Installing software

Note

Before installing software yourself, check if it has already been installed in a system-wide module or by one of your research colleagues.

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 system commands as a user. These include: apt-get install, yum install, su, or sudo.

As detailed in Environment Modules, software already installed by HPC staff is listed with:

module avail

Installing a binary package

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

Note

Centos 7, 64-bit, Intel x86_6 / AMD64

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 a more involved process than binary installation.

Note

It is best to install your software in your home directory, since it is backed up every night.

Github cloning

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.

Copy the web address revealed by the green ‘Code’ button on the repository. Creating a local copy of the repository is then as simple as:

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

The created folder will 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

Try to use the system compilers gcc and ld. However, many codes require 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. This allows you to set where the software is installed by using the –prefix flag. Again, it is best to install software within your home directory

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

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.

R and Python Packages

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

Note

If you do need assistance with software install after trying yourself, then send an email to itservicecentre@unsw.edu.au with Katana in the subject line.