diff --git a/README.md b/README.md index 2ff3fb9..852271a 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ -This repository hosts the content of 'Using resources effectively with VASP: exploring GPU and machine learning capability'. +This repository hosts the content of Using resources effectively with VASP: exploring GPU and machine learning capability. Workshop atendees can follow along with the material deployed using GitHub Pages, [here](https://johnryder23.github.io/VASP_workshop/). -The only other material needed are the scripts located in in the './content' directory of this repository. Simply clone this repo (with 'git clone git@github.com:Johnryder23/VASP_workshop.git') and the navigate into 'VASP_workshop/content'. The rest of the nessessary configurations are provided by host machine, Mahuika. +The only other material needed are the scripts located in in the `./content` directory of this repository. Simply clone this repo (with `git clone git@github.com:Johnryder23/VASP_workshop.git`) and the navigate into `VASP_workshop/content`. The rest of the nessessary configurations are provided by the host machine, Mahuika. ## If you would like to contribute to this workshop -Commits to the 'main' branch are deployed automatically at https://johnryder23.github.io/VASP_workshop/ . +Commits to the `main` branch are deployed automatically at https://johnryder23.github.io/VASP_workshop/ . If you would like to make your own edits and deploy them, create a new branch and install MkDocs in a Python virtual environment: ``` diff --git a/docs/interactive_job.md b/docs/interactive_job.md index 188d7b0..52c399c 100644 --- a/docs/interactive_job.md +++ b/docs/interactive_job.md @@ -1,11 +1,11 @@ ## General -This calculation is a standard ionic and electronic energy minimisation for ethane in vacuum. Because this calculation is short, we will run it interactively from the command line and use a Bash script to set up and submit the calculation. +This calculation is a standard ionic and electronic energy minimisation for ethane in vacuum. Because the calculation is short, it can be run interactively from the command line. A Bash script will be used to set up and submit the calculation. -To start an interactive Slurm job, we will execute `srun` directly from the terminal. Using `srun` instead of `sbatch` submits a parallel job (using MPI) for execution in real time, and prints 'stdout' and 'stderr' to the terminal. +To start an interactive Slurm job, we will execute `srun` directly - and not from *within* a batch script sumitted with `sbatch`. Subbmitting with `srun` instead of `sbatch` makes the job execute in real time, or, in other words, reads `stdin` from the terminal and prints 'stdout' and 'stderr' to the terminal. -!!! note -running a job in this way means if your connection with NeSI drops, the job will fail - as 'stdin'is diretly from the terminal. Therefore running jobs interactively is only appropriate for short calculations. +!!! warning + running a job in this way means if your connection with NeSI drops, the job will fail - as 'stdin'is diretly from the terminal. Therefore running jobs interactively is only appropriate for short calculations. ## Input parameters diff --git a/mkdocs.yml b/mkdocs.yml index cd7e887..95fc089 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -12,4 +12,5 @@ nav: markdown_extensions: - admonition - + - pymdownx.details + - pymdownx.superfences