Skip to content

New Mesh: WC14to60kmL60E3SMv2r03 #628

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 6 commits into from
Aug 17, 2020
Merged

New Mesh: WC14to60kmL60E3SMv2r03 #628

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
51890d3
Bump compass env to 0.1.8
xylar Jul 10, 2020
1bb7495
Bump WC14 revision to 03
xylar Jul 10, 2020
f4423ff
Add PR number to metadata
xylar Jul 10, 2020
40fbc08
Switch 60 layers to be the default vertical res
xylar Jul 10, 2020
23b073b
Update test_final_settings to run correctly
xylar Jul 13, 2020
48c29df
Update depreciated python plot label command.
mark-petersen Aug 17, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions testing_and_setup/compass/README_ocean.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@ To set up and run ocean test cases from COMPASS, you will need a conda
environment. First, install Miniconda3 (if miniconda is not already
installed), then create a new conda environment as follows:
``` bash
conda create -n compass_0.1.6 -c conda-forge -c e3sm python=3.7 compass=0.1.6
conda create -n compass_0.1.8 -c conda-forge -c e3sm python=3.7 compass=0.1.8
```
Each time you want to work with COMPASS, you will need to run:
```
conda activate compass_0.1.6
conda activate compass_0.1.8
```

An appropriate conda environment is already available on Los Alamos National
Expand Down
2 changes: 1 addition & 1 deletion testing_and_setup/compass/load_compass_env.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
version=0.1.6
version=0.1.8

# The rest of the script should not need to be modified
if [[ $HOSTNAME = "cori"* ]] || [[ $HOSTNAME = "dtn"* ]]; then
Expand Down
6 changes: 3 additions & 3 deletions testing_and_setup/compass/ocean/global_ocean/WC14/init/config_E3SM_coupling_files.ini
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
[main]
nprocs = 1
# the file name of the initial condition, possibly after spin-up
initial_condition = ../../spin_up/simulation/restarts/restart.0001-01-21_00.00.00.nc
initial_condition = ../../spin_up/test_final_settings/restarts/restart.0001-01-31_00.00.00.nc

[mesh]
short_name = ${prefix}${min_res}to${max_res}E${e3sm_version}r${mesh_version}
Expand All @@ -14,9 +14,9 @@ prefix = WC
description = MPAS North America and Arctic Focused Water Cycle mesh for E3SM version
${e3sm_version}, with a focused ${min_res}-km resolution
around North America and ${levels} vertical levels as documented at
https://github.com/MPAS-Dev/MPAS-Model/pull/584
https://github.com/MPAS-Dev/MPAS-Model/pull/628
e3sm_version = 2
mesh_version = 02
mesh_version = 03
creation_date = autodetect
min_res = 14
max_res = 60
Expand Down
1 change: 0 additions & 1 deletion testing_and_setup/compass/ocean/global_ocean/WC14/init/config_initial_state.xml
View file
Open in desktop

This file was deleted.

57 changes: 57 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/WC14/init/config_initial_state.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,57 @@
<?xml version="1.0"?>
<config case="initial_state">
<get_file dest_path="initial_condition_database" file_name="Salinity.01.filled.60levels.PHC.151106.nc">
<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="PotentialTemperature.01.filled.60levels.PHC.151106.nc">
<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>

<get_file dest_path="initial_condition_database" file_name="ETOPO2v2c_f4_151106.nc">
<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="chlorophyllA_monthly_averages_1deg.151201.nc">
<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/initial_condition_database/"/>
</get_file>

<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="script_core_dir" source="scripts/plots/plot_initial_state.py" dest="plot_initial_state.py"/>
<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="initial_condition_database" source="ETOPO2v2c_f4_151106.nc" dest="topography.nc"/>
<add_link source_path="initial_condition_database" source="chlorophyllA_monthly_averages_1deg.151201.nc" dest="swData.nc"/>

<namelist name="namelist.ocean" 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"/>
<option name="config_global_ocean_depth_file">'layer_depth.nc'</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_minimum_depth">10</option>
<option name="config_global_ocean_deepen_critical_passages">.false.</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"/>
</streams>

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">36</argument>
</step>
<model_run procs="36" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
<step executable="./plot_initial_state.py">
</step>
</run_script>
</config>
1 change: 0 additions & 1 deletion testing_and_setup/compass/ocean/global_ocean/WC14/init/config_initial_state_60_layers.xml
View file
Open in desktop

This file was deleted.

66 changes: 66 additions & 0 deletions testing_and_setup/compass/ocean/global_ocean/WC14/init/config_initial_state_64_layers.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
<?xml version="1.0"?>
<config case="initial_state_64_layers">
<get_file dest_path="initial_condition_database" file_name="layer_depth.80Layer.180619.nc">
<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="PTemp.Jan_p3.filled.mpas100levs.160127.nc">
<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="Salt.Jan_p3.noBlackCaspian.filled.mpas100levs.160127.nc">
<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>

<get_file dest_path="initial_condition_database" file_name="ETOPO2v2c_f4_151106.nc">
<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="chlorophyllA_monthly_averages_1deg.151201.nc">
<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/initial_condition_database/"/>
</get_file>


<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"/>
<copy_file source_path="script_test_dir" source="define_vertical_grid.py" dest="define_vertical_grid.py"/>
<add_link source_path="script_core_dir" source="scripts/vertical_grid/make_vertical_grid.py" dest="make_vertical_grid.py"/>
<add_link source_path="script_core_dir" source="scripts/plots/plot_initial_state.py" dest="plot_initial_state.py"/>
<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="initial_condition_database" source="ETOPO2v2c_f4_151106.nc" dest="topography.nc"/>
<add_link source_path="initial_condition_database" source="chlorophyllA_monthly_averages_1deg.151201.nc" dest="swData.nc"/>

<namelist name="namelist.ocean" 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"/>
<option name="config_global_ocean_depth_file">'vertical_grid.nc'</option>
<option name="config_global_ocean_depth_dimname">'nVertLevels'</option>
<option name="config_global_ocean_depth_varname">'refMidDepth'</option>
<option name="config_global_ocean_minimum_depth">10</option>
<option name="config_global_ocean_deepen_critical_passages">.false.</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"/>
</streams>

<run_script name="run.py">
<step executable="gpmetis">
<argument flag="graph.info">4</argument>
</step>
<step executable="./define_vertical_grid.py">
</step>
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
<step executable="./plot_initial_state.py">
</step>
</run_script>

</config>
8 changes: 4 additions & 4 deletions testing_and_setup/compass/ocean/global_ocean/WC14/init/define_base_mesh.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -186,10 +186,10 @@ def plot_cartopy(nPlot, varName, var, map_name):
alpha=0.5,
linestyle='-', zorder=2)
ax.coastlines()
gl.xlabels_top = False
gl.xlabels_bottom = False
gl.ylabels_right = False
gl.ylabels_left = False
gl.top_labels = False
gl.bottom_labels = False
gl.right_labels = False
gl.left_labels = False
plt.colorbar(im, shrink=.9)
plt.title(varName)

Expand Down
4 changes: 2 additions & 2 deletions testing_and_setup/compass/ocean/global_ocean/WC14/spin_up/config_test_final_settings.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
<namelist name="namelist.ocean" mode="forward">
<template file="template_forward.xml" path_base="script_configuration_dir"/>
<template file="template_forward.xml" path_base="script_resolution_dir"/>
<option name="config_run_duration">'00-01-00_00:00:00'</option>
<option name="config_run_duration">'00-00-24_00:00:00'</option>
<option name="config_do_restart">.true.</option>
<option name="config_start_time">'file'</option>
<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
Expand All @@ -29,7 +29,7 @@
<attribute name="output_interval">00-00-10_00:00:00</attribute>
</stream>
<stream name="restart">
<attribute name="output_interval">00-01-00_00:00:00</attribute>
<attribute name="output_interval">00-00-06_00:00:00</attribute>
</stream>

<template file="global_stats.xml" path_base="script_core_dir" path="templates/analysis_members"/>
Expand Down