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Clustering (fkmeans) with Mahout using Clojure
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clojurecluster-analysismahout
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I am trying to write a short script to cluster my data via clojure (calling Mahout classes though). I have my input data in this format (which is an output from a php script)

format: (tag) (image) (frequency)
tag_sit image_a 0
tag_sit image_b 1
tag_lorem image_a 1
tag_lorem image_b 0
tag_dolor image_a 0
tag_dolor image_b 1
tag_ipsum image_a 1
tag_ipsum image_b 1
tag_amit image_a 1
tag_amit image_b 0
... (more)

Then I write them into a SequenceFile using this script (clojure)

#!./bin/clj
(ns sensei.sequence.core)

(require 'clojure.string)
(require 'clojure.java.io)

(import org.apache.hadoop.conf.Configuration)
(import org.apache.hadoop.fs.FileSystem)
(import org.apache.hadoop.fs.Path)
(import org.apache.hadoop.io.SequenceFile)
(import org.apache.hadoop.io.Text)

(import org.apache.mahout.math.VectorWritable)
(import org.apache.mahout.math.SequentialAccessSparseVector)

(with-open [reader (clojure.java.io/reader *in*)]
  (let [hadoop_configuration ((fn []
                                (let [conf (new Configuration)]
                                  (. conf set "fs.default.name" "hdfs://localhost:9000/")
                                  conf)))
        hadoop_fs (FileSystem/get hadoop_configuration)]
    (reduce
      (fn [writer [index value]]
        (. writer append index value)
        writer)
      (SequenceFile/createWriter
        hadoop_fs
        hadoop_configuration
        (new Path "test/sensei")
        Text
        VectorWritable)
      (map
        (fn [[tag row_vector]]
          (let [input_index (new Text tag)
                input_vector (new VectorWritable)]
            (. input_vector set row_vector)
            [input_index input_vector]))
        (map
          (fn [[tag photo_list]]
            (let [photo_map (apply hash-map photo_list)
                  input_vector (new SequentialAccessSparseVector (count (vals photo_map)))]
              (loop [frequency_list (vals photo_map)]
                (if (zero? (count frequency_list))
                  [tag input_vector]
                  (when-not (zero? (count frequency_list))
                    (. input_vector set
                       (mod (count frequency_list) (count (vals photo_map)))
                       (Integer/parseInt (first frequency_list)))
                    (recur (rest frequency_list)))))))
          (reduce
            (fn [result next_line]
              (let [[tag photo frequency] (clojure.string/split next_line #" ")]
                (update-in result [tag]
                  #(if (nil? %)
                     [photo frequency]
                     (conj % photo frequency)))))
            {}
            (line-seq reader)))))))

Basically it turns the input into sequence file, in this format

key (Text): $tag_uri value (VectorWritable): a vector (cardinality = number of documents) with numeric index and the respective frequency <0:1 1:0 2:0 3:1 4:0 ...>

Then I proceed to do the actual cluster with this script (by referring to this blog post)

#!./bin/clj

(ns sensei.clustering.fkmeans)

(import org.apache.hadoop.conf.Configuration)
(import org.apache.hadoop.fs.Path)

(import org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver)
(import org.apache.mahout.common.distance.EuclideanDistanceMeasure)
(import org.apache.mahout.clustering.kmeans.RandomSeedGenerator)

(let [hadoop_configuration ((fn []
                                (let [conf (new Configuration)]
                                  (. conf set "fs.default.name" "hdfs://127.0.0.1:9000/")
                                  conf)))
      input_path (new Path "test/sensei")
      output_path (new Path "test/clusters")
      clusters_in_path (new Path "test/clusters/cluster-0")]
  (FuzzyKMeansDriver/run
    hadoop_configuration
    input_path
    (RandomSeedGenerator/buildRandom
      hadoop_configuration
      input_path
      clusters_in_path
      (int 2)
      (new EuclideanDistanceMeasure))
    output_path
    (new EuclideanDistanceMeasure)
    (double 0.5)
    (int 10)
    (float 5.0)
    true
    false
    (double 0.0)
    false)) '' runSequential

However I am getting output like this

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
11/08/25 15:20:16 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
11/08/25 15:20:16 INFO compress.CodecPool: Got brand-new compressor
11/08/25 15:20:16 INFO compress.CodecPool: Got brand-new decompressor
11/08/25 15:20:17 WARN mapred.JobClient: Use GenericOptionsParser for parsing the arguments. Applications should implement Tool for the same.
11/08/25 15:20:17 INFO input.FileInputFormat: Total input paths to process : 1
11/08/25 15:20:17 INFO mapred.JobClient: Running job: job_local_0001
11/08/25 15:20:17 INFO mapred.MapTask: io.sort.mb = 100
11/08/25 15:20:17 INFO mapred.MapTask: data buffer = 79691776/99614720
11/08/25 15:20:17 INFO mapred.MapTask: record buffer = 262144/327680
11/08/25 15:20:17 WARN mapred.LocalJobRunner: job_local_0001
java.lang.IllegalStateException: No clusters found. Check your -c path.
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansMapper.setup(FuzzyKMeansMapper.java:62)
        at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:142)
        at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:763)
        at org.apache.hadoop.mapred.MapTask.run(MapTask.java:369)
        at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:210)
11/08/25 15:20:18 INFO mapred.JobClient:  map 0% reduce 0%
11/08/25 15:20:18 INFO mapred.JobClient: Job complete: job_local_0001
11/08/25 15:20:18 INFO mapred.JobClient: Counters: 0
Exception in thread "main" java.lang.RuntimeException: java.lang.InterruptedException: Fuzzy K-Means Iteration failed processing test/clusters/cluster-0/part-randomSeed
        at clojure.lang.Util.runtimeException(Util.java:153)
        at clojure.lang.Compiler.eval(Compiler.java:6417)
        at clojure.lang.Compiler.load(Compiler.java:6843)
        at clojure.lang.Compiler.loadFile(Compiler.java:6804)
        at clojure.main$load_script.invoke(main.clj:282)
        at clojure.main$script_opt.invoke(main.clj:342)
        at clojure.main$main.doInvoke(main.clj:426)
        at clojure.lang.RestFn.invoke(RestFn.java:436)
        at clojure.lang.Var.invoke(Var.java:409)
        at clojure.lang.AFn.applyToHelper(AFn.java:167)
        at clojure.lang.Var.applyTo(Var.java:518)
        at clojure.main.main(main.java:37)
Caused by: java.lang.InterruptedException: Fuzzy K-Means Iteration failed processing test/clusters/cluster-0/part-randomSeed
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver.runIteration(FuzzyKMeansDriver.java:252)
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver.buildClustersMR(FuzzyKMeansDriver.java:421)
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver.buildClusters(FuzzyKMeansDriver.java:345)
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver.run(FuzzyKMeansDriver.java:295)
        at sensei.clustering.fkmeans$eval17.invoke(fkmeans.clj:35)
        at clojure.lang.Compiler.eval(Compiler.java:6406)
        ... 10 more

When runSequential is set to true

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
11/09/07 14:32:32 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
11/09/07 14:32:32 INFO compress.CodecPool: Got brand-new compressor
11/09/07 14:32:32 INFO compress.CodecPool: Got brand-new decompressor
Exception in thread "main" java.lang.IllegalStateException: Clusters is empty!
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver.buildClustersSeq(FuzzyKMeansDriver.java:361)
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver.buildClusters(FuzzyKMeansDriver.java:343)
        at org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver.run(FuzzyKMeansDriver.java:295)
        at sensei.clustering.fkmeans$eval17.invoke(fkmeans.clj:35)
        at clojure.lang.Compiler.eval(Compiler.java:6465)
        at clojure.lang.Compiler.load(Compiler.java:6902)
        at clojure.lang.Compiler.loadFile(Compiler.java:6863)
        at clojure.main$load_script.invoke(main.clj:282)
        at clojure.main$script_opt.invoke(main.clj:342)
        at clojure.main$main.doInvoke(main.clj:426)
        at clojure.lang.RestFn.invoke(RestFn.java:436)
        at clojure.lang.Var.invoke(Var.java:409)
        at clojure.lang.AFn.applyToHelper(AFn.java:167)
        at clojure.lang.Var.applyTo(Var.java:518)
        at clojure.main.main(main.java:37)

I have also rewritten the fkmeans script to this form

#!./bin/clj

(ns sensei.clustering.fkmeans)

(import org.apache.hadoop.conf.Configuration)
(import org.apache.hadoop.fs.Path)

(import org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver)
(import org.apache.mahout.common.distance.EuclideanDistanceMeasure)
(import org.apache.mahout.clustering.kmeans.RandomSeedGenerator)

(let [hadoop_configuration ((fn []
                                (let [conf (new Configuration)]
                                  (. conf set "fs.default.name" "hdfs://localhost:9000/")
                                  conf)))
      driver (new FuzzyKMeansDriver)]
  (. driver setConf hadoop_configuration)
  (. driver
     run
     (into-array String ["--input" "test/sensei"
                         "--output" "test/clusters"
                         "--clusters" "test/clusters/clusters-0"
                         "--clustering"
                         "--overwrite"
                         "--emitMostLikely" "false"
                         "--numClusters" "3"
                         "--maxIter" "10"
                         "--m" "5"])))

but is still getting same error as the first initial version :/

Command Line tool runs fine

$ bin/mahout fkmeans --input test/sensei --output test/clusters --clusters test/clusters/clusters-0 --clustering --overwrite --emitMostLikely false --numClusters 10 --maxIter 10 --m 5

However it would not return the points when I try clusterdumper even though --clustering option exists in the previous command and --pointsDir is defined here

$ ./bin/mahout clusterdump --seqFileDir test/clusters/clusters-1 --pointsDir test/clusters/clusteredPoints --output sensei.txt

Mahout version used: 0.6-snapshot, clojure 1.3.0-snapshot

Please let me know if I miss out anything

Nealey answered 25/8, 2011 at 7:36 Comment(3)
Can you check, does initial clusters are really were generated? – Vouchsafe
Yes, was it ever solved? If so you could post an answer. – Spectra
OOOOOOOps, erm, I actually changed my scripts to use graphlab instead, much easier to set up and uses all 4 cores of my CPU :) – Nealey
M
2

My guess is that the Mahout implementation of fuzzy-c-means needs initial clusters to start with, which you maybe did not supply?

Also it sounds a bit as if you are running single-node? Note that for single-node systems you should avoid all the Mahout/Hadoop overhead and just use a regular clustering algorithm. Hadoop/Mahout comes at quite a cost that only pays off when you can no longer process the data on a single system. It is not "map reduce" unless you do that on a large number of systems.

Marquise answered 17/8, 2012 at 3:31 Comment(0)

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