[gradsusr] HDF5 control file help
Meyerson, Joyce
hobo at atmos.ucla.edu
Tue Dec 22 15:57:42 EST 2015
Hi Jennifer,
Just getting back to this issue. I am now able to open the control file but when I try to display the variable pr I get the error below. I've tried on Linux and Mac with the same error.
Do you see what the problem is?
Joyce
(GrADS) Linux-Version 2.0.a9, Mac- Version 2.0.1
************
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 _FillValue
XDEF 3600 linear -179.95 0.1
YDEF 300 linear 20.05 0.1
ZDEF 1 levels 1000
TDEF 1 linear 01dec2015 1dy
VARS 1
Grid/precipitation=>pr 0 y,x precipitation mm/hr
ENDVARS
**************
ga-> d pr
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: ../../src/H5A.c line 615 in H5Aopen_by_name(): can't open attribute
major: Attribute
minor: Can't open object
#001: ../../src/H5A.c line 860 in H5A_open_by_name(): object not found
major: Attribute
minor: Object not found
#002: ../../src/H5Gloc.c line 480 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found
#003: ../../src/H5Gtraverse.c line 964 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#004: ../../src/H5Gtraverse.c line 714 in H5G_traverse_real(): can't look up component
major: Symbol table
minor: Object not found
#005: ../../src/H5Gobj.c line 1143 in H5G_obj_lookup(): can't locate object
major: Symbol table
minor: Object not found
#006: ../../src/H5Gstab.c line 839 in H5G_stab_lookup(): can't read message
major: Symbol table
minor: Unrecognized message
#007: ../../src/H5Omessage.c line 484 in H5O_msg_read(): unable to read object header message
major: Object header
minor: Read failed
#008: ../../src/H5Omessage.c line 539 in H5O_msg_read_oh(): message type not found
major: Object header
minor: Object not found
HDF5 attribute named "_FillValue" does not exist
h5setup warning: Could not retrieve undef attribute "_FillValue" -- using -9999.9 instead
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
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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