[gradsusr] SDF file error: does not have non-coordinate variables

Wed Jul 6 19:19:32 EDT 2016

Hi, Gary —
The comma-delimited list of coordinates in the variable declaration must match the order of dimensions in the ncdump output.

float ABF_mass_concentration(time, copy, vert, lat, lon) ;

This variable has to have "t,e,z,y,x”  since we are mapping the ‘copy’ coordinate to E and the ‘vert' coordinate to Z.
—Jennifer

On Jul 6, 2016, at 3:56 PM, Love, Mr. Gary, Contractor, Code 7542 <gary.love.ctr at nrlmry.navy.mil<mailto:gary.love.ctr at nrlmry.navy.mil>> wrote:

Thanks Jennifer,

I can open the file now. I just need to set the ctl parameters correctly.

I didn’t know you could set the coordinate order in the variable spec using t,e,z,y,x.  This is  a cool thing to know.

Thanks again,
Gary

From: gradsusr-bounces at gradsusr.org<mailto:gradsusr-bounces at gradsusr.org> [mailto:gradsusr-bounces at gradsusr.org] On Behalf Of Jennifer M Adams
Sent: Friday, July 01, 2016 6:42 AM
To: GrADS Users Forum
Subject: Re: [gradsusr] SDF file error: does not have non-coordinate variables

Hi, Gary —
Jim is right, you need a descriptor file for the “BAD” file with the extra dimensions. An example is below, but since your ncdump output didn’t show any metadata for the coordinates, I set everything to ‘abstract’ grid dimensions. You also need to alias the variables that have upper case letters and are >16 characters.

dset ^ENAAPS_2013080200_24hr.nc
dtype netcdf
undef -9.99e8
xdef 360 linear 1 1
ydef 180 linear 1 1
zdef  25 linear 1 1
tdef   2 linear 02aug2013 1dy
edef  12 names 1 2 3 4 5 6 7 8 9 10 11 12
vars 7
sigma  25 z mid-level sigma b
height 25 t,e,z,y,x elevation above surface [m]
pressure 25 t,e,z,y,x mid-level pressure [hPa]
ABF_mass_concentration=>abfmc  25 t,e,z,y,x  Anthropogenic and Biogenic fine mass concentration [ug/m^3]
dust_mass_concentration=>dustmc 25 t,e,z,y,x Dust mass concentration [ug/m^3]
smoke_mass_concentration=>smokemc 25 t,e,z,y,x Smoke mass concentration [ug/m^3]
seasalt_mass_concentration=>saltmc 25 t,e,z,y,x Seasalt mass concentration [ug/m^3]
endvars

—Jennifer

On Jun 30, 2016, at 9:32 PM, James T. Potemra <jimp at hawaii.edu<mailto:jimp at hawaii.edu>> wrote:

Hi Gary,

You are likely having problems because of the extra dimensions on your variables, specifically "copy" and "vert" (the good file has var(time,lat,lon) while the bad file has var(time,copy,vert,lat,lon).  You might be able to use a control file and map "vert" to ZDEF and "copy" to ensemble or something like that.

Jim

On 6/30/16 2:14 PM, Love, Mr. Gary, Contractor, Code 7542 wrote:

I have seen this problem reported earlier in the grads forum, but no clear

solution has emerged.

I'm using 2.0.2 on platform: Linux 2.6.32.59-0.7-default #1 SMP 2012-07-13

15:50:56 +0200 x86_64 x86_64 x86_64 GNU/Linux

Some .nc files do not open and give an error.

 gadsdf: SDF file does not have any non-coordinate variables.

No script is being used. This occurs at the command line when attempting to

sdfopen the file.

The results from ncdump -h for the bad file and a similar good file appear

below..

The issue may be related to the "copy" variable.

Thanks for any advice, I did not write these files but have access to the

author who doesn't know what the problem is either.

Gary Love

NRL Monterey, CA

BAD FILE

_______

netcdf ENAAPS_2013080200_24hr {

dimensions:

  lat = 180 ;

  lon = 360 ;

  vert = 25 ;

  copy = 12 ;

  time = 2 ;

variables:

  int time(time) ;

         time:units = "seconds since 2013-08-02 00:00:00" ;

         time:standard_name = "time" ;

  int forecast_reference_time ;

         forecast_reference_time:units = "seconds since 1970-01-01

00:00:00" ;

         forecast_reference_time:standard_name =

"forecast_reference_time" ;

  float lat(lat) ;

         lat:units = "degrees_north" ;

         lat:long_name = "latitude" ;

  float lon(lon) ;

         lon:units = "degrees_east" ;

         lon:long_name = "longitude" ;

  float sigma(vert) ;

         sigma:units = "sigma_level" ;

         sigma:long_name = "mid-level sigma b" ;

  float height(time, copy, vert, lat, lon) ;

         height:units = "m" ;

         height:long_name = "elevation above surface" ;

  float pressure(time, copy, vert, lat, lon) ;

         pressure:units = "hPa" ;

         pressure:long_name = "mid-level Pressure" ;

  float ABF_mass_concentration(time, copy, vert, lat, lon) ;

         ABF_mass_concentration:units = "ug/m^3" ;

         ABF_mass_concentration:long_name = "Anthropogenic and

Biogenic fine mass concentration" ;

  float dust_mass_concentration(time, copy, vert, lat, lon) ;

         dust_mass_concentration:units = "ug/m^3" ;

         dust_mass_concentration:long_name = "Dust mass

concentration" ;

  float smoke_mass_concentration(time, copy, vert, lat, lon) ;

         smoke_mass_concentration:units = "ug/m^3" ;

         smoke_mass_concentration:long_name = "Smoke mass

concentration" ;

  float seasalt_mass_concentration(time, copy, vert, lat, lon) ;

         seasalt_mass_concentration:units = "ug/m^3" ;

         seasalt_mass_concentration:long_name = "Seasalt mass

concentration" ;

// global attributes:

         :Conventions = "CF-1.0" ;

data:

 time = 0, 86400 ;

}

GOOD FILE

________

netcdf ENAAPS_2013081518_24hr_e1 {

dimensions:

  lat = 180 ;

  lon = 360 ;

  time = 5 ;

variables:

  int time(time) ;

         time:units = "seconds since 2013-08-15 18:00:00" ;

         time:standard_name = "time" ;

  int forecast_reference_time ;

         forecast_reference_time:units = "seconds since 1970-01-01

00:00:00" ;

         forecast_reference_time:standard_name =

"forecast_reference_time" ;

  float lat(lat) ;

         lat:units = "degrees_north" ;

         lat:long_name = "latitude" ;

  float lon(lon) ;

         lon:units = "degrees_east" ;

         lon:long_name = "longitude" ;

  float total_aod(time, lat, lon) ;

  float sulfate_aod(time, lat, lon) ;

  float dust_aod(time, lat, lon) ;

  float smoke_aod(time, lat, lon) ;

  float seasalt_aod(time, lat, lon) ;

// global attributes:

         :Conventions = "CF-1.0" ;

data:

 time = 0, 21600, 43200, 64800, 86400 ;

}

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--
Jennifer Miletta Adams
Center for Ocean-Land-Atmosphere Studies (COLA)
George Mason University

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--
Jennifer Miletta Adams
Center for Ocean-Land-Atmosphere Studies (COLA)
George Mason University

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