Software

Linux

The Linux distribution (RHEL) comes with its own native software stack managed by its package manager, YUM/RPM.

Software stacks

We also operate a number of custom software stacks to address specific needs of scientific research. These are in turn divided into several entities that progressively give more control to the user.

Software stack Location Environment Package Access
Linux [1] Standard Default RPM root
HPC [2] /cm/shared/apps /cm/shared/modulefiles source/binary root
MPS [2] /mnt/pactsw /mnt/pactsw/etc/modulefiles source/binary root
User [3] ~/apps [1] ~/privatemodules source/binary <user> [2]
Group [3] /research/<group>/apps [1] [2] /research/<group>/apps/etc/modulefiles [1] [2] source/binary <group> [2]
  1. We use CentOS and Scientific Linux, both varients of Red Hat Enterprise Linux (RHEL), in research computing at Sussex. These Linux distros use RPM packages, distributed via YUM repos, installed locally on each machine.
  2. For packages that do not come with our RHEL distro, we use the primary HPC software stack, supplemented by the MPS software stack to satisfy specific requirements of MPS users. These are managed by system administrators and requests should be sent to MPS Support if you would like more applications to be added.
  3. The User and Group software stacks allow a greater degree of flexibility, where users and groups have the ability to build their own applications and create Module files, see How do I create modulefiles?

OS X

ITS now manage the deployment of OS X, and their standard image includes popular applications that don’t come preinstalled on a standard shipment of OS X from Apple. These include, but not exclusively, Xcode and MacTeX.

University of Sussex licensed applications can also be included, for more information see IT Services Software.

Important

Users are given full system administration privilage on Apple laptops, as with all laptops provided to researchers at Sussex. So you are able to modify your machine any way you want.

Linux software on OS X?

For those who use Apple laptops, when it comes to research computing, nearly all computation is done on Linux and most software are designed for this platform. Unfortunately OS X does not have quite the same development environment as Linux, even though it is essentially UNIX based.

The software available on a standard OS X install may not include all the necessary dependencies required to run scientific analysis packages. To address this we recommend that you install MacPorts.

Note

There are several other options available, such as Fink and Homebrew, but in practice MacPorts has proved to be the most stable and well maintained.

Warning

Do not attempt to install more than one of these at the same time!

Footnotes

[1](1, 2, 3) These are merely suggested directories, in practice you can put them anywhere you have write permission.
[2](1, 2, 3, 4) Replace object within and including angle brackets, like <this>, with some relevant entry.