R on ARC

General

Text mode interactive shell

When you start R usual way you get into interactive R shell where you can type commands and get the results back. Like this:

$ module load R/3.6.2
$ R

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> Sys.info()
                              sysname                               release 
                              "Linux"              "3.10.0-1127.el7.x86_64" 
                              version                              nodename 
"#1 SMP Tue Mar 31 23:36:51 UTC 2020"                                 "arc" 
                              machine                                 login 
                             "x86_64"                            "drozmano" 
                                 user                        effective_user 
                           "drozmano"                            "drozmano" 

> quit()
$

Running R scripts from the command line

In order to run R scripts / programs on ARC as jobs you have to pre-record the commands you want in a text file, for example test.R, and run it as a script non-interactively.

If, for example we want to run a short R script, test.R:

cwd = getwd()
cat(" Current Directory: ", cwd, "\n")

t = Sys.time()
cat("      Current time: ", format(t), "\n")

u = Sys.info()["user"]
cat("         User name: ", u, "\n")

There are three ways to run an R script.

1. Sending the script file into the standard input of the R interactive shell. This is similar to typing the commands in R':

$ R --no-save < test.R

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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.

> cwd = getwd()
> cat(" Current Directory: ", cwd, "\n")
 Current Directory:  /global/software/src/r/tests 
> 
> t = Sys.time()
> cat("      Current time: ", format(t), "\n")
      Current time:  2020-05-07 15:16:12 
> 
> u = Sys.info()["user"]
> cat("         User name: ", u, "\n")
         User name:  drozmano 
> 
> 

After executing all the commands from the script, R terminates. Note that both the commands and the printed output are shown.

2. Using R's BATCH command. The output does not go to the screen, but is saved to the .Rout file:

$ R CMD BATCH test.R
$ ls -l
-rw-r--r-- 1 drozmano drozmano  176 May  7 15:03 test.R
-rw-r--r-- 1 drozmano drozmano 1121 May  7 15:19 test.Rout

$ cat test.Rout

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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.

> cwd = getwd()
> cat(" Current Directory: ", cwd, "\n")
 Current Directory:  /global/software/src/r/tests 
> 
> t = Sys.time()
> cat("      Current time: ", format(t), "\n")
      Current time:  2020-05-07 15:19:07 
> 
> u = Sys.info()["user"]
> cat("         User name: ", u, "\n")
         User name:  drozmano 
> 
> 
> proc.time()
   user  system elapsed 
  0.219   0.079   0.369 

The output if very similar to the first way, but contains some additional timing information. Again, both the commands and the output are shown.

3. Probably the best non-interactive way to run an R script is using a special non-interactive version of R, Rscript:

$ Rscript test.R
 Current Directory:  /global/software/src/r/tests 
      Current time:  2020-05-07 15:22:17 
         User name:  drozmano 

In this case R does not print any extra information and only explicitly printed values are shown in the output, the commands themselves are not printed.