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https://issues.apache.org/jira/browse/SPARK-17389?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15481490#comment-15481490
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Apache Spark commented on SPARK-17389:
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User 'yanboliang' has created a pull request for this issue:
https://github.com/apache/spark/pull/15050
> KMeans speedup with better choice of k-means|| init steps = 2
> -------------------------------------------------------------
>
> Key: SPARK-17389
> URL: https://issues.apache.org/jira/browse/SPARK-17389
> Project: Spark
> Issue Type: Improvement
> Components: MLlib
> Affects Versions: 2.0.0
> Reporter: Sean Owen
> Assignee: Sean Owen
> Priority: Minor
> Fix For: 2.1.0
>
>
> As reported in
> http://stackoverflow.com/questions/39260820/is-sparks-kmeans-unable-to-handle-bigdata#39260820
> KMeans can be surprisingly slow, and it's easy to see that most of the time
> spent is in kmeans|| initialization. For example, in this simple example...
> {code}
> import org.apache.spark.mllib.random.RandomRDDs
> import org.apache.spark.mllib.clustering.KMeans
> val data = RandomRDDs.uniformVectorRDD(sc, 1000000, 64,
> sc.defaultParallelism).cache()
> data.count()
> new KMeans().setK(1000).setMaxIterations(5).run(data)
> {code}
> Init takes 5:54, and iterations take about 0:15 each, on my laptop. Init
> takes about as long as 24 iterations, which is a typical run, meaning half
> the time is just in picking cluster centers. This seems excessive.
> There are two ways to speed this up significantly. First, the implementation
> has an old "runs" parameter that is always 1 now. It used to allow multiple
> clusterings to be computed at once. The code can be simplified significantly
> now that runs=1 always. This is already covered by SPARK-11560, but just a
> simple refactoring results in about a 13% init speedup, from 5:54 to 5:09 in
> this example. That's not what this change is about though.
> By default, k-means|| makes 5 passes over the data. The original paper at
> http://theory.stanford.edu/~sergei/papers/vldb12-kmpar.pdf actually shows
> that 2 is plenty, certainly when l=2k as is the case in our implementation.
> (See Figure 5.2/5.3; I believe the default of 5 was taken from Table 6 but
> it's not suggesting 5 is an optimal value.) Defaulting to 2 brings it down to
> 1:41 -- much improved over 5:54.
> Lastly, small thing, but the code will perform a local k-means++ step to
> reduce the number of centers to k even if there are already only <= k
> centers. This can be short-circuited. However this is really the topic of
> SPARK-3261 because this can cause fewer than k clusters to be returned where
> that would actually be correct, too.
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