Contents

Some random (unordered) content can be found in the Misc section. Previous versions of this workshop: 2019.

This workshop was recorded on February 18th, 2021, and is available here.

Materials

All the contents of this repository can be downloaded from the following github repository

https://github.com/USCbiostats/slurmR-workshop

You can also download all the contents of this repository (including R and bash scripts) using git:

git clone https://github.com/USCbiostats/slurmr-workshop.git

The slurmR R package can be installed directly from CRAN:

install.package("slurmR")

Or from Github using the remotes R package:

remotes::install_github("USCbiostats/slurmR")

All the examples here can be executed using GNU make. The command line entries used to run each one of the tasks follow (see the Makefile):

module load usc r
sbatch 00-hello-world.slurm
sbatch 01-sapply.slurm
sbatch 02-mclapply.slurm
# sbatch 03-parsapply-slurmr.slurm
sbatch 04-slurm_sapply.slurm #
# Rscript -e 'slurmR::sourceSlurm("05-sapply.R", plan = "submit")'

The last example can be executed directly while on the login node

module load usc r
Rscript -e 'slurmR::sourceSlurm("05-sapply.R", plan = "submit")'

This will submit a job without the need to write a slurm script!

Speaker

George G Vega Yon, Ph.D., Biostats Research Programmer