Giraph Shortest Paths Example ClassNotFoundException

I am trying to run the shortest paths example from the giraph incubator (https://cwiki.apache.org/confluence/display/GIRAPH/Shortest+Paths+Example). However instead of executing the example from the giraph-*-dependencies.jar, I have created my own job jar. When I created a single Job file as presented in the example, I was getting

java.lang.RuntimeException: java.lang.RuntimeException: java.lang.ClassNotFoundException: org.test.giraph.Test$SimpleShortestPathsVertexInputFormat

Then I have moved the inner classes (SimpleShortestPathsVertexInputFormat and SimpleShortestPathsVertexOutputFormat) to separates files and renamed them just in case (SimpleShortestPathsVertexInputFormat_v2, SimpleShortestPathsVertexOutputFormat_v2); the classes are not static anymore. This have solved the issues of class not found for the SimpleShortestPathsVertexInputFormat_v2, however I am still getting the same error for the SimpleShortestPathsVertexOutputFormat_v2. Below is my stack trace.

INFO mapred.JobClient: Running job: job_201205221101_0003
INFO mapred.JobClient:  map 0% reduce 0%
INFO mapred.JobClient: Task Id : attempt_201205221101_0003_m_000005_0, Status : FAILED
    java.lang.RuntimeException: java.lang.RuntimeException: java.lang.ClassNotFoundException: org.test.giraph.utils.SimpleShortestPathsVertexOutputFormat_v2
            at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:898)
            at org.apache.giraph.graph.BspUtils.getVertexOutputFormatClass(BspUtils.java:134)
            at org.apache.giraph.bsp.BspOutputFormat.getOutputCommitter(BspOutputFormat.java:56)
            at org.apache.hadoop.mapred.Task.initialize(Task.java:490)
            at org.apache.hadoop.mapred.MapTask.run(MapTask.java:352)
            at org.apache.hadoop.mapred.Child$4.run(Child.java:259)
            at java.security.AccessController.doPrivileged(Native Method)
            at javax.security.auth.Subject.doAs(Subject.java:415)
            at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1059)
            at org.apache.hadoop.mapred.Child.main(Child.java:253)
    Caused by: java.lang.RuntimeException: java.lang.ClassNotFoundException: org.test.giraph.utils.SimpleShortestPathsVertexOutputFormat_v2
            at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:866)
            at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:890)
            ... 9 more

I have inspected my job jar and all classes are there. Furthermore I am using hadoop 0.20.203 in a pseudo distributed mode. The way I launch my job is presented below.

hadoop jar giraphJobs.jar org.test.giraph.Test -libjars /path/to/giraph-0.2-SNAPSHOT-jar-with-dependencies.jar /path/to/input /path/to/output 0 3

Also I have defined HADOOP_CLASSPATH for the giraph-*-dependencies.jar. I can run the PageRankBenchmark example without a problem (directly from the giraph-*-dependencies.jar), and the shortes path example works as well (also directly from the giraph-*-dependencies.jar). Other hadoop jobs work without a problem (somewhere I have read to test if my "cluster" works correctly). Does anyone came across similar problem? Any help will be appreciated.

---

Solution (sorry to post it like this but I can't answer my own question for a couple of more hours)

To solve this issue I had to add my Job jar to the -libjars (no changes to HADOOP_CLASSPATH where made). The command to launch job now looks like this.

hadoop jar giraphJobs.jar org.test.giraph.Test -libjars /path/to/giraph-0.2-SNAPSHOT-jar-with-dependencies.jar,/path/to/job.jar /path/to/input /path/to/output 0 3

List of jars has to be comma separated. Though this has solved my problem. I am still curious why I have to pass my job jar as a "classpath" parameter? Can someone explain me what is the rational behind this? As I found it strange (to say the least) to invoke my job jar and then pass it again as a "classpath" jar. I am really curious about the explanation.

I found an alternative programmatic solution to the problem. We need to modify the run() method in the following way -

...
@Override
public int run(String[] argArray) throws Exception {
    Preconditions.checkArgument(argArray.length == 4,
        "run: Must have 4 arguments <input path> <output path> " +
        "<source vertex id> <# of workers>");

    GiraphJob job = new GiraphJob(getConf(), getClass().getName());
    // This is the addition - it will make hadoop look for other classes in the same     jar that contains this class
    job.getInternalJob().setJarByClass(getClass());
    job.setVertexClass(getClass());
    ...
}

setJarByClass() will make hadoop look for the missing classes in the same jar that contains the class returned by getClass(), and we will not need to add the job jar name separately to the -libjars option.