The Servers

The number of servers in the Maglab group has grown slowly over time as the requirements of the lab for computing power have grown. Because of this, the servers are a little messy in some respects and that needs to be taken into account when dealing with them.

Contents:

General Operation

Operating System

The default OS on all servers is Ubuntu 12.04 (excepting Maglab which uses an old 10.04 kernel). This is standardised to make it easier to keep things in shape and will be supported for a few more years yet.

Bioinformatics Programs

Bioinformatics programs are store in /opt with the previous versions used kept. They layout usually looks as follows:

/opt
├── cufflinks
│   ├── cufflinks-1.3.0
│   ├── cufflinks-2.0.0
│   └── cufflinks-2.0.2

Older programs may be required to replicate previous findings or to compare new and old findings if the program has been changed in a significant way.

These programs are then symlinked to /usr/local/bin. A helpful script (symlinkexec) allows you to quickly do this for an entire folder. It will also delete the old symlinks before adding the new ones.

R

R is an awkward one; all of the server where it has been installed use the official R repository rather than the default Ubuntu one. This ensure that R is kept up to date rather than lag behind (as the Ubuntu one does). All users keep their modules installed in the home directory to allow easy install of custom modules and to keep them up to date more easily.

Network Layout

Maglab network map

Life Sciences Server Room

All of the servers in the Life Sciences server room access the internet through Alfred (due to a lack of spare ethernet sockets). Alfred therefore acts as a gateway that all users need to log in to access the other servers. Internally they are all connected to a switch not owned by the group.

CSD Server Room

Because of a lack of space in the Life Sciences server room one machine sits in CSD. This is the storage machine and contains all of the home directories for the users. It is connected to the Life Sciences network as well as via a GRE tunnel to Alfred where it appears as a local machine.

Linode London

This is a VPS server hosted in a London datacentre. It hosts the lighter of the websites, ones that do not require large databases or heavy processing.