EOFException in org.apache.hadoop.io.SequenceFile $ Reader.init (SequenceFile.java:1508)

I tried to run the example of matrix multiplication presented by Mr. Norstadt at the following link http://www.norstad.org/matrix-multiply/index.html . I can run it successfully with hadoop 0.20.2, but I tried to run it with hadoop 1.0.3, but I get the following error. Is this a problem with my hadoop configuration or a compatibility issue in the code that was written in the hadoop 0.20 file. Also, please tell me how I can fix this error anyway. Here is the error I am getting.

in thread "main" java.io.EOFException
        at java.io.DataInputStream.readFully(DataInputStream.java:180)
        at java.io.DataInputStream.readFully(DataInputStream.java:152)
        at org.apache.hadoop.io.SequenceFile$Reader.init(SequenceFile.java:1508)
        at org.apache.hadoop.io.SequenceFile$Reader.<init>(SequenceFile.java:1486)
        at org.apache.hadoop.io.SequenceFile$Reader.<init>(SequenceFile.java:1475)
        at org.apache.hadoop.io.SequenceFile$Reader.<init>(SequenceFile.java:1470)
        at TestMatrixMultiply.fillMatrix(TestMatrixMultiply.java:60)
        at TestMatrixMultiply.readMatrix(TestMatrixMultiply.java:87)
        at TestMatrixMultiply.checkAnswer(TestMatrixMultiply.java:112)
        at TestMatrixMultiply.runOneTest(TestMatrixMultiply.java:150)
        at TestMatrixMultiply.testRandom(TestMatrixMultiply.java:278)
        at TestMatrixMultiply.main(TestMatrixMultiply.java:308)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.apache.hadoop.util.RunJar.main(RunJar.java:156)

Thanks in advance

Regards, Waqas