[gradsusr] [Possibly Spoofed] Re: netcdf group variable

Tue Nov 21 12:29:34 EST 2023

Respected Jennifer, 

Thanking you so much for your kind help, otherwise I would not have been able to display this data. I am lucky, data belongs to your GES DISC :). 

I had seen the gap between "IWC\ PressureGrid". But I was wrong, ... trying with "/IWC/~PressureGrid/", thinking "PressureGrid" as sub-group of 'IWC". Sorry! 

Thanks again. 

With Best Regards, 
Mahakur 

From: "Adams, Jennifer M. (GSFC-619.0)[ADNET SYSTEMS INC]" <jennifer.m.adams at nasa.gov> 
To: "GrADS Users Forum" <gradsusr at gradsusr.org> 
Sent: Tuesday, November 21, 2023 9:18:35 PM 
Subject: [Possibly Spoofed] Re: [gradsusr] netcdf group variable 

Hi, Mahakur -- 
Fortunately, you are looking at MLS data, which is archived here at GES DISC, so I was able to check the granule you are trying to access with GrADS. The error you are seeing is because of a space in the Group name in that file, which must be aliased with a ~ in the descriptor. The other issue is that the chunking parameters are set so that the entire variable is one chunk: 

float value(time, lev, lon, lat) ; 

string value:long_name = "Average Value of Cloud Ice" ; 

string value:units = "mg/m!U3!N" ; 

value:_FillValue = -999.99f ; 

string value:comments = "The average value in a bin" ; 

value:_Storage = "chunked" ; 

value:_ChunkSizes = 1, 29, 72, 45 ; 

value:_DeflateLevel = 5 ; 

value:_Endianness = "little" ; 

This requires you to override the default chunk cache size – otherwise you would get a warning message like this: 
*** WARNING! *** 

*** The I/O for this variable will be extremely slow 

*** because the chunks are too big to fit in the cache 

*** chunk size = 375840 bytes (45 * 72 * 29 * 1 * 4 bytes) 

*** cache size = 25920 bytes (scale factor)*(file cachesize) 

*** There are two ways to control the cache size: 

*** add a CACHESIZE entry to the descriptor file 

*** or change the scale factor with 'set cachesf' 

*** Please read http://cola.gmu.edu/grads/gadoc/compression.html 

So … below is a working descriptor file with changes highlighted in green: 

dset ^ MLS-Aura_L3DB-IWC_v04-24-c01_2022d365.nc 

title MLS IWC 

dtype hdf5_grid 

cachesize 500000 

undef -999.99 

xdef 72 linear -177.5 5.0 

ydef 45 linear -88.0 4.0 

zdef 29 levels 1000, 825.4042, 681.2921, 562.3413, 464.1589, 383.1187, 316.2278, 261.0157, 215.4435, 177.8279, 146.7799, 121.1528, 100, 82.54042, 68.1292, 56.23413, 46.41589, 38.31187, 31.62278, 26.10157, 21.54435, 17.78279, 14.67799, 12.11528, 10, 1, 0.1, 0.01, 0.001 

tdef 1 linear 31DEC2022 1dy 

vars 1 

/IWC~PressureGrid/value=>val 29 t,z,x,y IWC (mg/m3) 

endvars 

-- 
Jennifer Miletta Adams 
Senior Scientific Software Developer 
Goddard Earth Sciences Data and Information Services Center (GES DISC) 

NASA/GSFC, Code 619 

Building 32, Room S159 

From: gradsusr <gradsusr-bounces at gradsusr.org> on behalf of M.Mahakur <mmahakur at tropmet.res.in> 
Date: Tuesday, November 21, 2023 at 10:04 AM 
To: GrADS Users Forum <gradsusr at gradsusr.org> 
Subject: Re: [gradsusr] [Possibly Spoofed] Re: [EXTERNAL] [BULK] netcdf group variable 

CAUTION: This email originated from outside of NASA. Please take care when clicking links or opening attachments. Use the "Report Message" button to report suspicious messages to the NASA SOC. 

Respected Jennifer, 

Hi, Good morning! 

Thanks for your help. I changed the 'dtype' to 'hdf5_grid'. When I opened it i am getting errors while displaying 'val', the parameter; it says not in HDF5 file! 

Please suggest.. 

ga-> d val 
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: 
#000: H5D.c line 321 in H5Dopen2(): not found 
major: Dataset 
minor: Object not found 
#001: H5Gloc.c line 468 in H5G_loc_find(): can't find object 
major: Symbol table 
minor: Object not found 
#002: H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal failed 
major: Symbol table 
minor: Object not found 
#003: H5Gtraverse.c line 776 in H5G_traverse_real(): component not found 
major: Symbol table 
minor: Object not found 
Error: H5Dopen2 failed for variable /IWC/ PressureGrid/value 
Error: Variable /IWC/ PressureGrid/value not in HDF5 file 
Data Request Error: Error for variable 'val' 
Error ocurred at column 1 
DISPLAY error: Invalid expression 
Expression = val 
ga-> 

ga-> q file 
File 1 : MLS IWC 
Descriptor: mls.ctl 
Binary: MLS-Aura_L3DB-IWC_v04-24-c01_2022d365.nc 
Type = Gridded 
Xsize = 72 Ysize = 45 Zsize = 29 Tsize = 1 Esize = 1 
Number of Variables = 1 
val 29 t,z,x,y IWC (mg/m3) 

The ctl file: 

dset MLS-Aura_L3DB-IWC_v04-24-c01_2022d365.nc 
title MLS IWC 
dtype hdf5_grid 
undef -999.99 
xdef 72 linear -177.5 5.0 
ydef 45 linear -88.0 4.0 
zdef 29 levels 1000, 825.4042, 681.2921, 562.3413, 464.1589, 383.1187, 316.2278, 261.0157, 215.4435, 177.8279, 146.7799, 121.1528, 100, 82.54042, 68.1292, 56.23413, 46.41589, 38.31187, 31.62278, 26.10157, 21.54435, 17.78279, 14.67799, 12.11528, 10, 1, 0.1, 0.01, 0.001 
tdef 1 linear 31DEC2022 1dy 
vars 1 
/IWC/PressureGrid/value=>val 29 t,z,x,y IWC (mg/m3) 
endvars 

With Regards and Thanks, 

Mahakur 

From: "Adams, Jennifer M. (GSFC-619.0)[ADNET SYSTEMS INC]" <jennifer.m.adams at nasa.gov> 
To: "GrADS Users Forum" <gradsusr at gradsusr.org> 
Sent: Tuesday, November 21, 2023 1:22:58 AM 
Subject: [Possibly Spoofed] Re: [gradsusr] [EXTERNAL] [BULK] netcdf group variable 

It should work if you change: 
dtype netcdf 

to 

dtype hdf5_grid 

The HDF5 interface does support groups, and netcdf4 is really an hdf5 file under the hood. 
--Jennifer 

-- 
Jennifer Miletta Adams 
Senior Scientific Software Developer 
Goddard Earth Sciences Data and Information Services Center (GES DISC) 

NASA/GSFC, Code 619 

Building 32, Room S159 

From: gradsusr <gradsusr-bounces at gradsusr.org> on behalf of M.Mahakur <mmahakur at tropmet.res.in> 
Date: Monday, November 20, 2023 at 2:43 PM 
To: GrADS Users Forum <gradsusr at gradsusr.org> 
Subject: [EXTERNAL] [BULK] [gradsusr] netcdf group variable 

CAUTION: This email originated from outside of NASA. Please take care when clicking links or opening attachments. Use the "Report Message" button to report suspicious messages to the NASA SOC. 

Dear All, 

I like to display the variable "value" from the attached small netcdf file. I feel the pressure level variable is in the group 'IWC/PressureGrid'. For this I created the ctl : 

dset MLS-Aura_L3DB-IWC_v04-24-c01_2022d365.nc 
title MLS IWC 
dtype netcdf 
undef -999.99 
xdef 72 linear -177.5 5.0 
ydef 45 linear -88.0 4.0 
zdef 29 levels 1000, 825.4042, 681.2921, 562.3413, 464.1589, 383.1187, 316.2278, 261.0157, 215.4435, 177.8279, 146.7799, 121.1528, 100, 82.54042, 68.1292, 56.23413, 46.41589, 38.31187, 31.62278, 26.10157, 21.54435, 17.78279, 14.67799, 12.11528, 10, 1, 0.1, 0.01, 0.001 
tdef 1 linear 1DEC2022 1dy 
vars 1 
/IWC/PressureGrid/value=>val 29 t,z,x,y IWC (mg/m3) 
endvars 

But, it does not works. It seems it does not matches with the variable! 

ga-> d val 
Error: Variable /IWC/PressureGrid/value not in netcdf file 
Data Request Error: Error for variable 'val' 
Error ocurred at column 1 
DISPLAY error: Invalid expression 
Expression = val 

i am using Grads 2.0.a9. A portion from the ncdump is: 

========================= 

group: IWC\ PressureGrid { 
dimensions: 
lat = 45 ; 
lon = 72 ; 
lev = 29 ; 
time = 1 ; 
nv = 2 ; 
variables: 

.... 

... 

float value(time, lev, lon, lat) ; 
string value:long_name = "Average Value of Cloud Ice" ; 
string value:units = "mg/m!U3!N" ; 
value:_FillValue = -999.99f ; 
string value:comments = "The average value in a bin" ; 
============================ 

Please suggest, where to modify in the ctl. 

Thanks and Regards, 

Mahakur 

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