update to ESCOMP cmeps1.1.23

.github/workflows/extbuild.yml

@@ -5,9 +5,9 @@ name: extbuild
 # events but only for the main branch
 on:
   push:
-    branches: [ main ]
+    branches: [ noresm ]
   pull_request:
-    branches: [ main ]
+    branches: [ noresm ]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -23,8 +23,8 @@ jobs:
       ESMF_VERSION: v8.8.0
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_FORTRAN_VERSION: v4.6.1
-      PIO_VERSION: pio2_6_4
-      CDEPS_VERSION: cdeps1.0.64
+      PIO_VERSION: pio2_6_5
+      CDEPS_VERSION: cdeps1.0.80
     steps:
       - uses: actions/checkout@v4
         # Build the ESMF library, if the cache contains a previous build
@@ -75,7 +75,7 @@ jobs:
         with:
           path: /homme/runner/work/CMEPS/CMEPS/build-cdeps
           key: ${{ runner.os }}-${{ env.CDEPS_VERSION }}.cdeps1
-          
+
       - name: checkout CDEPS
         uses: actions/checkout@v4
         with:
@@ -85,7 +85,7 @@ jobs:
       - name: get genf90
         run: |
           cd cdeps-src
-          git submodule update --init 
+          git submodule update --init
       - name: Build CDEPS
         if: steps.cache-cdeps.outputs.cache-hit != 'true'
         uses: ESCOMP/CDEPS/.github/actions/buildcdeps@cdeps1.0.26
@@ -95,7 +95,7 @@ jobs:
           src_root: ${GITHUB_WORKSPACE}/cdeps-src
           cmake_flags: " -Wno-dev -DDISABLE_FoX=ON -DCMAKE_BUILD_TYPE=DEBUG -DWERROR=ON  -DCMAKE_Fortran_FLAGS=\"-DCPRGNU -g -Wall \
           -ffree-form -ffree-line-length-none -fallow-argument-mismatch \""
-      
+
       - name: Build CMEPS
         run: |
           export PIO=$HOME/pio

.github/workflows/srt.yml

@@ -6,9 +6,9 @@ name: scripts regression tests
 # events but only for the main branch
 on:
   push:
-    branches: [ main ]
+    branches: [ noresm ]
   pull_request:
-    branches: [ main ]
+    branches: [ noresm ]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -25,10 +25,10 @@ jobs:
       FC: mpifort
       CXX: mpicxx
       CPPFLAGS: "-I/usr/include -I/usr/local/include "
-      LDFLAGS: "-L/usr/lib/x86_64-linux-gnu -lnetcdf -lnetcdff -lpnetcdf"     
+      LDFLAGS: "-L/usr/lib/x86_64-linux-gnu -lnetcdf -lnetcdff -lpnetcdf"
       # Versions of all dependencies can be updated here
-      ESMF_VERSION: v8.6.1
-      PARALLELIO_VERSION: pio2_6_3
+      ESMF_VERSION: v8.9.0
+      PARALLELIO_VERSION: pio2_6_6
       CIME_MODEL: cesm
       CIME_DRIVER: nuopc
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -40,9 +40,9 @@ jobs:
         id: load-env
         run: |
           set -x
-          sudo apt-get update 
+          sudo apt-get update
           sudo apt-get install libxml2-utils
-          sudo apt-get install netcdf-bin 
+          sudo apt-get install netcdf-bin
           sudo apt-get install libnetcdf-dev
           sudo apt-get install libnetcdff-dev
           sudo apt-get install pnetcdf-bin
@@ -63,30 +63,30 @@ jobs:
       - run: echo "PyYAML" > requirements.txt
       - name: Install PyYAML
         run: pip install -r requirements.txt
-      # use the latest cesm main
-      - name: cesm checkout
+      # use the latest noresm main
+      - name: noresm checkout
         uses: actions/checkout@v4
         with:
-          repository: ESCOMP/CESM
-          path: cesm
+          repository: NorESMhub/NorESM
+          path: noresm
       # this cmeps commit
       - name: cmeps checkout
         uses: actions/checkout@v4
         with:
-          path: cesm/components/cmeps
-          
-      # Checkout cesm datamodels and support
+          path: noresm/components/cmeps
+
+      # Checkout noresm datamodels and support
       # cpl7 is needed - i think that's a bug
       - name: checkout externals
         run: |
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-          pushd cesm
+          pushd noresm
           ./bin/git-fleximod update cime ccs_config cdeps share mct parallelio
           cd ccs_config
-          git checkout main 
+          git checkout noresm
           cd ../cime
-          git checkout master
+          git checkout noresm
           git status
           if [[ ! -e "${PWD}/.gitmodules.bak" ]]
              then
@@ -96,11 +96,11 @@ jobs:
           fi
           git submodule update --init
           cd ../components/cdeps
-          git checkout main
+          git checkout noresm
           git submodule update --init
           cd ../../share
-          git checkout main
-          
+          git checkout noresm
+
       - name: Cache ESMF
         id: cache-esmf
         uses: actions/cache@v4
@@ -119,17 +119,17 @@ jobs:
         id: cache-inputdata
         uses: actions/cache@v4
         with:
-          path: $HOME/cesm/inputdata
+          path: $HOME/noresm/inputdata
           key: inputdata
 
       - name: Build ParallelIO
         if: steps.cache-PARALLELIO.outputs.cache-hit != 'true'
-        uses: NCAR/ParallelIO/.github/actions/parallelio_cmake@05173a6556ea8d80eb34e3881a5014ea8f4b7543
+        uses: NCAR/ParallelIO/.github/actions/parallelio_cmake@b38e34eeb9b75ce81ac94daf7c5245931de00b9d
         with:
           parallelio_version: ${{ env.ParallelIO_VERSION }}
           enable_fortran: True
           install_prefix: ${GITHUB_WORKSPACE}/pio
-          
+
       - name: Install ESMF
         uses: esmf-org/install-esmf-action@v1
         env:
@@ -150,10 +150,10 @@ jobs:
 
       - name: PREP for scripts regression test
         run: |
-          mkdir -p $HOME/cesm/scratch
-          mkdir -p $HOME/cesm/inputdata
-          pushd $GITHUB_WORKSPACE/cesm/cime/CIME/tests
-          export SRCROOT=$GITHUB_WORKSPACE/cesm/
+          mkdir -p $HOME/noresm/scratch
+          mkdir -p $HOME/noresm/inputdata
+          pushd $GITHUB_WORKSPACE/noresm/cime/CIME/tests
+          export SRCROOT=$GITHUB_WORKSPACE/noresm/
           export CIME_TEST_PLATFORM=ubuntu-latest
           export PIO_INCDIR=$GITHUB_WORKSPACE/pio/include
           export PIO_LIBDIR=$GITHUB_WORKSPACE/pio/lib
@@ -162,19 +162,34 @@ jobs:
           export NETCDF_PATH=/usr
           export PNETCDF_PATH=/usr
           export LD_LIBRARY_PATH=/usr/lib/libx86_64-linux-gnu/:$LD_LIBRARY_PATH
-          cat <<EOF >> $GITHUB_WORKSPACE/cesm/ccs_config/machines/cmake_macros/ubuntu-latest.cmake
+          cat <<EOF >> $GITHUB_WORKSPACE/noresm/ccs_config/machines/cmake_macros/ubuntu-latest.cmake
           set(NetCDF_Fortran_INCLUDE_DIR /usr/include)
           set(NetCDF_Fortran_LIBRARY /usr/lib/x86_64-gnu-Linux/libnetcdff.so)
           EOF
           printenv >> $GITHUB_ENV
           popd
       - name: scripts regression tests
         run: |
-          pushd $GITHUB_WORKSPACE/cesm/cime/CIME/tests
-          ./scripts_regression_tests.py  --no-fortran-run --compiler gnu --mpilib openmpi --machine ubuntu-latest 
+          pushd $GITHUB_WORKSPACE/noresm/cime/CIME/tests
+          ./scripts_regression_tests.py  --no-fortran-run --compiler gnu --mpilib openmpi --machine ubuntu-latest --no-teardown
           popd
+
+      # How to download artifacts:
+      # https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts
+
+#      - name: Upload test logs
+#        if: ${{ failure() }}
+#        steps:
+#        - name: Tar test logs
+#          run: tar zcf scratch-${{ matrix.python-version }}.tar.gz /home/runner/noresm/scratch
+#        - name: save artifact
+#          uses: actions/upload-artifact@v4
+#          with:
+#            name: test-logs-${{ matrix.python-version }}
+#            path: scratch-${{ matrix.python-version }}.tar.gz
+#            retention-days: 4
 #     the following can be used by developers to login to the github server in case of errors
 #     see https://github.com/marketplace/actions/debugging-with-tmate for further details
-#      - name: Setup tmate session
-#        if: ${{ failure() }}
-#        uses: mxschmitt/action-tmate@v3
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3

cesm/driver/esm.F90

@@ -9,7 +9,7 @@ module ESM
   use shr_mem_mod  , only : shr_mem_init
   use shr_log_mod  , only : shr_log_setLogunit, shr_log_error
   use esm_utils_mod, only : logunit, maintask, dbug_flag, chkerr
-  use esmf         , only : ESMF_FAILURE
+  use esmf         , only : ESMF_FAILURE, ESMF_VMBARRIER
   implicit none
   private
 
@@ -1557,6 +1557,9 @@ subroutine esm_finalize(driver, rc)
     call ESMF_VMGet(vm, mpiCommunicator=mpicomm, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
 
+    call ESMF_VMBarrier(vm, rc=rc)
+    if (chkerr(rc,__LINE__,u_FILE_u)) return
+
     call NUOPC_CompAttributeGet(driver, name="timing_dir",value=timing_dir, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
 

cesm/flux_atmocn/flux_atmocn_driver_mod.F90

@@ -54,7 +54,7 @@ subroutine flux_atmOcn_driver(logunit, nMax, &
     real(R8),intent(out)  ::  lwup (nMax)     ! heat flux: lw upward (W/m^2)
     real(R8),intent(out)  ::  evap (nMax)     ! water flux: evap ((kg/s)/m^2)
     real(R8),intent(out)  ::  taux (nMax)     ! surface stress, zonal (N)
-    real(R8),intent(out)  ::  tauy (nMax)     ! surface stress, maridional (N)
+    real(R8),intent(out)  ::  tauy (nMax)     ! surface stress, meridional (N)
     real(R8),intent(out)  ::  tref (nMax)     ! diag:  2m ref height T (K)
     real(R8),intent(out)  ::  qref (nMax)     ! diag:  2m ref humidity (kg/kg)
     real(R8),intent(out)  :: duu10n(nMax)     ! diag: 10m wind speed squared (m/s)^2

cesm/nuopc_cap_share/shr_megan_mod.F90

@@ -43,13 +43,13 @@ module shr_megan_mod
      integer               :: index
      real(r8), pointer     :: emis_factors(:) ! function of plant-function-type (PFT)
      integer               :: class_number    ! MEGAN class number
-     real(r8)              :: coeff           ! emissions component coeffecient
      real(r8)              :: molec_weight    ! molecular weight of the MEGAN compound (g/mole)
      type(shr_megan_megcomp_t), pointer :: next_megcomp ! points to next member in the linked list
   endtype shr_megan_megcomp_t
 
   type shr_megan_comp_ptr
-    type(shr_megan_megcomp_t), pointer :: ptr
+     type(shr_megan_megcomp_t), pointer :: ptr
+     real(r8) :: coeff           ! emissions component coeffecient
   endtype shr_megan_comp_ptr
 
   ! chemical compound in CAM mechanism that has MEGAN emissions
@@ -227,7 +227,8 @@ subroutine shr_megan_init( specifier)
        if (localPet==0) write(logunit,*) ' species : ', item%name
        do j = 1,item%n_terms
           if (localPet==0) write(logunit,'(f12.4,a,a)')  item%coeffs(j),' * ', item%vars(j)
-          shr_megan_mechcomps(i)%megan_comps(j)%ptr => add_megan_comp( item%vars(j), item%coeffs(j) )
+          shr_megan_mechcomps(i)%megan_comps(j)%ptr => add_megan_comp( item%vars(j) )
+          shr_megan_mechcomps(i)%megan_comps(j)%coeff = item%coeffs(j)
        enddo
        shr_megan_mechcomps_n = shr_megan_mechcomps_n+1
 
@@ -243,10 +244,9 @@ end subroutine shr_megan_init
 
   !-------------------------------------------------------------------------
 
-  function add_megan_comp( name, coeff ) result(megan_comp)
+  function add_megan_comp( name ) result(megan_comp)
 
     character(len=16), intent(in) :: name
-    real(r8),          intent(in) :: coeff
     type(shr_megan_megcomp_t), pointer :: megan_comp
 
     megan_comp => get_megan_comp_by_name(shr_megan_linkedlist, name)
@@ -264,7 +264,7 @@ function add_megan_comp( name, coeff ) result(megan_comp)
     megan_comp%index = shr_megan_megcomps_n+1
 
     megan_comp%name = trim(name)
-    megan_comp%coeff = coeff
+
     nullify(megan_comp%next_megcomp)
 
     call add_megan_comp_to_list(megan_comp)

cime_config/buildnml

@@ -7,7 +7,7 @@ _CIMEROOT = os.environ.get("CIMEROOT")
 if _CIMEROOT is None:
     raise SystemExit("ERROR: must set CIMEROOT environment variable")
 
-sys.path.append(os.path.join(_CIMEROOT, "scripts", "Tools"))
+sys.path.append(os.path.join(_CIMEROOT, "CIME", "Tools"))
 
 import shutil, glob, itertools
 from standard_script_setup import *
@@ -52,7 +52,6 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     )
     config["timer_level"] = "pos" if case.get_value("TIMER_LEVEL") >= 1 else "neg"
     config["continue_run"] = ".true." if case.get_value("CONTINUE_RUN") else ".false."
-    config["flux_epbal"] = "ocn" if case.get_value("CPL_EPBAL") == "ocn" else "off"
     config["mask_grid"] = case.get_value("MASK_GRID")
     for val in ("HIST", "REST", "STOP"):
         config[val.lower()+"_option"] = case.get_value(val+"_OPTION")
@@ -143,7 +142,8 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     elif case.get_value("RUN_TYPE") == "branch":
         config["run_type"] = "branch"
 
-    config['wav_ice_coupling'] = 'ww3' in config['COMP_WAV'] and config['COMP_ICE'] == 'cice'
+    if config['COMP_WAV'] == 'ww3' and config['COMP_ICE'] == 'cice':
+        config["wav_ice_coupling"] = "on"
 
     if config["COMP_OCN"] == "blom":
         if "ecosys" in case.get_value("BLOM_TRACER_MODULES"):
@@ -682,13 +682,37 @@ def compare_drv_flds_in(first, second, infile1, infile2):
                 % (infile1, infile2),
             )
 
+def cmeps_lib_list(case):
+    # provide a list of support libs that must be built for this case
+    # should be ordered with dependent libraries listed after those depended on
+    # the library names should match the keys in variable BUILD_LIB_FILE from config_files.xml
+    ufs_driver = os.environ.get("UFS_DRIVER")
+    if ufs_driver:
+        logger.info("UFS_DRIVER is set to {}".format(ufs_driver))
+
+    libs = case.get_values("CASE_SUPPORT_LIBRARIES")
+
+    mpilib = case.get_value("MPILIB")
+    if mpilib == "mpi-serial" and "mpi-serial" not in libs:
+        libs.insert(0, mpilib)
+
+    ocn_model = case.get_value("COMP_OCN")
+    # These will be handled by MOM and CAM, included here for backward compatibility.
+    atm_dycore = case.get_value("CAM_DYCORE")
+    if (ocn_model == "mom" or (atm_dycore and atm_dycore == "fv3")) and "FMS" not in libs:
+        libs.append("FMS")
+    return libs
 
 ###############################################################################
 def buildnml(case, caseroot, component):
     ###############################################################################
     if component != "drv":
         raise AttributeError
 
+    libs = cmeps_lib_list(case)
+    with Case(case.get_value("CASEROOT"), read_only=False) as case_tmp:
+        case_tmp.set_value("CASE_SUPPORT_LIBRARIES", ",".join(libs))
+
     esmfmkfile = os.getenv("ESMFMKFILE")
     expect(
         esmfmkfile and os.path.isfile(esmfmkfile),
@@ -779,7 +803,7 @@ def buildnml(case, caseroot, component):
 def _main_func():
     caseroot = parse_input(sys.argv)
 
-    with Case(caseroot) as case:
+    with Case(caseroot, read_only=False) as case:
         buildnml(case, caseroot, "drv")