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Re: [netcdf-java] Problem using Redefine mode in netcdf-java 4.1

Latest 4.1 release (2010-03-23 21:33:07) should have this fix in it.

James.Dempsey@xxxxxxxx wrote:

Hi John,

Thanks for that - we'll grab the update once it is ready and give a workout. At 
the moment we have used a workaround involving a temporary variable that we 
delete as part of the first add variable operation.

Thanks for the warning about define mode too - we'll keep an eye on that. The 
good news is that so far it seems to be working nicely other than this one 
issue.

Cheers,
James Dempsey
Java Technical Lead | Software Services
Information Management and Technology
CSIRO Australia


-----Original Message-----
From: John Caron [mailto:caron@xxxxxxxxxxxxxxxx] Sent: Tuesday, 23 March 2010 10:30 AM 
To: Dempsey, James (CSIRO IM&T, Yarralumla)
Cc: netcdf-java@xxxxxxxxxxxxxxxx
Subject: Re: [netcdf-java] Problem using Redefine mode in netcdf-java 4.1

Hi James:

Turns out its a bug when there are no variables in the file. Ill make a fix as 
soon as i can (probably tommorrow or day after).

BTW, im sorry to say going in and out of define mode is not very robust in 
netcdf-java. Id use it as minimally as possible, or at least be sure to test 
things are working correctly. Also its quite inefficient, as it forces a 
complete file rewrite in many cases.

Thanks for reporting the bug.

John

James.Dempsey@xxxxxxxx wrote:

Hi,
I am using the current 4.1 netcdf-java library (4.1.20100311.2157 or change 14 I believe) and encountering a problem when trying to use redefine mode. A similar problem also occurs using the latest 4.0 library . Our aim is to create some command line tools that allow a netCDF file to be build up. First, define a dimension, then add a variable to it, then populate the variable. However when we close and reopen the file, any attempt to add a variable results in the following stack trace: 

Exception in thread "main" _java.io.IOException_: The parameter is incorrect
at java.io.RandomAccessFile.setLength(_Native Method_)
at ucar.unidata.io.RandomAccessFile.close(_RandomAccessFile.java:339_)
at ucar.nc2.iosp.netcdf3.N3iosp.close(_N3iosp.java:878_)
at ucar.nc2.NetcdfFileWriteable.close(_NetcdfFileWriteable.java:769_)
at au.csiro.netcdf.CreateFile.main(_CreateFile.java:45_)

The following code demonstrates the problem.
package au.csiro.netcdf; import java.io.IOException; import ucar.ma2.DataType; 
import ucar.nc2.Dimension;
import ucar.nc2.NetcdfFileWriteable;
public class CreateFile { private static String dimensionName = "lat"; 
    private static int dimensionSize = 20;
    private static String variableName = "temp";
    private static DataType variableDataType = DataType.getType("Float");
public static void main(String[] args) throws IOException { 
        String outputFilename = args[0];
NetcdfFileWriteable ncFile = NetcdfFileWriteable.createNew(outputFilename, true); 
        try  {
Dimension dimension = new Dimension(dimensionName, dimensionSize, true /* isShared */, 
                    false /* isUnlimited */, false /* isVariableLength */);
            ncFile.addDimension(null, dimension);
            ncFile.create();
        } finally {
            ncFile.close();
        }
ncFile = NetcdfFileWriteable.openExisting(outputFilename, true); 
        try {
            ncFile.setRedefineMode(true);
ncFile.addVariable(variableName, variableDataType, dimensionName); 
            ncFile.setRedefineMode(false);
        } finally {
            ncFile.close();
        }
    }
} If the ncFile.close() and NetcdfFileWriteable.openExisting calls are commented out the file is successfully created with the variable. Could anyone advise if this is something I am doing wrong or a problem with the library please? Cheers, 
James Dempsey
Java Technical Lead | Software Services
Information Management and Technology
CSIRO Australia

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