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From kellrott <...@git.apache.org>
Subject [GitHub] spark pull request: Patch for SPARK-942
Date Sat, 01 Mar 2014 00:25:36 GMT
GitHub user kellrott opened a pull request:

    https://github.com/apache/spark/pull/50

    Patch for SPARK-942

    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.

You can merge this pull request into a Git repository by running:

    $ git pull https://github.com/kellrott/spark iterator-to-disk

Alternatively you can review and apply these changes as the patch at:

    https://github.com/apache/spark/pull/50.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 #50
    
----
commit efe1102c8a7436b2fe112d3bece9f35fedea0dc8
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2013-11-13T00:32:54Z

    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.

commit cac1fadeec964cfc254ee1f02b82665aac9a5690
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2013-11-13T21:49:50Z

    Fixing MemoryStore, so that it converts incoming iterators to ArrayBuffer objects. This
was previously done higher up the stack.

commit d32992fd55726d3aa26530136b9a711856e42bd5
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2013-11-13T22:10:28Z

    Merge remote-tracking branch 'origin/master' into iterator-to-disk

commit 81d670cb9ad9d2e2635a0eb6ecc74f117554a708
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2013-11-14T01:20:17Z

    Adding unit test for straight to disk iterator methods.

commit f40382630bceed95b2e56e3f76fbc924fdb9f2c8
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2013-11-15T06:36:59Z

    Merge branch 'master' into iterator-to-disk

commit 5eb2b7e53d5290fdf71a7addd672c7f4ffbf6ec7
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2013-11-17T06:19:19Z

    Changing the JavaSerializer reset to occur every 1000 objects.

commit 44ec35a3733a25df6038827f480e8cf6991f9344
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2013-11-17T06:35:51Z

    Adding some comments.

commit 56f71cd10782b3c65df04ff9b083d9fc4f5b2503
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-04T15:49:27Z

    Merge branch 'master' into iterator-to-disk
    
    Conflicts:
    	core/src/main/scala/org/apache/spark/CacheManager.scala

commit 95c7f67b131496de51587afa373eee9da1a5d46b
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-24T21:35:05Z

    Simplifying StorageLevel checks

commit 0e6f8084fe2e7cfb5129a016fcd65d62e4005031
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-24T23:56:09Z

    Deleting temp output directory when done

commit 2eeda75621eb1d60f10d1f4ab805acae75edd7c5
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T00:20:20Z

    Fixing dumb mistake ("||" instead of "&&")

commit a6424ba6b2551d4366a57cd1d5d32ffe5a4a3fd0
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T00:24:03Z

    Wrapping long line

commit 9df02765528d57935a9aed8daf754a065f5d0ef5
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T01:21:48Z

    Added check to make sure that streamed-to-dist RDD actually returns good data in the LargeIteratorSuite

commit 31fe08ed356c5fb37a985ea72a10d6e3e165c80b
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T01:34:27Z

    Removing un-needed semi-colons

commit 40fe1d7cf83ce2fe29a061ec2d6e6e54bd18a6ff
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T03:34:43Z

    Removing rouge space

commit 00c98e07334dac20085f51977d015cab6e2242bb
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T06:22:12Z

    Making the Java ObjectStreamSerializer reset rate configurable by the system variable
'spark.serializer.objectStreamReset', default is not 10000.

commit 8644ee83ffbc6f02f93abaef8c56906c4683e8db
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T07:30:42Z

    Merge branch 'master' into iterator-to-disk

commit 656c33e800a0f3c7926dd0857105e12e0cf5fb25
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T18:58:20Z

    Fixing the JavaSerializer to read from the SparkConf rather then the System property.

commit 0f28ec70853a6a5ab198bc113f6af77b78d34d51
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T19:03:23Z

    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.

commit 627a8b79d760103674f3c5b108900e911a6a7eeb
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-25T21:20:30Z

    Wrapping a few long lines

commit c2fb43056c836ebb520bd076da2b576c32e794cf
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-26T01:09:29Z

    Removing more un-needed array-buffer to iterator conversions

commit 16a4ceae706c3458e5a2721f8c27eebbf2cf4c89
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-26T19:05:27Z

    Streamlined the LargeIteratorSuite unit test. It should now run in ~25 seconds. Confirmed
that it still crashes an unpatched copy of Spark.

commit 7ccc74b7f7a2c58739cde2e4e83950e07e7fd3eb
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-27T21:34:56Z

    Moving the 'LargeIteratorSuite' to simply test persistance of iterators. It doesn't try
to invoke a OOM error any more

commit f70d06939bb9c164a0a6c9af42f663bc882c3211
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-27T21:36:06Z

    Adding docs for spark.serializer.objectStreamReset configuration

commit 2f684ea15053d1ad934d60c58e082c1edf57b3a0
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-27T21:36:42Z

    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.

commit 33ac3900b0b11c0646b85e41e1129734adf6ce5c
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-27T21:39:50Z

    Merge branch 'iterator-to-disk' of github.com:kellrott/incubator-spark into iterator-to-disk
    
    Conflicts:
    	core/src/test/scala/org/apache/spark/storage/LargeIteratorSuite.scala

commit 8aa31cdf94981887fcbc5c7db79a4f2d310dcb59
Author: Kyle Ellrott <kellrott@gmail.com>
Date:   2014-02-28T23:25:02Z

    Merge ../incubator-spark into iterator-to-disk

----


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