Update MPAS-O: 3d varying GM bolus and 2d varying phase speed #3057

mark-petersen · 2019-07-10T17:45:32Z

In the GM bolus calculation, there is a specified diffusivity and phase
speed (see Ferrari et al. 2010). Currently MPAS-O assumes these values
are fixed in time and space. This PR allows separate flags to enable
2D varying (+time) phase speed (based on the first baroclinic mode phase
speed) and a separate flag for 3D (+time) varying diffusivity.

See MPAS-Dev/MPAS-Model#288

[NML]
[non-BFB]

mark-petersen · 2019-07-10T17:48:06Z

@vanroekel this is a placeholder PR. The diffs won't be correct until MPAS-Dev/MPAS-Model#288 is merged in.

Based on the test results (see MPAS-Dev/MPAS-Model#288), I think we should make vertically varying GM-Bolus default ON for all low-res runs. That would make this a non-BFB PR.

rljacob · 2019-07-25T04:37:08Z

@mark-petersen, I found a design document in the old Ocean Group space:
https://acme-climate.atlassian.net/wiki/spaces/OCNICE/pages/980713736/ocean+GM+Parameter+function+of+depth

But this v2 feature needs a code review document added here:
https://acme-climate.atlassian.net/wiki/spaces/ED/pages/36176475/Proposed+New+Features

And approval of the above by @golaz

vanroekel · 2019-08-13T03:15:03Z

@rljacob the design doc is in place now.
https://acme-climate.atlassian.net/wiki/spaces/ED/pages/1023836492/W16+MPAS-Ocean+3D+varying+GM+bolus+kappa+Design+Document

vanroekel · 2019-08-13T03:25:03Z

NOTE that this still needs the corresponding E3SM changes to add namelist flags and set defaults. I'll try add my changes shortly

rljacob · 2019-08-13T14:56:17Z

@vanroekel that design document needs to be within a larger code review document. And "W16" was already taken so make it W17.

mark-petersen · 2019-08-16T18:19:08Z

@vanroekel this is ready for flag updates. @stephenprice this is the branch to use for your test, after Luke adds the namelist options.

mark-petersen · 2019-08-16T18:20:05Z

FYI, just rebased this on current master, so it should work on cori, but I haven't tested it.

flags are added to enable the 3D varying GM bolus Kappa, it is enabled by default and is on whenever the GM parameterization is on. output of kappaGM3D and the phase speed are added to monthly history as well

vanroekel · 2019-08-16T19:09:39Z

@stephenprice the branch is now ready for you to test.

mark-petersen · 2019-08-20T12:30:09Z

Passes these tests on cori-knl:

PASS PEM_Ln9.ne30_oECv3_ICG.A_WCYCL1850S.cori-knl_intel COMPARE_base_modpes
PASS PET_Ln3.T62_oEC60to30v3wLI.GMPAS-DIB-IAF-ISMF.cori-knl_intel COMPARE_base_single_thread
PASS PET_Ln9.T62_oEC60to30v3.GMPAS-IAF.cori-knl_intel COMPARE_base_single_thread

So I know the updated namelists work. Thanks @vanroekel and @jonbob

mark-petersen · 2019-08-20T13:14:59Z

OK, I updated the design document here. Added performance test and reviewed the rest, and filled in the meta-data information at the top that is collected in the page one level up.
https://acme-climate.atlassian.net/wiki/spaces/ED/pages/1023836492/W17+MPAS-Ocean+3D+varying+GM+bolus+kappa+Design+Document

@jonbob let's proceed with this one.

mark-petersen · 2019-08-20T15:43:21Z

@vanroekel please approve this PR.

@golaz, I think we are asking for team lead approval, and this falls under the water cycle. I think you just need to acknowledge that we filled out everything on the design document, see last post.

vanroekel

All looks good, just requesting two variables be added to the streams file by default.

components/mpas-ocean/cime_config/buildnml

mark-petersen · 2019-08-22T13:46:57Z

@jonbob I added those two variables, so all requests are completed.

jonbob · 2019-08-22T14:29:31Z

@mark-petersen - what was that last commit? This PR doesn't say anything about bringing in a new grid and doesn't have the CIME support for it

mark-petersen · 2019-08-22T14:37:08Z

Whoops - working on two things at once. I'll fix that, thanks for looking.

mark-petersen · 2019-08-22T14:45:13Z

OK, just rolled back the last commit. This is the only thing I added for Luke's requested variables:
6ff481a

vanroekel

changes look good. Thanks @mark-petersen

Update MPAS-O: 3d varying GM bolus and 2d varying phase speed n the GM bolus calculation, there is a specified diffusivity and phase speed (see Ferrari et al. 2010). Currently MPAS-O assumes these values are fixed in time and space. This PR allows separate flags to enable 2D varying (+time) phase speed (based on the first baroclinic mode phase speed) and a separate flag for 3D (+time) varying diffusivity. See MPAS-Dev/MPAS-Model #288 [NML] [non-BFB]

jonbob · 2019-08-29T17:08:48Z

merged to next

Update MPAS-O: 3d varying GM bolus and 2d varying phase speed In the GM bolus calculation, there is a specified diffusivity and phase speed (see Ferrari et al. 2010). Currently MPAS-O assumes these values are fixed in time and space. This PR allows separate flags to enable 2D varying (+time) phase speed (based on the first baroclinic mode phase speed) and a separate flag for 3D (+time) varying diffusivity. See MPAS-Dev/MPAS-Model #288 [NML] [non-BFB]

jonbob · 2019-08-30T14:23:47Z

merged to master and expected DIFF's blessed

This PR fixes a threading issue that was introduced in [E3SM PR#3057] (E3SM-Project/E3SM#3057) that brought in the initial implementation of 3D varying GM bolus. After that commit, some E3SM threading tests were observed to fail with different results. Tested with: * SMS_P12x2.T62_oQU240.CMPASO-NYF.compy_intel - BFB results 10 times * SMS_P12x2.ne4_oQU240.A_WCYCL1850.compy_intel.allactive-mach_mods - BFB * results 10 times This last test is one that was failing on sandiatoss3.

…3226) Fix threading issue in MPAS-O GM routine This PR brings in a new mpas-source submodule that fixes a threading issue that was introduced in E3SM PR #3057. After that commit, which brought in the initial implementation of 3D varying GM bolus, some E3SM threading tests were observed to fail with different results. Tested with: * SMS_P12x2.T62_oQU240.CMPASO-NYF.compy_intel - BFB results 10 times * SMS_P12x2.ne4_oQU240.A_WCYCL1850.compy_intel.allactive-mach_mods - BFB results 10 times This last test is one that was failing on sandiatoss3. Fixes #3200 [BFB]

Fix threading issue in MPAS-O GM routine This PR brings in a new mpas-source submodule that fixes a threading issue that was introduced in E3SM PR #3057. After that commit, which brought in the initial implementation of 3D varying GM bolus, some E3SM threading tests were observed to fail with different results. Tested with: * SMS_P12x2.T62_oQU240.CMPASO-NYF.compy_intel - BFB results 10 times * SMS_P12x2.ne4_oQU240.A_WCYCL1850.compy_intel.allactive-mach_mods - BFB results 10 times This last test is one that was failing on sandiatoss3. Fixes #3200 [BFB]

…(PR #3632) Adding E3SM support for 3DGM namelist options to maint-1.2 This adds changes from PR #3057 for E3SM support of 3DGM namelist options to the maint-1.2 branch. As part of this, 3DGM is turned on by default (as it was in PR #3057), so it is not BFB. The changes were copied directly from the E3SM (non mpas-source) file changes in #3057 (hash 9fc9d6f). [non-BFB] [NML]

…elop This PR fixes a threading issue that was introduced in [E3SM PR#3057] (E3SM-Project/E3SM#3057) that brought in the initial implementation of 3D varying GM bolus. After that commit, some E3SM threading tests were observed to fail with different results. Tested with: * SMS_P12x2.T62_oQU240.CMPASO-NYF.compy_intel - BFB results 10 times * SMS_P12x2.ne4_oQU240.A_WCYCL1850.compy_intel.allactive-mach_mods - BFB * results 10 times This last test is one that was failing on sandiatoss3.

…-orbital-parameter-type Automatically Merged using E3SM Pull Request AutoTester PR Title: Fix type in orbital parameter read PR Author: brhillman PR LABELS: radiation, AT: AUTOMERGE, bugfix, AT: Skip weaver, AT: Skip v1 Testing

mark-petersen added the mpas-ocean label Jul 10, 2019

mark-petersen requested a review from vanroekel July 10, 2019 17:45

mark-petersen assigned jonbob Jul 10, 2019

rljacob added this to the v2.0alpha milestone Jul 11, 2019

jonbob added NML non-BFB PR makes roundoff changes to answers. labels Jul 25, 2019

Update mpas-source for 3D GM and added GM output

5caa735

mark-petersen force-pushed the mark-petersen/ocean/gmBolus3Dvarying branch from 7d2c663 to 5caa735 Compare August 16, 2019 18:18

vanroekel added 2 commits August 16, 2019 11:38

Adds namelist options for 3D varying GM bolus Kappa

2f51169

flags are added to enable the 3D varying GM bolus Kappa, it is enabled by default and is on whenever the GM parameterization is on. output of kappaGM3D and the phase speed are added to monthly history as well

Updates mpas-source to GM varying branch

529c31b

vanroekel and others added 3 commits August 16, 2019 13:21

Adds GM eddy stat output to MPAS streams

f473c92

Merge auto-generated bld script updates due to Registry change

7ae8941

Update mpas-source to update GM in COMPASS

cf47b45

vanroekel requested changes Aug 20, 2019

View reviewed changes

components/mpas-ocean/cime_config/buildnml Show resolved Hide resolved

Add GMBolusVelocity variables to output stream

6ff481a

mark-petersen force-pushed the mark-petersen/ocean/gmBolus3Dvarying branch from a89b783 to 6ff481a Compare August 22, 2019 14:43

Correct tab to space on buildnml

b9f84d3

vanroekel approved these changes Aug 29, 2019

View reviewed changes

jonbob merged commit b9f84d3 into master Aug 30, 2019

jonbob deleted the mark-petersen/ocean/gmBolus3Dvarying branch August 30, 2019 14:23

wlin7 mentioned this pull request Sep 5, 2019

Implement O3v2 in Linoz #3047

Merged

This was referenced Sep 24, 2019

MPAS-O problem causing SMS_P12x2.ne4_oQU240.A_WCYCL1850.sandiatoss3_intel.allactive-mach_mods diffs #3200

Closed

Fix threading issue in MPAS-O GM routine MPAS-Dev/MPAS-Model#376

Merged

mark-petersen mentioned this pull request Oct 7, 2019

Fix threading issue in MPAS-O GM routine #3226

Merged

darincomeau mentioned this pull request Jun 11, 2020

Adding E3SM support for 3DGM namelist options to maint-1.2 #3632

Merged

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Update MPAS-O: 3d varying GM bolus and 2d varying phase speed #3057

Update MPAS-O: 3d varying GM bolus and 2d varying phase speed #3057

mark-petersen commented Jul 10, 2019 •

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Update MPAS-O: 3d varying GM bolus and 2d varying phase speed #3057

Update MPAS-O: 3d varying GM bolus and 2d varying phase speed #3057

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