[netcdf-java] Variable shape problem & EOFException

[Nick Bower]

Ok.  Could you clarify the version number?  I'm on 2.2.22 now - you mentioned 
2.22.14 just now.  Is there that much difference between the two?


John Caron wrote:
> release 2.22.14 should fix this problem. be sure to call flush() after 
> writing and before reading
>
> Nick Bower wrote:
>> Adding an ncFile.flush() to the submitted test case as suggested does 
>> not resolve the problem.  I think it needs to be marked as a bug 
>> until a documented way around it surfaces.
>>
>>
>> Ethan Davis wrote:
>>  
>>> Hi Nick,
>>>
>>> I'm not sure if this is a recommended way but you might try to 
>>> flush() the NetcdfFileWriteable before reading.
>>>
>>> John might have another answer. He is out of the office this week so 
>>> his email may be spotty.
>>>
>>> Hope that helps,
>>>
>>> Ethan
>>>
>>> Nick Bower wrote:
>>>    
>>>> Hello.  Is the lack of response here because this is not considered 
>>>> a bug?  Is there a another recommended way perhaps to safely 
>>>> increase a dimension and invalidate the memory cache in the process?
>>>>
>>>> Nick
>>>>
>>>>
>>>> Nick Bower wrote:
>>>>  
>>>>      
>>>>> I've found a problem in which cache/memory and disk shape 
>>>>> information about variables will disagree with v2.2.22 of Java 
>>>>> Netcdf library.
>>>>>
>>>>> When you add a new value to a variable, automatically increasing 
>>>>> the length of a dimension, subsequent reads can throw EOFException 
>>>>> because RandomAccessFile is instructed to read more values than 
>>>>> the file contains - the cached and actual shapes disagree.
>>>>>
>>>>> I've created a runnable test case below to explain and demonstrate 
>>>>> success and failure conditions.
>>>>>
>>>>> I am getting around this now by not interleaving read/write 
>>>>> operations on variables, but instead reading all variables' data 
>>>>> to memory, then performing any writes I need to after.
>>>>>
>>>>> TestInsertRecord.java:
>>>>>
>>>>>
>>>>> package com.metoceanengineers.datafeeds.netcdf.test;
>>>>>
>>>>> import java.io.File;
>>>>> import java.io.IOException;
>>>>> import java.text.DateFormat;
>>>>> import java.text.SimpleDateFormat;
>>>>>
>>>>> import junit.framework.TestCase;
>>>>> import ucar.ma2.Array;
>>>>> import ucar.ma2.ArrayInt;
>>>>> import ucar.ma2.DataType;
>>>>> import ucar.nc2.Dimension;
>>>>> import ucar.nc2.NetcdfFileWriteable;
>>>>>
>>>>> public class TestInsertRecord extends TestCase {
>>>>>       DateFormat dateFormat = new SimpleDateFormat("yyyyMMdd HHMM");
>>>>>       protected NetcdfFileWriteable createNc(String prefix) throws 
>>>>> IOException {
>>>>>               File mainline = File.createTempFile(prefix+"-", ".nc");
>>>>>        NetcdfFileWriteable mainlineNc = 
>>>>> NetcdfFileWriteable.createNew(mainline.getAbsolutePath(), false);
>>>>>
>>>>>        Dimension recordsDim = 
>>>>> mainlineNc.addUnlimitedDimension("records");
>>>>>               Dimension timeDims[] = {recordsDim};
>>>>>        Dimension var1Dims[] = {recordsDim}; // 1D
>>>>>               mainlineNc.addVariable("time", DataType.INT, timeDims);
>>>>>        mainlineNc.addVariable("var1", DataType.INT, var1Dims);
>>>>>
>>>>>        mainlineNc.create();
>>>>>        return mainlineNc;
>>>>>    }
>>>>>
>>>>>
>>>>>    protected String getNcInstance() throws Exception {
>>>>>
>>>>>        NetcdfFileWriteable mainlineNc = createNc("testfile");
>>>>>               int[] origin = {0};
>>>>>               ArrayInt.D1 timeArr = new ArrayInt.D1(2);
>>>>>        timeArr.set(0, (int)dateFormat.parse("20071130 
>>>>> 0924").getTime());
>>>>>        timeArr.set(1, (int)dateFormat.parse("20071130 
>>>>> 0926").getTime());
>>>>>        mainlineNc.write("time", origin, timeArr);
>>>>>               ArrayInt.D1 var1Arr = new ArrayInt.D1(2);
>>>>>        var1Arr.set(0, 10);
>>>>>        var1Arr.set(1, 12);
>>>>>        mainlineNc.write("var1", origin, var1Arr);
>>>>>
>>>>>        mainlineNc.close();
>>>>>
>>>>>        return mainlineNc.getLocation();
>>>>>    }
>>>>>      /**
>>>>>     * Append new data to end of existing variables.
>>>>>     *
>>>>>     * @throws Exception
>>>>>     */
>>>>>    public void testAppendWorksOk() throws Exception {
>>>>>               String ncFilename = getNcInstance();
>>>>>        NetcdfFileWriteable ncFile = 
>>>>> NetcdfFileWriteable.openExisting(ncFilename, false);
>>>>>
>>>>>        /*
>>>>>         * Append value (20071130 0924, 11) into (time, var1)
>>>>>         */
>>>>>               ArrayInt.D1 newTimeValue = new ArrayInt.D1(1);
>>>>>        newTimeValue.set(0, (int)dateFormat.parse("20071130 
>>>>> 0925").getTime());
>>>>>
>>>>>        ArrayInt.D1 newVarValue = new ArrayInt.D1(1);
>>>>>        newVarValue.set(0, 11);
>>>>>               int[] origin = {2};
>>>>>
>>>>>        /* The first write will expand the variables,
>>>>>         * but second write ok as we're just writing
>>>>>         * and not reading */
>>>>>               ncFile.write("time", origin, newTimeValue);
>>>>>        ncFile.write("var1", origin, newVarValue);
>>>>>               assertEquals(3, 
>>>>> ncFile.findDimension("records").getLength());
>>>>>           }
>>>>>
>>>>>    /**
>>>>>     * Test insertion of a record in between the 2 existing
>>>>>     * records by reading the existing tail, inserting new data
>>>>>     * and re-appending.
>>>>>     *
>>>>>     * Triggers EOFException through interleaved read/writes
>>>>>     *
>>>>>     * @throws Exception
>>>>>     */
>>>>>    public void testInsertFails() throws Exception {
>>>>>               String ncFilename = getNcInstance();
>>>>>        NetcdfFileWriteable ncFile = 
>>>>> NetcdfFileWriteable.openExisting(ncFilename, false);
>>>>>
>>>>>        ArrayInt.D1 newTimeValue = new ArrayInt.D1(1);
>>>>>        newTimeValue.set(0, (int)dateFormat.parse("20071130 
>>>>> 0925").getTime());
>>>>>
>>>>>        ArrayInt.D1 newVarValue = new ArrayInt.D1(1);
>>>>>        newVarValue.set(0, 11);
>>>>>               /* Going to insert at 1, so read existing value,
>>>>>         * write down new one, and re-append old tail.
>>>>>         */
>>>>>               int[] insertPointOrigin = {1};
>>>>>        int[] appendOrigin = {2};
>>>>>        int[] shape = {1};
>>>>>               Array tailTime = 
>>>>> ncFile.findVariable("time").read(insertPointOrigin, shape);
>>>>>        ncFile.write("time", insertPointOrigin, newTimeValue);
>>>>>        ncFile.write("time", appendOrigin, tailTime);
>>>>>               /* Next line excepts - why?  Because the last write 
>>>>> above at
>>>>>         * records index 2 triggers an increase in the CACHED/MEMORY
>>>>>         * length of all variables to 3, but on disk it's still the
>>>>>         * original length 2.
>>>>>         *
>>>>>         *  Therefore we get EOFException.
>>>>>         */
>>>>>               Array tailVar1 = 
>>>>> ncFile.findVariable("var1").read(insertPointOrigin, shape);
>>>>>        ncFile.write("var1", insertPointOrigin, newVarValue);
>>>>>        ncFile.write("var1", appendOrigin, tailVar1);
>>>>>               assertEquals(3, 
>>>>> ncFile.findDimension("records").getLength());
>>>>>           }
>>>>>
>>>>> }
>>>>>
>>>>>
>>>>>             
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