environment

Accessing software with Lmod

Accessing software with Lmod

Since October 2016 (Kebnekaise) and April 2017 (Abisko) we are using a set of tools called EasyBuild and Lmod to install and manage software packages and their accompanying modules.

This results in a different naming of the modules themselves and also a completely different module layout, compared to how it was done with Tcl modules.

The modules are installed hierarchically in such a way that not all modules are visible initially.

Using modules (Lmod)

Setting up the environment using Lmod

To set up your environment for using a particular (set of) software package(s), you can use the modules that are provided centrally.

On both Abisko and Kebnekaise, interacting with the modules is done via Lmod, using the module command or the handy shortcut command ml.

Using Environment Variables

Using Environment Variables

This page is assuming you use bash or another shell in the Bourne family of shells. Most of the informtation will be correct for other shells as well, but the examples cannot be assumed to be.

HPC2N recommends using bash, since it is the only shell that is fully supported by the batch system.

Environment variables are a set of dynamic named values, generally meant to make your life easier. Some are built-in, some are set by loading various modules, and you can also define extra to help yourself.

Environment Variables

Environment Variables

There are many environment variables. Some will be set automatically at login and some which you can change if needed. Many of the environment variables will be related to paths and storage locations, but there are also some which are set for specific applications (like compilers). These environment variables willl be set when you load the 'module' for the application in question. (Read more about modules in the section about them.)

HPC2N environment

HPC2N environment

The contents of your home directory are placed on an AFS name space and is backed up regularly. AFS (Andrew File System) is a distributed networked file system, which was developed for security and scalability. Read more about AFS here.

Most differences between AFS and traditional networked file systems (like NFS) are transparant for the user, but some important differences are:

The Environment

The Environment

The systems at HPC2N predominantly run various versions of Linux. If you have no experience with that, there are several good online sources that can be used to familiarize yourself with the basic commands. 

Updated: 2017-09-21, 11:05