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Similar to Python, the some basic R modules are included in the analysis_toolbox. Currently, there is no R-Studio available but we are planning to install it in the September-2023 update of the analysis_toolbox. Be aware that we still recommend against using graphical interfaces since that's not what an HPC is designed for. Our recommended workflow for using R is either with the interactive session and the R IDE, or via Rscript and sbatch script:
Interactive session with R
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command line interface
From Albedo's login node:
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From Albedo's login node:
$ module load analysis_-toolbox
The command Rscript allows you to run an R script you wrote from the shell (outside of R IDE or R-Studio). This means that you can also write a sbatch script (see Albedo-Slurm > Jobs) that runs your R scripts via Rscript and submit it to the slurm queue using sbatch command. You can even use the slurm array feature to launch the same R script multiple times in parallel if what your script does can be broken into multiple computing chunks. Depending on your R script it might need more or less changes, but it's probably worth to spend the time on chaning it to be able to benefit from this first order parallelization. For a simple example on slurm array + Rscript the following tutorial covers most of it: https://rcpedia.stanford.edu/topicGuides/jobArrayRExample.html
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module load panoply panoply.sh |
uftp-client
uftp is a parallel data transfer tool that uses multiple streams to transfer large ammounts of data efficiently between different systems. The tool has two main components: a server and a client. Albedo does not have a uftp server, but other HPC centers do have one (e.g. DKRZ and Jülich), which means you can efficiently transfer data from and to Albedo to and from these other HPC centers, using Albedo's uftp-client. For that follow these steps:
- Follow the steps to register an ssh-key in the target uftp-server, and read the full uftp-server documentation:
- For data transfers from/to Levante: https://docs.dkrz.de/doc/levante/data-transfer/uftp.html
- For data transfers from/to Jülich: https://apps.fz-juelich.de/jsc/hps/judac/uftp.html
- Load the module on Albedo:
Code Block module load uftp-client - Use the commands referred in the documentation (and uftp documentation) above to transfer your data.