[gradsusr] HDF5 control file help

Jennifer M Adams jadams21 at gmu.edu
Wed Dec 23 08:11:30 EST 2015


Hi, Joyce —
Try changing the variable declaration from “y,x” to “x,y” and see if that fixes it.
—Jennifer

On Dec 22, 2015, at 9:28 PM, Meyerson, Joyce <hobo at atmos.ucla.edu<mailto:hobo at atmos.ucla.edu>> wrote:

Hi Jennifer,

I removed _FillValue and most of the errors resolved however I'm left with the error below. The grid attributes are from 20N, 50N, -180, 180. Is there something I'm not seeing in the control file?

ga-> d pr
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
  #000: ../../src/H5Dio.c line 153 in H5Dread(): selection+offset not within extent
    major: Dataspace
    minor: Out of range
HDF5 read error for float data
Data Request Error:  Error for variable 'pr'
  Error ocurred at column 1
DISPLAY error:  Invalid expression
  Expression = pr

*********************
DSET ^3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5
OPTIONS template
DTYPE hdf5_grid
TITLE GPM precip
UNDEF -9999.9
XDEF 3600 linear -180 0.1
YDEF 300 linear 20 0.1
ZDEF 1 levels 1000
TDEF 100 linear 00Z01jan2015 6hr
VARS 1
Grid/precipitation=>pr          0 y,x   precipitation mm/hr
ENDVARS
********************

> h5dump 3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5 |more
HDF5 "3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5" {
GROUP "/" {
   ATTRIBUTE "FileHeader" {
      DATATYPE  H5T_STRING {
            STRSIZE 563;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "DOI=10.5067/GPM/IMERG/HH/3B;
           DOIauthority=http://dx.doi/org/;
           DOIshortName=3IMERGM;
           AlgorithmID=3IMERGMCAG;
           AlgorithmVersion=3IMERGM_1.0;
           FileName=3B-MO.MS.MRG.3IMERG.20150101-S000000-E235959.01.V03D.HDF5.ps.hdf;
           SatelliteName=MULTI;
           InstrumentName=MERGED;
           GenerationDateTime=2015-12-03T21:21:48.000Z;
           StartGranuleDateTime=2015-01-01T00:00:00.000Z;
           StopGranuleDateTime=2015-01-31T23:59:59.999Z;
           GranuleNumber=;
           NumberOfSwaths=0;
           NumberOfGrids=1;
           GranuleStart=;
           TimeInterval=MONTH;
           ProcessingSystem=PPS;
           ProductVersion=V03D;
           EmptyGranule=NOT_EMPTY;
           MissingData=;
           "
      }
   }
   ATTRIBUTE "FileInfo" {
      DATATYPE  H5T_STRING {
            STRSIZE 228;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "DataFormatVersion=bh;
           TKCodeBuildVersion=1;
           MetadataVersion=bh;
           FormatPackage=HDF5-1.8.9;
           BlueprintFilename=GPM.V1.3IMERGM.blueprint.xml;
           BlueprintVersion=BV_42;
           TKIOVersion=3.60.8;
           MetadataStyle=PVL;
           EndianType=LITTLE_ENDIAN;
           "
      }
   }
 GROUP "Grid" {
      ATTRIBUTE "GridHeader" {
         DATATYPE  H5T_STRING {
               STRSIZE 257;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
         DATASPACE  SCALAR
         DATA {
         (0): "BinMethod=ARITHMETIC_MEAN;
           Registration=CENTER;
           LatitudeResolution=0.1;
           LongitudeResolution=0.1;
           NorthBoundingCoordinate=50.000000;
           SouthBoundingCoordinate=20.000000;
           EastBoundingCoordinate=180.000000;
           WestBoundingCoordinate=-180.000000;
           Origin=SOUTHWEST;
           "
         }
      }

On Dec 10, 2015, at 4:59 AM, Jennifer M Adams <jadams21 at gmu.edu<mailto:jadams21 at gmu.edu>> wrote:

Hi, Joyce —
The first thing to try is set up aliases for those variable names, which are not GrADS-compliant. Something like this:
   Grid/precipitation=>p 0 y,x precipitation
   Grid/probabilityLiquidPrecipitation=>lp     0 y,x   liquid precip
—Jennifer


On Dec 9, 2015, at 7:06 PM, Meyerson, Joyce <hobo at atmos.ucla.edu<mailto:hobo at atmos.ucla.edu>> wrote:

Hi Users,

I have a hdf5 data file from NASA's Global Precipitation Measurement project and I'm having trouble writing the control file. I don't know what I'm doing wrong. Any help would be greatly appreciated. The error I'm getting is

open test.ctl
Open Error:  Invalid variable record
--> The invalid description file record is:
--> Grid/precipitation                0 y,x   precipitation


DSET ^3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5
OPTIONS template
DTYPE hdf5_grid
TITLE GPM precip
UNDEF -999.0 _FillValue
XDEF 3600 linear -180 0.1
YDEF 300 linear -20 0.1
ZDEF 1 levels 1000
TDEF 1 linear 01dec2015 1dy
VARS 2
Grid/precipitation              0 y,x   precipitation
Grid/probabilityLiquidPrecipitation     0 y,x   liquid precip
ENDVARS

Here's the file contents of
h5dump -n 3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5

HDF5 "3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5" {
FILE_CONTENTS {
group      /
group      /Grid
dataset    /Grid/gaugeRelativeWeighting
dataset    /Grid/lat
dataset    /Grid/lon
dataset    /Grid/precipitation
dataset    /Grid/probabilityLiquidPrecipitation
dataset    /Grid/randomError
}
}

and the dataset
h5dump -H -d/Grid/precipitation 3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5

HDF5 "3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5" {
DATASET "/Grid/precipitation" {
 DATATYPE  H5T_IEEE_F32LE
 DATASPACE  SIMPLE { ( 3600, 300 ) / ( 3600, 300 ) }
 ATTRIBUTE "CodeMissingValue" {
    DATATYPE  H5T_STRING {
          STRSIZE 8;
          STRPAD H5T_STR_NULLTERM;
          CSET H5T_CSET_ASCII;
          CTYPE H5T_C_S1;
       }
    DATASPACE  SCALAR
 }
 ATTRIBUTE "DIMENSION_LIST" {
    DATATYPE  H5T_VLEN { H5T_REFERENCE}
    DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
 }
 ATTRIBUTE "DimensionNames" {
    DATATYPE  H5T_STRING {
          STRSIZE 8;
          STRPAD H5T_STR_NULLTERM;
          CSET H5T_CSET_ASCII;
          CTYPE H5T_C_S1;
       }
    DATASPACE  SCALAR
 }
 ATTRIBUTE "Units" {
    DATATYPE  H5T_STRING {
          STRSIZE 6;
          STRPAD H5T_STR_NULLTERM;
          CSET H5T_CSET_ASCII;
          CTYPE H5T_C_S1;
       }
    DATASPACE  SCALAR
 }
 ATTRIBUTE "_FillValue" {
    DATATYPE  H5T_IEEE_F32LE
    DATASPACE  SCALAR
 }
 ATTRIBUTE "coordinates" {
    DATATYPE  H5T_STRING {
          STRSIZE 8;
          STRPAD H5T_STR_NULLTERM;
          CSET H5T_CSET_ASCII;
          CTYPE H5T_C_S1;
       }
    DATASPACE  SCALAR
 }
 ATTRIBUTE "units" {
    DATATYPE  H5T_STRING {
          STRSIZE 6;
          STRPAD H5T_STR_NULLTERM;
          CSET H5T_CSET_ASCII;
          CTYPE H5T_C_S1;
       }
    DATASPACE  SCALAR
 }
}
}


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