R workflow in ManeFrame

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• How to run R in ManeFrame

Objectives

• Learn how to run R & R Studio in ManeFrame

• Learn how to install package in R in ManeFrame

Run R in terminal via command line

Request a compute node if you do not have one (here I request for a node with 6 cpus and 16gb ram, running interactively):

$ srun -p htc -N 1 -c 6 --mem=16G --pty $SHELL

Load R module

$ module load r/3.6.2

Open R and run in Ineractive mode to install package:

$ R
> install.packages("doParallel")

Run R in batch mode

Make sure that you loaded R but not in R environment. Assume that you have an R script named hello.R (see next session if you do not have one) There are 2 ways to run an R script:

$ Rscript hello.R
$ R CMD BATCH hello.R

The latter method using R CMD BATCH will write the separate output file to your working directory

Now you are ready with the R pipeline running on ManeFrame

Prepare a simple script (skip if you already have one)

Here I create a simple R script with following information and named it hello.R

rm(list=ls())
setwd('/user/tuev')
print('welcome to R in ManeFrame')
print("hello from ManeFrame")
a <- 3
b <- 4
c <- a**b+b
print(c)

Running interactive Rn while in a login node using srun

While it is not recommended to run any job in a login node, we encourage every user to run their own job in compute node. If you are in a login node, you can run a job via this command:

$ module load r/3.6.2
$ srun -p htc --mem=6G R CMD BATCH hello.R

Running interactive R from a compute node

First, request an interactive node:

$ srun -p htc --mem=6G --pty $SHELL

Then load R and run your script:

$ module load r/3.6.2
$ R CMD BATCH hello.R

Running non-interactive R while in a login node using sbatch

Still in a login node, using sbatch –wrap to wrap a command in an sbatch script, then submitted to the queue to run in batch mode (non interactive)

$ sbatch -p htc --mem=6G --wrap "module load r/3.6.2; time R CMD BATCH hello.R"

You will find the output in the same folder with the format of slurm-$JobID.out.

Running non-interactive R while in a login node via a batch script (most advance)

First create a batch script named myR_batch.sh

#!/bin/bash
#SBATCH -J R
#SBATCH -o R_%j.out
#SBATCH -p htc
#SBATCH --mem=6G

module purge
module load r/3.6.2

time R CMD BATCH hello.R

Then, while in a login node, submit a batch script

$ sbatch myR_batch.sh

You can see the output as specified in the output file R_%j.out and hello.Rout

Key Points

• R workflow

• ManeFrame