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Archive additional metadata and other information #121

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merged 6 commits into from
Dec 11, 2024
Merged

Archive additional metadata and other information #121

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f7b859b
Archive additional metadata and other information to a metadata.out d…
andrew-c-ross Dec 5, 2024
ac899d4
Fix spelling of script/scripts
andrew-c-ross Dec 6, 2024
f6c127c
Fix copying of unmasked ocean_static
andrew-c-ross Dec 6, 2024
7011f77
Merge branch 'main' into update/archive-more-metadata
andrew-c-ross Dec 6, 2024
86b4cb8
Override names of truncation files so they can be found by FRE
andrew-c-ross Dec 6, 2024
0084211
Remove extra.results now that it's not needed
andrew-c-ross Dec 6, 2024
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37 changes: 22 additions & 15 deletions xmls/NEP10/CEFI_NEP_cobalt.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ frecheck -v -r restart -p ncrc6.intel23 -t repro -x CEFI_NEP_cobalt.xml CEFI_NE
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='ncrc5.intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='gfdl.ncrc5-intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='ncrc6.intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='gfdl.ncrc6-intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='gfdl.ncrc6-intel23'])"/>
</setup>

<!--= COMPILE =-->
Expand Down Expand Up @@ -600,10 +600,12 @@ cat > $work/INPUT/MOM_override << MOM_OVERRIDE_EOF
#override PHA_MLD_USE_DELTA_RHO = True
#override PHA_MLD_HREF = 10.0
#override PHA_MLD_DRHO = 0.03
#override HREF_FOR_MLD = 5.0
#override HREF_FOR_MLD = 5.0
#override DIAG_MLD_DENSITY_DIFF = 0.03
#override VISC_REM_BUG = True
#override GENERIC_TRACER_IC_FILE = "NEP_COBALT_spinup_2003.nc"
#override U_TRUNC_FILE = "U.velocity_truncations"
#override V_TRUNC_FILE = "V.velocity_truncations"
MOM_OVERRIDE_EOF

truncate -s 0 $work/INPUT/COBALT_override
Expand Down Expand Up @@ -681,28 +683,33 @@ COBALT_INPUT_EOF
<run days="2">
<resources jobWallclock="01:00:00">
<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>
<ocn ranks="2036" threads="1" layout = "32,80" io_layout = "1,1" mask_table="mask_table.524.32x80"/>
</resources>
</run>
</regression>
</runtime>

<postProcess>
<csh><![CDATA[
cd $work
#Make a directory to trick FRE to pick up and archive in ascii
mkdir extra.results
mv *velocity_truncations MOM_parameter_doc* SIS_parameter_doc* COBALT_parameter_doc* seaice.stats* ocean.stats* extra.results/
cp diag_table INPUT/*_input INPUT/*_override INPUT/*.xml extra.results/.
cp $scriptName extra.results/runscript.csh
#When the ocean uses a mask_table the ocean_static.nc file produced by the model run has holes in coordinates (geolon,geolat)
#This causes problems for ferret and python tools for analysis.
#Copy a non-masked version of ocean_static.nc to be saved as a history file to be used by the analysis scipts .
# Archive an assortment of model input files and model metadata
mkdir metadata.out
mv MOM_parameter_doc* SIS_parameter_doc* COBALT_parameter_doc* metadata.out/
cp diag_table input.nml metadata.out/
cp INPUT/*_input INPUT/*_override metadata.out/
# Save the Git commit hash for each source code submodule
git -C $root/$(LIBS_ROOT)/src/mom6 submodule status --recursive > metadata.out/git_submodule_status
# Archive a copy of the xml used to run the model and the run script (fre sets these)
cp $rtsxml metadata.out/
cp $scriptName metadata.out/runscript.csh
# When the ocean uses a mask_table the ocean_static.nc file produced by the model run has holes in coordinates (geolon,geolat)
# This causes problems for ferret and python tools for analysis.
# Copy a non-masked version of ocean_static.nc to be saved as a history file to be used by the analysis scripts.
cp $work/INPUT/ocean_static_no_mask_table.nc $work/ocean_static.nc
]]></csh>
<xi:include xpointer="xpointer(//freInclude[@name='MOM6_postprocess']/postProcess/node())"/>
<xi:include xpointer="xpointer(//freInclude[@name='COBALT_postprocess']/postProcess/node())"/>
<xi:include xpointer="xpointer(//freInclude[@name='COBALT_z_postprocess']/postProcess/node())"/>
<xi:include xpointer="xpointer(//freInclude[@name='COBALT_z_postprocess']/postProcess/node())"/>
</postProcess>

</experiment>
Expand Down Expand Up @@ -798,7 +805,7 @@ ln -sf nep_10km_glorys_obcs_${fyear}.nc obcs.nc
ln -sf glorys_monthly_NEP_sponge_${fyear}_clim.nc nep_10k_glorys_mnClim.nc

if ( $(target) == 'debug' ) then
echo "we are testing in debug mode. Need to re-create grid masks!"
echo "we are testing in debug mode. Need to re-create grid masks!"
cd $work/INPUT
rm -rf $work/INPUT/ocean_mask.nc
rm -rf $work/INPUT/ocean_mosaic.nc
Expand All @@ -809,7 +816,7 @@ make_solo_mosaic --num_tiles 1 --dir . --mosaic_name ocean_mosaic --tile_file oc
make_quick_mosaic --input_mosaic ocean_mosaic.nc --mosaic_name grid_spec --ocean_topog ocean_topog.nc
ln -fs $work/INPUT/ocean_topog.nc $work/INPUT/topog.nc
endif

]]>
</csh>
</input>
Expand Down
30 changes: 19 additions & 11 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 @@ -586,7 +586,7 @@ DT_OBC_SEG_UPDATE_OBGC = 1800
#override CHL_FROM_FILE = False
#override DO_GEOTHERMAL = True
#override GENERIC_TRACER_IC_FILE = "NWA12_COBALT_2023_10_spinup_2003.nc"
#override EPBL_ANSWER_DATE = 20231231
#override EPBL_ANSWER_DATE = 20231231
#override MLD_ITERATION_GUESS = False
#override REMAP_AUXILIARY_VARS = True
#override DIABATIC_FIRST = False
Expand All @@ -595,8 +595,10 @@ DT_OBC_SEG_UPDATE_OBGC = 1800
#override PHA_MLD_USE_DELTA_RHO = True
#override PHA_MLD_HREF = 10.0
#override PHA_MLD_DRHO = 0.03
#override HREF_FOR_MLD = 10.0
#override DIAG_MLD_DENSITY_DIFF = 0.03
#override HREF_FOR_MLD = 10.0
#override DIAG_MLD_DENSITY_DIFF = 0.03
#override U_TRUNC_FILE = "U.velocity_truncations"
#override V_TRUNC_FILE = "V.velocity_truncations"
MOM_OVERRIDE_EOF

truncate -s 0 $work/INPUT/COBALT_override
Expand Down Expand Up @@ -692,14 +694,20 @@ COBALT_INPUT_EOF
<postProcess>
<csh><![CDATA[
cd $work
#Make a directory to trick FRE to pick up and archive in ascii
mkdir extra.results
mv MOM_parameter_doc* SIS_parameter_doc* COBALT_parameter_doc* seaice.stats* ocean.stats* extra.results/
cp diag_table extra.results/.
#When the ocean uses a mask_table the ocean_static.nc file produced by the model run has holes in coordinates (geolon,geolat)
#This causes problems for ferret and python tools for analysis.
#Copy a non-masked version of ocean_static.nc to be saved as a history file to be used by the analysis scipts .
cp $work/INPUT/ocean_static_no_mask_table.nc $work/
# Archive an assortment of model input files and model metadata
mkdir metadata.out
mv MOM_parameter_doc* SIS_parameter_doc* COBALT_parameter_doc* metadata.out/
cp diag_table input.nml metadata.out/
cp INPUT/*_input INPUT/*_override metadata.out/
# Save the Git commit hash for each source code submodule
git -C $root/$(LIBS_ROOT)/src/mom6 submodule status --recursive > metadata.out/git_submodule_status
# Archive a copy of the xml used to run the model and the run script (fre sets these)
cp $rtsxml metadata.out/
cp $scriptName metadata.out/runscript.csh
# When the ocean uses a mask_table the ocean_static.nc file produced by the model run has holes in coordinates (geolon,geolat)
# This causes problems for ferret and python tools for analysis.
# Copy a non-masked version of ocean_static.nc to be saved as a history file to be used by the analysis scripts.
cp $work/INPUT/ocean_static_no_mask_table.nc $work/ocean_static.nc
]]></csh>
<xi:include xpointer="xpointer(//freInclude[@name='MOM6_postprocess']/postProcess/node())"/>
<xi:include xpointer="xpointer(//freInclude[@name='COBALT_postprocess']/postProcess/node())"/>
Expand Down
32 changes: 20 additions & 12 deletions xmls/NWA12/CEFI_NWA12_cobalt_fms2_yaml.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ frecheck -r layout -p ncrc6.intel23 -x CEFI_NWA12_cobalt_fms2_yaml.xml CEFI_NWA1
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='ncrc5.intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='gfdl.ncrc5-intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='ncrc6.intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='gfdl.ncrc6-intel23'])"/>
<xi:include href="../xml_include/xml_building_blocks/platforms.xml" xpointer="xpointer(//freInclude/platform[@name='gfdl.ncrc6-intel23'])"/>
</setup>

<!--= COMPILE =-->
Expand Down Expand Up @@ -586,7 +586,7 @@ DT_OBC_SEG_UPDATE_OBGC = 1800
#override CHL_FROM_FILE = False
#override DO_GEOTHERMAL = True
#override GENERIC_TRACER_IC_FILE = "NWA12_COBALT_2023_10_spinup_2003.nc"
#override EPBL_ANSWER_DATE = 20231231
#override EPBL_ANSWER_DATE = 20231231
#override MLD_ITERATION_GUESS = False
#override REMAP_AUXILIARY_VARS = True
#override DIABATIC_FIRST = False
Expand All @@ -595,8 +595,10 @@ DT_OBC_SEG_UPDATE_OBGC = 1800
#override PHA_MLD_USE_DELTA_RHO = True
#override PHA_MLD_HREF = 10.0
#override PHA_MLD_DRHO = 0.03
#override HREF_FOR_MLD = 10.0
#override HREF_FOR_MLD = 10.0
#override DIAG_MLD_DENSITY_DIFF = 0.03
#override U_TRUNC_FILE = "U.velocity_truncations"
#override V_TRUNC_FILE = "V.velocity_truncations"
MOM_OVERRIDE_EOF

truncate -s 0 $work/INPUT/COBALT_override
Expand All @@ -617,7 +619,7 @@ z_burial = 20.0
z_denit = 20.0
COBALT_INPUT_EOF

#hack to test yaml diag_table, convert the diag_table to yaml format
#hack to test yaml diag_table, convert the diag_table to yaml format
diag-table-to-yaml -f $work/diag_table -o $work/diag_table.yaml
]]>
</csh>
Expand Down Expand Up @@ -695,14 +697,20 @@ diag-table-to-yaml -f $work/diag_table -o $work/diag_table.yaml
<postProcess>
<csh><![CDATA[
cd $work
#Make a directory to trick FRE to pick up and archive in ascii
mkdir extra.results
mv MOM_parameter_doc* SIS_parameter_doc* COBALT_parameter_doc* seaice.stats* ocean.stats* extra.results/
cp diag_table extra.results/.
#When the ocean uses a mask_table the ocean_static.nc file produced by the model run has holes in coordinates (geolon,geolat)
#This causes problems for ferret and python tools for analysis.
#Copy a non-masked version of ocean_static.nc to be saved as a history file to be used by the analysis scipts .
cp $work/INPUT/ocean_static_no_mask_table.nc $work/
# Archive an assortment of model input files and model metadata
mkdir metadata.out
mv MOM_parameter_doc* SIS_parameter_doc* COBALT_parameter_doc* metadata.out/
cp diag_table input.nml metadata.out/
cp INPUT/*_input INPUT/*_override metadata.out/
# Save the Git commit hash for each source code submodule
git -C $root/$(LIBS_ROOT)/src/mom6 submodule status --recursive > metadata.out/git_submodule_status
# Archive a copy of the xml used to run the model and the run script (fre sets these)
cp $rtsxml metadata.out/
cp $scriptName metadata.out/runscript.csh
# When the ocean uses a mask_table the ocean_static.nc file produced by the model run has holes in coordinates (geolon,geolat)
# This causes problems for ferret and python tools for analysis.
# Copy a non-masked version of ocean_static.nc to be saved as a history file to be used by the analysis scripts.
cp $work/INPUT/ocean_static_no_mask_table.nc $work/ocean_static.nc
]]></csh>
<xi:include xpointer="xpointer(//freInclude[@name='MOM6_postprocess']/postProcess/node())"/>
<xi:include xpointer="xpointer(//freInclude[@name='COBALT_postprocess']/postProcess/node())"/>
Expand Down
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