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Updates for JEDI+UFS#824

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climbfuji wants to merge 55 commits intodevelopfrom
feature/ufs_dom
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Updates for JEDI+UFS#824
climbfuji wants to merge 55 commits intodevelopfrom
feature/ufs_dom

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@climbfuji
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WORK IN PROGRESS

Description

(Instructions: this, and all subsequent sections of text should be removed and filled in as appropriate.)
Provide a detailed description of what this PR does.
What bug does it fix, or what feature does it add?
Is a change of answers expected from this PR?

Issue(s) addressed

Link the issues to be closed with this PR, whether in this repository, or in another repository.
(Remember, issues should always be created before starting work on a PR branch!)

  • fixes #<issue_number>
  • fixes JCSDA/soca-bundle/issues/<issue_number>

Testing

How were these changes tested?
What compilers / HPCs was it tested with?
Are the changes covered by ctests? (If not, tests should be added first.)

Dependencies

If testing this branch requires non-default branches in other repositories, list them.
Those branches should have matching names for the automated TravisCI tests to pass

Do PRs in upstream repositories need to be merged first?
If so add the "waiting for other repos" label and list the upstream PRs

  • waiting on JCSDA/soca-bundle/pull/<pr_number>
  • waiting on JCSDA/oops/pull/<pr_number>

mark-a-potts and others added 30 commits January 25, 2022 17:28
@climbfuji climbfuji added INFRA JEDI Infrastructure ALGO JEDI Algorithms SOCA Sea-ice, Ocean, and Coupled Assimilation labels May 1, 2023
* Use SABER blocks chaining for training (#852)

* Adapt to name changes in ufo (#867)

* Use VertInterp instead of MarineVertInterp (#874)

* remove linear var change from ensevariance ctest (#881)

* Bugfixes for BUMP (#869)

* A few fixes to the Model to Analysis variable change (#847)

* Remove discontinuities in the balance op  (#885)

* set to min/max instead of 0

* ...

* vanilla vert conv

* tidy sign

* removed jac_mask

* tanh filt

* updated yamls and test refs

* merge develop and update answers after the develop history MESS i created

* code tidy/removed vanilla

---------

Co-authored-by: Travis Sluka <tsluka@ucar.edu>

* default plots (#888)

Co-authored-by: Travis Sluka <tsluka@ucar.edu>

* add VADER to SOCA (#887)

* add vader to build, but dont use it

* add State::fromFieldSet

* variablechange "uses" vader

* switched to ens. templ. (#894)

* Implementation of EnsMeanAndVariance (#892)

* added the ensmeanandvariance app

* ...

---------

Co-authored-by: Travis Sluka <tsluka@ucar.edu>

* Read the std. dev. instead of the variance (#896)

* skip sqrt, saving optional

* forgot test yaml

* Update test/testinput/varchange_bkgerrsoca_stddev.yml

Co-authored-by: Travis Sluka <tsluka@ucar.edu>

---------

Co-authored-by: Travis Sluka <tsluka@ucar.edu>

* Use the generic oops interpolator (#898)

* use oops interpolation

* to_fieldset_ad

* forgot some halo masks

* fix horizfilt

* fix some test answers

* letkf workaround for missing val bug

* work around for getvalues test

* change obs input to have 1 guaranteed land point

* Update version (#899)

* remove ewok repo (#889)

Co-authored-by: Yannick Trémolet <30638944+ytremolet@users.noreply.github.com>

* Merge B matrix-related applications (#890)

* Merge B matrix-related applications

* Trigger tests

---------

Co-authored-by: Benjamin Menetrier <benjamin.menetrier@irit.fr>
Co-authored-by: Travis Sluka <tsluka@ucar.edu>

* update for VADER PR#586 (#902)

* add ModelData

* fix coding norms

* Update CMakeLists.txt

* Fix vertical gradient (#914)

* a fix dvdz

* Updating test references

---------

Co-authored-by: Hyun-Chul.Lee <Hyun-Chul.Lee@noaa.gov>

* libs in soca

* Commend out dirac.x test and disable ecbuild_install_project as we did for fv3-jedi prevent the following error:

-- Configuring done
CMake Error in soca/src/soca/CMakeLists.txt:
  Target "soca" INTERFACE_LINK_DIRECTORIES property contains path:

    "/Users/heinzell/work/ufs-bundle/20230714/ufs-bundle-use-jedi-develop/soca/src/soca/."

  which is prefixed in the source directory.

-- Generating done
CMake Generate step failed.  Build files cannot be regenerated correctly.

* Apply same bug fix as for fv3-jedi to fix missing linker path for MPI libraries due to ESMF bug

---------

Co-authored-by: Benjamin Menetrier <benjamin.menetrier@irit.fr>
Co-authored-by: Wojciech Śmigaj <w.smigaj@gmail.com>
Co-authored-by: Travis Sluka <tsluka@ucar.edu>
Co-authored-by: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Co-authored-by: Yannick Trémolet <30638944+ytremolet@users.noreply.github.com>
Co-authored-by: Benjamin Menetrier <30638301+benjaminmenetrier@users.noreply.github.com>
Co-authored-by: Kriti Bhargava <kritib@ucar.edu>
Co-authored-by: Hyun-Chul.Lee <Hyun-Chul.Lee@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
@symoore90
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Is this still relevant?

@cmgas
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cmgas commented Aug 9, 2023

@symoore90, as explained earlier this year all the UFS integration is ongoing work that will continue until we have all of it merged. I don't know that we have an estimate for when that will be.

climbfuji and others added 15 commits December 12, 2023 16:13
…om_develop_20231212

Update feature/ufs_dom from develop 2023/12/12
Updates for building with UFS_APP=NG-GODAS
* Remove old static B code (#1020)

* deprecate horizfilt/vertconv

* remove old tests

* remove 3dvar_godas

* remove SocaError

* remove horizfilt

* remove vertconv

* WIP

* add explicit_diffusion sqrt multiply

* fix more tests

* update tests

* increase tolerances

* Remove MOM_restart_CS from src/soca/Model/ufs/soca_mom6.F90

* Comment out checkpoint test in test/CMakeLists.txt

---------

Co-authored-by: Travis Sluka <tsluka@ucar.edu>
@climbfuji
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@travissluka I believe this branch is no longer needed, correct?

@travissluka
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@travissluka I believe this branch is no longer needed, correct?

No, I don't think it is. Assuming https://github.com/JCSDA-internal/soca/tree/feature/mom6_fms_update works, all we would need in that branch is cmake logic to determine if mom6 should be built from the submodule or linked from the UFS build.

@climbfuji
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Oh great, thanks. I'll delete this branch and any other branch that starts with feature/ufs_dom!

@climbfuji climbfuji closed this Apr 26, 2024
@climbfuji climbfuji deleted the feature/ufs_dom branch April 26, 2024 02:25
@travissluka travissluka restored the feature/ufs_dom branch April 26, 2024 14:25
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7 participants