Installation of extra applications or libraries

If you want to use an application that is not installed as module yet, there are usually two options: either we can install it as a new module, or you can try to install it yourself into one of your own directories. The first allows other users to make use of the software as well, while the latter has the advantage that you keep control over the software and can easily change, update or delete the software.

If you want to request the installation of certain software, please contact us and specify which version of the software you would like to have installed. How you can install software yourself depends on the application. A lot of software for Linux is installed using a “configure, make, make install” procedure; in that case you could use the following to install it into your home directory:

# First, we load the foss toolchain to get access to recent compilers and libraries
module load foss/2022b

# Configure the software, and specify the installation directory
./configure --prefix=$HOME/some/installation/directory

# Build/compile the software
make

# Install the software
make install

To install a module for your account you can use EasyBuild, which is the framework we use on Hábrók for installing software as modules. You can find many already published easyconfig files at the easybuild-easyconfigs GitHub repository which you can adapt to suit your needs. Most of these are also readily accessible on Hábrók even if the applications themselves are not installed. To install software in this way, it is necessary to do some minimal setup and follow a few steps:

• Create a directory on your /home directory named easybuild (i.e.; mkdir $HOME/easybuild)
• Export the following environment variables by adding them to your .bashrc file

export EASYBUILD_PREFIX=$HOME/easybuild
export EASYBUILD_BUILDPATH=/tmp/$USER
export EASYBUILD_SOURCEPATH=$HOME/easybuild/sources:/easybuild/sources

• Log out and then log in again, or do source .bashrc
• Ensure you have no other loaded modules with module purge
• Upload the recipe and the patch files to the same directory, for example in $HOME
• Load the latest EasyBuild with module load EasyBuild
• Install your application as a user module with eb --robot --trace ModuleName-version-toolchain.eb. This may take a while and use quite a few resources. Please do this on interactive1.hb.hpc.rug.nl, or interactive2.hb.hpc.rug.nl and not one of the login nodes
• After the installation is finished, make the modules available by running: module use $HOME/easybuild/modules/all
• Load the newly installed module version with module load ModuleName/version-toolchain
• Use the module as usual. You can confirm you are using the correct module after loading it with module list

Keep in mind that unless you add the module use line to your .bashrc file, you will need to run it every time you want to make use of your custom installed modules.

Scripting or programming language like Perl, Python, and R allow you to easily install additional libraries/modules/packages to your own home directory. You can find more information about this on the respective pages for these tools in the Examples section.