Migrate to XIOS 3 by EdHone · Pull Request #805 · MetOffice/lfric_apps

Ed Hone (EdHone) · 2026-09-22T14:56:31Z

PR Summary

Sci/Tech Reviewer:
Code Reviewer:

The current iteration of XIOS 2 used by all the LFRic applications is no longer in development and will not be able to provide the I/O capability we will need going into the future. This PR migrates our applications to use an up-to-date version of XIOS 3. These changes will not be backwards compatible with the previous XIOS version.

linked Migrate to XIOS 3 lfric_core#472
is blocked-by Coupled checkpoint restart #774

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 Apps rose-stem suite
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

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

… | updated modules would be better

…S3. (MetOffice#6) Note these changes are likely not backwards-compatible with XIOS2.

* Changes in lfric_apps to be able to run the jedi-lfric tests with XIOS3. Note these changes are likely not backwards-compatible with XIOS2. * Fixes to axis definition for adjoint tests and linear model tests * Fix to stop adjoint tests from hanging after completion * Extra small fix needed for Linear Model tests to pass so I'm adding to the branch/PR for the adjoint

…ging fix)

This reverts commit 46d23af.

…ntext finalisation issue is fixed by PR #2 on the core feature branch

…and fix new iodefs

iboutle · 2026-09-28T14:02:21Z

Just adding a note that this is blocked by #774

… context is finalised as well as the jedi context before xios finalise is called.

Fixes to jedi lfric forecast test

github-actions · 2026-10-20T11:26:00Z

⚠️ Hello Ed Hone (@EdHone)!

Your CLA signature was found on the base branch, but you appear to have modified the CONTRIBUTORS.md file in this PR.

Please do not edit the CONTRIBUTORS.md file. If you have already signed the CLA, revert changes to the file and your signature will be picked up.

mo-marqh and others added 30 commits September 22, 2026 10:01

use XIOS3

5245e41

use linked core branch XIOS3

dae7068

p2p transport, no window manager

3178406

space from metadata X3 compatibility

ecaa15c

X3 settings oper_hres + XML alignment

4c5eb49

_field_group id typo

164500d

Fix field groups for jedi-lfric-tests (MetOffice#5)

5f7d62e

hard code paths for coupled env vars xios_path & prism-path | fragile…

63765eb

… | updated modules would be better

Changes in lfric_apps to be able to run the jedi-lfric tests with XIO…

b5798cf

…S3. (MetOffice#6) Note these changes are likely not backwards-compatible with XIOS2.

Fix new xios3 config option (MetOffice#7)

8d93ce6

fix references to buffer_factor_size (MetOffice#8)

cf1fe21

Various fixes needed for lfric_atm jobs (surface altitude fix and nud…

c0d1ad1

…ging fix)

correct use for jedi_lfric_comm_mod

3461fa4

clients_code_id XIOS3 compatibility

7199d63

query : memory milan to fix submit-fail due to memory request 238

90bacc4

remove use of final_comm for XIOS3

5723bb6

Extra fix needed for iodef for nudging test (MetOffice#11)

43060cf

XIOS3 drivers

4f7e275

Coupled test runs with XIOS3

4983dda

Add the xios_3 preprocessor key

2741482

Update NEMO package branch branch

93d7c45

Use the package branch

bd0b364

Add updated revision of core repository post merging sams changes

4f4a0c2

Revert "remove use of final_comm for XIOS3"

0df05d3

This reverts commit 46d23af.

Restore the core dependency to mo-marqh's clone

f2ee62d

fix lfric2lfric

3b3070f

fix some lfricinputs failures

f547f76

Fix lfric2lfric canned test

035213c

Reinstating final_comm() for adjoint and linear model tests as the co…

da53ea5

…ntext finalisation issue is fixed by PR #2 on the core feature branch

Adding back the call to final_comm() for this jedi-lfric test

18a1bf6

github-actions Bot added the cla-modified The CLA has been modified as part of this PR - added by GA label Sep 22, 2026

github-actions Bot assigned Ed Hone (EdHone) Sep 22, 2026

Ed Hone (EdHone) added 4 commits September 22, 2026 16:02

Update dependencies, replace final_comm, fix memory profile on spice …

ebbcb79

…and fix new iodefs

Merge branch 'main' into main-xios3adopt

fc367c1

Fix deprecated zoom_axis, fix gc6 iodef and others

79fa1df

Tweak CXI env setup and lfric2lfric iodefs

10145c9

iboutle mentioned this pull request Sep 28, 2026

Coupled checkpoint restart #774

Merged

18 of 28 tasks

Ed Hone (EdHone) and others added 8 commits September 29, 2026 12:59

Merge branch 'main' into main-xios3adopt

bc8592b

Fixes for jedi-lfric tests from Steve Sandbach

73b5a1f

Unused variable removed

88cb07f

close NL context

8c79cb2

fix close NL context

024949b

Fix lfric2lfric environment

6ab506f

Merge branch 'main' into main-xios3adopt

a37200d

Merge branch 'main' into main-xios3adopt

527eb16

Ed Hone (EdHone) added this to the Autumn 2026 milestone Oct 5, 2026

Ed Hone (EdHone) mentioned this pull request Oct 5, 2026

Migrate to XIOS 3 MetOffice/lfric_core#472

Draft

29 tasks

Ed Hone (EdHone) and others added 4 commits October 6, 2026 10:43

Merge branch 'main' into main-xios3adopt

55214e3

Fixes to jedi lfric forecast test to ensure that the LFRic model XIOS…

8b87570

… context is finalised as well as the jedi context before xios finalise is called.

Merge pull request #3 from svadams/jedi_lfric_forecast_fix

c0e8ed9

Fixes to jedi lfric forecast test

Merge branch 'main' into main-xios3adopt

ea464b9

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Migrate to XIOS 3 - #805

Migrate to XIOS 3#805
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Ed Hone (EdHone) commented Sep 22, 2026 •

edited

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iboutle commented Sep 28, 2026

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Ed Hone (EdHone) commented Sep 22, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR Summary

Code Quality Checklist

Testing

trac.log

Security Considerations

Performance Impact

AI Assistance and Attribution

Documentation

PSyclone Approval

Sci/Tech Review

Code Review

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iboutle commented Sep 28, 2026

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Ed Hone (EdHone) commented Sep 22, 2026 •

edited

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