NOAA-EMC · WalterKolczynski-NOAA · Jul 21, 2021 · Jun 8, 2021 · Jun 8, 2021 · Jun 8, 2021
diff --git a/README.md b/README.md
@@ -17,8 +17,14 @@ For aerosols:
 sh checkout.sh -a                           #Check out forecast model with active aerosols
 ```
 ## Compile code needed to run prototype and link fixed files and executable programs:
+For coupled (UFS APP=S2SW):
+```
+sh build_all.sh -c
+```
+For aerosols (UFS APP=ATMAERO):
+```
+sh build_all.sh -a
 ```
-sh build_all.sh -c           #This command will build only execs for coupled and aerosol-enabled model
 
 To link fixed files and executable programs for the coupled/aerosol application:
 On Hera: 

diff --git a/modulefiles/module_base.hera b/modulefiles/module_base.hera
@@ -4,15 +4,17 @@
 ##
 
 # Modules availble through hpc-stack
- module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack
+module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack
 
 module load hpc/1.1.0
 module load hpc-intel/18.0.5.274
 module load hpc-impi/2018.0.4
+# use shared memory and OpenFabrics Alliance (OFA) fabric with Intel MPI to circumvent RDMA-related bug in DAPL.
+setenv I_MPI_FABRICS shm:ofa
 
 # Non-MPI
-module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2/3.4.2
+module load g2tmpl/1.10.0
 module load grib_util/1.2.2
 module load crtm/2.3.0
 module load prod_util/1.2.2
@@ -30,7 +32,7 @@ module load png/1.6.35
 # MPI
 module load netcdf/4.7.4
 module load hdf5/1.10.6
-module load esmf/8_1_0_beta_snapshot_27
+module load esmf/8_1_1
 module load w3emc/2.7.3
 module load wgrib2/2.0.8
 setenv "WGRIB2" "wgrib2"

diff --git a/modulefiles/module_base.orion b/modulefiles/module_base.orion
@@ -20,8 +20,8 @@ module load hpc-intel/2018.4
 module load hpc-impi/2018.4
 
 # Non-MPI
-module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2/3.4.2
+module load g2tmpl/1.10.0
 module load grib_util/1.2.2
 module load crtm 2.3.0
 module load prod_util/1.2.2
@@ -38,7 +38,7 @@ module load png/1.6.35
 # MPI
 module load netcdf/4.7.4
 module load hdf5/1.10.6
-module load esmf/8_1_0_beta_snapshot_27
+module load esmf/8_1_1
 module load w3emc/2.7.3
 module load wgrib2/2.0.8
 setenv WGRIB2 wgrib2

diff --git a/modulefiles/module_base.wcoss_dell_p3 b/modulefiles/module_base.wcoss_dell_p3
@@ -11,8 +11,8 @@ module load CFP/2.0.2
 setenv USE_CFP YES
 
 # Non-MPI
-module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2/3.4.2
+module load g2tmpl/1.10.0
 module load grib_util/1.2.2
 module load crtm 2.3.0
 module load prod_util/1.2.2
@@ -28,12 +28,11 @@ module load png/1.6.35
 # MPI
 module load netcdf/4.7.4
 module load hdf5/1.10.6
-module load esmf/8_1_0_beta_snapshot_27
+module load esmf/8_1_1
 module load w3emc/2.7.3
 module load wgrib2/2.0.8
 setenv WGRIB2 wgrib2
 
-
 # Modules not under hpc-stack
 module load HPSS/5.0.2.5
 module load NCO/4.7.0

diff --git a/modulefiles/modulefile.ww3.hera b/modulefiles/modulefile.ww3.hera
@@ -15,3 +15,5 @@ module load png/1.6.35
 
 module load bacio/2.4.1
 module load g2/3.4.1
+
+module load netcdf/4.7.4
diff --git a/modulefiles/modulefile.ww3.orion b/modulefiles/modulefile.ww3.orion
@@ -16,3 +16,5 @@ module load png/1.6.35
 
 module load bacio/2.4.1
 module load g2/3.4.1
+
+module load netcdf/4.7.4
diff --git a/modulefiles/modulefile.ww3.wcoss_dell_p3 b/modulefiles/modulefile.ww3.wcoss_dell_p3
@@ -11,3 +11,5 @@ module load png/1.6.35
 
 module load bacio/2.4.1
 module load g2/3.4.1
+
+module load netcdf/4.7.4
diff --git a/parm/chem/gocart_tracer.list b/parm/chem/gocart_tracer.list
@@ -1,9 +1,7 @@
 so2
-sulf
+so4
 dms
 msa
-pp25
-pp10
 bc1
 bc2
 oc1
@@ -17,4 +15,11 @@ seas1
 seas2
 seas3
 seas4
-seas5
+seas5
+nh3
+nh4a
+no3an1
+no3an2
+no3an3
+pm25
+pm10
diff --git a/parm/mom6/MOM_input_template_025 b/parm/mom6/MOM_input_template_025
@@ -148,6 +148,8 @@ TOPO_FILE = "ocean_topog.nc"    ! default = "topog.nc"
                                 ! The file from which the bathymetry is read.
 TOPO_EDITS_FILE = "All_edits.nc" ! default = ""
                                 ! The file from which to read a list of i,j,z topography overrides.
+ALLOW_LANDMASK_CHANGES = MOM6_ALLOW_LANDMASK_CHANGES   ! default = "False"
+                                ! If true, allow topography overrides to change ocean points to land
 MAXIMUM_DEPTH = 6500.0          !   [m]
                                 ! The maximum depth of the ocean.
 MINIMUM_DEPTH = 9.5             !   [m] default = 0.0

diff --git a/parm/mom6/MOM_input_template_050 b/parm/mom6/MOM_input_template_050
@@ -147,6 +147,8 @@ TOPO_CONFIG = "file"            !
                                 !     USER - call a user modified routine.
 TOPO_FILE = "ocean_topog.nc"    ! default = "topog.nc"
                                 ! The file from which the bathymetry is read.
+ALLOW_LANDMASK_CHANGES = MOM6_ALLOW_LANDMASK_CHANGES   ! default = "False"
+                                ! If true, allow topography overrides to change ocean points to land
 MAXIMUM_DEPTH = 6500.0          !   [m]
                                 ! The maximum depth of the ocean.
 MINIMUM_DEPTH = 9.5             !   [m] default = 0.0

diff --git a/parm/mom6/MOM_input_template_100 b/parm/mom6/MOM_input_template_100
@@ -140,6 +140,8 @@ TOPO_CONFIG = "file"            !
                                 !     USER - call a user modified routine.
 TOPO_EDITS_FILE = "topo_edits_011818.nc" ! default = ""
                                 ! The file from which to read a list of i,j,z topography overrides.
+ALLOW_LANDMASK_CHANGES = MOM6_ALLOW_LANDMASK_CHANGES   ! default = "False"
+                                ! If true, allow topography overrides to change ocean points to land
 MAXIMUM_DEPTH = 6500.0          !   [m]
                                 ! The maximum depth of the ocean.
 MINIMUM_DEPTH = 9.5             !   [m] default = 0.0

diff --git a/parm/parm_fv3diag/diag_table_aer b/parm/parm_fv3diag/diag_table_aer
@@ -123,7 +123,7 @@
 # chemical tracers advected by FV3
 ###
 "gfs_dyn",     "so2",         "so2",       "fv3_history",    "all",  .false.,  "none",  2
-"gfs_dyn",     "sulf",        "sulf",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "so4",         "so4",       "fv3_history",    "all",  .false.,  "none",  2
 "gfs_dyn",     "dms",         "dms",       "fv3_history",    "all",  .false.,  "none",  2
 "gfs_dyn",     "msa",         "msa",       "fv3_history",    "all",  .false.,  "none",  2
 "gfs_dyn",     "bc1",         "bc1",       "fv3_history",    "all",  .false.,  "none",  2
@@ -145,8 +145,8 @@
 "gfs_dyn",     "no3an1",      "no3an1",    "fv3_history",    "all",  .false.,  "none",  2
 "gfs_dyn",     "no3an2",      "no3an2",    "fv3_history",    "all",  .false.,  "none",  2
 "gfs_dyn",     "no3an3",      "no3an3",    "fv3_history",    "all",  .false.,  "none",  2
-"gfs_dyn",     "pp25",        "pp25",      "fv3_history",    "all",  .false.,  "none",  2
-"gfs_dyn",     "pp10",        "pp10",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "pm25",        "pm25",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "pm10",        "pm10",      "fv3_history",    "all",  .false.,  "none",  2
 
 "gfs_phys",  "ALBDO_ave",     "albdo_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
 "gfs_phys",  "cnvprcp_ave",   "cprat_ave",   "fv3_history2d",         "all",  .false.,  "none",  2