Suneel,
I was trying -n 25 and -b 100 when I sent my e-mail about it not working
for me. Just tried -n 20 and got the same error message. Any other ideas?
Thanks,
Adam
On Mon, Aug 5, 2013 at 7:40 PM, Suneel Marthi <suneel_mar...@yahoo.com>wrote:
> Adam/Florian,
>
> Could you try running the clusterdump by limiting the number of terms from
> clusterdump, by specifying -n 20 (outputs the 20 top terms)?
>
>
>
>
> ________________________________
> From: Adam Baron <adam.j.ba...@gmail.com>
> To: user@mahout.apache.org
> Sent: Monday, August 5, 2013 8:03 PM
> Subject: Re: How to get human-readable output for large clustering?
>
>
> Florian,
>
> Any luck finding an answer over the past 5 months? I'm also dealing with
> similar out of memory errors when I run clusterdump. I'm using 50,000
> features and tried k=500. The kmeans command ran fine, but then I got the
> dreaded OutOfMemory error on with the clusterdump command:
>
> 2013-08-05 18:46:01,686 FATAL org.apache.hadoop.mapred.Child: Error running
> child : java.lang.OutOfMemoryError: Java heap space
> at
>
> org.apache.mahout.math.map.OpenIntDoubleHashMap.rehash(OpenIntDoubleHashMap.java:434)
> at
>
> org.apache.mahout.math.map.OpenIntDoubleHashMap.put(OpenIntDoubleHashMap.java:387)
> at
>
> org.apache.mahout.math.RandomAccessSparseVector.setQuick(RandomAccessSparseVector.java:139)
> at
> org.apache.mahout.math.VectorWritable.readFields(VectorWritable.java:118)
> at
>
> org.apache.hadoop.io.SequenceFile$Reader.getCurrentValue(SequenceFile.java:2114)
> at
> org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:2242)
> at
>
> org.apache.mahout.common.iterator.sequencefile.SequenceFileIterator.computeNext(SequenceFileIterator.java:95)
> at
>
> org.apache.mahout.common.iterator.sequencefile.SequenceFileIterator.computeNext(SequenceFileIterator.java:38)
> at
>
> com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
> at
>
> com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
> at
> com.google.common.collect.Iterators$5.hasNext(Iterators.java:543)
> at
>
> com.google.common.collect.ForwardingIterator.hasNext(ForwardingIterator.java:43)
> at
>
> org.apache.mahout.clustering.evaluation.RepresentativePointsMapper.getRepresentativePoints(RepresentativePointsMapper.java:103)
> at
>
> org.apache.mahout.clustering.evaluation.RepresentativePointsMapper.getRepresentativePoints(RepresentativePointsMapper.java:97)
> at
>
> org.apache.mahout.clustering.evaluation.RepresentativePointsMapper.setup(RepresentativePointsMapper.java:87)
> at
> org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:138)
> at
> org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:673)
> at
> org.apache.hadoop.mapred.MapTask.run(MapTask.java:331)
> at
> org.apache.hadoop.mapred.Child$4.run(Child.java:268)
> 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:1408)
> at
> org.apache.hadoop.mapred.Child.main(Child.java:262)
>
> Thanks,
> Adam
>
> On Mon, Mar 11, 2013 at 8:42 AM, Florian Laws <flor...@florianlaws.de
> >wrote:
>
> > Hi,
> >
> > I have difficulties with clusterdump and clusterpp.
> >
> > Experimenting with Mahout's k-means clusterer, I have successfully
> > obtained kmeans results and clusterdump output for small custom
> > datasets.
> >
> > However, when I try to use a larger dataset with 1M datapoints and
> > 1000 clusters, I start to run into problems with the clusterdump tool.
> > The kmeans step runs fine, but clusterdump fails with with an out of
> > memory error:
> >
> > mahout clusterdump
> > -i output/lda-vecs-1M-kmeans-k1000-x20/clusters-*-final
> > -o output/lda-vecs-1M-kmeans-k1000-x20/clusterdump
> > -dt sequencefile
> > -dm org.apache.mahout.common.distance.EuclideanDistanceMeasure
> > --pointsDir output/lda-vecs-1M-kmeans-k1000-x20/clusteredPoints/
> >
> > Running on hadoop, using /Users/issuu/florian/hadoop-1.0.3/bin/hadoop
> > and HADOOP_CONF_DIR=
> > MAHOUT-JOB:
> >
> /Users/issuu/florian/mahout/mahout-distribution-0.7/mahout-examples-0.7-job.jar
> > 13/03/11 16:21:04 INFO common.AbstractJob: Command line arguments:
> > {--dictionaryType=[sequencefile],
> >
> >
> --distanceMeasure=[org.apache.mahout.common.distance.EuclideanDistanceMeasure],
> > --endPhase=[2147483647],
> > --input=[output/lda-vecs-1M-kmeans-k1000-x20/clusters-*-final],
> > --output=[output/lda-vecs-1M-kmeans-k1000-x20/clusterdump],
> > --outputFormat=[TEXT],
> > --pointsDir=[output/lda-vecs-1M-kmeans-k1000-x20/clusteredPoints/],
> > --startPhase=[0], --tempDir=[temp]}
> > 2013-03-11 16:21:04.631 java[79418:1203] Unable to load realm info
> > from SCDynamicStore
> >
> > Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> > at org.apache.mahout.math.DenseVector.<init>(DenseVector.java:44)
> > at org.apache.mahout.math.DenseVector.<init>(DenseVector.java:39)
> > at
> > org.apache.mahout.math.VectorWritable.readFields(VectorWritable.java:99)
> > at
> >
> org.apache.mahout.clustering.classify.WeightedVectorWritable.readFields(WeightedVectorWritable.java:56)
> > at
> >
> org.apache.hadoop.io.SequenceFile$Reader.getCurrentValue(SequenceFile.java:1809)
> > at
> > org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:1937)
> > at
> >
> org.apache.mahout.common.iterator.sequencefile.SequenceFileIterator.computeNext(SequenceFileIterator.java:95)
> > at
> >
> org.apache.mahout.common.iterator.sequencefile.SequenceFileIterator.computeNext(SequenceFileIterator.java:38)
> > at
> >
> com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:141)
> > at
> >
> com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:136)
> > at
> > com.google.common.collect.Iterators$5.hasNext(Iterators.java:525)
> > at
> >
> com.google.common.collect.ForwardingIterator.hasNext(ForwardingIterator.java:43)
> > at
> >
> org.apache.mahout.utils.clustering.ClusterDumper.readPoints(ClusterDumper.java:292)
> > at
> >
> org.apache.mahout.utils.clustering.ClusterDumper.init(ClusterDumper.java:245)
> > at
> >
> org.apache.mahout.utils.clustering.ClusterDumper.run(ClusterDumper.java:152)
> > at
> >
> org.apache.mahout.utils.clustering.ClusterDumper.main(ClusterDumper.java:102)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke(Method.java:597)
> > at
> >
> org.apache.hadoop.util.ProgramDriver$ProgramDescription.invoke(ProgramDriver.java:68)
> > at
> > org.apache.hadoop.util.ProgramDriver.driver(ProgramDriver.java:139)
> > at
> > org.apache.mahout.driver.MahoutDriver.main(MahoutDriver.java:195)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke(Method.java:597)
> > at org.apache.hadoop.util.RunJar.main(RunJar.java:156)
> >
> >
> > How do I increase the heap space in a way that the mahout command accepts
> > it?
> > I've set both MAHOUT_HEAPSIZE to 40000 and JAVA_HEAP_MAX to -Xmx40g
> > with no effect.
> >
> >
> > I also read that this is because clusterdump tries to read the whole
> > clustering input into memory,
> > and that one one instead use clusterpp to separate the clusters, so I
> > also tried to use the clusterpp utility as suggested in
> >
> >
> http://mail-archives.apache.org/mod_mbox/mahout-user/201210.mbox/%3CCAPa28_KPzBzhn5Ug0jQNstbzFOBMhADdfGTrcg2p1HCw5GXWWw%40mail.gmail.com%3E
> >
> > However that fails because it apparently can't determine the number of
> > clusters.
> >
> > $ mahout clusterpp
> > -i output/lda-vecs-1M-kmeans-k1000-x20/clusters-20-final/
> > -o /user/issuu/output/lda-vecs-1M-kmeans-k1000-x20/clusterGroups
> >
> > Running on hadoop, using /Users/issuu/florian/hadoop-1.0.3/bin/hadoop
> > and HADOOP_CONF_DIR=
> > MAHOUT-JOB:
> >
> /Users/issuu/florian/mahout/mahout-distribution-0.7/mahout-examples-0.7-job.jar
> > 13/03/11 16:34:55 INFO common.AbstractJob: Command line arguments:
> > {--endPhase=[2147483647],
> > --input=[output/lda-vecs-1M-kmeans-k1000-x20/clusters-20-final/],
> > --method=[mapreduce],
> > --output=[/user/issuu/output/lda-vecs-1M-kmeans-k1000-x20/clusterGroups],
> > --startPhase=[0], --tempDir=[temp]}
> > 2013-03-11 16:34:55.925 java[79653:1203] Unable to load realm info
> > from SCDynamicStore
> >
> > Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
> > at
> >
> org.apache.mahout.clustering.topdown.postprocessor.ClusterCountReader.getNumberOfClusters(ClusterCountReader.java:53)
> > at
> >
> org.apache.mahout.clustering.topdown.postprocessor.ClusterOutputPostProcessorDriver.postProcessMR(ClusterOutputPostProcessorDriver.java:150)
> > at
> >
> org.apache.mahout.clustering.topdown.postprocessor.ClusterOutputPostProcessorDriver.run(ClusterOutputPostProcessorDriver.java:104)
> > at
> >
> org.apache.mahout.clustering.topdown.postprocessor.ClusterOutputPostProcessorDriver.run(ClusterOutputPostProcessorDriver.java:70)
> > at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:65)
> > at
> >
> org.apache.mahout.clustering.topdown.postprocessor.ClusterOutputPostProcessorDriver.main(ClusterOutputPostProcessorDriver.java:81)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke(Method.java:597)
> > at
> >
> org.apache.hadoop.util.ProgramDriver$ProgramDescription.invoke(ProgramDriver.java:68)
> > at
> > org.apache.hadoop.util.ProgramDriver.driver(ProgramDriver.java:139)
> > at
> > org.apache.mahout.driver.MahoutDriver.main(MahoutDriver.java:195)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke(Method.java:597)
> > at org.apache.hadoop.util.RunJar.main(RunJar.java:156)
> >
> > I'm running Mahout 0.7 on Hadoop 1.0.3 in pseudo-distributed mode.
> >
> > What am I doing wrong?
> > What is the recommended way to get the output of a large(-ish)
> > clustering job into some human-readable format?
> >
> >
> > Thanks,
> >
> > Florian
> >
>
