Removed accidentally checked in comment

It looks like this comment was added a while ago by @mridulm as part of a merge and was accidentally checked in.  We should remove it.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #61 from kayousterhout/remove_comment and squashes the following commits:

0b2b3f2 [Kay Ousterhout] Removed accidentally checked in comment
update proportion of memory

The default value of "spark.storage.memoryFraction" has been changed from 0.66 to 0.6 . So it should be 60% of the memory to cache while 40% used for task execution.

Author: Chen Chao <crazyjvm@gmail.com>

Closes #66 from CrazyJvm/master and squashes the following commits:

0f84d86 [Chen Chao] update proportion of memory
Remove the remoteFetchTime metric.

This metric is confusing: it adds up all of the time to fetch
shuffle inputs, but fetches often happen in parallel, so
remoteFetchTime can be much longer than the task execution time.

@squito it looks like you added this metric -- do you have a use case for it?

cc @shivaram -- I know you've looked at the shuffle performance a lot so chime in here if this metric has turned out to be useful for you!

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #62 from kayousterhout/remove_fetch_variable and squashes the following commits:

43341eb [Kay Ousterhout] Remote the remoteFetchTime metric.
Added a unit test for PairRDDFunctions.lookup

Lookup didn't have a unit test. Added two tests, one for with a partitioner, and one for without.

Author: Bryn Keller <bryn.keller@intel.com>

Closes #36 from xoltar/lookup and squashes the following commits:

3bc0d44 [Bryn Keller] Added a unit test for PairRDDFunctions.lookup
SPARK-1158: Fix flaky RateLimitedOutputStreamSuite.

There was actually a problem with the RateLimitedOutputStream implementation where the first second doesn't write anything because of integer rounding.

So RateLimitedOutputStream was overly aggressive in throttling.

Author: Reynold Xin <rxin@apache.org>

Closes #55 from rxin/ratelimitest and squashes the following commits:

52ce1b7 [Reynold Xin] SPARK-1158: Fix flaky RateLimitedOutputStreamSuite.
Remove broken/unused Connection.getChunkFIFO method.

This method appears to be broken -- since it never removes
anything from messages, and it adds new messages to it,
the while loop is an infinite loop.  The method also does not appear
to have ever been used since the code was added in 2012, so
this commit removes it.

cc @mateiz who originally added this method in case there's a reason it should be here! (https://github.com/apache/spark/commit/63051dd2bcc4bf09d413ff7cf89a37967edc33ba)

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #69 from kayousterhout/remove_get_fifo and squashes the following commits:

053bc59 [Kay Ousterhout] Remove broken/unused Connection.getChunkFIFO method.
[java8API] SPARK-964 Investigate the potential for using JDK 8 lambda expressions for the Java/Scala APIs

Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Patrick Wendell <pwendell@gmail.com>

Closes #17 from ScrapCodes/java8-lambdas and squashes the following commits:

95850e6 [Patrick Wendell] Some doc improvements and build changes to the Java 8 patch.
85a954e [Prashant Sharma] Nit. import orderings.
673f7ac [Prashant Sharma] Added support for -java-home as well
80a13e8 [Prashant Sharma] Used fake class tag syntax
26eb3f6 [Prashant Sharma] Patrick's comments on PR.
35d8d79 [Prashant Sharma] Specified java 8 building in the docs
31d4cd6 [Prashant Sharma] Maven build to support -Pjava8-tests flag.
4ab87d3 [Prashant Sharma] Review feedback on the pr
c33dc2c [Prashant Sharma] SPARK-964, Java 8 API Support.
SPARK-1164 Deprecated reduceByKeyToDriver as it is an alias for reduceByKeyLocally

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #72 from ScrapCodes/SPARK-1164/deprecate-reducebykeytodriver and squashes the following commits:

ee521cd [Prashant Sharma] SPARK-1164 Deprecated reduceByKeyToDriver as it is an alias for reduceByKeyLocally
SPARK-1178: missing document of spark.scheduler.revive.interval

https://spark-project.atlassian.net/browse/SPARK-1178

The configuration on spark.scheduler.revive.interval is undocumented but actually used

https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/scheduler/cluster/CoarseGrainedSchedulerBackend.scala#L64

Author: CodingCat <zhunansjtu@gmail.com>

Closes #74 from CodingCat/SPARK-1178 and squashes the following commits:

783ec69 [CodingCat] missing document of spark.scheduler.revive.interval
SPARK-1109 wrong API docs for pyspark map function

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #73 from ScrapCodes/SPARK-1109/wrong-API-docs and squashes the following commits:

1a55b58 [Prashant Sharma] SPARK-1109 wrong API docs for pyspark map function
SPARK-1171: when executor is removed, we should minus totalCores instead of just freeCores on that executor

https://spark-project.atlassian.net/browse/SPARK-1171

When the executor is removed, the current implementation will only minus the freeCores of that executor. Actually we should minus the totalCores...

Author: CodingCat <zhunansjtu@gmail.com>
Author: Nan Zhu <CodingCat@users.noreply.github.com>

Closes #63 from CodingCat/simplify_CoarseGrainedSchedulerBackend and squashes the following commits:

f6bf93f [Nan Zhu] code clean
19c2bb4 [CodingCat] use copy idiom to reconstruct the workerOffers
43c13e9 [CodingCat] keep WorkerOffer immutable
af470d3 [CodingCat] style fix
0c0e409 [CodingCat] simplify the implementation of CoarseGrainedSchedulerBackend
Improve  building with maven  docs

     mvn -Dhadoop.version=... -Dsuites=spark.repl.ReplSuite test

to

     mvn -Dhadoop.version=... -Dsuites=org.apache.spark.repl.ReplSuite test

Author: liguoqiang <liguoqiang@rd.tuan800.com>

Closes #70 from witgo/building_with_maven and squashes the following commits:

6ec8a54 [liguoqiang] spark.repl.ReplSuite to org.apache.spark.repl.ReplSuite
SPARK-1184: Update the distribution tar.gz to include spark-assembly jar

See JIRA for details.

Author: Mark Grover <mark@apache.org>

Closes #78 from markgrover/SPARK-1184 and squashes the following commits:

12b78e6 [Mark Grover] SPARK-1184: Update the distribution tar.gz to include spark-assembly jar
SPARK-1156: allow user to login into a cluster without slaves

Reported in https://spark-project.atlassian.net/browse/SPARK-1156

The current spark-ec2 script doesn't allow user to login to a cluster without slaves. One of the issues brought by this behaviour is that when all the worker died, the user cannot even login to the cluster for debugging, etc.

Author: CodingCat <zhunansjtu@gmail.com>

Closes #58 from CodingCat/SPARK-1156 and squashes the following commits:

104af07 [CodingCat] output ERROR to stderr
9a71769 [CodingCat] do not allow user to start 0-slave cluster
24a7c79 [CodingCat] allow user to login into a cluster without slaves
SPARK-1187, Added missing Python APIs

The following Python APIs are added,
RDD.id()
SparkContext.setJobGroup()
SparkContext.setLocalProperty()
SparkContext.getLocalProperty()
SparkContext.sparkUser()

was raised earlier as a part of  apache/incubator-spark#486

Author: Prabin Banka <prabin.banka@imaginea.com>

Closes #75 from prabinb/python-api-backup and squashes the following commits:

cc3c6cd [Prabin Banka] Added missing Python APIs
SPARK-942: Do not materialize partitions when DISK_ONLY storage level is used

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.
SPARK-1189: Add Security to Spark - Akka, Http, ConnectionManager, UI use servlets

resubmit pull request.  was https://github.com/apache/incubator-spark/pull/332.

Author: Thomas Graves <tgraves@apache.org>

Closes #33 from tgravescs/security-branch-0.9-with-client-rebase and squashes the following commits:

dfe3918 [Thomas Graves] Fix merge conflict since startUserClass now using runAsUser
05eebed [Thomas Graves] Fix dependency lost in upmerge
d1040ec [Thomas Graves] Fix up various imports
05ff5e0 [Thomas Graves] Fix up imports after upmerging to master
ac046b3 [Thomas Graves] Merge remote-tracking branch 'upstream/master' into security-branch-0.9-with-client-rebase
13733e1 [Thomas Graves] Pass securityManager and SparkConf around where we can. Switch to use sparkConf for reading config whereever possible. Added ConnectionManagerSuite unit tests.
4a57acc [Thomas Graves] Change UI createHandler routines to createServlet since they now return servlets
2f77147 [Thomas Graves] Rework from comments
50dd9f2 [Thomas Graves] fix header in SecurityManager
ecbfb65 [Thomas Graves] Fix spacing and formatting
b514bec [Thomas Graves] Fix reference to config
ed3d1c1 [Thomas Graves] Add security.md
6f7ddf3 [Thomas Graves] Convert SaslClient and SaslServer to scala, change spark.authenticate.ui to spark.ui.acls.enable, and fix up various other things from review comments
2d9e23e [Thomas Graves] Merge remote-tracking branch 'upstream/master' into security-branch-0.9-with-client-rebase_rework
5721c5a [Thomas Graves] update AkkaUtilsSuite test for the actorSelection changes, fix typos based on comments, and remove extra lines I missed in rebase from AkkaUtils
f351763 [Thomas Graves] Add Security to Spark - Akka, Http, ConnectionManager, UI to use servlets
SPARK-1197. Change yarn-standalone to yarn-cluster and fix up running on YARN docs

This patch changes "yarn-standalone" to "yarn-cluster" (but still supports the former).  It also cleans up the Running on YARN docs and adds a section on how to view logs.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #95 from sryza/sandy-spark-1197 and squashes the following commits:

563ef3a [Sandy Ryza] Review feedback
6ad06d4 [Sandy Ryza] Change yarn-standalone to yarn-cluster and fix up running on YARN docs
Example for cassandra CQL read/write from spark

Cassandra read/write using CqlPagingInputFormat/CqlOutputFormat

Author: anitatailor <tailor.anita@gmail.com>

Closes #87 from anitatailor/master and squashes the following commits:

3493f81 [anitatailor] Fixed scala style as per review
19480b7 [anitatailor] Example for cassandra CQL read/write from spark
Small clean-up to flatmap tests