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Name: Bob Yantosca
Institution: Harvard + GCST

Describe the update

This PR seeks to merge the updates from GCHP 14.5.2 into the GCHP 14.6.0 development stream (branch dev/14.6.0).

Expected changes

This will be a zero-diff update as 14.5.2 did not contain any updates that change benchmark simulations.

Related Github Issue

yantosca and others added 17 commits January 16, 2025 14:23
docs/requirements.txt
- Bumped jinja2 to version 3.1.5, as suggested by GitHub Dependabot.
  This is a security fix.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR #469 (Bump jinja2 to 3.1.5 as suggested by
Dependabot, by @yantosca) into the GCClassic "no-diff-to-benchmark"
development stream.

This PR updates a Python package used by ReadTheDocs to implement
a security fix.  This was suggested by GitHub Dependabot.

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

255a13d88 Merge PR #2690 (Add .zenodo.json to auto-populate DOI fields)

and to the GitHub geoschem/HEMCO repository:

9cf873a Merge PR #304 (Add .zenodo.json; Update jinja2 to 3.1.5)

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the GCClassic superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

a3e623f7e Merge PR #2684 (Fix CO2 weekly scale factors in GCHP)

This PR fixes a typo in the ExtData.rc.carbon file so that the
CO2 weekly scale factors are read and applied properly.

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the GCHP superproject about the following
commits that were pushed to the geos-chem-shared-docs repository:

acf07e2 Updated GEOS-Chem Input Data doc to say download is free

Also updated the CHANGELOG.md accordingly

Signed-off-by: Bob Yantosca <[email protected]>
Submodule src/GCHP_GridComp/GEOSChem_GridComp/geos-chem 6b056e0..8ea94bc:
  > Merge pull request #2692 from geoschem/feature/updated_cluster_env_and_run_scripts
  > Merge pull request #2616 from yuanjianz/feature/geosit_preprocessed_cs

Submodule src/MAPL 9ad63ae..6207fd0:
  > Merge pull request #38 from geoschem/bugfix/intel_build_error_in_AbstractComponent

Signed-off-by: Lizzie Lundgren <[email protected]>
CMakeScripts/GC-ConfigureClassic.cmake
- Added boolean cache variable KPPSA and print its value

src/CMakeLists.txt
- Only execute the block where KPPSA_FILE_NAME is defined as a target
  if the KPPSA boolean variable is true.  This will only build the
  KPP-Standalone executable when -DKPPSA=y is passed from the cmd line.

src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt
- Added boolean cache variable KPPSA

CHANGELOG.md
- Updated accordingly

TODO: Update KPP-Standalone documentation accordingly in ReadTheDocs,
which is located in the geos-chem-shared-docs submodule

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

60381876d  Merge PR #2712 (Only build KPP-Standalone upon request)

This PR now asks the user if they wish to build the KPP-Standalone
executable at run directory creation time.  A reminder will be
printed to configure with -DKPPSA=y, and the kpp_standalone_interface.yml
file will be copies to the run directory.

Signed-off-by: Bob Yantosca <[email protected]>
This merge brings PR #473 (Do not build KPP-Standalone executable unless
specifically requested at compile time, by @yantosca) into the GEOS-Chem
"no-diff-to-benchmark" development stream.

This PR adds updates to the CMake files so that the KPP-Standalone will
only be built if the user configures with -DKPPSA=y.

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the GCClassic superproject about the following
commits that were pushed to the GitHub geos-chem-shared-docs repository:

02c4c26 Update KPP-Standalone guide for on-request build

Signed-off-by: Bob Yantosca <[email protected]>
docs/source/user-guide/rundir-init.rst
- Add a section explaining that the user will be prompted
  if they wish to build the KPP-Standalone Box Model.  Also provide
  a link to the KPP-Standalone supplemental guide.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>
This commit informs the GCHP superproject about the following
commits that were pushed to the GitHub geoschem/geos-chem repository:

aeeb8e9 Add link to KPP-Standalone documentation on GCPy ReadTheDocs

This PR adds a paragraph to the KPP-Standalone documentation
stating that plotting scripts are available on GCPy (with link to
documentation).

Signed-off-by: Bob Yantosca <[email protected]>
CHANGELOG.md
CMakeLists.txt
docs/source/conf.py
- Updated version numbers to 14.5.2

src/GEOS-Chem
- Now points to GEOS-Chem (sci codebase) 14.5.2 release commit

src/HEMCO
- Points to HEMCO 3.10.1 release
    Signed-off-by: Bob Yantosca <[email protected]>

Signed-off-by: Bob Yantosca <[email protected]>
We have merged the most recent documentation updates for
GCHP into the release/14.5.2 branch.

Signed-off-by: Bob Yantosca <[email protected]>
This is the official release commit of GCHP 14.5.2.

Updated version numbers in:
- CHANGELOG.md
- CMakeLists.txt
- docs/source/conf.py

Updated GEOS-Chem submodule to version 14.5.2

Updated geos-chem-shared-docs submodule to commit aeeb8e9

Also updated CHANGELOG.md with the latest information.

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca added category: Feature Request New feature or request no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations labels Feb 14, 2025
@yantosca yantosca added this to the 14.6.0 milestone Feb 14, 2025
@yantosca yantosca requested a review from msulprizio February 14, 2025 21:34
@yantosca yantosca self-assigned this Feb 14, 2025
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Integration tests are running

@yantosca yantosca merged commit 503fe2c into dev/14.6.0 Feb 18, 2025
8 of 9 checks passed
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All GEOS-Chem Classic integration tests passed:

==============================================================================
GEOS-Chem Classic: Execution Test Results

CodeDir   : 71b86c6 Merge GCClassic 14.5.2 into dev/14.6.0
GEOS-Chem : b07fab7d7 Merge GEOS-Chem 14.5.2 into dev/14.6.0
HEMCO     : 2423647 Merge PR #279 (Use USTAR from met in DustDEAD extension)
Cloud-J   : f8a2b7f Update version number for 8.0.1 release
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 3855867
============================================================================== 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

All tests were zero-diff w/r/t 14.5.0-alpha.5 except:

  • CH4 (new rice emissions)
  • carbon (new rice emissions)
  • carbon_CH4 (new rice emissions)
  • TOMAS15 (parallelization error?)
  • APM (parallelization error?)
  • fullchem_alldiags (KppDiags and ObsPack diagnostic diffs, but restarts are identical)

All GCHP integration tests passed:

==============================================================================
GCHP: Execution Test Results

CodeDir       : 503fe2c Merge GCHP 14.5.2 into dev/14.6.0
MAPL          : 6207fd0 Merge pull request #38 from geoschem/bugfix/intel_build_error_in_AbstractComponent
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared   : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS           : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem     : b07fab7d7 Merge GEOS-Chem 14.5.2 into dev/14.6.0
HEMCO         : 2423647 Merge PR #279 (Use USTAR from met in DustDEAD extension)
yaFyaml       : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger      : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J       : f8a2b7f Update version number for 8.0.1 release
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Number of execution tests: 12

Submitted as SLURM job: 3856235
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

All tests were zero-diff w/r/t 14.6.0-alpha.6 except for:

  • carbon (new rice emissions)
  • carbon_CH4 (new rice emissions)

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category: Feature Request New feature or request no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations

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4 participants