Attention

GPU users: GPU nodes run EL9, while this documentation still reflects the EL7 software stack.

Run module avail on an EL9 login node, or within an interactive session on the relevant GPU type, to see the software available.

The documentation will be updated once all nodes have migrated to EL9.

Autogenerated - All Package Index

The All Packages Index is autogenerated using this repository .

The autogenerated files can serve as a foundation to enhance more detailed documentation in the first four sections of Software on Stanage .

We can use the autogenerated imports to ensure for example, module list versions are up to date:

.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst

The most useful autogenerated imports are:

.. include:: /referenceinfo/imports/stanage/packages/software-name-sdbr-el7-icelake-znver-stanage.rst                   # sidebar
.. include:: /referenceinfo/imports/stanage/packages/software-name-dscr-el7-icelake-znver-stanage.rst                   # description
.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst                     # module load (versions)
.. include:: /referenceinfo/imports/stanage/packages/software-name-inst-el7-icelake-znver-stanage.rst                   # installation notes
.. include:: /referenceinfo/imports/stanage/packages/software-name-dpnd-el7-icelake-znver-stanage.rst                   # dependencies of latest version

Using API ReST Files as Templates for Software Pages

If we want to add a fully documented page which does not currently exist for a software that is already installed on Stanage to, for example, stanage/software/apps within sheffield_hpc, then we would do the following:

cd stanage/software/apps
cp ../stacks/el7-icelake-znver-stanage/Bio/<package-name>.rst .

Here Bio is the module class of the package, The module class of a package can be found in it’s easyconfig.

Alternatively, find module class and also remove lines not needed:

cd stanage/software/apps
module_class=$(grep -r <package-name> ../stacks/el7-icelake-znver-stanage/All/index.rst | sed -E 's/-/\n/g' | tail -n 5 | head -n 1 | sed 's/./\U&/')
awk '/packages_note| -cust-/{getline; next} {print}' ../stacks/el7-icelake-znver-stanage/${module_class}/<package-name>.rst > ./<package-name>.rst

Now we can edit the template which looks like the following:

.. _software-name-bio-el7-icelake-znver-stanage:                                                                         # Edit this line to avoid conflicts

software-name
=============

.. include:: /referenceinfo/imports/stanage/packages/software-name-sdbr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dscr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/packages_note.rst                                                   # Delete this line as not needed

.. include:: /referenceinfo/imports/scheduler/SLURM/common_commands/srun_start_interactive_session_import_stanage.rst

A version of software-name can then be made available with *one* of the following:

.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/custom/software-name-cust-el7-icelake-znver-stanage.rst             # Delete this line as not needed

Notes
-----

.. include:: /referenceinfo/imports/stanage/packages/software-name-inst-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dpnd-el7-icelake-znver-stanage.rst

.. _software-name-bio-el7-icelake-znver-stanage:                                                                         # Edit this line to avoid conflicts

software-name
=============

.. include:: /referenceinfo/imports/stanage/packages/software-name-sdbr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dscr-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/scheduler/SLURM/common_commands/srun_start_interactive_session_import_stanage.rst

A version of software-name can then be made available with *one* of the following:

.. include:: /referenceinfo/imports/stanage/packages/software-name-ml-el7-icelake-znver-stanage.rst

Notes
-----

.. include:: /referenceinfo/imports/stanage/packages/software-name-inst-el7-icelake-znver-stanage.rst

.. include:: /referenceinfo/imports/stanage/packages/software-name-dpnd-el7-icelake-znver-stanage.rst

Note

In this example, the internal page reference _software-name-bio-el7-icelake-znver-stanage:, should be updated to _softwarename_stanage: for consitency with fully documented software page references.