Exercises

Load and run

Try yourself to load R, start it, check libraries, load a library, quit R

1) Load R version 4.1.1
2) Start R. Check which libraries are installed. Load one of them.
3) Quit R

Remember to check if a module you are loading has prerequisites, and load those first if it does. In this case it depends on whether you do the exercises on Kebnekaise or Rackham.

Solution

UPPMAXHPC2N

This is for Rackham.

$ ml spider R/4.1.1

----------------------------------------------------------------------------
R: R/4.1.1
----------------------------------------------------------------------------

   This module can be loaded directly: module load R/4.1.1

Help:
   R - use R Version 4.1.1

   https://www.r-project.org

Many, many R and Bioconductor packages are available in the module
'R_packages/4.1.1'

$ module load R/4.1.1
Nearly all CRAN and BioConductor packages are installed and available by loading the module R_packages/4.1.1
$

$ R

   R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
   Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> installed.packages()
Package      LibPath                                    Version
base       "base"       "/sw/apps/R/4.1.1/rackham/lib64/R/library" "4.1.1"
boot       "boot"       "/sw/apps/R/4.1.1/rackham/lib64/R/library" "1.3-28"
class      "class"      "/sw/apps/R/4.1.1/rackham/lib64/R/library" "7.3-19"
cluster    "cluster"    "/sw/apps/R/4.1.1/rackham/lib64/R/library" "2.1.2"
codetools  "codetools"  "/sw/apps/R/4.1.1/rackham/lib64/R/library" "0.2-18"
compiler   "compiler"   "/sw/apps/R/4.1.1/rackham/lib64/R/library" "4.1.1"
datasets   "datasets"   "/sw/apps/R/4.1.1/rackham/lib64/R/library" "4.1.1"
foreign    "foreign"    "/sw/apps/R/4.1.1/rackham/lib64/R/library" "0.8-81"
graphics   "graphics"   "/sw/apps/R/4.1.1/rackham/lib64/R/library" "4.1.1"
grDevices  "grDevices"  "/sw/apps/R/4.1.1/rackham/lib64/R/library" "4.1.1"
grid       "grid"       "/sw/apps/R/4.1.1/rackham/lib64/R/library" "4.1.1"
KernSmooth "KernSmooth" "/sw/apps/R/4.1.1/rackham/lib64/R/library" "2.23-20"
lattice    "lattice"    "/sw/apps/R/4.1.1/rackham/lib64/R/library" "0.20-45"
MASS       "MASS"       "/sw/apps/R/4.1.1/rackham/lib64/R/library" "7.3-54"
Matrix     "Matrix"     "/sw/apps/R/4.1.1/rackham/lib64/R/library" "1.3-4"
...

> library("parallel")
> quit()
Save workspace image? [y/n/c]:

The list of installed packages is very long, as you will see for yourself.

Load R and run a short R script from the command line

1. Load R version 4.1.x (if you have not done so already)

2. Run the small R script called hello.R, using Rscript

Remember to check if a module you are loading has prerequisites, and load those first if it does. In this case it depends on whether you do the exercises on Kebnekaise or Rackham. Remember, Kebnekaise has 4.1.2 and Rackham has 4.1.1.

“hello.R” (it can also be found under “R” in the “Exercises” directory on the course GitHub repository (https://github.com/UPPMAX/R-python-julia-HPC).

message <-"Hello World!"
print(message)

Solution

UPPMAXHPC2N

This is for Rackham.

$ Rscript hello.R
[1] "Hello World!"
$

As you can see, it is working the same way.

Packages

Install a package with automatic download

1) First do the setup of .Renviron and create the directory for installing R packages. Remember to load any modules you need.

2. Install a package from the command line. Suggestion: the package “anomalize”

3. Install a package from inside R. Suggestion: the package “tidyr”

4. Start R and see if the library can be loaded.

These are both on CRAN, and this way any dependencies will be installed as well.

Remember to pick a repo that is nearby, to install from: https://cran.r-project.org/mirrors.html

Solution

SetupCommand lineInside RLoad library

$ echo R_LIBS_USER=\"$HOME/R-packages-%V\" > ~/.Renviron R_LIBS_USER="/home/bbrydsoe/R-packages-%V"
$ mkdir -p $HOME/R-packages-4.0.4

Batch mode

Serial batch script for R

Run the serial batch script shown in the session “Running R in batch mode”, but for the add2.R code (see the Exercise/R directory on GitHub). Remember the arguments.

Solution for UPPMAX

Serial script on Rackham

#!/bin/bash
#SBATCH -A naiss2024-22-107 # Change to your own after the course
#SBATCH --time=00:10:00 # Asking for 10 minutes
#SBATCH -n 1 # Asking for 1 core

# Load any modules you need, here for R/4.1.1
module load R/4.1.1

# Run your R script
R --no-save --quiet < add2.R 2 3

Solution for HPC2N

Serial script on Kebnekaise

#!/bin/bash
#SBATCH -A hpc2n2024-025 # Change to your own project ID
#SBATCH --time=00:10:00 # Asking for 10 minutes
#SBATCH -n 1 # Asking for 1 core

# Load any modules you need, here for R/4.1.2
module load R/4.1.2

# Run your R script
R --no-save --quiet < add2.R 2 3

Parallel job run

Try running the parallel example with “foreach” from the session “Running R in batch mode”.

R for ML

Run the ML examples shown in the session “ML with R”.