE Training courses. It is thus open for academics and people who work in industry in the PRACE member countries.

Preliminary Schedule

DAY 1

• 09:00-09:10 Welcome
• 09:10-09:40 What is Parallelization
• 09:40-10:20 Introduction to HPC2N
• 10:20-10:35 Coffee Break (on your own)
• 10:35-10:50 How to use RStudio
• 10:50-11:15 Lab: Login using RStudio/ThinLinc
• 11:15-11:30 Serial R using HPC2N clusters
• 11:30-12:00 Lab: Serial computing in R

DAY 2

• 09:00-09:30 Parallel Computing in R
• 09:30-10:15 Lab: Shared memory computing
• 10:15-10:30 Coffee Break (on your own)
• 10:30-11:00 Best Practices for R in HPC
• 11:00-11:30 Usable parallelized R functions
• 11:30-12:00 Questions and comments

Requirements: 

• Basic knowledge of R. 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/2022/R-in-HPC/setup

Slides from the course: https://github.com/menzzana/parallel_R_course/tree/master/presentations

All the materials for the R course can be found here: https://github.com/menzzana/parallel_R_course

Q/A from the course [PDF].

Recordings of the lectures can be found on HPC2N's Youtube channel. The direct link to the playlist for the recordings from the course is here.

Participation is free and open to all users from the SNIC HPC centres and academics throughout the Nordic region. 

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: 2022-12-(14-15)
Time: 09:00-12:00 (both days)
Location: ONLINE. Zoom: connection information will be sent to participants before the course
Instructors: Pedro Ojeda-May, Henric Zazzi
Helper: Birgitte Brydsö
Deadline for registration: 2022-12-05

Contact Person: bbrydsoe@hpc2n.umu.se

Registration

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