Cluster Software

Basic linux software is installed on the cluster for general use. For scientific computation users are welcome to install software in their hpc/home/ space if sudo access is not required. Most commonly, users may self install Conda to use Python and other supported langauges.

For all other software we recommend building and deploying your container to NCShare.

Conda / Python Install

A full guide is available on how to install Conda and manage your own environments.

Software Containers

NCShare provides the following containers for use on the the cluster: * Jupyter (get link from Mike) * RStudio (get link from Mike)

Adding containers to NCShare

Pre-built Docker and Singularity containers are often available within scientific repositories and on GitHub. Images can be moved to the cluster using the same methods as any other file.

!! info Because many images are quite large, we recommend storing them in /opt/apps/containers/user.

Most Docker containers are fully supported with singularity and can be run using Apptainer.

Useful Singularity Container repositories

Pre-built containers are also available in external repositories and can be loaded to the DCC using singularity pull or singularity build commands.

• Sylab's Container Library
• Docker Hub
• Red Hat's Quay
• NVIDIA GPU Cloud

Creating your own apptainer containers

Singularity containers cannot be created on the DCC directly because you need root access to the build system. Generally to build a container, you will need root access to a Linux machine. If you do not have a Linux VM, you can obtain one through Duke Virtual Computing Manager, or lab groups may have access to a RAPID VM through their Faculty/PIs allocation. Helpful documentation:

• Install Singularity on Linux
• Singularity Definition Files
• Instructions to Build a Container