Introduction R

../_images/r_logo_50.png

  • see a first overview of the R programming language

  • see the overview of the course

Course learning objectives

  • use the module system to load R

  • use the module system to load site-installed R packages

  • find out which versions of R and packages are installed

  • run R scripts

  • write a batch script for running R

  • install R packages from CRAN

  • see how to install other R packages yourself

  • start batch jobs

  • run RStudio

on HPC2N or UPPMAX

Course non-goals

  • improve R coding skills

  • use R on other HPC clusters

First overview of R

R is a programming language for statistical computing and data visualization (from Wikipedia).

flowchart TD subgraph r[R] r_interpreter[the R interpreter] r_packages[R packages] r_language[the R programming language] r_dev[R software development] rstudio[RStudio] interpreted_language[Interpreted] cran[CRAN] end r_language --> |has| r_dev r_language --> |is| interpreted_language r_language --> |uses| r_packages interpreted_language --> |done by| r_interpreter r_packages --> |maintained by| cran r_dev --> |commonly done in| rstudio

The main general R resources are:

R is used in many NAISS centres:

R Exercise files

  • On HPC2N, you can copy the R exercise tarball from /proj/nobackup/hpc2n2024-025/exercises-r.tar.gz

  • On UPPMAX, you can copy the R exercise tarball from /proj/naiss2024-22-107/exercises-r.tar.gz

Schedule

flowchart TD subgraph login[HPC login] ssh[0. SSH] remote_desktop_website[5. Remote desktop website] remote_desktop_local_thinlinc_client[5. Remote desktop with local ThinLinc client] end subgraph scheduler[scheduler] running_batch_jobs[3. Running batch jobs] running_interactive_session[5. Running an interactive session] end login --> |allows for| scheduler flowchart TD subgraph r[R] r_interpreter[1. the R interpreter] r_packages[2. R packages] r_virtual_environments[2. R virtual environments] r_language[1. the R programming language] parallel_and_multithreaded_functions[3. Parallel and multithreaded functions] r_dev[5. R software development] rstudio[5. RStudio] ml[4. Machine learning] interpreted_language[1. Interpreted] cran[1. CRAN] end subgraph modules[modules] r_module[1. R module] r_packages_module[2. R_packages module] rstudio_module[5. RStudio module] end r_language --> |has| r_dev r_language --> |is| interpreted_language r_language --> |uses| r_packages interpreted_language --> |done by| r_interpreter r_packages --> |maintained by| cran r_packages --> |isolated by|r_virtual_environments r_language --> |allows| parallel_and_multithreaded_functions r_language --> |provides for| ml r_dev --> |commonly done in| rstudio r_interpreter --> |loaded by|r_module r_packages --> |loaded by|r_packages_module rstudio --> |loaded by|rstudio_module rstudio_module --> |automatically loads latest| r_packages_module r_packages_module --> |automatically loads corresponding version of| r_module
Schedule

Time

Topic

Teacher(s)

9:00

First login

BB + PO + RB

9:45

Break

.

10:00

First login

BB + PO + RB

10:10

Syllabus

RB

10:20

Load modules and run

RB

10:45

Break

.

11:00

Packages

BB

11:30

Isolated environments

BB

12:00

Lunch

.

13:00

Batch

BB

13:30

Parallel

PO

14:15

Break

.

14:30

Simultaneous session

PO * RB * ?RP

15:15

Break

.

15:30

Machine learning

BB or PO

16:00

Summary and evaluation

RB

16:15

Done

.

Simultaneous session:

  • HPC2N: ThinLinc & RStudio, by PO

  • UPPMAX: ThinLinc, RStudio, interactive, by RB

  • LUNARC, by ?RP