HPC documentation



If you're already familiar with HPC and grid engine you can go to the quick start guide. The primary source of information on using Rosalind can be found on our user wiki. This is essential reading even if you're already familiar with HPC and grid engine. You may also want to check back from time to time to find out whats been added. In future all users will be required to take an online test before being allowed to user Rosalind's HPC resources.

If you're unfamiliar with working in a linux environment then we'd suggest you start by trying to learn some basic bash commands(see links below). Most advanced users have worked out how to make things happen with a combination of self study, learning on the job and advice from colleagues with linux experience. In addition to learning how to use unix shell commands its a good idea to try to learn about bash scripting or how to use another scripting language like python or perl. Scripting languages are essentially the tools of the trade when it comes to using a cluster like Rosalind. Not everyone will have to become an expert in these but there are massive gains to be had in becoming proficient in some form of scripting language. Chances are, you'll find that the time invested in learning these will pay off hansomely.

The scope of research on the Rosalind cluster is quite varied and while everything is run on more or less the same hardware, different tasks require different approaches. For example while bioinformatics users ususally have a need to examine large datasets, physicists often need optimum CPU throughput and require MPI for communication between parallel tasks. Code for some types of research, for example molecular modelling, can be up to 30 years old has has gone through many revisions and optimisation cycles, in contrast, software for experiments using next generation sequencing is more often than not at an early stage in the development cycle and in a constant state of flux. It has often been written and tested on a single workstation and hasn't been opimised for a shared environment.



Links

User wiki. (internal only)https://user-wiki.rosalind.kcl.ac.uk/doku.php
Quick Start Guide.HPCquickStart.html
Open grid scheduler.http://gridscheduler.sourceforge.net
Environment modules.http://modules.sourceforge.net/
Bash Guide For Beginnershttp://www.tldp.org/LDP/Bash-Beginners-Guide/html/
Advanced Bash Scriptinghttp://www.tldp.org/LDP/abs/html/
A useful bash reference.http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html


xkcd.com