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

• To: James.Dempsey@xxxxxxxx
• Subject: Re: [netcdf-java] Problem using Redefine mode in netcdf-java 4.1
• From: John Caron <caron@xxxxxxxxxxxxxxxx>
• Date: Mon, 22 Mar 2010 17:30:15 -0600

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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