Merge pull request #5 from NOAA-EMC/community_develop

Community develop

Externals.cfg

@@ -30,7 +30,7 @@ protocol = git
 repo_url = https://github.com/NOAA-EMC/EMC_post
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 78078f62
+hash = 172bab0
 local_path = sorc/EMC_post
 required = True
 

modulefiles/module-setup.sh.inc

@@ -57,12 +57,6 @@ elif [[ -L /usrx && "$( readlink /usrx 2> /dev/null )" =~ dell ]] ; then
 	source /usrx/local/prod/lmod/lmod/init/$__ms_shell
     fi
     module purge
-elif [[ -d /glade ]] ; then
-    # We are on NCAR Yellowstone
-    if ( ! eval module help > /dev/null 2>&1 ) ; then
-        . /usr/share/Modules/init/$__ms_shell
-    fi
-    module purge
 elif [[ -d /lustre && -d /ncrc ]] ; then
     # We are on GAEA. 
     if ( ! eval module help > /dev/null 2>&1 ) ; then

ush/cmp_expt_to_baseline.sh

@@ -263,8 +263,8 @@ Exiting script with nonzero exit code.
 #-----------------------------------------------------------------------
 #
     cd ${expt_dir}/$subdir
-#    num_files=$( ls -1 *.${file_ext} 2>/dev/null | wc -l )
-    num_files=$( count_files *.${file_ext} 2>/dev/null | wc -l )
+    num_files=$( ls -1 *.${file_ext} 2>/dev/null | wc -l )
+#   num_files=$( count_files *.${file_ext} 2>/dev/null | wc -l )
     printf "
     Number of files with extension \"${file_ext}\" in subdirectory \"$subdir\" 
     of the experiment directory is:  ${num_files}
@@ -343,7 +343,7 @@ done # Loop over subdirectories.
 #
 msg="Summary of regression test:"
 msglen=${#msg}
-msg="$msg  ${result_str}"
+msg="$msg"
 printf "\n%s\n" "$msg"
 printf "%0.s=" $(seq 1 $msglen)
 printf "\n"

ush/generate_FV3SAR_wflow.sh

@@ -298,6 +298,9 @@ cat "${MAKE_LBCS_TN}.local" >> "${MAKE_LBCS_TN}"
 ln_vrfy -fs "${UFS_WTHR_MDL_DIR}/NEMS/src/conf/modules.nems" \
             "${RUN_FCST_TN}"
 
+ln_vrfy -fs "${EMC_POST_DIR}/modulefiles/post/v8.0.0-$machine" \
+            "${RUN_POST_TN}"
+
 cd_vrfy -
 #
 #-----------------------------------------------------------------------

ush/get_extrn_mdl_file_dir_info.sh

@@ -528,6 +528,9 @@ bination of external model (extrn_mdl_name) and analysis or forecast
     "ODIN")
       sysdir=""
       ;;
+    "CHEYENNE")
+      sysdir=""
+      ;;
     *)
       print_err_msg_exit "\
 The system directory in which to look for external model output files 
@@ -556,6 +559,9 @@ has not been specified for this external model and machine combination:
     "ODIN")
       sysdir="$sysbasedir/${yyyymmdd}"
       ;;
+    "CHEYENNE")
+      sysdir="$sysbasedir/gfs.${yyyymmdd}/${hh}"
+      ;;
     *)
       print_err_msg_exit "\
 The system directory in which to look for external model output files 
@@ -584,6 +590,9 @@ has not been specified for this external model and machine combination:
     "ODIN")
       sysdir="$sysbasedir"
       ;;
+    "CHEYENNE")
+      sysdir="$sysbasedir"
+      ;;
     *)
       print_err_msg_exit "\
 The system directory in which to look for external model output files 
@@ -612,6 +621,9 @@ has not been specified for this external model and machine combination:
     "ODIN")
       sysdir="$sysbasedir"
       ;;
+    "CHEYENNE")
+      sysdir="$sysbasedir"
+      ;;
     *)
       print_err_msg_exit "\
 The system directory in which to look for external model output files 

ush/set_extrn_mdl_params.sh

@@ -70,6 +70,9 @@ else
     "ODIN")
       EXTRN_MDL_FILES_SYSBASEDIR_ICS=""
       ;;
+    "CHEYENNE")
+      EXTRN_MDL_FILES_SYSBASEDIR_ICS="/glade/p/ral/jntp/UFS_CAM/COMGFS"
+      ;;
     *)
       print_err_msg_exit "\
 The system directory in which to look for the files generated by the ex-
@@ -99,6 +102,9 @@ this machine and external model combination:
     "ODIN")
       EXTRN_MDL_FILES_SYSBASEDIR_ICS="/scratch/ywang/test_runs/FV3_regional/gfs"
       ;;
+    "CHEYENNE")
+      EXTRN_MDL_FILES_SYSBASEDIR_ICS="/glade/p/ral/jntp/UFS_CAM/COMGFS"
+      ;;
     *)
       print_err_msg_exit "\
 The system directory in which to look for the files generated by the ex-
@@ -219,6 +225,9 @@ else
     "ODIN")
       EXTRN_MDL_FILES_SYSBASEDIR_LBCS=""
       ;;
+    "CHEYENNE")
+      EXTRN_MDL_FILES_SYSBASEDIR_LBCS="/glade/p/ral/jntp/UFS_CAM/COMGFS"
+      ;;
     *)
       print_err_msg_exit "\
 The system directory in which to look for the files generated by the ex-

ush/setup.sh

@@ -323,16 +323,11 @@ Then remove this message and rerun."
 #
 "CHEYENNE")
 #
-  print_err_msg_exit "\
-Don't know how to set several parameters on MACHINE=\"$MACHINE\".
-Please specify the correct parameters for this machine in the setup script.  
-Then remove this message and rerun."
-
-  NCORES_PER_NODE=
-  SCHED=""
-  QUEUE_DEFAULT=${QUEUE_DEFAULT:-""}
+  NCORES_PER_NODE=36
+  SCHED="pbs"
+  QUEUE_DEFAULT=${QUEUE_DEFAULT:-"regular"}
   QUEUE_HPSS=${QUEUE_HPSS:-""}
-  QUEUE_FCST=${QUEUE_FCST:-""}
+  QUEUE_FCST=${QUEUE_FCST:-"regular"}
 #
 esac
 #
@@ -683,6 +678,10 @@ case $MACHINE in
   FIXgsm="/scratch/ywang/fix/theia_fix/fix_am"
   SFC_CLIMO_INPUT_DIR="/scratch1/NCEPDEV/da/George.Gayno/ufs_utils.git/climo_fields_netcdf"
   ;;
+"CHEYENNE")
+  FIXgsm="/glade/p/ral/jntp/UFS_CAM/fix_am"
+  SFC_CLIMO_INPUT_DIR="/glade/p/ral/jntp/UFS_CAM/climo_fields_netcdf"
+  ;;
 
 *)
   print_err_msg_exit "\
@@ -707,7 +706,7 @@ esac
 mng_extrns_cfg_fn="$HOMErrfs/Externals.cfg"
 property_name="local_path"
 #
-# Get the base directory of the FV3 forecast model code code.
+# Get the base directory of the FV3 forecast model code.
 #
 external_name="ufs_weather_model"
 UFS_WTHR_MDL_DIR=$( \
@@ -764,6 +763,25 @@ Please clone the external repository containing the code in this direct-
 ory, build the executable, and then rerun the workflow."
 fi
 #
+# Get the base directory of the EMC_post code.
+#
+external_name="EMC_post"
+EMC_POST_DIR=$( \
+get_manage_externals_config_property \
+"${mng_extrns_cfg_fn}" "${external_name}" "${property_name}" ) || \
+print_err_msg_exit "\
+Call to function get_manage_externals_config_property failed."
+
+EMC_POST_DIR="$HOMErrfs/${EMC_POST_DIR}"
+if [ ! -d "${EMC_POST_DIR}" ]; then
+  print_err_msg_exit "\
+The base directory in which the EMC_post source code should be located
+(EMC_POST_DIR) does not exist:
+  EMS_POST_DIR = \"${EMC_POST_DIR}\"
+Please clone the external repository containing the code in this directory,
+build the executable, and then rerun the workflow."
+fi
+#
 #-----------------------------------------------------------------------
 #
 # Set the names of the various tasks in the rocoto workflow XML.

ush/templates/diag_table.FV3_CPT_v0

@@ -271,7 +271,12 @@
 "gfs_phys",    "nbdsf_ave",    "nbdsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "nddsf_ave",    "nddsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "trans_ave",    "trans_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
-
+# Stochastic physics
+"gfs_phys",    "sppt_wts",      "sppt_wts",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebu_wts",     "skebu_wts",     "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebv_wts",     "skebv_wts",     "fv3_history",  "all", .false., "none", 2
+"dynamics",    "diss_est",      "diss_est",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "shum_wts",      "shum_wts",      "fv3_history",  "all", .false., "none", 2
 #=============================================================================================
 #
 #====> This file can be used with diag_manager/v2.0a (or higher) <====

ush/templates/diag_table.FV3_GFS_2017_gfdlmp

@@ -270,7 +270,12 @@
 "gfs_phys",    "nbdsf_ave",    "nbdsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "nddsf_ave",    "nddsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "trans_ave",    "trans_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
-
+# Stochastic physics
+"gfs_phys",    "sppt_wts",      "sppt_wts",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebu_wts",     "skebu_wts",     "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebv_wts",     "skebv_wts",     "fv3_history",  "all", .false., "none", 2
+"dynamics",    "diss_est",      "diss_est",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "shum_wts",      "shum_wts",      "fv3_history",  "all", .false., "none", 2
 #=============================================================================================
 #
 #====> This file can be used with diag_manager/v2.0a (or higher) <====

ush/templates/diag_table.FV3_GFS_v15p2

@@ -270,6 +270,12 @@
 "gfs_phys",    "nbdsf_ave",    "nbdsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "nddsf_ave",    "nddsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "trans_ave",    "trans_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+# Stochastic physics
+"gfs_phys",    "sppt_wts",      "sppt_wts",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebu_wts",     "skebu_wts",     "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebv_wts",     "skebv_wts",     "fv3_history",  "all", .false., "none", 2
+"dynamics",    "diss_est",      "diss_est",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "shum_wts",      "shum_wts",      "fv3_history",  "all", .false., "none", 2
 
 #=============================================================================================
 #

ush/templates/diag_table.FV3_GFS_v16beta

@@ -270,6 +270,12 @@
 "gfs_phys",    "nbdsf_ave",    "nbdsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "nddsf_ave",    "nddsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_phys",    "trans_ave",    "trans_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+# Stochastic physics
+"gfs_phys",    "sppt_wts",      "sppt_wts",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebu_wts",     "skebu_wts",     "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebv_wts",     "skebv_wts",     "fv3_history",  "all", .false., "none", 2
+"dynamics",    "diss_est",      "diss_est",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "shum_wts",      "shum_wts",      "fv3_history",  "all", .false., "none", 2
 
 #=============================================================================================
 #

ush/templates/diag_table.FV3_GSD_SAR

@@ -319,6 +319,12 @@
 # Prognostic/diagnostic variables from RUC LSM
 "gfs_sfc",     "snowfall_acc",     "snowfall_acc",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_sfc",     "swe_snowfall_acc", "swe_snowfall_acc", "fv3_history2d",  "all",  .false.,  "none",  2
+# Stochastic physics
+"gfs_phys",    "sppt_wts",      "sppt_wts",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebu_wts",     "skebu_wts",     "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebv_wts",     "skebv_wts",     "fv3_history",  "all", .false., "none", 2
+"dynamics",    "diss_est",      "diss_est",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "shum_wts",      "shum_wts",      "fv3_history",  "all", .false., "none", 2
 
 #=============================================================================================
 #

ush/templates/diag_table.FV3_GSD_v0

@@ -319,6 +319,12 @@
 # Prognostic/diagnostic variables from RUC LSM
 "gfs_sfc",     "snowfall_acc",     "snowfall_acc",     "fv3_history2d",  "all",  .false.,  "none",  2
 "gfs_sfc",     "swe_snowfall_acc", "swe_snowfall_acc", "fv3_history2d",  "all",  .false.,  "none",  2
+# Stochastic physics
+"gfs_phys",    "sppt_wts",      "sppt_wts",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebu_wts",     "skebu_wts",     "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "skebv_wts",     "skebv_wts",     "fv3_history",  "all", .false., "none", 2
+"dynamics",    "diss_est",      "diss_est",      "fv3_history",  "all", .false., "none", 2
+"gfs_phys",    "shum_wts",      "shum_wts",      "fv3_history",  "all", .false., "none", 2
 
 #=============================================================================================
 #

ush/templates/input.nml.FV3_CPT_v0

@@ -325,28 +325,31 @@
        FSNOS    = 99999,
        FSICS    = 99999,
 /
+
 &nam_stochy
-  lon_s=768,
-  lat_s=384,
-  ntrunc=382,
-  SKEBNORM=1,
-  SKEB_NPASS=30,
-  SKEB_VDOF=5,
-  SKEB=-999.,
-  SKEB_TAU=2.16E4,
-  SKEB_LSCALE=1000.E3,
-  SHUM=-999.,
-  SHUM_TAU=21600,
-  SHUM_LSCALE=500000,
-  SPPT=-999.,
-  SPPT_TAU=21600,
-  SPPT_LSCALE=500000,
-  SPPT_LOGIT=.TRUE.,
-  SPPT_SFCLIMIT=.TRUE.,
-  ISEED_SHUM=1,
-  ISEED_SKEB=2,
-  ISEED_SPPT=3,
+     new_lscale=.true.,
+     sppt=1.0,
+     sppt_tau = 2.16E4,
+     sppt_lscale=150.E3,
+     USE_ZMTNBLCK=.FALSE.,
+     SPPT_LOGIT=.TRUE.,
+     SPPT_SFCLIMIT=.FALSE.,
+     ISEED_SPPT=1,
+     SHUM=0.006,
+     SHUM_TAU=21600,
+     SHUM_LSCALE=150.E3,
+     ISEED_SHUM=2,
+     SKEBNORM=1,
+     SKEB=0.5,
+     SKEB_VDOF=10,
+     SKEB_TAU=21600.,
+     SKEB_LSCALE=150.E3,
+     ISEED_SKEB=3,
+     skebint=3600,
+     spptint=3600,
+     shumint=3600,
 /
+
 &nam_sfcperts
 /
 

ush/templates/input.nml.FV3_GSD_SAR

@@ -272,26 +272,27 @@
 /
 
 &nam_stochy
-     lon_s=768,
-     lat_s=384, 
-     ntrunc=382,
-     SKEBNORM=1,
-     SKEB_NPASS=30,
-     SKEB_VDOF=5,
-     SKEB=@[SKEB],
-     SKEB_TAU=2.16E4,
-     SKEB_LSCALE=1000.E3,
-     SHUM=@[SHUM],
-     SHUM_TAU=21600,
-     SHUM_LSCALE=500000,
-     SPPT=@[SPPT],
-     SPPT_TAU=21600,
-     SPPT_LSCALE=500000,
+     new_lscale=.true.,
+     sppt=1.0,
+     sppt_tau = 2.16E4,
+     sppt_lscale=150.E3,
+     USE_ZMTNBLCK=.FALSE.,
      SPPT_LOGIT=.TRUE.,
-     SPPT_SFCLIMIT=.TRUE.,
-     ISEED_SHUM=1,
-     ISEED_SKEB=2,
-     ISEED_SPPT=3,
+     SPPT_SFCLIMIT=.FALSE.,
+     ISEED_SPPT=1,
+     SHUM=0.006,
+     SHUM_TAU=21600,
+     SHUM_LSCALE=150.E3,
+     ISEED_SHUM=2,
+     SKEBNORM=1,
+     SKEB=0.5,
+     SKEB_VDOF=10,
+     SKEB_TAU=21600.,
+     SKEB_LSCALE=150.E3,
+     ISEED_SKEB=3,
+     skebint=3600,
+     spptint=3600,
+     shumint=3600,
 /
 
 &nam_sfcperts