Merge pull request #107 from grantfirl/ufs-dev-PR69

UFS-dev PR#69

.github/pull_request_template.md

@@ -1,20 +1,32 @@
+<!-- THE FOLLOWING IS FOR THE PR AUTHOR TO FILL OUT
+PLEASE DO NOT MODIFY THE TEMPLATE BEYOND FILLING OUT THE PROPER SECTIONS -->
+## PR Author Checklist:
+<!--  Please complete all items in list. -->
+- [ ] I have linked PR's from all sub-components involved in section below. <!-- PLEASE DO NOT LINK SUBCOMPONENT ISSUES -->
+- [ ] I am confirming reviews are completed in ALL sub-component PR's.
+- [ ] I have run the full RT suite on either Hera/Cheyenne AND have attached the log to this PR below this line:
+  - LOG: 
+- [ ] I have added the list of all failed regression tests to "Anticipated changes" section.
+- [ ] I have filled out all sections of the template.
+
 ## Description
-<!--
-Provide a detailed description of what this PR does. What bug does it fix, or what feature does it add? Is a change of answers expected from this PR? Are any library updates included in this PR (modulefiles etc.)?
--->
+<!-- Provide a detailed description of what this PR does in the space provided below-->
 
-### Input data additions/changes
-- [ ] No changes are expected to input data.
-- [ ] Changes are expected to input data:
-  - [ ] New input data.
-  - [ ] Updated input data.
 
-### Anticipated changes to regression tests:
-- [ ] No changes are expected to any regression test.
-- [ ] Changes are expected to the following tests:
-<!-- Please insert what RT's change and why you expect them to change -->
+## Linked Issues and Pull Requests
+### Associated UFSWM Issue to close
+<!-- Example: "- Closes #1698" -->
 
-## Subcomponents involved:
+
+### Subcomponent Pull Requests
+<!-- format: - <community>/<repo>/pull/<PR number> i.e.: - NOAA-EMC/fv3atm/pull/33 or "None" -->
+
+
+### Blocking Dependencies
+<!-- Example: "- Depends on #1733" or "None" -->
+
+
+### Subcomponents involved:
 - [ ] AQM
 - [ ] CDEPS
 - [ ] CICE
@@ -29,44 +41,38 @@ Provide a detailed description of what this PR does. What bug does it fix, or wh
 - [ ] stochastic_physics
 - [ ] none
 
-### Library Updates/Changes
+## Anticipated Changes
+### Input data
+- [ ] No changes are expected to input data.
+- [ ] Changes are expected to input data:
+  - [ ] New input data.
+  - [ ] Updated input data.
+
+### Regression Tests:
+- [ ] No changes are expected to any regression test.
+- [ ] Changes are expected to the following tests:
+<!-- Please insert what RT's change and why you expect them to change in the space provided below -->
+<details><summary>Tests effected by changes in this PR:</summary>
+<!-- ADD ITEMS HERE or add "None" -->
+
+</details>
+
+### Libraries
 <!-- Library updates take time. If this PR needs updates to libraries, please make sure to accomplish the following tasks -->
 - [ ] Not Needed
-- [ ] Create separate issue in [JCSDA/spack-stack](https://github.com/JCSDA/spack-stack) asking for update to library. Include library name, library version.
-- [ ] Add issue link from JCSDA/spack-stack following this item
-<!-- for example: "- JCSDA/spack-stack/issue/1757" -->
-
-### Combined with PR's (If Applicable):
-
-## Commit Queue Checklist:
-<!-- 
-Please complete all items in list. Make sure to attach logs from RT testing in comment, not in repository. Once all boxes are checked, please add the label "Ready for Commit Queue".
--->
-- [ ] Link PR's from all sub-components involved in section below
-- [ ] Confirm reviews completed in ALL sub-component PR's
-- [ ] Add all appropriate labels to this PR.
-- [ ] Run full RT suite on either Hera/Cheyenne AND attach log to a PR comment.
-- [ ] Add list of any failed regression tests to "Anticipated changes to regression tests" section.
-
-## Linked PR's and Issues:
-<!--
-Please link dependent pull requests.
-EXAMPLE: "- Depends on NOAA-EMC/fv3atm/pull/<pullrequest_number>"
-
-Please link the related issues to be closed with this PR, whether in this repository, or in another repository.
-EXAMPLE: "- Closes NOAA-EMC/fv3atm/issues/<issue_number>"
-
-PLEASE MAKE SURE TO USE THE - with a space before the "Depends on" or "Closes" as they show up well on github.
--->
-
-## Testing Day Checklist:
-<!--
-Please consult the ufs-weather-model [wiki](https://github.com/ufs-community/ufs-weather-model/wiki/Making-code-changes-in-the-UFS-weather-model-and-its-subcomponents) if you are unsure how to do this.
--->
+- [ ] Needed
+  - [ ] Create separate issue in [JCSDA/spack-stack](https://github.com/JCSDA/spack-stack) asking for update to library. Include library name, library version.
+  - [ ] Add issue link from JCSDA/spack-stack following this item <!-- for example: "- JCSDA/spack-stack/issue/1757" -->
+
+
+<!-- THE FOLLOWING IS FOR CODE MANAGERS ONLY DO NOT FILL OUT -->
+<details><summary>Code Managers Log</summary>
+
 - [ ] This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR.
 - [ ] Move new/updated input data on RDHPCS Hera and propagate input data changes to all supported systems.
+  - [ ] N/A
 
-### Testing Log (for CM's):
+### Testing Log:
 - RDHPCS
   - [ ] Hera
   - [ ] Orion
@@ -81,3 +87,4 @@ Please consult the ufs-weather-model [wiki](https://github.com/ufs-community/ufs
 - opnReqTest
   - [ ] N/A
   - [ ] Log attached to comment
+</details>

MOM6-interface/mom6_files.cmake

@@ -58,15 +58,19 @@ list(APPEND mom6_src_files
   MOM6/src/diagnostics/MOM_obsolete_params.F90
   MOM6/src/diagnostics/MOM_sum_output.F90
   MOM6/src/diagnostics/MOM_wave_speed.F90
-  MOM6/src/diagnostics/MOM_wave_structure.F90
 
   MOM6/src/equation_of_state/MOM_EOS.F90
-  MOM6/src/equation_of_state/MOM_EOS_NEMO.F90
+  MOM6/src/equation_of_state/MOM_EOS_Jackett06.F90
+  MOM6/src/equation_of_state/MOM_EOS_Roquet_SpV.F90
+  MOM6/src/equation_of_state/MOM_EOS_Roquet_rho.F90
   MOM6/src/equation_of_state/MOM_EOS_TEOS10.F90
   MOM6/src/equation_of_state/MOM_EOS_UNESCO.F90
   MOM6/src/equation_of_state/MOM_EOS_Wright.F90
+  MOM6/src/equation_of_state/MOM_EOS_Wright_full.F90
+  MOM6/src/equation_of_state/MOM_EOS_Wright_red.F90
   MOM6/src/equation_of_state/MOM_EOS_linear.F90
   MOM6/src/equation_of_state/MOM_TFreeze.F90
+  MOM6/src/equation_of_state/MOM_temperature_convert.F90
 
   MOM6/src/equation_of_state/TEOS10/gsw_chem_potential_water_t_exact.f90
   MOM6/src/equation_of_state/TEOS10/gsw_ct_freezing_exact.f90
@@ -160,6 +164,7 @@ list(APPEND mom6_src_files
   MOM6/src/parameterizations/lateral/MOM_spherical_harmonics.F90
   MOM6/src/parameterizations/lateral/MOM_thickness_diffuse.F90
   MOM6/src/parameterizations/lateral/MOM_tidal_forcing.F90
+  MOM6/src/parameterizations/lateral/MOM_Zanna_Bolton.F90
 
   MOM6/src/parameterizations/vertical/MOM_ALE_sponge.F90
   MOM6/src/parameterizations/vertical/MOM_CVMix_KPP.F90

modulefiles/ufs_cheyenne.gnu.lua

@@ -22,7 +22,7 @@ load(pathJoin("ncarcompilers", ncarcompilers_ver))
 
 unload("netcdf")
 
-prepend_path("MODULEPATH", "/glade/work/epicufsrt/contrib/hpc-stack/gnu10.1.0/modulefiles/stack")
+prepend_path("MODULEPATH", "/glade/work/epicufsrt/contrib/hpc-stack/gnu10.1.0_ncdf492/modulefiles/stack")
 
 hpc_ver=os.getenv("hpc_ver") or "1.2.0"
 load(pathJoin("hpc", hpc_ver))

modulefiles/ufs_cheyenne.intel.lua

@@ -23,7 +23,7 @@ load(pathJoin("ncarcompilers", ncarcompilers_ver))
 
 unload("netcdf")
 
-prepend_path("MODULEPATH", "/glade/work/epicufsrt/contrib/hpc-stack/intel2022.1/modulefiles/stack")
+prepend_path("MODULEPATH", "/glade/work/epicufsrt/contrib/hpc-stack/intel2022.1_ncdf492/modulefiles/stack")
 
 hpc_ver=os.getenv("hpc_ver") or "1.2.0"
 load(pathJoin("hpc", hpc_ver))

modulefiles/ufs_common.lua

@@ -6,11 +6,11 @@ local ufs_modules = {
   {["jasper"]      = "2.0.25"},
   {["zlib"]        = "1.2.11"},
   {["libpng"]      = "1.6.37"},
-  {["hdf5"]        = "1.10.6"},
-  {["netcdf"]      = "4.7.4"},
-  {["pio"]         = "2.5.7"},
-  {["esmf"]        = "8.3.0b09"},
-  {["fms"]         = "2022.04"},
+  {["hdf5"]        = "1.14.0"},
+  {["netcdf"]      = "4.9.2"},
+  {["pio"]         = "2.5.10"},
+  {["esmf"]        = "8.4.2"},
+  {["fms"]         = "2023.01"},
   {["bacio"]       = "2.4.1"},
   {["crtm"]        = "2.4.0"},
   {["g2"]          = "3.4.5"},
@@ -19,7 +19,7 @@ local ufs_modules = {
   {["sp"]          = "2.3.3"},
   {["w3emc"]       = "2.9.2"},
   {["gftl-shared"] = "v1.5.0"},
-  {["mapl"]        = "2.22.0-esmf-8.3.0b09"},
+  {["mapl"]        = "2.35.2-esmf-8.4.2"},
 }
 
 for i = 1, #ufs_modules do

modulefiles/ufs_gaea.intel.lua

@@ -7,7 +7,7 @@ whatis([===[Loads libraries needed for building the UFS Weather Model on Gaea ]=
 
 load_any(pathJoin("cmake", os.getenv("cmake_ver") or "3.20.1"),"cmake")
 
-prepend_path("MODULEPATH","/lustre/f2/dev/role.epic/contrib/hpc-stack/intel-classic-2022.0.2/modulefiles/stack")
+prepend_path("MODULEPATH","/lustre/f2/dev/role.epic/contrib/hpc-stack/intel-classic-2022.0.2_ncdf492/modulefiles/stack")
 load(pathJoin("hpc", os.getenv("hpc_ver") or "1.2.0"))
 
 load(pathJoin("intel-classic", os.getenv("intel_classic_ver") or "2022.0.2"))

modulefiles/ufs_hera.gnu.lua

@@ -11,7 +11,7 @@ load(pathJoin("cmake", cmake_ver))
 gnu_ver=os.getenv("gnu_ver") or "9.2.0"
 load(pathJoin("gnu", gnu_ver))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-9.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-9.2_ncdf492/modulefiles/stack")
 
 hpc_ver=os.getenv("hpc_ver") or "1.2.0"
 load(pathJoin("hpc", hpc_ver))

modulefiles/ufs_hera.intel.lua

@@ -14,7 +14,7 @@ load(pathJoin("intel", intel_ver))
 impi_ver=os.getenv("impi_ver") or "2022.1.2"
 load(pathJoin("impi", impi_ver))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2_ncdf492/modulefiles/stack")
 
 hpc_ver=os.getenv("hpc_ver") or "1.2.0"
 load(pathJoin("hpc", hpc_ver))

modulefiles/ufs_jet.intel.lua

@@ -8,7 +8,7 @@ load("sutils")
 cmake_ver=os.getenv("cmake_ver") or "3.20.1"
 load(pathJoin("cmake", cmake_ver))
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/hpc-stack/libs/intel-2022.1.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/hpc-stack/libs/intel-2022.1.2_ncdf492/modulefiles/stack")
 
 hpc_ver=os.getenv("hpc_ver") or "1.2.0"
 load(pathJoin("hpc", hpc_ver))

modulefiles/ufs_orion.intel.lua

@@ -8,7 +8,7 @@ load("noaatools")
 cmake_ver=os.getenv("cmake_ver") or "3.22.1"
 load(pathJoin("cmake", cmake_ver))
 
-prepend_path("MODULEPATH", "/work/noaa/epic-ps/role-epic-ps/hpc-stack/libs/intel-2022.1.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/work/noaa/epic-ps/role-epic-ps/hpc-stack/libs/intel-2022.1.2_ncdf492/modulefiles/stack")
 
 hpc_ver=os.getenv("hpc_ver") or "1.2.0"
 load(pathJoin("hpc", hpc_ver))

modulefiles/ufs_wcoss2.intel.lua

@@ -12,71 +12,16 @@ load(pathJoin("intel", intel_ver))
 craype_ver=os.getenv("craype_ver") or "2.7.13"
 load(pathJoin("craype", craype_ver))
 
-cray_mpich_ver=os.getenv("cray_mpich_ver") or "8.1.7"
+cray_mpich_ver=os.getenv("cray_mpich_ver") or "8.1.12"
 load(pathJoin("cray-mpich", cray_mpich_ver))
 
 cmake_ver=os.getenv("cmake_ver") or "3.20.2"
 load(pathJoin("cmake", cmake_ver))
 
-jasper_ver=os.getenv("jasper_ver") or "2.0.25"
-load(pathJoin("jasper", jasper_ver))
+prepend_path("MODULEPATH", "/apps/test/hpc-stack/i-19.1.3.304__m-8.1.12__h-1.14.0__n-4.9.2__p-2.5.10__e-8.4.2/modulefiles/compiler/intel/19.1.3.304")
+prepend_path("MODULEPATH", "/apps/test/hpc-stack/i-19.1.3.304__m-8.1.12__h-1.14.0__n-4.9.2__p-2.5.10__e-8.4.2/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.12")
 
-zlib_ver=os.getenv("zlib_ver") or "1.2.11"
-load(pathJoin("zlib", zlib_ver))
-
-libpng_ver=os.getenv("libpng_ver") or "1.6.37"
-load(pathJoin("libpng", libpng_ver))
-
-hdf5_ver=os.getenv("hdf5_ver") or "1.10.6"
-load(pathJoin("hdf5", hdf5_ver))
-
-netcdf_ver=os.getenv("netcdf_ver") or "4.7.4"
-load(pathJoin("netcdf", netcdf_ver))
-
-fms_ver=os.getenv("fms_ver") or "2022.04"
-load(pathJoin("fms", fms_ver))
-
-bacio_ver=os.getenv("bacio_ver") or "2.4.1"
-load(pathJoin("bacio", bacio_ver))
-
-crtm_ver=os.getenv("crtm_ver") or "2.4.0"
-load(pathJoin("crtm", crtm_ver))
-
-g2_ver=os.getenv("g2_ver") or "3.4.5"
-load(pathJoin("g2", g2_ver))
-
-g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
-load(pathJoin("g2tmpl", g2tmpl_ver))
-
-ip_ver=os.getenv("ip_ver") or "3.3.3"
-load(pathJoin("ip", ip_ver))
-
-sp_ver=os.getenv("sp_ver") or "2.3.3"
-load(pathJoin("sp", sp_ver))
-
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
-load(pathJoin("w3emc", w3emc_ver))
-
--- Second, look for libraries in "para"
-setenv("HPC_OPT", "/apps/ops/para/libs")
-prepend_path("MODULEPATH", "/apps/ops/para/libs/modulefiles/compiler/intel/19.1.3.304")
-prepend_path("MODULEPATH", "/apps/ops/para/libs/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.7")
-
-pio_ver=os.getenv("pio_ver") or "2.5.7"
-load(pathJoin("pio", pio_ver))
-
--- Finally, look for libraries in "dev" space
-prepend_path("MODULEPATH", "/apps/dev/lmodules/intel/19.1.3.304")
-prepend_path("MODULEPATH", "/apps/dev/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.9")
-
-gftl_shared_ver=os.getenv("gftl_shared_ver") or "1.5.0"
-load(pathJoin("gftl_shared", gftl_shared_ver))
-
-esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
-load(pathJoin("esmf", esmf_ver))
-
-mapl_ver=os.getenv("mapl_ver") or "2.23.1-esmf-8.3.0b09"
-load(pathJoin("mapl", mapl_ver))
+load("ufs_common")
 
 setenv("CC", "cc")
 setenv("CXX", "CC")

tests/auto-jenkins/jobs/bl.py

@@ -20,7 +20,7 @@ def set_directories(job_obj):
     logger = logging.getLogger('BL/SET_DIRECTORIES')
     if job_obj.machine == 'hera':
         workdir = '/scratch1/NCEPDEV/nems/emc.nemspara/autort/pr'
-        blstore = '/scratch1/NCEPDEV/nems/emc.nemspara/RT/NEMSfv3gfs'
+        blstore = '/scratch2/NAGAPE/epic/UFS-WM_RT/NEMSfv3gfs'
         rtbldir = '/scratch1/NCEPDEV/stmp4/emc.nemspara/FV3_RT/'\
                  f'REGRESSION_TEST'
     elif job_obj.machine == 'jet':

tests/bl_date.conf

@@ -1,2 +1,2 @@
-export BL_DATE=20230720
+export BL_DATE=20230816
 

tests/bl_date.ncar.conf

@@ -1,2 +1,2 @@
-export BL_DATE=20231031
+export BL_DATE=20240110
 

tests/ci/Dockerfile

@@ -1,4 +1,4 @@
-From noaaepic/ubuntu20.04-gnu9.3-hpc-stack:v1.2
+From noaaepic/ubuntu20.04-gnu9.3-hpc-stack:v2.0
 
 CMD ["/bin/bash"]