Installing Software

In addition to the software already available on Hopper, users can install custom software. Because Hopper is a shared system, users do not have root access and cannot install software using administrative commands as you might on a home computer. Instead, software must be installed locally (to a location within your /home or /projects or /groups directory). The following are some common methods of installing user software:

Python Packages

Python packages can be installed into a python virtual environment. This is the preferred method of installing python packages on all machines. For instructions on creating python virtual environments and installing packages using pip, see Python Virtual Environments Hopper.

Conda

Conda is a popular tool for managing and installing software. To search for software which can be installed using conda see Conda Forge, Bioconda, and Anaconda repositories. To install any conda software, see Conda Environments on Hopper

Building from Source

Some software is availabe only as source code (often hosted on github or similar shared repositories). Building and installing software from source is an advanced topic for experienced users. To build software, first ensure that you have loaded software modules for any compilers and libraries required by the code (e.g. the command ml gnu12 will load the GCC 12.3 Compiler Suite). Then download the source code (often with a git clone or wget command). If a configure script is part of the software installation process, you can specify the target installation directory using ./configure --prefix=$HOME/target_directory.

Running Docker/Singularity/Apptainer Containers Images

For software which is available as a Docker or Singularity/Apptainer Container Image, the software can be run using Singularity.