GEOS-Chem 14.4 and dependencies #1093
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lizziel
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ACOM (e.g., @tilmes, Doug Kinnison) think Cloud-J would be a great option to include in CESM3, as an alternative to TUV-x for now. |
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The tests failed due to git-fleximod errors. I am looking into them now. |
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Looks pretty good. I have a few questions and change requests.
test/system/TR8.sh needs to be updated to skip over the new submodules.
Have you ran the aux_cam regression test suite to ensure that these changes to mo_neu_wetdep do not affect CAMChem or WACCM?
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When I run submit aux_cam test suite I get a lot of errors because I am on derecho instead of izumi. Is it still useful for me to test with it? |
This is how I submit the tests on derecho: |
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I now have lots of tests in ~elundgren/scratch. Could you tell me what tests to look at? Or do you run a script to evaluate all of them at once? |
To get a summary of the test results try thist: I see that you have a izumi tests as well as derecho tests. You must be launching the tests differntly. When I use the test_driver.sh script it creates an aux_cam sub dir under my scratch. For an example, see |
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@fvitt, here are the aux_cam test results. Let me know if we should be concerned about any of these. I am not sure why some are still pending given this was done last week. |
Good to know. I submitted via this since it is what I use for |
Using the example that Francis provided, you can add a flag In summary:
The |
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Thanks for the tips @cacraigucar. @fvitt, could you give me an update on where this PR stands. I see there are now conflicts due to new commits in cam_development. I can rebase and test again next week. Otherwise there are no remaining updates to add since I believe I addressed all of your comments. I am not sure about the test results above for non-GEOS-Chem runs and will need help deciphering those. |
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@fvitt, I have rebased locally and will run tests on derecho and izumi prior to pushing. However, when I try to use test_driver.sh I get this error: Should I set this to the GEOS-Chem project or to some other account? |
Yes, use the GEOS-Chem project number. |
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@fvitt, now I am getting |
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@lizziel |
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Still not working... |
Did you try this on izumi? |
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Ah, I did not notice you switched to izumi. I am trying to run tests using test_driver.sh on derecho prior to pushing. I do not have the code on izumi right now. |
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- Increase time requested for GEOS-Chem climo tests - Update default lower boundary condition file for FCHIST_GC/FCnudged_GC/: New file will enable runs past 2015-01-16. - Add MWs for new species FURA and BUTDI to adv_mass in GEOS-Chem mo_sim_dat Signed-off-by: Lizzie Lundgren <[email protected]>
- Add fine-grained timers; minor comment fixes - Fix wrong function call - Change GC_ to GEOSChem_ to avoid prefix misunderstandings - Fix to emissions unit conversion to kg/m2 - Programmatically generate the species list - Update comments for clarity on the sources of the species lists - Remove comment as separator
- Update GEOS-Chem from 14.3.1 to 14.4 and build successfully: - Update .gitmodules with temporary branches for needed submodule updates - Code updates in geoschem/chemistry.F90 for the version change - Add HETP submodule for aerosol thermodynamics in GEOS-Chem - bld/configure updates to build HETP if using GEOS-Chem - Add Cloud-J as a submodule - Update commit hashes for HEMCO_CESM and GEOS-Chem submodules - Add new namelist entry for aerosol optical property files: These files are used in GEOS-Chem outside of Cloud-J photolysis. - Fix temporary branch name for GEOS-Chem in .gitmodules Signed-off-by: Lizzie Lundgren <[email protected]>
- Fixes to Cloud-J data reading in CAM-SE - Update to CPU_Subdomain_ID and CPU_Subdomain_FirstID
- Update GEOS-Chem and dependencies in .gitmodules - Remove obsolete Externals files Signed-off-by: Lizzie Lundgren <[email protected]> Update changelog Update GEOS-Chem to version 14.4.2 release tag Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
This commit also moves the location of the GEOS-Chem compsets within the config_compsets.xml file to be by their corresponding cam-chem compset. Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
…tted Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
… def Including %NUDG after %HEMCO rather than before it results in the omission of the nudging_nl namelist in atm_in. Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
Updates for compatibility with GEOS-Chem are now merged into HETP and released as tag HETPv1.1. This removes the prior need to use the fork in the GEOS-Chem github organization. This is a zero diff update. Signed-off-by: Lizzie Lundgren <[email protected]>
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Signed-off-by: Lizzie Lundgren <[email protected]>
Signed-off-by: Lizzie Lundgren <[email protected]>
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@cacraigucar This is ready for review by others. |
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I did not review the code in src/chemistry as that is more something @fvitt is familiar with.
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Regarding input files, is there a procedure for detecting when new inputs files are added? Should I be creating an issue when there are files I add, or alerting someone via email? |
@lizziel |
It is good to made a note in the issue when new files are added and make sure they are added to the svn repo. That is something I try to check during review, but it is error prone. Before an official release (like CESM3), the CESM tester runs a special test to check for files not in the repo. Missing files would be found at that time. The only other way they are found, is when a user runs on a machine other than derecho and reports back to us that they can't access the file. |
This update is a zero diff update. The url may change again in the future once an institutional github is available for Environment and Climate Change Canada. In the meantime the GEOS-Chem fork will be used. Signed-off-by: Lizzie Lundgren <[email protected]>
This PR updates GEOS-Chem from version 14.1.2 to 14.4.3 It also includes updating HEMCO_CESM to 2.0.0 and HEMCO to 3.9.0. In addition, there are two new submodules in CAM: (1) Cloud-J 7.7.3, now used in GEOS-Chem for computing J-values, and (2) HETP v1.1, an improved ISORROPIA for aerosol thermodynamics in GEOS-Chem.
This PR supercedes #996 which was updating to an older version of GEOS-Chem.
Closes #959