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From Nick West <nick.w...@benchmarksolutions.com>
Subject Re: Heterogeneous Vertex Types
Date Mon, 30 Jul 2012 13:21:36 GMT
Joh, Etienne and Avery,

Thank you all for your replies.  I have settled on using a container class with different
functionalities implemented with in it, and one message type that wraps all the different
types of messages.

Avery and Jon:  I ended up with the same conclusion that a parametrized type for a vertex
would be difficult for the de/serialization process.

Thanks for all the feedback.

-Nick


On Jul 28, 2012, at 3:43 AM, Avery Ching wrote:

Hi Nick,

Giraph needs to have be able to instantiate the vertex id, value, edges, and messages and
there can only be a single type for each of them.

That being said, since all the types are user chosen, you can basically implement types that
support multiple types inside of it.  As a simple, stupid example

class MessageA {
...
}

class MessageB {
...
}

class MultiMessage implements Writable {
    private MessageA msgA;
    private MessageB msgB;

    private boolean useMsgA;

    pubic MessageA getMsgA(){
        return msgA;
    }

    pubic MessageB getMsgB(){
        return msgB;
    }

    ...
}

I didn't try and compile it, but hopefully you get the idea.  =)

On 7/27/12 9:52 AM, Jonathan Bishop wrote:
Nick,

I am guessing it is because Giraph needs to move vertices around and needs to construct them
before it reads in their serialization. I am new to Giraph myself so this may be incorrect.
Maybe Avery could comment.

Jon

On Fri, Jul 27, 2012 at 6:32 AM, Nick West <nick.west@benchmarksolutions.com<mailto:nick.west@benchmarksolutions.com>>
wrote:
Thanks for the quick reply.

That (using one uber-class) was my initial thought when I ran into this problem, however I
was wondering if there was a solution that would use the type hierarchy (which admittedly
is a bit more flexible in scala than java, so this may not be possible).  Is there something
in the Giraph architecture that precludes this?

Thanks,
Nick

On Jul 25, 2012, at 7:11 PM, Jonathan Bishop wrote:

Nick,

You may want to reconsider your approach as I don't think Giraph will be happy with this.

How about using a new vertex value class with BasicVertex which can do both behaviours for
you? Same for edge and message classes. This should be enough do what you want.

Jon

On Wed, Jul 25, 2012 at 3:29 PM, Nick West <nick.west@benchmarksolutions.com<mailto:nick.west@benchmarksolutions.com>>
wrote:
Hi,

I'm working on implementing a belief propagation algorithm over Giraph.  (Do you know if anyone
has done this before?)  This requires having (at least) two different types of vertices implemented
(values and factors) and different types of messages sent between different vertices.

I've been able to set up and run my own vertices (with my own custom readers and writers),
however, whenever I try to extend this to a more complex  case I run into problems.  For example,
suppose aI have the following two vertex types:

class FooVertex() extends BasicVertex[IntWritable, IntWritable, Text, IntWritable]
class BarVertex() extends BasicVertex[IntWritable, IntWritable, Text, IntWritable]

(both of which run fine in the basic set up), and I then configure the GiraphJob with the
following,

job.setVertexClass(classOf[BasicVertex[IntWritable, IntWritable, Text, IntWritable]])

(as opposed to with FooVertex or BarVertex).

I get a null pointer error in GraphMapper (at line 204 in the version of the code that I am
using - just after the log statement about the input format vertex index type not being known,
and at the line where it checks if the vertextIndexTypes are the same).

Do you know what is causing this? (The stack trace is below.)  Have you tried to instantiate
different classes for different vertices in the past?

One last piece of info that might explain things: I'm developing in scala, which I have seen
behave a little bit poorly with java reflection - could that be a cause?

Thanks,
Nick West

Stack Trace:

./bin/hadoop jar ~/code/watchdog/modules/inference/target/inference-assembly-1.0.jar bmrk.inference.giraph.IdiotRunner
ising ising_out 4
Input arguments:
[0] = ising
[1] = ising_out
[2] = 4
setting vertex class to: org.apache.giraph.graph.BasicVertex
setting vertex input class to: bmrk.inference.giraph.IdiotVertexInputFormat
setting vertex output class to: bmrk.inference.giraph.IdiotVertexOutputFormat
12/07/25 17:48:54 INFO mapred.JobClient: Running job: job_201207250932_0012
12/07/25 17:48:55 INFO mapred.JobClient:  map 0% reduce 0%
12/07/25 17:52:43 INFO mapred.JobClient: Task Id : attempt_201207250932_0012_m_000000_0, Status
: FAILED
java.lang.NullPointerException
at org.apache.giraph.graph.GraphMapper.determineClassTypes(GraphMapper.java:204)
at org.apache.giraph.graph.GraphMapper.setup(GraphMapper.java:392)
at org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:655)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:764)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370)
at org.apache.hadoop.mapred.Child$4.run(Child.java:255)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1121)
at org.apache.hadoop.mapred.Child.main(Child.java:249)


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Nick West

Benchmark Solutions
101 Park Avenue - 7th Floor
New York, NY 10178
Tel +1.212.220.4739<tel:%2B1.212.220.4739> | Mobile +1.646.267.4324<tel:%2B1.646.267.4324>
www.benchmarksolutions.com <http://www.benchmarksolutions.com/>
<Mail Attachment.png>









Nick West

Benchmark Solutions
101 Park Avenue - 7th Floor
New York, NY 10178
Tel +1.212.220.4739 | Mobile +1.646.267.4324
www.benchmarksolutions.com <http://www.benchmarksolutions.com/>
[cid:image001.png@01CCA50E.43B4A860]






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