Merge branch 'develop' into feature/ocn-letkf-init

AndrewEichmann-NOAA · Jun 5, 2024 · 8881e2c · 8881e2c
2 parents 500db0f + 205d0c2
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diff --git a/ci/cases/pr/C96C48_ufs_hybatmDA.yaml b/ci/cases/pr/C96C48_ufs_hybatmDA.yaml
@@ -21,5 +21,4 @@ skip_ci_on_hosts:
   - hera
   - orion
   - hercules
-  - wcoss2
 
diff --git a/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml b/ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml
@@ -1,6 +1,5 @@
 defaults:
   !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
 base:
-  DOIAU: "NO"
   DO_JEDISNOWDA: "YES"
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
diff --git a/ci/scripts/clone-build_ci.sh b/ci/scripts/clone-build_ci.sh
@@ -74,7 +74,7 @@ set +e
 source "${HOMEgfs}/ush/module-setup.sh"
 export BUILD_JOBS=8
 rm -rf log.build
-./build_all.sh -gk  >> log.build 2>&1
+./build_all.sh -guk  >> log.build 2>&1
 build_status=$?
 
 DATE=$(date +'%D %r')

diff --git a/docs/source/hpc.rst b/docs/source/hpc.rst
@@ -22,7 +22,7 @@ HPC helpdesks
 * Hercules:  rdhpcs.hercules.help@noaa.gov
 * HPSS: rdhpcs.hpss.help@noaa.gov
 * Gaea: oar.gfdl.help@noaa.gov
-* S4: david.huber@noaa.gov
+* S4: innocent.souopgui@noaa.gov
 * Jet: rdhpcs.jet.help@noaa.gov
 * Cloud: rdhpcs.cloud.help@noaa.gov
 
@@ -48,7 +48,7 @@ https://aim.rdhpcs.noaa.gov/
 Optimizing the global workflow on S4
 ====================================
 
-The S4 cluster is relatively small and so optimizations are recommended to improve cycled runtimes. Please contact David Huber (david.huber@noaa.gov) if you are planning on running a cycled experiment on this system to obtain optimized configuration files.
+The S4 cluster is relatively small and so optimizations are recommended to improve cycled runtimes. Please contact Innocent Souopgui (innocent.souopgui@noaa.gov) if you are planning on running a cycled experiment on this system to obtain optimized configuration files.
 
 ============
 Git settings

diff --git a/docs/source/init.rst b/docs/source/init.rst
@@ -315,7 +315,7 @@ Manual Generation
 *****************
 
 .. note::
-   Initial conditions cannot be generated on S4. These must be generated on another supported platform then pushed to S4. If you do not have access to a supported system or need assistance, please contact David Huber (david.huber@noaa.gov).
+   Initial conditions cannot be generated on S4. These must be generated on another supported platform then pushed to S4. If you do not have access to a supported system or need assistance, please contact Innocent Souopgui (innocent.souopgui@noaa.gov).
 
 .. _coldstarts:
 

diff --git a/jobs/JGLOBAL_ATMOS_SFCANL b/jobs/JGLOBAL_ATMOS_SFCANL
@@ -4,40 +4,35 @@ source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "sfcanl" -c "base sfcanl"
 
 
-##############################################
-# Set variables used in the script
-##############################################
-export CDUMP="${RUN/enkf}"
-
-
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
-GDATE=$(${NDATE} -"${assim_freq}" "${PDY}${cyc}")
-# shellcheck disable=
-gPDY=${GDATE:0:8}
-gcyc=${GDATE:8:2}
-export GDUMP="gdas"
+GDATE=$(date --utc -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
+export GDATE
+
+RUN="gdas" YMD=${GDATE:0:8} HH=${GDATE:8:2} declare_from_tmpl -rx \
+  COMIN_OBS_PREV:COM_OBS_TMPL \
+  COMIN_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
+
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+  COMIN_OBS:COM_OBS_TMPL \
+  COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
+  COMIN_SNOW_ANALYSIS:COM_SNOW_ANALYSIS_TMPL
 
-export OPREFIX="${CDUMP}.t${cyc}z."
-export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${CDUMP}.t${cyc}z."
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+  COMOUT_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS COM_ATMOS_ANALYSIS COM_ATMOS_RESTART \
-    COM_SNOW_ANALYSIS
+mkdir -p "${COMOUT_ATMOS_RESTART}"
 
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COM_OBS_PREV:COM_OBS_TMPL \
-    COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
 
 ###############################################################
 # Run relevant script
 
 ${SFCANALSH:-${SCRgfs}/exglobal_atmos_sfcanl.sh}
 status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
+(( status != 0 )) && exit "${status}"
 
 
 ##############################################
@@ -48,14 +43,14 @@ status=$?
 # Final processing
 ##############################################
 if [[ -e "${pgmout}" ]] ; then
-  cat ${pgmout}
+  cat "${pgmout}"
 fi
 
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd ${DATAROOT}
-[[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}
+cd "${DATAROOT}"
+[[ "${KEEPDATA}" == "NO" ]] && rm -rf "${DATA}"
 
 
 exit 0
diff --git a/parm/archive/arcdir.yaml.j2 b/parm/archive/arcdir.yaml.j2
@@ -2,84 +2,118 @@
 {% set cycle_YMDH = current_cycle | to_YMDH %}
 {% set cycle_YMD = current_cycle | to_YMD %}
 {% set head = RUN + ".t" + cycle_HH + "z." %}
-{% if RUN == "gdas" or RUN == "gfs" %}
-deterministic:
-    mkdir:
-        - "{{ ARCDIR }}"
-        {% if RUN == "gfs" %}
-        - "{{ ARCDIR }}/tracker.{{ cycle_YMDH }}/{{ RUN }}"
-        {% endif %}
-        {% if FITSARC %}
-        {% set VFYARC = ROTDIR + "/vrfyarch" %}
-        - "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}"
-        {% endif %}
-    copy:
-        {% if current_cycle != SDATE and MODE == "cycled" %}
-        {% if DO_JEDIATMVAR %}
-        - ["{{ COM_ATMOS_ANALYSIS }}/{{ head }}atmstat", "{{ ARCDIR }}/atmstat.{{ RUN }}.{{ cycle_YMDH }}"]
-        {% else %}
-        - ["{{ COM_ATMOS_ANALYSIS }}/{{ head }}gsistat", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}"]
-        {% endif %}
-        {% if DO_JEDISNOWDA %}
-        - ["{{ COM_SNOW_ANALYSIS }}/{{ head }}snowstat.tgz", "{{ ARCDIR }}/snowstat.{{ RUN }}.{{ cycle_YMDH }}.tgz"]
-        {% endif %}
-        {% if AERO_ANL_CDUMP == RUN or AERO_ANL_CDUMP == "both" %}
-        - ["{{ COM_CHEM_ANALYSIS }}/{{ head }}aerostat", "{{ ARCDIR }}/aerostat.{{ RUN }}.{{ cycle_YMDH }}"]
-        {% endif %}
-        - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.anl", "{{ ARCDIR }}/pgbanl.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
-        {% endif %}  # Full cycle
-        {% if RUN == "gfs" %}
-        {% set fhmax, fhout = FHMAX_GFS, FHOUT_GFS %}
-        {% elif RUN == "gdas" %}
-        {% set fhmax, fhout = FHMAX, FHOUT %}
-        {% endif %}
-        {% for fhr in range(0, fhmax + fhout, fhout) %}
-        - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
-        {% endfor %}
-        {% if RUN == "gfs" %}
-        {% if FITSARC %}
-        {% if FHMAX_FITS is defined %}
-        {% set fhmax = FHMAX_FITS %}
-        {% else %}
-        {% set fhmax = FHMAX_GFS %}
-        {% endif %}
-        {% for fhr in range(0, fhmax + 6, 6) %}
-        {% set sfcfile = "/" + head + "sfcf" + '%03d'|format(fhr) + ".nc" %}
-        {% set sigfile = "/" + head + "atmf" + '%03d'|format(fhr) + ".nc" %}
-        - ["{{COM_ATMOS_HISTORY}}/{{ sfcfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sfcfile }}"]
-        - ["{{COM_ATMOS_HISTORY}}/{{ sigfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sigfile }}"]
-        {% endfor %}
-        {% endif %} ## FITSARC
-        {% if path_exists(COM_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH) %}
-        - ["{{ COM_ATMOS_GENESIS }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}"]
-        - ["{{ COM_ATMOS_GENESIS }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}"]
-        {% endif %}
-        {% if path_exists(COM_ATMOS_GENESIS ~ "/trak.gfso.atcfunix." ~ cycle_YMDH) %}
-        - ["{{ COM_ATMOS_GENESIS }}/trak.gfso.atcfunix.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.{{ cycle_YMDH }}"]
-        - ["{{ COM_ATMOS_GENESIS }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}"]
-        {% endif %}
-        ## Only created if tracking is on and there were systems to track
-        {% for basin in ["epac", "natl"] %}
-        {% if path_exists(COM_ATMOS_TRACK + "/" + basin) %}
-        - ["{{ COM_ATMOS_TRACK }}/{{ basin }}", "{{ ARCDIR }}/{{ basin }}"]
-        {% endif %}
-        {% endfor %}
-        {% endif %} ## RUN == "gfs"
-        {% if path_exists(COM_ATMOS_TRACK ~ "/atcfunix." ~ RUN ~ "." ~ cycle_YMDH) %}
-        - ["{{ COM_ATMOS_TRACK }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}"]
-        - ["{{ COM_ATMOS_TRACK }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}"]
-        {% endif %}
-{% endif %} # gfs or gdas
-{% if current_cycle != SDATE and (RUN == "enkfgdas" or RUN == "enkfgfs") %}
-ensemble:
-    mkdir:
-        - "{{ ARCDIR }}"
-    copy:
-        {% if DO_JEDIATMENS %}
-        - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atmensstat", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}"]
-        - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atminc.ensmean.nc", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}.ensmean.nc"]
-        {% else %}
-        - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}enkfstat", "{{ ARCDIR }}/enkfstat.{{ RUN }}.{{ cycle_YMDH }}"]
-        - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}gsistat.ensmean", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}.ensmean"]
-        {% endif %}
-{% endif %}  # enkfgdas or enkfgfs
+
+# Select data to store in the ARCDIR and VFYARC from deterministic runs
+Base: &base # GDAS, GFS, ENKFGDAS, or ENKFGFS
+    common:
+        mkdir:
+            - "{{ ARCDIR }}"
+
+# Common files to be added to both the gfs and gdas keys below
+Deterministic: &deterministic
+    cyclone:
+        copy:
+            # Cyclone forecasts, produced for both gdas and gfs cycles
+            ## Only created if tracking is on and there were systems to track
+            {% if path_exists(COM_ATMOS_TRACK ~ "/atcfunix." ~ RUN ~ "." ~ cycle_YMDH) %}
+            - ["{{ COM_ATMOS_TRACK }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunix.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COM_ATMOS_TRACK }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}", "{{ ARCDIR }}/atcfunixp.{{ RUN }}.{{ cycle_YMDH }}"]
+            {% endif %}
+
+            # Cyclone tracking data
+            {% for basin in ["epac", "natl"] %}
+                {% if path_exists(COM_ATMOS_TRACK + "/" + basin) %}
+            - ["{{ COM_ATMOS_TRACK }}/{{ basin }}", "{{ ARCDIR }}/{{ basin }}"]
+                {% endif %}
+            {% endfor %}
+
+    {% if MODE == "cycled" %}
+    analysis:
+        copy:
+            # Analysis data (if we are running in cycled mode)
+            - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.anl", "{{ ARCDIR }}/pgbanl.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
+
+            {% if DO_JEDIATMVAR %}
+            - ["{{ COM_ATMOS_ANALYSIS }}/{{ head }}atmstat", "{{ ARCDIR }}/atmstat.{{ RUN }}.{{ cycle_YMDH }}"]
+            {% else %}
+            - ["{{ COM_ATMOS_ANALYSIS }}/{{ head }}gsistat", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}"]
+            {% endif %}
+
+            {% if DO_JEDISNOWDA %}
+            - ["{{ COM_SNOW_ANALYSIS }}/{{ head }}snowstat.tgz", "{{ ARCDIR }}/snowstat.{{ RUN }}.{{ cycle_YMDH }}.tgz"]
+            {% endif %}
+
+            {% if AERO_ANL_CDUMP == RUN or AERO_ANL_CDUMP == "both" %}
+            - ["{{ COM_CHEM_ANALYSIS }}/{{ head }}aerostat", "{{ ARCDIR }}/aerostat.{{ RUN }}.{{ cycle_YMDH }}"]
+            {% endif %}
+
+    {% endif %}
+
+{% if RUN == "gfs" %}
+gfs:  # GFS specific
+    <<: *base
+    <<: *deterministic
+
+    gfs:
+        copy:
+            {% for fhr in range(0, FHMAX_GFS + 1, FHOUT_GFS) %}
+            - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
+            {% endfor %}
+
+            # Cyclone genesis data (only present if there are storms)
+            {% if path_exists(COM_ATMOS_GENESIS ~ "/storms.gfso.atcf_gen." ~ cycle_YMDH) %}
+            - ["{{ COM_ATMOS_GENESIS }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.{{ cycle_YMDH }}"]
+            - ["{{ COM_ATMOS_GENESIS }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/storms.gfso.atcf_gen.altg.{{ cycle_YMDH }}"]
+            {% endif %}
+
+            {% if path_exists(COM_ATMOS_GENESIS ~ "/trak.gfso.atcfunix." ~ cycle_YMDH) %}
+            - ["{{ COM_ATMOS_GENESIS }}/trak.gfso.atcfunix.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.{{ cycle_YMDH }}"]
+            - ["{{ COM_ATMOS_GENESIS }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}", "{{ ARCDIR }}/trak.gfso.atcfunix.altg.{{ cycle_YMDH }}"]
+            {% endif %}
+
+    {% if DO_FIT2OBS %}
+    fit2obs:
+
+        mkdir:
+            {% set VFYARC = ROTDIR + "/vrfyarch" %}
+            - "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}"
+
+        copy:
+            {% for fhr in range(0, FHMAX_FITS + 1, 6) %}
+                {% set sfcfile = "/" + head + "sfcf" + '%03d'|format(fhr) + ".nc" %}
+                {% set sigfile = "/" + head + "atmf" + '%03d'|format(fhr) + ".nc" %}
+            - ["{{COM_ATMOS_HISTORY}}/{{ sfcfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sfcfile }}"]
+            - ["{{COM_ATMOS_HISTORY}}/{{ sigfile }}", "{{ VFYARC }}/{{ RUN }}.{{ cycle_YMD }}/{{ cycle_HH }}/{{ sigfile }}"]
+            {% endfor %}
+
+    {% endif %}
+{% endif %}
+
+{% if RUN == "gdas" %}
+gdas:  # GDAS specific
+    <<: *base
+    <<: *deterministic
+    gdas:
+        copy:
+            {% for fhr in range(0, FHMAX + 1, FHOUT) %}
+            - ["{{ COM_ATMOS_GRIB_1p00 }}/{{ head }}pgrb2.1p00.f{{ '%03d' % fhr }}", "{{ ARCDIR }}/pgbf{{ '%02d' % fhr }}.{{ RUN }}.{{ cycle_YMDH }}.grib2"]
+            {% endfor %}
+{% endif %}
+
+Ensemble: &ensemble # ENKFGDAS or ENKFGFS
+    analysis:
+        copy:
+            # Copy ensemble analyses
+            {% if DO_JEDIATMENS %}
+            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atmensstat", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}atminc.ensmean.nc", "{{ ARCDIR }}/atmensstat.{{ RUN }}.{{ cycle_YMDH }}.ensmean.nc"]
+            {% else %}
+            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}enkfstat", "{{ ARCDIR }}/enkfstat.{{ RUN }}.{{ cycle_YMDH }}"]
+            - ["{{ COM_ATMOS_ANALYSIS_ENSSTAT }}/{{ head }}gsistat.ensmean", "{{ ARCDIR }}/gsistat.{{ RUN }}.{{ cycle_YMDH }}.ensmean"]
+            {% endif %}
+
+{% if "enkf" in RUN %}
+{{ RUN }}:
+    <<: *base
+    <<: *ensemble
+{% endif %}