[gradsusr] GrADS Control File for Array with Spectral Band Dimension

James E. Johnson James.Johnson at nasa.gov
Thu Sep 19 18:11:44 EDT 2013


On Thursday 19 September 2013 04:55:58 pm Jennifer Adams wrote:
> First of all, thank you for providing all the information and data I needed
>  to reproduce the error! The failure of method 1 (using array indices in
>  the units field of the variable declaration instead of x,y,z,t,e) is
>  indeed a bug that is unique to the hdf5 data type. The critical bit of
>  information in the error message from the HDF5 library was this: "src and
>  dest data spaces have different sizes." In method 1, the variables are
>  described to GrADS as being only 2-dimensional (i.e., not Z-varying) even
>  though they really have 3 varying dimensions, and the library trips on
>  this deception. The netcdf library is not as fussy. I will put a fix in
>  version 2.1, but for now you will have to use method 2. --Jennifer

Thanks Jennifer,

I think there may be another bug. I have a more extensive control file with 
all the variables from the file. I can successfully display data from the 
first variable I read, but subsequent variables complain:

HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
  #000: H5Shyper.c line 6593 in H5Sselect_hyperslab(): not a data space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5 Error: unable to select dataspace hyperslab
Data Request Error:  Error for variable 'uvai'
  Error ocurred at column 1
DISPLAY error:  Invalid expression
  Expression = uvai

Here is the complete config file for this product:
DSET OMI-Aura_L3-OMAEROe_2013m0601_v003-2013m0603t015851.he5
DTYPE hdf5_grid
TITLE OMI/Aura Multi-wavelength Aerosol Optical Depth and Single Scattering 
Albedo Daily L3 Global 0.25x0.25 deg Lat/Lon Grid
UNDEF -32767 _FillValue
UNPACK ScaleFactor Offset
XDEF 1440 linear -180 0.25
YDEF 720 linear -90 0.25
ZDEF 5 levels 342.5 388.0 442.0 463.0 483.5
TDEF 5000 linear 1oct2004 1dy
VARS 15
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AbsorbingAerosolOpticalThicknessMW=>aaod  
5  z,y,x  Absorbing Aerosol Optical Thickness
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AerosolModelMW=>amod 0 y,x  
Aerosol Model
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AerosolOpticalThicknessMW=>aod  
5  z,y,x  Aerosol Optical Thickness
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AerosolOpticalThicknessPassedThresholdMean=>aodptm  
0  y,x  Aerosol Optical Thickness Passed Threshold Mean
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AerosolOpticalThicknessPassedThresholdStd=>aodpts  
0  y,x  Aerosol Optical Thickness Passed Threshold Standard Deviation
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/Latitude=>lat  0  y,x  Latitude
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/Longitude=>lon  0  y,x  
Longitude
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/SingleScatteringAlbedoMW=>ssa  5  
z,y,x  Single Scattering Albedo
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/SingleScatteringAlbedoPassedThresholdMean=>ssaptm  
0  y,x  Single Scattering Albedo Passed Threshold Mean
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/SingleScatteringAlbedoPassedThresholdStd=>ssapts  
0  y,x  Single Scattering Albedo Passed Threshold Standard Deviation
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/SolarZenithAngle=>sza  0  y,x  
Solar Zenith Angle
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/TerrainReflectivity=>tref  0  
y,x  Terrain Reflectivity
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/UVAerosolIndex=>uvai  0  y,x  UV 
Aerosol Index
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/VISAerosolIndex=>visai  0  y,x  
VIS Aerosol Index
/HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/ViewingZenithAngle=>vza  0  y,x 
Viewing Zenith Angle
ENDVARS


Does the optional CACHESIZE attribute needed to be set?

James Johnson

> On Sep 19, 2013, at 3:29 PM, James E. Johnson wrote:
> > I'm using grads-2.0.2-bin-CentOS5.8-x86_64.tar.gz
> >
> > I have an HDF-EOS5 file with some data arrays that are 3 dimensional,
> > with the third dimension representing wavelength/spectral band. I created
> > a control file for this data following the description at
> > http://www.iges.org/grads/gadoc/gadocindex.html (section VAR subsection
> > units). It says there are two ways to implement this, first with an array
> > index in the units dimension list, the second with dimension values
> > specified in the Z axis. The second method works, however the first
> > method keeps giving me errors:
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
> >  #000: H5Dio.c line 174 in H5Dread(): can't read data
> >    major: Dataset
> >    minor: Read failed
> >  #001: H5Dio.c line 348 in H5D_read(): src and dest data spaces have
> > different sizes
> >    major: Invalid arguments to routine
> >    minor: Bad value
> > H5Dread failed for short data
> > Data Request Error:  Error for variable 'aaod342'
> >  Error ocurred at column 1
> > DISPLAY error:  Invalid expression
> >  Expression = aaod342
> >
> >
> >
> > The sample data file is:
> > ftp://acdisc.gsfc.nasa.gov/data/s4pa/Aura_OMI_Level3/OMAEROe.003/2013/OMI
> >- Aura_L3-OMAEROe_2013m0601_v003-2013m0603t015851.he5
> >
> >
> > First method (array index) control file:
> > DSET OMI-Aura_L3-OMAEROe_2013m0601_v003-2013m0603t015851.he5
> > DTYPE hdf5_grid
> > TITLE OMI/Aura Multi-wavelength Aerosol Optical Depth and Single
> > Scattering Albedo Daily L3 Global 0.25x0.25 deg Lat/Lon Grid for 1 June
> > 2013 UNDEF -32767 _FillValue
> > XDEF 1440 linear -180 0.25
> > YDEF 720 linear -90 0.25
> > ZDEF 1 levels 1
> > TDEF 1 linear 1jun2013 1dy
> > VARS 5
> > /HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AbsorbingAerosolOpticalThic
> >knessMW=>aaod342 0  0,y,x  Absorbing Aerosol Optical Thickness at 342.5 nm
> > /HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AbsorbingAerosolOpticalThic
> >knessMW=>aaod388 0  1,y,x  Absorbing Aerosol Optical Thickness at 388.0 nm
> > /HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AbsorbingAerosolOpticalThic
> >knessMW=>aaod442 0  2,y,x  Absorbing Aerosol Optical Thickness at 442.0 nm
> > /HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AbsorbingAerosolOpticalThic
> >knessMW=>aaod463 0  3,y,x  Absorbing Aerosol Optical Thickness at 463.0 nm
> > /HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AbsorbingAerosolOpticalThic
> >knessMW=>aaod483 0  4,y,x  Absorbing Aerosol Optical Thickness at 483.5 nm
> > ENDVARS
> >
> >
> > Second method (Z dimension) control file:
> > DSET OMI-Aura_L3-OMAEROe_2013m0601_v003-2013m0603t015851.he5
> > DTYPE hdf5_grid
> > TITLE OMI/Aura Multi-wavelength Aerosol Optical Depth and Single
> > Scattering Albedo Daily L3 Global 0.25x0.25 deg Lat/Lon Grid for 1 June
> > 2013 UNDEF -32767 _FillValue
> > XDEF 1440 linear -180 0.25
> > YDEF 720 linear -90 0.25
> > ZDEF 5 levels 342.5 388.0 442.0 463.0 483.5
> > TDEF 1 linear 1jun2013 1dy
> > VARS 1
> > /HDFEOS/GRIDS/ColumnAmountAerosol/Data~Fields/AbsorbingAerosolOpticalThic
> >knessMW=>aaod 5  z,y,x  Absorbing Aerosol Optical Thickness
> > ENDVARS
> >
> >
> > How do I get method 1 (array index) to work? Is there something wrong
> > with ZDEF? Or is this a GrADS bug?
> >
> > -------------------------------------------------------------------------
> >-----
> >
> > | James E. Johnson                   | address:                          
> > |    | ADNET Systems, Inc.                |  NASA Goddard Space Flight
> > | Center     | e-mail: james.johnson at nasa.gov     |  Data and Information
> > | Services Center | phone:  301-614-5121               |  Code 610.2,
> > | Bldg 32, Room S130G      | fax:    301-614-5268               | 
> > | Greenbelt, MD  20771                 |
> >
> > -------------------------------------------------------------------------
> >----- _______________________________________________
> > gradsusr mailing list
> > gradsusr at gradsusr.org
> > http://gradsusr.org/mailman/listinfo/gradsusr
> 
> --
> Jennifer M. Adams
> Center for Ocean-Land-Atmosphere Studies (COLA)
> 111 Research Hall, Mail Stop 2B3
> George Mason University
> 4400 University Drive
> Fairfax, VA 22030
> 




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