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Posted to reviews@spark.apache.org by maropu <gi...@git.apache.org> on 2015/01/21 17:18:32 UTC
[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
GitHub user maropu opened a pull request:
https://github.com/apache/spark/pull/4136
[SPARK-5351][GraphX] Do not use Partitioner.defaultPartitioner as a partitioner of EdgeRDDImp...
If the value of 'spark.default.parallelism' does not match the number of partitoins in EdgePartition(EdgeRDDImpl),
the following error occurs in ReplicatedVertexView.scala:72;
object GraphTest extends Logging {
def run[VD: ClassTag, ED: ClassTag](graph: Graph[VD, ED]): VertexRDD[Int] = {
graph.aggregateMessages[Int](
ctx => {
ctx.sendToSrc(1)
ctx.sendToDst(2)
},
_ + _)
}
}
val g = GraphLoader.edgeListFile(sc, "graph.txt")
val rdd = GraphTest.run(g)
java.lang.IllegalArgumentException: Can't zip RDDs with unequal numbers of partitions
at org.apache.spark.rdd.ZippedPartitionsBaseRDD.getPartitions(ZippedPartitionsRDD.scala:57)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:206)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:204)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:204)
at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:32)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:206)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:204)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:204)
at org.apache.spark.ShuffleDependency.<init>(Dependency.scala:82)
at org.apache.spark.rdd.ShuffledRDD.getDependencies(ShuffledRDD.scala:80)
at org.apache.spark.rdd.RDD$$anonfun$dependencies$2.apply(RDD.scala:193)
at org.apache.spark.rdd.RDD$$anonfun$dependencies$2.apply(RDD.scala:191)
...
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/maropu/spark EdgePartitionBugFix
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/4136.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 #4136
----
commit 0a2f32b0283b4fe319a23f7f4541d1531ddcbab2
Author: Takeshi Yamamuro <li...@gmail.com>
Date: 2015-01-21T15:59:58Z
Do not use Partitioner.defaultPartitioner as a partitioner of EdgeRDDImpl
----
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71155268
This is a spurious test failure due to a build break in SQL. Let's retest:
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71160729
Test PASSed.
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Test PASSed.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71155272
Jenkins, retest this please.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71160721
[Test build #26004 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/26004/consoleFull) for PR 4136 at commit [`0a2f32b`](https://github.com/apache/spark/commit/0a2f32b0283b4fe319a23f7f4541d1531ddcbab2).
* This patch **passes all tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by ankurdave <gi...@git.apache.org>.
Github user ankurdave commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71265542
@JoshRosen No, it doesn't seem to trigger the Snappy error! After the previous attempted fix (#1763, 9b225ac3072de522b40b46aba6df1f1c231f13ef), the GraphX unit tests (`for i in {1..10}; do sbt/sbt 'graphx/test:test-only org.apache.spark.graphx.*'; done`) would fail 3 out of 10 times, but they always succeed now.
I think we can merge this! I'm just going to bisect to see what fixed the error.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71268887
@ankurdave Don't know if you've already seen this, but check out https://issues.apache.org/jira/browse/SPARK-3630 and its linked tickets for some related Snappy errors that and how they've been fixed. It's possible that one of those patches may have fixed the GraphX manifestation of the Snappy problem.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by maropu <gi...@git.apache.org>.
Github user maropu commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71305053
Thanks for your quick commits! I got trouble in this bug for my graphx application :))
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/4136
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70930842
[Test build #25916 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/25916/consoleFull) for PR 4136 at commit [`0a2f32b`](https://github.com/apache/spark/commit/0a2f32b0283b4fe319a23f7f4541d1531ddcbab2).
* This patch merges cleanly.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70930354
@ankurdave Does it still trigger that bug? How reliably? I've spent a huge amount of time fighting nondeterministic Snappy stream corruption errors in Spark, so I'd be _very_ interested if you've found a semi-reliable reproduction in the current Spark master.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by ankurdave <gi...@git.apache.org>.
Github user ankurdave commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71298562
Merged into master & branch-1.2.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70938045
[Test build #25916 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/25916/consoleFull) for PR 4136 at commit [`0a2f32b`](https://github.com/apache/spark/commit/0a2f32b0283b4fe319a23f7f4541d1531ddcbab2).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70918281
[Test build #25910 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/25910/consoleFull) for PR 4136 at commit [`0a2f32b`](https://github.com/apache/spark/commit/0a2f32b0283b4fe319a23f7f4541d1531ddcbab2).
* This patch merges cleanly.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70938054
Test FAILed.
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Test FAILed.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by ankurdave <gi...@git.apache.org>.
Github user ankurdave commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70918331
This is the same fix as was originally proposed for [SPARK-2823](https://issues.apache.org/jira/browse/SPARK-2823): apache/spark#1763. The problem is that it seems to trigger a Spark bug ([SPARK-3400](https://issues.apache.org/jira/browse/SPARK-3400), [SPARK-3630](https://issues.apache.org/jira/browse/SPARK-3630)) that causes deserialization errors.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by ankurdave <gi...@git.apache.org>.
Github user ankurdave commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70917802
ok to test
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71155446
[Test build #26004 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/26004/consoleFull) for PR 4136 at commit [`0a2f32b`](https://github.com/apache/spark/commit/0a2f32b0283b4fe319a23f7f4541d1531ddcbab2).
* This patch merges cleanly.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70924225
Test FAILed.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by ankurdave <gi...@git.apache.org>.
Github user ankurdave commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71297997
Oh, thanks! Looks like that was the problem all along; stopping the SparkContext fixes the problem. I'm going to merge this with the amended test now.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70930130
Jenkins, retest this please.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by ankurdave <gi...@git.apache.org>.
Github user ankurdave commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71286155
@JoshRosen Actually, it seems the test failures still occur, but only when I add a [unit test](https://github.com/apache/spark/commit/9b225ac3072de522b40b46aba6df1f1c231f13ef#diff-3ade47bc293ef06e43c25f1ac1f6783bR354) that sets spark.default.parallelism.
Adding the test causes subsequent tests within the same run to fail with exceptions like
```
java.io.IOException: org.apache.spark.SparkException: Failed to get broadcast_0_piece0 of broadcast_0
```
and
```
java.io.IOException: PARSING_ERROR(2)
```
The exception traces always occur in TorrentBroadcast.
It seems like setting spark.default.parallelism is causing some kind of side effect that corrupts broadcasts in later unit tests, which is strange since (1) each unit test should have its own SparkContext and therefore its own temp directory, and (2) I'm only passing spark.default.parallelism to SparkConf/SparkContext, not setting it as a system property.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by JoshRosen <gi...@git.apache.org>.
Github user JoshRosen commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-71293352
@ankurdave The exception from the new unit test sounds suspiciously similar to https://issues.apache.org/jira/browse/SPARK-4133. Your new test creates a new `sc` local variable then never stops it, so if that test runs first then its leaked context will keep running and will interfere with contexts created in the other tests.
Because some SparkSQL tests could not pass without it, our unit tests set `spark.driver.allowMultipleContexts=false` to disable the check, so this might be hard to notice. If you have `unit-tests.log`, though, I'd take a look to see whether there are any warning messages about multiple contexts.
I'd check to see if those failures still persist after properly cleaning up the SparkContext created in your new test.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70924211
[Test build #25910 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/25910/consoleFull) for PR 4136 at commit [`0a2f32b`](https://github.com/apache/spark/commit/0a2f32b0283b4fe319a23f7f4541d1531ddcbab2).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: [SPARK-5351][GraphX] Do not use Partitioner.de...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/4136#issuecomment-70867791
Can one of the admins verify this patch?
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