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From Jeff Eastman <j...@windwardsolutions.com>
Subject Re: Clustering from DB
Date Wed, 15 Jul 2009 15:30:17 GMT
Glad to hear KMeans is working reliably now. Your performance problems 
will require some additional tuning. Here are some suggestions:
- You did not mention how many mappers are running in your job. With 
60gb in a single input file, I would think Hadoop would allocate 
multiple mapper tasks automatically, since there are thousands of 
potential splits. If this is not happening (is the file compressed?), 
then breaking it into multiple parts in a preprocessing step would allow 
you to get more concurrency in the map phase.
- Same with the reducers; how many are you running and what is your K? 
The default number of reducers is 2, but you can increase this up to the 
number of clusters to increase parallelism. Unlike Canopy and Mean 
Shift, KMeans can use multiple reducers up to that limit.
- Finally, what is the size of your cluster? Adding machines would be 
another way to increase concurrency, since map and reduce tasks are 
spread across the entire cluster.

60 gb is a small dataset for Hadoop. I don't think it should be taking 
that long.
Jeff

nfantone wrote:
> After updating to the latest revision, everything seems to be working
> just fine. However, the task I set up to do, user clustering by
> KMeans, is taking forever to complete: I initiated the job yesterday's
> morning and it's still running today (an elapsed time of nearly 18hs
> and counting...). Of course, the main reason behind it it's the huge
> size of the data set I'm trying to process (a ~60Gb HDFS file), but
> I'm looking for ways to improve the performance. Would splitting the
> input file into smaller parts do any difference? Is it even possible
> to set the Driver in order to use more than one input (right now, I'm
> specifying a full path to a single file, including its filename)? What
> about setting a higher number of reducers? Is there any drawbacks to
> that? Running multiple KMeans' job in several threads?
>
> Or perhaps, I'm just doing something wrong and should not be taking
> this long. Surely, I'm not the first one to encounter this running
> time issue with large datasets. Ideas, anyone?
>
>
> On Mon, Jul 13, 2009 at 2:39 PM, nfantone<nfantone@gmail.com> wrote:
>   
>> Great work. It works like a charm now. Thank you very much.
>>
>> On Mon, Jul 13, 2009 at 1:41 PM, Jeff Eastman<jdog@windwardsolutions.com> wrote:
>>     
>>> r793620 fixes the KMeansDriver.isConverged() method to iterate over all
>>> cluster part files. Unit test now runs without error and the synthetic
>>> control job completes too.
>>>
>>>
>>> Jeff Eastman wrote:
>>>       
>>>> In this case, the code should be reading all of the clusters into memory
>>>> to see if they have all converged. These may be split into multiple part
>>>> files if more than one reducer is specified. So /* is the correct file
>>>> pattern and it is the calling site that should remove the /part-0000
>>>> reference. The code in isConverged should loop through all the parts,
>>>> returning if they have all converged or not.
>>>>
>>>> I'll take a detailed look tomorrow.
>>>>
>>>>
>>>> Grant Ingersoll wrote:
>>>>         
>>>>> Hmm, that might be a mistake on my part when trying to resolve how Hadoop
>>>>> 0.20 now resolves globs.  I somewhat blindly applied "/*" where needed,
but
>>>>> I think it is likely worth revistiing here where a specific file is needed?
>>>>>
>>>>> -Grant
>>>>>
>>>>> On Jul 10, 2009, at 3:08 PM, nfantone wrote:
>>>>>
>>>>>           
>>>>>> This error is still bugging me. The exception:
>>>>>>
>>>>>> WARNING: java.io.FileNotFoundException: File
>>>>>> output/clusters-0/part-00000/* does not exist.
>>>>>> java.io.FileNotFoundException: File output/clusters-0/part-00000/*
>>>>>> does not exist.
>>>>>>
>>>>>> ocurrs first at:
>>>>>>
>>>>>>
>>>>>> org.apache.mahout.clustering.kmeans.KMeansDriver.isConverged(KMeansDriver.java:298)
>>>>>>
>>>>>> which corresponds to:
>>>>>>
>>>>>>  private static boolean isConverged(String filePath, JobConf conf,
>>>>>> FileSystem fs)
>>>>>>     throws IOException {
>>>>>>   Path outPart = new Path(filePath + "/*");
>>>>>>   SequenceFile.Reader reader = new SequenceFile.Reader(fs, outPart,
>>>>>> conf);  <-- THIS
>>>>>>   ...
>>>>>>  }
>>>>>>
>>>>>> where isConverged() is called in this fashion:
>>>>>>
>>>>>> return isConverged(clustersOut + "/part-00000", conf, fs);
>>>>>>
>>>>>> by runIteration(), which is previously invoked by runJob() like:
>>>>>>
>>>>>>    String clustersOut = output + "/clusters-" + iteration;
>>>>>>     converged = runIteration(input, clustersIn, clustersOut,
>>>>>> measureClass,
>>>>>>         delta, numReduceTasks, iteration);
>>>>>>
>>>>>> Consequently, assuming its the first iteration and the output folder
>>>>>> has been named "output" by the user, the SequenceFile.Reader receives
>>>>>> "output/clusters-0/part-00000/*" as a path, which is non-existent.
I
>>>>>> believe the path should end in "part-00000" and the  + "/*" should
be
>>>>>> removed... although someone, evidently, thought otherwise.
>>>>>>
>>>>>> Any feedback?
>>>>>>
>>>>>> On Mon, Jul 6, 2009 at 5:39 PM, nfantone<nfantone@gmail.com>
wrote:
>>>>>>             
>>>>>>> I was using Canopy to create input clusters, but the error appeared
>>>>>>> while running kMeans (if I run kMeans' job only with previously
>>>>>>> created clusters from Canopy placed in output/canopies as initial
>>>>>>> clusters, it still fails). I noticed no other problems. I was
using
>>>>>>> revision 790979 before updating.  Strangely, there were no changes
in
>>>>>>> the job and drivers class from that revision. svn diff shows
that the
>>>>>>> only classes that changed in org.apache.mahout.clustering.kmeans
>>>>>>> package were KMeansInfo.java and RandomSeedGenerator.java
>>>>>>>
>>>>>>> On Mon, Jul 6, 2009 at 3:55 PM, Jeff
>>>>>>> Eastman<jdog@windwardsolutions.com> wrote:
>>>>>>>               
>>>>>>>> Hum, no, it's looking for the output of the first iteration.
Were
>>>>>>>> there
>>>>>>>> other errors? What was the last revision you were running?
It does
>>>>>>>> look like
>>>>>>>> something got horked, as it should be looking for output/clusters-0/*.
>>>>>>>> Can
>>>>>>>> you diff the job and driver class to see what changed?
>>>>>>>>
>>>>>>>> Jeff
>>>>>>>>
>>>>>>>> nfantone wrote:
>>>>>>>>                 
>>>>>>>>> Fellows, today I updated to revision 791558 and while
running kMeans
>>>>>>>>> I
>>>>>>>>> got the following exception:
>>>>>>>>>
>>>>>>>>> WARNING: java.io.FileNotFoundException: File
>>>>>>>>> output/clusters-0/part-00000/* does not exist.
>>>>>>>>> java.io.FileNotFoundException: File output/clusters-0/part-00000/*
>>>>>>>>> does not exist.
>>>>>>>>>
>>>>>>>>> The algorithm isn't interrupted, though. But this exception
wasn't
>>>>>>>>> thrown before the update and, to me, its message is not
quite clear.
>>>>>>>>> It seems as it's looking for any file inside a "part-00000"
>>>>>>>>> directory,
>>>>>>>>> which doesn't exist; and, as far as I know, "part-xxxxx"
are default
>>>>>>>>> names for output files.
>>>>>>>>>
>>>>>>>>> I could show the entire stack trace, if needed. Any pointers?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Jul 2, 2009 at 3:16 PM, nfantone<nfantone@gmail.com>
wrote:
>>>>>>>>>
>>>>>>>>>                   
>>>>>>>>>> Thanks for the feedback, Jeff.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>                     
>>>>>>>>>>> The logical format of input to KMeans is <Key,
Vector> as it is in
>>>>>>>>>>> sequence
>>>>>>>>>>> file format, but the Key is never used. To my
knowledge, there is
>>>>>>>>>>> no
>>>>>>>>>>> requirement to assign identifiers to the input
points*. Users are
>>>>>>>>>>> free
>>>>>>>>>>> to
>>>>>>>>>>> associate an arbitrary name field with each vector
- also label
>>>>>>>>>>> mappings
>>>>>>>>>>> may
>>>>>>>>>>> be assigned - but these are not manipulated by
KMeans or any of the
>>>>>>>>>>> other
>>>>>>>>>>> clustering applications. The name field is now
used as a vector
>>>>>>>>>>> identifier
>>>>>>>>>>> by the KMeansClusterMapper - if it is non-null
- in the output step
>>>>>>>>>>> only.
>>>>>>>>>>>
>>>>>>>>>>>                       
>>>>>>>>>> The key may not be used internally, but externally
they can prove to
>>>>>>>>>> be pretty useful. For me, keys are userIDs and each
Vector
>>>>>>>>>> represents
>>>>>>>>>> his/her historical behavior. Being able to collect
the output
>>>>>>>>>> information as <UserID, ClusterID> is quite
neat as it allows me to,
>>>>>>>>>> for instance, retrieve user information using data
directly from a
>>>>>>>>>> HDFS file's field.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>                     
>>>>>>>>>
>>>>>>>>>                   
>>>>>>>>                 
>>>>> --------------------------
>>>>> Grant Ingersoll
>>>>> http://www.lucidimagination.com/
>>>>>
>>>>> Search the Lucene ecosystem (Lucene/Solr/Nutch/Mahout/Tika/Droids) using
>>>>> Solr/Lucene:
>>>>> http://www.lucidimagination.com/search
>>>>>
>>>>>
>>>>>
>>>>>           
>>>>
>>>>         
>>>       
>
>
>   


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