Versions
As of this article update, we have the following versions of R installed on Talapas, :
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3.3.3 3.3.3_intel-17 3.4.1 3.4.2 3.4.3 3.4.4 3.5.1 3.5.3 3.6.1 3.6.1_gcc7 3.6.2 4.0.2 4.0.2_gcc7 |
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Note: packages within each version of R are not the same! There may be different packages or different package versions. |
Intel R
Intel is the default. To run an Intel compiled version of R, run,e.g 4.0.2, run:
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$ module load R/4.0.2 $ R |
gcc R
We have 2 versions of R compiled with gcc7 (3.6.1_gcc7 and 4.0.2_gcc7) built specifically to support RStan. To use these versions you must first load gcc. E.g. 4.0.2, run:
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$ module load gcc Lmod is automatically replacing "intel/17" with "gcc/7.3". $ module load R/4.0.2 $ R |
Verify the path of the R executable that is loaded use the bash command which
:
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$ which R /packages/R/4.0.2_gcc7/bin/R |
The output above shows the executable to R version 4.0.2 built with gcc7.
R Packages
To list installed packages and version information, run:
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$ module load R/4.0.2 $ R > installed.packages()[,c("Package","Version")] Package Version abind "abind" "1.4-5" ... |
Running R Interactive
ssh onto a talapas login node, How-to Log Into Talapas
Start an interactive job, How-to Start an Interactive Job
Once on the allocated node enter,
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$ module load R/4.0.2 $ R |
Running R in Batch
For longer running non-interactive use cases call R in batch.
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#!/bin/bash #SBATCH --account=<pirg-name> #SBATCH --job-name=r-job #SBATCH --output=r-job.out #SBATCH --error=r-job.err module load R/4.0.2 R --save < /gpfs/projects/<pirg-name>/<user-name>/demo.r |
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‘Save current workspace’ with |
The example above preserves R session output. Also include the save.image
function in your demo.r
file, e.g. save.image("/gpfs/projects/<pirg-name>/<user-name>/demo.RData")
in your demo.r
file
Submit the job
Use the sbatch command to submit the job.
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