Merge branch 'feature/prepobs_fit2obs_versions' of https://github.com…

…/KateFriedman-NOAA/global-workflow into feature/prepobs_fit2obs_versions * 'feature/prepobs_fit2obs_versions' of https://github.com/KateFriedman-NOAA/global-workflow: Adds contents of constructor and initialize methods to marine LETKF class (NOAA-EMC#2635) Fix GDAS group B restart archiving (NOAA-EMC#2735) Add fcst dependency to ocnanalprep (NOAA-EMC#2728)
KateFriedman-NOAA · Jul 11, 2024 · 4293469 · 4293469
2 parents 1540921 + 3a0e553
commit 4293469
Show file tree

Hide file tree

Showing 13 changed files with 330 additions and 235 deletions.
diff --git a/env/HERA.env b/env/HERA.env
@@ -140,13 +140,13 @@ elif [[ "${step}" = "ocnanalecen" ]]; then
     [[ ${NTHREADS_OCNANALECEN} -gt ${nth_max} ]] && export NTHREADS_OCNANALECEN=${nth_max}
     export APRUN_OCNANALECEN="${launcher} -n ${npe_ocnanalecen} --cpus-per-task=${NTHREADS_OCNANALECEN}"
 
-elif [[ "${step}" = "ocnanalletkf" ]]; then
+elif [[ "${step}" = "marineanalletkf" ]]; then
 
-    nth_max=$((npe_node_max / npe_node_ocnanalletkf))
+    nth_max=$((npe_node_max / npe_node_marineanalletkf))
 
-    export NTHREADS_OCNANALLETKF=${nth_ocnanalletkf:-${nth_max}}
-    [[ ${NTHREADS_OCNANALLETKF} -gt ${nth_max} ]] && export NTHREADS_OCNANALLETKF=${nth_max}
-    export APRUN_OCNANALLETKF="${launcher} -n ${npe_ocnanalletkf} --cpus-per-task=${NTHREADS_OCNANALLETKF}"
+    export NTHREADS_MARINEANALLETKF=${nth_marineanalletkf:-${nth_max}}
+    [[ ${NTHREADS_MARINEANALLETKF} -gt ${nth_max} ]] && export NTHREADS_MARINEANALLETKF=${nth_max}
+    export APRUN_MARINEANALLETKF="${launcher} -n ${npe_marineanalletkf} --cpus-per-task=${NTHREADS_MARINEANALLETKF}"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 

diff --git a/env/ORION.env b/env/ORION.env
@@ -148,13 +148,13 @@ elif [[ "${step}" = "ocnanalecen" ]]; then
     [[ ${NTHREADS_OCNANALECEN} -gt ${nth_max} ]] && export NTHREADS_OCNANALECEN=${nth_max}
     export APRUN_OCNANALECEN="${launcher} -n ${npe_ocnanalecen} --cpus-per-task=${NTHREADS_OCNANALECEN}"
 
-elif [[ "${step}" = "ocnanalletkf" ]]; then
+elif [[ "${step}" = "marineanalletkf" ]]; then
 
-    nth_max=$((npe_node_max / npe_node_ocnanalletkf))
+    nth_max=$((npe_node_max / npe_node_marineanalletkf))
 
-    export NTHREADS_OCNANALLETKF=${nth_ocnanalletkf:-${nth_max}}
-    [[ ${NTHREADS_OCNANALLETKF} -gt ${nth_max} ]] && export NTHREADS_OCNANALLETKF=${nth_max}
-    export APRUN_OCNANALLETKF="${launcher} -n ${npe_ocnanalletkf} --cpus-per-task=${NTHREADS_OCNANALLETKF}"
+    export NTHREADS_MARINEANALLETKF=${nth_marineanalletkf:-${nth_max}}
+    [[ ${NTHREADS_MARINEANALLETKF} -gt ${nth_max} ]] && export NTHREADS_MARINEANALLETKF=${nth_max}
+    export APRUN_MARINEANALLETKF="${launcher} -n ${npe_marineanalletkf} --cpus-per-task=${NTHREADS_MARINEANALLETKF}"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF → jobs/JGLOBAL_MARINE_ANALYSIS_LETKF b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF → jobs/JGLOBAL_MARINE_ANALYSIS_LETKF
@@ -1,6 +1,6 @@
 #!/bin/bash
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalletkf" -c "base ocnanal ocnanalletkf"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanalletkf" -c "base ocnanal marineanalletkf"
 
 ##############################################
 # Set variables used in the script
@@ -13,8 +13,10 @@ gPDY=${GDATE:0:8}
 gcyc=${GDATE:8:2}
 
 YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-   COM_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
-   COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL
+   COMIN_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
+   COMIN_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL
+
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_OBS:COM_OBS_TMPL 
 
 ##############################################
 # Begin JOB SPECIFIC work

diff --git a/jobs/rocoto/ocnanalletkf.sh → jobs/rocoto/marineanalletkf.sh b/jobs/rocoto/ocnanalletkf.sh → jobs/rocoto/marineanalletkf.sh
@@ -8,7 +8,7 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="ocnanalletkf"
+export job="marineanalletkf"
 export jobid="${job}.$$"
 
 ###############################################################
@@ -18,6 +18,6 @@ export PYTHONPATH
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF"
+"${HOMEgfs}/jobs/JGLOBAL_MARINE_ANALYSIS_LETKF"
 status=$?
 exit "${status}"
diff --git a/parm/archive/master_enkf.yaml.j2 b/parm/archive/master_enkf.yaml.j2
@@ -6,108 +6,111 @@
 
 # Split IAUFHRS into a list; typically either "3,6,9" or 6 (integer)
 {% if IAUFHRS is string %}
-# "3,6,9"
-{% set iaufhrs = [] %}
-{% for iaufhr in IAUFHRS.split(",") %}
-{% do iaufhrs.append(iaufhr | int) %}
-{% endfor %}
+    # "3,6,9"
+    {% set iaufhrs = [] %}
+    {% for iaufhr in IAUFHRS.split(",") %}
+        {% do iaufhrs.append(iaufhr | int) %}
+    {% endfor %}
 {% else %}
-# 6 (integer)
-{% set iaufhrs = [IAUFHRS] %}
+    # 6 (integer)
+    {% set iaufhrs = [IAUFHRS] %}
 {% endif %}
 
 # Repeat for IAUFHRS_ENKF
 {% if IAUFHRS_ENKF is string %}
-{% set iaufhrs_enkf = [] %}
-{% for iaufhr in IAUFHRS_ENKF.split(",") %}
-{% do iaufhrs_enkf.append(iaufhr | int) %}
-{% endfor %}
+    {% set iaufhrs_enkf = [] %}
+    {% for iaufhr in IAUFHRS_ENKF.split(",") %}
+        {% do iaufhrs_enkf.append(iaufhr | int) %}
+    {% endfor %}
 {% else %}
-{% set iaufhrs_enkf = [IAUFHRS_ENKF] %}
+    {% set iaufhrs_enkf = [IAUFHRS_ENKF] %}
 {% endif %}
 
 # Determine which data to archive
 datasets:
 {% if ENSGRP == 0 %}
-{% filter indent(width=4) %}
-# Archive the ensemble means and spreads
+    {% filter indent(width=4) %}
+        # Archive the ensemble means and spreads
 {% include "enkf.yaml.j2" %}
-{% endfilter %}
+    {% endfilter %}
 {% else %}
 
-# Archive individual member data
-# First, construct individual member directories from templates
-#    COMIN_ATMOS_ANALYSIS_MEM, COMIN_ATMOS_HISTORY_MEM, and COMIN_ATMOS_RESTART_MEM
-
-# Declare to-be-filled lists of member COM directories
-{% set COMIN_ATMOS_ANALYSIS_MEM_list = [] %}
-{% set COMIN_ATMOS_RESTART_MEM_list = [] %}
-{% set COMIN_ATMOS_HISTORY_MEM_list = [] %}
-
-# Determine which ensemble members belong to this group
-{% set first_group_mem = (ENSGRP - 1) * NMEM_EARCGRP + 1 %}
-{% set last_group_mem = [ ENSGRP * NMEM_EARCGRP, nmem_ens ] | min %}
-
-# Construct member COM directories for the group
-{% for mem in range(first_group_mem, last_group_mem + 1) %}
-
-# Declare a dict of search and replace terms to run on each template
-{% set tmpl_dict = {'ROTDIR':ROTDIR,
-                    'RUN':RUN,
-                    'YMD':cycle_YMD,
-                    'HH':cycle_HH,
-                    'MEMDIR':"mem" + '%03d' % mem} %}
-
-# Replace template variables with tmpl_dict, one key at a time
-# This must be done in a namespace to overcome jinja scoping
-#  Variables set inside of a for loop are lost at the end of the loop
-#  unless they are part of a namespace
-{% set com_ns = namespace(COMIN_ATMOS_ANALYSIS_MEM = COM_ATMOS_ANALYSIS_TMPL,
-                          COMIN_ATMOS_HISTORY_MEM = COM_ATMOS_HISTORY_TMPL,
-                          COMIN_ATMOS_RESTART_MEM = COM_ATMOS_RESTART_TMPL) %}
-
-{% for key in tmpl_dict.keys() %}
-{% set search_term = '${' + key + '}' %}
-{% set replace_term = tmpl_dict[key] %}
-{% set com_ns.COMIN_ATMOS_ANALYSIS_MEM = com_ns.COMIN_ATMOS_ANALYSIS_MEM.replace(search_term, replace_term) %}
-{% set com_ns.COMIN_ATMOS_HISTORY_MEM = com_ns.COMIN_ATMOS_HISTORY_MEM.replace(search_term, replace_term) %}
-{% set com_ns.COMIN_ATMOS_RESTART_MEM = com_ns.COMIN_ATMOS_RESTART_MEM.replace(search_term, replace_term) %}
-{% endfor %}
-
-# Append the member COM directories
-{% do COMIN_ATMOS_ANALYSIS_MEM_list.append(com_ns.COMIN_ATMOS_ANALYSIS_MEM)%}
-{% do COMIN_ATMOS_HISTORY_MEM_list.append(com_ns.COMIN_ATMOS_HISTORY_MEM)%}
-{% do COMIN_ATMOS_RESTART_MEM_list.append(com_ns.COMIN_ATMOS_RESTART_MEM)%}
-
-{% endfor %}
-
-# Archive member data
-{% filter indent(width=4) %}
+    # Archive individual member data
+    # First, construct individual member directories from templates
+    #    COMIN_ATMOS_ANALYSIS_MEM, COMIN_ATMOS_HISTORY_MEM, and COMIN_ATMOS_RESTART_MEM
+
+    # Declare to-be-filled lists of member COM directories
+    {% set COMIN_ATMOS_ANALYSIS_MEM_list = [] %}
+    {% set COMIN_ATMOS_RESTART_MEM_list = [] %}
+    {% set COMIN_ATMOS_HISTORY_MEM_list = [] %}
+
+    # Determine which ensemble members belong to this group
+    {% set first_group_mem = (ENSGRP - 1) * NMEM_EARCGRP + 1 %}
+    {% set last_group_mem = [ ENSGRP * NMEM_EARCGRP, nmem_ens ] | min %}
+
+    # Construct member COM directories for the group
+    {% for mem in range(first_group_mem, last_group_mem + 1) %}
+
+        # Declare a dict of search and replace terms to run on each template
+        {% set tmpl_dict = {'ROTDIR':ROTDIR,
+                            'RUN':RUN,
+                            'YMD':cycle_YMD,
+                            'HH':cycle_HH,
+                            'MEMDIR':"mem" + '%03d' % mem} %}
+
+        # Replace template variables with tmpl_dict, one key at a time
+        # This must be done in a namespace to overcome jinja scoping
+        #  Variables set inside of a for loop are lost at the end of the loop
+        #  unless they are part of a namespace
+        {% set com_ns = namespace(COMIN_ATMOS_ANALYSIS_MEM = COM_ATMOS_ANALYSIS_TMPL,
+                                  COMIN_ATMOS_HISTORY_MEM = COM_ATMOS_HISTORY_TMPL,
+                                  COMIN_ATMOS_RESTART_MEM = COM_ATMOS_RESTART_TMPL) %}
+
+        {% for key in tmpl_dict.keys() %}
+            {% set search_term = '${' + key + '}' %}
+            {% set replace_term = tmpl_dict[key] %}
+            {% set com_ns.COMIN_ATMOS_ANALYSIS_MEM =
+                com_ns.COMIN_ATMOS_ANALYSIS_MEM.replace(search_term, replace_term) %}
+            {% set com_ns.COMIN_ATMOS_HISTORY_MEM =
+                com_ns.COMIN_ATMOS_HISTORY_MEM.replace(search_term, replace_term) %}
+            {% set com_ns.COMIN_ATMOS_RESTART_MEM =
+                com_ns.COMIN_ATMOS_RESTART_MEM.replace(search_term, replace_term) %}
+        {% endfor %}
+
+        # Append the member COM directories
+        {% do COMIN_ATMOS_ANALYSIS_MEM_list.append(com_ns.COMIN_ATMOS_ANALYSIS_MEM)%}
+        {% do COMIN_ATMOS_HISTORY_MEM_list.append(com_ns.COMIN_ATMOS_HISTORY_MEM)%}
+        {% do COMIN_ATMOS_RESTART_MEM_list.append(com_ns.COMIN_ATMOS_RESTART_MEM)%}
+
+    {% endfor %}
+
+    # Archive member data
+    {% filter indent(width=4) %}
 {% include "enkf_grp.yaml.j2" %}
-{% endfilter %}
+    {% endfilter %}
 
-# Determine if restarts should be saved
-{% set save_warm_start_forecast, save_warm_start_cycled = ( False, False ) %}
+    # Determine if restarts should be saved
+    {% set save_warm_start_forecast, save_warm_start_cycled = ( False, False ) %}
 
-# Save the increments and restarts every ARCH_WARMICFREQ days
-# The ensemble increments (group a) should be saved on the ARCH_CYC
-{% if (current_cycle - SDATE).days % ARCH_WARMICFREQ == 0 %}
-{% if ARCH_CYC == cycle_HH | int %}
-{% filter indent(width=4) %}
+    # Save the increments and restarts every ARCH_WARMICFREQ days
+    # The ensemble increments (group a) should be saved on the ARCH_CYC
+    {% if (current_cycle - SDATE).days % ARCH_WARMICFREQ == 0 %}
+        {% if ARCH_CYC == cycle_HH | int %}
+            {% filter indent(width=4) %}
 {% include "enkf_restarta_grp.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-{% endif %}
-
-# The ensemble ICs (group b) are restarts and always lag increments by assim_freq
-{% set ics_offset = (assim_freq | string + "H") | to_timedelta %}
-{% if (current_cycle | add_to_datetime(ics_offset) - SDATE).days % ARCH_WARMICFREQ == 0 %}
-{% if (ARCH_CYC - assim_freq) % 24 == cycle_HH | int %}
-{% filter indent(width=4) %}
+            {% endfilter %}
+        {% endif %}
+    {% endif %}
+
+    # The ensemble ICs (group b) are restarts and always lag increments by assim_freq
+    {% set ics_offset = (assim_freq | string + "H") | to_timedelta %}
+    {% if (current_cycle | add_to_datetime(ics_offset) - SDATE).days % ARCH_WARMICFREQ == 0 %}
+        {% if (ARCH_CYC - assim_freq) % 24 == cycle_HH | int %}
+            {% filter indent(width=4) %}
 {% include "enkf_restartb_grp.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-{% endif %}
+            {% endfilter %}
+        {% endif %}
+    {% endif %}
 
-# End of individual member archiving
+    # End of individual member archiving
 {% endif %}