Revert "[SPARK-1150] fix repo location in create script"

This reverts commit 9aa095711858ce8670e51488f66a3d7c1a821c30.
[SPARK-1150] fix repo location in create script (re-open)

reopen for https://spark-project.atlassian.net/browse/SPARK-1150

Author: CodingCat <zhunansjtu@gmail.com>

Closes #52 from CodingCat/script_fixes and squashes the following commits:

fc05a71 [CodingCat] fix repo location in create script
[SPARK-1100] prevent Spark from overwriting directory silently

Thanks for Diana Carroll to report this issue (https://spark-project.atlassian.net/browse/SPARK-1100)

the current saveAsTextFile/SequenceFile will overwrite the output directory silently if the directory already exists, this behaviour is not desirable because

overwriting the data silently is not user-friendly

if the partition number of two writing operation changed, then the output directory will contain the results generated by two runnings

My fix includes:

add some new APIs with a flag for users to define whether he/she wants to overwrite the directory:
if the flag is set to true, then the output directory is deleted first and then written into the new data to prevent the output directory contains results from multiple rounds of running;

if the flag is set to false, Spark will throw an exception if the output directory already exists

changed JavaAPI part

default behaviour is overwriting

Two questions

should we deprecate the old APIs without such a flag?

I noticed that Spark Streaming also called these APIs, I thought we don't need to change the related part in streaming? @tdas

Author: CodingCat <zhunansjtu@gmail.com>

Closes #11 from CodingCat/SPARK-1100 and squashes the following commits:

6a4e3a3 [CodingCat] code clean
ef2d43f [CodingCat] add new test cases and code clean
ac63136 [CodingCat] checkOutputSpecs not applicable to FSOutputFormat
ec490e8 [CodingCat] prevent Spark from overwriting directory silently and leaving dirty directory
Initialized the regVal for first iteration in SGD optimizer

Ported from https://github.com/apache/incubator-spark/pull/633

In runMiniBatchSGD, the regVal (for 1st iter) should be initialized
as sum of sqrt of weights if it's L2 update; for L1 update, the same logic is followed.

It maybe not be important here for SGD since the updater doesn't take the loss
as parameter to find the new weights. But it will give us the correct history of loss.
However, for LBFGS optimizer we implemented, the correct loss with regVal is crucial to
find the new weights.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #40 from dbtsai/dbtsai-smallRegValFix and squashes the following commits:

77d47da [DB Tsai] In runMiniBatchSGD, the regVal (for 1st iter) should be initialized as sum of sqrt of weights if it's L2 update; for L1 update, the same logic is followed.
Merge the old sbt-launch-lib.bash with the new sbt-launcher jar downloading logic.

This allows developers to pass options (such as -D) to sbt.  I also modified the SparkBuild to ensure spark specific properties are propagated to forked test JVMs.

Author: Michael Armbrust <michael@databricks.com>

Closes #14 from marmbrus/sbtScripts and squashes the following commits:

c008b18 [Michael Armbrust] Merge the old sbt-launch-lib.bash with the new sbt-launcher jar downloading logic.
Update io.netty from 4.0.13 Final to 4.0.17.Final

This update contains a lot of bug fixes and some new perf improvements.
It is also binary compatible with the current 4.0.13.Final

For more information: http://netty.io/news/2014/02/25/4-0-17-Final.html

Author: Binh Nguyen <ngbinh@gmail.com>

Author: Binh Nguyen <ngbinh@gmail.com>

Closes #41 from ngbinh/master and squashes the following commits:

a9498f4 [Binh Nguyen] update io.netty to 4.0.17.Final
Remove remaining references to incubation

This removes some loose ends not caught by the other (incubating -> tlp) patches. @markhamstra this updates the version as you mentioned earlier.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #51 from pwendell/tlp and squashes the following commits:

d553b1b [Patrick Wendell] Remove remaining references to incubation
SPARK-1137: Make ZK PersistenceEngine not crash for wrong serialVersionUID

Previously, ZooKeeperPersistenceEngine would crash the whole Master process if
there was stored data from a prior Spark version. Now, we just delete these files.

Author: Aaron Davidson <aaron@databricks.com>

Closes #4 from aarondav/zookeeper2 and squashes the following commits:

fa8b40f [Aaron Davidson] SPARK-1137: Make ZK PersistenceEngine not crash for wrong serialVersionUID
Ignore RateLimitedOutputStreamSuite for now.

This test has been flaky. We can re-enable it after @tdas has a chance to look at it.

Author: Reynold Xin <rxin@apache.org>

Closes #54 from rxin/ratelimit and squashes the following commits:

1a12198 [Reynold Xin] Ignore RateLimitedOutputStreamSuite for now.
SPARK-1084.2 (resubmitted)

(Ported from https://github.com/apache/incubator-spark/pull/650 )

This adds one more change though, to fix the scala version warning introduced by json4s recently.

Author: Sean Owen <sowen@cloudera.com>

Closes #32 from srowen/SPARK-1084.2 and squashes the following commits:

9240abd [Sean Owen] Avoid scala version conflict in scalap induced by json4s dependency
1561cec [Sean Owen] Remove "exclude *" dependencies that are causing Maven warnings, and that are apparently unneeded anyway
SPARK-1121: Include avro for yarn-alpha builds

This lets us explicitly include Avro based on a profile for 0.23.X
builds. It makes me sad how convoluted it is to express this logic
in Maven. @tgraves and @sryza curious if this works for you.

I'm also considering just reverting to how it was before. The only
real problem was that Spark advertised a dependency on Avro
even though it only really depends transitively on Avro through
other deps.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #49 from pwendell/avro-build-fix and squashes the following commits:

8d6ee92 [Patrick Wendell] SPARK-1121: Add avro to yarn-alpha profile
Add Jekyll tag to isolate "production-only" doc components.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #56 from pwendell/jekyll-prod and squashes the following commits:

1bdc3a8 [Patrick Wendell] Add Jekyll tag to isolate "production-only" doc components.
SPARK-1173. Improve scala streaming docs.

Clarify imports to add implicit conversions to DStream and
fix other small typos in the streaming intro documentation.

Tested by inspecting output via a local jekyll server, c&p'ing the scala commands into a spark terminal.

Author: Aaron Kimball <aaron@magnify.io>

Closes #64 from kimballa/spark-1173-streaming-docs and squashes the following commits:

6fbff0e [Aaron Kimball] SPARK-1173. Improve scala streaming docs.
SPARK-1173. (#2) Fix typo in Java streaming example.

Companion commit to pull request #64, fix the typo on the Java side of the docs.

Author: Aaron Kimball <aaron@magnify.io>

Closes #65 from kimballa/spark-1173-java-doc-update and squashes the following commits:

8ce11d3 [Aaron Kimball] SPARK-1173. (#2) Fix typo in Java streaming example.
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.