Merge remote-tracking branch 'origin/develop' into fix_qr_tests

ufs-community · Aug 29, 2023 · 3137bb9 · 3137bb9
2 parents ff6dbe8 + 03fad6f
commit 3137bb9
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Showing 113 changed files with 9,453 additions and 13,238 deletions.
diff --git a/CMEPS-interface/CMEPS b/CMEPS-interface/CMEPS
diff --git a/CMEPS-interface/CMakeLists.txt b/CMEPS-interface/CMakeLists.txt
@@ -31,6 +31,8 @@ list(APPEND _nems_util_files
   CMEPS/ufs/ufs_kind_mod.F90
   CMEPS/ufs/perf_mod.F90
   CMEPS/ufs/ufs_const_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_orb_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_const_mod.F90
   ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_abort_mod.F90
   ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_strconvert_mod.F90
   ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_log_mod.F90

diff --git a/GOCART b/GOCART
diff --git a/HYCOM-interface/HYCOM b/HYCOM-interface/HYCOM
diff --git a/MOM6-interface/MOM6 b/MOM6-interface/MOM6
diff --git a/MOM6-interface/mom6_files.cmake b/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

diff --git a/modulefiles/ufs_acorn.intel.lua b/modulefiles/ufs_acorn.intel.lua
@@ -2,30 +2,20 @@ help([[
 Load environment to build UFS on Acorn with Intel compiler
 ]])
 
-PrgEnv_intel_ver=os.getenv("PrgEnv_intel_ver") or "8.1.0"
-load(pathJoin("PrgEnv-intel", PrgEnv_intel_ver))
+prepend_path("MODULEPATH", "/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.4.1/envs/ufs-pio-2.5.10/install/modulefiles/Core")
 
-intel_ver=os.getenv("intel_ver") or "19.1.3.304"
-load(pathJoin("intel", intel_ver))
+load("stack-intel")
+load("stack-cray-mpich")
+load("stack-python")
 
-craype_ver=os.getenv("craype_ver") or "2.7.13"
-load(pathJoin("craype", craype_ver))
-
-cray_mpich_ver=os.getenv("cray_mpich_ver") or "8.1.9"
-load(pathJoin("cray-mpich", cray_mpich_ver))
-
-cmake_ver=os.getenv("cmake_ver") or "3.20.2"
-load(pathJoin("cmake", cmake_ver))
-
-prepend_path("MODULEPATH", "/lfs/h1/emc/nceplibs/noscrub/hpc-stack/libs/hpc-stack/modulefiles/stack")
-
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-hpc_intel_ver=os.getenv("hpc_intel_ver") or "19.1.3.304"
-hpc_cray_mpich_ver=os.getenv("hpc_cray_mpich_ver") or "8.1.9"
-load(pathJoin("hpc", hpc_ver))
-load(pathJoin("hpc-intel", hpc_intel_ver))
-load(pathJoin("hpc-cray-mpich", hpc_cray_mpich_ver))
+--Avoid production installations; use spack-stack only:
+remove_path("MODULEPATH", "/apps/ops/prod/libs/modulefiles/compiler/intel/19.1.3.304")
+remove_path("MODULEPATH", "/apps/ops/prod/libs/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.4")
+remove_path("MODULEPATH", "/apps/ops/prod/libs/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.7")
+remove_path("MODULEPATH", "/apps/prod/lmodules/intel/19.1.3.304")
+remove_path("MODULEPATH", "/apps/prod/lmodules/INTEL_cray_mpich/19.1.3.304/cray-mpich/8.1.4")
 
+load("cmake")
 load("ufs_common")
 
 prepend_path("MODULEPATH", "/lfs/h1/emc/nceplibs/noscrub/UPP_IFI/modulefiles")

diff --git a/modulefiles/ufs_cheyenne.gnu.lua b/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))
@@ -33,10 +33,24 @@ load(pathJoin("hpc-gnu", hpc_gnu_ver))
 hpc_mpt_ver=os.getenv("hpc_mpt_ver") or "2.25"
 load(pathJoin("hpc-mpt", hpc_mpt_ver))
 
-scotch_ver=os.getenv("scotch_ver") or "7.0.3"
-load(pathJoin("scotch", scotch_ver))
+load("jasper/2.0.25")
+load("zlib/1.2.11")
+load("hdf5/1.14.0")
+load("netcdf/4.9.2")
+load("pio/2.5.10")
+load("esmf/8.4.2")
+load("fms/2023.01")
+load("bacio/2.4.1")
+load("crtm/2.4.0")
+load("g2/3.4.5")
+load("g2tmpl/1.10.2")
+load("ip/3.3.3")
+load("sp/2.3.3")
+load("w3emc/2.9.2")
+load("gftl-shared/v1.5.0")
+load("mapl/2.35.2-esmf-8.4.2")
+load("scotch/7.0.3")
 
-load("ufs_common")
 
 setenv("CC", "mpicc")
 setenv("CXX", "mpicxx")

diff --git a/modulefiles/ufs_cheyenne.intel.lua b/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))
@@ -34,10 +34,24 @@ load(pathJoin("hpc-intel", hpc_intel_ver))
 hpc_mpt_ver=os.getenv("hpc_mpt_ver") or "2.25"
 load(pathJoin("hpc-mpt", hpc_mpt_ver))
 
-scotch_ver=os.getenv("scotch_ver") or "7.0.3"
-load(pathJoin("scotch", scotch_ver))
+load("jasper/2.0.25")
+load("zlib/1.2.11")
+load("hdf5/1.14.0")
+load("netcdf/4.9.2")
+load("pio/2.5.10")
+load("esmf/8.4.2")
+load("fms/2023.01")
+load("bacio/2.4.1")
+load("crtm/2.4.0")
+load("g2/3.4.5")
+load("g2tmpl/1.10.2")
+load("ip/3.3.3")
+load("sp/2.3.3")
+load("w3emc/2.9.2")
+load("gftl-shared/v1.5.0")
+load("mapl/2.35.2-esmf-8.4.2")
+load("scotch/7.0.3")
 
-load("ufs_common")
 
 setenv("CC", "mpicc")
 setenv("CXX", "mpicxx")

diff --git a/modulefiles/ufs_common.lua b/modulefiles/ufs_common.lua
@@ -3,23 +3,25 @@ whatis("Description: UFS build environment common libraries")
 help([[Load UFS Model common libraries]])
 
 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"},
-  {["bacio"]       = "2.4.1"},
-  {["crtm"]        = "2.4.0"},
-  {["g2"]          = "3.4.5"},
-  {["g2tmpl"]      = "1.10.2"},
-  {["ip"]          = "3.3.3"},
-  {["sp"]          = "2.3.3"},
-  {["w3emc"]       = "2.9.2"},
-  {["gftl-shared"] = "v1.5.0"},
-  {["mapl"]        = "2.22.0-esmf-8.3.0b09"},
+  {["jasper"]          = "2.0.32"},
+  {["zlib"]            = "1.2.13"},
+  {["libpng"]          = "1.6.37"},
+  {["hdf5"]            = "1.14.0"},
+  {["netcdf-c"]        = "4.9.2"},
+  {["netcdf-fortran"]  = "4.6.0"},
+  {["parallelio"]      = "2.5.10"},
+  {["esmf"]            = "8.4.2"},
+  {["fms"]             = "2023.01"},
+  {["bacio"]           = "2.4.1"},
+  {["crtm"]            = "2.4.0"},
+  {["g2"]              = "3.4.5"},
+  {["g2tmpl"]          = "1.10.2"},
+  {["ip"]              = "3.3.3"},
+  {["sp"]              = "2.3.3"},
+  {["w3emc"]           = "2.9.2"},
+  {["gftl-shared"]     = "1.5.0"},
+  {["mapl"]            = "2.35.2-esmf-8.4.2"},
+  {["scotch"]          = "7.0.3"},
 }
 
 for i = 1, #ufs_modules do

diff --git a/modulefiles/ufs_common_spack.lua b/modulefiles/ufs_common_spack.lua
diff --git a/modulefiles/ufs_gaea.intel.lua b/modulefiles/ufs_gaea.intel.lua
@@ -5,23 +5,32 @@ help([[
 
 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")
+unload("intel")
+unload("cray-mpich")
+unload("cray-python")
+unload("darshan")
 
-prepend_path("MODULEPATH","/lustre/f2/dev/role.epic/contrib/hpc-stack/intel-classic-2022.0.2/modulefiles/stack")
-load(pathJoin("hpc", os.getenv("hpc_ver") or "1.2.0"))
+prepend_path("MODULEPATH", "/lustre/f2/dev/wpo/role.epic/contrib/spack-stack/spack-stack-1.4.1-c4/envs/ufs-pio-2.5.10/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/lustre/f2/pdata/esrl/gsd/spack-stack/modulefiles")
 
-load(pathJoin("intel-classic", os.getenv("intel_classic_ver") or "2022.0.2"))
-load(pathJoin("cray-mpich", os.getenv("cray_mpich_ver") or "7.7.20"))
-load(pathJoin("hpc-intel-classic", os.getenv("hpc_intel_classic_ver") or "2022.0.2"))
-load(pathJoin("hpc-cray-mpich", os.getenv("hpc_cray_mpich_ver") or "7.7.20"))
-load(pathJoin("libpng", os.getenv("libpng_ver") or "1.6.37"))
+stack_intel_ver=os.getenv("stack_intel_ver") or "2022.0.2"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_cray_mpich_ver=os.getenv("stack_cray_mpich_ver") or "7.7.20"
+load(pathJoin("stack-cray-mpich", stack_cray_mpich_ver))
+
+stack_python_ver=os.getenv("stack_python_ver") or "3.9.12"
+load(pathJoin("stack-python", stack_python_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
 
 -- Needed at runtime:
 load("alps")
 
 load("ufs_common")
 
 setenv("CC","cc")
-setenv("FC","ftn")
 setenv("CXX","CC")
+setenv("FC","ftn")
 setenv("CMAKE_Platform","gaea.intel")
diff --git a/modulefiles/ufs_hera.gnu.lua b/modulefiles/ufs_hera.gnu.lua
@@ -2,33 +2,25 @@ help([[
 loads UFS Model prerequisites for Hera/GNU
 ]])
 
-prepend_path("MODULEPATH", "/contrib/sutils/modulefiles")
-load("sutils")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.4.1/envs/ufs-pio-2.5.10/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
 
-cmake_ver=os.getenv("cmake_ver") or "3.20.1"
-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")
+stack_gnu_ver=os.getenv("stack_gnu_ver") or "9.2.0"
+load(pathJoin("stack-gcc", stack_gnu_ver))
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_openmpi_ver=os.getenv("stack_openmpi_ver") or "4.1.5"
+load(pathJoin("stack-openmpi", stack_openmpi_ver))
 
-hpc_gnu_ver=os.getenv("hpc_gnu_ver") or "9.2"
-load(pathJoin("hpc-gnu", hpc_gnu_ver))
+stack_python_ver=os.getenv("stack_python_ver") or "3.9.12"
+load(pathJoin("stack-python", stack_python_ver))
 
-hpc_mpich_ver=os.getenv("hpc_mpich_ver") or "3.3.2"
-load(pathJoin("hpc-mpich", hpc_mpich_ver))
-
-scotch_ver=os.getenv("scotch_ver") or "7.0.3"
-load(pathJoin("scotch", scotch_ver))
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
 setenv("CC", "mpicc")
-setenv("CXX", "mpicxx")
+setenv("CXX", "mpic++")
 setenv("FC", "mpif90")
 setenv("CMAKE_Platform", "hera.gnu")