Enable the use of layered CF output for checkpoint-restart

[Ed Hone (EdHone)]

PR Summary

Sci/Tech Reviewer: Mike Hobson (@mike-hobson)
Code Reviewer:

The checkpointing I/O system used by some applications in lfric_apps uses 'legacy' checkpointing domains which are extremely non-performance at scale. The aim is convert to using the same UGRID format for output as the diagnostic files, which would involve changing the way that fields on the W2 function space are set up for I/O in XIOS. However, progress has been difficult for implementing this goal, as the UGRID implementation inside XIOS has some requirements and bugs which we cannot circumvent at the required timescales.
To get a performant checkpointing system working as soon as possible, this PR enables these applications to use checkpoint files to use a layered CF I/O implementation, which will circumvent the bugs in UGRID whilst maintaining the improved performance gains.

• linked Convert checkpoint files from legacy domains to layered CF lfric_apps#782

Code Quality Checklist

• I have performed a self-review of my own code
• My code follows the project's style guidelines
• Comments have been included that aid understanding and enhance the readability of the code
• My changes generate no new warnings
• All automated checks in the CI pipeline have completed successfully

Testing

• I have tested this change locally, using the LFRic Core rose-stem suite
• If required (e.g. API changes) I have also run the LFRic Apps test suite using this branch
• If any tests fail (rose-stem or CI) the reason is understood and acceptable (e.g. kgo changes)
• I have added tests to cover new functionality as appropriate (e.g. system tests, unit tests, etc.)
• Any new tests have been assigned an appropriate amount of compute resource and have been allocated to an appropriate testing group (i.e. the developer tests are for jobs which use a small amount of compute resource and complete in a matter of minutes)

trac.log

Test Suite Results - lfric_core - lfric_core-ugrid-ckp-flag/run3

Suite Information

Item	Value
Suite Name	lfric_core-ugrid-ckp-flag/run3
Suite User	edward.hone
Workflow Start	2026-09-30T14:22:35
Groups Run	developer

Dependency	Reference	Main Like
lfric_core	EdHone/lfric_core@ugrid-ckp-flag	False
SimSys_Scripts	MetOffice/SimSys_Scripts@cab3315	True

Task Information

✅ succeeded tasks - 433

Security Considerations

• I have reviewed my changes for potential security issues
• Sensitive data is properly handled (if applicable)
• Authentication and authorisation are properly implemented (if applicable)

Performance Impact

• Performance of the code has been considered and, if applicable, suitable performance measurements have been conducted

AI Assistance and Attribution

• Some of the content of this change has been produced with the assistance of Generative AI tool name (e.g., Met Office Github Copilot Enterprise, Github Copilot Personal, ChatGPT GPT-4, etc) and I have followed the Simulation Systems AI policy (including attribution labels)

Documentation

• Where appropriate I have updated documentation related to this change and confirmed that it builds correctly

PSyclone Approval

• If you have edited any PSyclone-related code (e.g. PSyKAl-lite, Kernel interface, optimisation scripts, LFRic data structure code) then please contact the HPC Optimisation Team

Sci/Tech Review

• I understand this area of code and the changes being added
• The proposed changes correspond to the pull request description
• Documentation is sufficient (do documentation papers need updating)
• Sufficient testing has been completed

(Please alert the code reviewer via a tag when you have approved the SR)

Code Review

• All dependencies have been resolved
• Related Issues have been properly linked and addressed
• CLA compliance has been confirmed
• Code quality standards have been met
• Tests are adequate and have passed
• Documentation is complete and accurate
• Security considerations have been addressed
• Performance impact is acceptable