Merge branch 'master' of https://github.com/ESMCI/cime

NordicESMhub · Jan 25, 2020 · 695a06c · 695a06c
2 parents 224a2d3 + d3624d9
commit 695a06c
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Showing 150 changed files with 7,768 additions and 2,477 deletions.
diff --git a/ChangeLog b/ChangeLog
diff --git a/config/cesm/config_archive.xml b/config/cesm/config_archive.xml
@@ -1,27 +1,4 @@
 <components version="2.0">
-  <comp_archive_spec compname="clm" compclass="lnd">
-    <rest_file_extension>r</rest_file_extension>
-    <rest_file_extension>rh\d?</rest_file_extension>
-    <hist_file_extension>h\d*.*\.nc$</hist_file_extension>
-    <hist_file_extension>e</hist_file_extension>
-    <rest_history_varname>locfnh</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer.lnd$NINST_STRING</rpointer_file>
-      <rpointer_content>./$CASE.clm2$NINST_STRING.r.$DATENAME.nc</rpointer_content>
-    </rpointer>
-    <test_file_names>
-      <tfile disposition="copy">rpointer.lnd</tfile>
-      <tfile disposition="copy">rpointer.lnd_9999</tfile>
-      <tfile disposition="copy">casename.clm2.r.1976-01-01-00000.nc</tfile>
-      <tfile disposition="copy">casename.clm2.rh4.1976-01-01-00000.nc</tfile>
-      <tfile disposition="move">casename.clm2.h0.1976-01-01-00000.nc</tfile>
-      <tfile disposition="ignore">casename.clm2.h0.1976-01-01-00000.nc.base</tfile>
-      <tfile disposition="move">casename.clm2_0002.e.postassim.1976-01-01-00000.nc</tfile>
-      <tfile disposition="move">casename.clm2_0002.e.preassim.1976-01-01-00000.nc</tfile>
-      <tfile disposition="ignore">anothercasename.clm2.i.1976-01-01-00000.nc</tfile>
-    </test_file_names>
-  </comp_archive_spec>
-
   <comp_archive_spec compname="cice" compclass="ice">
     <rest_file_extension>[ri]</rest_file_extension>
     <hist_file_extension>h\d*.*\.nc$</hist_file_extension>
@@ -63,7 +40,7 @@
       <tfile disposition="move">casename.pop.h.1976-01-01-00000.nc</tfile>
       <tfile disposition="move">casename.pop.h.1975-02-01-00000.nc</tfile>
       <tfile disposition="move">casename.pop.h0.1976-01-01-00000.nc</tfile>
-      <tfile disposition="move">casename.pop.dd.1976-01-01-00000.nc</tfile>
+      <tfile disposition="move">casename.pop.dd.1976-01-01-00000</tfile>
       <tfile disposition="ignore">casename.pop.r.1975-01-01-00000.nc</tfile>
       <tfile disposition="ignore">anothercasename.pop.r.1976-01-01-00000.nc</tfile>
     </test_file_names>

diff --git a/config/cesm/config_files.xml b/config/cesm/config_files.xml
@@ -92,6 +92,7 @@
       <value>$CIMEROOT/config/config_tests.xml</value>
       <!-- component specific config_tests files -->
       <value component="clm">$COMP_ROOT_DIR_LND/cime_config/config_tests.xml</value>
+      <value component="cam">$COMP_ROOT_DIR_ATM/cime_config/config_tests.xml</value>
     </values>
     <group>test</group>
     <file>env_test.xml</file>
@@ -110,7 +111,7 @@
       <value component="satm"      >$CIMEROOT/src/components/stub_comps/satm</value>
       <value component="xatm"      >$CIMEROOT/src/components/xcpl_comps/xatm</value>
       <value component="cam"      >$SRCROOT/components/cam/</value>
-      <value component="fv3gfs"      >$SRCROOT/components/fv3/</value>
+      <value component="ufsatm"      >$SRCROOT/components/fv3/</value>
     </values>
     <group>case_comps</group>
     <file>env_case.xml</file>
@@ -255,7 +256,7 @@
       <value component="allactive">$SRCROOT/cime_config/config_compsets.xml</value>
       <value component="drv"      >$COMP_ROOT_DIR_CPL/cime_config/config_compsets.xml</value>
       <value component="cam"      >$COMP_ROOT_DIR_ATM/cime_config/config_compsets.xml</value>
-      <value component="fv3gfs"   >$COMP_ROOT_DIR_ATM/cime_config/config_compsets.xml</value>
+      <value component="ufsatm"   >$COMP_ROOT_DIR_ATM/cime_config/config_compsets.xml</value>
       <value component="cism"     >$COMP_ROOT_DIR_GLC/cime_config/config_compsets.xml</value>
       <value component="clm"      >$COMP_ROOT_DIR_LND/cime_config/config_compsets.xml</value>
       <value component="cice"     >$COMP_ROOT_DIR_ICE/cime_config/config_compsets.xml</value>
@@ -276,7 +277,7 @@
       <value component="allactive">$SRCROOT/cime_config/config_pes.xml</value>
       <value component="drv"      >$COMP_ROOT_DIR_CPL/cime_config/config_pes.xml</value>
       <value component="cam"      >$COMP_ROOT_DIR_ATM/cime_config/config_pes.xml</value>
-      <value component="fv3gfs"   >$COMP_ROOT_DIR_ATM/cime_config/config_pes.xml</value>
+      <value component="ufsatm"   >$COMP_ROOT_DIR_ATM/cime_config/config_pes.xml</value>
       <value component="cism"     >$COMP_ROOT_DIR_GLC/cime_config/config_pes.xml</value>
       <value component="clm"      >$COMP_ROOT_DIR_LND/cime_config/config_pes.xml</value>
       <value component="cice"     >$COMP_ROOT_DIR_ICE/cime_config/config_pes.xml</value>

diff --git a/config/cesm/config_grids.xml b/config/cesm/config_grids.xml
@@ -197,6 +197,13 @@
       <mask>gx1v7</mask>
     </model_grid>
 
+    <model_grid alias="T5_T5_mg37" not_compset="_POP">
+      <grid name="atm">T5</grid>
+      <grid name="lnd">T5</grid>
+      <grid name="ocnice">T5</grid>
+      <mask>gx3v7</mask>
+    </model_grid>
+
     <model_grid alias="T85_T85_mg16" not_compset="_POP">
       <grid name="atm">T85</grid>
       <grid name="lnd">T85</grid>
@@ -954,6 +961,13 @@
       <mask>gx1v7</mask>
     </model_grid>
 
+    <model_grid alias="ne120pg3_ne120pg3_mt13" not_compset="_POP">
+      <grid name="atm">ne120np4.pg3</grid>
+      <grid name="lnd">ne120np4.pg3</grid>
+      <grid name="ocnice">ne120np4.pg3</grid>
+      <mask>tx0.1v3</mask>
+    </model_grid>
+
     <model_grid alias="ne240pg3_ne240pg3_mg17" not_compset="_POP|_CLM">
       <grid name="atm">ne240np4.pg3</grid>
       <grid name="lnd">ne240np4.pg3</grid>
@@ -968,6 +982,13 @@
       <mask>gx1v7</mask>
     </model_grid>
 
+    <model_grid alias="ne120pg3_t13">
+      <grid name="atm">ne120np4.pg3</grid>
+      <grid name="lnd">ne120np4.pg3</grid>
+      <grid name="ocnice">gx1v7</grid>
+      <mask>tx0.1v3</mask>
+    </model_grid>
+
     <!--  spectral element grids with 4x4 FVM physics grid -->
 
     <model_grid alias="ne30pg4_ne30pg4_mg17" not_compset="_POP|_CLM">
@@ -1134,54 +1155,63 @@
     <domain name="CLM_USRDAT">
       <nx>1</nx> <ny>1</ny>
       <file>$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.${CLM_USRDAT_NAME}_navy.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>user specified domain - only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="1x1_numaIA">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.1x1pt-numaIA_navy.110106.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>1x1 Numa Iowa -- only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="1x1_brazil">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.1x1pt-brazil_navy.090715.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>1x1 Brazil -- only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="1x1_smallvilleIA">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.1x1pt-smallvilleIA_test.110106.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>1x1 Smallville Iowa Crop Test Case -- only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="1x1_camdenNJ">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.1x1pt-camdenNJ_navy.111004.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>1x1 Camden New Jersey -- only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="1x1_mexicocityMEX">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.1x1pt-mexicocityMEX_navy.090715.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>1x1 Mexico City Mexico -- only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="1x1_vancouverCAN">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.1x1pt-vancouverCAN_navy.090715.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>1x1 Vancouver Canada -- only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="1x1_urbanc_alpha">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.1x1pt-urbanc_alpha_test.110201.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>1x1 Urban C Alpha Test Case -- only valid for DATM/CLM compset</desc>
     </domain>
 
     <domain name="5x5_amazon">
       <nx>1</nx> <ny>1</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.5x5pt-amazon_navy.090715.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>5x5 Amazon regional case -- only valid for DATM/CLM compset</desc>
     </domain>
 
@@ -1198,6 +1228,7 @@
     <domain name="360x720cru">
       <nx>720</nx> <ny>360</ny>
       <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.clm/domain.lnd.360x720_cruncep.100429.nc</file>
+      <mesh driver="nuopc">create_mesh</mesh>
       <desc>Exact half-degree CRUNCEP datm forcing grid with CRUNCEP land-mask -- only valid for DATM/CLM compset</desc>
     </domain>
 
@@ -1288,6 +1319,13 @@
       <support>Backward compatible for very high resolution Spectral-dycore experiments</support>
     </domain>
 
+    <domain name="T5">
+      <nx>16</nx> <ny>8</ny>
+      <file grid="atm|lnd" mask="gx3v7">$DIN_LOC_ROOT/share/domains/domain.lnd.T5_gx3v7.181009.nc</file>
+      <file grid="ocnice"  mask="gx3v7">$DIN_LOC_ROOT/share/domains/domain.ocn.T5_gx3v7.181009.nc</file>
+      <desc>T5 is Gaussian grid:</desc>
+    </domain>
+
     <domain name="T85">
       <!-- global spectral (eulerian dycore) grids-->
       <nx>256</nx>  <ny>128</ny>
@@ -1455,6 +1493,8 @@
       <nx>777600</nx> <ny>1</ny>
       <file grid="atm|lnd" mask="gx1v7">$DIN_LOC_ROOT/share/domains/domain.lnd.ne120np4.pg3_gx1v7.190718.nc</file>
       <file grid="ocnice"  mask="gx1v7">$DIN_LOC_ROOT/share/domains/domain.ocn.ne120np4.pg3_gx1v7.190718.nc</file>
+      <file grid="atm|lnd" mask="tx0.1v3">$DIN_LOC_ROOT/share/domains/domain.lnd.ne120np4.pg3_tx0.1v3.190820.nc</file>
+      <file grid="ocnice"  mask="tx0.1v3">$DIN_LOC_ROOT/share/domains/domain.ocn.ne120np4.pg3_tx0.1v3.190820.nc</file>
       <desc>ne120np4.pg3 is a Spectral Elem 0.25-deg grid with a 3x3 FVM physics grid:</desc>
       <support>EXPERIMENTAL FVM physics grid</support>
     </domain>
@@ -1652,6 +1692,7 @@
 
     <domain name="gland4">
       <nx>416</nx> <ny>704</ny>
+      <mesh driver="nuopc">$DIN_LOC_ROOT/share/meshes/greenland_4km_epsg3413_c170414_ESMFmesh_c20190729.nc</mesh>
       <desc>4-km Greenland grid, for use with the glissade dycore</desc>
     </domain>
 

diff --git a/config/cesm/config_grids_common.xml b/config/cesm/config_grids_common.xml
@@ -214,8 +214,8 @@
       <map name="ROF2OCN_ICE_RMAPNAME">cpl/gridmaps/r05/map_r05_to_tx0.66v1_e1000r300_190314.nc</map>
     </gridmap>
     <gridmap rof_grid="JRA025" ocn_grid="tx0.66v1" >
-      <map name="ROF2OCN_LIQ_RMAPNAME">cpl/gridmaps/rJRA025/map_JRA025m_to_tx0.66v1_nnsm_e333r100_190326.nc</map>
-      <map name="ROF2OCN_ICE_RMAPNAME">cpl/gridmaps/rJRA025/map_JRA025m_to_tx0.66v1_nnsm_e333r100_190326.nc</map>
+      <map name="ROF2OCN_LIQ_RMAPNAME">cpl/gridmaps/rJRA025/map_JRA025m_to_tx0.66v1_nnsm_e333r100_190910.nc</map>
+      <map name="ROF2OCN_ICE_RMAPNAME">cpl/gridmaps/rJRA025/map_JRA025m_to_tx0.66v1_nnsm_e333r100_190910.nc</map>
     </gridmap>
 
     <!-- ======================================================== -->

diff --git a/config/cesm/config_grids_mct.xml b/config/cesm/config_grids_mct.xml
@@ -191,6 +191,13 @@
       <map name="OCN2ATM_FMAPNAME">cpl/gridmaps/gx1v7/map_gx1v7_TO_ne120np4.pg3_aave.190718.nc</map>
       <map name="OCN2ATM_SMAPNAME">cpl/gridmaps/gx1v7/map_gx1v7_TO_ne120np4.pg3_aave.190718.nc</map>
     </gridmap>
+    <gridmap atm_grid="ne120np4.pg3" ocn_grid="tx0.1v3">
+      <map name="ATM2OCN_FMAPNAME">cpl/gridmaps/ne120np4.pg3/map_ne120np4.pg3_TO_tx0.1v3_aave.190820.nc</map>
+      <map name="ATM2OCN_SMAPNAME">cpl/gridmaps/ne120np4.pg3/map_ne120np4.pg3_TO_tx0.1v3_blin.190820.nc</map>
+      <map name="ATM2OCN_VMAPNAME">cpl/gridmaps/ne120np4.pg3/map_ne120np4.pg3_TO_tx0.1v3_blin.190820.nc</map>
+      <map name="OCN2ATM_FMAPNAME">cpl/gridmaps/tx0.1v3/map_tx0.1v3_TO_ne120np4.pg3_aave.190820.nc</map>
+      <map name="OCN2ATM_SMAPNAME">cpl/gridmaps/tx0.1v3/map_tx0.1v3_TO_ne120np4.pg3_aave.190820.nc</map>
+    </gridmap>
     <gridmap atm_grid="ne120np4.pg3" wav_grid="ww3a">
       <map name="ATM2WAV_SMAPNAME">cpl/gridmaps/ne120np4.pg3/map_ne120np4.pg3_TO_ww3a_blin.190503.nc</map>
     </gridmap>

diff --git a/config/cesm/machines/Depends.nag b/config/cesm/machines/Depends.nag
@@ -1,4 +1,4 @@
 wrap_mpi.o: wrap_mpi.F90
-	$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<
+	$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) -mismatch_all $(FFLAGS_NOOPT) $(FREEFLAGS) $<
 fft99.o: fft99.F90
-	$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<
+	$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) -mismatch_all $(FFLAGS_NOOPT) $(FREEFLAGS) $<
diff --git a/config/cesm/machines/config_compilers.xml b/config/cesm/machines/config_compilers.xml
@@ -72,14 +72,14 @@ using a fortran linker.
     <!-- This should be removed AFTER MOM6 cap is fully unified -->
     <append> -DCESMCOUPLED </append>
     <append MODEL="pop"> -D_USE_FLOW_CONTROL </append>
-    <append MODEL="fv3gfs"> -DSPMD </append>
+    <append MODEL="ufsatm"> -DSPMD </append>
   </CPPDEFS>
 
   <INCLDIR>
-        <append MODEL="fv3gfs"> -I$(EXEROOT)/atm/obj/FMS </append>
+        <append MODEL="ufsatm"> -I$(EXEROOT)/atm/obj/FMS </append>
   </INCLDIR>
   <FFLAGS>
-    <append MODEL="fv3gfs"> $(FC_AUTO_R8) </append>
+    <append MODEL="ufsatm"> $(FC_AUTO_R8) </append>
     <append MODEL="mom"> $(FC_AUTO_R8) -Duse_LARGEFILE</append>
   </FFLAGS>
   <SUPPORTS_CXX>FALSE</SUPPORTS_CXX>
@@ -554,38 +554,6 @@ using a fortran linker.
   </FFLAGS>
 </compiler>
 
-<compiler MACH="athena">
-  <CPPDEFS>
-    <!-- these flags enable nano timers -->
-    <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
-  </CPPDEFS>
-  <NETCDF_PATH>$ENV{NETCDF}</NETCDF_PATH>
-  <PIO_FILESYSTEM_HINTS>gpfs</PIO_FILESYSTEM_HINTS>
-  <PNETCDF_PATH>$ENV{PNETCDF}</PNETCDF_PATH>
-  <AR>xiar</AR>
-  <ARFLAGS>
-    <base>cru</base>
-  </ARFLAGS>
-</compiler>
-
-<compiler MACH="athena" COMPILER="intel">
-  <CFLAGS>
-    <append>  -xHost </append>
-  </CFLAGS>
-  <CPPDEFS>
-    <append> -DINTEL_MKL -DHAVE_SSE2 </append>
-  </CPPDEFS>
-  <FFLAGS>
-    <append>  -xHost </append>
-  </FFLAGS>
-  <MPICXX MPILIB="mpich2">mpiicpc</MPICXX>
-  <MPICC MPILIB="mpich2">mpiicc</MPICC>
-  <MPIFC MPILIB="mpich2">mpiifort</MPIFC>
-  <SCC>icc</SCC>
-  <SFC>ifort</SFC>
-  <TRILINOS_PATH MPILIB="mpich2">$ENV{TRILINOS_PATH}</TRILINOS_PATH>
-</compiler>
-
 <compiler MACH="aleph" COMPILER="intel">
   <CONFIG_ARGS>
     <base> --host=Linux </base>
@@ -804,7 +772,7 @@ using a fortran linker.
     <append> -L$(NETCDF_DIR) -lnetcdff -Wl,--as-needed,-L$(NETCDF_DIR)/lib -lnetcdff -lnetcdf </append>
   </SLIBS>
     <CPPDEFS>
-    <append MODEL="gptl"> -DHAVE_PAPI -DHAVE_SLASHPROC </append>
+    <append MODEL="gptl"> -DHAVE_SLASHPROC </append>
   </CPPDEFS>
   <LDFLAGS>
     <append>-mkl </append>