Fesom2.6 recom tra diags and CI test by ogurses · Pull Request #802 · FESOM/fesom2

ogurses · 2025-10-29T14:24:22Z

No description provided.

Define new variables to track tracer changes due to advection and diffusion. We want to save for now diffusion and advection contribution to the tracer changes. Horizontal and vertical diffusion includes Redi parametrization (if it is set .true.).

Fill __ciso directive to ensure that carbon isotope code works. Medusa interface is added.

Use __coccos in src/CMakeLists.txt to include 2 more phytoplankton classes FESOM2.6-REcoM setup with 4 phytoplankton, 3 zooplankton and 2 detritus functional types. BREAKING CHANGE: FESOM2.6-REcoM setup with 4p3z2d

Correct temperature function for small phytoplankton and diatoms. Previous update for the fouth phytoplankton class and new temperature functions for small phytoplankton and diatoms resulted in very low Phaeocystis biomass. We recognised that this is related to missing code lines in the temperature function which we correct with this update.

…ostics Use namelist.io to activate diagnostics. Sinking velocity of particle (fast and slow) are calculated but not written into a file before. We fix the missing diagnostics for sinking velocity of detritus classes. Besides we Extracted the K0, solubility which is computed in gasx.F90.

…esom2.6_recom_tra_diags

We add __coccos directive to get the correct temperature function in silicate assimilation. In the coccos and Phaeocystis version, it should be dependent on the new temperature function, Temp_diatoms. Use the original Arrhenius function in simpler phytoplankton version. Besides, light limitation diagnostics is corrected. It does affect only the diatoms related output.

Correct reported salt flux bug in oce_ale_tracer.F90. #721

We commented out the linear model where degradation is directly proportional to light intensity and the chlorophyll degradation rate is capped at a maximum of 0.3. Reason for this is the unrealistic air2sea co2 fluxes in the 2p3z2d setup. The reactivated saturation model is more realistic. It accounts for light saturation effects. At low light, degradation increases roughly linearly with PAR At high light, the degradation rate approaches an asymptotic maximum

…tives with namelist parameters Replace preprocessor directives with namelist parameters: * `__3Zoo2Det` → `enable_3zoo2det` * `__coccos` → `enable_coccos` * Enhanced inline comments with ecological significance and biological context *Complete variable/parameter documentation with units and descriptions * Clear sectioning with visual separators and variable definitions * Equation explanations showing mathematical relationships and biological processes * Logic documentation for decision trees and conditional blocks * Comments now explain "why" not just "what" **Sequence Validation** * Generates expected tracer ID list based on configuration * Shows exact ID order and position-by-position comparison **Configuration-Specific Clash Detection** * Full Model (both flags): Don't use IDs 1023-1024 * Coccos-only: Use 1023-1028 (NOT 1029-1034) * 3Zoo2Det-only: Use 1029-1030 for microzoo (NOT 1035-1036) **Validation Checks** * Exact sequence matching against expected IDs * Duplicate ID detection *Forbidden ID detection per configuration BREAKING CHANGE: replace directives with namelist parameter for model configuration

ogurses · 2025-10-29T14:35:52Z

CI test for recom is on the way. Any help is welcome @suvarchal

JanStreffing · 2025-10-29T14:38:31Z

! O:G
! Save horizontal and vertical advective fluxes.
! We have the values on the nodes
! We do not know how much each edge contributes
! to the nodes it connects
! Notes from Patrick: del_ttf includes
! Low-order solution. But, del_ttf_advhoriz and
! del_ttf_advvert contain antidiffusive fluxes 
! from the FCT scheme

!if (.FALSE.) then
! O:G - tra_diag
!#if defined (__recom)
!        if (tracers%data(tr_num)%ltra_diag) then
!           do n=1, myDim_nod2D+eDim_nod2D
!              nu1 = ulevels_nod2D(n)
!              nl1 = nlevels_nod2D(n)
!              do nz = nu1, nl1-1
                 ! Horizontal advection part
!                 tracers%work%tra_advhoriz(nz,n,tr_num) = tracers%work%del_ttf_advhoriz(nz,n)
                 ! Vertical advection part
!                 tracers%work%tra_advvert (nz,n,tr_num) = tracers%work%del_ttf_advvert(nz,n)
!              end do
!           end do
!        end if
!#endif
!endif

Still needed @ogurses?

JanStreffing · 2025-10-29T14:55:31Z

src/oce_ale_tracer.F90

+!#if defined (__recom)           ! not necessarily should belong to recom case
+!    tracers%work%tra_advhoriz = 0.0 ! O:G - tra_diag
+!    tracers%work%tra_advvert  = 0.0
+    ttf_rhs_bak = 0.0


Has no impact on CI test, so probably ok. Just flagging to be checked by @patrickscholz

suvarchal · 2025-10-29T14:58:35Z

CI test for recom is on the way. Any help is welcome @suvarchal

last-minute working on compute time reporting and proposal, can take a look tomorrow

JanStreffing · 2026-02-25T08:30:30Z

@ogurses, @suvarchal, @patrickscholz
I think we should try to resolve the last issues on the CI test and merge this branch. I'm at AWI to join next week Monday to Wednesday. After that, I'm away for some weeks.

patrickscholz · 2026-02-25T10:06:38Z

src/oce_ale_tracer.F90

+    if (tracers%data(tr_num)%ltra_diag) then
+          do n=1, myDim_nod2D+eDim_nod2D
+          nu1 = ulevels_nod2D(n)
+          nl1 = nlevels_nod2D(n)
+          do nz = nu1, nl1-1
+             ttf_rhs_bak(nz,n) = del_ttf(nz,n)
+          end do
+       end do
+    end if


it would be nice if we could encapsulate this in a subroutine not to make our code messy and unreadable! Especially that this pieces repeat itself

patrickscholz · 2026-02-25T10:07:51Z

src/oce_ale_tracer.F90

+    if (tracers%data(tr_num)%ltra_diag) then
+       do n=1, myDim_nod2D+eDim_nod2D
+          nu1 = ulevels_nod2D(n)
+          nl1 = nlevels_nod2D(n)
+          do nz = nu1, nl1-1
+             ! horizontal diffusion (w/out Redi)           
+             tracers%work%tra_diff_part_hor_redi(nz,n,tr_num) = (del_ttf(nz,n) - ttf_rhs_bak(nz,n)) / hnode_new(nz,n) ! Unit [Conc]
+             !if (mype==0)  print *, tracers%work%tra_diff_part_hor_redi(nz,n,tr_num)
+          end do
+       end do
+    end if


Here that same this, this structure repeats itself and could be a re-callable subroutine

patrickscholz · 2026-02-25T10:18:27Z

I talked a while a ago with Sergey about this, and we should try to encapsulate as much of RECOM as we can, To achieve that as much of RECOM lives within the recom_...F90 code files and is only called by function and subroutines (e.g boundary conditions, initialisation, ...). We have been a bit sloppy about this with all the iceberg and transient tracer stuff in the past, which made large part of the FESOM code especially the initialisation, tracer and boundary condition part very crowded and messy and more difficult to maintain.

JanStreffing · 2026-02-25T10:25:36Z

Perfect task for the AI. I had it search for more cases:

Similar repeated-structure cases in REcoM code (candidates for future refactor)

src/int_recom/recom_main.F90
- Pattern: In the main node loop (do n=1,myDim_nod2D) there is a recurring
  "backup state -> do work -> compute diagnostic delta" idiom.
- Example: ttf_rhs_bak is filled for all tracers with ltra_diag, and later
  tracers%work%tra_recom_sms(...) is computed as values - ttf_rhs_bak.
- Why it’s similar: conceptually the same as the backup/delta calculation
  refactored in src/oce_ale_tracer.F90 (just organized differently).
src/int_recom/recom_sinking.F90
- Pattern: long sequences of if(tracer ID == ...) blocks repeat nearly the same
  update structure for different element pools:
  - update Benthos(n,k)
  - optionally update SinkFlx_tr(n,k,tr_num) when use_MEDUSA
  - optionally update Benthos_tr(n,k,tr_num)
    repeated for N/C/Si/CaCO3 and also isotope variants.
- Why it’s similar: repetitive boilerplate where only the tracer-ID set and the
  target index (k) changes.
src/int_recom/recom_init.F90
- Pattern: repeated min/max scanning over nodes for multiple REcoM tracers,
  followed by repeated MPI_Allreduce calls with identical structure.
- Why it’s similar: repeated blocks of the same operation on different tracer IDs.
src/int_recom/recom_sms.F90 (benthic remineralization section)
- Pattern: repeated update equations with the same shape:
  decayBenthos(i) = rate(i) * LocBenthos(i)
  LocBenthos(i) = LocBenthos(i) - decayBenthos(i) * dt_b
  repeated across elements and (optionally) isotopes.
- Why it’s similar: identical structure differing only by indices/parameters.

Recom refactoring dedup

JanStreffing · 2026-03-03T13:53:15Z

I tried my hands on this, but I was not able to figure out what is wrong with the DIC_PI file. Could your try this out @ogurses ?

Runs the same steps as the GitHub Actions fesom2_recom workflow inside the CI container on Levante. Requires pre-pulling the SIF image on the login node (compute nodes have read-only TMPDIR).

Root cause: copy-paste bug in recom_init.F90 where ErosionTON2D was initialized twice and ErosionTOC2D was never initialized. Uninitialized memory (NaN) propagated through bc_surface for DIC via IEEE 754 NaN * 0.0 = NaN, even when erosion input was disabled. Also adds a guard for nodes with nzmax < 1 in the REcoM main loop and hardens tracer initialization in gen_ic3d.F90 to clean up NaN values from CDO/NCO interpolation artifacts.

…ce values The io_list used explicit "DIN" and "DIC" variable names, but the model only outputs these via the generic "otracers" keyword. Changed to "otracers" and updated fcheck reference values from actual CI run output.

JanStreffing · 2026-04-08T09:07:10Z

Remaining build check failures indicate some YAC issue? Any idea what happened there @nils3er, @suvarchal, @sveta-loza?

Or maybe some change in the docker? @koldunovn

Upstream libfyaml (commit 902a981, March 3 2026) split the monolithic libfyaml.h into an umbrella header that #includes 13 sub-headers from libfyaml/. The install command only ran install-includeHEADERS (the umbrella), not install-libfyamlHEADERS (the sub-headers). When YAC's configure tested #include <libfyaml.h>, the compiler could not find the sub-headers and reported "libfyaml.h not found".

JanStreffing · 2026-04-08T09:38:55Z

Alright, all CI tests pass. Ready to merge when you give the ok @ogurses

ogurses and others added 17 commits October 15, 2024 15:08

add recom_sms diag

3e84a88

feat(recom): add ciso and medusa components

434f0e6

Fill __ciso directive to ensure that carbon isotope code works. Medusa interface is added.

input to bc_surface from medusa added and Sed_input deleted

0864237

fix(recom) Add missing directives

eafe8e9

two small fixes

4408f0e

feat(recom)!: FESOM2.6-REcoM setup with 4p3z2d

db00bd1

Use __coccos in src/CMakeLists.txt to include 2 more phytoplankton classes FESOM2.6-REcoM setup with 4 phytoplankton, 3 zooplankton and 2 detritus functional types. BREAKING CHANGE: FESOM2.6-REcoM setup with 4p3z2d

Merge remote-tracking branch 'origin/fesom2.6_recom_tra_diags' into f…

2836492

…esom2.6_recom_tra_diags

fix(recom) clean merge conflicts

66a5aeb

fix(recom): Correct Light limitation diagnostics(continued)

4258874

fix(recom): Correct namelist.recom files in config folder

d82dbcb

fix(fesom): Bugfix: sign of real salt flux

502d4d6

Correct reported salt flux bug in oce_ale_tracer.F90. #721

JanStreffing requested review from JanStreffing and patrickscholz October 29, 2025 14:25

JanStreffing assigned ogurses Oct 29, 2025

JanStreffing added the RECOM label Oct 29, 2025

JanStreffing added this to the FESOM 2.7 milestone Oct 29, 2025

JanStreffing changed the title ~~Fesom2.6 recom tra diags~~ Fesom2.6 recom tra diags and CI test Oct 29, 2025

JanStreffing linked an issue Oct 29, 2025 that may be closed by this pull request

Create REcoM CI test #620

Closed

ogurses requested a review from suvarchal October 29, 2025 14:34

Merge branch 'main' into fesom2.6_recom_tra_diags

80bbbe7

JanStreffing reviewed Oct 29, 2025

View reviewed changes

JanStreffing force-pushed the fesom2.6_recom_tra_diags branch from e5e0fe2 to 075f709 Compare January 26, 2026 16:00

JanStreffing modified the milestones: FESOM 2.7.1, FESOM 2.8 Feb 18, 2026

Merge branch 'main' into fesom2.6_recom_tra_diags

e296ae8

Merge branch 'main' into fesom2.6_recom_tra_diags

87fbce9

patrickscholz reviewed Feb 25, 2026

View reviewed changes

Refactor tracer diag loops

f56ee08

JanStreffing added 4 commits February 25, 2026 11:30

REcoM: deduplicate ltra_diag backup/delta

b1e09a8

REcoM: deduplicate benthos accumulation

cd2928f

REcoM: deduplicate init sanity-check reductions

f179d3c

REcoM: deduplicate benthos decay updates

c9287bc

This was referenced Feb 25, 2026

Recom refactoring dedup #863

Merged

Fesom2.7 recom3.1 #864

Draft

patrickscholz approved these changes Feb 27, 2026

View reviewed changes

Merge pull request #863 from FESOM/recom_refactoring_dedup

6056444

Recom refactoring dedup

JanStreffing added 6 commits April 7, 2026 14:39

Add script to run REcoM CI test locally via Singularity

316339a

Runs the same steps as the GitHub Actions fesom2_recom workflow inside the CI container on Levante. Requires pre-pulling the SIF image on the login node (compute nodes have read-only TMPDIR).

Merge branch 'main' into fesom2.6_recom_tra_diags

95a3282

move ci test run script to work folder

067418c

update truth

06ec4bc

ogurses merged commit 36c5d41 into main Apr 8, 2026
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Fesom2.6 recom tra diags and CI test#802

Fesom2.6 recom tra diags and CI test#802
ogurses merged 75 commits intomainfrom
fesom2.6_recom_tra_diags

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