HPC with Slurm, R and the slurmR package
Contents
Part 1: HPC fundamentals (source code here)
Part 2: Simulating pi (again) (source code here)
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.gitThe 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!
Featured Happy Scientist: Lynn Conway
Lynn Ann Conway (born January 2, 1938) is an American computer scientist, electrical engineer, inventor, and transgender activist. Conway is notable for a number of pioneering achievements. She worked at IBM in the 1960s and is credited with the invention of generalized dynamic instruction handling, a key advance used in out-of-order execution, used by most modern computer processors to improve performance. – (Wiki)