Merge branch 'develop' into prod2dev

ufs-community · Jun 3, 2024 · ced5e01 · ced5e01
2 parents 486c056 + 5bec704
commit ced5e01
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Showing 46 changed files with 3,277 additions and 2,855 deletions.
diff --git a/CICE-interface/CICE b/CICE-interface/CICE
diff --git a/CMEPS-interface/CMEPS b/CMEPS-interface/CMEPS
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -73,6 +73,7 @@ set(JEDI_DRIVER OFF CACHE BOOL "Enable JEDI as top level driver")
 set(CMEPS_AOFLUX OFF CACHE BOOL "Enable atmosphere-ocean flux calculation in mediator")
 set(PDLIB OFF CACHE BOOL "Enable Domain Decomposition in WW3 via PDLIB")
 set(CDEPS_INLINE OFF CACHE BOOL "Enable CDEPS inline capability")
+set(HYDRO OFF CACHE BOOL "Enable hydrostatic set")
 
 set(CMAKE_Platform $ENV{CMAKE_Platform})
 if(CMAKE_Platform)
@@ -122,6 +123,7 @@ message("PARALLEL_NETCDF .. ${PARALLEL_NETCDF}")
 message("JEDI_DRIVER ...... ${JEDI_DRIVER}")
 message("CMEPS_AOFLUX ..... ${CMEPS_AOFLUX}")
 message("CDEPS_INLINE ..... ${CDEPS_INLINE}")
+message("HYDRO ........... ${HYDRO}")
 
 message("")
 

diff --git a/FV3 b/FV3
diff --git a/MOM6-interface/MOM6 b/MOM6-interface/MOM6
diff --git a/NOAHMP-interface/CMakeLists.txt b/NOAHMP-interface/CMakeLists.txt
@@ -56,8 +56,10 @@ endif()
 
 #------------------------------------------------------------------------------
 # Add model-specific flags for C/C++/Fortran preprocessor
-add_definitions(-DMOIST_CAPPA -DUSE_COND -DNEMS_GSM)
-add_definitions(-DINTERNAL_FILE_NML)
+if (NOT HYDRO)
+add_definitions(-DMOIST_CAPPA -DUSE_COND)
+endif()
+add_definitions(-DINTERNAL_FILE_NML -DNEMS_GSM)
 
 #------------------------------------------------------------------------------
 # NOAHMP

diff --git a/NOAHMP-interface/noahmp b/NOAHMP-interface/noahmp
diff --git a/doc/UsersGuide/requirements.txt b/doc/UsersGuide/requirements.txt
@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
 # pip-compile requirements.in
@@ -12,6 +12,8 @@ certifi==2024.2.2
  # via requests
 charset-normalizer==3.3.2
  # via requests
+colorama==0.4.6
+ # via sphinx
 docutils==0.20.1
  # via
  # pybtex-docutils
@@ -22,10 +24,6 @@ idna==3.7
  # via requests
 imagesize==1.4.1
  # via sphinx
-importlib-metadata==7.0.1
- # via
- # sphinx
- # sphinxcontrib-bibtex
 jinja2==3.1.4
  # via sphinx
 latexcodec==2.0.1
@@ -44,7 +42,7 @@ pygments==2.17.2
  # via sphinx
 pyyaml==6.0.1
  # via pybtex
-requests==2.31.0
+requests==2.32.0
  # via sphinx
 six==1.16.0
  # via
@@ -78,5 +76,3 @@ sphinxcontrib-serializinghtml==1.1.10
  # via sphinx
 urllib3==2.2.1
  # via requests
-zipp==3.17.0
- # via importlib-metadata
diff --git a/doc/UsersGuide/source/BuildingAndRunning.rst b/doc/UsersGuide/source/BuildingAndRunning.rst
@@ -582,7 +582,9 @@ To run a single test, users can try the following command instead of creating a
 
 .. code-block:: console
 
- ./rt.sh -r -k -n control_p8
+ ./rt.sh -r -k -n "control_p8 <compiler>"
+
+where ``<compiler>`` is ``gnu`` or ``intel``. 
 
 Troubleshooting
 ^^^^^^^^^^^^^^^^^^

diff --git a/doc/UsersGuide/source/Glossary.rst b/doc/UsersGuide/source/Glossary.rst
@@ -68,7 +68,7 @@ Glossary
  Global atmospheric model based on fluid dynamics principles, including Euler's equations of motion.
 
  EMC
- The `Environmental Modeling Center <https://www.emc.ncep.noaa.gov/emc_new.php>`__ is one of :term:`NCEP`'s nine centers and leads the :term:`National Weather Service <NWS>`'s modeling efforts.
+ The `Environmental Modeling Center <https://www.emc.ncep.noaa.gov/emc.php>`_ is one of :term:`NCEP`'s nine centers and leads the :term:`National Weather Service <NWS>`'s modeling efforts.
 
  ESMF
  `Earth System Modeling Framework <https://earthsystemmodeling.org/docs/release/latest/ESMF_usrdoc/>`__. The ESMF defines itself as "a suite of software tools for developing high-performance, multi-component Earth science modeling applications." It is a community-developed software infrastructure for building and coupling models. 

diff --git a/modulefiles/ufs_wcoss2.intel.lua b/modulefiles/ufs_wcoss2.intel.lua
@@ -18,27 +18,28 @@ 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", "/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")
+append_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-8.6.0_pnetcdf/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.12")
 
 local ufs_modules = {
- {["jasper"] = "2.0.25"},
- {["zlib"] = "1.2.11"},
- {["libpng"] = "1.6.37"},
- {["hdf5-B"] = "1.14.0"},
- {["netcdf-B"] = "4.9.2"},
- {["pio-B"] = "2.5.10"},
- {["esmf-B"] = "8.5.0"},
- {["fms"] = "2023.02.01"},
- {["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"] = "1.6.1"},
- {["mapl-B"] = "2.40.3"},
+ {["jasper"] = "2.0.25"},
+ {["zlib"] = "1.2.11"},
+ {["libpng"] = "1.6.37"},
+ {["hdf5"] = "1.14.0"},
+ {["netcdf"] = "4.9.2"},
+ {["pio"] = "2.5.10"},
+ {["esmf"] = "8.6.0"},
+ {["fms"] = "2023.04"},
+ {["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"] = "1.6.1"},
+ {["mapl"] = "2.40.3-esmf-8.6.0"},
+ {["pnetcdf"] = "1.12.2"},
+ {["scotch"] = "7.0.4"},
 }
 
 for i = 1, #ufs_modules do
@@ -48,10 +49,6 @@ for i = 1, #ufs_modules do
  end
 end
 
-prepend_path("MODULEPATH", "/apps/prod/lmodules/INTEL_cray_mpich/19.1.3.304/cray-mpich/8.1.9")
-scotch_ver=os.getenv("scotch_ver") or "7.0.4"
-load(pathJoin("scotch",scotch_ver))
-
 setenv("CC", "cc")
 setenv("CXX", "CC")
 setenv("FC", "ftn")

diff --git a/stochastic_physics b/stochastic_physics
diff --git a/tests/bl_date.conf b/tests/bl_date.conf
@@ -1 +1 @@
-export BL_DATE=20240503
+export BL_DATE=20240530
diff --git a/tests/ci/Jenkinsfile.combined b/tests/ci/Jenkinsfile.combined
@@ -69,6 +69,10 @@ def generateStage(nodeLabel) {
  cd $WORKSPACE/tests/
  elif [[ $machine =~ "Orion" ]]
  then
+ cd ..
+ module load git/2.28.0
+ git submodule update --init --recursive
+ cd tests
  echo "Creating baselines on $machine"
  export dprefix=/work2/noaa/$ACCNR/$USER
  sed -i 's|/work/noaa/stmp/${USER}|/work/noaa/epic/stmp/role-epic/|g' rt.sh
@@ -214,6 +218,10 @@ def generateStage(nodeLabel) {
  elif [[ $machine =~ "Orion" ]]
  then
  echo "Running regression tests on $machine"
+ cd ..
+ module load git/2.28.0
+ git submodule update --init --recursive
+ cd tests
  export dprefix=/work2/noaa/$ACCNR/$USER
  sed "s|/noaa/stmp/|/noaa/$ACCNR/stmp/|g" -i rt.sh
  ./rt.sh -a ${ACCNR} -e -l rt.conf | tee $WORKSPACE/tests/logs/RT-run-$machine.log

diff --git a/tests/default_vars.sh b/tests/default_vars.sh
@@ -556,6 +556,14 @@ export EXTERNAL_IC=.true.
 export MAKE_NH=.true.
 export MOUNTAIN=.false.
 export NA_INIT=1
+export DO_VORT_DAMP=.true.
+export HYDROSTATIC=.false.
+export KORD_XX=9
+export KORD_TM=-9
+export D_CON=1.
+export HORD_XX=5
+export HORD_DP=-5
+export HORD_TR=8
 
 # Radiation
 export DO_RRTMGP=.false.
@@ -910,10 +918,6 @@ export_cice6() {
  export CICE_RESTART_DEFLATE=0
 
  export CICE_HISTORY_FORMAT='pnetcdf2'
- if [[ ${MACHINE_ID} == wcoss2 ]]; then
- export CICE_RESTART_FORMAT='hdf5'
- export CICE_HISTORY_FORMAT='hdf5'
- fi
  export CICE_HISTORY_IOTASKS=-99
  export CICE_HISTORY_REARR='box'
  export CICE_HISTORY_ROOT=-99

diff --git a/tests/fv3_conf/control_run.IN b/tests/fv3_conf/control_run.IN
@@ -133,7 +133,7 @@ fi
 #merra2
 if [ $USE_MERRA2 = .true. ]; then
  for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
- cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m${n}.nc aeroclim.m${n}.nc
+ cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
  done
  cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat optics_BC.dat
  cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat optics_OC.dat

diff --git a/tests/fv3_conf/cpld_control_run.IN b/tests/fv3_conf/cpld_control_run.IN
@@ -173,7 +173,7 @@ fi
 #merra2
 if [ $IAER = 1011 ]; then
  for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
- cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m${n}.nc aeroclim.m${n}.nc
+ cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
  done
  cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat optics_BC.dat
  cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat optics_OC.dat

diff --git a/tests/fv3_conf/fv3_gocart.IN b/tests/fv3_conf/fv3_gocart.IN
@@ -7,9 +7,8 @@ else
  cp -r @[INPUTDATA_ROOT]/FV3_input_data/RESTART/* ./INPUT
 fi
 cp @[INPUTDATA_ROOT]/FV3_input_data/*grb .
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2C.aerclim.2003-2014.*nc .
 for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
-ln -sf merra2C.aerclim.2003-2014.m${n}.nc  aeroclim.m${n}.nc
+ cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
 done
 cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/mg2_IN_CCN/cam5_4_143_NAAI_monclimo2.nc cam5_4_143_NAAI_monclimo2.nc
 cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/mg2_IN_CCN/cam5_4_143_NPCCN_monclimo2.nc cam5_4_143_NPCCN_monclimo2.nc

diff --git a/tests/fv3_conf/lake_control_run.IN b/tests/fv3_conf/lake_control_run.IN
@@ -123,7 +123,7 @@ fi
 #merra2
 if [ $USE_MERRA2 = .true. ]; then
  for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
- cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m${n}.nc aeroclim.m${n}.nc
+ cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
  done
  cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat optics_BC.dat
  cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat optics_OC.dat

diff --git a/tests/fv3_conf/regional_rrfs_a_run.IN b/tests/fv3_conf/regional_rrfs_a_run.IN
@@ -5,18 +5,9 @@ mkdir INPUT RESTART
 
 rsync -arv @[INPUTDATA_ROOT]/FV3_regional_rrfs_a/INPUT/. INPUT/.
 
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m01.nc aeroclim.m01.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m02.nc aeroclim.m02.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m03.nc aeroclim.m03.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m04.nc aeroclim.m04.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m05.nc aeroclim.m05.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m06.nc aeroclim.m06.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m07.nc aeroclim.m07.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m08.nc aeroclim.m08.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m09.nc aeroclim.m09.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m10.nc aeroclim.m10.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m11.nc aeroclim.m11.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m12.nc aeroclim.m12.nc
+for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
+ cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
+done
 
 cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat optics_BC.dat
 cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat

diff --git a/tests/fv3_conf/regional_run.IN b/tests/fv3_conf/regional_run.IN
@@ -5,18 +5,10 @@ rsync -arv @[INPUTDATA_ROOT]/FV3_regional/INPUT/. INPUT/.
 
 cp @[INPUTDATA_ROOT]/FV3_fix/CCN_ACTIVATE.BIN .
 
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m01.nc aeroclim.m01.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m02.nc aeroclim.m02.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m03.nc aeroclim.m03.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m04.nc aeroclim.m04.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m05.nc aeroclim.m05.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m06.nc aeroclim.m06.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m07.nc aeroclim.m07.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m08.nc aeroclim.m08.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m09.nc aeroclim.m09.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m10.nc aeroclim.m10.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m12.nc aeroclim.m11.nc
-cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2/merra2.aerclim.2003-2014.m12.nc aeroclim.m12.nc
+for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
+ cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
+done
+
 
 cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat optics_BC.dat
 cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat