R Using Anaconda Environment

Step 1: Installing R Additional Package with Anaconda

To install R additional packages with Anaconda, 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 Anaconda Environment Module
$ module load anaconda

# Add conda-forge Channels
$ conda config --add channels conda-forge

# Create Anaconda Virtual Environment
$ conda create –n <environment name> <packages to install>

# Create Anaconda Virtual Environment (Example)
$ conda create -n R_test_env r-base=4.3 r-cairo r-gifi

# Install Missing Package (Example)
$ ${CONDA_ENV_PATH}/R_test_env/bin/Rscript -e "install.packages(c('MPsychoR'), repos='https://cran.r-project.org')"

# 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_conda.sh

#!/bin/bash
#SBATCH --job-name=MPsychoR_test_conda ## 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 anaconda

## Run user command in conda environemnt
## Do not use conda activate command, use absolute path instead
${CONDA_ENV_PATH}/R_test_env/bin/Rscript \
/home/${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: Remove user’s Conda (R) environment (Optional)

# Remove user’s Conda (R) environment
$ rm –rf /home/$USER/.conda/envs/<environment name>

# Remove user’s Conda (R) environment (Example)
$ rm –rf /home/$USER/.conda/envs/R_test_env