Running R scripts on Mox

[yaaminiv]

Based on advice from this discussion, I'm going to run my methylKit R scripts on Mox. I have a few questions about running R scripts on Mox that I can't find the answer to in our lab's Mox guide.

1. Is there a list of R packages that have been installed on Mox, or do I need to install every new R run?
2. If I run a command (ex. head(myDataframe)), does that output get written to the slurm-out file?
3. Looking the Hyak documentation, I can run R or R Studio interactively. Does anyone have experience with this/what are the pros and cons of running an interactive node vs. using a SBATCH script?

[yaaminiv]

Is there a list of R packages that have been installed on Mox, or do I need to install every new R run?

Answered my own question based on Hyak documentation. I can install and save packages in my gscratch directory

[yaaminiv]

I created this script to run R on mox based on a suggestion from @kubu4 in this discussion. When I ran the script on mox I got the following error:

I'm not sure what it means, and I don't see this information in the hyak documentation.

Where would I specify the above arguments, and what exactly are they? Alternatively, I could move my R code to a separate file, and call it within a SLURM script.

edited because I was missing a sentence

[kubu4]

Sorry! Change the shebang to:

#!/gscratch/srlab/programs/R-3.6.2/bin/Rscript

[kubu4]

And, alternatively, you could stick with the documentation provided. With that said, here's better documentation:

https://www.chpc.utah.edu/documentation/software/r-language.php

Specifically the section titled, "Runing a R batch script on the cluster (using SLURM)".

[yaaminiv]

Thanks! That worked and now I have new issues.

[kubu4]

Yay? 😆

BTW, which worked: change shebang or calling Rscript in SLURM script?

[yaaminiv]

I changed the shebang and ran the script! But now I'm having trouble actually loading packages with require(). I think R doesn't know where to find the packages (I go into it in this discussion).