Make stochastic physics independent of fv3atm and its submodules

[climbfuji]

This PR and associated PRs make the stochastic_physics submodule independent of fv3atm and its submodules.

The approach taken is to provide independent calls to generic MPI routines and supply specific halo exchange routines for the FV3 model. If other models are added in the future, only the file halo_exchange.fv3.F90 needs to be swapped with another halo_exchange.myothermodel.F90 file (and the cmake build system can take care of which one of these to compile).

There is a lot more room for cleanup and improvement, notably the redundant storage of MPI-specific information (gis_stochy%me, ...) and the looping over blocks (as a consequence of the use of blocked data structures in fv3atm), but this is beyond the scope of the current PRs.

Fixes #24.

Not addressed in this PR: gnu-make build, standalone builds.

Associated PRs:

#27
NOAA-EMC/ufsatm#145
ufs-community/ufs-weather-model#171

For regression testing information, see ufs-community/ufs-weather-model#171.

[climbfuji]

@pjpegion Please add @lisa-bengtsson as reviewer. Thanks.

[pjpegion]

Changes look good to me. This will go in after #26

[climbfuji]

@pjpegion @lisa-bengtsson for your information, I updated the PRs with the latest changes from "develop" for this repository, fv3atm and ufs-weather-model. I ran the regression tests against the existing baseline, fv3_ccpp_stochy passes, fv3_ccpp_ca has different results. This is because of commenting out the if (kstep== test around the count4 initialization in cellular_automata_global and cellular_automata_sgs. If I make those changes manually in the current develop version of the files and create a new baseline, then this PR gives the same answer (even in PROD mode!).

I will keep updating and testing these three PRs until it is our time to commit.

[lisa-bengtsson]

@climbfuji Thank you Dom, this is great!

[pjpegion]

@climbfuji I see you issued some more PRS at the fv3atm and ufs-weather-model level. Are you ready for me to accept your PR for stochastic_physics? -Phil

…

On Fri, Jul 31, 2020 at 2:34 PM lisa-bengtsson ***@***.***> wrote: @climbfuji <https://github.com/climbfuji> Thank you Dom, this is great! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#27 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJIRVJCL4Z62LAUBD2ZQRRTR6MTEVANCNFSM4PDVJNRA> .

-- Philip Pegion NOAA/Physical Sciences Laboratory-CIRES (303) 497-7897 philip.pegion@noaa.gov

[climbfuji]

Hi Phil, we are working on this now - just need to get the old gnumake build going again (some issues after the FMS downgrade). But yes, it will be the next in line. Please wait for another day or so to merge, if possible. Thanks!

…

On Aug 5, 2020, at 9:15 AM, Phil Pegion ***@***.***> wrote: Hi Dom, I see you issued some more PRS at the fv3atm and ufs-weather-model level. Are you ready for me to accept your PR for stochastic_physics? -Phoil On Fri, Jul 31, 2020 at 2:34 PM lisa-bengtsson ***@***.***> wrote: > @climbfuji <https://github.com/climbfuji> Thank you Dom, this is great! > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#27 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AJIRVJCL4Z62LAUBD2ZQRRTR6MTEVANCNFSM4PDVJNRA> > . > -- Philip Pegion NOAA/Physical Sciences Laboratory-CIRES (303) 497-7897 ***@***.*** — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#27 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5C2RPGGFJZEG65ESE5NZTR7FZQZANCNFSM4PDVJNRA>.

[lisa-bengtsson]

Hi Dom, Could you tell me the git command for me to download your version from git so I can check the CA pattern output. I am sure it is OK given your results reproduce, but I just want to make sure. Thanks! Lisa

…

--------------------------------- --------------------------------- Dr. Lisa Bengtsson Phone : 1 (303) 497 5971 Research Scientist - Meteorologist University of Colorado/NOAA Earth System Research Lab Email: lisa.bengtsson@noaa.gov 325 Broadway Office: Skaggs Research Cntr 1D-702 Boulder, CO, USA 80303-3328 On Wed, Aug 5, 2020 at 9:28 AM Dom Heinzeller <notifications@github.com> wrote:

Hi Phil, we are working on this now - just need to get the old gnumake build going again (some issues after the FMS downgrade). But yes, it will be the next in line. Please wait for another day or so to merge, if possible. Thanks! > On Aug 5, 2020, at 9:15 AM, Phil Pegion ***@***.***> wrote: > > > Hi Dom, > I see you issued some more PRS at the fv3atm and ufs-weather-model level. > Are you ready for me to accept your PR for stochastic_physics? > -Phoil > > On Fri, Jul 31, 2020 at 2:34 PM lisa-bengtsson ***@***.*** > > wrote: > > > @climbfuji <https://github.com/climbfuji> Thank you Dom, this is great! > > > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub > > < #27 (comment) >, > > or unsubscribe > > < https://github.com/notifications/unsubscribe-auth/AJIRVJCL4Z62LAUBD2ZQRRTR6MTEVANCNFSM4PDVJNRA > > > . > > > > > -- > Philip Pegion > NOAA/Physical Sciences Laboratory-CIRES > (303) 497-7897 > ***@***.*** > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub < #27 (comment)>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AB5C2RPGGFJZEG65ESE5NZTR7FZQZANCNFSM4PDVJNRA >. > — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#27 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM7EFLDLXB6KDCGFBO5JWSLR7F275ANCNFSM4PDVJNRA> .

[climbfuji]

Hi Dom, Could you tell me the git command for me to download your version from git so I can check the CA pattern output. I am sure it is OK given your results reproduce, but I just want to make sure. Thanks! Lisa
…

git clone -b stochastic_physics_independent_of_fv3atm --recursive https://github.com/climbfuji/ufs-weather-model

Please make sure to use compile_cmake.sh.

[lisa-bengtsson]

Thanks, Lisa

…

--------------------------------- --------------------------------- Dr. Lisa Bengtsson Phone : 1 (303) 497 5971 Research Scientist - Meteorologist University of Colorado/NOAA Earth System Research Lab Email: lisa.bengtsson@noaa.gov 325 Broadway Office: Skaggs Research Cntr 1D-702 Boulder, CO, USA 80303-3328

On Wed, Aug 5, 2020 at 9:33 AM Dom Heinzeller ***@***.***> wrote: Hi Dom, Could you tell me the git command for me to download your version from git so I can check the CA pattern output. I am sure it is OK given your results reproduce, but I just want to make sure. Thanks! Lisa … <#m_-7209020552485726087_> git clone -b stochastic_physics_independent_of_fv3atm --recursive https://github.com/climbfuji/ufs-weather-model Please make sure to use compile_cmake.sh. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#27 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM7EFLAQS5SFQD7IIY65RH3R7F3TDANCNFSM4PDVJNRA> .

[climbfuji]

@pjpegion @lisa-bengtsson we are ready for merging this. Can you please review/approve and merge, if ok? Thanks.

[pjpegion]

Look good

[lisa-bengtsson]

I don't think I am assigned as a reviewer, but changes look good.

[pjpegion]

@lisa-bengtsson I just added you as a reviewer, but no need to complete the review. I will do the merge.