R

Running R Interactively from command line

[test@login31 ~]$ srun --pty bash
srun: job 3176550 queued and waiting for resources
srun: job 3176550 has been allocated resources
[test@compute-152 ~]$ module load conda_R
Loading conda_R/4.3.x
(4.3.x)[test@compute-152 ~]$ module list

Currently Loaded Modules:
  1) JHPCE_ROCKY9_DEFAULT_ENV   2) JHPCE_tools/3.0   3) conda/3-23.3.1   4) conda_R/4.3.x

(4.3.x)[test@compute-152 ~]$ R

R version 4.3.2 Patched (2024-02-08 r85876) -- "Eye Holes"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
...
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
...
> 

Running R in batch mode

1. Write your R source in a file with .r extension (e.g. plot1.r)

   # Set output file name
   pdf("plot1-R-results.pdf")
   
   # Define 2 vectors
   cars <- c(1, 3, 6, 4, 9)
   trucks <- c(2, 5, 4, 5, 12)
   
   # Graph cars using a y axis that ranges from 0 to 12
   plot(cars, type="o", col="blue", ylim=c(0,12))
   
   # Graph trucks with red dashed line and square points
   lines(trucks, type="o", pch=22, lty=2, col="red")
   
   # Create a title with a red, bold/italic font
   title(main="Autos", col.main="red", font.main=4)
   

2. Write a submit job script (e.g. plot1.sh)

   #!/bin/bash
   
   #SBATCH --mem=2G
   #SBATCH --time=2:00
   
   module load conda_R
   R CMD BATCH plot1.r
   

3. Submit your R job

   [test@login31 ~]$ sbatch plot1.sh 
   Submitted batch job 3177833
   

4. Monitor the job status

   [test@login31 ~]$ squeue --me
                JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
              3177833    shared plot1.sh    test  R       0:03      1 compute-095
   

5. When the job is finished, the output files are created in your Current Working Directory

   -rw-r--r--    1 test test        22 Mar 13 16:29  slurm-3177833.out
   -rw-r--r--    1 test test      4988 Mar 13 16:29  plot1-R-results.pdf
   

6. Look at the result file, plot1-R-results.pdf; you can use xpdf to view it if you have set X11 forward when login. Otherwise, you need download the file to local machine to view it.

   [test@login31 ~]$ xpdf plot1-R-results.pdf
   

Running RStudio

[test@login31 ~]$ srun --mem 10G --x11 --pty bash
srun: job 3244190 queued and waiting for resources
srun: job 3244190 has been allocated resources
[test@compute-097 ~]$ module load R
Loading R/4.3
(4.3)[test@compute-097 ~]$ module load rstudio
(4.3)[test@compute-097 ~]$ rstudio

Note

X Windows Setup
- For Windows, MobaXterm has an X server built into it
- For Mac, you need to have the XQuartz program installed (which requires a reboot), and you need to add the "-X" option to ssh:

ssh -X yourusername@jhpce01.jhsph.edu

Running RStudio via web

You can run RStudio via JHPCE Application Portal by login with your JHED ID and password.

Note

This web site is only available on campus, so if you are outside of the school network, you will need login to the JHU VPN first.