The programming language R(4.0.3) is available in SQUID. Also, Anaconda is installed, so users can prepare any version by themselves. For the procedure using Anaconda, please refer to this page.

How to use

Environmental setting

    You need to set up the environment using "environment modules".

    $ module load BaseCPU
    $ module load BaseR

    Also, specify a large work area as the installation destination for the library.
    In the following example, we create a directory named R_lib under the work area and specify it as the installation directory for the library.

    $ mkdir /sqfs/work/[group name]/[user name]/R_lib
    $ export R_LIBS=/sqfs/work/[group name]/[user name]/R_lib


package install

    Any package can be installed on the front-end node of SQUID.
    Since connection to the outside world is prohibited from the computation node, please install the packages necessary for the calculation on the front-end node beforehand.
    The steps to install the "data.table" package on the front-end node are shown below.

    Launch the R prompt.
    $ R
    Install the data.table package.
    > install.packages("data.table")

    Displays the installed packages
    $ library()
      パッケージ  (ライブラリ ‘/sqfs/work/【グループ名】/【ユーザ名】/R_libs’ 中):
    data.table              Extension of data.frame


Execute R script in SQUID

    Please run the script as a batch job when using R. The following is an example of a job script when using R. The R script file (file.R) is given as the input file.


Reference information