Load and run R

Learning outcomes

  • Practice using the documentation of your HPC cluster
  • Load an R module
  • Start the R interpreter
  • Run an R script
  • Download and extract the exercise files
  • (optional) Find the different R modules
  • (optional) See the list of installed R packages
Learning outcomes

Teaching goals are:

  • Learners have practiced using the documentation of their HPC clusters
  • Learners have loaded the module to be able to run R
  • Learners have run the R interpreter
  • Learners have run an R script from the command-line
  • Learners have downloaded and extracted the exercise files
  • (optional) Learners have found the different R modules
  • (optional) Learners have seen the list of installed R packages

Prior:

  • What is ‘HPC’ in ‘HPC cluster’?
  • What is ‘cluster’ in ‘HPC cluster’?
  • What is a software module?
  • What is a script?
  • What are features of using an HPC cluster?
  • What problem would arise if users can install their own software?

Introduction

You want to run R on an HPC cluster. For this, you’ll need to read the documentation of your HPC cluster.

In this session, we will use the documentation of your HPC cluster to start R.

Only do lightweight things!

Only do lightweight things!

We are still on the login node, which is shared with many other users. This means, that if we do heavy calculations, all the other users are affected.

How to do heavy calculations will be shown in this course later.

Exercises

Prefer this session as video?

HPC cluster| Login method | Location | -----------+------------------------+------------------------------------- COSMOS | Local ThinLinc client | Here Dardel | Local ThinLinc client | Here Kebnekaise | Local ThinLinc client | Here Rackham | Local ThinLinc client | Here Tetralith | Local ThinLinc client | Here

+------------------+-------------------+ | HPC cluster name |Main breakout room | +------------------+-------------------+ | COSMOS |Room 1 | +------------------+-------------------+ | Dardel |Room 2 | +------------------+-------------------+ | Kebnekaise |Room 3 | +------------------+-------------------+ | Rackham |Room 4 | +------------------+-------------------+ | Tetralith |Room 5 | +------------------+-------------------+

Exercise 1: start the R interpreter

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  • Find the documentation of your HPC cluster

.. admonition:: Answer :class: dropdown

+------------+-----------------------------------------------------------------------------------+
| HPC cluster| Location                                                                          |
+============+===================================================================================+
| COSMOS     | `Here <https://lunarc-documentation.readthedocs.io/en/latest/>`__                 |
+------------+-----------------------------------------------------------------------------------+
| Dardel     | `Here <https://support.pdc.kth.se/doc/contact/contact_support/>`__                                |
+------------+-----------------------------------------------------------------------------------+
| Kebnekaise | `Here <https://docs.hpc2n.umu.se/>`__                                             |
+------------+-----------------------------------------------------------------------------------+
| Rackham    | `Here <http://docs.uppmax.uu.se/>`__                                              |
+------------+-----------------------------------------------------------------------------------+
| Tetralith  | `Here <https://www.nsc.liu.se/support/systems/tetralith-getting-started/>`__      |
+------------+-----------------------------------------------------------------------------------+
  • Within the documentation of your HPC cluster, search for the documentation about R

.. admonition:: Answer :class: dropdown

+------------+----------------------------------------------------------------------------------------------------------------+
| HPC cluster| Page name and location                                                                                         |
+============+================================================================================================================+
| COSMOS     | `R Software environment <https://lunarc-documentation.readthedocs.io/en/latest/guides/applications/Rscript/>`__|
+------------+----------------------------------------------------------------------------------------------------------------+
| Dardel     | `R <https://support.pdc.kth.se/doc/applications/?sub=r/>`__                                                    |
+------------+----------------------------------------------------------------------------------------------------------------+
| Kebnekaise | `R <https://www.hpc2n.umu.se/resources/software/r>`__                                                          |
+------------+----------------------------------------------------------------------------------------------------------------+
| Rackham    | `R <https://docs.uppmax.uu.se/software/r/>`__                                                                  |
+------------+----------------------------------------------------------------------------------------------------------------+
| Tetralith  | `R <https://www.nsc.liu.se/software/catalogue/tetralith/modules/r.html>`__                                     |
+------------+----------------------------------------------------------------------------------------------------------------+
  • From the terminal, load the module(s) for R, of the recommend version as shown below

+----------+---------+ |HPC center|R version| +==========+=========+ |COSMOS |4.2.1 | +----------+---------+ |Dardel |4.1.1 | +----------+---------+ |Kebnekaise|4.1.2 | +----------+---------+ |Rackham |4.1.1 | +----------+---------+ |Tetralith |4.2.2 | +----------+---------+

.. admonition:: Answer :class: dropdown

+------------+----------------------------------------------------------------------------------------------------------------+
| HPC cluster| How to load the module(s) for R                                                                                |
+============+================================================================================================================+
| COSMOS     | :code:`module load GCC/11.3.0 OpenMPI/4.1.4 R/4.2.1`                                                           |
+------------+----------------------------------------------------------------------------------------------------------------+
| Dardel     | :code:`module load PDC/23.12 R/4.1.1`                                                                          |
+------------+----------------------------------------------------------------------------------------------------------------+
| Kebnekaise | :code:`module load GCC/11.2.0 OpenMPI/4.1.1 R/4.1.2`                                                           |
+------------+----------------------------------------------------------------------------------------------------------------+
| Rackham    | :code:`module load R/4.1.1`                                                                                    |
+------------+----------------------------------------------------------------------------------------------------------------+
| Tetralith  | :code:`module load R/4.2.2-hpc1-gcc-11.3.0-bare`                                                               |
+------------+----------------------------------------------------------------------------------------------------------------+
  • From the terminal, start the R interpreter

.. admonition:: Answer :class: dropdown

+------------+----------------------------------+
| HPC cluster| How to start the R interpreter   |
+============+==================================+
| COSMOS     | :code:`R`                        |
+------------+----------------------------------+
| Dardel     | :code:`R`                        |
+------------+----------------------------------+
| Kebnekaise | :code:`R`                        |
+------------+----------------------------------+
| Rackham    | :code:`R`                        |
+------------+----------------------------------+
| Tetralith  | :code:`R`                        |
+------------+----------------------------------+

  • From the R interpreter, run the R code :code:message("Hello") to verify if this makes the R interpreter show the text ‘Hello’

  • From the R interpreter, run the R code :code:quit() to quit the R interpreter and go back to the terminal

Exercise 2: run an R script ~~~~~~~~~~~~~~~~~~~~~~~~~~~

To run an R script, we’ll download one, after which we’ll run it:

  • From the terminal, run :code:wget https://raw.githubusercontent.com/UPPMAX/R-python-julia-HPC/main/exercises/r/hello.R

  • From the terminal, run :code:Rscript hello.R

Exercise 3: download and extract the tarball with exercises ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

See here <https://uppmax.github.io/R-matlab-julia-HPC/common/use_tarball.html>_ how to download and extract the tarball with exercises.

Exercise X1: find and use installed R packages

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  • From the R interpreter, check which packages are installed, using :code:installed.packages()

.. admonition:: Answer :class: dropdown

+------------+----------------------------------+
| HPC cluster| Answe                            |
+============+==================================+
| COSMOS     | :code:`installed.packages()`     |
+------------+----------------------------------+
| Dardel     | :code:`installed.packages()`     |
+------------+----------------------------------+
| Kebnekaise | :code:`installed.packages()`     |
+------------+----------------------------------+
| Rackham    | :code:`installed.packages()`     |
+------------+----------------------------------+
| Tetralith  | :code:`installed.packages()`     |
+------------+----------------------------------+
  • From the R interpreter, load the parallel package, using :code:library(parallel)

.. admonition:: Answer :class: dropdown

+------------+----------------------------------+
| HPC cluster| Answe                            |
+============+==================================+
| COSMOS     | :code:`library(parallel)`        |
+------------+----------------------------------+
| Dardel     | :code:`library(parallel)`        |
+------------+----------------------------------+
| Kebnekaise | :code:`library(parallel)`        |
+------------+----------------------------------+
| Rackham    | :code:`library(parallel)`        |
+------------+----------------------------------+
| Tetralith  | :code:`library(parallel)`        |
+------------+----------------------------------+

Exercise X2: search for other R versions ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Use the module system to find which versions of R are provided by your cluster’s module system.

.. admonition:: Answer :class: dropdown

+------------+----------------------------------+
| HPC cluster| How to search for the R modules  |
+============+==================================+
| COSMOS     | :code:`module spider R`          |
+------------+----------------------------------+
| Dardel     | :code:`module spider R`          |
+------------+----------------------------------+
| Kebnekaise | :code:`module spider R`          |
+------------+----------------------------------+
| Rackham    | :code:`module spider R`          |
+------------+----------------------------------+
| Tetralith  | :code:`module spider R`          |
+------------+----------------------------------+