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5. Software in the HPC environment
One of the advantages of using the HPC is that it has an extensive library of scientific software already installed and available to users. This enables users to access the functionalities of various software applications without cumbersome setup procedures.
To explore the available software, users can invoke the 'catalogue' command, generating a list of installed programs and tools:
catalogue
If you include the –search option, just the matching software will be returned
catalogue –search package_name
In addition, there is a browser based version of the software catalogue (https://software.hpc.nbi.ac.uk/) which has more information on each package, including the .def (or recipe) file used to install the software.
To load any installed software into your local environment, use the source command:
source package package_UUID
In instances where a required software package is not yet available, refer to the Research Computing (RC) documentation for guidance on deploying a Singularity container version locally first, which can subsequently be deployed in the EI software area.
Should users encounter challenges during the installation process, a ticket can be raised with Research Computing team to troubleshoot the issue.
- Induction
- HPC Best practice
- Job Arrays - RC documentation
- Methods to Improve I/O Performance - RC documentation
- Customising your bash profile for ease and efficiency
- Customise bash profile: Logging Your Command History Automatically
- Using the ei-gpu partition on the Earlham Institute computing cluster
- Using the GPUs at EI
- HPC Job Summary Tool
- EI Cloud (CyVerse)
- Git and GitHub
- Worked examples
- Job Arrays
- Using Parabricks on the GPUs
- dependencies
- Software installations
- Workflow management system
- Transfers
- Local (mounting HPC storage)
- Remote - <1gb (ood)
- Remote - <50gb (nbi drop off)
- Remote - No limit (globus)
- mv command