R-Sapelo2

Category

Statistics

Program On

Sapelo2

Version

3.5.0, 3.6.2, 4.0.0

Author / Distributor

See http://www.r-project.org/

Description

R is a language and environment for statistical computing and graphics. It provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques.

Running Program

Also refer to Running Jobs on Sapelo2

R version 4.0.0

R version 4.0.0 is installed in /apps/eb/R/4.0.0-foss-2019b and add-on packages are installed in /apps/eb/R/4.0.0-foss-2019b/lib64/R/library. You can list all files in this dir to see the packages installed with this version of R.

To use this version of R, please first load the module with

module load R/4.0.0-foss-2019b

Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.

A number of R packages are provided by other module files. For example, many packages that depend on the GDAL library are provided by the rgdal/1.4-8-foss-2019b-R-4.0.0 module, which can be loaded with

module load rgdal/1.4-8-foss-2019b-R-4.0.0

R version 3.6.2

R version 3.6.2 is installed in /apps/eb/R/3.6.2-foss-2019b and add-on packages are installed in /apps/eb/R/3.6.2-foss-2019b/lib64/R/library. You can list all files in this dir to see the packages installed with this version of R.

To use this version of R, please first load the module with

module load R/3.6.2-foss-2019b

Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.

A number of R packages are provided by other module files. For example, many packages that depend on the GDAL library are provided by the rgdal/1.4-8-foss-2019b-R-3.6.2 module, which can be loaded with

module load rgdal/1.4-8-foss-2019b-R-3.6.2

For R 3.6.2 some of the Bioconductor packages are installed in a separate R-bundle-Bioconductor/3.10-foss-2019b module, with can be loaded with

module load R-bundle-Bioconductor/3.10-foss-2019b

R version 3.5.0

R version 3.5.0 is installed in /apps/eb/R/3.5.0-foss-2019b and add-on packages are installed in /apps/eb/R/3.5.0-foss-2019b/lib64/R/library. You can list all files in this dir to see the packages installed with this version of R.

To use this version of R, please first load the module with

module load R/3.5.0-foss-2019b

Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash<br>
#SBATCH --job-name=testRjob
#SBATCH --partition=batch        
#SBATCH --mail-type=ALL 
#SBATCH --mail-user=username@uga.edu  
#SBATCH --ntasks=1
#SBATCH --mem=10gb   
#SBATCH --time=08:00:00   
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err
 
cd $SLURM_SUBMIT_DIR

ml R/4.0.0-foss-2019b   

R CMD BATCH program.R   

where program.R is just a sample program name and needs to be changed. The settings in the header lines, such as the job name, the email address, the number of cores, memory and walltime limit, need to be changed appropriately as well.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

Please see http://www.r-project.org/

Installation

Source code downloaded from https://www.r-project.org/

System

64-bit Linux