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 > > >