Enable jedi_lfric to run lfric_atm forecast configurations by ss421 · Pull Request #512 · MetOffice/lfric_apps

Steven Sandbach (ss421) · 2026-05-20T22:24:30Z

PR Summary

Sci/Tech Reviewer: Matt Shin (@matthewrmshin)
Code Reviewer: Ricky Wong (@mo-rickywong)

This update requires the changes applied in: #502. This branch Update forecast config ifdefphys was created from the branch in that PR: cjohnson-pi/ifdefphys. The change being applied in this PR can be seen via: cjohnson-pi/lfric_apps@ifdefphys...ss421:lfric_apps:update_forecast_config_ifdefphys

This PR updates jedi_lfric_tests to enable running of model forecast based on lfric_atm configurations. This requires setting UM_PHYSICS to true. The update largely follows the lfric_atm build configurations. I did not:

Add the optimization scripts as it is not yet clear how this should be done. Some follow up work is required to better understand this.
Update the build flags FFLAG_GROUPS because I encountered build issues that may be linked to Adjoint code which is included in the jedi_lfric library.

A small bug was fixed (removal of clock double tick).

Three new lfric_atm based configurations have been added: nwp_gal9-C12, nwp_gal9-C12_da and nwp_gal9-C48_MG. The existing gh-si-for-linear-C12 was removed as it was only a placeholder configuration and no longer required.

Note: The C48 test requires a new input file reference directly at: /home/users/darth/srv/mobb-data/lfric-jedi/lfric-diag/lfric_bg_mi-be607_C48_20210602_la354.nc currently and used in JEDI testing. Documentation on the file is included in: https://github.com/MetOffice/jjdocs/blob/38d5cfad6fd30cbea67e825775c5a20798490430/docs/Interfaces/ModelInterfaces/Input-Data/lfric-jedi-dir.rst?plain=1#L169

The applications/jedi_lfric_tests/integration-test was removed as it was problematic when integrating the UM physics and currently not testing anything useful. Furthermore, none of the other applications include integration tests.

linked MetOffice/mo-bundle#1072
linked JCSDA-internal/lfric-jedi#1274

Note: given the nature of this change I would like to test this branch again before the branch is merged into main.

is blocked-by linear_model app with UM_PHYSICS compiler flag set to true #502

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)

Tested via lfric-jedi: https://github.com/JCSDA-internal/lfric-jedi/pull/1274 using a sepearte branch at the head of main (see: ss421#2).

trac.log

Test Suite Results - lfric_apps - update_forecast_config_ifdefphys/run5

Suite Information

Item	Value
Suite Name	update_forecast_config_ifdefphys/run5
Suite User	steven.sandbach
Workflow Start	2026-05-22T13:29:40
Groups Run	developer

Dependency	Reference	Main Like
casim	MetOffice/casim@2026.03.2	True
jules	MetOffice/jules@2026.03.2	True
lfric_apps	ss421/lfric_apps@update_forecast_config_ifdefphys	False
lfric_core	MetOffice/lfric_core@2026.03.2	True
moci	MetOffice/moci@2026.03.2	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2026.03.2	True
socrates	MetOffice/socrates@2026.03.2	True
socrates-spectral	MetOffice/socrates-spectral@2026.03.2	True
ukca	MetOffice/ukca@2026.03.2	True

Task Information

✅ succeeded tasks - 1172

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 TCD 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

…cast_config_ifdefphys

Steven Sandbach (ss421) · 2026-05-22T15:28:21Z

Thanks reviewing Matt Shin (@matthewrmshin) - I see this has now been moved to code review and is now with Ricky Wong (@mo-rickywong)

Matthew Hambley (MatthewHambley)

Code owner (build system) review: A few things seem off. Please explain why the are necessary.

Matthew Hambley (MatthewHambley) · 2026-06-02T10:34:10Z

If you want to override compiler arguments on a per-file bases the FFLAGS_EXTRA variable is provided for this. Did you try this and find it didn't work?

I did not and Im not sure what I need to do to test that. Can you help with this?

I've been following the structure of lfric_atm so all of these files are based on/copies from that. From what I understand, these are profile specific and needed because the per-file flag overrides differ between profiles. The FFLAGS_EXTRA in compile_options.mk is profile agnostic.

Matthew Hambley (MatthewHambley) · 2026-06-02T10:35:26Z

+
+$(info UM physics specific compile options)
+
+include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk


I don't think this should be needed.

This is in the equivalent lfric_atm file but I can try to remove it here.

I tired removing that but it failed during build so it appears to be needed. The failure relates to code that is now being built. This File seems to include settings that are currently required by lfric-atm. See:

https://cylchub/services/cylc-review/view/steven.sandbach?&suite=update_forecast_config_ifdefphys1%2Frun1&no_fuzzy_time=0&path=log/job/1/build_jedi_lfric_tests_azspice_gnu_fast-debug-64bit/01/job.err

Matthew Hambley (MatthewHambley) · 2026-06-02T10:37:30Z

 	$(Q)echo > /dev/null

-include $(APPS_ROOT_DIR)/build/extract/extract_meta.mk
 include $(CORE_ROOT_DIR)/infrastructure/build/lfric.mk
 include $(INTERNAL_DEPENDENCIES:=/build/import.mk)
-include $(PROJECT_DIR)/build/project.mk
+include build/project.mk


Why make this change?

Im not sure, I made a bunch of changes to get this to work. I will try reverting it and see what happens.

I've reverted and retested and all good so committed at: 89c3bba

Matthew Hambley (MatthewHambley) · 2026-06-02T10:38:38Z

+	$(call MESSAGE,Extracting coupled_interface component)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/coupled_interface/source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,Extracting Gungho dynamical core)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/science/gungho/source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,Extracting UM physics)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(APPS_ROOT_DIR)/build/extract/extract_physics.mk
+	$(call MESSAGE,========================================)


The INTERNAL_DEPENDENCIES list is provided for doing exactly this.

As noted I've been following lfric_atm in the minimal way possible. I'm not sure what I tried that didn't work but I think I did try to minimize what is included here. Can I clarify on your comment: do you think it should be possible to remove all of the highlighted text (131-144)? I can try that if so.

Matthew Hambley (MatthewHambley) · 2026-06-02T10:39:30Z

+	$(call MESSAGE,PSycloning interface components)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/coupled_interface/source \
+	          OPTIMISATION_PATH=$(OPTIMISATION_PATH)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/jules_interface/source \
+	          OPTIMISATION_PATH=$(OPTIMISATION_PATH)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/socrates_interface/source \
+	          OPTIMISATION_PATH=$(OPTIMISATION_PATH)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/physics_schemes_interface/source \
+	          OPTIMISATION_PATH=$(OPTIMISATION_PATH)
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,PSycloning Gungho dynamical core)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/science/gungho/source \
+	          OPTIMISATION_PATH=$(OPTIMISATION_PATH)
+	$(call MESSAGE,========================================)


The INTERNAL_DEPENDENCIES should do away with this as well.

As with previous comment - I can test with this section (157-177) removed if you think that should work?

Matthew Hambley (MatthewHambley) · 2026-06-02T10:57:56Z

 export FFLAGS_UM_PHYSICS = -s real64

-include $(PROJECT_DIR)/build/fortran/crayftn/$(PROFILE).mk
+include $(PROJECT_DIR)/../lfric_atm/build/fortran/crayftn/$(PROFILE).mk


This change seems unnecessary.

This is a branch from: cjohnson-pi:ifdefphys in #502 where this particular change is being added. I see you have commented on that so it will be fixed by that PR.

Matthew Hambley (MatthewHambley) · 2026-06-02T11:55:56Z

+
+$(info UM physics specific compile options)
+
+include $(LFRIC_ATM_DIR)/build/fortran/$(FORTRAN_COMPILER).mk


I don't think this should be necessary.

This is a branch from: cjohnson-pi:ifdefphys in #502 where this particular change is being added. I see you have commented on that so it will be fixed by that PR.

cjohnson-pi and others added 22 commits May 12, 2026 16:57

Add ifdef UM_PHYS, linear_model example runs

42c51b7

retry copying optimisation from lfric_atm]

3f79afc

linear_model and lfric_atm run

f6f1a06

clearwhitespace

0f9e2be

removing PHYSICS_ROOT change

9bf79cb

increase build wallclock

5f68c17

Merge remote-tracking branch 'upstream/stable' into ifdefphys

70c1ce1

use_physics false

0efabc0

correct for validate_rose-meta. Test suite completes.

23a5abb

Adding updates from my HEAD branch...

fa5e41d

use lfric_atm optimisation options

eaaba2a

tidy

3d3e72e

revert jedi changes

bcad2f5

whitespace

db5d9a2

Merge remote-tracking branch 'cjohnson-pi/ifdefphys' into update_fore…

ab70eb4

…cast_config_ifdefphys

update build

339b0b0

Make switch less strict, for jedi tests

b9da623

Merge remote-tracking branch 'cjohnson-pi/ifdefphys' into update_fore…

6f79e5b

…cast_config_ifdefphys

Merge remote-tracking branch 'cjohnson-pi/ifdefphys' into update_fore…

f0261b9

…cast_config_ifdefphys

Fix rose validate - need to use upgrade macro

f3090de

Fix/add KGOs

80831af

Relabeled the name of the chcksum

f039571

Steven Sandbach (ss421) self-assigned this May 20, 2026

Steven Sandbach (ss421) requested review from a team, Matthew Hambley (MatthewHambley), Hacka Fett (christophermaynard), cjohnson-pi, Joerg Henrichs (hiker), James Bruten (james-bruten-mo) and mo-cjsmith as code owners May 20, 2026 22:24

Steven Sandbach (ss421) requested review from a team and Matt Shin (matthewrmshin) as code owners May 20, 2026 22:24

Steven Sandbach (ss421) added the Linked Jedi This PR is linked to a Jedi PR - this will be managed by the DA team label May 20, 2026

Steven Sandbach (ss421) changed the title ~~Update forecast config ifdefphys~~ Enable jedi_lfric to run lfric_atm forecast configurations May 20, 2026

Code tidy

d240f12

cjohnson-pi approved these changes May 21, 2026

View reviewed changes

Steven Sandbach (ss421) mentioned this pull request May 21, 2026

linear_model app with UM_PHYSICS compiler flag set to true #502

Open

27 tasks

Matt Shin (matthewrmshin) approved these changes May 21, 2026

View reviewed changes

Update to fix rose validate correctly

09d22e1

github-actions Bot requested a review from Ricky Wong (mo-rickywong) May 21, 2026 22:39

mo-cjsmith approved these changes May 22, 2026

View reviewed changes

Update the forecast configuration

d5a18cd

Matthew Hambley (MatthewHambley) reviewed Jun 2, 2026

View reviewed changes

Update to revert previous change as noted by reviewer.

89c3bba


		$(info UM physics specific compile options)

		include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk


		$(info UM physics specific compile options)

		include $(LFRIC_ATM_DIR)/build/fortran/$(FORTRAN_COMPILER).mk

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PR Summary

Code Quality Checklist

Testing

trac.log

Test Suite Results - lfric_apps - update_forecast_config_ifdefphys/run5

Suite Information

Task Information

Security Considerations

Performance Impact

AI Assistance and Attribution

Documentation

PSyclone Approval

Sci/Tech Review

Code Review

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Steven Sandbach (ss421) commented May 22, 2026

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Steven Sandbach (ss421) commented May 20, 2026 •

edited

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