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Can I aggregate multiple collections of NetCDF files using NcML?

I have 40 NetCDF files that make up one simulation from an ocean model. The time series of data for each variable is divided into several files, so the list of directories looks like this:

$ ls ./output/*.nc
1_hvel.nc           3_hvel.nc           5_hvel.nc           7_hvel.nc
1_MeanPeriod.nc     3_MeanPeriod.nc     5_MeanPeriod.nc     7_MeanPeriod.nc
1_PeakPeriod.nc     3_PeakPeriod.nc     5_PeakPeriod.nc     7_PeakPeriod.nc
1_pwd.nc            3_pwd.nc            5_pwd.nc            7_pwd.nc
1_SigWaveHeight.nc  3_SigWaveHeight.nc  5_SigWaveHeight.nc  7_SigWaveHeight.nc
1_WaterLevel.nc     3_WaterLevel.nc     5_WaterLevel.nc     7_WaterLevel.nc
2_hvel.nc           4_hvel.nc           6_hvel.nc           8_hvel.nc
2_MeanPeriod.nc     4_MeanPeriod.nc     6_MeanPeriod.nc     8_MeanPeriod.nc
2_PeakPeriod.nc     4_PeakPeriod.nc     6_PeakPeriod.nc     8_PeakPeriod.nc
2_pwd.nc            4_pwd.nc            6_pwd.nc            8_pwd.nc
2_SigWaveHeight.nc  4_SigWaveHeight.nc  6_SigWaveHeight.nc  8_SigWaveHeight.nc
2_WaterLevel.nc     4_WaterLevel.nc     6_WaterLevel.nc     8_WaterLevel.nc

Is it possible to aggregate each variable by time size, and then combine all these aggregates?

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Yes, you can group aggregates using NcML, so you can use type aggregation unionaround multiple type aggregates join_existingon time.

join_existing time , time time2 , .

:

<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
 <attribute name="title" type="string" value="SELFE - Ike - Ultralite - Variable Drag - Waves - 3D"/>
 <attribute name="institution" type="string"
  value="Virginia Institute of Marine Science -- http://web.vims.edu/physical/"/>
 <attribute name="source" type="string"
  value="SELFE run  (version v.vvv  compiled yyyy-mm-dd) for Hurricane Ike on the Ultralight mesh using variable drag, wind waves from WWM and 3D depth-averaged physics"/>
 <attribute name="history" type="string" value="ncml aggregation of .../whole_domain/ datafiles"/>
 <attribute name="references" type="string"
  value="testbed.sura.org:/data/ftp/upload/Inundation/vims/selfe_tropical/runs/Ike/3D_varied_roughness_windstress_with_wave/Inundation_Model_Metadata_Template_v3_for_3D_windstress_sv_with_wave_Rita.docx"/>
 <variable name="selfe_mesh" shape="" type="int">
  <attribute name="cf_role" value="mesh_topology"/>
  <attribute name="topology_dimension" type="int" value="2"/>
  <attribute name="node_coordinates" value="x y"/>
  <attribute name="face_node_connectivity" value="ele"/>
 </variable>
 <variable name="time">
  <attribute name="units" value="seconds since 2005-09-18 00:00:00"/>
  <attribute name="standard_name" value="time"/>
 </variable>
 <variable name="ele" shape="nface nele" type="int">
  <attribute name="cf_role" value="face_node_connnectivity"/>
  <attribute name="start_index" type="short" value="1"/>
 </variable>
 <variable name="x" shape="node" type="float">
  <attribute name="units" value="degrees_east"/>
 </variable>
 <variable name="y" shape="node" type="float">
  <attribute name="units" value="degrees_north"/>
 </variable>
 <variable name="depth" shape="node" type="float">
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="m"/>
  <attribute name="standard_name" value="depth_below_geoid"/>
  <remove type="attribute" name="positive"/>
 </variable>
 <variable name="sigma" shape="sigma" type="float">
  <attribute name="long_name" value="S coordinates at whole levels"/>
  <attribute name="units" value="non-dimensional"/>
  <attribute name="positive" value="up"/>
 </variable>
 <variable name="Cs" shape="sigma" type="float">
  <attribute name="long_name" value="Function C(s) at whole levels"/>
  <attribute name="units" value="non-dimensional"/>
  <attribute name="positive" value="up"/>
 </variable>
 <variable name="elev" shape="time node" type="float">
  <attribute name="long_name" value="free_surface_elevation"/>
  <attribute name="standard_name" value="sea_surface_height_above_geoid"/>
  <attribute name="missing_value" type="float" value="-999.00"/>
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="m"/>
 </variable>
 <variable name="wwm_1" shape="time node" type="float">
  <attribute name="long_name" value="significant_wave_height"/>
  <attribute name="standard_name" value="sea_surface_wave_significant_height"/>
  <attribute name="missing_value" type="float" value="-999.00"/>
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="m"/>
 </variable>
 <variable name="wwm_3" shape="time node" type="float">
  <attribute name="long_name" value="mean_period"/>
  <attribute name="standard_name" value="sea_surface_wave_period_at_variance_spectral_density_mean"/>
  <attribute name="missing_value" type="float" value="-999.00"/>
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="s"/>
 </variable>
 <variable name="wwm_9" shape="time node" type="float">
  <attribute name="long_name" value="peak_period"/>
  <attribute name="standard_name"
   value="sea_surface_wave_period_at_variance_spectral_density_maximum"/>
  <attribute name="missing_value" type="float" value="-999.00"/>
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="s"/>
 </variable>
 <variable name="wwm_15" shape="time node" type="float">
  <attribute name="long_name" value="peak_direction"/>
  <attribute name="standard_name"
   value="sea_surface_wave_from_direction_at_variance_spectral_density_maximum"/>
  <attribute name="missing_value" type="float" value="-999.00"/>
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="degrees_east"/>
 </variable>
 <variable name="u" shape="time2 sigma node" type="float">
  <attribute name="standard_name" value="barotropic_eastward_sea_water_velocity"/>
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="m/s"/>
 </variable>
 <variable name="v" shape="time2 sigma node" type="float">
  <attribute name="standard_name" value="barotropic_northward_sea_water_velocity"/>
  <attribute name="mesh" value="selfe_mesh"/>
  <attribute name="location" value="node"/>
  <attribute name="coordinates" value="y x"/>
  <attribute name="units" value="m/s"/>
 </variable>
 <aggregation type="union">
  <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
   <aggregation dimName="time" type="joinExisting">
    <scan
     location="/data/ftp/upload/Inundation/vims/selfe_tropical/runs/Rita/3D_varied_roughness_windstress_with_wave/output/"
     regExp=".*[0-9]{1}_WaterLevel\.nc$"/>
   </aggregation>
  </netcdf>
  <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
   <aggregation dimName="time" type="joinExisting">
    <scan
     location="/data/ftp/upload/Inundation/vims/selfe_tropical/runs/Rita/3D_varied_roughness_windstress_with_wave/output/"
     regExp=".*[0-9]{1}_SigWaveHeight\.nc$"/>
   </aggregation>
  </netcdf>
  <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
   <aggregation dimName="time" type="joinExisting">
    <scan
     location="/data/ftp/upload/Inundation/vims/selfe_tropical/runs/Rita/3D_varied_roughness_windstress_with_wave/output/"
     regExp=".*[0-9]{1}_MeanPeriod\.nc$"/>
   </aggregation>
  </netcdf>
  <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
   <aggregation dimName="time" type="joinExisting">
    <scan
     location="/data/ftp/upload/Inundation/vims/selfe_tropical/runs/Rita/3D_varied_roughness_windstress_with_wave/output/"
     regExp=".*[0-9]{1}_PeakPeriod\.nc$"/>
   </aggregation>
  </netcdf>
  <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
   <aggregation dimName="time" type="joinExisting">
    <scan
     location="/data/ftp/upload/Inundation/vims/selfe_tropical/runs/Rita/3D_varied_roughness_windstress_with_wave/output/"
     regExp=".*[0-9]{1}_pwd\.nc$"/>
   </aggregation>
  </netcdf>
  <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
   <dimension name="time2" orgName="time"/>
   <variable name="time2" orgName="time"/>
   <aggregation dimName="time" type="joinExisting">
    <scan
     location="/data/ftp/upload/Inundation/vims/selfe_tropical/runs/Rita/3D_varied_roughness_windstress_with_wave/output/"
     regExp=".*[0-9]{1}_hvel\.nc$"/>
   </aggregation>
  </netcdf>
 </aggregation>
</netcdf>
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