Merge development HEAD into main #64
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…s possible; note that CMAKE_PREFIX_PATH is now ignored
Submodule src/GCHP_GridComp/HEMCO_GridComp/HEMCO 9561eef..edff3a4: > Ensure box height is initialized for calculation if pressures available > Fix incorrect module names in error handling messages > Fix bug in xyL option in HEMCO standalone if box height not available Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Fixed make install
Fixed OMP switch for GCHP
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
This update restores previous behavior for using the following commands to build GCHP from a run directory: mkdir -p build; cd build; cmake ../CodeDir; make -j; make install This allows the recommended procedure for building GCHP to match that of GEOS-Chem Classic. Changes to the recommended procedure in the future will be applied to both at the same time so that a common set of instructions may always be used. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…tory (previously they were relative to src/ subdirectory)
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…brary
Updates include:
1. Remove unnecessary HCOI_GCHP library from HEMCO and link instead to
HCOI_MAPL_ESMF. This is possible since HEMCO will not be an ESMF
component in GCHPctm and therefore the more generic MAPL/ESMF library
in HEMCO can be linked to rather than a GCHPctm-specific library.
2. Remove extraneous print in HEMCO that clutters the log file
3. Remove git add for sample run scripts during run directory creation
since run scripts are now linked to via sym link to source code.
Submodule src/GCHP_GridComp/HEMCO_GridComp/HEMCO edff3a4..db95516:
> Remove "testing only" print that is on even with verbose off
> Remove Interfaces/GCHPctm directory since unnecessary
Submodule src/GCHP_GridComp/GEOSChem_GridComp/geos-chem d18addc..478045f:
> Minor fix in GCHP run directory creation script
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Submodule src/GCHP_GridComp/HEMCO_GridComp/HEMCO db95516..a225cd3: > Merge pull request #55 from geoschem/feature/sphinx-docs Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…update The ESMA_cmake submodule commit was on a branch separate from dev since the merge of PR 50. Updates in that PR are now merged into the 13.0.0 dev branch Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
This issue came in with PR 50 when OpenMP became disabled by default. It remains disabled if using GNU compilers to avoid slow-down due to a separate bug under investigation. However, it is now enabled if using Intel compilers pending determination of the problem in MAPL. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…ttings Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Submodule src/GCHP_GridComp/GEOSChem_GridComp/geos-chem f172723..030cf89: > Rename HEMCO diagnostics for lightning flash rates / convective cld top ht > Updates to GCHP and GEOS diagnostic handling based on names in HISTORY.rc Submodule src/GCHP_GridComp/HEMCO_GridComp/HEMCO 7917490..465db7b: > Change lightning NOx Ext diagnostic names for compatibility with GCHP/GEOS Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Submodule ESMA_cmake 61bed9f..0981bed: > Turn off recursion check in debug mode if using GNU fortran compiler Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Add runtime CI test for transport tracer simulation
… build updates Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
This commit informs the GCHPctm superproject about the following updates that were committed to the geos-chem submodule: 7f3d9d7 Fixed typos in intTestCreate.sh; Expand root path in intTest_*.sh scripts 38373e1 Minor tweaks to GCClassic integration tests d6986a9 Merge branch 'dev/13.0.0' of https://github.com/geoschem/geos-chem.git into dev/13.0.0+iTests c304239 Updates to run-directory creation scripts bc5c23a Now declare fieldId array with the proper number of slots 48764bd Bug fix: remove SOAP and SOAS from input.geos for complexSOA* simulations 1df4e3d Restore TOMAS compilation and execution jobs in GCClassic intTests 6cc7c0a Resolve compilation issues for TOMAS 14305c2 Merge branch 'dev/13.0.0' into dev/13.0.0+iTests 7b5d30b Bug fix: make sure that the number of integration tests is displayed: 0e0d87c Use -DRUNDIR="" option; reduce requested time in intTestExecute.sh 19a5157 createRunDir.sh now copies APM configuration files to run directories 6600069 Fix outstanding issues for GCClassic integration tests 97a5e9c Update GCClassic integration test scripts to compile only a few times a47f19b Enable offline lightning emissions by default in GCHP fullchem HISTORY.rc 07abebb Merge branch 'feature/bmy/iTests' of https://github.com/geoschem/geos-chem.git into dev/13.0.0+iTests Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCHPctm superproject about the following updates that were committed to the HEMCO submodule: 133e60e Merge pull request #60 from geoschem/feature/build-updates Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCHPctm superproject about the following updates that were committed into the geos-chem submodule: 3e24b95 Use the srun commmand to run the executable in intTestExecute_slurm.sh Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
We have added a symbolic link from the top-level GCHPctm superproject folder to the directory: GCHP_GridComp/GEOSChem_GridComp/geos-chem/test/GCHPctm which contains the scripts for setting up GCHPctm integration tests. This mirrors what we have done for GCClassic. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GEOS-Chem submodule about the following updates that were committed to the geos-chem submodule 4f5f6bb Fix minor bugs in GCClassic and GCHPctm integration test scripts Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCClassic superproject about the following updates that were committed to the src/GEOS-Chem submodule: 86779cc Bug fix in intTestResults.sh: Remove typo and display proper text eb33255 Add more unit tests and a script to write results from execution tests ff02f8c Exclude certain emission diagnostics from HISTORY.rc.fullchem template 0006734 Updates to ensure that GCHPctm execution tests are submitted as SLURM jobs Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCHPctm superproject about the following updates that were committed to the geos-chem submodule: 3d9cefb Fix more GCHPctm integration test script issues Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCHPctm superproject about the following updates that were committed to the geos-chem submodule: 1abad25 GCHPctm bug fix: Comment out EmisGLYX_Total from HISTORY.rc.fullchem Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCHPctm superproject about the following updates that were committed to the geos-chem superproject: 06a5b41 Updates to make GCHP integration tests start faster and not pend Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCClassic submodule about the following updates that were committed to the src/GEOS-Chem superproject: fba5465 Merge branch 'patch-5' of git://github.com/sdeastham/geos-chem into dev/13.0.0+CreateRunDir Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCHPctm superproject about the following updates that were committed to the geos-chem submodule 40a1601 (HEAD -> test) Merge branch 'dev/13.0.0' into dev/13.0.0+iTests Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This commit informs the GCClassic superproject about the following updates that were committed to the src/GEOS-Chem submodule: 4551d18 Merge branch 'bugfix/sg-param-updating' into dev/13.0.0 8d9a5de Further updates to make createRunDir.sh files consistent with each other Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
…bug print This commit informs the GCClassic wrapper about the following updates that were committed to the src/GEOS-Chem submodule: a57449e Remove debug print from test/GCClassic/intTestCreate.sh b131c21 Use a better algorithm in function absolute_path Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
ExtData updates fixing monthly/annual inputs and leap days
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Therefore, I'm going to merge the developement HEAD into main so that any new users that try GCHP and don't checkout a specific prerelease get a version of GCHPctm that works.