Update CMEPS for postphases, ice sheets and glc->ocn dynamic mapping

.github/pull_request_template.md

@@ -16,18 +16,26 @@ Any User Interface Changes (namelist or namelist defaults changes)?
  - [ ] No
 
 Testing performed if application target is CESM:(either UFS-S2S or CESM testing is required):
-- [ ] (required) CIME_DRIVER=nuopc scripts_regression_tests.py
+- [ ] (recommended) CIME_DRIVER=nuopc scripts_regression_tests.py
    - machines:
    - details (e.g. failed tests):
-- [ ] (required) CESM testlist_drv.xml
+- [ ] (recommended) CESM testlist_drv.xml
    - machines and compilers:
    - details (e.g. failed tests):
 - [ ] (optional) CESM prealpha test
    - machines and compilers
    - details (e.g. failed tests):
+- [ ] (other) please described in detail
+   - machines and compilers
+   - details (e.g. failed tests):
 
 Testing performed if application target is UFS-S2S:
-- [ ] (required) UFS-S2S testing
+- [ ] (recommended) UFS-S2S testing
+   - description:
+   - details (e.g. failed tests):
+
+Testing performed if application target is UFS-HAFS:
+- [ ] (recommended) UFS-HAFS testing
    - description:
    - details (e.g. failed tests):
 
@@ -40,3 +48,7 @@ Hashes used for testing:
   - repository to check out:
   - branch:
   - hash:
+- [ ] UFS-HAFS, then umbrella repostiory to check out and associated hash:
+  - repository to check out:
+  - branch:
+  - hash:

CMakeLists.txt

@@ -0,0 +1,48 @@
+cmake_minimum_required(VERSION 3.10)
+include(ExternalProject)
+
+if (DEFINED CIMEROOT)
+  message("Using CIME in ${CIMEROOT} with compiler ${COMPILER}")
+  include(${CASEROOT}/Macros.cmake)
+  if (${PIO_VERSION} LESS 2)
+    message( FATAL_ERROR "Version 2 of the PIO library required")
+  endif()
+  if (${MPILIB} STREQUAL "mpi-serial")
+    set(CMAKE_C_COMPILER ${SCC})
+    set(CMAKE_Fortran_COMPILER ${SFC})
+    set(CMAKE_CXX_COMPILER ${SCXX})
+  else()
+    set(CMAKE_C_COMPILER ${MPICC})
+    set(CMAKE_Fortran_COMPILER ${MPIFC})
+    set(CMAKE_CXX_COMPILER ${MPICXX})
+  endif()
+  set(CMAKE_Fortran_FLAGS "${FFLAGS} -I${LIBROOT}/include -I${LIBROOT}/finclude -I${LIBROOT}/nuopc/esmf/${NINST_VALUE}/include")
+else()
+  set(BLD_STANDALONE TRUE)
+endif()
+
+project(CMEPS LANGUAGES Fortran VERSION 0.1)
+
+list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
+
+message("CMAKE_MODULE_PATH is ${CMAKE_MODULE_PATH}")
+
+find_package(ESMF REQUIRED)
+if (DEFINED PIO)
+  set(PIO_PATH ${PIO})
+else()
+  set(PIO_PATH $ENV{PIO})
+endif()
+find_package(PIO REQUIRED COMPONENT C Fortran PATH ${PIO_PATH})
+
+if (NOT DEFINED MPILIB OR NOT ${MPILIB} STREQUAL "mpi-serial")
+  find_package(MPI REQUIRED)
+endif()
+
+if(BLD_STANDALONE)
+  add_subdirectory(nems/util)
+  list(APPEND EXTRA_LIBS cmeps_share)
+  list(APPEND EXTRA_INCLUDES "${CMAKE_BINARY_DIR}/nems/util")
+endif()
+
+add_subdirectory(mediator)

cime_config/buildnml

@@ -399,8 +399,6 @@ def _create_runseq(case, coupling_times, valid_comps):
                 from runseq_D import gen_runseq
             elif (comp_lnd == 'dlnd' and comp_glc == "cism"):
                 from runseq_TG import gen_runseq
-            elif (comp_atm == 'ufsatm' and comp_ocn == "mom" and comp_ice == 'cice'):
-                from runseq_NEMS import gen_runseq
             else:
                 from runseq_general import gen_runseq
 
@@ -571,10 +569,8 @@ def buildnml(case, caseroot, component):
         filename = os.path.join(fd_dir,"fd_cesm.yaml")
     elif coupling_mode == 'hafs':
         filename = os.path.join(fd_dir,"fd_hafs.yaml")
-    elif 'nems' in coupling_mode:
-        filename = os.path.join(fd_dir,"fd_nems.yaml")
     else:
-        expect(False, "coupling mode currently only supports cesm, hafs and nems")
+        expect(False, "coupling mode currently only supports cesm")
     shutil.copy(filename, os.path.join(rundir, "fd.yaml"))
 
 ###############################################################################

cime_config/namelist_definition_drv.xml

@@ -18,15 +18,6 @@
     </values>
   </entry>
 
-  <entry id="Profiling@driver_attributes" modify_via_xml="ESMF_PROFILING_LEVEL">
-    <type>char</type>
-    <category>nuopc</category>
-    <group>DRIVER_attributes</group>
-    <values>
-      <value>$ESMF_PROFILING_LEVEL</value>
-    </values>
-  </entry>
-
   <entry id="Verbosity@med_attributes" modify_via_xml="ESMF_VERBOSITY_LEVEL">
     <type>char</type>
     <category>nuopc</category>
@@ -393,6 +384,15 @@
   <!-- All components orbital attributes           -->
   <!-- =========================================== -->
 
+  <entry id="Profiling" modify_via_xml="ESMF_PROFILING_LEVEL">
+    <type>char</type>
+    <category>nuopc</category>
+    <group>ALLCOMP_attributes</group>
+    <values>
+      <value>$ESMF_PROFILING_LEVEL</value>
+    </values>
+  </entry>
+
   <entry id="orb_mode">
     <type>char</type>
     <category>orbital</category>
@@ -768,6 +768,31 @@
     </values>
   </entry>
 
+  <entry id="ocn2glc_coupling">
+    <type>logical</type>
+    <category>flds</category>
+    <group>ALLCOMP_attributes</group>
+    <desc>
+      .true. if ocean sends fields at multiple ocean levels to the land-ice component
+    </desc>
+    <values>
+      <value>.false.</value>
+    </values>
+  </entry>
+
+  <entry id="ocn2glc_levels">
+    <type>char</type>
+    <category>flds</category>
+    <group>ALLCOMP_attributes</group>
+    <desc>
+      if the ocean component sends fields at multiple ocean levels to the
+      land-ice component, these are the colon deliminted level indices
+    </desc>
+    <values>
+      <value>1:10:19:26:30:33:35</value>
+    </values>
+  </entry>
+
   <entry id="tfreeze_option" modify_via_xml="TFREEZE_SALTWATER_OPTION">
     <type>char</type>
     <category>control</category>
@@ -826,6 +851,161 @@
   <!-- MED general attributes                      -->
   <!-- =========================================== -->
 
+  <entry id="atm_nx" modify_via_xml="ATM_NX">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of atm cells in i direction
+    </desc>
+    <values>
+      <value>$ATM_NX</value>
+    </values>
+  </entry>
+  <entry id="atm_ny" modify_via_xml="ATM_NY">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of atm cells in j direction
+    </desc>
+    <values>
+      <value>$ATM_NY</value>
+    </values>
+  </entry>
+  <entry id="ice_nx" modify_via_xml="ICE_NX">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of ice cells in i direction
+    </desc>
+    <values>
+      <value>$ICE_NX</value>
+    </values>
+  </entry>
+  <entry id="ice_ny" modify_via_xml="ICE_NY">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of ice cells in j direction
+    </desc>
+    <values>
+      <value>$ICE_NY</value>
+    </values>
+  </entry>
+  <entry id="glc_nx" modify_via_xml="GLC_NX">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of glc cells in i direction
+    </desc>
+    <values>
+      <value>$GLC_NX</value>
+    </values>
+  </entry>
+  <entry id="glc_ny" modify_via_xml="GLC_NY">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of glc cells in j direction
+    </desc>
+    <values>
+      <value>$GLC_NY</value>
+    </values>
+  </entry>
+  <entry id="lnd_nx" modify_via_xml="LND_NX">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of lnd cells in i direction
+    </desc>
+    <values>
+      <value>$LND_NX</value>
+    </values>
+  </entry>
+  <entry id="lnd_ny" modify_via_xml="LND_NY">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of lnd cells in j direction
+    </desc>
+    <values>
+      <value>$LND_NY</value>
+    </values>
+  </entry>
+  <entry id="ocn_nx" modify_via_xml="OCN_NX">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of ocn cells in i direction
+    </desc>
+    <values>
+      <value>$OCN_NX</value>
+    </values>
+  </entry>
+  <entry id="ocn_ny" modify_via_xml="OCN_NY">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of ocn cells in j direction
+    </desc>
+    <values>
+      <value>$OCN_NY</value>
+    </values>
+  </entry>
+  <entry id="rof_nx" modify_via_xml="ROF_NX">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of rof cells in i direction
+    </desc>
+    <values>
+      <value>$ROF_NX</value>
+    </values>
+  </entry>
+  <entry id="rof_ny" modify_via_xml="ROF_NY">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of rof cells in j direction
+    </desc>
+    <values>
+      <value>$ROF_NY</value>
+    </values>
+  </entry>
+  <entry id="wav_nx" modify_via_xml="WAV_NX">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of wav cells in i direction
+    </desc>
+    <values>
+      <value>$WAV_NX</value>
+    </values>
+  </entry>
+  <entry id="wav_ny" modify_via_xml="WAV_NY">
+    <type>integer</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      number of wav cells in j direction
+    </desc>
+    <values>
+      <value>$WAV_NY</value>
+    </values>
+  </entry>
+
   <entry id="coupling_mode" modify_via_xml="COUPLING_MODE">
     <type>char</type>
     <category>control</category>

cime_config/runseq/runseq_D.py

@@ -31,32 +31,38 @@ def gen_runseq(case, coupling_times):
 
         runseq.enter_time_loop(ocn_cpl_time, newtime=((ocn_cpl_time)))
 
-        runseq.add_action("MED med_phases_prep_ocn_accum_avg", med_to_ocn)
-        runseq.add_action("MED -> OCN :remapMethod=redist"   , med_to_ocn)
+        runseq.add_action("MED med_phases_prep_ocn_avg"    , med_to_ocn)
+        runseq.add_action("MED -> OCN :remapMethod=redist" , med_to_ocn)
 
         runseq.enter_time_loop(atm_cpl_time, newtime=((atm_cpl_time < ocn_cpl_time)))
 
-        runseq.add_action ("MED med_phases_prep_ocn_map"        , med_to_ocn)
-        runseq.add_action ("MED med_phases_aofluxes_run"        , run_ocn and run_atm and (med_to_ocn or med_to_atm))
-        runseq.add_action ("MED med_phases_prep_ocn_merge"      , med_to_ocn)
-        runseq.add_action ("MED med_phases_prep_ocn_accum_fast" , med_to_ocn)
-        runseq.add_action ("MED med_phases_ocnalb_run"          , med_to_ocn)
-        runseq.add_action ("MED med_phases_prep_ice"            , med_to_ice)
-        runseq.add_action ("MED -> ICE :remapMethod=redist"     , med_to_ice)
-        runseq.add_action ("ICE"                                , run_ice)
-        runseq.add_action ("ROF"                                , run_rof)
-        runseq.add_action ("ATM"                                , run_atm)
-        runseq.add_action ("ICE -> MED :remapMethod=redist"     , run_ice)
-        runseq.add_action ("MED med_fraction_set"               , run_ice)
-        runseq.add_action ("ROF -> MED :remapMethod=redist"     , run_rof)
-        runseq.add_action ("ATM -> MED :remapMethod=redist"     , run_atm)
-        runseq.add_action ("MED med_phases_history_write"       , atm_cpl_time == ocn_cpl_time)
+        runseq.add_action ("MED med_phases_aofluxes_run"   , run_ocn and run_atm and (med_to_ocn or med_to_atm))
+        runseq.add_action ("MED med_phases_prep_ocn_accum" , med_to_ocn)
+        runseq.add_action ("MED med_phases_ocnalb_run"     , med_to_ocn)
+
+        runseq.add_action ("MED med_phases_prep_ice"        , med_to_ice)
+        runseq.add_action ("MED -> ICE :remapMethod=redist" , med_to_ice)
+
+        runseq.add_action ("ICE" , run_ice)
+        runseq.add_action ("ROF" , run_rof)
+        runseq.add_action ("ATM" , run_atm)
+
+        runseq.add_action ("ICE -> MED :remapMethod=redist" , run_ice)
+        runseq.add_action("MED med_phases_post_ice"         , run_ice)
+
+        runseq.add_action ("ROF -> MED :remapMethod=redist" , run_rof)
+        runseq.add_action("MED med_phases_post_rof"         , run_rof)
+
+        runseq.add_action ("ATM -> MED :remapMethod=redist" , run_atm)
+        runseq.add_action ("MED med_phases_history_write"   , atm_cpl_time == ocn_cpl_time)
+        runseq.add_action ("MED med_phases_post_atm"        , run_atm)
 
         runseq.leave_time_loop(run_rof and (atm_cpl_time < ocn_cpl_time))
 
-        runseq.add_action ("OCN", run_ocn)
-        runseq.add_action ("OCN -> MED :remapMethod=redist"     , run_ocn)
-        runseq.add_action ("MED med_phases_history_write"       , atm_cpl_time < ocn_cpl_time)
+        runseq.add_action ("OCN"                            , run_ocn)
+        runseq.add_action ("OCN -> MED :remapMethod=redist" , run_ocn)
+        runseq.add_action ("MED med_phases_history_write"   , atm_cpl_time < ocn_cpl_time)
+        runseq.add_action ("MED med_phases_post_ocn"        , run_ocn)
 
         runseq.leave_time_loop(True)