README.md

In MansMeg/slurmr: Convenience Package to handle batch processing in slurm systems

slurmr

Repository containing functionality to generate batch files for slurm cluster system

Installation

To install, just use:

devtools::install_github("MansMeg/slurmr")

Usage

The package is built upon the object sbatch that is one sbatch script file. To create a sbatch job just use the constructor sbatch():

> a_job <- slurmr::sbatch(code = "Rscript -e \"print('Hello World')\"", add_status = TRUE)
> a_job
#!/bin/bash 
# 
#SBATCH -t 01:00:00 
#SBATCH --output="slurm-%j.out" 

# Run status sbatch script  
echo "username: $USER" 
date 
projinfo 
git log -n 1 
pwd 

# Main code 
Rscript -e "print('Hello World')"

See documentation for all installed arguments to the constructor. The main argument is code that is used to set the code to run.

To write the files to a folder together with a run_all.sh script to submit all sbatch files use:

> slurmr::write_sbatch_list(a_job)

MansMeg/slurmr documentation built on May 7, 2019, 2:46 p.m.