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From Vasiliki Kalavri <vasilikikala...@gmail.com>
Subject Re: RuntimeException Gelly API: Memory ran out. Compaction failed.
Date Wed, 18 Mar 2015 21:49:20 GMT
haha, yes, actually I just confirmed!
If I flip my args, I get the error you mention in the first e-mail. you're
trying to generate a graph giving the edge list as a vertex list and this
is a way too big dataset for your memory settings (cmp. ~15m edges vs. the
actual 400k).

I hope that clear everything out :-)

Cheers,
V.

On 18 March 2015 at 23:44, Vasiliki Kalavri <vasilikikalavri@gmail.com>
wrote:

> Well, one thing I notice is that your vertices and edges args are flipped.
> Might be the source of error :-)
>
> On 18 March 2015 at 23:04, Mihail Vieru <vieru@informatik.hu-berlin.de>
> wrote:
>
>>  I'm also using 0 as sourceID. The exact program arguments:
>>
>> 0 /home/vieru/dev/flink-experiments/data/social_network.edgelist
>> /home/vieru/dev/flink-experiments/data/social_network.verticeslist
>> /home/vieru/dev/flink-experiments/sssp-output-higgstwitter 10
>>
>> And yes, I call both methods on the initialized Graph *mappedInput*. I
>> don't understand why the distances are computed correctly for the small
>> graph (also read from files) but not for the larger one.
>> The messages appear to be wrong in the latter case.
>>
>>
>> On 18.03.2015 21:55, Vasiliki Kalavri wrote:
>>
>>  hmm, I'm starting to run out of ideas...
>> What's your source ID parameter? I ran mine with 0.
>> About the result, you call both createVertexCentricIteration() and
>> runVertexCentricIteration() on the initialized graph, right?
>>
>> On 18 March 2015 at 22:33, Mihail Vieru <vieru@informatik.hu-berlin.de>
>> wrote:
>>
>>>  Hi Vasia,
>>>
>>> yes, I am using the latest master. I just did a pull again and the
>>> problem persists. Perhaps Robert could confirm as well.
>>>
>>> I've set the solution set to unmanaged in SSSPUnweighted as Stephan
>>> proposed and the job finishes. So I am able to proceed using this
>>> workaround.
>>>
>>> An odd thing occurs now though. The distances aren't computed correctly
>>> for the SNAP graph and remain the one set in InitVerticesMapper(). For the
>>> small graph in SSSPDataUnweighted they are OK. I'm currently investigating
>>> this behavior.
>>>
>>> Cheers,
>>> Mihail
>>>
>>>
>>> On 18.03.2015 20:55, Vasiliki Kalavri wrote:
>>>
>>>  Hi Mihail,
>>>
>>>  I used your code to generate the vertex file, then gave this and the
>>> edge list as input to your SSSP implementation and still couldn't reproduce
>>> the exception. I'm using the same local setup as I describe above.
>>> I'm not aware of any recent changes that might be relevant, but, just in
>>> case, are you using the latest master?
>>>
>>>  Cheers,
>>> V.
>>>
>>> On 18 March 2015 at 19:21, Mihail Vieru <vieru@informatik.hu-berlin.de>
>>> wrote:
>>>
>>>>  Hi Vasia,
>>>>
>>>> I have used a simple job (attached) to generate a file which looks like
>>>> this:
>>>>
>>>> 0 0
>>>> 1 1
>>>> 2 2
>>>> ...
>>>> 456629 456629
>>>> 456630 456630
>>>>
>>>> I need the vertices to be generated from a file for my future work.
>>>>
>>>> Cheers,
>>>> Mihail
>>>>
>>>>
>>>>
>>>> On 18.03.2015 17:04, Vasiliki Kalavri wrote:
>>>>
>>>>  Hi Mihail, Robert,
>>>>
>>>>  I've tried reproducing this, but I couldn't.
>>>> I'm using the same twitter input graph from SNAP that you link to and
>>>> also Scala IDE.
>>>> The job finishes without a problem (both the SSSP example from Gelly
>>>> and the unweighted version).
>>>>
>>>>  The only thing I changed to run your version was creating the graph
>>>> from the edge set only, i.e. like this:
>>>>
>>>>  Graph<Long, Long, NullValue> graph = Graph.fromDataSet(edges,
>>>>  new MapFunction<Long, Long>() {
>>>>  public Long map(Long value) {
>>>>  return Long.MAX_VALUE;
>>>>  }
>>>>  }, env);
>>>>
>>>> Since the twitter input is an edge list, how do you generate the vertex
>>>> dataset in your case?
>>>>
>>>>  Thanks,
>>>> -Vasia.
>>>>
>>>> On 18 March 2015 at 16:54, Mihail Vieru <vieru@informatik.hu-berlin.de>
>>>> wrote:
>>>>
>>>>>  Hi,
>>>>>
>>>>> great! Thanks!
>>>>>
>>>>> I really need this bug fixed because I'm laying the groundwork for my
>>>>> Diplom thesis and I need to be sure that the Gelly API is reliable and
can
>>>>> handle large datasets as intended.
>>>>>
>>>>> Cheers,
>>>>> Mihail
>>>>>
>>>>>
>>>>> On 18.03.2015 15:40, Robert Waury wrote:
>>>>>
>>>>>   Hi,
>>>>>
>>>>>  I managed to reproduce the behavior and as far as I can tell it seems
>>>>> to be a problem with the memory allocation.
>>>>>
>>>>>  I have filed a bug report in JIRA to get the attention of somebody
>>>>> who knows the runtime better than I do.
>>>>>
>>>>> https://issues.apache.org/jira/browse/FLINK-1734
>>>>>
>>>>>  Cheers,
>>>>>  Robert
>>>>>
>>>>> On Tue, Mar 17, 2015 at 3:52 PM, Mihail Vieru <
>>>>> vieru@informatik.hu-berlin.de> wrote:
>>>>>
>>>>>>  Hi Robert,
>>>>>>
>>>>>> thank you for your reply.
>>>>>>
>>>>>> I'm starting the job from the Scala IDE. So only one JobManager and
>>>>>> one TaskManager in the same JVM.
>>>>>> I've doubled the memory in the eclipse.ini settings but I still get
>>>>>> the Exception.
>>>>>>
>>>>>> -vmargs
>>>>>> -Xmx2048m
>>>>>> -Xms100m
>>>>>> -XX:MaxPermSize=512m
>>>>>>
>>>>>> Best,
>>>>>> Mihail
>>>>>>
>>>>>>
>>>>>> On 17.03.2015 10:11, Robert Waury wrote:
>>>>>>
>>>>>>   Hi,
>>>>>>
>>>>>>  can you tell me how much memory your job has and how many workers
>>>>>> you are running?
>>>>>>
>>>>>>  From the trace it seems the internal hash table allocated only 7
MB
>>>>>> for the graph data and therefore runs out of memory pretty quickly.
>>>>>>
>>>>>>  Skewed data could also be an issue but with a minimum of 5 pages
>>>>>> and a maximum of 8 it seems to be distributed fairly even to the
different
>>>>>> partitions.
>>>>>>
>>>>>>  Cheers,
>>>>>>  Robert
>>>>>>
>>>>>> On Tue, Mar 17, 2015 at 1:25 AM, Mihail Vieru <
>>>>>> vieru@informatik.hu-berlin.de> wrote:
>>>>>>
>>>>>>> And the correct SSSPUnweighted attached.
>>>>>>>
>>>>>>>
>>>>>>> On 17.03.2015 01:23, Mihail Vieru wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I'm getting the following RuntimeException for an adaptation
of the
>>>>>>>> SingleSourceShortestPaths example using the Gelly API (see
attachment).
>>>>>>>> It's been adapted for unweighted graphs having vertices with
Long values.
>>>>>>>>
>>>>>>>> As an input graph I'm using the social network graph (~200MB
>>>>>>>> unpacked) from here:
>>>>>>>> https://snap.stanford.edu/data/higgs-twitter.html
>>>>>>>>
>>>>>>>> For the small SSSPDataUnweighted graph (also attached) it
>>>>>>>> terminates and computes the distances correctly.
>>>>>>>>
>>>>>>>>
>>>>>>>> 03/16/2015 17:18:23    IterationHead(WorksetIteration
>>>>>>>> (Vertex-centric iteration
>>>>>>>> (org.apache.flink.graph.library.SingleSourceShortestPathsUnweighted$VertexDistanceUpdater@dca6fe4
>>>>>>>> |
>>>>>>>> org.apache.flink.graph.library.SingleSourceShortestPathsUnweighted$MinDistanceMessenger@6577e8ce)))(2/4)
>>>>>>>> switched to FAILED
>>>>>>>> java.lang.RuntimeException: Memory ran out. Compaction failed.
>>>>>>>> numPartitions: 32 minPartition: 5 maxPartition: 8 number
of overflow
>>>>>>>> segments: 176 bucketSize: 217 Overall memory: 20316160 Partition
memory:
>>>>>>>> 7208960 Message: Index: 8, Size: 7
>>>>>>>>     at
>>>>>>>> org.apache.flink.runtime.operators.hash.CompactingHashTable.insert(CompactingHashTable.java:390)
>>>>>>>>     at
>>>>>>>> org.apache.flink.runtime.operators.hash.CompactingHashTable.buildTable(CompactingHashTable.java:337)
>>>>>>>>     at
>>>>>>>> org.apache.flink.runtime.iterative.task.IterationHeadPactTask.readInitialSolutionSet(IterationHeadPactTask.java:216)
>>>>>>>>     at
>>>>>>>> org.apache.flink.runtime.iterative.task.IterationHeadPactTask.run(IterationHeadPactTask.java:278)
>>>>>>>>     at
>>>>>>>> org.apache.flink.runtime.operators.RegularPactTask.invoke(RegularPactTask.java:362)
>>>>>>>>     at
>>>>>>>> org.apache.flink.runtime.execution.RuntimeEnvironment.run(RuntimeEnvironment.java:205)
>>>>>>>>     at java.lang.Thread.run(Thread.java:745)
>>>>>>>>
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Mihail
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>

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