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Posted to reviews@spark.apache.org by hhbyyh <gi...@git.apache.org> on 2016/04/01 05:23:37 UTC
[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
GitHub user hhbyyh opened a pull request:
https://github.com/apache/spark/pull/12106
[SPARK-14322] [MLlib] Use treeReduce instead of reduce in OnlineLDAOptimizer
## What changes were proposed in this pull request?
OnlineLDAOptimizer uses RDD.reduce in two places where it could use treeReduce. This can cause scalability issues. This should be an easy fix.
## How was this patch tested?
unit tests
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/hhbyyh/spark ldaTreeReduce
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/12106.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #12106
----
commit 38cf0f3cc90d09435f12ad86021469eff32985db
Author: Yuhao Yang <hh...@gmail.com>
Date: 2016-04-01T03:17:43Z
change reduce to treeReduce for lda
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by hhbyyh <gi...@git.apache.org>.
Github user hhbyyh commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58645358
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
Get it. Thanks
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58334794
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
Whoops, that's a long-standing bug... Perhaps we can just backport this PR.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by hhbyyh <gi...@git.apache.org>.
Github user hhbyyh commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-206094396
@jkbradley Updated. I used flatMap to replace the second reduce.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-206098699
Merged build finished. Test PASSed.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58422643
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
+ val statsSum: BDM[Double] = stats.map(_._1).treeReduce(_ += _)
expElogbetaBc.unpersist()
val gammat: BDM[Double] = breeze.linalg.DenseMatrix.vertcat(
- stats.map(_._2).reduce(_ ++ _).map(_.toDenseMatrix): _*)
+ stats.map(_._2).treeReduce(_ ++ _).map(_.toDenseMatrix): _*)
--- End diff --
Let's just use aggregate here for now. I made [https://issues.apache.org/jira/browse/SPARK-14371] to fix the issue with concatenating lists.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-206098700
Test PASSed.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by hhbyyh <gi...@git.apache.org>.
Github user hhbyyh commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58478599
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
I'm thinking `.treeReduce(_ + _)` is fine here. Internally it will transform it into treeAggregate
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-204240409
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58586792
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
It would be better to modify the first argument, which treeAggregate should support. (Actually I noticed treeAggregate does not say it supports it in the docs, but it should be OK to assume. I just created [https://issues.apache.org/jira/browse/SPARK-14408] for that.)
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-206089752
**[Test build #55081 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/55081/consoleFull)** for PR 12106 at commit [`42ae469`](https://github.com/apache/spark/commit/42ae4692bb483f85c4fc46425ac312d2657ba451).
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-204240413
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by hhbyyh <gi...@git.apache.org>.
Github user hhbyyh commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58367523
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
As far as I understand, this does not generate any computation error since it still gives the correct sum, right?
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-206507031
LGTM
Merging with master, and backporting to 1.6, 1.5, 1.4 if possible
Thanks!
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58335017
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
+ val statsSum: BDM[Double] = stats.map(_._1).treeReduce(_ += _)
expElogbetaBc.unpersist()
val gammat: BDM[Double] = breeze.linalg.DenseMatrix.vertcat(
- stats.map(_._2).reduce(_ ++ _).map(_.toDenseMatrix): _*)
+ stats.map(_._2).treeReduce(_ ++ _).map(_.toDenseMatrix): _*)
--- End diff --
aggregate would send stats.numPartitions elements back to the driver, whereas treeAggregate would send fewer (for large enough numPartitions), right?
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-204229682
**[Test build #54684 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/54684/consoleFull)** for PR 12106 at commit [`38cf0f3`](https://github.com/apache/spark/commit/38cf0f3cc90d09435f12ad86021469eff32985db).
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58168561
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
This doesn't seem right because the first arg is modified in-place, which violates reduce contract. It should be an aggregate (or treeAggregate) instead.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58420665
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
This is the line which caused the original failure, so using treeAggregate here should help.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-205435882
I just updated the JIRA to indicate the bug here. Could you please update the PR title and description?
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58168589
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
+ val statsSum: BDM[Double] = stats.map(_._1).treeReduce(_ += _)
expElogbetaBc.unpersist()
val gammat: BDM[Double] = breeze.linalg.DenseMatrix.vertcat(
- stats.map(_._2).reduce(_ ++ _).map(_.toDenseMatrix): _*)
+ stats.map(_._2).treeReduce(_ ++ _).map(_.toDenseMatrix): _*)
--- End diff --
I don't think treeReduce helps here because the partial reduce doesn't reduce the size of the result.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by jkbradley <gi...@git.apache.org>.
Github user jkbradley commented on a diff in the pull request:
https://github.com/apache/spark/pull/12106#discussion_r58412527
--- Diff: mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAOptimizer.scala ---
@@ -451,10 +451,10 @@ final class OnlineLDAOptimizer extends LDAOptimizer {
}
Iterator((stat, gammaPart))
}
- val statsSum: BDM[Double] = stats.map(_._1).reduce(_ += _)
--- End diff --
I would expect so, but I'm not familiar enough about Spark internals to know if this might return corrupted results.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeReduce instead o...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-204240344
**[Test build #54684 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/54684/consoleFull)** for PR 12106 at commit [`38cf0f3`](https://github.com/apache/spark/commit/38cf0f3cc90d09435f12ad86021469eff32985db).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/12106
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[GitHub] spark pull request: [SPARK-14322] [MLlib] Use treeAggregate instea...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/12106#issuecomment-206098633
**[Test build #55081 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/55081/consoleFull)** for PR 12106 at commit [`42ae469`](https://github.com/apache/spark/commit/42ae4692bb483f85c4fc46425ac312d2657ba451).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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