High Throughput Computing using Condor

R

Overview

R is a language and environment for statistical computing and graphics developed by the R community. R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible.

Restrictions on use/License information

R is released under the GNU GPL v2.

There is no restriction on the number of simultaneously running programs on HTCondor.

Versions installed

R version HTCondor ClassAd
3.2.4 HAS_R_3_2
3.4.3 HAS_R_3_4
3.5.3 HAS_R_3_5_3
3.6.0 HAS_R_3_6_0
4.0.3 HAS_R_4_0_3

Set up procedure on submit node

R can be enabled using the command:

module load R/<R version>

and then run using the command R.

Running the application

The following lines are the contents of a simple generic HTCondor submit text file for submitting an R job that does not require the installation of any additional R packages to HTCondor:

Universe = vanilla

Requirements = (Target.Opsys == "LINUX" && Target.Arch == "X86_64" && <HTCondor ClassAd>=?=True)
Request_Memory = 1000

Log = R.log
Output = R.out
Error = R.error
Notification = Error

Should_Transfer_Files = Yes
When_To_Transfer_Output = ON_EXIT

Executable = /opt/R-<R version>/bin/Rscript
Transfer_Executable = False
Arguments = --no-save <script>.R <input arguments>
Transfer_Input_Files = <script>.R

Queue

If your submit file is called submit.txt then your job can be submitted to HTCondor using the command condor_submit submit.txt.

Sample R HTCondor jobs

  1. R code for calculating Pi using n terms of the Gregory series.
  2. R code for listing available R packages.
  3. Sample code that demonstrates how to use additional R packages.

Last modified on February 1, 2022 at 4:35 pm by Peter Crowther