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, such as adegenet, pegas, poppr, rgdal, sf, and spdepare, 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

The WGCNA package does not work on the AMD Opteron processors. If using functions in this package, please add a --constraint=EDR option to sbatch to exclude Opteron processors. For batch jobs, you can add the header line:

#SBATCH --constraint=EDR

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, which 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.

How to run R programs with multithreads

Some functions in the R packages are written with OpenMP and can run in parallel using multithreads. The R module files set the variable OMP_NUM_THREADS=1, to specify using only one thread. If you are using a function in an R package that is enabled to run with multithreads, please set the OMP_NUM_THREADS variable to the number of threads you want to use and request the same number of cores for your job. Note that you would need to set this variable after you load the R module, for it to have effect. For example, to use 6 threads, request 6 cores on the same node with

#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6

and set

export OMP_NUM_THREADS=6

You can set OMP_NUM_THREADS to automatically correspond to the number of cores per task requested for the job, by setting it to $SLURM_CPUS_PER_TASK, with

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

A sample job submission to run a multithread job is provided below.

Sample Job Submission Scripts

Here is an example of a shell script, sub.sh, to run a serial R script 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

module load R/4.0.0-foss-2019b   

R CMD BATCH program.R   

where program.R is just a sample program name and needs to be replaced by the name of the program you wish to run. 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 a shell script, sub.sh, to run a multithread R script 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 --cpus-per-task=6
#SBATCH --mem=10gb   
#SBATCH --time=08:00:00   
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err
 
cd $SLURM_SUBMIT_DIR

module load R/4.0.0-foss-2019b   

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

R CMD BATCH program.R   

where program.R is just a sample program name and needs to be replaced by the name of the program you wish to run. 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