large file support

[Christopher.Moore at noaa.gov]

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
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