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Add -i and -o flags to all mesh conversion calls in ocean test cases #1148

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Add -i and -o flags to all mesh conversion calls in ocean test cases #1148

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6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/baroclinic_channel/10km/decomp_test/config_init1.xml
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Expand Up @@ -50,14 +50,14 @@

<run_script name="run.py">
<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>

<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/baroclinic_channel/10km/default/config_init1.xml
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Expand Up @@ -50,14 +50,14 @@

<run_script name="run.py">
<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>

<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/baroclinic_channel/10km/restart_test/config_init1.xml
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Expand Up @@ -50,14 +50,14 @@

<run_script name="run.py">
<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>

<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/baroclinic_channel/10km/threads_test/config_init1.xml
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Expand Up @@ -50,14 +50,14 @@

<run_script name="run.py">
<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>

<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/EC_60to30km/default/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/EC_60to30km/spin_up/config_init1.xml
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Expand Up @@ -15,7 +15,7 @@
<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
4 changes: 2 additions & 2 deletions test_cases/ocean/ocean/global_ocean/EC_60to30km/with_land_ice/config_init1.xml
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Expand Up @@ -15,8 +15,8 @@
<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_cavities"></argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_cavities</argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_120km/default/config_init1.xml
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Expand Up @@ -15,7 +15,7 @@
<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_120km/ecosys_60_layer/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
4 changes: 2 additions & 2 deletions test_cases/ocean/ocean/global_ocean/QU_120km/with_land_ice/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_cavities"></argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_cavities</argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_240km/analysis_test/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_240km/default/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_240km/performance_test/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_240km/restart_test/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_240km/rk4_blocks_test/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_240km/se_blocks_test/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
4 changes: 2 additions & 2 deletions test_cases/ocean/ocean/global_ocean/QU_240km/with_land_ice/config_init1.xml
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Expand Up @@ -15,8 +15,8 @@
<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_cavities"></argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_cavities</argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
4 changes: 2 additions & 2 deletions test_cases/ocean/ocean/global_ocean/QU_240km/with_land_ice_no_iter/config_init1.xml
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Expand Up @@ -15,8 +15,8 @@
<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_cavities"></argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_cavities</argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_240km/zstar_128_layers/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/QU_480km/default/config_init1.xml
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<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_critical_passages"></argument>
<argument flag="">--with_critical_passages</argument>
</step>
</run_script>
</config>
2 changes: 1 addition & 1 deletion test_cases/ocean/ocean/global_ocean/RRS_30to10km/with_land_ice/config_init1.xml
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Expand Up @@ -15,7 +15,7 @@
<run_script name="run.py">
<step executable="./init_step1.py">
<argument flag="-p">geometric_features</argument>
<argument flag="--with_cavities"></argument>
<argument flag="">--with_cavities</argument>
</step>
</run_script>
</config>
32 changes: 16 additions & 16 deletions test_cases/ocean/ocean/global_ocean/init_step1.py
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Expand Up @@ -65,8 +65,8 @@

# create the land mask based on the land coverage
# Run command is:
# ./MpasMaskCreator.x base_mesh.nc land_mask.nc -f land_coverage.geojson
subprocess.check_call(['./MpasMaskCreator.x', 'base_mesh.nc', 'land_mask.nc',
# ./MpasMaskCreator.x -i base_mesh.nc -o land_mask.nc -f land_coverage.geojson
subprocess.check_call(['./MpasMaskCreator.x', '-i', 'base_mesh.nc', '-o', 'land_mask.nc',
'-f', 'land_coverage.geojson'], env=os.environ.copy())

# create seed points for a flood fill of the ocean
Expand All @@ -91,54 +91,54 @@

# create masks from the transects
# Run command is:
# ./MpasMaskCreator.x base_mesh.nc critical_passages_mask.nc -f critical_passages.geojson
args = ['./MpasMaskCreator.x', 'base_mesh.nc', 'critical_passages_mask.nc',
# ./MpasMaskCreator.x -i base_mesh.nc -o critical_passages_mask.nc -f critical_passages.geojson
args = ['./MpasMaskCreator.x', '-i', 'base_mesh.nc', '-o', 'critical_passages_mask.nc',
'-f', 'critical_passages.geojson']
print "running", ' '.join(args)
subprocess.check_call(args, env=os.environ.copy())


# cull the mesh based on the land mask and keeping critical passages open
# Run command is:
# ./MpasCellCuller.x base_mesh.nc culled_mesh.nc -m land_mask.nc -p critical_passages_mask.nc
args = ['./MpasCellCuller.x', 'base_mesh.nc', 'culled_mesh.nc',
# ./MpasCellCuller.x -i base_mesh.nc -o culled_mesh.nc -m land_mask.nc -p critical_passages_mask.nc
args = ['./MpasCellCuller.x', '-i', 'base_mesh.nc', '-o', 'culled_mesh.nc',
'-m', 'land_mask.nc', '-p', 'critical_passages_mask.nc']
print "running", ' '.join(args)
subprocess.check_call(args, env=os.environ.copy())
else:

# cull the mesh based on the land mask
# Run command is:
# ./MpasCellCuller.x base_mesh.nc culled_mesh.nc -m land_mask.nc
args = ['./MpasCellCuller.x', 'base_mesh.nc', 'culled_mesh.nc',
# ./MpasCellCuller.x -i base_mesh.nc -o culled_mesh.nc -m land_mask.nc
args = ['./MpasCellCuller.x', '-i', 'base_mesh.nc', '-o', 'culled_mesh.nc',
'-m', 'land_mask.nc']
print "running", ' '.join(args)
subprocess.check_call(args, env=os.environ.copy())

# create a mask for the flood fill seed points
# Run command is:
# ./MpasMaskCreator.x culled_mesh.nc seed_mask.nc -s seed_points.geojson
args = ['./MpasMaskCreator.x', 'culled_mesh.nc', 'seed_mask.nc',
# ./MpasMaskCreator.x -i culled_mesh.nc -o seed_mask.nc -s seed_points.geojson
args = ['./MpasMaskCreator.x', '-i', 'culled_mesh.nc', '-o', 'seed_mask.nc',
'-s', 'seed_points.geojson']
print "running", ' '.join(args)
subprocess.check_call(args, env=os.environ.copy())


# cull the mesh a second time using a flood fill from the seed points
# Run command is:
# ./MpasCellCuller.x culled_mesh.nc culled_mesh_final.nc -i seed_mask.nc
args = ['./MpasCellCuller.x', 'culled_mesh.nc', 'culled_mesh_final.nc',
'-i', 'seed_mask.nc']
# ./MpasCellCuller.x -i culled_mesh.nc -o culled_mesh_final.nc -v seed_mask.nc
args = ['./MpasCellCuller.x', '-i', 'culled_mesh.nc', '-o', 'culled_mesh_final.nc',
'-v', 'seed_mask.nc']

print "running", ' '.join(args)
subprocess.check_call(args, env=os.environ.copy())

if options.with_critical_passages:
# make a new version of the critical passages mask on the culled mesh
# Run command is:
# ./MpasMaskCreator.x culled_mesh_final.nc critical_passages_mask_final.nc -f critical_passages.geojson
args = ['./MpasMaskCreator.x', 'culled_mesh_final.nc',
'critical_passages_mask_final.nc',
# ./MpasMaskCreator.x -i culled_mesh_final.nc -o critical_passages_mask_final.nc -f critical_passages.geojson
args = ['./MpasMaskCreator.x', '-i', 'culled_mesh_final.nc',
'-o', 'critical_passages_mask_final.nc',
'-f', 'critical_passages.geojson']
print "running", ' '.join(args)
subprocess.check_call(args, env=os.environ.copy())
Expand Down
6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/isomip/10km/expt1.01/config_init1.xml
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Expand Up @@ -24,8 +24,8 @@

<run_script name="run.py">
<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>

<step executable="./metis">
Expand All @@ -34,7 +34,7 @@
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/isomip/10km/expt2.01/config_init1.xml
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Expand Up @@ -29,8 +29,8 @@

<run_script name="run.py">
<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>

<step executable="./metis">
Expand All @@ -39,7 +39,7 @@
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/isomip_plus/2km/Ocean0/config_init1.xml
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Expand Up @@ -39,8 +39,8 @@
</step>

<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>
<step executable="./metis">
<argument flag="graph.info">4</argument>
Expand All @@ -49,7 +49,7 @@
<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
6 changes: 3 additions & 3 deletions test_cases/ocean/ocean/isomip_plus/2km/Ocean1/config_init1.xml
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Expand Up @@ -39,8 +39,8 @@
</step>

<step executable="./MpasMeshConverter.x">
<argument flag="">base_mesh.nc</argument>
<argument flag="">mesh.nc</argument>
<argument flag="-i">base_mesh.nc</argument>
<argument flag="-o">mesh.nc</argument>
</step>
<step executable="./metis">
<argument flag="graph.info">16</argument>
Expand All @@ -49,7 +49,7 @@
<model_run procs="16" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

<step executable="./MpasCellCuller.x">
<argument flag="">ocean.nc</argument>
<argument flag="-i">ocean.nc</argument>
</step>
</run_script>
</config>
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