Sync with NoahMP Github version with all NoahMP updates since v4.3 #1641

cenlinhe · 2022-01-13T03:47:16Z

TYPE: new feature

KEYWORDS: NoahMP

SOURCE: Cenlin He (NCAR)

DESCRIPTION OF CHANGES:
This is step one to synchronize with latest NoahMP Github code version in order to prepare for connecting WRF directly to NoahMP unified Github repo.

Specifically, the updates in NoahMP since version 4.3:

three additional runoff schemes added (OPT_RUN=6, 7, 8)
new tile drainage capability/scheme added (OPT_TDRN)
New soil time step control capability added to allow users specify a different soil time step from main
NoahMP time step
additional water and energy budget terms added for output and diagnosis
updated flood irrigation parameters
add constraints for snow thickness during compaction
updated snow viscosity coefficient in compaction process
add canopy heat storage in canopy temperature calculation
updated formulation and parameter values for TOPMODEL groundwater scheme (OPT_RUN=1)
Bug fixes: SWE cap value in initialization, NoahMP snow depth update, snow layer index update, floating
issues in runoff scheme, and BATS albedo scheme

LIST OF MODIFIED FILES: list of changed files (use git diff --name-status master to get formatted list)
M Registry/Registry.EM_COMMON
M Registry/registry.noahmp
M dyn_em/module_first_rk_step_part1.F
M dyn_em/start_em.F
M phys/module_diag_misc.F
M phys/module_diagnostics_driver.F
M phys/module_physics_init.F
M phys/module_sf_noahmp_glacier.F
M phys/module_sf_noahmp_groundwater.F
M phys/module_sf_noahmpdrv.F
M phys/module_sf_noahmplsm.F
M phys/module_surface_driver.F
M run/MPTABLE.TBL
M run/README.namelist
M run/SOILPARM.TBL

TESTS CONDUCTED:

successfully compiled and tested for running in NCAR supercomputer by Cenlin He (NCAR)
Jenkins tests are all pass.

RELEASE NOTE: Updates from NoahMP and linking WRF directly to NoahMP Github repo.

Synchronize the develop branch from official WRF GitHub

sync up develop branch

…ntrol

cenlinhe · 2022-01-13T21:52:16Z

I just found a bug in defining an "inout" variable and am re-doing all the tests for the bug fix. I will update this PR soon after successful test.

weiwangncar · 2022-01-13T22:00:08Z

run/README.namelist

+                                                     2 = Hooghoudt's equation based tile drainage
+ soiltstep                          = 0.0,      ! Noah-MP soil process timestep (seconds) for solving soil water and temperature
+                                                     0 = default, the same as main NoahMP model timestep
+                                                     N * dt_noahmp, typically 15min or 30min


@cenlinhe Can you add noahmp_output, noahmp_acc_dt, and possibly opt_infdv, opt_tdrn to this file?

cenlinhe · 2022-01-13T23:45:27Z

The PR is now updated. I fixed the bugs and add info to README.namelist.

davegill · 2022-01-15T01:53:50Z

@weiwangncar @dudhia
Folks,
If people are OK with these mods (and really, these are in the NoahMP repo, so we are basically given these AS-IS), we should approve to merge in the next step as quickly as possible.

dudhia · 2022-01-17T16:03:43Z

I could approve but some of these mods are mine. Dave could go ahead and do the software approve.

TYPE: bug fix KEYWORDS: netcdfpar, Error SOURCE: internal DESCRIPTION OF CHANGES: IMPORTANT: Without these mods, every commit since the parallel netcdf4 IO mods will fail the DA build test in the regression test. For example, at least these commits: ``` fed10f4 Adding the WRF-Solar EPS model (#1547) 0bda5e0 Fix 4dvar build failure after commit 8b5bfe5 (#1652) 8b5bfe5 Thompson AA enhancements: BC aerosol, biomass burning emissions, and … (#1616) 9dc68ca After testing with UFS/GFS/FV-3, some tuning knob changes to Thompson-MP and icloud3 (cloud fraction) scheme (#1626) 96fd889 Update HONO, TERP, and CO2 emissions (#1644) 64fb190 SFCLAY=1, add shallow water roughness calculation (#1543) 609c2fc New module firebrand_spotting for WRF-Fire (#1540) 75bfe6d MYNN PBL clouds in photolysis option 4 (TUV) (#1622) f8c4b13 Fix runtime error when using sf_surface_mosaic = 1 with use_wudapt_lcz = 0 (#1638) b511c70 Run-time option for climate GHG for radiation (#1625) 8194c66 Bug fix for configuration option INTEL:HSW/BDW (#1645) 16c9287 bug fixes for radar_rf_opt=2 (#1642) a82ce24 Sync with NoahMP Github version with all NoahMP updates since v4.3 (#1641) 7b642cc Bug fix for TAMDAR T VarBC (#1632) 92fd706 fix WRFDA build for Parallel netcdf-4 IO (#1634) ``` Problem: With PR #1552 "Parallel netcdf-4 IO option" (SHA1 3cd4713), when then code was built without the new parallel NetCDF4 compression, the build log had an `Error`. ``` > grep Error compile.log Fatal Error: Cannot open module file ‘wrf_data_ncpar.mod’ for reading at (1): No such file or directory make[2]: [diffwrf] Error 1 (ignored) make[2]: [diffwrf] Error 1 (ignored) wrf_io.f:117: Error: Can't open included file 'mpif.h' make[2]: [wrf_io.o] Error 1 (ignored) Fatal Error: Cannot open module file ‘wrf_data_ncpar.mod’ for reading at (1): No such file or directory make[2]: [field_routines.o] Error 1 (ignored) make[2]: [libwrfio_nfpar.a] Error 127 (ignored) make[2]: [libwrfio_nfpar.a] Error 1 (ignored) ``` The problem was related to constructing the object files in the io_netcdfpar directory. When the option is not selected at compile time, then we do not care about errors in the directory that will never be used. Solution: If the NETCDFPAR option is not selected at compile time, then SKIP going into the io_netcdfpar directory all together. LIST OF MODIFIED FILES: m Makefile m arch/Config.pl m arch/configure.defaults m configure TESTS CONDUCTED: 1. Without the NETCDFPAR parameter set, the build for the io_netcdfpar directory is bypassed: ``` cd ../io_netcdfpar ; \ echo SKIPPING make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.7.3/gnu/9.1.0" \ cd ../io_netcdfpar ; \ echo SKIPPING make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.7.3/gnu/9.1.0" \ ``` 2. When the NETCDFPAR env variable is set, the build includes the io_netcdfpar directory: cd ../io_netcdfpar ; \ make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.8.0/gnu/9.1.0" \ cd ../io_netcdfpar ; \ make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.8.0/gnu/9.1.0" \ ``` 3. Jenkins tests are all PASS.

Fix a memory problem in Noah LSM after PR#[1641](#1641) TYPE: bug fix KEYWORDS: memory issue, Noah LSM, WRF-Hydro SOURCE: internal DESCRIPTION OF CHANGES: Problem: After PR#1641 merge, which consisted modification and additions to NoahMP, problems showed up in the model when Noah LSM is used. Errors include random failures when running with a relatively large domain (581x501x56 in one test) and nests, and when model is trying to write output. Solution: Using 'configure -D' with gfortran identified the failure in module_sf_noahdrv.F. Examination of the routine suggests the code related to WRF-Hydro implementation could be an issue when WRF-Hydro is not used. Revision is made to the driver so that variables related to WRF-Hydro are properly defined when WRF-Hydro is not used or arrays are not defined. LIST OF MODIFIED FILES: M phys/module_sf_noahdrv.F M phys/module_surface_driver.F TESTS CONDUCTED: 1. Previously failed large domain and nest tests are working now. 2. The Jenkins tests are all passing.

…l#1671) Fix a memory problem in Noah LSM after PR#[1641](wrf-model#1641) TYPE: bug fix KEYWORDS: memory issue, Noah LSM, WRF-Hydro SOURCE: internal DESCRIPTION OF CHANGES: Problem: After PR#1641 merge, which consisted modification and additions to NoahMP, problems showed up in the model when Noah LSM is used. Errors include random failures when running with a relatively large domain (581x501x56 in one test) and nests, and when model is trying to write output. Solution: Using 'configure -D' with gfortran identified the failure in module_sf_noahdrv.F. Examination of the routine suggests the code related to WRF-Hydro implementation could be an issue when WRF-Hydro is not used. Revision is made to the driver so that variables related to WRF-Hydro are properly defined when WRF-Hydro is not used or arrays are not defined. LIST OF MODIFIED FILES: M phys/module_sf_noahdrv.F M phys/module_surface_driver.F TESTS CONDUCTED: 1. Previously failed large domain and nest tests are working now. 2. The Jenkins tests are all passing.

…rf-model#1641) TYPE: new feature KEYWORDS: NoahMP SOURCE: Cenlin He (NCAR) DESCRIPTION OF CHANGES: This is step one to synchronize with latest NoahMP Github code version in order to prepare for connecting WRF directly to NoahMP unified Github repo. Specifically, the updates in NoahMP since version 4.3: 1. three additional runoff schemes added (OPT_RUN=6, 7, 8) 2. new tile drainage capability/scheme added (OPT_TDRN) 3. New soil time step control capability added to allow users specify a different soil time step from main NoahMP time step 4. additional water and energy budget terms added for output and diagnosis 5. updated flood irrigation parameters 6. add constraints for snow thickness during compaction 7. updated snow viscosity coefficient in compaction process 8. add canopy heat storage in canopy temperature calculation 9. updated formulation and parameter values for TOPMODEL groundwater scheme (OPT_RUN=1) 10. Bug fixes: SWE cap value in initialization, NoahMP snow depth update, snow layer index update, floating issues in runoff scheme, and BATS albedo scheme LIST OF MODIFIED FILES: list of changed files (use `git diff --name-status master` to get formatted list) M Registry/Registry.EM_COMMON M Registry/registry.noahmp M dyn_em/module_first_rk_step_part1.F M dyn_em/start_em.F M phys/module_diag_misc.F M phys/module_diagnostics_driver.F M phys/module_physics_init.F M phys/module_sf_noahmp_glacier.F M phys/module_sf_noahmp_groundwater.F M phys/module_sf_noahmpdrv.F M phys/module_sf_noahmplsm.F M phys/module_surface_driver.F M run/MPTABLE.TBL M run/README.namelist M run/SOILPARM.TBL TESTS CONDUCTED: 1. successfully compiled and tested for running in NCAR supercomputer by Cenlin He (NCAR) 2. Jenkins tests are all pass. RELEASE NOTE: Updates from NoahMP and linking WRF directly to NoahMP Github repo.

TYPE: bug fix KEYWORDS: netcdfpar, Error SOURCE: internal DESCRIPTION OF CHANGES: IMPORTANT: Without these mods, every commit since the parallel netcdf4 IO mods will fail the DA build test in the regression test. For example, at least these commits: ``` fed10f4 Adding the WRF-Solar EPS model (wrf-model#1547) 0bda5e0 Fix 4dvar build failure after commit 8b5bfe5 (wrf-model#1652) 8b5bfe5 Thompson AA enhancements: BC aerosol, biomass burning emissions, and … (wrf-model#1616) 9dc68ca After testing with UFS/GFS/FV-3, some tuning knob changes to Thompson-MP and icloud3 (cloud fraction) scheme (wrf-model#1626) 96fd889 Update HONO, TERP, and CO2 emissions (wrf-model#1644) 64fb190 SFCLAY=1, add shallow water roughness calculation (wrf-model#1543) 609c2fc New module firebrand_spotting for WRF-Fire (wrf-model#1540) 75bfe6d MYNN PBL clouds in photolysis option 4 (TUV) (wrf-model#1622) f8c4b13 Fix runtime error when using sf_surface_mosaic = 1 with use_wudapt_lcz = 0 (wrf-model#1638) b511c70 Run-time option for climate GHG for radiation (wrf-model#1625) 8194c66 Bug fix for configuration option INTEL:HSW/BDW (wrf-model#1645) 16c9287 bug fixes for radar_rf_opt=2 (wrf-model#1642) a82ce24 Sync with NoahMP Github version with all NoahMP updates since v4.3 (wrf-model#1641) 7b642cc Bug fix for TAMDAR T VarBC (wrf-model#1632) 92fd706 fix WRFDA build for Parallel netcdf-4 IO (wrf-model#1634) ``` Problem: With PR wrf-model#1552 "Parallel netcdf-4 IO option" (SHA1 3cd4713), when then code was built without the new parallel NetCDF4 compression, the build log had an `Error`. ``` > grep Error compile.log Fatal Error: Cannot open module file ‘wrf_data_ncpar.mod’ for reading at (1): No such file or directory make[2]: [diffwrf] Error 1 (ignored) make[2]: [diffwrf] Error 1 (ignored) wrf_io.f:117: Error: Can't open included file 'mpif.h' make[2]: [wrf_io.o] Error 1 (ignored) Fatal Error: Cannot open module file ‘wrf_data_ncpar.mod’ for reading at (1): No such file or directory make[2]: [field_routines.o] Error 1 (ignored) make[2]: [libwrfio_nfpar.a] Error 127 (ignored) make[2]: [libwrfio_nfpar.a] Error 1 (ignored) ``` The problem was related to constructing the object files in the io_netcdfpar directory. When the option is not selected at compile time, then we do not care about errors in the directory that will never be used. Solution: If the NETCDFPAR option is not selected at compile time, then SKIP going into the io_netcdfpar directory all together. LIST OF MODIFIED FILES: m Makefile m arch/Config.pl m arch/configure.defaults m configure TESTS CONDUCTED: 1. Without the NETCDFPAR parameter set, the build for the io_netcdfpar directory is bypassed: ``` cd ../io_netcdfpar ; \ echo SKIPPING make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.7.3/gnu/9.1.0" \ cd ../io_netcdfpar ; \ echo SKIPPING make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.7.3/gnu/9.1.0" \ ``` 2. When the NETCDFPAR env variable is set, the build includes the io_netcdfpar directory: cd ../io_netcdfpar ; \ make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.8.0/gnu/9.1.0" \ cd ../io_netcdfpar ; \ make -i -r NETCDFPARPATH="/glade/u/apps/ch/opt/netcdf/4.8.0/gnu/9.1.0" \ ``` 3. Jenkins tests are all PASS.

…l#1671) Fix a memory problem in Noah LSM after PR#[1641](wrf-model#1641) TYPE: bug fix KEYWORDS: memory issue, Noah LSM, WRF-Hydro SOURCE: internal DESCRIPTION OF CHANGES: Problem: After PR#1641 merge, which consisted modification and additions to NoahMP, problems showed up in the model when Noah LSM is used. Errors include random failures when running with a relatively large domain (581x501x56 in one test) and nests, and when model is trying to write output. Solution: Using 'configure -D' with gfortran identified the failure in module_sf_noahdrv.F. Examination of the routine suggests the code related to WRF-Hydro implementation could be an issue when WRF-Hydro is not used. Revision is made to the driver so that variables related to WRF-Hydro are properly defined when WRF-Hydro is not used or arrays are not defined. LIST OF MODIFIED FILES: M phys/module_sf_noahdrv.F M phys/module_surface_driver.F TESTS CONDUCTED: 1. Previously failed large domain and nest tests are working now. 2. The Jenkins tests are all passing.

cenlinhe added 9 commits December 17, 2020 12:06

Merge pull request #1 from wrf-model/develop

45d1380

Synchronize the develop branch from official WRF GitHub

Merge pull request #2 from wrf-model/develop

c8d86d3

sync up develop branch

Merge branch 'wrf-model:develop' into develop

3d62e5e

Merge branch 'wrf-model:develop' into develop

08e71b9

all noahmp-related file updates since WRFv4.3 release

fcb9faa

modify WRF-related driver & registry to work with updated NoahMP code

ca2e1d6

update NOAHMP_INIT in phy_init & start_em

0ca37ba

add additional NoahMP water & energy budget output & soil timestep co…

452d3c7

…ntrol

bug fix for water balance check

569ca50

cenlinhe requested review from a team as code owners January 13, 2022 03:47

bug fix for inout variable

70defeb

weiwangncar reviewed Jan 13, 2022

View reviewed changes

edit namelist readme & bug

a31fe47

davegill requested review from dudhia and weiwangncar January 15, 2022 01:51

davegill added PHYSICS Enhancement Develop Branch labels Jan 15, 2022

weiwangncar approved these changes Jan 15, 2022

View reviewed changes

davegill self-requested a review January 17, 2022 16:27

davegill approved these changes Jan 17, 2022

View reviewed changes

davegill merged commit a82ce24 into wrf-model:develop Jan 17, 2022

davegill mentioned this pull request Jan 24, 2022

NoahMP as a submodule in WRF #1646

Closed

weiwangncar mentioned this pull request Feb 9, 2022

Fix a invalid memory reference error identified by gfortran #1668

Closed

weiwangncar mentioned this pull request Feb 10, 2022

Fix a invalid memory reference error identified by gfortran #1671

Merged

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Sync with NoahMP Github version with all NoahMP updates since v4.3 #1641

Sync with NoahMP Github version with all NoahMP updates since v4.3 #1641

cenlinhe commented Jan 13, 2022 •

edited by davegill

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cenlinhe commented Jan 13, 2022

weiwangncar Jan 13, 2022

cenlinhe commented Jan 13, 2022

davegill commented Jan 15, 2022

dudhia commented Jan 17, 2022

Sync with NoahMP Github version with all NoahMP updates since v4.3 #1641

Sync with NoahMP Github version with all NoahMP updates since v4.3 #1641

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cenlinhe commented Jan 13, 2022 • edited by davegill Loading

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dudhia commented Jan 17, 2022

cenlinhe commented Jan 13, 2022 •

edited by davegill

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