R Using CRAN Packages

Step 1: Installing R Additional Package from CRAN

To install R additional packages from CRAN, run below command in the SSH terminal (CLI), for tutorial in accessing CLI, please refer to SSH Shell Access to EdUHK HPC Platform and Cluster (Web-based Shell Access)

# Load R Environment Module
$ module load R/4.3

# Start R CLI
$ R

# Package Install Path:/home/$USER/R
> install.packages(c('<packages to install>'), repos='<repository_url>')

# Install Package (Example)
> install.packages(c('MPsychoR', 'Gifi', 'Cairo'), repos='https://cran.r-project.org')

# Exit R CLI
> quit()

# Purge Module
$ module purge

Step 2: Prepare R Program Source Code

For the example source code please refer to R Program Source Code (Example)

Step 3: Prepare Job Template Script

Pre-configured template script path → /home/$USER/job_template/slurm_job/MPsychoR_test.sh

#!/bin/bash
#SBATCH --job-name=MPsychoR_test ## Job Name
#SBATCH --partition=shared_cpu ## Partition for Running Job
#SBATCH --nodes=1 ## Number of Compute Node
#SBATCH --ntasks-per-node=1 # Number of Task per Compute Node
#SBATCH --cpus-per-task=2 ## Number of CPU per task
#SBATCH --time=60:00 ## Job Time Limit (i.e. 60 Minutes)
#SBATCH --mem=10GB ## Total Memory for Job
#SBATCH --output=./%x%j.out ## Output File Path
#SBATCH --error=./%x%j.err ## Error Log Path

## Initiate Environment Module
source /usr/share/modules/init/profile.sh

## Reset the Environment Module components
module purge

## Load Module
module load R/4.3

## Run user command
Rscript /home/${USER}/job_template/R/MPsychoR_test.R

## Clear Environment Module components
module purge

Step 4: Submit HPC Job

Guides for submitting HPC job, please refer to: HPC Job Submission (For CLI) and HPC Job Submission (For Web Portal)

Step 5: Reset user’s R Environment (Optional)

# Reset User’s R Environment
$ rm -rf /home/$USER/R