large file support

[John Caron]

Hi Chris:

Sounds like a bug!
Any way tou can put your data on an ftp or http server so I can recreate the problem?

thanks

Christopher.Moore at noaa.gov wrote:
> 
> Hi John & others,
> 
> A lot of us are creating large netcdf files these days, and I was 
> wondering if anyone is having the same kind of problems I am:
> 
> When I open a large (~2Gb) netcdf file using the latest stable release, 
> I've been getting an error.  The code was working when the file size was 
> smaller (fewer time steps, smaller lat/lon resolution).
> 
> My data is simply
> dimensions:
>         LON = 1276 ;
>         LAT = 950 ;
>         TIME = UNLIMITED ; // (601 currently)
> variables:
>         double LON(LON) ;
>                 LON:units = "degrees_east" ;
>                 LON:point_spacing = "even" ;
>         double LAT(LAT) ;
>                 LAT:units = "degrees_north" ;
>                 LAT:point_spacing = "uneven" ;
>         double TIME(TIME) ;
>                 TIME:units = "SECONDS" ;
>         float HA(TIME, LAT, LON) ;
> 
> I start by opening the file, getting the time dimension & variable.  It 
> croaks when reading the variable into an Array (note that I'm only 
> reading the TIME axis array, fairly small):
> 
>             ...
>             Variable testVar = timeDim.getCoordinateVariable();
>             System.out.println("testVar.getName: " + testVar.getName());
>             System.out.println("testVar.getDataType: " + 
> testVar.getDataType());
>             System.out.println("testVar.getRank: " + testVar.getRank());
>             int[] testShape = testVar.getShape();
>             for (int q=0; q<testShape.length; q++)
>                 System.out.println("testShape["+q+"]: " + testShape[q]);
>             int[] testOrigin = new int[testVar.getRank()];
>             Array testArr2 = testVar.read(testOrigin,testShape);
> 
> error: java.io.IOException: Negative seek offset
> java.io.IOException: Negative seek offset
>         at java.io.RandomAccessFile.seek(Native Method)
>         at ucar.netcdf.RandomAccessFile.read_(RandomAccessFile.java:508)
>         at ucar.netcdf.RandomAccessFile.seek(RandomAccessFile.java:350)
>         at 
> ucar.netcdf.NetcdfFile$V1DoubleIo.readArray(NetcdfFile.java:1520)
>         at ucar.netcdf.NetcdfFile$V1Io.copyout(NetcdfFile.java:896)
>         at ucar.netcdf.Variable.copyout(Variable.java:276)
>         at ucar.nc2.Variable.read(Variable.java:237)
> 
> 
> I immediately thought it was a Large File Support problem, but a little 
> investigation turned up the fact that I don't (yet) need 64-bit 
> addressing because my record sizes are small.  In fact, I can read the 
> file fine with applications that use the C and FORTRAN netcdf libraries 
> (version 3.6 or higher).  And ncdump works.
> 
> But I went ahead and created the large file with 64-bit addressing 
> anyway by simply changing one line in my FORTRAN model from
> 
>         iret = nf_create(ncfn, NF_CLOBBER, ncid)
> to
> 
>         iret = nf_create(ncfn, OR(NF_CLOBBER, NF_64BIT_OFFSET), ncid)
> 
> It creates the file just fine, checking with:
> 
>       od -An -c -N4 foo.nc
> gives the expected
>       C    D    F 002
> 
> and ncdump gives
> 
>      netcdf s_2903-563_ha64 { // format variant: 64bit
>      dimensions: ...
> 
> but my java code still croaks (in the same way Ferret does if not 
> compiled against netcdf lib > 3.6):
> 
> Exception in thread "AWT-EventQueue-0" 
> java.lang.IllegalArgumentException: Not a netcdf file
>         at ucar.netcdf.NetcdfFile.readV1(NetcdfFile.java:1745)
>         at ucar.netcdf.NetcdfFile.<init>(NetcdfFile.java:130)
>         at ucar.netcdf.NetcdfFile.<init>(NetcdfFile.java:148)
>         at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:61)
> 
> 
> Anybody else out there creating java applications that read large files?
> 
> I'm running RHEL4 on an EMT64 x86_64 machine, with java 1.5.0_06 and 
> java netcdf version 2.2.16
> 
> Yours,
> Chris
> 
> __________________________________________________________________
> Christopher W. Moore             email: Christopher.Moore at noaa.gov
> Research Scientist, Oceanography                 tel: 206.526.6779
> University of Washington/JISAO/NOAA-PMEL         fax: 206.526.6744
> NOAA Center for Tsunami Research                       Seattle, WA
> ------------------------------------------------------------------
> 
> =============================================================================== 
> 
> To unsubscribe netcdf-java, visit:
> http://www.unidata.ucar.edu/mailing-list-delete-form.html
> =============================================================================== 
> 

==============================================================================
To unsubscribe netcdf-java, visit:
http://www.unidata.ucar.edu/mailing-list-delete-form.html
==============================================================================