Using Modules: FAQs

Owned by Simon Alexander
Last updated: Sep 30, 2024
5 min read

Goal: Present a list of commonly asked questions that might not be addressed specifically during the workshop.

Do I Need to Load Modules slurm/latest and arcc/1.0?

As mentioned earlier these two modules will be loaded automatically on the start of any session.

As long as you do not --force purge nor unload these, they stay within your session and essentially you do not need to re-load them.

The arcc/<version> module can be considered as a dependency for everything, which is why ARCC loads it. But there is no harm if you wish to include it within any scripts.

Dependencies: Remember

  • If a library/application has been installed with a compiler, you need to load that compiler first.

  • If a library/application has been built with openmpi, you need to load that next. Libraries will be post fixed with -ompi.

  • Software based on containers and conda environments do not have dependencies.

  • Some Linux binaries might have might have dependencies. These will be automatically loaded and specified in the module spider help details.

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Relationships with Dependencies

Remember: Use module spider to find if something has dependencies.

Are There Modules For Python Packages?

Are There Modules For R Packages?

Can Not Find a Previous Module I Used

[]$ module spider samtools -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- samtools: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Versions: samtools/1.14 samtools/1.16.1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- For detailed information about a specific "samtools" package (including how to load the modules) use the module's full name. Note that names that have a trailing (E) are extensions provided by other modules. For example: $ module spider samtools/1.16.1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- []$ module spider samtools/1.16.1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- samtools: samtools/1.16.1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- You will need to load all module(s) on any one of the lines below before the "samtools/1.16.1" module is available to load. arcc/1.0 gcc/12.2.0 Help: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
[]$ module spider samtools ---------------------------------------------------------------------------- samtools: samtools/1.20 ---------------------------------------------------------------------------- This module can be loaded directly: module load samtools/1.20 Additional variants of this module can also be loaded after loading the following modules: arcc/1.0 gcc/14.2.0 Help: samtools : 1.20 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. https://www.htslib.org/ []$ module spider samtools/1.20 ---------------------------------------------------------------------------- samtools: samtools/1.20 ---------------------------------------------------------------------------- This module can be loaded directly: module load samtools/1.20 Additional variants of this module can also be loaded after loading the following modules: arcc/1.0 gcc/14.2.0 Help: samtools : 1.20 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. https://www.htslib.org/

Module Names Can Update

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Using Modules: Considerations and Defaults

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Intro to using the Module System

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