Re: [netcdf-java] Differing results reading an unlimited dimension between Java and C (?) binary distribution

• To: Jean-Michel.Perraud@xxxxxxxx
• Subject: Re: [netcdf-java] Differing results reading an unlimited dimension between Java and C (?) binary distribution
• From: John Caron <caron@xxxxxxxxxxxxxxxx>
• Date: Tue, 02 Jun 2009 06:06:37 -0600

Hi Jean-Michel:

Thats pretty strange. Can you put the file on an ftp or http server so we can 
look at it?

BTW, which version on netcdf-java are you using?


Jean-Michel.Perraud@xxxxxxxx wrote:

Hi,

I have a lat/lon/time data set for which the lat dimension is unlimited. On 
disk the file is ~14 GiB. It was created using the Java API. More precisely, a 
C# application calling netCDF-Java through IKVM; worked beautifully. Colleagues 
and I tried to read this file from other tools (R via Rnetcdf, ncdump, etc.). 
The values of the lat variable are not read correctly (either all zeroes, or a 
mix with other numbers presumably from other variables).

Has anyone had similar issues? This is really not a blocking issue and can live 
with it, but I am intrigued. Below are sample code and CDL. I cannot 
investigate more in-depth due to approaching milestones, but happy to provide 
clarifications if needed.
I am reluctant to cross-post for now, but this may well be an issue outside of 
the Java API.

Cheers

### From IronPython or Jython, using the Java API, read works as expected:
clr.AddReferenceToFileAndPath(r"C:\lib\netcdf\netcdfAll-4.0.dll")
clr.AddReferenceToFileAndPath(r"C:\bin\ikvm\bin\IKVM.OpenJDK.ClassLibrary.dll")
from ucar.nc2 import NetcdfFile
netcdfFile = NetcdfFile.open(r"\\somename\tmp\scenarioA.nc")
latVar = netcdfFile.findVariable("lat")
latArray = latVar.read()
latArray
# prints:
# <ucar.ma2.ArrayFloat+D1 object at 0x000000000000002B [-39.097 -39.047 -38.997 
-3
# 8.947 -38.897 -38.847 -38.797 -38.747 -38.697 -38.647 -38.597 -38.547 -38.497 
-3

netcdfFile.close()

### using ncdump from a linux distro on a ncks subset. Same behavior without 
the full 14GB data set.

netcdf smallScenarioA {
dimensions:
        lat = UNLIMITED ; // (4 currently)
        lon = 9 ;
        time = 40907 ;
variables:
        char cellId(lat, lon) ;
                cellId:long_name = "Cell ID" ;
        float lat(lat) ;
                lat:units = "degrees_north" ;
                lat:axis = "Y" ;
                lat:standard_name = "latitude" ;
        float lon(lon) ;
                lon:units = "degrees_east" ;
                lon:axis = "X" ;
                lon:standard_name = "longitude" ;
        float runoff(lat, lon, time) ;
                runoff:long_name = "runoff" ;
                runoff:units = "mm" ;
                runoff:missing_value = -9999.f ;
                runoff:_FillValue = -9999.f ;
        int time(time) ;
                time:units = "days since 1895-01-01" ;
                time:axis = "T" ;
                time:standard_name = "time" ;
                time:long_name = "time" ;

// global attributes:
                :history = "Sat May 30 19:58:55 2009: ncks -d lat,30,33 -d 
lon,160,168 scenarioA.nc smallScenarioA.nc" ;
data:

 cellId =
  "",
  "",
  "",
  "" ;

 lat = 0, 0, 0, 0 ;

 lon = 146.6, 146.65, 146.7, 146.75, 146.8, 146.85, 146.9, 146.95, 147 ;
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• References:
  • [netcdf-java] Differing results reading an unlimited dimension between Java and C (?) binary distribution
    • From: Jean-Michel.Perraud