Skip to content

Installing software

Checking if a package is installed

Note

Before installing software yourself, check if it has already been installed as part of the environment or as a module. You may also want to speak to one of your research colleagues to find out if they have installed it for themselves.

Some common software packages are already available as part of katana's the operating system. They are listed by: 

    yum list installed

Warning

Do not try to run administration commands as a user. These include: apt-get install, yum install, su, or sudo.

You can see the list of software applications already installed on Katana using the Environment Module command:

   module avail

R and Python Packages

Many Python and R packages are installed on katana. We have specific documentation to install your own packages in Python` and R

Note

If you have tried to install packages software yourself, but you need further assistance, then please send an email to restech.support@unsw.edu.au.

Installing a binary package

While installing from source is preferred for effeciency reasons, sometimes only precompiled binaries are available. When downloading binaries, make sure you select the correct architecture and operating system for Katana.

Note

The login and compute nodes of Katana are currently Rocky Linux 8.9, 64-bit, Intel x86_64 / AMD64.

If the software is small then you may want to install it in your home directory to take advantage of the nightly backup. Otherwise you should install the software in your scratch directory.

wget https://website.org/binary/application

Change file permissions to make the application readable and executable

chmod u+rx ./application

Compiling from source

Compiling from source is preferred for efficiency reasons but is generally a more complicted process than a binary installation.

Note

If the software is small then you may want to install it in your home directory to take advantage of the nightly backup. Otherwise you should install the software in your scratch directory.

Installing software from Github

Source code is commonly stored on GitHub for easy version control. Git is available by default on katana. Remember: UNSW has its own GitHub organisation.

The process to install code which comes from GitHub depends on how the author of the code has set it up.

Installing a Github software release

Often the software owner will create a software release which is a copy of the software with everything frozen at that point in time. This helps with reproducability of results as you can refer to a specific version of the software and someone else can easily install the same version on their computer. You will often be able to choose between a binary version and downloading the source. Downloading the binary and the source versions will look something like:

   wget https://github.com/project/project/releases/download/v1.48.1/project.linux_8.zip

   wget https://github.com/project/project/archive/refs/tags/v1.48.1.tar.gz

Github cloning

If the owner of the software has not created a release or the latest release is too old then you can download the repository and use it to compile the software. Copy the web address revealed by the green 'Code' button on the repository. Creating a local copy of the repository uses the following command:

   git clone https://github.com/project/project.git

The created folder will then contain the source code and some documentation files.

README and INSTALL files

The README file contains general information for the software, and often a brief installation guide. INSTALL will contain more detailed installation instructions, including configuration for certain archictures. Please read the README and INSTALL files in full before attempting compilation.

Compilers

It is generally best to use the system compilers gcc and ld. However, many code requires specific compilers and versions. Katana has many compilers available as modules including the Intel Compilers and Software Libraries

Note

Please install software using an interactive session, qsub -I, not directly on the login node.

Configuring installation files

Commonly, a configuration script is available which allows you to set where the software is installed by using the --prefix flag as well as other options. To install the software in your Katana home directory you can use the following command:

   ./configure --prefix=$HOME/apps/{PACKAGE}/{VERSION}

The software can then be installed according to the rules in the MakeFile. This is typically invoked with

   make
   make install

Creating module files

Much like katana's Environment Modules, you can also have multiple versions of the application available through your own modules.

The template for environment modules is in:

/apps/modules/templates/module_file

The template module file makes some assumptions and examples, which may not be applicable to your software. Key sections will likely need to modify are:

  • set basepath $env(HOME)/apps/{SOFTWARE_NAME}

  • set version {VERSION_NUMBER}

  • set url

  • set installed

  • set compiled_with

  • set mpiversion

  • prereq {PREREQUISITE_SOFTWARE)

Note

Insert "module use --append $HOME/apps/Modules" into your ~/.bashrc to enable using your own modules upon login.

You should be able to module load your own software module as your own.