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Clean up diag_table files to provide a default CEFI diag_table #108

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merged 14 commits into from
Nov 18, 2024
Merged

Clean up diag_table files to provide a default CEFI diag_table #108

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a1597f4
added draft CEFI diag_table
yichengt900 Nov 1, 2024
7dfe5ca
Removed COBALT budget diags
yichengt900 Nov 1, 2024
02dc961
forget to remove ocean_cobalt_tracers_instant
yichengt900 Nov 1, 2024
4f87550
Removed omip_tracers_year_z and rates_year_z
yichengt900 Nov 1, 2024
2ddedc7
remove ocean snapshot diags
yichengt900 Nov 1, 2024
b48a1dc
Merge remote-tracking branch 'origin' into feature/diag_table_cleanup
yichengt900 Nov 1, 2024
5f812d5
Split diag_table and add variable description
yichengt900 Nov 4, 2024
dcb2f13
rename CEFI diag_tables
yichengt900 Nov 4, 2024
92fce78
Update xml files
yichengt900 Nov 4, 2024
4959856
update NEP xml
yichengt900 Nov 4, 2024
b7c2d08
fix typos in xmls and remove unused diag_tables
yichengt900 Nov 5, 2024
aba43d3
Merge branch 'main' into feature/diag_table_cleanup
yichengt900 Nov 7, 2024
82d02cd
Merge branch 'main' into feature/diag_table_cleanup
yichengt900 Nov 12, 2024
724e425
Merge branch 'main' into feature/diag_table_cleanup
yichengt900 Nov 18, 2024
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56 changes: 18 additions & 38 deletions xmls/NEP10/CEFI_NEP_cobalt.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ frecheck -v -r restart -p ncrc6.intel23 -t repro -x CEFI_NEP_cobalt.xml CEFI_NE
<property name="ICEPACK_GIT_TAG" value="Icepack1.3.3"/>

<!-- customize as needed -->
<property name="FRE_STEM" value="fre/cefi/NEP/2024_10"/>
<property name="FRE_STEM" value="fre/cefi/NEP/2024_11"/>

<!-- Please make sure to change your group, such as b, f, g, m, o... -->
<!-- NCRC_GROUP will only have impact for your root dir and work dir on gaea c5/c6-->
Expand Down Expand Up @@ -145,7 +145,7 @@ frecheck -v -r restart -p ncrc6.intel23 -t repro -x CEFI_NEP_cobalt.xml CEFI_NE
</compile>
</component>

<component name="Icepack" paths="mom6/src/Icepack/columnphysics" requires="fms mom6_symmetric" includeDir="$HOME/$(stem)/$(LIBS_ROOT)/src/mom6/src/MOM6/src/framework" >
<component name="Icepack" paths="mom6/src/Icepack/columnphysics" requires="fms mom6_symmetric" includeDir="$root/$(LIBS_ROOT)/src/mom6/src/MOM6/src/framework" >
<source versionControl="git" root="https://github.com/CICE-Consortium/">
<codeBase version="$(ICEPACK_GIT_TAG)"> Icepack.git </codeBase>
</source>
Expand All @@ -154,7 +154,7 @@ frecheck -v -r restart -p ncrc6.intel23 -t repro -x CEFI_NEP_cobalt.xml CEFI_NE
</compile>
</component>

<component name="sis2" paths="mom6/src/SIS2/config_src/dynamic_symmetric mom6/src/SIS2/src mom6/src/icebergs/src mom6/src/ice_param" requires="fms mom6_symmetric Icepack" includeDir="$HOME/$(stem)/$(LIBS_ROOT)/src/mom6/src/MOM6/src/framework" >
<component name="sis2" paths="mom6/src/SIS2/config_src/dynamic_symmetric mom6/src/SIS2/src mom6/src/icebergs/src mom6/src/ice_param" requires="fms mom6_symmetric Icepack" includeDir="$root/$(LIBS_ROOT)/src/mom6/src/MOM6/src/framework" >
<source versionControl="git" root="https://github.com/NOAA-GFDL">
<codeBase version="$(RELEASE)"> ice_param.git </codeBase>
</source>
Expand Down Expand Up @@ -568,12 +568,12 @@ $name
$baseDate
</diagTable>
<dataFile label="diagTable" target="INPUT/" chksum="" size="" timestamp="">
<dataSource site="ncrc">/ncrc/home2/Andrew.C.Ross/nwa-xml/diag_tables/diag_table_COBALT_2024-04</dataSource>
<dataSource site="ncrc">/ncrc/home2/Andrew.C.Ross/nwa-xml/diag_tables/diag_table_MOM6_2024-04</dataSource>
<dataSource site="ncrc">/ncrc/home2/Andrew.C.Ross/nwa-xml/diag_tables/diag_table.SIS</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table_COBALT_2024-04</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table_MOM6_2024-04</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table.SIS</dataSource>
<dataSource site="ncrc">../NWA12/diag_tables/diag_table_CEFI_MOM6_default</dataSource>
<dataSource site="ncrc">../NWA12/diag_tables/diag_table_CEFI_SIS_default</dataSource>
<dataSource site="ncrc">../NWA12/diag_tables/diag_table_CEFI_COBALT_default</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_CEFI_MOM6_default</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_CEFI_SIS_default</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_CEFI_COBALT_default</dataSource>
</dataFile>
<csh type='always'>
<![CDATA[
Expand Down Expand Up @@ -636,11 +636,19 @@ COBALT_INPUT_EOF
<regression name="month">
<run months="1">
<resources jobWallclock="04:00:00">
<ice layout = "40,40" io_layout = "1,1" mask_table="MOM_mask_table"/>
<ice layout = "40,40" io_layout = "1,1" mask_table="MOM_mask_table"/>
<ocn ranks="1600" threads="1" layout = "40,40" io_layout = "1,1" mask_table="MOM_mask_table"/>
</resources>
</run>
</regression>
<regression name="year">
<run months="12">
<resources jobWallclock="12:00:00">
<ice layout = "32,80" io_layout = "1,1" mask_table="mask_table.524.32x80"/>
<ocn ranks="2036" threads="1" layout = "32,80" io_layout = "1,1" mask_table="mask_table.524.32x80"/>
</resources>
</run>
</regression>
<regression name="test">
<run days="2">
<resources jobWallclock="01:00:00">
Expand Down Expand Up @@ -946,12 +954,6 @@ endif
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_B)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_tracers_instant" start="$(PP_START_YEAR)" source="ocean_cobalt_tracers_instant">
<!-- No monthly for this because it's an annual field -->
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_B)" />
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_sfc" start="$(PP_START_YEAR)" source="ocean_cobalt_sfc">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
Expand All @@ -968,17 +970,6 @@ endif
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_B)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_daily" start="$(PP_START_YEAR)" source="ocean_cobalt_daily">
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_A)" />
</component>
<component type="ocean_cobalt_tracers_month" start="$(PP_START_YEAR)" source="ocean_cobalt_tracers_month">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_B)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_B)" />
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_B)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_omip_2d" start="$(PP_START_YEAR)" source="ocean_cobalt_omip_2d">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
Expand All @@ -991,12 +982,6 @@ endif
</freInclude>
<freInclude name="COBALT_z_postprocess">
<postProcess>
<component type="ocean_cobalt_omip_tracers_month_z" start="$(PP_START_YEAR)" source="ocean_cobalt_omip_tracers_month_z">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_A)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_A)"/>
</component>
<component type="ocean_cobalt_tracers_month_z" start="$(PP_START_YEAR)" source="ocean_cobalt_tracers_month_z">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
Expand All @@ -1005,11 +990,6 @@ endif
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_B)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_rates_year_z" start="$(PP_START_YEAR)" source="ocean_cobalt_rates_year_z">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
<timeAverage source="annual" interval="$(CHUNK_LENGTH_A)"/>
</component>
</postProcess>
</freInclude>
<freInclude name="MOM6_postprocess">
Expand Down
59 changes: 9 additions & 50 deletions xmls/NWA12/CEFI_NWA12_cobalt.xml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ frecheck -r layout -p ncrc6.intel23 -x CEFI_NWA12_cobalt.xml CEFI_NWA12_COBALT_V
<property name="MOM6_GIT_FIX" value="main"/> <!-- Trying new branch with bug fix for bgc obc index -->

<!-- customize as needed -->
<property name="FRE_STEM" value="fre/cefi/NWA/2024_09"/>
<property name="FRE_STEM" value="fre/cefi/NWA/2024_11"/>

<!-- Please make sure to change your group, such as b, f, g, m, o... -->
<property name="NCRC_GROUP" value="ira-cefi"/>
Expand Down Expand Up @@ -556,16 +556,16 @@ $name
$baseDate
</diagTable>
<dataFile label="diagTable" target="INPUT/" chksum="" size="" timestamp="">
<dataSource site="ncrc">./diag_tables/diag_table_COBALT_2023-04</dataSource>
<dataSource site="ncrc">./diag_tables/diag_table_MOM6_2024-09</dataSource>
<dataSource site="ncrc">./diag_tables/diag_table.SIS</dataSource>
<dataSource site="ncrc">./diag_tables/diag_table_CEFI_MOM6_default</dataSource>
<dataSource site="ncrc">./diag_tables/diag_table_CEFI_SIS_default</dataSource>
<dataSource site="ncrc">./diag_tables/diag_table_CEFI_COBALT_default</dataSource>
<dataSource site="ncrc">./diag_tables/diag_table_COBALT_neus</dataSource>
<dataSource site="ncrc">./diag_tables/diag_table_MOM6_neus</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table_COBALT_2023-04</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table_MOM6_2023-03</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table.SIS</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table_COBALT_neus</dataSource>
<dataSource site="gfdl">/home/Andrew.C.Ross/git/nwa-xml/diag_tables/diag_table_MOM6_neus</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_CEFI_MOM6_default</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_CEFI_SIS_default</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_CEFI_COBALT_default</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_COBALT_neus</dataSource>
<dataSource site="gfdl">/home/ynt/git/CEFI-regional-MOM6/xmls/NWA12/diag_tables/diag_table_MOM6_neus</dataSource>
</dataFile>
<dataFile label="initCond" target="INPUT/" chksum="" size="" timestamp="">
<dataSource site="ncrc">$(NWA12_WORLD)/restarts/NWA12_COBALT_2023_10_spinup/NWA12_COBALT_2023_10_spinup_2003.nc</dataSource>
Expand Down Expand Up @@ -924,18 +924,10 @@ endif
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_B)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_daily_2D" start="$(PP_START_YEAR)" source="ocean_cobalt_daily_2D">
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_B)" />
</component>
<component type="ocean_cobalt_daily_2d" start="$(PP_START_YEAR)" source="ocean_cobalt_daily_2d">
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_B)" />
</component>
<component type="ocean_cobalt_omip_daily" start="$(PP_START_YEAR)" source="ocean_cobalt_omip_daily">
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_B)" />
</component>
<component type="ocean_cobalt_omip_sfc" start="$(PP_START_YEAR)" source="ocean_cobalt_omip_sfc">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
Expand Down Expand Up @@ -970,22 +962,10 @@ endif
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_B)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_daily" start="$(PP_START_YEAR)" source="ocean_cobalt_daily">
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_B)" />
</component>
<component type="ocean_cobalt_neus" start="$(PP_START_YEAR)" source="ocean_cobalt_neus">
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_A)" source="ocean_cobalt_neus"/>
<timeSeries freq="daily" chunkLength="$(CHUNK_LENGTH_B)" source="ocean_cobalt_neus"/>
</component>
<component type="ocean_cobalt_tracers_month" start="$(PP_START_YEAR)" source="ocean_cobalt_tracers_month">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_B)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_B)" />
<timeAverage source="monthly" interval="$(CHUNK_LENGTH_B)"/>
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_tracers_month_z" start="$(PP_START_YEAR)" source="ocean_cobalt_tracers_month_z">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
Expand All @@ -1004,27 +984,6 @@ endif
</component>
</postProcess>
</freInclude>
<freInclude name="COBALT_budget_postprocess">
<postProcess>
<component type="ocean_cobalt_budget_annual" start="$(PP_START_YEAR)" source="ocean_cobalt_budget_annual">
<!-- No monthly for this because it's an annual field -->
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_B)" />
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<component type="ocean_cobalt_budget_instant" start="$(PP_START_YEAR)" source="ocean_cobalt_budget_instant">
<!-- No monthly for this because it's an annual field -->
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_A)" />
<timeSeries freq="annual" chunkLength="$(CHUNK_LENGTH_B)" />
<timeAverage source="annual" interval="$(CHUNK_LENGTH_B)"/>
</component>
<!-- don't process this; it is 14 day averages
<component type="ocean_cobalt_budget" start="$(PP_START_YEAR)" source="ocean_cobalt_budget">
<timeSeries freq="monthly" chunkLength="$(CHUNK_LENGTH_SHORT)" />
</component>
-->
</postProcess>
</freInclude>
<freInclude name="MOM6_postprocess">
<postProcess>
<!--PostProcessing component models-->
Expand Down
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