Add GEFS capability to setup_expt

Allows GEFS experiment directories to be set up using `setup_expt.py`.
To facilitate this, a new positional argument is added in the first
position to specify which system to set up: `gfs` or `gefs`. If gfs is
chosen, the second positional argument is to choose the mode, and allows
the same values as before: `cycled` and `forecast-only`. If gefs is
chosen, forecast-only is assumed and no second positional argument is
required.

To allow both gfs and gefs configure files to exist in workflow
concurrently, the `parm/config` directory contains two new directories:
gfs and gefs. All of the old config files have been moved into the gfs
directory. A few select config files have also been copied to the gefs
directory. As yet, they are unmodified (except the changes noted below).
These config files will be updated in a future PR so the modifications
for GEFS are not hidden in the new file creation. The `yaml/defaults`
is also copied over, but the contents were removed since GEFS will not
be running its own analyses.

A couple variables have been renamed to be more appropriate for use in
both systems: `NMEM_ENKF`, `NMEM_EFCS`, and `CASE_ENKF` are now
`NMEM_ENS`, `NMEM_ENS_GFS`, and `CASE_ENS` respectively. Further,
`NMEM_EFCS` and `HOMEfv3gfs` were removed as unused.

Finally, resolution validation was extended to the ensemble resolution
as well.

Fixes: NOAA-EMC#1576

docs/source/setup.rst

@@ -84,12 +84,13 @@ The following command examples include variables for reference but users should
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC] [--resdet $RESDET]
+   ./setup_expt.py gfs forecast-only --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC] [--resdet $RESDET]
      [--pslot $PSLOT] [--configdir $CONFIGDIR] [--comrot $COMROT] [--expdir $EXPDIR]
 
 where:
 
-   * ``forecast-only`` is the first positional argument that instructs the setup script to produce an experiment directory for forecast only experiments.
+   * ``gfs`` is the first positional argument that instructs the setup script to produce a GFS experiment directory
+   * ``forecast-only`` is the second positional argument that instructs the setup script to produce an experiment directory for forecast only experiments.
    * ``$APP`` is the target application, one of:
 
      - ATM: atmosphere-only [default]
@@ -116,21 +117,21 @@ Atm-only:
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --pslot test --idate 2020010100 --edate 2020010118 --resdet 384 --gfs_cyc 4 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
+   ./setup_expt.py gfs forecast-only --pslot test --idate 2020010100 --edate 2020010118 --resdet 384 --gfs_cyc 4 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
 
 Coupled:
 
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --app S2SW --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
+   ./setup_expt.py gfs forecast-only --app S2SW --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
 
 Coupled with aerosols:
 
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --app S2SWA --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
+   ./setup_expt.py gfs forecast-only --app S2SWA --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
 
 ****************************************
 Step 2: Set user and experiment settings
@@ -193,13 +194,14 @@ The following command examples include variables for reference but users should
 ::
 
    cd workflow
-   ./setup_expt.py cycled --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC]
+   ./setup_expt.py gfs cycled --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC]
      [--resdet $RESDET] [--resens $RESENS] [--nens $NENS] [--cdump $CDUMP]
      [--pslot $PSLOT] [--configdir $CONFIGDIR] [--comrot $COMROT] [--expdir $EXPDIR] [--icsdir $ICSDIR]
 
 where:
 
-   * ``cycled`` is the first positional argument that instructs the setup script to produce an experiment directory for cycled experiments.
+   * ``gfs`` is the first positional argument that instructs the setup script to produce a GFS experiment directory
+   * ``cycled`` is the second positional argument that instructs the setup script to produce an experiment directory for cycled experiments.
    * ``$APP`` is the target application, one of:
 
      - ATM: atmosphere-only [default]
@@ -226,13 +228,13 @@ Example:
 ::
 
    cd workflow
-   ./setup_expt.py cycled --pslot test --configdir /home/Joe.Schmo/git/global-workflow/parm/config --idate 2020010100 --edate 2020010118 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir --resdet 384 --resens 192 --nens 80 --gfs_cyc 4
+   ./setup_expt.py gfs cycled --pslot test --configdir /home/Joe.Schmo/git/global-workflow/parm/config --idate 2020010100 --edate 2020010118 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir --resdet 384 --resens 192 --nens 80 --gfs_cyc 4
 
 Example ``setup_expt.py`` on Orion:
 
 ::
 
-   Orion-login-3$ ./setup_expt.py cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
+   Orion-login-3$ ./setup_expt.py gfs cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
    EDITED:  /work/noaa/global/jschmo/expdir/test/config.base as per user input.
    EDITED:  /work/noaa/global/jschmo/expdir/test/config.aeroanl as per user input.
    EDITED:  /work/noaa/global/jschmo/expdir/test/config.ocnanal as per user input.
@@ -243,7 +245,7 @@ What happens if I run ``setup_expt.py`` again for an experiment that already exi
 
 ::
 
-   Orion-login-3$ ./setup_expt.py cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
+   Orion-login-3$ ./setup_expt.py gfs cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
 
    directory already exists in /work/noaa/stmp/jschmo/comrot/test
 

jobs/JGDAS_ENKF_DIAG

@@ -24,7 +24,7 @@ export gcyc=${GDATE:8:2}
 export GDUMP="gdas"
 export GDUMP_ENS="enkf${GDUMP}"
 
-export CASE=${CASE_ENKF}
+export CASE=${CASE_ENS}
 
 export OPREFIX="${CDUMP}.t${cyc}z."
 export APREFIX="${RUN}.t${cyc}z."

jobs/JGDAS_ENKF_ECEN

@@ -21,7 +21,7 @@ export gcyc=${GDATE:8:2}
 export GDUMP="gdas"
 export GDUMP_ENS="enkf${GDUMP}"
 
-export CASE=${CASE_ENKF}
+export CASE=${CASE_ENS}
 
 export OPREFIX="${CDUMP}.t${cyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."

jobs/JGDAS_ENKF_FCST

@@ -14,7 +14,7 @@ export rCDUMP="enkfgdas"
 # Begin JOB SPECIFIC work
 ##############################################
 
-export CASE=${CASE_ENKF}
+export CASE=${CASE_ENS}
 
 YMD=${PDY} HH=${cyc} generate_com -rx COM_TOP
 

jobs/JGDAS_ENKF_SFC

@@ -25,7 +25,7 @@ export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
-export CASE=${CASE_ENKF}
+export CASE=${CASE_ENS}
 
 export OPREFIX="${CDUMP}.t${cyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."

parm/config/config.base.emc.dyn → parm/config/gefs/config.base.emc.dyn

@@ -75,7 +75,6 @@ export MODE="@MODE@" # cycled/forecast-only
 ####################################################
 # Build paths relative to $HOMEgfs
 export FIXgsi="${HOMEgfs}/fix/gsi"
-export HOMEfv3gfs="${HOMEgfs}/sorc/fv3gfs.fd"
 export HOMEpost="${HOMEgfs}"
 export HOMEobsproc="${BASE_GIT}/obsproc/v1.1.2"
 
@@ -159,8 +158,8 @@ export OPS_RES="C768" # Do not change
 # Resolution specific parameters
 export LEVS=128
 export CASE="@CASECTL@"
-export CASE_ENKF="@CASEENS@"
-# TODO: This should not depend on $CASE or $CASE_ENKF
+export CASE_ENS="@CASEENS@"
+# TODO: This should not depend on $CASE or $CASE_ENS
 # These are the currently available grid-combinations
 case "${CASE}" in
     "C48") export OCNRES=500;;
@@ -306,8 +305,8 @@ export DO_MERGENSST="NO"
 
 # Hybrid related
 export DOHYBVAR="@DOHYBVAR@"
-export NMEM_ENKF=@NMEM_ENKF@
-export NMEM_EFCS=30
+export NMEM_ENS=@NMEM_ENS@
+export NMEM_ENS_GFS=@NMEM_ENS@
 export SMOOTH_ENKF="NO"
 export l4densvar=".true."
 export lwrite4danl=".true."

parm/config/config.efcs → parm/config/gefs/config.efcs

@@ -13,7 +13,7 @@ export DO_WAVE=${DO_WAVE_ENKF:-"NO"}
 
 # TODO: Possibly need OCNRES_ENKF, ICERES_ENKF, WAVRES_ENKF too
 if [[ ${DO_OCN} == "YES" ]]; then
-  case "$CASE_ENKF" in
+  case "$CASE_ENS" in
     "C48") export OCNRES=500;;
     "C96") export OCNRES=100;;
     "C192") export OCNRES=050;;
@@ -26,7 +26,7 @@ fi
 [[ ${DO_WAVE} == "YES" ]] && export waveGRD=${waveGRD_ENKF:-$waveGRD}  # TODO: will we run waves with a different resolution in the ensemble?
 
 # Source model specific information that is resolution dependent
-string="--fv3 $CASE_ENKF"
+string="--fv3 $CASE_ENS"
 [[ ${DO_OCN} == "YES" ]] && string="$string --mom6 $OCNRES"
 [[ ${DO_ICE} == "YES" ]] && string="$string --cice6 $ICERES"
 [[ ${DO_WAVE} == "YES" ]] && string="$string --ww3 ${waveGRD// /;}"
@@ -84,7 +84,7 @@ fi
 export cplwav=.false.
 
 # ocean model resolution
-case "$CASE_ENKF" in
+case "$CASE_ENS" in
     "C48") export OCNRES=500;;
     "C96") export OCNRES=100;;
     "C192") export OCNRES=050;;

parm/config/gefs/yaml/defaults.yaml

@@ -0,0 +1 @@
+# This file intentionally left blank