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https://issues.apache.org/jira/browse/SPARK-5081?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14319948#comment-14319948
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Dr. Christian Betz commented on SPARK-5081:
-------------------------------------------
>From SPARK-5715
I see a *factor four performance loss* in my Spark jobs when migrating from
Spark 1.1.0 to Spark 1.2.0 or 1.2.1.
Also, I see an *increase in the size of shuffle writes* (which is also reported
by Kevin Jung on the mailing list:
http://apache-spark-user-list.1001560.n3.nabble.com/Shuffle-write-increases-in-spark-1-2-tt20894.html
Together with this I experience a *huge number of disk spills*.
I'm experiencing these with my job under the following circumstances:
* Spark 1.2.0 with Sort-based Shuffle
* Spark 1.2.0 with Hash-based Shuffle
* Spark 1.2.1 with Sort-based Shuffle
All three combinations show the same behavior, which contrasts from Spark
1.1.0.
In Spark 1.1.0, my job runs for about an hour, in Spark 1.2.x it runs for
almost four hours. Configuration is identical otherwise - I only added
org.apache.spark.scheduler.CompressedMapStatus to the Kryo registrator for
Spark 1.2.0 to cope with https://issues.apache.org/jira/browse/SPARK-5102.
As a consequence (I think, but causality might be different) I see lots and
lots of disk spills.
I cannot provide a small test case, but maybe the log entries for a single
worker thread can help someone investigate on this. (See below.)
I will also open up an issue, if nobody stops me by providing an answer ;)
Any help will be greatly appreciated, because otherwise I'm stuck with Spark
1.1.0, as quadrupling runtime is not an option.
Sincerely,
Chris
2015-02-09T14:06:06.328+01:00 INFO org.apache.spark.executor.Executor Running
task 9.0 in stage 18.0 (TID 300) Executor task launch worker-18
2015-02-09T14:06:06.351+01:00 INFO org.apache.spark.CacheManager Partition
rdd_35_9 not found, computing it Executor task launch worker-18
2015-02-09T14:06:06.351+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Getting 10 non-empty
blocks out of 10 blocks Executor task launch worker-18
2015-02-09T14:06:06.351+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Started 0 remote fetches
in 0 ms Executor task launch worker-18
2015-02-09T14:06:07.396+01:00 INFO org.apache.spark.storage.MemoryStore
ensureFreeSpace(2582904) called with curMem=300174944, maxMe... Executor task
launch worker-18
2015-02-09T14:06:07.397+01:00 INFO org.apache.spark.storage.MemoryStore Block
rdd_35_9 stored as bytes in memory (estimated size 2.5... Executor task launch
worker-18
2015-02-09T14:06:07.398+01:00 INFO org.apache.spark.storage.BlockManagerMaster
Updated info of block rdd_35_9 Executor task launch worker-18
2015-02-09T14:06:07.399+01:00 INFO org.apache.spark.CacheManager Partition
rdd_38_9 not found, computing it Executor task launch worker-18
2015-02-09T14:06:07.399+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Getting 10 non-empty
blocks out of 10 blocks Executor task launch worker-18
2015-02-09T14:06:07.400+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Started 0 remote fetches
in 0 ms Executor task launch worker-18
2015-02-09T14:06:07.567+01:00 INFO org.apache.spark.storage.MemoryStore
ensureFreeSpace(944848) called with curMem=302757848, maxMem... Executor task
launch worker-18
2015-02-09T14:06:07.568+01:00 INFO org.apache.spark.storage.MemoryStore Block
rdd_38_9 stored as values in memory (estimated size 92... Executor task launch
worker-18
2015-02-09T14:06:07.569+01:00 INFO org.apache.spark.storage.BlockManagerMaster
Updated info of block rdd_38_9 Executor task launch worker-18
2015-02-09T14:06:07.573+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Getting 34 non-empty
blocks out of 50 blocks Executor task launch worker-18
2015-02-09T14:06:07.573+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Started 0 remote fetches
in 1 ms Executor task launch worker-18
2015-02-09T14:06:38.931+01:00 INFO org.apache.spark.CacheManager Partition
rdd_41_9 not found, computing it Executor task launch worker-18
2015-02-09T14:06:38.931+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Getting 3 non-empty blocks
out of 10 blocks Executor task launch worker-18
2015-02-09T14:06:38.931+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Started 0 remote fetches
in 0 ms Executor task launch worker-18
2015-02-09T14:06:38.945+01:00 INFO org.apache.spark.storage.MemoryStore
ensureFreeSpace(0) called with curMem=307529127, maxMem=9261... Executor task
launch worker-18
2015-02-09T14:06:38.945+01:00 INFO org.apache.spark.storage.MemoryStore Block
rdd_41_9 stored as bytes in memory (estimated size 0.0... Executor task launch
worker-18
2015-02-09T14:06:38.946+01:00 INFO org.apache.spark.storage.BlockManagerMaster
Updated info of block rdd_41_9 Executor task launch worker-18
2015-02-09T14:06:38.946+01:00 WARN org.apache.spark.storage.BlockManager Block
rdd_41_9 replicated to only 0 peer(s) instead of 1 pee... Executor task launch
worker-18
2015-02-09T14:06:39.088+01:00 INFO org.apache.spark.storage.BlockManager Found
block rdd_3_9 locally Executor task launch worker-18
2015-02-09T14:06:41.389+01:00 INFO org.apache.spark.CacheManager Partition
rdd_7_9 not found, computing it Executor task launch worker-18
2015-02-09T14:06:41.389+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Getting 1 non-empty blocks
out of 1 blocks Executor task launch worker-18
2015-02-09T14:06:41.389+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Started 0 remote fetches
in 0 ms Executor task launch worker-18
2015-02-09T14:06:41.402+01:00 INFO org.apache.spark.storage.MemoryStore
ensureFreeSpace(38144) called with curMem=307529151, maxMem=... Executor task
launch worker-18
2015-02-09T14:06:41.402+01:00 INFO org.apache.spark.storage.MemoryStore Block
rdd_7_9 stored as values in memory (estimated size 37.... Executor task launch
worker-18
2015-02-09T14:06:41.404+01:00 INFO org.apache.spark.storage.BlockManagerMaster
Updated info of block rdd_7_9 Executor task launch worker-18
2015-02-09T14:07:00.019+01:00 INFO org.apache.spark.CacheManager Partition
rdd_73_9 not found, computing it Executor task launch worker-18
2015-02-09T14:07:00.019+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Getting 1 non-empty blocks
out of 1 blocks Executor task launch worker-18
2015-02-09T14:07:00.019+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Started 0 remote fetches
in 0 ms Executor task launch worker-18
2015-02-09T14:07:00.185+01:00 INFO org.apache.spark.storage.MemoryStore
ensureFreeSpace(826250) called with curMem=307567295, maxMem... Executor task
launch worker-18
2015-02-09T14:07:00.185+01:00 INFO org.apache.spark.storage.MemoryStore Block
rdd_73_9 stored as values in memory (estimated size 80... Executor task launch
worker-18
2015-02-09T14:07:00.186+01:00 INFO org.apache.spark.storage.BlockManagerMaster
Updated info of block rdd_73_9 Executor task launch worker-18
2015-02-09T14:07:00.190+01:00 INFO org.apache.spark.storage.BlockManager Found
block rdd_35_9 locally Executor task launch worker-18
2015-02-09T14:07:00.190+01:00 INFO org.apache.spark.storage.BlockManager Found
block rdd_38_9 locally Executor task launch worker-18
2015-02-09T14:07:00.194+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Getting 34 non-empty
blocks out of 50 blocks Executor task launch worker-18
2015-02-09T14:07:00.194+01:00 INFO
org.apache.spark.storage.ShuffleBlockFetcherIterator Started 0 remote fetches
in 1 ms Executor task launch worker-18
2015-02-09T14:07:17.967+01:00 INFO
org.apache.spark.util.collection.ExternalAppendOnlyMap Thread 117 spilling
in-memory map of 670.2 MB to disk (1 tim... Executor task launch worker-18
2015-02-09T14:07:46.716+01:00 INFO org.apache.spark.storage.BlockManager Found
block rdd_41_9 locally Executor task launch worker-18
2015-02-09T14:07:47.603+01:00 INFO org.apache.spark.storage.BlockManager Found
block rdd_3_9 locally Executor task launch worker-18
2015-02-09T14:07:47.897+01:00 INFO
org.apache.spark.util.collection.ExternalAppendOnlyMap Thread 117 spilling
in-memory map of 5.0 MB to disk (1 time ... Executor task launch worker-18
2015-02-09T14:07:48.270+01:00 INFO
org.apache.spark.util.collection.ExternalAppendOnlyMap Thread 117 spilling
in-memory map of 5.0 MB to disk (2 times... Executor task launch worker-18
2015-02-09T14:07:48.727+01:00 INFO
org.apache.spark.util.collection.ExternalAppendOnlyMap Thread 117 spilling
in-memory map of 5.0 MB to disk (3 times... Executor task launch worker-18
2015-02-09T14:07:49.021+01:00 INFO
org.apache.spark.util.collection.ExternalAppendOnlyMap Thread 117 spilling
in-memory map of 5.0 MB to disk (4 times... Executor task launch worker-18
> Shuffle write increases
> -----------------------
>
> Key: SPARK-5081
> URL: https://issues.apache.org/jira/browse/SPARK-5081
> Project: Spark
> Issue Type: Bug
> Components: Shuffle
> Affects Versions: 1.2.0
> Reporter: Kevin Jung
>
> The size of shuffle write showing in spark web UI is much different when I
> execute same spark job with same input data in both spark 1.1 and spark 1.2.
> At sortBy stage, the size of shuffle write is 98.1MB in spark 1.1 but 146.9MB
> in spark 1.2.
> I set spark.shuffle.manager option to hash because it's default value is
> changed but spark 1.2 still writes shuffle output more than spark 1.1.
> It can increase disk I/O overhead exponentially as the input file gets bigger
> and it causes the jobs take more time to complete.
> In the case of about 100GB input, for example, the size of shuffle write is
> 39.7GB in spark 1.1 but 91.0GB in spark 1.2.
> spark 1.1
> ||Stage Id||Description||Input||Shuffle Read||Shuffle Write||
> |9|saveAsTextFile| |1169.4KB| |
> |12|combineByKey| |1265.4KB|1275.0KB|
> |6|sortByKey| |1276.5KB| |
> |8|mapPartitions| |91.0MB|1383.1KB|
> |4|apply| |89.4MB| |
> |5|sortBy|155.6MB| |98.1MB|
> |3|sortBy|155.6MB| | |
> |1|collect| |2.1MB| |
> |2|mapValues|155.6MB| |2.2MB|
> |0|first|184.4KB| | |
> spark 1.2
> ||Stage Id||Description||Input||Shuffle Read||Shuffle Write||
> |12|saveAsTextFile| |1170.2KB| |
> |11|combineByKey| |1264.5KB|1275.0KB|
> |8|sortByKey| |1273.6KB| |
> |7|mapPartitions| |134.5MB|1383.1KB|
> |5|zipWithIndex| |132.5MB| |
> |4|sortBy|155.6MB| |146.9MB|
> |3|sortBy|155.6MB| | |
> |2|collect| |2.0MB| |
> |1|mapValues|155.6MB| |2.2MB|
> |0|first|184.4KB| | |
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