Introduction to Unix and Grid Engine for beginners

This is a guide on using unix systems and the Grid Engine cluster environment.

First chapter will introduce basic usage for unix systems. The second chapter will explore the Grid Engine environment and show how to use the queuing system from users perspective.

What will you get out of this ?

After reading, you will:

• be able to use unix commands to navigate the file system
• use unix commands to interrogate files
• understand and write basic bash scripts
• understand Grid Engine and queueing system
• be able to submit jobs to a Grid Engine cluster and troubleshoot

Contribute to the development

You can contribute to the development of this guide using github features such as pull-requests and issue creation.

Build the book

This book is compiled with pandoc.

Run guix environment -m manifest.scm to enter a suitable environment to hack on this book. Then run npm install to install the lunr JavaScript library for the search index.

How to update the book

Edit the .md files using markdown syntax and run bash build.sh. This will regenerate the book and store the files in the book directory. Copy the contents of this directory to the gh-pages branch (the contents of this branch are served by GitHub pages) and push those changes to “gh-pages” branch of the online repository. You should also commit the changes you made in the “master” branch via git commit. Basically, “master” branch has the markdown files, “gh-pages” branch has the html website.

Acknowledgements

Initially created by Altuna Akalin. Some of the material is based on Martin Siegert’s documentation of the Grid Engine cluster.