Nemo merge requestshttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests2024-03-19T16:15:32Zhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/471Resolve "refactor zdf_drg and fix issue with rCdU_top when using linear drag"2024-03-19T16:15:32ZDaley CalvertResolve "refactor zdf_drg and fix issue with rCdU_top when using linear drag"Closes #383.
#### Tests
**Regular checks**
- [x] Can this change be shown to produce expected impact (option activated)?
- [x] Can this change be shown to have a null impact (option not activated)?
- [x] Results of the required bit co...Closes #383.
#### Tests
**Regular checks**
- [x] Can this change be shown to produce expected impact (option activated)?
- [x] Can this change be shown to have a null impact (option not activated)?
- [x] Results of the required bit comparability tests been run: are there no differences when activating the development?
- [ ] ~If some differences appear, is reason for the change valid/understood?~
- [ ] ~If some differences appear, is the impact as expected on model configurations?~
- [x] Is this change expected to preserve all diagnostics?
- [ ] ~If no, is reason for the change valid/understood?~
- [x] Are there significant changes in run time/memory?
SETTE passes, but it doesn't cover the specific configuration settings (`key_si3` + `key_isf` + `ln_isfcav` + `ln_lin` + `ln_drgice_imp`) that would recreate this issue.
**Other tests**
Testing was performed using 10-day runs of ORCA2_ICE_PISCES with passive tracers turned off. The restartability failures caused by this issue have been addressed, which causes an expected change in results.
#### Review
**Assessments**
- [ ] Is the proposed methodology now implemented?
- [ ] Are the code changes in agreement with the flowchart defined at preview step?
- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?
- [ ] If, not, are the discrepancies acceptable?
- [ ] Is the in-line documentation accurate and sufficient?
- [ ] Do the code changes comply with NEMO coding standards?
- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?NEMO 5.0-betaDaley CalvertDaley Calverthttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/457Resolve "1.d notation should not be used"2024-02-07T13:28:28ZSebastien MassonResolve "1.d notation should not be used"Closes #373Closes #373NEMO 5.0-betaSebastien MassonSebastien Massonhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/322Reduce dimensionality of working arrays in ZDF2024-02-01T15:42:20ZDaley CalvertReduce dimensionality of working arrays in ZDFCloses #234
### Summary of changes
* `trazdf.F90`
* Some cleanup of commented code
* `zdfddm.F90`
* All working arrays have been reduced from 2D (i,j) to scalar
* `zdfevd.F90`
* Replaced 2 3D (i,j,k) working arrays (`zav[tm]_evd`...Closes #234
### Summary of changes
* `trazdf.F90`
* Some cleanup of commented code
* `zdfddm.F90`
* All working arrays have been reduced from 2D (i,j) to scalar
* `zdfevd.F90`
* Replaced 2 3D (i,j,k) working arrays (`zav[tm]_evd`) with 1 (`zav_evd`)
* `zdfgls.F90`
* Renamed all local working arrays that did not conform to the variable naming conventions
* e.g. `prod` => `zprod`
* Reduced 10 3D (i,j,k) working arrays to 2D (i,k), 2 2D (i,j) working arrays to 1D (i), 3 2D (i,j) working arrays to scalar
* Converted 4 module-level arrays to local working arrays and reduced them from 3D (i,j,k) to 2D (i,k), 2D (i,j) to 1D (i)
* These are not used outside of `zdfgls.F90`
* Loop order is now i-k-j instead of i-j-k
* This is because the tridiagonal solver prohibits 2D slices over k; instead they have to be done over j
* Some code was moved to avoid duplicate calculations
* Some unnecessary calculations were removed
* `zdfmfc.F90`
* Removed `diag_mfc` and `rhs_mfc` subroutines
* As of 16443a0b, these are no longer being used by `tra_zdf`. Instead, the code from these subroutines is executed directly in `tra_zdf`.
* I've kept this approach- the commented out code in `tra_zdf` has been removed but I've kept the 'note' comments, some of which were moved into `zdf_mfc`
* Removed 3 module-level arrays (`edmf[abc]`)
* With the removal of `diag_mfc`, these are no longer used
* Removed 2 3D (i,j,k) working arrays (`zedmf`, `zn2`) and 10 2D (i,j) working arrays, and added 1 2D (i,j) working array (`zwrk`)
* The first use of `zedmf` (to calculate the surface boundary condition of the mass flux) has been replaced by the 2D (i,j) working array `zwrk`
* The second use of `zedmf` (to calculate the mass flux at W-levels) has been replaced by re-using `edmfm`
* `edmfm(ji,jj,jk)` is calculated as the mass flux at W-levels
* `edmfm(ji,jj,jk-1)` is then calculated as the mass flux at T-levels using the half-sum of `edmfm(ji,jj,jk)` and `edmfm(ji,jj,jk-1)`
* `zn2` was not used
* The 2D arrays were removed either by inlining the calculations or by using `zwrk` instead
* Reduced 1 4D (i,j,k,trc) working array to 3D (i,j,trc), 2 3D (i,j,k) working arrays to 2D (i,j), 1 3D (i,j,k) working array to scalar, 2 2D (i,j) working arrays to scalar
* Some unnecessary calculations were removed
* `zdfric.F90`
* Converted the 2D (i,j) working array from automatic to allocatable
* This only needs to be declared when `ln_mldw = .TRUE.`
* `zdftke.F90`
* Reduced 6 3D (i,j,k) working arrays to 2D (i,k), 5 2D (i,j) working arrays to 1D (i)
* Loop order is now i-k-j instead of i-j-k
* This is because the tridiagonal solver prohibits 2D slices over k; instead they have to be done over j
* Some code was moved to avoid duplicate calculations
* Converted module-level array `apdlr` to local working array `z_pdlr`
* This only needs to be declared when `nn_pdl = 1` and is not used outside of `zdftke.F90`
* Some unnecessary calculations were removed
### Testing and review
#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test.
**Regular checks**
- [x] Can this change be shown to produce expected impact (option activated)?
- [x] Can this change be shown to have a null impact (option not activated)?
- [x] Results of the required bit comparability tests been run: are there no differences when activating the development?
- [ ] ~~If some differences appear, is reason for the change valid/understood?~~
- [ ] ~~If some differences appear, is the impact as expected on model configurations?~~
- [x] Is this change expected to preserve all diagnostics?
- [ ] ~~If no, is reason for the change valid/understood?~~
- [x] Are there significant changes in run time/memory?
- \~40% reduction in `zdf_tke` runtime for ORCA025-L75
- No reduction for ORCA2-L31
- 25% - 50% reduction in `zdf_gls` runtime for ORCA025-L75
- 15% - 35% reduction for ORCA2-L31
- \~65% reduction in `zdf_mfc` runtime for ORCA025-L75
- \~55% for ORCA2-L31
- This only ran for RK3, MLF crashed with a grid point instability
- MLF runs if `key_vco_3d` is used instead of `key_vco_1d3d`
#### Review
A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).
**Assessments**
- [x] Is the proposed methodology now implemented?
- [x] Are the code changes in agreement with the flowchart defined at preview step?
- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?
- [ ] If, not, are the discrepancies acceptable?
- [ ] Is the in-line documentation accurate and sufficient?
- [x] Do the code changes comply with NEMO coding standards?
- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?2023 WPDaley CalvertDaley Calverthttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/427Resolve "Issue in Richardson number"2023-12-19T14:56:32ZAimie MoulinResolve "Issue in Richardson number"Closes #343
Sette passed after the rebasedCloses #343
Sette passed after the rebasedTag 4.2.2https://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/428Correction langmuir cell in coupled mode issue #3442023-12-18T14:18:46ZAimie MoulinCorrection langmuir cell in coupled mode issue #344Clean the Langmuir code + Closes #344Clean the Langmuir code + Closes #344Tag 4.2.2https://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/421Resolve "Error langmuir cells with wave coupling"2023-12-11T08:31:10ZAimie MoulinResolve "Error langmuir cells with wave coupling"Closes #344 for branch 4.2Closes #344 for branch 4.2Tag 4.2.2Aimie MoulinAimie Moulinhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/420Resolve "Issue in Richardson number"2023-12-08T09:15:40ZAimie MoulinResolve "Issue in Richardson number"Closes #343 for branch 4.2Closes #343 for branch 4.2Tag 4.2.2https://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/99"adaptive-implicit vertical advection with RK3"2023-08-29T16:30:35ZAndrew Coward"adaptive-implicit vertical advection with RK3"Closes #63Closes #632022 WPAndrew CowardAndrew Cowardhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/302Fix `zdf_tke` when using `ln_mxhsw` and tiling2023-06-09T10:14:06ZDaley CalvertFix `zdf_tke` when using `ln_mxhsw` and tilingCloses #241
#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and ...Closes #241
#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test.
**Regular checks**
- [x] Can this change be shown to produce expected impact (option activated)?
- [x] Can this change be shown to have a null impact (option not activated)?
- [x] Results of the required bit comparability tests been run: are there no differences when activating the development?
- [ ] ~~If some differences appear, is reason for the change valid/understood?~~
- [ ] ~~If some differences appear, is the impact as expected on model configurations?~~
- [x] Is this change expected to preserve all diagnostics?
- [ ] ~~If no, is reason for the change valid/understood?~~
- [ ] Are there significant changes in run time/memory?
#### Review
A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).
**Assessments**
- [ ] Is the proposed methodology now implemented?
- [ ] Are the code changes in agreement with the flowchart defined at preview step?
- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?
- [ ] If, not, are the discrepancies acceptable?
- [ ] Is the in-line documentation accurate and sufficient?
- [ ] Do the code changes comply with NEMO coding standards?
- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?Tag 4.2.1Daley CalvertDaley Calverthttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/301Resolve several diagnostic issues in branch_4.22023-05-16T16:27:34ZDaley CalvertResolve several diagnostic issues in branch_4.2Closes #243
#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and ...Closes #243
#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test.
**Regular checks**
- [x] Can this change be shown to produce expected impact (option activated)?
- [x] Can this change be shown to have a null impact (option not activated)?
- [x] Results of the required bit comparability tests been run: are there no differences when activating the development?
- [ ] ~~If some differences appear, is reason for the change valid/understood?~~
- [ ] ~~If some differences appear, is the impact as expected on model configurations?~~
- [ ] Is this change expected to preserve all diagnostics?
- [x] If no, is reason for the change valid/understood?
- Some diagnostics were giving different results with the tiling active- these changes address this
- [ ] Are there significant changes in run time/memory?
#### Review
A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).
**Assessments**
- [ ] Is the proposed methodology now implemented?
- [ ] Are the code changes in agreement with the flowchart defined at preview step?
- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?
- [ ] If, not, are the discrepancies acceptable?
- [ ] Is the in-line documentation accurate and sufficient?
- [ ] Do the code changes comply with NEMO coding standards?
- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?Tag 4.2.1Daley CalvertDaley Calverthttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/226Resolve "small bug in array size for zdfgls in main branch"2023-03-15T14:01:09ZGuillaume SamsonResolve "small bug in array size for zdfgls in main branch"Closes #155Closes #1552023 WPGuillaume SamsonGuillaume Samsonhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/168Resolve "Completion of the OSMOSIS diagnostic output"2023-03-15T12:01:28ZSimon MuellerResolve "Completion of the OSMOSIS diagnostic output"Closes #108Closes #108Tag 4.2.1Simon MuellerSimon Muellerhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/172Resolve "Transfer of a bug fix from a previous OSMOSIS development branch"2023-03-15T11:59:37ZSimon MuellerResolve "Transfer of a bug fix from a previous OSMOSIS development branch"Closes #111Closes #111Tag 4.2.1Simon MuellerSimon Muellerhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/49Ice thickness dependent roughness in GLS and TKE2023-03-15T11:58:54ZJérôme ChanutIce thickness dependent roughness in GLS and TKEPrevent from using nn_mxlice==(2,3) without a sea-ice model (nn_ice==0)
Closes #29Prevent from using nn_mxlice==(2,3) without a sea-ice model (nn_ice==0)
Closes #29Tag 4.2.1Jérôme ChanutJérôme Chanuthttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/212remove wrong top limit condition on tke for cavities in gls2022-12-28T15:35:55ZClément Bricaudremove wrong top limit condition on tke for cavities in glsCloses #143Closes #1432022 WPClément BricaudClément Bricaudhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/109Resolve "Summer 2022 work- ZDF halo cleanup"2022-12-15T15:51:11ZDaley CalvertResolve "Summer 2022 work- ZDF halo cleanup"#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and reproducibili...#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test.
**Regular checks**
- [ ] Can this change be shown to produce expected impact (option activated)?
- [ ] Can this change be shown to have a null impact (option not activated)?
- [ ] Results of the required bit comparability tests been run: are there no differences when activating the development?
- [ ] If some differences appear, is reason for the change valid/understood?
- [ ] If some differences appear, is the impact as expected on model configurations?
- [ ] Is this change expected to preserve all diagnostics?
- [ ] If no, is reason for the change valid/understood?
- [ ] Are there significant changes in run time/memory?
#### Review
A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).
**Assessments**
- [ ] Is the proposed methodology now implemented?
- [ ] Are the code changes in agreement with the flowchart defined at preview step?
- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?
- [ ] If, not, are the discrepancies acceptable?
- [ ] Is the in-line documentation accurate and sufficient?
- [ ] Do the code changes comply with NEMO coding standards?
- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?2022 WPDaley CalvertDaley Calverthttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/182Merge branch '111-transfer-of-a-bug-fix-from-a-previous-osmosis-development-b...2022-11-11T19:30:01ZSimon MuellerMerge branch '111-transfer-of-a-bug-fix-from-a-previous-osmosis-development-branch' into 'main'Merge branch '111-transfer-of-a-bug-fix-from-a-previous-osmosis-development-branch' into 'branch_4.2'
Resolve "Transfer of a bug fix from a previous OSMOSIS development branch"
See merge request nemo/nemo!172
(cherry picked from commi...Merge branch '111-transfer-of-a-bug-fix-from-a-previous-osmosis-development-branch' into 'branch_4.2'
Resolve "Transfer of a bug fix from a previous OSMOSIS development branch"
See merge request nemo/nemo!172
(cherry picked from commit 05678c0df79ea3c9ea6c6e575f6b4a0e630bd643)
b8c86a0d Application of an OSMOSIS bug fix previously lagging behind (see issue #111)2022 WPSimon MuellerSimon Muellerhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/176Merge branch '108-completion-of-the-osmosis-diagnostic-output' into 'main'2022-11-07T08:52:58ZSimon MuellerMerge branch '108-completion-of-the-osmosis-diagnostic-output' into 'main'Resolve "Completion of the OSMOSIS diagnostic output"
See merge request nemo/nemo!168
(cherry picked from commit 84511c3357018a57097528ea438b9fbfcaedf9b2)
52b5e71c Adjustments and additions to the OSMOSIS diagnostic-output implementat...Resolve "Completion of the OSMOSIS diagnostic output"
See merge request nemo/nemo!168
(cherry picked from commit 84511c3357018a57097528ea438b9fbfcaedf9b2)
52b5e71c Adjustments and additions to the OSMOSIS diagnostic-output implementation (see issue #108)2022 WPSimon MuellerSimon Muellerhttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/54Resolve "Prevent from using specific sea ice boundary conditions in zdftke an...2022-04-02T16:23:43ZJérôme ChanutResolve "Prevent from using specific sea ice boundary conditions in zdftke and zdfgls if nn_ice=0 (i.e. no ice model but key_si3 || key_cice)"Closes #29Closes #292022 WPJérôme ChanutJérôme Chanuthttps://forge.nemo-ocean.eu/nemo/nemo/-/merge_requests/10import commits from dev_r15388_updated_zdfiwm SVN branch2022-04-02T14:13:47ZGuillaume Samsonimport commits from dev_r15388_updated_zdfiwm SVN branch```
[belenoslogin3 ~/SRC/NEMO/nemo/sette (dev_r15388_updated_zdfiwm *)]$ ./sette_rpt.sh -V main -R 21342_d47e9a4
Current code is : dev_r15388_updated_zdfiwm @ 21350_fb2dd32 ( with local changes )
SETTE validation report generated for ...```
[belenoslogin3 ~/SRC/NEMO/nemo/sette (dev_r15388_updated_zdfiwm *)]$ ./sette_rpt.sh -V main -R 21342_d47e9a4
Current code is : dev_r15388_updated_zdfiwm @ 21350_fb2dd32 ( with local changes )
SETTE validation report generated for :
dev_r15388_updated_zdfiwm @ 21350_fb2dd32 (with local changes)
on X64_BELENOS_INTEL_IMPI_DEBUG arch file
!!---------------1st pass------------------!!
!----restart----!
GYRE_PISCES directory MISSING : 21350_fb2dd32+
ORCA2_ICE_PISCES run.stat restartability passed : 21350_fb2dd32+
ORCA2_ICE_PISCES tracer.stat restartability passed : 21350_fb2dd32+
ORCA2_OFF_PISCES directory MISSING : 21350_fb2dd32+
AMM12 directory MISSING : 21350_fb2dd32+
ORCA2_SAS_ICE directory MISSING : 21350_fb2dd32+
AGRIF_DEMO directory MISSING : 21350_fb2dd32+
WED025 directory MISSING : 21350_fb2dd32+
ISOMIP+ directory MISSING : 21350_fb2dd32+
OVERFLOW directory MISSING : 21350_fb2dd32+
LOCK_EXCHANGE directory MISSING : 21350_fb2dd32+
VORTEX directory MISSING : 21350_fb2dd32+
ICE_AGRIF directory MISSING : 21350_fb2dd32+
SWG directory MISSING : 21350_fb2dd32+
!----repro----!
GYRE_PISCES directory MISSING : 21350_fb2dd32+
ORCA2_ICE_PISCES run.stat reproducibility passed : 21350_fb2dd32+
ORCA2_ICE_PISCES tracer.stat reproducibility passed : 21350_fb2dd32+
ORCA2_OFF_PISCES directory MISSING : 21350_fb2dd32+
AMM12 directory MISSING : 21350_fb2dd32+
ORCA2_SAS_ICE directory MISSING : 21350_fb2dd32+
ORCA2_ICE_OBS directory MISSING : 21350_fb2dd32+
AGRIF_DEMO directory MISSING : 21350_fb2dd32+
WED025 directory MISSING : 21350_fb2dd32+
ISOMIP+ directory MISSING : 21350_fb2dd32+
VORTEX directory MISSING : 21350_fb2dd32+
ICE_AGRIF directory MISSING : 21350_fb2dd32+
SWG directory MISSING : 21350_fb2dd32+
!----agrif check----!
non-existent test directory
!----result comparison check----!
check result differences between :
VALID directory : /home/ext/mr/smer/samsong/NEMO_VALIDATION/dev_r15388_updated_zdfiwm at rev 21350_fb2dd32+
and
REFERENCE directory : /home/ext/mr/smer/samsong/NEMO_VALIDATION/main at rev 21342_d47e9a4
GYRE_PISCES VALID directory at 21350_fb2dd32+ is MISSING
ORCA2_ICE_PISCES run.stat files are DIFFERENT (results are different after 1 time steps)
ORCA2_ICE_PISCES tracer.stat files are DIFFERENT (results are different after 1 time steps)
ORCA2_OFF_PISCES VALID directory at 21350_fb2dd32+ is MISSING
AMM12 VALID directory at 21350_fb2dd32+ is MISSING
ORCA2_SAS_ICE VALID directory at 21350_fb2dd32+ is MISSING
AGRIF_DEMO VALID directory at 21350_fb2dd32+ is MISSING
WED025 VALID directory at 21350_fb2dd32+ is MISSING
ISOMIP+ VALID directory at 21350_fb2dd32+ is MISSING
VORTEX VALID directory at 21350_fb2dd32+ is MISSING
ICE_AGRIF VALID directory at 21350_fb2dd32+ is MISSING
OVERFLOW VALID directory at 21350_fb2dd32+ is MISSING
LOCK_EXCHANGE VALID directory at 21350_fb2dd32+ is MISSING
SWG VALID directory at 21350_fb2dd32+ is MISSING
Report timing differences between REFERENCE and VALID (if available) :
ORCA2_ICE_PISCES ref. time: 275.569 cur. time: 271.984 diff.: -3.585
```Release 4.2Clement RoussetClement Rousset