debug mode for NEMS, additional minor changes in component mk files (N…

…OAA-EMC#21)

* minor updates to component*.mk files

* Syno for ice_fraction and sea_ice_concentration

* updated syno for ice-frac

* * adding DATM-MOM6-CICE5 as a test
* updating NEMSfv3gfs and FV3-MOM6-CICE5 to github URLs
* adding extra platforms for some of the apps

* fix divide by zero in non-CMEPS version of NEMS

* update clean command for newest MOM6

* remove unintended changes

Co-authored-by: Jessica Meixner <jessica.meixner@noaa.gov>

src/incmake/component_CICE.mk

@@ -4,7 +4,7 @@ all_component_mk_files+=$(cice_mk)
 
 # Location of source code and installation
 CICE_SRCDIR?=$(ROOTDIR)/CICE
-CICE_BINDIR?=$(ROOTDIR)/CICE_INSTALL
+CICE_BINDIR?=$(ROOTDIR)/CICE/CICE_INSTALL
 
 CICE_CAPDIR?=$(ROOTDIR)/CICE_CAP
 

src/incmake/component_MOM6.mk

@@ -4,7 +4,7 @@ all_component_mk_files+=$(mom6_mk)
 
 # Location of source code and installation
 MOM6_SRCDIR?=$(ROOTDIR)/MOM6
-MOM6_BINDIR?=$(ROOTDIR)/MOM6_INSTALL
+MOM6_BINDIR?=$(ROOTDIR)/MOM6/MOM6_INSTALL
 
 # Make sure the expected directories exist and are non-empty:
 $(call require_dir,$(MOM6_SRCDIR),MOM6 source directory)
@@ -16,7 +16,7 @@ MOM6_ALL_OPTS=\
   COMP_SRCDIR="$(MOM6_SRCDIR)" \
   COMP_BINDIR="$(MOM6_BINDIR)" \
   FMS_BINDIR="$(FMS_BINDIR)" \
-  MACHINE_ID="$(MACHINE_ID)"
+  MACHINE_ID="$(FULL_MACHINE_ID)"
 
 # Workaround: if MOM6 is built twice, it fails because files in
 # $(MOM6_SRCDIR)/exec/ already exist.
@@ -26,11 +26,11 @@ $(mom6_mk): $(fms_mk) configure
 	$(MODULE_LOGIC) ; export $(MOM6_ALL_OPTS)                     ; \
 	set -e                                                        ; \
 	cd $(MOM6_SRCDIR)                                             ; \
-	./compile.sh --platform $(MACHINE_ID) --fms-dir "$(FMS_BINDIR)"
+	./compile.sh --platform $(FULL_MACHINE_ID) --fms-dir "$(FMS_BINDIR)"
 	+$(MODULE_LOGIC) ; cd $(MOM6_SRCDIR)                          ; \
 	  exec $(MAKE) -f makefile.nuopc $(MOM6_ALL_OPTS)               \
 	  "FMSDIR=$(FMS_BINDIR)"                                        \
-	  "NEMSMOMDIR=$(MOM6_SRCDIR)/exec/$(MACHINE_ID)"                \
+	  "NEMSMOMDIR=$(MOM6_SRCDIR)/exec/$(FULL_MACHINE_ID)"                \
 	  "INSTALLDIR=$(MOM6_BINDIR)" install
 	test -d "$(MOM6_BINDIR)"
 	test -s "$(mom6_mk)"
@@ -41,7 +41,7 @@ clean_MOM6:
 	cd $(MOM6_SRCDIR)                                                ; \
 	set +e                                                           ; \
 	rm -rf exec src/path_names_shared                                ; \
-	find . -name '*.o' -o -name '*.mod' -o -name '*.a' | xargs rm -f
+	find . -type f -name '*.o' -o -type f -name '*.mod' -o -type f -name '*.a' | xargs rm -f
 
 distclean_MOM6: clean_MOM6
 	rm -f $(MOM6_SRCDIR)/src/MOM6/config_src/nems_cap/mom5.mk.install

src/incmake/component_WW3.mk

@@ -7,7 +7,7 @@ WW3_SRCDIR?=$(ROOTDIR)/WW3/model
 WW3_BINDIR?=$(ROOTDIR)/WW3/WW3_INSTALL
 
 # Make sure the source directory exists and is non-empty
-$(call require_dir,$(WW3_SRCDIR),WaveWatch3 source directory)
+$(call require_dir,$(WW3_SRCDIR),WW3 source directory)
 
 # Rule for building this component:
 build_WW3: $(ww3_mk)

src/module_EARTH_GRID_COMP.F90

@@ -2610,6 +2610,25 @@ SUBROUTINE EARTH_REGISTER(EARTH_GRID_COMP,RC_REG)
         file=__FILE__)) &
         return  ! bail out
 
+      if (.not. NUOPC_FieldDictionaryHasEntry( &
+        "sea_ice_concentration")) then
+        call NUOPC_FieldDictionaryAddEntry( &
+          standardName="sea_ice_concentration", &
+          canonicalUnits="1", &
+          rc=rc)
+        if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+          line=__LINE__, &
+          file=__FILE__)) &
+          return  ! bail out
+      endif
+      call NUOPC_FieldDictionarySetSyno( &
+        standardNames = (/"ice_fraction",&
+                          "sea_ice_concentration"/), rc=rc)
+      if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+        line=__LINE__, &
+        file=__FILE__)) &
+        return  ! bail out
+
       !For MOM6 and WW3 variables to match: 
       call NUOPC_FieldDictionarySetSyno( &
         standardNames = (/"surface_eastward_sea_water_velocity",&

src/module_MEDIATOR.F90

@@ -5143,10 +5143,12 @@ subroutine MedPhase_atm_ocn_flux(gcomp, rc)
       zbot1(1)  = zbot(i,j)
       ubot1(1)  = ubot(i,j)
       vbot1(1)  = vbot(i,j)
-      thbot1(1) = tbot(i,j)*((100000._ESMF_KIND_R8/pbot(i,j))**0.286_ESMF_KIND_R8)  ! tcx temporary
+      if(pbot(i,j) .gt. 0.0) &
+     thbot1(1) = tbot(i,j)*((100000._ESMF_KIND_R8/pbot(i,j))**0.286_ESMF_KIND_R8)  ! tcx temporary
 !tcx      thbot1(1) = thbot(i,j)
       qbot1(1)  = qbot(i,j)
-      rbot1(1)  =pbot(i,j)/(287.058_ESMF_KIND_R8*(1._ESMF_KIND_R8+0.608_ESMF_KIND_R8*qbot(i,j))*tbot(i,j)) ! tcx temporary
+      if(tbot(i,j) .gt. 0.0) &
+      rbot1(1)  = pbot(i,j)/(287.058_ESMF_KIND_R8*(1._ESMF_KIND_R8+0.608_ESMF_KIND_R8*qbot(i,j))*tbot(i,j)) ! tcx temporary
 !tcx      rbot1(1)  = rbot(i,j)
       tbot1(1)  = tbot(i,j)
       us1(1)    = us(i,j)

tests/apps.def

@@ -7,13 +7,13 @@ PLATFORM wcoss_dell_p3     NAME WCOSS Phase 3
 
 # List of known apps and the compsets to run for each app.
 APP NEMSfv3gfs      COMPSETS -f
-APP WW3-FV3         COMPSETS -f
+APP FV3-GSDCHEM-WW3 COMPSETS -f
 APP FV3-MOM6-CICE5  COMPSETS -f
 APP FV3GFS-GSDCHEM  COMPSETS -f
 
 # URLs of each application's repository.  Default is gerrit:APPNAME
 APP NEMSfv3gfs      URL https://github.com/ufs-community/ufs-weather-model
-APP WW3-FV3         URL gerrit:EMC_FV3-GSDCHEM-WW3
+APP FV3-GSDCHEM-WW3 URL gerrit:EMC_FV3-GSDCHEM-WW3
 APP FV3-MOM6-CICE5  URL https://github.com/ufs-community/ufs-s2s-model
 APP FV3GFS-GSDCHEM  URL gerrit:EMC_FV3GFS-GSDCHEM
 
@@ -26,12 +26,11 @@ ON wcoss_cray        SCRUB /gpfs/hps2/ptmp/$username
 ON wcoss_dell_p3     SCRUB /gpfs/dell2/ptmp/$username
 
 # List of apps to run on each platform.
-#ON hera.intel         APPS NEMSfv3gfs FV3-MOM6-CICE5 WW3-FV3
-ON hera.intel         APPS NEMSfv3gfs FV3-MOM6-CICE5
+ON hera.intel         APPS NEMSfv3gfs FV3-MOM6-CICE5 FV3-GSDCHEM-WW3
 ON wcoss1             APPS NEMSfv3gfs
-ON wcoss2             APPS NEMSfv3gfs WW3-FV3
-ON wcoss_cray         APPS NEMSfv3gfs FV3GFS-GSDCHEM
-ON wcoss_dell_p3      APPS NEMSfv3gfs
+ON wcoss2             APPS NEMSfv3gfs FV3-GSDCHEM-WW3 
+ON wcoss_cray         APPS NEMSfv3gfs FV3GFS-GSDCHEM FV3-GSDCHEM-WW3
+ON wcoss_dell_p3      APPS NEMSfv3gfs FV3-GSDCHEM-WW3
 
 # Extra arguments to rt.sh for each platform
 ON hera.intel        EXTRA_ARGS --platform hera.intel