Merge NSSL branch v8merge into the MPAS GSL-develop #1

tanyasmirnova · 2024-03-15T17:20:16Z

The title above should be a 1 line short summary of the pull request (i.e. what the project the PR represents is intended to do).

Merged NSSL code to the GSL MPAS branch.

Enter a description of this PR. This should include why this PR was created, and what it does.
This merge adds RUC LSM and NSSL microphysics, initial/BC conditions for all hydrometeors, and more diagnostics.

Testing and relations to other Pull Requests should be added as subsequent comments.

See the below examples for more information.
MPAS-Dev/MPAS#930
MPAS-Dev/MPAS#931

This commit adds a copy of the SMIOL library source code in src/external/SMIOL, and it updates recipes in Makefiles to build the SMIOL library and link it with MPAS executables. At present, however, the SMIOL library is not actually used.

In order to isolate all code that is specific to the PIO library, this commit adds pre-processing directives to include PIO-specific code only if MPAS_PIO_SUPPORT is defined at build time. The top-level Makefile defines MPAS_PIO_SUPPORT only if the PIO environment variable is defined. Although it is now possible to compile MPAS without any reference to the PIO library, doing so does not result in a useful model executable, since, e.g., no mesh information can be read during model bootstrapping. Besides the obvious additions of #idef MPAS_PIO_SUPPORT directives, there are several other aspects of the changes in this commit worth noting: 1) The optional 'io_system' argument to mpas_framework_init_phase2 and mpas_framework_finalize is an integer when MPAS_PIO_SUPPORT is not defined. 2) When MPAS_PIO_SUPPORT is not defined, MPAS_IO_OFFSET_KIND is defined as an I8KIND integer in mpas_io_types.inc. 3) The MPAS_*_FILLVAL constants have been provided with alternate defininitions when MPAS_PIO_SUPPORT is not defined.

If the PIO environment variable is not defined, the top-level Makefile defines the pre-processing macro MPAS_SMIOL_SUPPORT; otherwise, MPAS_PIO_SUPPORT is defined as before.

Still to do: 1) Ensure that all cores compile 2) Remove debugging print statements from mpas_io.F

* framework/smiol-iocomm: Update SMIOL to 36e0f0e on io_comm branch WIP: Implement SMIOL If PIO is not available, define MPAS_SMIOL_SUPPORT in top-level Makefile Wrap all PIO-specific code in MPAS_PIO_SUPPORT preprocessing directives Add SMIOL library code in src/external/SMIOL, and add Makefile hooks

This reverts commit 1e53460.

(Add back the io_comm changes on top of aggregation changes) This reverts commit 18b7b91.

…ng prints

…icrophysics (adds refl. moment variables for rain, graupel, hail: zrw, zgw, zhw). Also added code to compute the composite and 1-km reflectivity for NSSL2M (not actually tested yet)

…RTMG range.

… sets n_microp)

On case-insensitive filesystems, having the name of a build target the same as a directory -- specifically, 'smiol' and 'SMIOL', respectively -- leads make to infer that the target is already up to date. This is problematic in the case of SMIOL, since the library will never be compiled.

mpas_io_streams.F : pass ioformat to def_var mpas_io.F : add conditional to set deflate on variables if ioformat is netcdf4 (needs netcdf-4.7.4 or later)

…ls/nprocs

…eded if the libraries are static only.

MPAS Version 7.3 This minor release addresses one issue in the MPAS-Atmosphere model. MPAS-Atmosphere: ---------------- * Update the checkout_data_files.sh script to use HTTPS rather than the unencrypted Git protocol when obtaining the MPAS-Data repository from GitHub. * tag 'v7.3': (26 commits) Switch from unencrypted Git protocol to HTTPS when obtaining MPAS-Data repo Increment version number to 7.3 Correct units and descriptions for GWDO fields var2d, con, oa[1-4], ol[1-4] Halo exchange inTropo in flood fill to find DT. Fix parallel reproducibility error in 'smstav' field Correct check on availability of dtheta_dt_mix when computing depv_dt_mix Fix bug in vertical interp of r.h. and s.h. when levels are given top-to-bottom Initialize qvb to zero before its first use in init_atm_case_squall_line Remove redundant mpas_pool_get_array calls for dtheta_dt_mp computation Use dt_dyn rather than dt_microp when computing dtheta_dt_mp Remove trailing whitespace and adjust indentation of dtheta_dt_mp computation Obtain 'rvord' from mpas_constants for computation of dtheta_dt_mp Increment version number to 7.2 Calculate dtheta_dt_mp by finite difference around microphysics call. Update test for libpio to skip libpio.settings When calculating mosit air density, should use virtual T instead of T modified: src/core_init_atmosphere/mpas_init_atm_cases.F Enable all runtime checks when DEBUG=true in gfortran build target Remove -m64 from all compiler flag sets in gfortran build target Change -O3 to -g in CXXFLAGS_DEBUG for gfortran build target Fix non-standard BOZ-literal integer constant in module_ra_cam_support ...

…evelopment

…ging

In order to enable the use of regional first-guess datasets given on a Lambert conformal conic projection for regional MPAS-A ICs (including terrain blending), LBCs, surface updates, several places in the init_atmosphere core have been updated with code to set up Lambert conformal projections. This commit also adds 'else' cases in the map projection set-up to catch future uses of unsupported map projections.

…here/nssl_v7.3_smiol_lcc

…l_v7.3_smiol_lcc

…ecast/MPAS-Model into atmosphere/nssl_v7.3_smiol_lcc

…arnOnForecast/MPAS-Model into atmosphere/sfclayrev

… atmoshere/v8merge

…es-NOAA/MPAS-Model into atmoshere/v8merge

… develop

…eres The methods previously employed in the mpas_sphere_angle function for computing the side lengths of a spherical triangle were only applicable to unit-radius spheres. This commit generalizes the computation of these side lengths so that the mpas_sphere_angle function can be used to compute spherical angles on spheres of arbitrary radius.

joeolson42 · 2024-03-28T17:23:40Z

src/core_atmosphere/dynamics/mpas_atm_time_integration.F

+         end if
+         if (index_nc > 0) then
+            scalars_driving(index_nc,1:nVertLevels,1:nCells+1) = mpas_atm_get_bdy_state( clock, block, nVertLevels, nCells, 'nc', dt)
+         end if


Note to Anders: i guess ifa & wfa need to be added here too

I meant to tag @AndersJensen-NOAA

Yes, @joeolson42, I have ifa and nwfa and nc added in my PR.

joeolson42 · 2024-03-28T17:26:41Z

src/core_atmosphere/physics/mpas_atmphys_control.F

+             dzs(6,iCell) = 0.35_RKIND
+             dzs(7,iCell) = 0.50_RKIND
+             dzs(8,iCell) = 1.00_RKIND
+             dzs(9,iCell) = 0.70_RKIND


@tanyasmirnova : is this really correct? the 9th layer is thinner than the 8th?

@joeolson42 Joe, these are the thicknesses between the middles of the layers. The first and last values are actually 0.5 of the thickness.

OK. Thanks.

joeolson42 · 2024-03-28T17:32:36Z

src/core_atmosphere/physics/mpas_atmphys_manager.F

+      n_microp  = max(nint(dt_dyn/60._RKIND),2)
+      dt_microp = dt_dyn / n_microp
+    ENDIF
+ endif


@AndersJensen-NOAA : do we need anything like this for TEMPO?

@joeolson42, likely. Though we'll have to look at timestep sensitivity in MPAS first. There already is something defined in the lines above for Thompson, a limit of 90 s.

joeolson42

I left a few comments. I don't know much of anything about the majority of the modules changed, so my review isn't worth much. Under these time constraints, we have no choice but to accept the changes.

AndersJensen-NOAA

The commits from Michael Duda before 2021 are related to the use of SMIOL, which is a built-in I/O layer. If we don't intent on using that, then we can ignore those commits. There are also a lot of commits related to the addition of severe convection diagnostics, that we could ignore for now as well. I added suggestions for files to ignore; here's the caveat: I don't what will or won't break if we ignore files that I suggest we ignore.

AndersJensen-NOAA · 2024-03-28T17:46:12Z

src/core_atmosphere/Registry.xml

-                             packages="mp_thompson_in"/>
+                             packages="mp_thompson_in;mp_nssl2m_in"/>
+
+                        <var name="nc" array_group="number" units="nb kg^{-1}"


I added this in my PR.
Setting packages="mp_thompson_in;mp_nssl2m_in" will solve the merge conflict for this.

AndersJensen-NOAA · 2024-03-28T17:52:17Z

src/core_atmosphere/diagnostics/Registry_convective.xml

Can we ignore this registry for convective diagnostics?

AndersJensen-NOAA · 2024-03-28T17:53:01Z

src/core_atmosphere/diagnostics/mpas_atm_diagnostics_manager.F

These changes could be ignored.

AndersJensen-NOAA · 2024-03-28T17:53:26Z

src/core_atmosphere/diagnostics/mpas_convective_diagnostics.F

These changes could be ignored.

AndersJensen-NOAA · 2024-03-28T17:57:24Z

src/core_atmosphere/dynamics/mpas_atm_time_integration.F

+         end if
+         if (index_nc > 0) then
+            scalars_driving(index_nc,1:nVertLevels,1:nCells+1) = mpas_atm_get_bdy_state( clock, block, nVertLevels, nCells, 'nc', dt)
+         end if


Yes, @joeolson42, I have ifa and nwfa and nc added in my PR.

AndersJensen-NOAA · 2024-03-28T18:40:10Z

src/core_atmosphere/physics/mpas_atmphys_constants.F

+ real(kind=RKIND),parameter :: epsq2=0.2         ! initial TKE for camuw PBL scheme                      [m2 s^-2]
+ real(kind=RKIND),parameter :: a2=17.2693882
+ real(kind=RKIND),parameter :: a3=273.16
+ real(kind=RKIND),parameter :: a4=35.86


a2, a3, and a4 replace a2s, a3s, and a4s defined as parameters in the scheme itself.

AndersJensen-NOAA · 2024-03-28T18:45:43Z

src/core_atmosphere/physics/physics_wrf/module_mp_thompson.F

Do not merge changes to this file: module_mp_thompson.F

AndersJensen-NOAA · 2024-03-28T18:49:44Z

src/core_init_atmosphere/Makefile

Since some of these commit are old, I'd ignore changes to the Makefile.

AndersJensen-NOAA · 2024-03-28T18:52:23Z

src/driver/Makefile

Ignore this.

AndersJensen-NOAA · 2024-03-28T18:53:11Z

src/framework/Makefile

tanyasmirnova · 2024-03-28T19:37:52Z

I left a few comments. I don't know much of anything about the majority of the modules changed, so my review isn't worth much. Under these time constraints, we have no choice but to accept the changes.

@joeolson42 Joe, I think we could make a separate branch: NCAR_NSSLv8_merge. And another option isto add our physics to NCAR MPAS one at a time as you suggested. I am working now on separating RUC LSM changes from the rest of NSSL changes. Hopefully it will not take too long, maybe by next week it will be ready. The NCAR_NSSLv8_merge branch could be used untill we are ready with the NCAR_GSL/develop.

jderrico-noaa · 2024-03-29T01:11:51Z

@joeolson42 Joe, I think we could make a separate branch: NCAR_NSSLv8_merge. And another option isto add our physics to NCAR MPAS one at a time as you suggested. I am working now on separating RUC LSM changes from the rest of NSSL changes. Hopefully it will not take too long, maybe by next week it will be ready. The NCAR_NSSLv8_merge branch could be used until we are ready with the NCAR_GSL/develop.

I think this makes sense, I can add @tanyasmirnova 's branch from this PR as a separate branch to our repo for now and then work on pulling out what @AndersJensen-NOAA flagged and we can see how (if) it compiles and runs. In the mean time we can start with Anders's PR #2, I need one more approval and then I'll merge it

… microphysics features (#2) * Add microphysics submodule and updated graupel lookup table support (#1) * microphysics Makefiles for submodule * Add submodule support for microphysics * Fix bug in Makefile directory path * Thompson table updates for two-moment graupel * Add aerosol aware microphysics capability (#2) * Add microphysics aerosol information to initialization * Link microphysics aerosol tables for runtime * Update submodule * Fix link to microphysics aerosol tables * Add water- and ice-friendly aerosols to model for transport (#3) * Update pointer for microphysics * Update pointer to microphysics submodule * Add microphysics aerosol information to LBCs * Add aerosol-aware microphysics to LBCs (#4) * Add microphysics aerosol information to LBCs * Support for water- and ice-friendly aerosols in LBCs * Add documentation to subroutine init_microphysics_aerosols_lbc * Time interpolation for microphysics aerosols ICs * Add time interpolation for microphysics aerosols to LBCs * Aerosol time interpolation (#5) * Add microphysics aerosol information to LBCs * Time interpolation for microphysics aerosols ICs * Add time interpolation for microphysics aerosols to LBCs * Nc microphysics (#6) * Updates for aerosol aware * Add support for nc microphysics * Add nc to interface * point to develop branch of Thompson submodule * Import nwfa and nifa into microphysics (#7) * Add microphysics submodule makefile (#8) * Import nwfa and nifa into microphysics * Add makefile support for microphysics submodule * Update location for microphysics submodule * remove GSL_cloud_physics directory * Point to microphysics submodule * Point to microphysics submodule * Remove old submodule * Bug fix in Makefile to deal with old version of microphysics

tanyasmirnova · 2024-03-29T20:32:47Z

@jderrico-noaa @joeolson42 @AndersJensen-NOAA This merged with NSSL version of MPAS code has been tested on the 13-km CONUS test case from Anders Jensen. Although the versions of MYNN, Thompson and RUC LSM are old, the results appear to be reasonable. Below is the 2-m T verification produced by @AndersJensen-NOAA:

This code could be used in HFIP as a backup until the gsl/develp is ready.

mgduda and others added 30 commits September 21, 2020 17:49

If PIO is not available, define MPAS_SMIOL_SUPPORT in top-level Makefile

afce155

If the PIO environment variable is not defined, the top-level Makefile defines the pre-processing macro MPAS_SMIOL_SUPPORT; otherwise, MPAS_PIO_SUPPORT is defined as before.

WIP: Implement SMIOL

62b98bb

Still to do: 1) Ensure that all cores compile 2) Remove debugging print statements from mpas_io.F

Update SMIOL to 36e0f0e on io_comm branch

1e53460

Revert "Update SMIOL to 36e0f0e on io_comm branch"

18b7b91

This reverts commit 1e53460.

Add aggregation changes

0d6c685

Revert "Revert "Update SMIOL to 36e0f0e on io_comm branch""

a924d12

(Add back the io_comm changes on top of aggregation changes) This reverts commit 18b7b91.

Use non-blocking (bput) interface to PnetCDF

b614abb

Increase buffer size to 1 GB, change agg_factor to 20, remove debuggi…

714dcda

…ng prints

Initial implementation of NSSL 2-moment microphysics

2d96219

Added a package (nssl_moments) to turn on 3-moment version of NSSL m…

8669ec4

…icrophysics (adds refl. moment variables for rain, graupel, hail: zrw, zgw, zhw). Also added code to compute the composite and 1-km reflectivity for NSSL2M (not actually tested yet)

Limit ice crystal effective radius to 130um to stay within allowed R…

5eebcc8

…RTMG range.

Enable substepping for mp_nssl2m when dt_dyn is large (automatically…

80cab0e

… sets n_microp)

Added new variables to LBC code in time_integration

4421a8b

Checkpoint SMIOL prototype implementation -- 28 Sept 2022

5badd46

Incorporate bugfix from MPAS v7.3

ef4bab3

Add support for compression for netcdf4

9f19611

mpas_io_streams.F : pass ioformat to def_var mpas_io.F : add conditional to set deflate on variables if ioformat is netcdf4 (needs netcdf-4.7.4 or later)

Hack to set chunksizes along the nCells dimension. Chunksize is nCel…

c576543

…ls/nprocs

Added check in Makefile for HDF5 env. variable, which seems to be ne…

37e3be9

…eded if the libraries are static only.

Silence a few messages in mpas_io.F that were primarily used during d…

f7fe473

…evelopment

Comment-out some print statements in smiol.c that were used for debug…

ca96c22

…ging

Merge remote-tracking branch 'remotes/ted/nssl2m-deflate' into atmosp…

318c2fd

…here/nssl_v7.3_smiol_lcc

Merge remote-tracking branch 'ted/nssl2m-deflate' into atmosphere/nss…

2ff5e2e

…l_v7.3_smiol_lcc

Fixed null pointer issue with program init_atmosphere on Jet

e2267af

Merge branch 'atmosphere/nssl_v7.3_smiol_lcc' of github.com:WarnOnFor…

bbf6f07

…ecast/MPAS-Model into atmosphere/nssl_v7.3_smiol_lcc

LarissaReames and others added 14 commits June 29, 2023 21:28

Merge branch 'atmosphere/nssl_v7.3_smiol_lcc' of https://github.com/W…

28bb77c

…arnOnForecast/MPAS-Model into atmosphere/sfclayrev

Fixed computation of minimum UH fields.

f79481a

Merge branch 'develop' of https://github.com/MPAS-Dev/MPAS-Model into…

591b15c

… atmoshere/v8merge

Merge branch 'MPAS-Dev:master' into update_static_ruclsm

c0836c9

Merge branch 'update_static_ruclsm' of https://github.com/LarissaReam…

be69abd

…es-NOAA/MPAS-Model into atmoshere/v8merge

Additional content from previous merge commit

a4638f9

Merge branch 'develop' of https://github.com/MPAS-Dev/MPAS-Model into…

49886f6

… develop

Bug fixes for init_atmosphere

64eadf7

Updates to fix bugs with forecast.

c284080

Updated RUC LSM init to work with new VEGPARM.TBL

cbe0b4e

Replaced erroneously deleted line.

768cee2

Merge remote-tracking branch 'remotes/origin/v8merge' into gsl/develop

bbc87d9

Fixed syntax error in MYJ PBL.

fce2c71

jderrico-noaa assigned joeolson42, haiqinli, AndersJensen-NOAA and mdtoyNOAA Mar 27, 2024

joeolson42 reviewed Mar 28, 2024

View reviewed changes

joeolson42 approved these changes Mar 28, 2024

View reviewed changes

mdtoyNOAA approved these changes Mar 28, 2024

View reviewed changes

AndersJensen-NOAA requested changes Mar 28, 2024

View reviewed changes

jderrico-noaa marked this pull request as draft March 29, 2024 18:29

jderrico-noaa closed this May 23, 2024

Merge NSSL branch v8merge into the MPAS GSL-develop #1

Merge NSSL branch v8merge into the MPAS GSL-develop #1

Uh oh!

Conversation

tanyasmirnova commented Mar 15, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

joeolson42 left a comment

Choose a reason for hiding this comment

Uh oh!

AndersJensen-NOAA left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

tanyasmirnova commented Mar 28, 2024

Uh oh!

jderrico-noaa commented Mar 29, 2024

Uh oh!

tanyasmirnova commented Mar 29, 2024

Uh oh!

Uh oh!

tanyasmirnova commented Mar 15, 2024 •

edited

Loading