tin6150/r4eta repository overview

⁠r4eta

Container for R with libraries for LBNL Energy Technology Area project Now with Jupyter Notebook server

Start jupyter notebook web server (on specific port, eg 5997):

docker run -p 5997:5997 -v "$PWD":/mnt -it --entrypoint=/opt/conda/bin/jupyter tin6150/r4eta lab --allow-root --no-browser --port=5997 --ip=0.0.0.0

Point web browser to something like http://127.0.0.1:5997/⁠ http://hima.lbl.gov:5997/⁠ and paste the token URL link shown on the terminal console

/mnt is a mount of the current dir (PWD) where you started the docker process, and files written there will persist after the container is terminated. (Other files inside the container are ephemeral!)

⁠Repo info

• source: https://github.com/tin6150/r4eta⁠
• docker hub: https://hub.docker.com/repository/docker/tin6150/r4eta⁠
• singularity hub: https://singularity-hub.org/collections/4160⁠

⁠Text Terminal based run

⁠Examples for using the singularity container

Pull the container from the cloud :: singularity pull --name myR shub://tin6150/r4eta

Run R interactively :: ./myR q() # exit R and container session.

Run rstudio interactively :: singularity exec myR rstudio -or- singularity exec shub://tin6150/r4eta rstudio

Interact with the container, run bash, R, Rscript INSIDE the container :: singularity exec myR bash ls # current working directory should be bind mounted R # run R interactively, use q() to quit, return back to shell INSIDE the container Rscript helloWorld.R # invoke an R script exit # exit the container, return to host prompt

Run R script in "batch mode", find out what version it is :: singularity exec myR /usr/bin/Rscript --version

Run Rscript with a specific command specified on the command line [ library() ] :: singularity exec myR /usr/bin/Rscript -e 'library()'

Run Rscript invoking a script file. This is a bit more elaborate as the container need to map (bind) the file system in the outside to the inside of the container. This example maps home dir from outside the container ($HOME) to a path inside the container (/tmp/home ), then run the script on the mapped dir (/tmp/home/helloWorld.R) :: singularity exec --bind $HOME:/tmp/home myR /usr/bin/Rscript /tmp/home/helloWorld.R

Alternate example for mapping only the current dir on host to /mnt on the container. Output is send to current dir on the host ( > output.txt) :: singularity exec --bind .:/mnt myR /usr/bin/Rscript /mnt/helloWorld.R > output.txt

Additional singularity and docker container build and troubleshooting notes in DevNote.txt

-Tin 2020.09.07

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