This is a port of a pull request original targeted at incubator-spark: https://github.com/apache/incubator-spark/pull/180
Essentially if a user returns a generative iterator (from a flatMap operation), when trying to persist the data, Spark would first unroll the iterator into an ArrayBuffer, and then try to figure out if it could store the data. In cases where the user provided an iterator that generated more data then available memory, this would case a crash. With this patch, if the user requests a persist with a 'StorageLevel.DISK_ONLY', the iterator will be unrolled as it is inputed into the serializer.
To do this, two changes where made:
1) The type of the 'values' argument in the putValues method of the BlockStore interface was changed from ArrayBuffer to Iterator (and all code interfacing with this method was modified to connect correctly.
2) The JavaSerializer now calls the ObjectOutputStream 'reset' method every 1000 objects. This was done because the ObjectOutputStream caches objects (thus preventing them from being GC'd) to write more compact serialization. If reset is never called, eventually the memory fills up, if it is called too often then the serialization streams become much larger because of redundant class descriptions.
Author: Kyle Ellrott <kellrott@gmail.com>
Closes#50 from kellrott/iterator-to-disk and squashes the following commits:
9ef7cb8 [Kyle Ellrott] Fixing formatting issues.
60e0c57 [Kyle Ellrott] Fixing issues (formatting, variable names, etc.) from review comments
8aa31cd [Kyle Ellrott] Merge ../incubator-spark into iterator-to-disk
33ac390 [Kyle Ellrott] Merge branch 'iterator-to-disk' of github.com:kellrott/incubator-spark into iterator-to-disk
2f684ea [Kyle Ellrott] Refactoring the BlockManager to replace the Either[Either[A,B]] usage. Now using trait 'Values'. Also modified BlockStore.putBytes call to return PutResult, so that it behaves like putValues.
f70d069 [Kyle Ellrott] Adding docs for spark.serializer.objectStreamReset configuration
7ccc74b [Kyle Ellrott] Moving the 'LargeIteratorSuite' to simply test persistance of iterators. It doesn't try to invoke a OOM error any more
16a4cea [Kyle Ellrott] Streamlined the LargeIteratorSuite unit test. It should now run in ~25 seconds. Confirmed that it still crashes an unpatched copy of Spark.
c2fb430 [Kyle Ellrott] Removing more un-needed array-buffer to iterator conversions
627a8b7 [Kyle Ellrott] Wrapping a few long lines
0f28ec7 [Kyle Ellrott] Adding second putValues to BlockStore interface that accepts an ArrayBuffer (rather then an Iterator). This will allow BlockStores to have slightly different behaviors dependent on whether they get an Iterator or ArrayBuffer. In the case of the MemoryStore, it needs to duplicate and cache an Iterator into an ArrayBuffer, but if handed a ArrayBuffer, it can skip the duplication.
656c33e [Kyle Ellrott] Fixing the JavaSerializer to read from the SparkConf rather then the System property.
8644ee8 [Kyle Ellrott] Merge branch 'master' into iterator-to-disk
00c98e0 [Kyle Ellrott] Making the Java ObjectStreamSerializer reset rate configurable by the system variable 'spark.serializer.objectStreamReset', default is not 10000.
40fe1d7 [Kyle Ellrott] Removing rouge space
31fe08e [Kyle Ellrott] Removing un-needed semi-colons
9df0276 [Kyle Ellrott] Added check to make sure that streamed-to-dist RDD actually returns good data in the LargeIteratorSuite
a6424ba [Kyle Ellrott] Wrapping long line
2eeda75 [Kyle Ellrott] Fixing dumb mistake ("||" instead of "&&")
0e6f808 [Kyle Ellrott] Deleting temp output directory when done
95c7f67 [Kyle Ellrott] Simplifying StorageLevel checks
56f71cd [Kyle Ellrott] Merge branch 'master' into iterator-to-disk
44ec35a [Kyle Ellrott] Adding some comments.
5eb2b7e [Kyle Ellrott] Changing the JavaSerializer reset to occur every 1000 objects.
f403826 [Kyle Ellrott] Merge branch 'master' into iterator-to-disk
81d670c [Kyle Ellrott] Adding unit test for straight to disk iterator methods.
d32992f [Kyle Ellrott] Merge remote-tracking branch 'origin/master' into iterator-to-disk
cac1fad [Kyle Ellrott] Fixing MemoryStore, so that it converts incoming iterators to ArrayBuffer objects. This was previously done higher up the stack.
efe1102 [Kyle Ellrott] Changing CacheManager and BlockManager to pass iterators directly to the serializer when a 'DISK_ONLY' persist is called. This is in response to SPARK-942.
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