feat(chunker): add cli chunker helper

[jourdain]

No description provided.

[jourdain]

I get the following error when running

quickview-chunk --input ../NERSC-bigdata/output.scream.Cess.monthly_ne1024.AVERAGE.nmonths_x1.2019-09-01-00000.nc
  time                 shape=(1,) chunks=None read=   0.0s write=   0.0s size=0.00GB
  time_bnds            shape=(1, 2) chunks=None read=   0.0s write=   0.0s size=0.00GB
  IceWaterPath         shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  LW_clrsky_flux_dn_at_model_bot shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.1s size=0.10GB
  LW_clrsky_flux_up_at_model_top shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  LW_flux_dn_at_model_bot shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  LW_flux_up_at_model_bot shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  LW_flux_up_at_model_top shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  LiqWaterPath         shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  LongwaveCloudForcing shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  MeridionalVapFlux    shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  PotentialTemperature_at_1000hPa shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  PotentialTemperature_at_700hPa shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  RainWaterPath        shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  RelativeHumidity     shape=(1, 25165824, 128) chunks=(1, 1048576, 1) read=   4.8s write=  47.2s size=12.88GB
  RelativeHumidity_at_700hPa shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SW_clrsky_flux_dn_at_model_bot shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SW_clrsky_flux_up_at_model_bot shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SW_clrsky_flux_up_at_model_top shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SW_flux_dn_at_model_bot shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SW_flux_dn_at_model_top shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SW_flux_up_at_model_bot shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SW_flux_up_at_model_top shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  SeaLevelPressure     shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  ShortwaveCloudForcing shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  T_2m                 shape=(1, 25165824) chunks=(1, 1048576) read=   0.0s write=   0.0s size=0.10GB
  T_mid                shape=(1, 25165824, 128) chunks=(1, 1048576, 1) read=   5.4s write=  54.4s size=12.88GB
  U                    shape=(1, 25165824, 128) chunks=(1, 1048576, 1) read=   5.5s write=  57.2s size=12.88GB

Traceback (most recent call last):
  File "/Users/sebastien.jourdain/Documents/code/BER/QuickView/src/e3sm_quickview/cli/chunk.py", line 67, in convert
    out_var[:] = data
    ~~~~~~~^^^
  File "src/netCDF4/_netCDF4.pyx", line 5630, in netCDF4._netCDF4.Variable.__setitem__
  File "src/netCDF4/_netCDF4.pyx", line 5917, in netCDF4._netCDF4.Variable._put
  File "src/netCDF4/_netCDF4.pyx", line 2164, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: HDF error

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/sebastien.jourdain/miniforge3/envs/quickview/bin/quickview-chunk", line 7, in <module>
    sys.exit(main())
             ~~~~^^
  File "/Users/sebastien.jourdain/Documents/code/BER/QuickView/src/e3sm_quickview/cli/chunk.py", line 90, in main
    convert(args.input, args.output)
    ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/sebastien.jourdain/Documents/code/BER/QuickView/src/e3sm_quickview/cli/chunk.py", line 36, in convert
    with netCDF4.Dataset(dst_file, "w", format="NETCDF4") as dst:
         ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "src/netCDF4/_netCDF4.pyx", line 2551, in netCDF4._netCDF4.Dataset.__exit__
  File "src/netCDF4/_netCDF4.pyx", line 2669, in netCDF4._netCDF4.Dataset.close
  File "src/netCDF4/_netCDF4.pyx", line 2636, in netCDF4._netCDF4.Dataset._close
  File "src/netCDF4/_netCDF4.pyx", line 2164, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: HDF error

[jourdain]

quickview-chunk --input ../NERSC-bigdata/output.scream.Cess.hourly2DVars.INSTANT.nhours_x1.2019-09-02-03600.nc
  time                 shape=(96,) chunks=None read=   0.0s write=   0.0s size=0.00GB
Traceback (most recent call last):
  File "/Users/sebastien.jourdain/Documents/code/BER/QuickView/src/e3sm_quickview/cli/chunk.py", line 67, in convert
    out_var[:] = data
    ~~~~~~~^^^
  File "src/netCDF4/_netCDF4.pyx", line 5630, in netCDF4._netCDF4.Variable.__setitem__
  File "src/netCDF4/_netCDF4.pyx", line 5917, in netCDF4._netCDF4.Variable._put
  File "src/netCDF4/_netCDF4.pyx", line 2164, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: HDF error

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/sebastien.jourdain/miniforge3/envs/quickview/bin/quickview-chunk", line 7, in <module>
    sys.exit(main())
             ~~~~^^
  File "/Users/sebastien.jourdain/Documents/code/BER/QuickView/src/e3sm_quickview/cli/chunk.py", line 90, in main
    convert(args.input, args.output)
    ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/sebastien.jourdain/Documents/code/BER/QuickView/src/e3sm_quickview/cli/chunk.py", line 36, in convert
    with netCDF4.Dataset(dst_file, "w", format="NETCDF4") as dst:
         ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "src/netCDF4/_netCDF4.pyx", line 2551, in netCDF4._netCDF4.Dataset.__exit__
  File "src/netCDF4/_netCDF4.pyx", line 2669, in netCDF4._netCDF4.Dataset.close
  File "src/netCDF4/_netCDF4.pyx", line 2636, in netCDF4._netCDF4.Dataset._close
  File "src/netCDF4/_netCDF4.pyx", line 2164, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: HDF error

[jourdain]

nerver mind, I was running of disk space...