[gradsusr] Control File Issues for HDF5 file

Justin Hicks jhicks2014 at gmail.com
Thu Jan 14 11:04:49 EST 2016


Jennifer,

Thank you. I will play around with this. However, it seems I would have to
know the xdef, ydef, and zdef to take advantage of this. Any hints on how I
could find out what these would be? What I have in my control file isn't
correct; I just placed it there with the intention of fixing it later after
the variables worked.

-Justin

On Thu, Jan 14, 2016 at 10:42 AM, Jennifer M Adams <jadams21 at gmu.edu> wrote:

> Hi, Justin —
> That message looks like your delcaration of the coordinates (“x,y”) is
> wrong. Look at the DATASPACE SIMPLE attribute in the h5dump output, that
> should give you a clue as to how many and what size the dimensions are. It
> looks like ‘hist’ has one more dimension than ‘mean’ and these variables
> have 6 or 7 dimensions.  Have a look at item #4 in the Usage Notes of
> http://cola.gmu.edu/grads/gadoc/SDFdescriptorfile.html for how to handle
> this situation.
> —Jennifer
>
> On Jan 14, 2016, at 10:04 AM, Justin Hicks <jhicks2014 at gmail.com> wrote:
>
> Jennifer,
>
> I put in the dataset names, like you said, but I still get a different
> error. The error says:
>
> ga-> d plrcnt
> HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
>   #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
>     major: Dataspace
>     minor: Out of range
> H5Dread failed for int data
> Data Request Error:  Error for variable 'plrcnt'
>   Error ocurred at column 1
> DISPLAY error:  Invalid expression
>   Expression = plrcnt
>
>
>
> -Justin
>
> On Wed, Jan 13, 2016 at 8:07 AM, Jennifer M Adams <jadams21 at gmu.edu>
> wrote:
>
>> Justin,
>> It looks like the variables in your descriptor files are group names not
>> dataset names. Try this instead:
>> /Grids/G1/precipLiqRate/count=>plrcnt            0 x,y  liquid
>> precipitation rate count
>> /Grids/G1/precipLiqRate/hist=>plrhist            0 x,y  liquid
>> precipitation rate hist
>> /Grids/G1/precipLiqRate/mean=>plrmean            0 x,y  liquid
>> precipitation rate mean
>> /Grids/G1/precipLiqRate/stdev=>plrcstd           0 x,y  liquid
>> precipitation rate stdev
>> —Jennifer
>>
>> On Jan 11, 2016, at 2:42 PM, Justin Hicks <jhicks2014 at gmail.com> wrote:
>>
>> Grads Users,
>>
>> I was able to open the control file in grads, but i get an error when I
>> try to display a variable:
>>
>> ga-> d plrate
>> HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
>>   #000: H5D.c line 341 in H5Dopen2(): not a dataset
>>     major: Dataset
>>     minor: Inappropriate type
>> Error: H5Dopen2 failed for variable /Grids/G1/precipLiqRate
>> Error: Variable /Grids/G1/precipLiqRate not in HDF5 file
>> Data Request Error:  Error for variable 'plrate'
>>   Error ocurred at column 1
>> DISPLAY error:  Invalid expression
>>   Expression = plrate
>>
>> The control file is below:
>>
>> DSET
>> /data2/GPM/GPM_3CMB.03/2015/3B-MO.GPM.DPRGMI.CORRAGM.20150301-S000000-E235959.03.V03D.HDF5
>> OPTIONS template
>> DTYPE hdf5_grid
>> TITLE GPM precip
>> UNDEF -999.0
>> XDEF 3600 linear -180 0.1
>> YDEF 300 linear -20 0.1
>> ZDEF 1 levels 1000
>> TDEF 1 linear 01mar2015 1dy
>> VARS 4
>> /Grids/G1/precipLiqRate=>plrate            0 x,y  liquid precipitation
>> rate
>> /Grids/G1/precipLiqWaterContent=>plcon     0 x,y   liquid precipitation
>> content
>> /Grids/G1/precipTotDm=>ptot                0 x,y   precipitation total
>> /Grids/G1/precipTotRate=>ptotr             0 x,y  precipitation total rate
>> ENDVARS
>>
>>
>> I don't think the xdef and ydef are completely accurate, but I shouldn't
>> get that error message even if the edef and ydef are wrong. The file
>> contents of h5dump are below:
>>
>> /home/jhicks/h5dump -n
>> 3B-MO.GPM.DPRGMI.CORRAGM.20150301-S000000-E235959.03.V03D.HDF5
>> HDF5 "3B-MO.GPM.DPRGMI.CORRAGM.20150301-S000000-E235959.03.V03D.HDF5" {
>> FILE_CONTENTS {
>>  group      /
>>  group      /Grids
>>  group      /Grids/G1
>>  dataset    /Grids/G1/precipAllObs
>>  group      /Grids/G1/precipLiqRate
>>  dataset    /Grids/G1/precipLiqRate/count
>>  dataset    /Grids/G1/precipLiqRate/hist
>>  dataset    /Grids/G1/precipLiqRate/mean
>>  dataset    /Grids/G1/precipLiqRate/stdev
>>  group      /Grids/G1/precipLiqWaterContent
>>  dataset    /Grids/G1/precipLiqWaterContent/count
>>  dataset    /Grids/G1/precipLiqWaterContent/hist
>>  dataset    /Grids/G1/precipLiqWaterContent/mean
>>  dataset    /Grids/G1/precipLiqWaterContent/stdev
>>  group      /Grids/G1/precipTotDm
>>  dataset    /Grids/G1/precipTotDm/count
>>  dataset    /Grids/G1/precipTotDm/hist
>>  dataset    /Grids/G1/precipTotDm/mean
>>  dataset    /Grids/G1/precipTotDm/stdev
>>  group      /Grids/G1/precipTotLogNw
>>  dataset    /Grids/G1/precipTotLogNw/count
>>  dataset    /Grids/G1/precipTotLogNw/hist
>>  dataset    /Grids/G1/precipTotLogNw/mean
>>  dataset    /Grids/G1/precipTotLogNw/stdev
>>  group      /Grids/G1/precipTotRate
>>  dataset    /Grids/G1/precipTotRate/count
>>  dataset    /Grids/G1/precipTotRate/hist
>>  dataset    /Grids/G1/precipTotRate/mean
>>  dataset    /Grids/G1/precipTotRate/stdev
>>  group      /Grids/G1/precipTotWaterContent
>>  dataset    /Grids/G1/precipTotWaterContent/count
>>  dataset    /Grids/G1/precipTotWaterContent/hist
>>  dataset    /Grids/G1/precipTotWaterContent/mean
>>  dataset    /Grids/G1/precipTotWaterContent/stdev
>>  dataset    /Grids/G1/surfPrecipLiqRateProb
>>  dataset    /Grids/G1/surfPrecipLiqRateUn
>>  group      /Grids/G1/surfPrecipTotRateDiurnal
>>  dataset    /Grids/G1/surfPrecipTotRateDiurnal/count
>>  dataset    /Grids/G1/surfPrecipTotRateDiurnal/mean
>>  dataset    /Grids/G1/surfPrecipTotRateDiurnal/stdev
>>  dataset    /Grids/G1/surfPrecipTotRateDiurnalAllObs
>>  dataset    /Grids/G1/surfPrecipTotRateProb
>>  dataset    /Grids/G1/surfPrecipTotRateUn
>>  group      /Grids/G2
>>  dataset    /Grids/G2/precipAllObs
>>  group      /Grids/G2/precipLiqRate
>>  dataset    /Grids/G2/precipLiqRate/count
>>  dataset    /Grids/G2/precipLiqRate/mean
>>  dataset    /Grids/G2/precipLiqRate/stdev
>>  group      /Grids/G2/precipLiqWaterContent
>>  dataset    /Grids/G2/precipLiqWaterContent/count
>>  dataset    /Grids/G2/precipLiqWaterContent/mean
>>  dataset    /Grids/G2/precipLiqWaterContent/stdev
>>  group      /Grids/G2/precipTotDm
>>  dataset    /Grids/G2/precipTotDm/count
>>  dataset    /Grids/G2/precipTotDm/mean
>>  dataset    /Grids/G2/precipTotDm/stdev
>>  group      /Grids/G2/precipTotLogNw
>>  dataset    /Grids/G2/precipTotLogNw/count
>>  dataset    /Grids/G2/precipTotLogNw/mean
>>  dataset    /Grids/G2/precipTotLogNw/stdev
>>  group      /Grids/G2/precipTotRate
>>  dataset    /Grids/G2/precipTotRate/count
>>  dataset    /Grids/G2/precipTotRate/mean
>>  dataset    /Grids/G2/precipTotRate/stdev
>>  group      /Grids/G2/precipTotWaterContent
>>  dataset    /Grids/G2/precipTotWaterContent/count
>>  dataset    /Grids/G2/precipTotWaterContent/mean
>>  dataset    /Grids/G2/precipTotWaterContent/stdev
>>  dataset    /Grids/G2/surfPrecipLiqRateProb
>>  dataset    /Grids/G2/surfPrecipLiqRateUn
>>  group      /Grids/G2/surfPrecipTotRateDiurnal
>>  dataset    /Grids/G2/surfPrecipTotRateDiurnal/count
>>  dataset    /Grids/G2/surfPrecipTotRateDiurnal/mean
>>  dataset    /Grids/G2/surfPrecipTotRateDiurnal/stdev
>>  dataset    /Grids/G2/surfPrecipTotRateDiurnalAllObs
>>  dataset    /Grids/G2/surfPrecipTotRateProb
>>  dataset    /Grids/G2/surfPrecipTotRateUn
>>  dataset    /InputAlgorithmVersions
>>  dataset    /InputFileNames
>>  dataset    /InputGenerationDateTimes
>>  }
>> }
>>
>>
>> The group contents of /Grids/G1/precipLiqRate are below:
>>
>> h5dump -H -g/Grids/G1/precipLiqRate
>> 3B-MO.GPM.DPRGMI.CORRAGM.20150301-S000000-E235959.03.V03D.HDF5
>> HDF5 "3B-MO.GPM.DPRGMI.CORRAGM.20150301-S000000-E235959.03.V03D.HDF5" {
>> GROUP "/Grids/G1/precipLiqRate" {
>>    DATASET "count" {
>>       DATATYPE  H5T_STD_I32LE
>>       DATASPACE  SIMPLE { ( 3, 3, 16, 2, 72, 28 ) / ( 3, 3, 16, 2, 72, 28
>> ) }
>>       ATTRIBUTE "CodeMissingValue" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 101;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>       ATTRIBUTE "DimensionNames" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 21;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>    }
>>    DATASET "hist" {
>>       DATATYPE  H5T_STD_I32LE
>>       DATASPACE  SIMPLE { ( 30, 3, 3, 16, 2, 72, 28 ) / ( 30, 3, 3, 16,
>> 2, 72, 28 ) }
>>       ATTRIBUTE "CodeMissingValue" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 101;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>       ATTRIBUTE "DimensionNames" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 25;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>    }
>>    DATASET "mean" {
>>       DATATYPE  H5T_IEEE_F32LE
>>       DATASPACE  SIMPLE { ( 3, 3, 16, 2, 72, 28 ) / ( 3, 3, 16, 2, 72, 28
>> ) }
>>       ATTRIBUTE "CodeMissingValue" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 101;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>       ATTRIBUTE "DimensionNames" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 21;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>    }
>>    DATASET "stdev" {
>>       DATATYPE  H5T_IEEE_F32LE
>>       DATASPACE  SIMPLE { ( 3, 3, 16, 2, 72, 28 ) / ( 3, 3, 16, 2, 72, 28
>> ) }
>>       ATTRIBUTE "CodeMissingValue" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 101;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>       ATTRIBUTE "DimensionNames" {
>>          DATATYPE  H5T_STRING {
>>                STRSIZE 21;
>>                STRPAD H5T_STR_NULLTERM;
>>                CSET H5T_CSET_ASCII;
>>                CTYPE H5T_C_S1;
>>             }
>>          DATASPACE  SCALAR
>>       }
>>    }
>> }
>> }
>>
>>
>> Any help would be appreciated.
>>
>> Thanks,
>>
>> -Justin
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>>
>>
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