Merge branch 'develop' into feature/jdas_enkf_diag_com_in_out

mingshichen-noaa · Oct 10, 2024 · 2e83482 · 2e83482
2 parents 268190e + a0771f8
commit 2e83482
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diff --git a/ci/cases/pr/C48_S2SWA_gefs.yaml b/ci/cases/pr/C48_S2SWA_gefs.yaml
@@ -15,7 +15,7 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_ci_defaults.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_defaults_ci.yaml
 
 skip_ci_on_hosts:
   - wcoss2
diff --git a/ci/cases/pr/C96_S2SWA_gefs_replay_ics.yaml b/ci/cases/pr/C96_S2SWA_gefs_replay_ics.yaml
@@ -0,0 +1,19 @@
+experiment:
+  system: gefs
+  mode: forecast-only
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: S2SWA
+  resdetatmos: 96
+  resdetocean: 1.0
+  resensatmos: 96
+  nens: 2
+  gfs_cyc: 1
+  start: warm
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  idate: 2020110100
+  edate: 2020110100
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_replay_ci.yaml
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96mx100/20240610
diff --git a/ci/cases/yamls/gefs_ci_defaults.yaml → ci/cases/yamls/gefs_defaults_ci.yaml b/ci/cases/yamls/gefs_ci_defaults.yaml → ci/cases/yamls/gefs_defaults_ci.yaml
diff --git a/ci/cases/yamls/gefs_replay_ci.yaml b/ci/cases/yamls/gefs_replay_ci.yaml
@@ -0,0 +1,14 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
+base:
+  ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  REPLAY_ICS: "YES"
+  FCST_BREAKPOINTS: ""
+  FHMAX_GFS: 48
+  FHMAX_HF_GFS: 24
+  DO_EXTRACTVARS: "YES"
+  FHOUT_HF_GFS: 3
+  FHOUT_OCN_GFS: 24
+  FHOUT_ICE_GFS: 24
+  HOMEDIR: {{ 'RUNTESTS' | getenv }}/GLOBAL
+
diff --git a/jobs/JGLOBAL_WAVE_POST_PNT b/jobs/JGLOBAL_WAVE_POST_PNT
@@ -25,7 +25,7 @@ export WAV_MOD_TAG=${RUN}wave${waveMEMB}
 
 export CFP_VERBOSE=1
 
-export FHMAX_WAV_PNT=${FHMAX_WAV}
+export FHMAX_WAV_PNT=$(( FHMAX_WAV - OFFSET_START_HOUR ))
 export DOSPC_WAV='YES' # Spectral post
 export DOBLL_WAV='YES' # Bulletin post
 export DOBNDPNT_WAV='NO'  #not boundary points

diff --git a/parm/archive/enkf.yaml.j2 b/parm/archive/enkf.yaml.j2
@@ -4,15 +4,15 @@ enkf:
     required:
         # Logs
         {% for mem in range(1, nmem_ens + 1) %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}fcst_mem{{ '%03d' % mem }}.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_fcst_mem{{ '%03d' % mem }}.log"
         {% endfor %}
         {% for fhr in range(fhmin, fhmax + 1, fhout) %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}epos{{ '%03d' % (fhr - fhmin) }}.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_epos{{ '%03d' % (fhr - fhmin) }}.log"
         {% endfor %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}echgres.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}esfc.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_echgres.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_esfc.log"
         {% for grp in range(IAUFHRS | length) %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ecen{{ '%03d' % grp }}.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_ecen{{ '%03d' % grp }}.log"
         {% endfor %}
 
         {% if lobsdiag_forenkf %}
@@ -33,7 +33,7 @@ enkf:
         {% endif %}
 
         {% for step in steps %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}{{ step }}.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_{{ step }}.log"
         {% endfor %}
 
         # Ensemble mean and spread

diff --git a/parm/archive/gdas.yaml.j2 b/parm/archive/gdas.yaml.j2
@@ -5,33 +5,33 @@ gdas:
     required:
         {% if MODE == "cycled" %}
         # Cycled logs
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlprod.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}prep.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmanlprod.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_prep.log"
             {% if DO_JEDIATMVAR %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}prepatmiodaobs.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlinit.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlprod.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlfinal.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlfv3inc.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlvar.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_prepatmiodaobs.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmanlinit.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmanlprod.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmanlfinal.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmanlfv3inc.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmanlvar.log"
             {% else %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}anal.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}analdiag.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_anal.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_analdiag.log"
             {% endif %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlupp.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmanlupp.log"
             {% if DO_JEDIOCNVAR %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}prepoceanobs.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlinit.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}marinebmat.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlvar.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlfinal.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlchkpt.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_prepoceanobs.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_marineanlinit.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_marinebmat.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_marineanlvar.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_marineanlfinal.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_marineanlchkpt.log"
                 {% if DOHYBVAR %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalecen.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_ocnanalecen.log"
                 {% endif %}
             {% endif %}
             {% if DO_VRFY_OCEANDA %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalvrfy.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_ocnanalvrfy.log"
             {% endif %}
 
         # Analysis GRIB2 (sub-sampled) data
@@ -85,7 +85,7 @@ gdas:
         - "{{ COMIN_ATMOS_OZNMON | relpath(ROTDIR) }}/time/bad_pen.{{ cycle_YMDH }}"
         - "{{ COMIN_ATMOS_OZNMON | relpath(ROTDIR) }}/time/stdout.time.tar.gz"
         - "{{ COMIN_ATMOS_OZNMON | relpath(ROTDIR) }}/horiz/stdout.horiz.tar.gz"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}verfozn.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_verfozn.log"
             {% endif %}
 
         # Radiance verification
@@ -94,7 +94,7 @@ gdas:
         - "{{ COMIN_ATMOS_RADMON | relpath(ROTDIR) }}/radmon_bcoef.tar.gz"
         - "{{ COMIN_ATMOS_RADMON | relpath(ROTDIR) }}/radmon_bcor.tar.gz"
         - "{{ COMIN_ATMOS_RADMON | relpath(ROTDIR) }}/radmon_time.tar.gz"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}verfrad.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_verfrad.log"
             {% endif %}
 
         # Minimization monitor
@@ -104,18 +104,18 @@ gdas:
         - "{{ COMIN_ATMOS_MINMON | relpath(ROTDIR) }}/{{ cycle_YMDH }}.gnorms.ieee_d"
         - "{{ COMIN_ATMOS_MINMON | relpath(ROTDIR) }}/{{ cycle_YMDH }}.reduction.ieee_d"
         - "{{ COMIN_ATMOS_MINMON | relpath(ROTDIR) }}/gnorm_data.txt"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}vminmon.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_vminmon.log"
             {% endif %}
         {% endif %}  # End of cycled data
 
         # Forecast and post logs
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}fcst_seg0.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_fcst_seg0.log"
 
         {% for fhr in range(0, FHMAX + 1, 3) %}
             {% set fhr3 = '%03d' % fhr %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmos_prod_f{{ fhr3 }}.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmos_prod_f{{ fhr3 }}.log"
             {% if not WRITE_DOPOST %}
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}atmos_upp_f{{ fhr3 }}.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}_atmos_upp_f{{ fhr3 }}.log"
             {% endif %}  ## not WRITE_DOPOST
         # Forecast GRIB2 data
         - "{{ COMIN_ATMOS_GRIB_0p25 | relpath(ROTDIR) }}/{{ head }}pgrb2.0p25.f{{ fhr3 }}"

diff --git a/parm/archive/gefs_arcdir.yaml.j2 b/parm/archive/gefs_arcdir.yaml.j2
@@ -17,11 +17,17 @@
 
 {% set COMIN_ATMOS_ENSSTAT_1p00 = COM_ATMOS_GRIB_GRID_TMPL | replace_tmpl(tmpl_dict) %}
 
+{% if REPLAY_ICS %}
+    {% set ofst_hr = FHOUT_GFS %}
+{% else %}
+    {% set ofst_hr = FHMIN_GFS %}
+{% endif %}
+
 # Select ensstat files to copy to the arcdir
 {% if RUN == "gefs" %}
     {% set ensstat_files = [] %}
     {% if path_exists(COMIN_ATMOS_ENSSTAT_1p00) %}
-        {% for fhr in range(FHMIN_GFS, FHMAX_GFS + FHOUT_GFS, FHOUT_GFS) %}
+        {% for fhr in range(ofst_hr, FHMAX_GFS + FHOUT_GFS, FHOUT_GFS) %}
             {% do ensstat_files.append([COMIN_ATMOS_ENSSTAT_1p00 ~ "/" ~ head ~ "mean.pres_." ~
                                         "1p00" ~ ".f" ~ '%03d'|format(fhr) ~ ".grib2",
                                         GEFS_ARCH]) %}

diff --git a/parm/archive/gfsa.yaml.j2 b/parm/archive/gfsa.yaml.j2
@@ -6,7 +6,7 @@ gfsa:
         # Logs
         # TODO explicitly name all logs to include
         {% for log in glob("logs/" ~ cycle_YMDH ~ "/gfs*.log") %}
-        {% if not "gfsarch.log" in log %}
+        {% if not "gfs_arch.log" in log %}
         - "{{ log }}"
         {% endif %}
         {% endfor %}

diff --git a/parm/config/gefs/config.atmos_products b/parm/config/gefs/config.atmos_products
@@ -16,7 +16,12 @@ export INTERP_ATMOS_MASTERSH="${USHgfs}/interp_atmos_master.sh"
 export INTERP_ATMOS_SFLUXSH="${USHgfs}/interp_atmos_sflux.sh"
 
 export downset=2
-export FHOUT_PGBS=${FHOUT_GFS:-3}  # Output frequency of supplemental gfs pgb file at 1.0 and 0.5 deg
+
+if [[ "${FHMAX_HF_GFS:-0}" == "0" ]]; then
+    export FHOUT_PGBS=${FHOUT_GFS:-3}  # Output frequency of supplemental gfs pgb file at 1.0 and 0.5 deg
+else
+    export FHOUT_PGBS=${FHOUT_HF_GFS:-1}
+fi
 export FLXGF="NO"  # Create interpolated sflux.1p00 file
 
 # paramlist files for the different forecast hours and downsets

diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
@@ -229,6 +229,15 @@ export FHOUT_ICE=3
 # GFS cycle info
 export gfs_cyc=@gfs_cyc@ # 0: no GFS cycle, 1: 00Z only, 2: 00Z and 12Z only, 4: all 4 cycles.
 
+# set variables needed for use with REPLAY ICs
+export REPLAY_ICS=@REPLAY_ICS@
+if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
+    export OFFSET_START_HOUR=$(( assim_freq / 2 ))
+else
+    export OFFSET_START_HOUR=0
+fi
+
+
 # GFS output and frequency
 export FHMIN_GFS=0
 export FHMAX_GFS="@FHMAX_GFS@"
@@ -238,10 +247,10 @@ export FCST_SEGMENTS="${FHMIN_GFS},${breakpnts:+${breakpnts},}${FHMAX_GFS}"
 
 export FHOUT_GFS=6
 export FHMAX_HF_GFS=@FHMAX_HF_GFS@
-export FHOUT_HF_GFS=1
-export FHOUT_OCN_GFS=6
-export FHOUT_ICE_GFS=6
-export FHMIN_WAV=0
+export FHOUT_HF_GFS=@FHOUT_HF_GFS@
+export FHOUT_OCN_GFS=@FHOUT_OCN_GFS@
+export FHOUT_ICE_GFS=@FHOUT_ICE_GFS@
+export FHMIN_WAV=${OFFSET_START_HOUR:-0}
 export FHOUT_WAV=3
 export FHMAX_HF_WAV=120
 export FHOUT_HF_WAV=1
@@ -290,20 +299,9 @@ export NMEM_ENS=@NMEM_ENS@
 export ENSMEM=${ENSMEM:-"000"}
 export MEMDIR="mem${ENSMEM}"
 
-# initialize ocean ensemble members with perturbations
-#   if true, only occurs for members greater than zero
-export REPLAY_ICS=@REPLAY_ICS@
-if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
-    export OFFSET_START_HOUR=$(( assim_freq / 2 ))
-else
-    export OFFSET_START_HOUR=0
-fi
-
 export DOIAU="NO"  # While we are not doing IAU, we may want to warm start w/ IAU in the future
-# Check if cycle is cold starting
-if [[ "${EXP_WARM_START}" = ".false." ]]; then
-  export IAU_FHROT=${OFFSET_START_HOUR}
-else
+# Check if cycle is warm starting with IAU
+if [[ "${EXP_WARM_START}" = ".true." ]]; then
   if [[ "${DOIAU}" = "YES" ]]; then
     export IAU_FHROT=3
   else

diff --git a/parm/config/gefs/config.efcs b/parm/config/gefs/config.efcs
@@ -46,10 +46,6 @@ export SKEB_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
 export SKEBNORM=1
 export SKEB_NPASS=30
 export SKEB_VDOF=5
-export DO_SHUM="YES"
-export SHUM=0.005
-export SHUM_TAU=21600.
-export SHUM_LSCALE=500000.
 export DO_SPPT="YES"
 export SPPT="0.56,0.28,0.14,0.056,0.028"
 export SPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"

diff --git a/parm/config/gefs/config.extractvars b/parm/config/gefs/config.extractvars
@@ -14,7 +14,7 @@ export compress_ice=1 #1: Compress extracted ice product, 0: Do not compress ext
 
 export ocnres="1p00" # Resolution of ocean products
 export iceres="native" # Resolution of ice products
-export wavres="0p25" # Resolution of wave products
+export wavres="${waveGRD:4:1}p${waveGRD:5:2}"  # Resolution of wave products
 
 export depthvar_name="z_l" # Name of depth variable in NetCDF ocean products
 export zmin="0." # Minimum depth to extract from NetCDF ocean products

diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
@@ -11,7 +11,11 @@ base:
   DO_EXTRACTVARS: "NO"
   FHMAX_GFS: 120
   FHMAX_HF_GFS: 0
+  FHOUT_HF_GFS: 1
   FCST_BREAKPOINTS: "48"
   REPLAY_ICS: "NO"
   USE_OCN_PERTURB_FILES: "false"
+  FHOUT_OCN_GFS: 6
+  FHOUT_ICE_GFS: 6
+  HPSSARCH: "NO"
   LOCALARCH: "NO"
diff --git a/parm/product/gefs.0p25.fFFF.paramlist.a.txt b/parm/product/gefs.0p25.fFFF.paramlist.a.txt
@@ -12,13 +12,14 @@
 :CSNOW:surface:
 :CFRZR:surface:
 :CICEP:surface:
+:FDNSSTMP:surface:
 :PWAT:entire atmosphere (considered as a single layer):
 :CAPE:180-0 mb above ground:
 :CAPE:surface:
 :CIN:180-0 mb above ground:
 :CIN:surface:
 :HLCY:3000-0 m above ground:
-:TCDC:entire atmosphere:
+:TCDC:entire atmosphere (considered as a single layer):
 :WEASD:surface:
 :SNOD:surface:
 :ULWRF:top of atmosphere:

diff --git a/parm/product/gefs.0p25.fFFF.paramlist.b.txt b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
@@ -346,6 +346,7 @@
 :TMP:surface:
 :TMP:tropopause:
 :TOZNE:entire atmosphere (considered as a single layer):
+:TSNOWP:surface:
 :TSOIL:0.1-0.4 m below ground:
 :TSOIL:0.4-1 m below ground:
 :TSOIL:1-2 m below ground:

diff --git a/parm/stage/atmosphere_perturbation.yaml.j2 → ...tage/atmosphere_ens_perturbations.yaml.j2 b/parm/stage/atmosphere_perturbation.yaml.j2 → ...tage/atmosphere_ens_perturbations.yaml.j2
@@ -1,12 +1,12 @@
-atmosphere_perturbation:
+atmosphere_ens_perturbation:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
     copy:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.fv3_perturbation.nc", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}/{{ RUN }}.t{{ current_cycle_HH }}z.atminc.nc"]

diff --git a/parm/stage/master_gefs.yaml.j2 b/parm/stage/master_gefs.yaml.j2
@@ -116,7 +116,7 @@
 
 {% if REPLAY_ICS %}
 {% filter indent(width=4) %}
-{% include "atmosphere_perturbation.yaml.j2" %}
+{% include "atmosphere_ens_perturbations.yaml.j2" %}
 {% endfilter %}
 {% endif %}
 
@@ -137,7 +137,7 @@
 {% endif %}
 {% if REPLAY_ICS %}
 {% filter indent(width=4) %}
-{% include "ocean_replay.yaml.j2" %}
+{% include "ocean_ens_perturbations.yaml.j2" %}
 {% endfilter %}
 {% endif %}
 {% if EXP_WARM_START %}

diff --git a/parm/stage/ocean_replay.yaml.j2 → parm/stage/ocean_ens_perturbations.yaml.j2 b/parm/stage/ocean_replay.yaml.j2 → parm/stage/ocean_ens_perturbations.yaml.j2
@@ -1,12 +1,12 @@
-ocean_replay:
+ocean_ens_perturbation:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_OCEAN_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
     copy:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}
         - ["{{ ICSDIR }}/{{ COMOUT_OCEAN_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.mom6_perturbation.nc", "{{ COMOUT_OCEAN_ANALYSIS_MEM }}/mom6_increment.nc"]

diff --git a/scripts/exgfs_wave_post_pnt.sh b/scripts/exgfs_wave_post_pnt.sh
@@ -252,7 +252,9 @@ source "${USHgfs}/preamble.sh"
                                ww3_outp_spec.inp.tmpl > ww3_outp.inp
 
     ${NLN} mod_def.$waveuoutpGRD mod_def.ww3
-    HMS="${cyc}0000"
+    #export OFFSET_START_HOUR=$( printf "%02d" ${half_assim} )
+    hh=$( printf "%02d" $(( cyc + OFFSET_START_HOUR )) )
+    HMS="${hh}0000"
     if [[ -f "${COMIN_WAVE_HISTORY}/${WAV_MOD_TAG}.out_pnt.${waveuoutpGRD}.${PDY}.${HMS}" ]]; then
       ${NLN} "${COMIN_WAVE_HISTORY}/${WAV_MOD_TAG}.out_pnt.${waveuoutpGRD}.${PDY}.${HMS}" \
         "./out_pnt.${waveuoutpGRD}"

diff --git a/ush/extractvars_tools.sh b/ush/extractvars_tools.sh
@@ -17,7 +17,8 @@ check_atmos() {
   done
   mapfile -t requestedvar_in_allgrb2file_arr < "${requestedvar_in_allgrb2file}"
   while read -r vari; do
-    if [[ ! ${requestedvar_in_allgrb2file_arr[*]} =~ ${vari} ]] ;then
+    # shellcheck disable=SC2076
+    if [[ ! ${requestedvar_in_allgrb2file_arr[*]} =~ "${vari}" ]] ;then
       echo "WARNING: PARM VARIABLE (${vari}) is not available in pgrb and pgrb2b for f${fnhl}."
     fi
   done <"${varlistl}"