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From "Jan Ebbing" <Jan.Ebb...@gmx.de>
Subject AW: Questions after writing some giraph code
Date Mon, 06 Jul 2015 20:01:23 GMT
Hello,

 

thanks for the quick answer.

1.       I will look into changing my code to use static methods, I think this should be possible.

2.       Aggregators: Each aggregators stores the load (=#vertices) of a partition, in the
very first step this is 1 for every partition. Then partitions will be merged together, leaving
most at 0, and only really using k (for n >> k) Aggregators to track the state of the
surviving partitions. I only check the state of all aggregators once in a complete iteration
of the algorithm (after 1 complete graph partitioning iteration)

3.       I wrote some unit tests, there’s usually a larger difference I would like between
what runs locally and what works in giraph (might be my fault for writing too little/the wrong
tests though). I’m using giraph on a pseudodistributed Ubuntu machine on very small graphs
since I’m implementing the algorithms at the moment. I just had several problems with things
that worked in eclipse but gave strange errors when I ran the whole algorithm in giraph. (e.g.
the VertexValue not remembering its partition even though the setPartition method was called
or an aggregator value that was 0 because I obtained it in an odd superstep, since it held
a value in even supersteps)

4.       Sure, in [1] at line 311 they call ComputeNewPartition.requestMigration() and the
method ends there, requestMigration calls VertexValue.setNewPartition() which is a basic setter
without calling setValue at any point.

 

Could you shed some light on where I can place a job-specific config file which holds information
obtainable with MasterCompute.getContext().getConfiguration().getInt()/getDouble()/… ?

 

Regards,

Jan

 

[1] https://github.com/grafos-ml/okapi/blob/master/src/main/java/ml/grafos/okapi/spinner/Spinner.java#L311


 

Von: Sergey Edunov [mailto:edunov@gmail.com] 
Gesendet: Montag, 6. Juli 2015 21:41
An: user@giraph.apache.org
Betreff: Re: Questions after writing some giraph code

 

Hi Jan, 

It's a bit hard to advise without seeing actual code, so my reply might seem too generic.
Feel free to send specific questions with code samples to get more detailed advice. 

"Is there a way to do this without duplicating a lot of code of the “standalone” MasterCompute
class of algorithm" - this sort of thing is usually done by abstracting your algorithm out
of giraph-related classes. You can have a class with static methods that implement your algorithm
and then all you need to do is to pass data from vertices or master compute into this class.
This approach has other benefits such as easy testability. E.g. you can write unit tests for
algorithm. 

 

"I need to register n aggregators (n = number of vertices)" - this is generally a bad sign.
How much data you want to store in aggregators? Remeber, they will be send other the wire
between workers and master. You can, of course, get around by registering single Map as aggregator.
You'll need to wrap it into another class that implements Writable and then implement readFields
and write functions. 

 

"My biggest problem right now is debugging" - unit tests are usually very good approach. Again,
depends a lot on your configuration. We also use downsampled graphs a lot to quickly test
on cluster.


" After reading through another giraph algorithm, I noticed that they do the same" - can you
point to the example? I suspect that's because they use mutable data types or some helper
functions to change value. 

 

Regards,

Sergey Edunov

 

 

On Mon, Jul 6, 2015 at 8:18 AM, Jan Ebbing <Jan.Ebbing@gmx.de <mailto:Jan.Ebbing@gmx.de>
> wrote:

Hello everybody,

 

first of all thank you for all your work on giraph.

I’m a student writing his bachelor thesis using giraph.

I have already implemented an algorithm that isn’t completely trivial, with my new task,
however, I’m running into problems.

 

I implemented my first algorithm as a subclass of MasterCompute where I register aggregators
etc and then do a switch on the superstep and call setComputation() with the appropriate AbstractComputation
subclass I wrote. (I hope this is how you’re supposed to do it)

Now I want to implement a new algorithm that calls my new algorithm as a subroutine: While
the halting condition is not fulfilled, I first partition the graph using algorithm 1, then
continue to work on it with algorithm 1. Is there a way to do this without duplicating a lot
of code of the “standalone” MasterCompute class of algorithm 1? An additional problem
that arises with this is that the Vertex- and EdgeValue classes would have to be exactly the
same. I tried to work around this by defining a writable interface that defines all the methods
needed for my algorithms which would make the actual classes exchangeable. However, giraph
uses reflection to create a new instance of exactly the type the computation uses (an interface),
which leads to an error. Is there any good way to do this or are giraph jobs not that flexible?


 

In a variation of the first algorithm, I need to register n aggregators (n = number of vertices).
However, the documentation reads like I have to register aggregators in MasterCompute.initialize()
(nowhere else) and at that point, getTotalNumVertices() does not work yet. I am aware that
this is a very costly operation (I do not use all of those aggregators but I do not know beforehand
which of them I will use and which I will not use), but currently the only workaround I can
think of is using Configuration.getInt(). (and writing the total number of vertices in such
a config file beforehand)

Also a question on the config files: I understood that there are several of them that overwrite
each other and that e.g. I should not change the core-default.xml or core-site.xml since they
will change my complete Hadoop installation. I also read somewhere that it’s possible to
write a config file just for one job (which would be what I need) but I never found out how
that file should be called/where I have to place it.

 

My biggest problem right now is debugging, though: Is there an easy way to test giraph code
on small sample graphs? Right now, to test my implementations I have to package my code with
maven, copy the long command into the terminal to run the giraph job (changing the output
folder since they have to be different each time), wait a few minutes for the job to complete,
open the web GUI, click through a few pages there until I see my debug statements/if the job
completed I have to run through a text file via the console. Compared to what I was used to
(1 click in eclipse and almost instantly seeing the output on the console) this is very annoying,
especially since I do dumb small mistakes like switching the if and else blocks more often
than I’d like to and have to go through the whole process each time that happens.

I also searched for that, I found GRAFT which seemed to be a useful debugging tool, but more
for suitable for testing on real input and not to quickly test if the code runs at all on
a small input graph.

After searching through this mailing list archive, there were a few references to running
a giraph job with one click in eclipse aswell (see also [1]), but most descriptions were very
vague and I could not reproduce them.

 

Lastly, one small question: In my first algorithm I had a small bug where I would use getVertexValue,
then change the java object but not call setVertexValue which resulted in my changes not being
saved leading to undesired behavior. After reading through another giraph algorithm, I noticed
that they do the same (maybe it was with an EdgeValue, I’m not 100% sure on that) and don’t
call setXValue, but apparently their code works. Can anybody shed some light on that? (I understand
why it’s useful to have an explicit setVertexValue method for writing/reading vertices to/from
disk, I just don’t understand why it is not necessary for them?)

 

Thanks,

Jan

 

 

[1] http://ben-tech.blogspot.in/2011/08/how-to-debug-hadoop-mapreduce-jobs-in.html

 


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