CSC8306 -- Systems Administration

Practical Classes

Introduction

Bioinformatics research often requires use of advanced machinery. At Newcastle we have a number of large cluster machines, which are used for a variety of different purposes.

This sort of machinery can speed up research enormously. Work which would previously have taken months can be performed in days. However, this machinery doesn't come without cost—apart from the financial cost of buying the hardware—installing and maintaining a system in a working state is no small issue. Partly this is because the hardware fails — a large scale disk store may have 100s of disks, disk failure is to be expected at least once a month. The biggest problem, however, is getting the software which actually makes the machines useful to work properly.

In these module, you will learn the basics of systems administration. For many bioinformaticians, based in small biological research labs, there is no access to a professional systems administrator. Even where there is such a person, the specialist requirements of bioinformatics is often beyond their training and expertise. For this reason, a knowledge of systems administration is likely to be useful, to enable you to get to research answers more quickly and accurately than would otherwise be possible. This is likely to be an issue for a number of you during your research projects.

Outline

The module will take you through the basics of installing and using a linux operating system; this OS is probably the most widely used for "hard-core" bioinformatics analysis.

These web pages will be your main guide. Either I or a demonstrator will be on hand during the practical sessions. As with all the courses on the MSc the timetabled sessions are unlikely to be long enough to complete the work; you are expected to continue with the work in your own time.

During the course, you will be introduced to the various sources of documentation and advice on systems administration; there is an enourmous wealth of information available on the web which is freely available. In fact, this quantity of information available is one of the main reasons for the success of linux. You should familiarise yourself with this documentation and are expected to use it. A modern UNIX based system is huge, complex and regularly changes. System Administration is less about pre-existing knowledge and more about finding things out quickly.

Throughout the practical classes, you will find suitable references and keywords. These references may be out of date, so please use Google, the Linux documentation project or any of the many help sites and forums out there ¹. Demonstrators will not provide answers to things that you could look up easily for yourself ². There is also a book associated with this course, which is O'Reilly's "Essential Systems Administration". This book is fairly out-of-date now, but it provides a useful, all-in-one overview. Books on the internal workings of operating systems tend to go out-of-date, are often not specific to the system you are using and, worse, are not searchable. Use of the web is recommended. Remember that you should cite and reference your work appropriately.

Tasks

The practical work is split into sections. Each section is then split into a number of tasks. You should work through the tasks one by one in the practical classes and your own private study time.

Assessment

You will need to maintain a log book detailing your progression through the phases. The log should be submitted using Word — comments and coursework for this module will be returned using change tracking ³.

Each task description may be annotated in one of two ways.

This type of task requires some bookwork to be carried out and a solution provided in your log. For example,1.3 requires you to provide answers to a Linux exercise. These answers should be provided in your log.

This type of task requires you to do something to your operating system. If you don't do all of the actions, later parts of the coursework may not work.

You need to do two things with your coursework.

• You need to fill in a sign-off sheet that I or the demonstrator will have with them. There are two reasons for this. First, it enables to check the work that you will eventually submit so that we can discover problems earlier. Second, it helps us to ensure that the work is your own, which will help to avoid difficulties when the exams approach.
• The coursework log book needs to be submitted to NESS. This will happen in three blocks. The first three sections will be submitted first, then the next three, and finally the last three. Coursework deadlines will appear in NESS.

Contents

1. Please be careful when using forums. In general, people are pleased to help, but occasionally some are malicious. Don't tell people the name of your machine, do not tell people your username and do not, UNDER ANY CIRCUMSTANCES, reveal passwords. A few years ago, our local system admin found a text file in the root directory of an important machine at Newcastle saying "Revealing your password on a forum will get your machine hacked". In this case, no harm was done, but this was just luck not design.

2. This is also true on web based mailing lists and forums. Do not expect people to do your coursework for you. Ask simple, straight-forward and directed questions if you are having difficulties. If you paste your coursework in, it's really obvious, and you will irritate people on the list. It's the quickest way to loose any good will that you might otherwise have.

3. Using word for a course using linux seems a bit strange, but marking is a nightmare if I get coursework in multiple different formats. You may find it easier to use a simple text file. You can cut and paste it into word when you submit.