Update linear integration tests #170

cjohnson-pi · 2026-01-21T11:16:24Z

PR Summary

Sci/Tech Reviewer: @tommbendall
Code Reviewer: @mo-marqh

#115

Add a new nwp_gal9 configuration in the linear integration tests (to match the default configuration for the linear_model). This includes using data read from file to initialise the tests.
Update the integration tests linear drivers to match the linear model driver (this required a safety switch added to gungho_step)
Reduce the number of tests for the semi-implicit and runge-kutta configs (as nwp_gal9 is running most tests)
Update the plot_convergence.sh script (this is not part of the test suite but is useful to have) - this runs the integration tests multiple times and creates plots of the data.
Improve how the convergence rate in the integration tests is tested.

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)

Plot convergence results

#115 (comment)

trac.log

Test Suite Results - lfric_apps - update_integration_test/run1

Suite Information

Item	Value
Suite Name	update_integration_test/run1
Suite User	christine.johnson
Workflow Start	2026-01-28T15:09:36
Groups Run	suite_default

Dependency	Reference	Main Like
casim	MetOffice/casim@2025.12.1	True
jules	MetOffice/jules@2025.12.1	True
lfric_apps	cjohnson-pi/lfric_apps@update_integration_t	False
lfric_core	MetOffice/lfric_core@aa32824	True
moci	MetOffice/moci@2025.12.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True
socrates	MetOffice/socrates@2025.12.1	True
socrates-spectral	MetOffice/socrates-spectral@2025.12.1	True
ukca	MetOffice/ukca@2025.12.1	True

Task Information

✅ succeeded tasks - 1106

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

cjohnson-pi · 2026-01-21T12:07:25Z

test

tommbendall

This PR does quite a lot of things, and I have to admit to finding it difficult to navigate!

One of the larger changes seems to be to include moisture in several of the test algorithms, such as tl_test_rhs_alg_mod.x90 and tl_test_semi_imp_alg_mod.x90. There are a couple of changes that I don't understand, so have left comments on them.

It's an welcome change to use the appropriate driver level code in the control routines for the integration tests.

I appreciate the level of instructions in plot_convergence.sh. I checked out a copy of this branch and ran the script. It seems to take a very long time and hasn't finished yet -- I will report back it this fails.

tommbendall · 2026-01-26T12:10:14Z

science/gungho/source/driver/gungho_step_mod.x90

@@ -123,10 +123,13 @@ module gungho_step_mod
    call log_event( log_scratch_space, LOG_LEVEL_INFO )

    temp_corr_io_value => get_io_value( modeldb%values, 'temperature_correction_io_value')


It seems sensible to wrap the lines below in an if statement. Would it also make sense to wrap this line in an if statement about the energy correction?

Now included

tommbendall · 2026-01-26T17:03:53Z

science/linear/plot_convergence/plot_convergence.sh

@@ -0,0 +1,112 @@
+##############################################################################
+# (c) Crown copyright 2022 Met Office. All rights reserved.


Should the year be 2026?

I've just moved this script from another directory, so the origin date is correct.

tommbendall · 2026-01-26T17:04:04Z

science/linear/plot_convergence/plot_convergence.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+##############################################################################
+# (c) Crown copyright 2021 Met Office. All rights reserved.


Should the year be 2026?

tommbendall · 2026-01-26T17:09:59Z

science/linear/plot_convergence/plot_convergence.sh

+        echo "Do not need to build the executable as $exe exists"
+    else
+        echo "$exe does not exist, so now building the executable"
+        cd ../../../build


Does this mean we could only run this script from the plot_convergence directory? Could this be an absolutely path instead of a relative one?

Absolute paths created

tommbendall · 2026-01-26T17:12:27Z

science/linear/plot_convergence/plot_convergence.py

+    plt.ylabel('Relative error')
+    plt.title('Validity of the tangent linear model')
+
+    #plt.show()


I don't know if you want to remove this comment? Or leave it in with an instruction to uncomment to show the plots?

An extra comment added

tommbendall · 2026-01-26T17:29:50Z

science/linear/integration-test/tl_test/tl_test_timesteps_random_alg_mod.x90

+  !> @param[in] norm_diff_prev  Previous norm
+  !> @param[inout] pass_str     Pass string (either PASS or FAIL)
+  !> @param[in] tol             Test Tolerance
+  subroutine convergence_pass_string( norm_diff, norm_diff_prev, pass_str, tol )


Could this convergence_pass_string routine be removed, and could this file import the public routine from tl_test_convergence_rate_check.f90 instead? And if not, could there be an explanation here for the extra implementation?

A brief explanation has been added to the description. What has happened is the original code applied the square roots to the norms before checking in the convergence test. But I improved this so that when there are multiple variables, the convergence rate is checked for each variable and for the sum (but this needs the square root to be done after). But I kept this original code to allow the plot convergence graphs to be created.

tommbendall · 2026-01-26T17:31:02Z

science/linear/integration-test/tl_test/tl_test_timesteps_random_alg_mod.x90

+        ! Clean up solvers and timestep method left over from running
+        ! the model to set up model state and linear state
+        call final_si_operators()
+        call semi_implicit_solver_alg_final


Suggested change

call semi_implicit_solver_alg_final

call semi_implicit_solver_alg_final()

tommbendall · 2026-01-26T17:31:24Z

science/linear/integration-test/tl_test/tl_test_timesteps_random_alg_mod.x90

+                     setval_X( exner, n1_exner ) )
+        do i = 1, nummr
+          call invoke( setval_X( mr(i), n1_mr(i) ) )
+        enddo


Suggested change

enddo

end do

tommbendall · 2026-01-26T17:38:41Z

science/linear/integration-test/tl_test/tl_test_rhs_alg_mod.x90

                 setval_X(ls_state(igh_d), ls_rho  ), &
                 setval_X(ls_state(igh_p), ls_exner) )

-    call invoke( assign_field_random_kernel_type( random(igh_u), 1.0_r_def ) , &


Are these removed because the incoming u, exner, etc fields are already initialised to random values? I'm struggling to find where that happened

yes the perturbations are now initialised from real data. This is better as we used to have set with random data and gamma values - and choosing the gamma values was tricky. The real data seems more robust.

tommbendall · 2026-01-26T17:39:45Z

science/linear/integration-test/tl_test/tl_test_semi_imp_alg_mod.x90

+                 setval_X(r_theta, theta), &
+                 setval_X(r_rho, rho  ) )

+    ! Overwrite the moisture fields with potential temperature


explanation added

tommbendall

Thanks for the explanation. I'm happy with the changes and that my suggestions have been addressed.

I have two final suggestions:

Can you delete the applications/linear_model/plot_convergence folder?
It would be nice to get the plot_convergence.sh script working if executed from a different directory. I've put a suggestion on how to do this

tommbendall · 2026-01-29T10:41:33Z

science/linear/plot_convergence/plot_convergence.sh

+config_list=(nwp_gal9 semi_implicit runge_kutta)
+
+# Define directories using the current working directory
+export Linear_dir="$(dirname $PWD)"


So I think this command still prevents us from running the script from folders that aren't science/linear/plot_convergence. I realise this is not a big deal, but I think this suggestion will fix it:

Suggested change

export Linear_dir="$(dirname $PWD)"

SCRIPT_DIR="$(dirname "$(realpath "$BASH_SOURCE")")"

export Linear_dir="$(dirname $SCRIPT_DIR)"

I've checked that it at least starts running correctly with this change

cjohnson-pi · 2026-01-29T11:33:57Z

Thanks for the helpful suggestions. Both addressed.

tommbendall

Thanks for the responses, this passes science review. @mo-marqh this is ready for code review

ss421

This has no impact on JEDI.

cjohnson-pi added 3 commits January 12, 2026 15:07

changes from fcm for linear integration tests

eee6f28

Merge remote-tracking branch 'origin/stable' into update_integration_t

ad30c2e

integration tests pass for local build

43039e7

github-actions bot added the cla-required The CLA has not yet been signed by the author of this PR - added by GA label Jan 21, 2026

CLA

f6ff358

github-actions bot removed the cla-required The CLA has not yet been signed by the author of this PR - added by GA label Jan 21, 2026

cjohnson-pi added 2 commits January 21, 2026 11:41

Merge branch 'main' into update_integration_t

3f1f649

style

650bdf0

style

50bc604

cjohnson-pi marked this pull request as ready for review January 21, 2026 12:20

james-bruten-mo assigned cjohnson-pi and unassigned cjohnson-pi Jan 21, 2026

cjohnson-pi added this to the Spring 2026 milestone Jan 22, 2026

cjohnson-pi added the cla-signed The CLA has been signed as part of this PR - added by GA label Jan 22, 2026

For gungho_model hot jupiter cases

f4bfe9e

cjohnson-pi requested a review from tommbendall January 22, 2026 14:49

cjohnson-pi mentioned this pull request Jan 22, 2026

Update linear integration tests configs #115

Open

tommbendall requested changes Jan 26, 2026

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mo-marqh self-requested a review January 27, 2026 08:51

science review

433b032

cjohnson-pi requested review from matthewrmshin and ss421 as code owners January 28, 2026 14:59

tommbendall requested changes Jan 29, 2026

View reviewed changes

science review response

814f038

tommbendall approved these changes Jan 29, 2026

View reviewed changes

ss421 approved these changes Jan 29, 2026

View reviewed changes

		@@ -123,10 +123,13 @@ module gungho_step_mod
		call log_event( log_scratch_space, LOG_LEVEL_INFO )

		temp_corr_io_value => get_io_value( modeldb%values, 'temperature_correction_io_value')

		@@ -0,0 +1,112 @@
		##############################################################################
		# (c) Crown copyright 2022 Met Office. All rights reserved.

	call semi_implicit_solver_alg_final
	call semi_implicit_solver_alg_final()

	export Linear_dir="$(dirname $PWD)"
	SCRIPT_DIR="$(dirname "$(realpath "$BASH_SOURCE")")"
	export Linear_dir="$(dirname $SCRIPT_DIR)"

Update linear integration tests #170

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PR Summary

Code Quality Checklist

Testing

Plot convergence results

trac.log

Test Suite Results - lfric_apps - update_integration_test/run1

Suite Information

Task Information

Security Considerations

Performance Impact

AI Assistance and Attribution

Documentation

PSyclone Approval

Sci/Tech Review

Code Review

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cjohnson-pi commented Jan 21, 2026

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cjohnson-pi Jan 28, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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cjohnson-pi commented Jan 29, 2026

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cjohnson-pi commented Jan 21, 2026 •

edited by tommbendall

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cjohnson-pi Jan 28, 2026 •

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