Installing (Third Party) applications

NeSI provides a long list of various applications on its systems. Nevertheless, if you need additional applications or libraries (below called package), we distinguish:

• you need a newer version of an already installed package: Contact our Support Team for an update
• you need an older version of an installed package: please use the Easybuild installation procedure (below) to install it into your working space
• you want to test a new (not installed) package: below we collected some hints, how you can install it in your user space.

In any case, if you have issues, do not hesitate to Contact our Support Team.

Additional Packages for Python, R, etc.

See Python or R, or for other languages check if we have additional documentation for it in our application documentation.

Third party applications

Installation instruction vary from application to application. In any case we suggest to read the provided installing instructions. Nevertheless, the following should give you an impression which steps you usually need to consider:

• Change into a desired source code directory. We suggest to use /nesi/nobackup/<projectID> or /nesi/project/<projectID>
• download the source code. This could be done via a repository checkout (git clone <URL to the application source repository>) or via downloading a tarball (wget <URL to the tarball>). Unpack the tarball using tar xf <tar file name>. Change into source directory.
• load compiler module and modules for additional libraries (module load gimkl FFTW)
• run the configure with appropriate options ./configure --prefix=<desired install directory> --use-fftw=$EBROOTFFTW(options can be listed using ./configure --help)
• In other applications you need to adjust the provided Makefile to reflect compiler, and library options (see below)
• compile code (make)
• install the binaries and libraries into the specified directory (make install)

Create your own modules (Optional)

You can create personalised module environments, which can load modules and set up environment variables. For example, you could define a modules in a project directory /nesi/project/<projectID>/modulefiles/ProdXY as the following:

In the first lines, we can set conflicts with other modules (here named ProdABC). Then we load some dependency modules and provide some description. The additional lines depend on your requirements for the module. With set you can define internal variables (within this module file). The command setenv defines a environment variable. And prepend-path and append-path extend an environment variable at the front or end.

There are common environment variables like:

• PATH for providing executabl,
• LD_LIBRARY_PATH for self created libraries,
• PYTHONPATH for providing Python modules,
• CONDA_ENVS_PATH for providing Conda environments,
• etc.

And others which are very application specific.

To use the module (or all in that directory and sub-directories) we need to register that directory to the module environment. This can be done by setting the following environment variable:

by adding that line to your $HOME/.bashrc you will have the modules always available.

The module then can be loaded by:

These modules can easily be shared with collaborators. They just need to specify the last two steps.