Add submesoscale eddy parametrization by mwarusz · Pull Request #438 · E3SM-Project/Omega

mwarusz · 2026-06-20T05:40:22Z

This PR adds the submesoscale eddy parametrization in the form presented in Fox-Kemper et al. 2011. The parametrization class provides three main methods that

determine mixed layer depth
compute buoyancy gradient
compute submesoscale induced velocity

respectively. A new auxiliary variable named NormalTransportVelocity has been added. This velocity variable is used to advect pseudo-thickness and tracers, and can optionally include the submesocale induced velocity.

Checklist

mwarusz · 2026-06-20T05:58:13Z

The parametrization unit tests are passing. However, after turning it on in the baroclinic channel polaris test with the default parameters, I see NaNs after about 3 hours of simulation time, so there is still some debugging to be done. Moreover, user and developer documentation needs to be added.

Copilot

Pull request overview

This PR introduces a new submesoscale eddy parameterization module (Fox-Kemper
et al. 2011) into Omega’s ocean model, wires it into initialization/finalization
and tendency/auxiliary-state workflows, and adds a dedicated unit test plus
broad test-harness updates to support new analytic-field helper signatures.

Changes:

Add SubmesoEddies module (config-driven) and integrate it into ocean module
init/finalize and auxiliary-state computation.
Introduce TransportAuxVars::NormalTransportVelocity and use it in thickness
and tracer tendency computations as the transport velocity (optionally
including submesoscale-induced velocity).
Update unit test utilities and many tests to accommodate updated analytic
field setters; add SubmesoEddiesTest.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
components/omega/test/timeStepping/TimeStepperTest.cpp	Initialize/destroy `SubmesoEddies` in the time stepper test harness.
components/omega/test/ocn/TendencyTermsTest.cpp	Update analytic-field lambdas to match updated `setScalar`/`setVectorEdge` signatures.
components/omega/test/ocn/TendenciesTest.cpp	Initialize/destroy `SubmesoEddies`; update analytic-field lambdas and `setScalar`/`setVectorEdge` call signatures.
components/omega/test/ocn/SubmesoEddiesTest.cpp	New unit test covering mixed-layer depth, buoyancy gradient, and eddy velocity computations.
components/omega/test/ocn/OceanTestCommon.h	Extend `setScalar`/`setVectorEdge` helpers to pass element indices and optional Z coordinates.
components/omega/test/ocn/HorzOperatorsTest.cpp	Update analytic-field lambdas to match updated helper signatures.
components/omega/test/ocn/AuxiliaryVarsTest.cpp	Update analytic-field lambdas to match updated helper signatures.
components/omega/test/ocn/AuxiliaryStateTest.cpp	Initialize/destroy `SubmesoEddies`; update analytic-field lambdas and helper call signatures.
components/omega/test/CMakeLists.txt	Register new `SUBMESOEDDIES_TEST`.
components/omega/src/timeStepping/ForwardBackwardStepper.cpp	Pass tracer array into thickness tendency computation.
components/omega/src/ocn/Tendencies.h	Extend thickness tendency API to accept a tracer array (for aux-state computations).
components/omega/src/ocn/Tendencies.cpp	Route thickness/tracer tendencies through new aux-state compute routines and use `NormalTransportVelocity`.
components/omega/src/ocn/SubmesoEddies.h	New `SubmesoEddies` public interface.
components/omega/src/ocn/SubmesoEddies.cpp	New implementation and IO field registration for `SubmesoEddies`.
components/omega/src/ocn/OceanInit.cpp	Initialize `SubmesoEddies` during ocean module init.
components/omega/src/ocn/OceanFinal.cpp	Destroy `SubmesoEddies` during ocean finalize.
components/omega/src/ocn/auxiliaryVars/TransportAuxVars.h	New aux-var container for `NormalTransportVelocity`.
components/omega/src/ocn/auxiliaryVars/TransportAuxVars.cpp	Register/unregister IO field for `NormalTransportVelocity`.
components/omega/src/ocn/AuxiliaryState.h	Add `TransportAuxVars` member and new aux compute entry points.
components/omega/src/ocn/AuxiliaryState.cpp	Compute Brunt–Väisälä frequency, compute transport velocity (optionally + submeso), and use it for vertical pseudo-velocity.
components/omega/configs/Default.yml	Add `Omega.Submeso` configuration group and defaults.

+       KOKKOS_LAMBDA(int IEdge, const TeamMember &Team) {
+          const int KMin   = MinLayerEdgeBot(IEdge);
+          const int KMax   = MaxLayerEdgeTop(IEdge);
+          const int KRange = vertRangeChunked(KMin, KMax);
+
+          parallelForInner(
+              Team, KRange, INNER_LAMBDA(int KChunk) {
+                 LocPseudoThicknessAux.computeVarsOnEdge(
+                     IEdge, KChunk, PseudoThick, NormalVelEdge);
+              });


+/// Destroy instance of SubmesoEddies
+void SubmesoEddies::destroyInstance() {
+   delete Instance;
+   Instance = nullptr;
+}


mwarusz · 2026-07-15T23:22:59Z

Testing

CTest unit tests

Machine: pm-cpu / pm-gpu / frontier
Compiler: gnu / gnugpu / craygnu-mphipcc
Build type: Release
Result: All tests passed (on all machines)

Polaris `omega_pr` suite

Baseline workdir: /pscratch/sd/m/mwarusz/omega-pr-testing/submeso/baseline-gnu
Baseline build: /pscratch/sd/m/mwarusz/omega-pr-testing/submeso/baseline-gnu/build
PR build: /pscratch/sd/m/mwarusz/omega-pr-testing/submeso/build-gnu
PR workdir: /pscratch/sd/m/mwarusz/omega-pr-testing/submeso/pr-gnu
Machine: pm-cpu
Compiler: gnu
Build type: Release
Log: /pscratch/sd/m/mwarusz/omega-pr-testing/submeso/pr-gnu/polaris_omega_pr.o55955301
Result: All tests passed

mwarusz · 2026-07-15T23:29:40Z

The baroclinic channel test is now running stably with the submesoscale eddy parametrization turned on. This PR is ready for review. However, I haven't checked that the parametrization has the intended effect, and I'm not sure that I'm the best person to do that. @vanroekel could you help with this kind of testing ?

vanroekel · 2026-07-23T00:01:41Z

@mwarusz I ran a couple tests with baroclinic channel and it's too hard to tell what the effects must be. We need to add a mixed layer. Let me look and see how straight forward that might be.

vanroekel · 2026-07-24T22:23:49Z

update - I have a mixed layer variant of baroclinic channel I have a test run in the queue on frontier. Hopefully will have results by Monday

vanroekel · 2026-08-11T21:38:03Z

+                 PseudoThickML, GradBuoyML, BVFreqML);
+
+             GradBuoyML /= PseudoThickML;
+             BVFreqML /= PseudoThickML;


@mwarusz for small ML this could be be problematic, it's not clear above in the MLD code if there is a floor. maybe it's not an issue though

I agree that we should probably add a tiny value here. MPAS-O has it.

vanroekel · 2026-08-11T21:38:50Z

+                 Team, Range{MinLyrEdgeBot, IndexMLEdge},
+                 INNER_LAMBDA(int K, Real &AccumThick, Real &AccumGradBuoy,
+                              Real &AccumBVFreq) {
+                    const Real PseudoThickKm1 =


If your function starts at MinLyrEdgeBot can this lead to values lower than min layer edge?

No, this variable is set to

((K - 1) >= MinLyrEdgeBot ? MeanPseudoThickEdge(IEdge, K - 1) : 0)

which is 0 for K = MinLyrEdgeBot. In the end an average of PseudoThickKm1 and PseudoThickK is used. This means that for K = MinLyrEdgeBot you get

PseudoThickAvg = 0.5 * (0 + MeanPseudoThickEdge(IEdge, MinLyrEdgeBot));

This is a kinda hacky treatment of the first half layer. I will add a comment to explain this.

vanroekel · 2026-08-11T21:43:11Z

@mwarusz in testing I'm getting NaN for EddyVelocity quickly. CoPilot added some guards on the ML average and zero initializing and it fixed the NaN issue. I can point you at what the changes made were if you'd like

mwarusz · 2026-08-11T22:05:33Z

@vanroekel

@mwarusz in testing I'm getting NaN for EddyVelocity quickly. CoPilot added some guards on the ML average and zero initializing and it fixed the NaN issue. I can point you at what the changes made were if you'd like

Please do.

vanroekel · 2026-08-11T22:15:43Z

here it is - https://github.com/vanroekel/E3SM/tree/temp-submeso-branch

There is some extra stuff that is adding more diagnostics as well.

mwarusz · 2026-08-11T22:39:20Z

Hmm, Copilot added this check

if (PseudoThickML > Tiny && MLDepthEdge > Tiny)

but afterwards it is also explicitly checking for NaNs and skipping calculations if it finds any. It would good to see if the first check is enough.

sbrus89 · 2026-09-08T16:06:49Z

+
+   // Compute mixed layer index and  depth based on the density difference
+   // criterion
+   void computeDenMixLayerDepth(const Array2DReal &SpecVol);


@mwarusz, you were going to move this to an aux variable, correct?

Yes. I haven't worked on this PR in a while. I was planning to get back to it after the split-explicit is merged, since the transport velocity refactoring that I did there affects this PR in non-trivial ways.

Sounds good. Thanks!

mwarusz · 2026-09-21T21:46:13Z

To test this branch after rebasing on develop and fixing a couple of bugs I ran ocean/spherical/realistic_global/EC30to60E2r2/analysis_members_test for about one year using Omega and MPAS-O with the following changes to both models:

enable submesoscale eddy parametrization
use split-explicit time stepping (RK2 with 45 min time step for Omega, AB2 with 30 min time step for MPAS-O)
use monotonic third-order horizontal advection

Here are some plots comparing temperature, mixed layer depth, and eddy velocity kinetic energy at the final time. @vanroekel Do you think these look reasonable ?

Omega

MPAS-O

vanroekel · 2026-09-29T04:31:11Z

+- `Tau`: MLI timescale parameter (s).
+- `Ce`: nondimensional efficiency coefficient.
+- `LfMin`: minimum frontal width limiter (m).
+- `DsMax`: maximum grid-length limiter used in the closure (m).


somewhere, either here or in the SubmesoEddy class we should include reasonable ranges of these parameters.

vanroekel · 2026-09-30T16:18:22Z

+
+   parallelForOuter(
+       LaunchConfig({Mesh->NEdgesAll},
+                    TeamScratch<Real>(3 * NVertLayers + 3 * NVertLayersP1)),


Could you explain the 3 * here? I don't understand where they come from

This is the number of scratch arrays used in this loop. Three scratch arrays for layer data and three for interface data. I added a comment and changed the code slightly to hopefully make it more clear.

vanroekel · 2026-09-30T16:20:37Z

+                 const int K      = MaxLyrEdgeTop + 1;
+                 const int JCell0 = CellsOnEdge(IEdge, 0);
+                 const int JCell1 = CellsOnEdge(IEdge, 1);
+                 BVFSqEdge(K)     = 0.5_Real * (BruntVaisalaFreqSq(JCell1, K) +


how is this part different than just above on L183?

It's not. In addition to BVF, the loop above interpolates fields that are located at layer mid-points (SpecVol), so it only loops over layers. This code handles the last interface interpolation for BVF. I rephrased the comment above to make it more clear.

I see. thanks. Maybe say 'ocean bottom' instead of 'bottom interface' in the comment or 'bottom of the column'? But also on second read I clearly see the 'MaxLayerEdge' definition in K that I missed earlier

Co-authored-by: Luke Van Roekel <lvanroekel@lanl.gov>

katsmith133 · 2026-10-19T16:39:26Z

I've looked over the code and it looks good to me, but Copilot found the following two issues:

Boundary initialization is dropped by both compatibility overloads. The bounds-taking setScalar overload accepts SetBndOpt but does not forward it, so the implementation uses SetBoundary::No; the same happens in setVectorEdge. Calls that explicitly request boundary setup—such as those in TendenciesTest.cpp:88-108—leave the special boundary element unwritten. See the forwarding calls in OceanTestCommon.h:263-273 and OceanTestCommon.h:470-482.
Vector functors may be invoked four times per element. The independent if constexpr branches all run when a generic or overloaded functor matches multiple supported signatures. That can repeat side effects and overwrite the vector result; the adapter should select one matching signature. See OceanTestCommon.h:290-306.

@mwarusz, if you don't think these are an issue, I am happy to approve.

mwarusz · 2026-10-19T17:41:27Z

@katsmith133

I pushed a fix for the first issue. I think the second one doesn't need a fix. I believe we never call the setX functions with generic or overloaded functors, and I don't think there is any use case for this.

katsmith133

@katsmith133

I pushed a fix for the first issue. I think the second one doesn't need a fix. I believe we never call the setX functions with generic or overloaded functors, and I don't think there is any use case for this.

Great, thanks @mwarusz! I am happy to approve this now. Approving based on visual inspection and testing done by @mwarusz.

sbrus89 · 2026-10-19T19:11:56Z

Testing on frontier

Tested the merge of #438 (6f4378a243) into develop (a341e65245) as 8d0c87c076, against Polaris' Omega submodule (cdb935bb5a).

Row	CTests	`omega_pr`	New build warnings
frontier, craygnu, mpich	61 of 61 passed	32 of 32 passed	0
frontier, craygnu-mphipcc, mpich	61 of 61 passed	32 of 32 passed	0

frontier, craygnu, mpich

Polaris `omega_pr` suite

Baseline workdir: /ccs/home/brus/run/omega_pr_test/baselines/frontier_craygnu_polaris-46a013b_omega-cdb935b/omega_pr
Baseline build: /ccs/home/brus/run/omega_pr_test/baselines/frontier_craygnu_polaris-46a013b_omega-cdb935b/build
PR build: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu/build
PR workdir: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu/omega_pr
Polaris: 46a013b426fecdccba7c5f3a6be6830caacec322 (1.1.0-182-g46a013b42)
Baseline Omega: cdb935bb5a8d995b0878616e001a2701a2627519 (Omega-v0.1.0-alpha.1-6142-gcdb935bb5a)
PR Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Machine: frontier
Partition: batch
Compiler: craygnu
Build type: Release
Log: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu/omega_pr/polaris_omega_pr.o5711232
Result: All tests passed

Recent commits

Polaris:

46a013b42 Merge remote-tracking branch 'origin/main' into HEAD
1b660aa0a Merge remote-tracking branch 'xylar/add-omega-testing-workflow' into HEAD
2a2c8ad4b Merge pull request #855 from xylar/fix-float32-diff-summary
2e0ae95f5 Merge pull request #787 from xylar/add-realistic-global-analysis-run
44c4d5601 Merge pull request #776 from xylar/check-cf-in-omega-output

Baseline Omega:

cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop
9aba4a8032 Merge pull request #597 from xylar/omega/fix-real-literal-nvcc

PR Omega:

8d0c87c076 Test merge of E3SM-Project/Omega#438 (6f4378a243) into develop (a341e65245)
a341e65245 Merge pull request #562 from andrewdnolan/omega/guard-division-by-zero
46aa54cd68 Merge pull request #603 from vanroekel/vanroekel/omega/kpp-bug-fix
9656466bb6 Merge PR #570 into develop, resolving Tendencies.cpp initializer order
d1d3ea6506 Merge pull request #466 from alicebarthel/omega/add-frazil-basic-rebased

CTest unit tests:

Machine: frontier
Compiler: craygnu
Build type: Release
Build: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu/build
Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Result: All tests passed
Log: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu/build/ctests.log

Build warnings

No new warnings (3 in the PR build, 3 in the baseline build).

Baseline build log: /ccs/home/brus/run/omega_pr_test/baselines/frontier_craygnu_polaris-46a013b_omega-cdb935b/build/build_omega.log
PR build log: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu/build/build_omega.log

frontier, craygnu-mphipcc, mpich

Polaris `omega_pr` suite

Baseline workdir: /ccs/home/brus/run/omega_pr_test/baselines/frontier_craygnu-mphipcc_polaris-46a013b_omega-cdb935b/omega_pr
Baseline build: /ccs/home/brus/run/omega_pr_test/baselines/frontier_craygnu-mphipcc_polaris-46a013b_omega-cdb935b/build
PR build: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu-mphipcc/build
PR workdir: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu-mphipcc/omega_pr
Polaris: 46a013b426fecdccba7c5f3a6be6830caacec322 (1.1.0-182-g46a013b42)
Baseline Omega: cdb935bb5a8d995b0878616e001a2701a2627519 (Omega-v0.1.0-alpha.1-6142-gcdb935bb5a)
PR Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Machine: frontier
Partition: batch
Compiler: craygnu-mphipcc
Build type: Release
Log: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu-mphipcc/omega_pr/polaris_omega_pr.o5711240
Result: All tests passed

Recent commits

Polaris:

46a013b42 Merge remote-tracking branch 'origin/main' into HEAD
1b660aa0a Merge remote-tracking branch 'xylar/add-omega-testing-workflow' into HEAD
2a2c8ad4b Merge pull request #855 from xylar/fix-float32-diff-summary
2e0ae95f5 Merge pull request #787 from xylar/add-realistic-global-analysis-run
44c4d5601 Merge pull request #776 from xylar/check-cf-in-omega-output

Baseline Omega:

cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop
9aba4a8032 Merge pull request #597 from xylar/omega/fix-real-literal-nvcc

PR Omega:

8d0c87c076 Test merge of E3SM-Project/Omega#438 (6f4378a243) into develop (a341e65245)
a341e65245 Merge pull request #562 from andrewdnolan/omega/guard-division-by-zero
46aa54cd68 Merge pull request #603 from vanroekel/vanroekel/omega/kpp-bug-fix
9656466bb6 Merge PR #570 into develop, resolving Tendencies.cpp initializer order
d1d3ea6506 Merge pull request #466 from alicebarthel/omega/add-frazil-basic-rebased

CTest unit tests:

Machine: frontier
Compiler: craygnu-mphipcc
Build type: Release
Build: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu-mphipcc/build
Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Result: All tests passed
Log: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu-mphipcc/build/ctests.log

Build warnings

No new warnings (6 in the PR build, 6 in the baseline build).

Baseline build log: /ccs/home/brus/run/omega_pr_test/baselines/frontier_craygnu-mphipcc_polaris-46a013b_omega-cdb935b/build/build_omega.log
PR build log: /ccs/home/brus/run/omega_pr_test/pr438-6f4378a/frontier_craygnu-mphipcc/build/build_omega.log

xylar · 2026-10-19T23:44:34Z

While testing this branch with a new Polaris mixed-layer-eddies task, I found that DenMixLayerDepth and EddyVelocity in the same output often don't come from the same state. In SplitExplicitRK2Stepper::doStep, EddyVelocity is last computed in the Stage 3 tendencies. After that, VertMixImplicit calls computeMomVertAux on the new state (VertMix.cpp:778), which updates DenMixLayerDepth (and BruntVaisalaFreqSq) but not EddyVelocity, and the tracers are then mixed before output.

In a nearly neutral mixed layer the density-threshold depth can jump by whole layers between the two. At 8 km on day 1, the output depth was the one the eddy velocity was computed with on only about a third of the edges in the frontal zone (about 80% by day 7). Within the scheme the two are consistent, so this only affects anyone diagnosing it from output. Writing the edge mixed-layer depth the scheme used, or a note in the user guide, would help. I only looked at the split-explicit stepper.

Posted by Claude Code on @xylar's behalf. The testing, analysis and wording above are AI-authored; please check them accordingly.

sbrus89 · 2026-10-20T00:52:58Z

Testing on pm-cpu and pm-gpu

Tested the merge of #438 (6f4378a243) into develop (a341e65245) as 8d0c87c076, against Polaris' Omega submodule (cdb935bb5a).

Row	CTests	`omega_pr`	New build warnings
pm-cpu, gnu, mpich	58 of 58 passed	32 of 32 passed	0
pm-gpu, gnugpu, mpich	61 of 61 passed	32 of 32 passed	5

pm-cpu, gnu, mpich

Polaris `omega_pr` suite

Baseline workdir: /global/homes/s/sbrus/scratch/omega_pr_test/baselines/pm-cpu_gnu_polaris-e9e74eb_omega-cdb935b/omega_pr
Baseline build: /global/homes/s/sbrus/scratch/omega_pr_test/baselines/pm-cpu_gnu_polaris-e9e74eb_omega-cdb935b/build
PR build: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-cpu_gnu/build
PR workdir: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-cpu_gnu/omega_pr
Polaris: e9e74eb869cc2afbc38789af7fd75efd05733a95 (1.0.0-1102-ge9e74eb869)
Baseline Omega: cdb935bb5a8d995b0878616e001a2701a2627519 (Omega-v0.1.0-alpha.1-6142-gcdb935bb5a)
PR Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Machine: pm-cpu
Compiler: gnu
Build type: Release
Log: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-cpu_gnu/omega_pr/polaris_omega_pr.o60005347
Result: All tests passed

Recent commits

Polaris:

e9e74eb869 Merge PR testing utility into main for local testing
662796b1b7 Merge pull request #864 from xylar/add-release-notes-skill
2a2c8ad4b9 Merge pull request #855 from xylar/fix-float32-diff-summary
2e0ae95f5b Merge pull request #787 from xylar/add-realistic-global-analysis-run
44c4d56012 Merge pull request #776 from xylar/check-cf-in-omega-output

Baseline Omega:

cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop
9aba4a8032 Merge pull request #597 from xylar/omega/fix-real-literal-nvcc

PR Omega:

8d0c87c076 Test merge of E3SM-Project/Omega#438 (6f4378a243) into develop (a341e65245)
a341e65245 Merge pull request #562 from andrewdnolan/omega/guard-division-by-zero
46aa54cd68 Merge pull request #603 from vanroekel/vanroekel/omega/kpp-bug-fix
9656466bb6 Merge PR #570 into develop, resolving Tendencies.cpp initializer order
d1d3ea6506 Merge pull request #466 from alicebarthel/omega/add-frazil-basic-rebased

CTest unit tests:

Machine: pm-cpu
Compiler: gnu
Build type: Release
Build: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-cpu_gnu/build
Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Result: All tests passed
Log: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-cpu_gnu/build/ctests.log

Build warnings

No new warnings (4 in the PR build, 4 in the baseline build).

Baseline build log: /global/homes/s/sbrus/scratch/omega_pr_test/baselines/pm-cpu_gnu_polaris-e9e74eb_omega-cdb935b/build/build_omega.log
PR build log: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-cpu_gnu/build/build_omega.log

pm-gpu, gnugpu, mpich

Polaris `omega_pr` suite

Baseline workdir: /global/homes/s/sbrus/scratch/omega_pr_test/baselines/pm-gpu_gnugpu_polaris-e9e74eb_omega-cdb935b/omega_pr
Baseline build: /global/homes/s/sbrus/scratch/omega_pr_test/baselines/pm-gpu_gnugpu_polaris-e9e74eb_omega-cdb935b/build
PR build: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-gpu_gnugpu/build
PR workdir: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-gpu_gnugpu/omega_pr
Polaris: e9e74eb869cc2afbc38789af7fd75efd05733a95 (1.0.0-1102-ge9e74eb869)
Baseline Omega: cdb935bb5a8d995b0878616e001a2701a2627519 (Omega-v0.1.0-alpha.1-6142-gcdb935bb5a)
PR Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Machine: pm-gpu
Compiler: gnugpu
Build type: Release
Log: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-gpu_gnugpu/omega_pr/polaris_omega_pr.o60006009
Result: All tests passed

Recent commits

Polaris:

e9e74eb869 Merge PR testing utility into main for local testing
662796b1b7 Merge pull request #864 from xylar/add-release-notes-skill
2a2c8ad4b9 Merge pull request #855 from xylar/fix-float32-diff-summary
2e0ae95f5b Merge pull request #787 from xylar/add-realistic-global-analysis-run
44c4d56012 Merge pull request #776 from xylar/check-cf-in-omega-output

Baseline Omega:

cdb935bb5a Merge pull request #600 from xylar/omega/fix-pm-mpi-flags
b90c3dae8d Merge pull request #601 from andrewdnolan/omega/cxx20-for-coupled
9641c6cf9e Merge pull request #546 from xylar/omega/fix-cf-units
55c3de8c15 Merge pull request #566: e3sm/master into omega/develop
9aba4a8032 Merge pull request #597 from xylar/omega/fix-real-literal-nvcc

PR Omega:

8d0c87c076 Test merge of E3SM-Project/Omega#438 (6f4378a243) into develop (a341e65245)
a341e65245 Merge pull request #562 from andrewdnolan/omega/guard-division-by-zero
46aa54cd68 Merge pull request #603 from vanroekel/vanroekel/omega/kpp-bug-fix
9656466bb6 Merge PR #570 into develop, resolving Tendencies.cpp initializer order
d1d3ea6506 Merge pull request #466 from alicebarthel/omega/add-frazil-basic-rebased

CTest unit tests:

Machine: pm-gpu
Compiler: gnugpu
Build type: Release
Build: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-gpu_gnugpu/build
Omega: 8d0c87c0766af598ae1b8dc9f579c0cd0f2bb6e8 (Omega-v0.1.0-alpha.1-6225-g8d0c87c076)
Result: All tests passed
Log: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-gpu_gnugpu/build/ctests.log

Build warnings

5 new warnings, 2 in files this PR changes (853 in the PR build, 842 in the baseline build). Those in files the PR changes are marked *.

New warnings

* components/omega/src/ocn/AuxiliaryState.cpp: [#177-D] variable "MaxLayerEdgeTop" was declared but never referenced (10 -> 12)
* components/omega/src/ocn/AuxiliaryState.cpp: [#177-D] variable "MinLayerEdgeBot" was declared but never referenced (10 -> 12)
  components/omega/src/ocn/Frazil.cpp: [#177-D] variable "LocIceRefSal" was declared but never referenced (0 -> 2)
  components/omega/src/ocn/Frazil.cpp: [#177-D] variable "LocLatIce" was declared but never referenced (0 -> 2)
  components/omega/test/ocn/FrazilTest.cpp: [#177-D] variable "RTol" was declared but never referenced (0 -> 3)

Baseline build log: /global/homes/s/sbrus/scratch/omega_pr_test/baselines/pm-gpu_gnugpu_polaris-e9e74eb_omega-cdb935b/build/build_omega.log
PR build log: /global/homes/s/sbrus/scratch/omega_pr_test/pr438-6f4378a/pm-gpu_gnugpu/build/build_omega.log

Notes

On pm-cpu, the three KPP config tests (KPP_CONFIG_GRADIENT_TEST, KPP_CONFIG_UNSUPPORTED_TEST, KPP_CONFIG_PARABOLIC_TEST) were left out of the CTests (58 of 61 run). They are expected to abort, and today on pm-cpu the Slurm step stays running after MPI_Abort, so each test hangs until it times out and blocks the tests after it. They hang the same way with the build from #603's testing, where they passed this morning, so this is a pm-cpu problem, not this PR. They pass on pm-gpu.

Two of the new pm-gpu warnings are from this PR: in AuxiliaryState::computeTransportVelocity, the const auto &MinLayerEdgeBot and MaxLayerEdgeTop declared inside the SubEddies->Enable block are never used (they shadow the OMEGA_SCOPE copies above), so they can be removed. The three Frazil warnings come from #466, merged into develop after the baseline, and are unrelated to this PR.

sbrus89 · 2026-10-20T00:56:32Z

@mwarusz, how would you like to address @xylar's comment above?

mwarusz · 2026-10-20T01:40:03Z

@sbrus89 @xylar

@mwarusz, how would you like to address @xylar's comment above?

I think this is #532. This is an issue that keeps coming up, but I don't think this PR is the right place to address it. We need a general solution.

The new develop head brings in Omega's submesoscale eddy parameterization (E3SM-Project/Omega#438), which the mixed_layer_eddies tasks validate, along with frazil, penetrating shortwave, a KPP sea-ice buoyancy-flux fix and a division-by-zero guard. Steven Brus's testing of E3SM-Project#438 merged into this develop found omega_pr bit-for-bit with the previous submodule. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

mwarusz requested a review from Copilot June 20, 2026 05:59

Copilot started reviewing on behalf of mwarusz June 20, 2026 05:59

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Copilot AI reviewed Jun 20, 2026

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mwarusz force-pushed the omega/submesoscale-eddies branch 2 times, most recently from 1d3f283 to 9825eda Compare July 14, 2026 21:14

mwarusz requested review from katsmith133 and vanroekel July 15, 2026 23:29

vanroekel reviewed Aug 11, 2026

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mwarusz force-pushed the omega/submesoscale-eddies branch 2 times, most recently from 3660296 to a7bd36d Compare August 24, 2026 22:33

sbrus89 reviewed Sep 8, 2026

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mwarusz force-pushed the omega/submesoscale-eddies branch from a7bd36d to 0bf23ad Compare September 18, 2026 23:10

vanroekel reviewed Sep 26, 2026

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Comment thread components/omega/doc/userGuide/SubmesoEddies.md Outdated

vanroekel reviewed Sep 26, 2026

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Comment thread components/omega/doc/userGuide/SubmesoEddies.md Outdated

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Comment thread components/omega/doc/userGuide/SubmesoEddies.md Outdated

vanroekel reviewed Sep 28, 2026

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Comment thread components/omega/src/ocn/auxiliaryVars/MixedLayerAuxVars.h Outdated

vanroekel reviewed Sep 29, 2026

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vanroekel reviewed Sep 30, 2026

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Comment thread components/omega/src/ocn/SubmesoEddies.cpp

vanroekel reviewed Sep 30, 2026

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mwarusz and others added 12 commits October 19, 2026 09:35

Refactor setScalar and setVector

b5c5a55

Add submesocale eddies

5ce1111

Add Omega user and developer docs for submesoscale eddies

e43d2bd

Add computation of Brunt-Vaisala freq in vert aux

13cbc16

Add submesoscale contribution to transport velocity

014c92e

Clamp mixed layer depth

36c8b03

Make mixed layer depth an auxiliary variable

7779488

Update tau description in submesoscale user docs

dd97b03

Co-authored-by: Luke Van Roekel <lvanroekel@lanl.gov>

Update docs to reflect move of DenMixLayerDepth to aux

7fa0b01

Return early in mixed layer depth computation for shallow columns

2a6ed0c

Expand some comments in submesoscale code

8020f41

Update transport velocity description in submesoscale user docs

b97fb83

Co-authored-by: Luke Van Roekel <lvanroekel@lanl.gov>

mwarusz force-pushed the omega/submesoscale-eddies branch from 4648e59 to b97fb83 Compare October 19, 2026 15:36

Improve a comment

6f4378a

Fix propagation of SetBnd option

ccb835c

katsmith133 approved these changes Oct 19, 2026

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mwarusz mentioned this pull request Oct 19, 2026

Brunt-Vaisala frequency computation in vertical mixing should be using mid-layer pressure #614

Open

xylar mentioned this pull request Oct 20, 2026

Add mixed_layer_eddies tasks for the submesoscale eddy parameterization E3SM-Project/polaris#865

Open

5 tasks done

sbrus89 merged commit 135755f into E3SM-Project:develop Oct 20, 2026
8 checks passed

This was referenced Oct 21, 2026

Compute MeshScaling for variable-resolution meshes #506

Merged

Update Omega submodule E3SM-Project/polaris#870

Merged

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Pull request overview

Reviewed changes

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mwarusz commented Jul 15, 2026

Testing

CTest unit tests

Polaris omega_pr suite

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mwarusz commented Jul 15, 2026

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vanroekel commented Jul 23, 2026

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vanroekel commented Aug 11, 2026

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mwarusz commented Sep 21, 2026

Omega

MPAS-O

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vanroekel Oct 12, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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katsmith133 commented Oct 19, 2026

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mwarusz commented Jun 20, 2026 •

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Polaris `omega_pr` suite

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vanroekel Oct 12, 2026 •

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Polaris `omega_pr` suite

Polaris `omega_pr` suite

Polaris `omega_pr` suite

Polaris `omega_pr` suite