[gradsusr] Control File Issues for HDF5 file
Jennifer M Adams
jadams21 at gmu.edu
Thu Jan 14 10:42:11 EST 2016
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<mailto: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<mailto: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<mailto: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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