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Smooth topography before interp to MPAS #489

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Smooth topography before interp to MPAS #489

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20 changes: 15 additions & 5 deletions testing_and_setup/compass/ocean/global_ocean/EC60to30wISC/init/config_initial_state.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/initial_condition_database/"/>
</get_file>


<get_file dest_path="initial_condition_database" file_name="windStress.ncep_1958-2000avg.interp3600x2431.151106.nc">
<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/initial_condition_database/"/>
</get_file>
Expand All @@ -25,12 +24,15 @@
<add_link source="../culled_mesh/culled_mesh.nc" dest="mesh.nc"/>
<add_link source="../culled_mesh/culled_graph.info" dest="graph.info"/>
<add_link source="../culled_mesh/critical_passages_mask_final.nc" dest="critical_passages.nc"/>
<add_link source_path="initial_condition_database" source="Salinity.01.filled.60levels.PHC.151106.nc" dest="layer_depth.nc"/>
<add_link source="../culled_mesh/land_ice_mask.nc" dest="land_ice_mask.nc"/>
<add_link source="../base_mesh/cellWidthVsLatLon.nc" dest="cellWidthVsLatLon.nc"/>
<add_link source_path="initial_condition_database" source="Salinity.01.filled.60levels.PHC.151106.nc" dest="layer_depth.nc"/>
<add_link source_path="initial_condition_database" source="PotentialTemperature.01.filled.60levels.PHC.151106.nc" dest="temperature.nc"/>
<add_link source_path="initial_condition_database" source="Salinity.01.filled.60levels.PHC.151106.nc" dest="salinity.nc"/>
<add_link source_path="initial_condition_database" source="windStress.ncep_1958-2000avg.interp3600x2431.151106.nc" dest="wind_stress.nc"/>
<add_link source_path="bathymetry_database" source="BedMachineAntarctica_and_GEBCO_2019_0.05_degree.200128.nc" dest="topography.nc"/>
<add_link source_path="initial_condition_database" source="chlorophyllA_monthly_averages_1deg.151201.nc" dest="swData.nc"/>
<add_link source_path="script_configuration_dir" source="scripts/smooth_topo.py" dest="smooth_topo.py"/>

<namelist name="namelist.ocean" mode="init">
<template file="template_initial_state.xml" path_base="script_configuration_dir"/>
Expand All @@ -40,20 +42,28 @@
<option name="config_global_ocean_depth_file">'layer_depth.nc'</option>
<option name="config_global_ocean_minimum_depth">10</option>
<option name="config_global_ocean_deepen_critical_passages">.false.</option>
<option name="config_global_ocean_depth_conversion_factor">0.01</option>
<option name="config_global_ocean_tracer_depth_conversion_factor">0.01</option>
<option name="config_global_ocean_depth_conversion_factor">0.01</option>
<option name="config_global_ocean_tracer_depth_conversion_factor">0.01</option>
<option name="config_global_ocean_topography_file">'topography_smoothed.nc'</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="init">
<template file="template_initial_state.xml" path_base="script_configuration_dir"/>
<template file="template_critical_passages.xml" path_base="script_core_dir" path="global_ocean"/>
<template file="template_init_with_land_ice.xml" path_base="script_configuration_dir"/>
</streams>

<run_script name="run.py">
<step executable="./smooth_topo.py">
<argument flag="--iter">100</argument>
<argument flag="--smoothing">1.0</argument>
<argument flag="--mpi_tasks">4</argument>
<argument flag="--include_cavities"></argument>
</step>
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
</run_script>
</run_script>

</config>
9 changes: 9 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/config_files_ISC/config_initial_state.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,12 +29,14 @@
<add_link source="../culled_mesh/culled_graph.info" dest="graph.info"/>
<add_link source="../culled_mesh/critical_passages_mask_final.nc" dest="critical_passages.nc"/>
<add_link source="../culled_mesh/land_ice_mask.nc" dest="land_ice_mask.nc"/>
<add_link source="../base_mesh/cellWidthVsLatLon.nc" dest="cellWidthVsLatLon.nc"/>
<add_link source_path="initial_condition_database" source="layer_depth.80Layer.180619.nc" dest="layer_depth.nc"/>
<add_link source_path="initial_condition_database" source="PTemp.Jan_p3.filled.mpas100levs.160127.nc" dest="temperature.nc"/>
<add_link source_path="initial_condition_database" source="Salt.Jan_p3.noBlackCaspian.filled.mpas100levs.160127.nc" dest="salinity.nc"/>
<add_link source_path="initial_condition_database" source="windStress.ncep_1958-2000avg.interp3600x2431.151106.nc" dest="wind_stress.nc"/>
<add_link source_path="bathymetry_database" source="BedMachineAntarctica_and_GEBCO_2019_0.05_degree.200128.nc" dest="topography.nc"/>
<add_link source_path="initial_condition_database" source="chlorophyllA_monthly_averages_1deg.151201.nc" dest="swData.nc"/>
<add_link source_path="script_configuration_dir" source="scripts/smooth_topo.py" dest="smooth_topo.py"/>

<namelist name="namelist.ocean" mode="init">
<template file="template_initial_state.xml" path_base="script_configuration_dir"/>
Expand All @@ -44,6 +46,7 @@
<option name="config_global_ocean_depth_file">'layer_depth.nc'</option>
<option name="config_global_ocean_minimum_depth">10</option>
<option name="config_global_ocean_deepen_critical_passages">.false.</option>
<option name="config_global_ocean_topography_file">'topography_smoothed.nc'</option>
</namelist>

<streams name="streams.ocean" keep="immutable" mode="init">
Expand All @@ -53,6 +56,12 @@
</streams>

<run_script name="run.py">
<step executable="./smooth_topo.py">
<argument flag="--iter">100</argument>
<argument flag="--smoothing">1.0</argument>
<argument flag="--mpi_tasks">4</argument>
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It's annoying that the number of MPI tasks is repeatedly hard coded and not part of the config file or some kind of machine config file. We need to think if there's a better way to do this. This is just one example of where the problem arises.

<argument flag="--include_cavities"></argument>
</step>
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
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