slurm-knitr-spin

Tool to automatically create a SLURM submission script to spin an R script. Relies on the knitr package developed by Yihui Xie.

Table of Contents

• Installation
• Usage

Installation

To install, execute the following steps from the remote server:

1. Cone this repository

   git clone https://github.com/funkhou9/slurm-knitr-spin

2. cd into slurm-knitr-spin and ensure both spin and knitr_spin.R are executable

   cd slurm-knitr-spin
   chmod +x spin
   chmod +x knitr_spin.R

3. Add slurm-knitr-spin to your path, however you like. For instance in your ~/.bashrc file add:

   export PATH=$PATH:/path/to/slurm-knitr-spin/

Usage

Spin must be used with the following command line arguments $ spin <my-script.R> <qos> <constraints> <time> <mem (in Gb)>. See SLURM manual for description of arguments.

Internally, knitr::spin(<script.R>) is used to convert <script.R> into <script.md>, the markdown version of the same script.

Additionally your project space will be updated. Assuming your project space looks something like this:

project/
│   README.md    
│
└───subfolder1
    │   subfolder1.md
    │   1-script.R
    │
    └───subfolder2
    │   subfolder2.md
    │   1-script.R
    ...

and $ spin 1.script.R ... is called from within subfolder1, the project space will update to:

project/
│   README.md    
│
└───subfolder1/
    │   subfolder1.md
    │   1-script.R
    |	1-script/
    |	|
    |	└─ 1-script.md
    |      1-script.out
    |	   figure/
    │
    └───subfolder2/
    │   subfolder2.md
    │   1-script.R
    ...

1-script.out contains standard output from the cluster run, which may contain useful information like walltime used, RAM used, etc. figure/ is a directory produced by the knitr package, which contains all figures generated from 1-script.R