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From "Sardeshmukh, Vivek" <vivek-sardeshm...@uiowa.edu>
Subject RE: Setting variable value in Compute class and using it in the next superstep
Date Wed, 23 Jul 2014 17:23:31 GMT
Sorry, my bad! Sorry for spamming your inbox!

Adding "public" keyword in front of class DeltaVertexWritable did the trick! I should have
tested this before sending out the previous email.
Thank you.


Vivek
________________________________
From: Sardeshmukh, Vivek <vivek-sardeshmukh@uiowa.edu>
Sent: Wednesday, July 23, 2014 12:10 PM
To: user@giraph.apache.org
Subject: RE: Setting variable value in Compute class and using it in the next superstep


Hello again,


As Tom and Matthew suggested I wrote my own custom vertex value class and input format class.
I followed Matthew's example to create my own custom vertex class but now I'm getting the
following error while running the program


java.lang.IllegalStateException: newInstance: Illegal access org.apache.giraph.examples.DeltaVertexWritable
    at org.apache.giraph.utils.ReflectionUtils.newInstance(ReflectionUtils.java:84)
    at org.apache.giraph.utils.WritableUtils.createWritable(WritableUtils.java:68)
    at org.apache.giraph.factories.DefaultVertexValueFactory.newInstance(DefaultVertexValueFactory.java:48)
    at org.apache.giraph.conf.ImmutableClassesGiraphConfiguration.createVertexValue(ImmutableClassesGiraphConfiguration.java:729)
    at org.apache.giraph.utils.VertexIterator.resetEmptyVertex(VertexIterator.java:69)
    at org.apache.giraph.utils.VertexIterator.<init>(VertexIterator.java:60)
    at org.apache.giraph.comm.requests.SendWorkerVerticesRequest.doRequest(SendWorkerVerticesRequest.java:108)
    at org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.doRequest(NettyWorkerClientRequestProcessor.java:466)
    at org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.flush(NettyWorkerClientRequestProcessor.java:412)
    at org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:241)
    at org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:60)
    at org.apache.giraph.utils.LogStacktraceCallable.call(LogStacktraceCallable.java:51)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:744)





Here is my DeltaVertexWritable class - https://gist.github.com/sar-vivek/df09cca17cc3f6b5ac60


I tried digging a bit but I couldn't get any success [at the first place I even didn't understand
the error message!]



Thank you.

Vivek
________________________________
From: Sardeshmukh, Vivek <vivek-sardeshmukh@uiowa.edu>
Sent: Monday, July 21, 2014 6:06 PM
To: user@giraph.apache.org
Subject: RE: Setting variable value in Compute class and using it in the next superstep


Thank you Matthew. Now writing a custom vertex class and input format seems doable! Thank
you.



--
Vivek
________________________________
From: Matthew Saltz <saltzm@gmail.com>
Sent: Monday, July 21, 2014 5:50 PM
To: user@giraph.apache.org
Subject: Re: Setting variable value in Compute class and using it in the next superstep

Yeah, that's true. Sorry I forgot that part. Luckily, it isn't too tricky either, depending
on the input format of your graph. Here's another example<https://gist.github.com/saltzm/ab7172c57dec927061be>
to get you started, for a very simple input format for edges with no values. I basically took
the code straight from here<http://giraph.apache.org/apidocs/org/apache/giraph/io/formats/LongLongNullTextInputFormat.html>
and modified where I needed to it to return the InputFormat that I needed for my code. You'll
probably be better off digging through some of the already implemented InputFormat classes
that come with Giraph to do something similar, since I'm guessing your input files will be
different than mine. Take a look at the subclasses of TextVertexInputFormat<http://giraph.apache.org/apidocs/org/apache/giraph/io/formats/TextVertexInputFormat.html>,
since they deal with a lot of common input format styles, and see if you can modify their
code to work with your custom vertex data format. Now, the example I give you is also easy
because I just use the default constructor of the class, but if you need to load additional
data from the file into your vertex data and the default constructor isn't appropriate, you
may have to do some extra parsing and legwork for that.

Best of luck,
Matthew



On Tue, Jul 22, 2014 at 12:28 AM, Sardeshmukh, Vivek <vivek-sardeshmukh@uiowa.edu<mailto:vivek-sardeshmukh@uiowa.edu>>
wrote:

Thank you Matthew for the example link. It is helpful. I'll give it a shot.


If I have a custom vertex class isn't it necessary to change the VertexInputFormat class too?
Since this class "loads" the data into the vertex and if vertex has a custom value field then
it doesn't know how to load the input. Am I right?


Vivek
________________________________
From: Schweiger, Tom <thschweiger@ebay.com<mailto:thschweiger@ebay.com>>
Sent: Monday, July 21, 2014 5:16 PM
To: user@giraph.apache.org<mailto:user@giraph.apache.org>
Subject: RE: Setting variable value in Compute class and using it in the next superstep


For more than one flag, a custom class is necessary (unless you're able to, say, toggle the
sign bit to get double usage out or a value).

I've started a private thread with Vivek to get a better understanding of what he was trying
to solve.

And you are also correct that there isn't much to writing a custom vertex class.  The key
is making sure you read and write in the same order.  Likewise, extending a vertex reader
can be quite simple.

________________________________
From: Matthew Saltz [saltzm@gmail.com<mailto:saltzm@gmail.com>]
Sent: Monday, July 21, 2014 3:09 PM
To: user@giraph.apache.org<mailto:user@giraph.apache.org>
Subject: Re: Setting variable value in Compute class and using it in the next superstep

Tom,

If it's necessary to store more than one flag though, for example, won't a custom class be
necessary? I'm a beginner too, so I apologize if I'm incorrect about that. Just to be clarify,
to keep persistent data for a vertex from one superstep to the next, it is necessary to encapsulate
it in the type used for the 'V', right? In other words, if Vivek tries to use a normal member
variable for the Computation class, it won't work will it?

Also, just to point out, there actually isn't too much involved with writing your own custom
vertex class. Here's a quick example<https://gist.github.com/saltzm/692fba1d3aade035ce9c>
to get you started. Within your compute() method you can access the data in this class by
doing

SampleVertexData d = vertex.getValue();

and then using d.setFlag(true) or boolean currentFlag = d.getFlag() for example.  And your
computation class is now something like

public class MyComputation extends BasicComputation<IdType, SampleVertexData, EdgeType,
MessageType> {
    @Override
    public void compute(Vertex<IdType, SampleVertexData, EdgeType> vertex, Iterable<MessageType>
messages) {.....}

    ...

}

As a warning, for this class I'm using Hadoop 0.20.203 and I'm also a beginner, so take everything
I say with a grain of salt, and Tom please correct me if I'm wrong.

Best of luck,
Matthew


On Mon, Jul 21, 2014 at 11:37 PM, Schweiger, Tom <thschweiger@ebay.com<mailto:thschweiger@ebay.com>>
wrote:
And in answer of :


This post also suggests (along with what I described above) to have a field in the vertex
value itself. For that I need to change the vertex input format and also create my own custom
vertex class. Is it really necessary?
No, you don't need a custom vertex class or vertex input format. You can create/initialize
the value at the beginning of the first superstep.

________________________________
From: Sardeshmukh, Vivek [vivek-sardeshmukh@uiowa.edu<mailto:vivek-sardeshmukh@uiowa.edu>]
Sent: Monday, July 21, 2014 2:05 PM
To: user@giraph.apache.org<mailto:user@giraph.apache.org>
Subject: Setting variable value in Compute class and using it in the next superstep


Hi, all--


In my algorithm, I need to set a flag if certain conditions hold (locally at a vertex v).
If this flag is set then execute some other block of code *only once*, and do nothing until
some other condition is hold.


My question is, can I declare a flag variable in the class where I override compute function?
I defined the flag as a public variable and setting it once the conditions are met but it
seems the value is not "carried" over to the next superstep.

I dig a little bit in this mailing list and found this

https://www.mail-archive.com/user@giraph.apache.org/msg01266.html


This post also suggests (along with what I described above) to have a field in the vertex
value itself. For that I need to change the vertex input format and also create my own custom
vertex class. Is it really necessary?


By the way, I am using Giraph 1.1.0 compiled against Hadoop 1.0.3. I was able to run SimpleShortestPathComputation
successfully.


Here are more technical details of my algorithm: I am trying to implement Delta-stepping shortest
path algorithm ( http://dl.acm.org/citation.cfm?id=740136 or http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.46.2200
). This was mentioned in Pregel paper. A vertex "relax" light edges if it belongs to the minimum
bucket index (of course, aggregators!). Once a vertex is done with relaxing light edges it
relaxes heavy edges (here is where I need a flag) once. A vertex may be "re-inserted" to a
newer bucket and may have to execute all the steps that I described here again.


Thanks.


Sincerely,

Vivek
A beginner in Giraph (and Java too!)




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