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1331 commits

Author SHA1 Message Date
Kai Jiang 9a73b33a9a [MINOR][DOCS] typo in docs/configuration.md
`<\code>` end tag missing backslash in
docs/configuration.md{L308-L339}

ref #8795

Author: Kai Jiang <jiangkai@gmail.com>

Closes #9715 from vectorijk/minor-typo-docs.
2015-11-14 11:59:37 +00:00
Xusen Yin 912b94363b [SPARK-11336] Add links to example codes
https://issues.apache.org/jira/browse/SPARK-11336

mengxr I add a hyperlink of Spark on Github and a hint of their existences in Spark code repo in each code example. I remove the config key for changing the example code dir, since we assume all examples  should be in spark/examples.

The hyperlink, though we cannot use it now, since the Spark v1.6.0 has not been released yet, can be used after the release. So it is not a problem.

I add some screen shots, so you can get an instant feeling.

<img width="949" alt="screen shot 2015-10-27 at 10 47 18 pm" src="https://cloud.githubusercontent.com/assets/2637239/10780634/bd20e072-7cfc-11e5-8960-def4fc62a8ea.png">

<img width="1144" alt="screen shot 2015-10-27 at 10 47 31 pm" src="https://cloud.githubusercontent.com/assets/2637239/10780636/c3f6e180-7cfc-11e5-80b2-233589f4a9a3.png">

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9320 from yinxusen/SPARK-11336.
2015-11-13 13:14:25 -08:00
Yanbo Liang 99693fef0a [SPARK-11723][ML][DOC] Use LibSVM data source rather than MLUtils.loadLibSVMFile to load DataFrame
Use LibSVM data source rather than MLUtils.loadLibSVMFile to load DataFrame, include:
* Use libSVM data source for all example codes under examples/ml, and remove unused import.
* Use libSVM data source for user guides under ml-*** which were omitted by #8697.
* Fix bug: We should use ```sqlContext.read().format("libsvm").load(path)``` at Java side, but the API doc and user guides misuse as ```sqlContext.read.format("libsvm").load(path)```.
* Code cleanup.

mengxr

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9690 from yanboliang/spark-11723.
2015-11-13 08:43:05 -08:00
Rishabh Bhardwaj 61a28486cc [SPARK-11445][DOCS] Replaced example code in mllib-ensembles.md using include_example
I have made the required changes and tested.
Kindly review the changes.

Author: Rishabh Bhardwaj <rbnext29@gmail.com>

Closes #9407 from rishabhbhardwaj/SPARK-11445.
2015-11-13 08:36:46 -08:00
Yanbo Liang ea5ae2705a [SPARK-11629][ML][PYSPARK][DOC] Python example code for Multilayer Perceptron Classification
Add Python example code for Multilayer Perceptron Classification, and make example code in user guide document testable. mengxr

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9594 from yanboliang/spark-11629.
2015-11-12 21:29:43 -08:00
Andrew Or 12a0784ac0 [SPARK-11667] Update dynamic allocation docs to reflect supported cluster managers
Author: Andrew Or <andrew@databricks.com>

Closes #9637 from andrewor14/update-da-docs.
2015-11-12 15:48:42 -08:00
Andrew Or cf38fc7551 [SPARK-11670] Fix incorrect kryo buffer default value in docs
<img width="931" alt="screen shot 2015-11-11 at 1 53 21 pm" src="https://cloud.githubusercontent.com/assets/2133137/11108261/35d183d4-889a-11e5-9572-85e9d6cebd26.png">

Author: Andrew Or <andrew@databricks.com>

Closes #9638 from andrewor14/fix-kryo-docs.
2015-11-12 15:47:29 -08:00
Nick Evans dd77e278b9 [SPARK-11335][STREAMING] update kafka direct python docs on how to get the offset ranges for a KafkaRDD
tdas koeninger

This updates the Spark Streaming + Kafka Integration Guide doc with a working method to access the offsets of a `KafkaRDD` through Python.

Author: Nick Evans <me@nicolasevans.org>

Closes #9289 from manygrams/update_kafka_direct_python_docs.
2015-11-11 13:29:30 -08:00
Josh Rosen 529a1d3380 [SPARK-6152] Use shaded ASM5 to support closure cleaning of Java 8 compiled classes
This patch modifies Spark's closure cleaner (and a few other places) to use ASM 5, which is necessary in order to support cleaning of closures that were compiled by Java 8.

In order to avoid ASM dependency conflicts, Spark excludes ASM from all of its dependencies and uses a shaded version of ASM 4 that comes from `reflectasm` (see [SPARK-782](https://issues.apache.org/jira/browse/SPARK-782) and #232). This patch updates Spark to use a shaded version of ASM 5.0.4 that was published by the Apache XBean project; the POM used to create the shaded artifact can be found at https://github.com/apache/geronimo-xbean/blob/xbean-4.4/xbean-asm5-shaded/pom.xml.

http://movingfulcrum.tumblr.com/post/80826553604/asm-framework-50-the-missing-migration-guide was a useful resource while upgrading the code to use the new ASM5 opcodes.

I also added a new regression tests in the `java8-tests` subproject; the existing tests were insufficient to catch this bug, which only affected Scala 2.11 user code which was compiled targeting Java 8.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #9512 from JoshRosen/SPARK-6152.
2015-11-11 11:16:39 -08:00
Pravin Gadakh 638c51d938 [SPARK-11550][DOCS] Replace example code in mllib-optimization.md using include_example
Author: Pravin Gadakh <pravingadakh177@gmail.com>

Closes #9516 from pravingadakh/SPARK-11550.
2015-11-10 14:47:04 -08:00
Xusen Yin a81f47ff74 [SPARK-11382] Replace example code in mllib-decision-tree.md using include_example
https://issues.apache.org/jira/browse/SPARK-11382

B.T.W. I fix an error in naive_bayes_example.py.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9596 from yinxusen/SPARK-11382.
2015-11-10 10:05:53 -08:00
gatorsmile 2f38378856 [SPARK-11360][DOC] Loss of nullability when writing parquet files
This fix is to add one line to explain the current behavior of Spark SQL when writing Parquet files. All columns are forced to be nullable for compatibility reasons.

Author: gatorsmile <gatorsmile@gmail.com>

Closes #9314 from gatorsmile/lossNull.
2015-11-09 16:06:48 -08:00
Rishabh Bhardwaj b7720fa455 [SPARK-11548][DOCS] Replaced example code in mllib-collaborative-filtering.md using include_example
Kindly review the changes.

Author: Rishabh Bhardwaj <rbnext29@gmail.com>

Closes #9519 from rishabhbhardwaj/SPARK-11337.
2015-11-09 14:27:36 -08:00
sachin aggarwal 51d41e4b1a [SPARK-11552][DOCS][Replaced example code in ml-decision-tree.md using include_example]
I have tested it on my local, it is working fine, please review

Author: sachin aggarwal <different.sachin@gmail.com>

Closes #9539 from agsachin/SPARK-11552-real.
2015-11-09 14:25:42 -08:00
Bharat Lal 860ea0d386 [SPARK-11581][DOCS] Example mllib code in documentation incorrectly computes MSE
Author: Bharat Lal <bharat.iisc@gmail.com>

Closes #9560 from bharatl/SPARK-11581.
2015-11-09 11:33:01 -08:00
chriskang90 874cd66d4b [DOCS] Fix typo for Python section on unifying Kafka streams
1) kafkaStreams is a list.  The list should be unpacked when passing it into the streaming context union method, which accepts a variable number of streams.
2) print() should be pprint() for pyspark.

This contribution is my original work, and I license the work to the project under the project's open source license.

Author: chriskang90 <jckang@uchicago.edu>

Closes #9545 from c-kang/streaming_python_typo.
2015-11-09 19:39:22 +01:00
Yanbo Liang d50a66cc04 [SPARK-10689][ML][DOC] User guide and example code for AFTSurvivalRegression
Add user guide and example code for ```AFTSurvivalRegression```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9491 from yanboliang/spark-10689.
2015-11-09 08:57:29 -08:00
Rohit Agarwal b541b31630 [DOC][MINOR][SQL] Fix internal link
It doesn't show up as a hyperlink currently. It will show up as a hyperlink after this change.

Author: Rohit Agarwal <mindprince@gmail.com>

Closes #9544 from mindprince/patch-2.
2015-11-09 13:28:00 +01:00
xin Wu 26739059bc [SPARK-10046][SQL] Hive warehouse dir not set in current directory when not …
Doc change to align with HiveConf default in terms of where to create `warehouse` directory.

Author: xin Wu <xinwu@us.ibm.com>

Closes #9365 from xwu0226/spark-10046-commit.
2015-11-08 12:28:19 -08:00
Rohit Agarwal 5c4e6d7ec9 [DOC][SQL] Remove redundant out-of-place python snippet
This snippet seems to be mistakenly introduced at two places in #5348.

Author: Rohit Agarwal <mindprince@gmail.com>

Closes #9540 from mindprince/patch-1.
2015-11-08 14:24:26 +00:00
Sean Owen d981902101 [SPARK-11476][DOCS] Incorrect function referred to in MLib Random data generation documentation
Fix Python example to use normalRDD as advertised

Author: Sean Owen <sowen@cloudera.com>

Closes #9529 from srowen/SPARK-11476.
2015-11-08 11:15:58 +00:00
Yanbo Liang 72634f27e3 [MINOR][ML][DOC] Rename weights to coefficients in user guide
We should use ```coefficients``` rather than ```weights``` in user guide that freshman can get the right conventional name at the outset. mengxr vectorijk

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9493 from yanboliang/docs-coefficients.
2015-11-05 08:59:06 -08:00
Josh Rosen ce5e6a2849 [SPARK-11491] Update build to use Scala 2.10.5
Spark should build against Scala 2.10.5, since that includes a fix for Scaladoc that will fix doc snapshot publishing: https://issues.scala-lang.org/browse/SI-8479

Author: Josh Rosen <joshrosen@databricks.com>

Closes #9450 from JoshRosen/upgrade-to-scala-2.10.5.
2015-11-04 16:58:38 -08:00
Wenchen Fan e0fc9c7e59 [SPARK-11197][SQL] add doc for run SQL on files directly
Author: Wenchen Fan <wenchen@databricks.com>

Closes #9467 from cloud-fan/doc.
2015-11-04 09:33:30 -08:00
Xusen Yin 9b214cea89 [SPARK-11443] Reserve space lines
The trim_codeblock(lines) function in include_example.rb removes some blank lines in the code.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9400 from yinxusen/SPARK-11443.
2015-11-04 08:36:55 -08:00
Pravin Gadakh 820064e613 [SPARK-11380][DOCS] Replace example code in mllib-frequent-pattern-mining.md using include_example
Author: Pravin Gadakh <pravingadakh177@gmail.com>
Author: Pravin Gadakh <prgadakh@in.ibm.com>

Closes #9340 from pravingadakh/SPARK-11380.
2015-11-04 08:32:08 -08:00
lewuathe d648a4ad54 [DOC] Missing link to R DataFrame API doc
Author: lewuathe <lewuathe@me.com>
Author: Lewuathe <lewuathe@me.com>

Closes #9394 from Lewuathe/missing-link-to-R-dataframe.
2015-11-03 16:38:22 -08:00
felixcheung a9676cc710 [SPARK-11407][SPARKR] Add doc for running from RStudio
![image](https://cloud.githubusercontent.com/assets/8969467/10871746/612ba44a-80a4-11e5-99a0-40b9931dee52.png)
(This is without css, but you get the idea)
shivaram

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #9401 from felixcheung/rstudioprogrammingguide.
2015-11-03 11:53:10 -08:00
Rishabh Bhardwaj 2804674a7a [SPARK-11383][DOCS] Replaced example code in mllib-naive-bayes.md/mllib-isotonic-regression.md using include_example
I have made the required changes in mllib-naive-bayes.md/mllib-isotonic-regression.md and also verified them.
Kindle Review it.

Author: Rishabh Bhardwaj <rbnext29@gmail.com>

Closes #9353 from rishabhbhardwaj/SPARK-11383.
2015-11-02 14:03:50 -08:00
Sean Owen 643c49c75e [SPARK-11305][DOCS] Remove Third-Party Hadoop Distributions Doc Page
Remove Hadoop third party distro page, and move Hadoop cluster config info to configuration page

CC pwendell

Author: Sean Owen <sowen@cloudera.com>

Closes #9298 from srowen/SPARK-11305.
2015-11-01 12:25:49 +00:00
felixcheung bb5a2af034 [SPARK-11340][SPARKR] Support setting driver properties when starting Spark from R programmatically or from RStudio
Mapping spark.driver.memory from sparkEnvir to spark-submit commandline arguments.

shivaram suggested that we possibly add other spark.driver.* properties - do we want to add all of those? I thought those could be set in SparkConf?
sun-rui

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #9290 from felixcheung/rdrivermem.
2015-10-30 13:51:32 -07:00
tedyu f304f9c9a1 [SPARK-11318] Include hive profile in make-distribution.sh command
Author: tedyu <yuzhihong@gmail.com>

Closes #9281 from tedyu/master.
2015-10-29 15:02:13 +01:00
Mageswaran.D fd9e345cee Typo in mllib-evaluation-metrics.md
Recall by threshold snippet was using "precisionByThreshold"

Author: Mageswaran.D <mageswaran1989@gmail.com>

Closes #9333 from Mageswaran1989/Typo_in_mllib-evaluation-metrics.md.
2015-10-28 08:46:30 -07:00
Xusen Yin d77d198fcc [SPARK-11297] Add new code tags
mengxr https://issues.apache.org/jira/browse/SPARK-11297

Add new code tags to hold the same look and feel with previous documents.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9265 from yinxusen/SPARK-11297.
2015-10-26 23:53:41 -07:00
Xusen Yin 943d4fa204 [SPARK-11289][DOC] Substitute code examples in ML features extractors with include_example
mengxr https://issues.apache.org/jira/browse/SPARK-11289

I make some changes in ML feature extractors. I.e. TF-IDF, Word2Vec, and CountVectorizer. I add new example code in spark/examples, hope it is the right place to add those examples.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9266 from yinxusen/SPARK-11289.
2015-10-26 21:17:53 -07:00
Josh Rosen b67dc6a434 [SPARK-11299][DOC] Fix link to Scala DataFrame Functions reference
The SQL programming guide's link to the DataFrame functions reference points to the wrong location; this patch fixes that.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #9269 from JoshRosen/SPARK-11299.
2015-10-25 10:31:44 +01:00
Sun Rui 2462dbcce8 [SPARK-10971][SPARKR] RRunner should allow setting path to Rscript.
Add a new spark conf option "spark.sparkr.r.driver.command" to specify the executable for an R script in client modes.

The existing spark conf option "spark.sparkr.r.command" is used to specify the executable for an R script in cluster modes for both driver and workers. See also [launch R worker script](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/api/r/RRDD.scala#L395).

BTW, [envrionment variable "SPARKR_DRIVER_R"](https://github.com/apache/spark/blob/master/launcher/src/main/java/org/apache/spark/launcher/SparkSubmitCommandBuilder.java#L275) is used to locate R shell on the local host.

For your information, PYSPARK has two environment variables serving simliar purpose:
PYSPARK_PYTHON	      Python binary executable to use for PySpark in both driver and workers (default is `python`).
PYSPARK_DRIVER_PYTHON	Python binary executable to use for PySpark in driver only (default is PYSPARK_PYTHON).
pySpark use the code [here](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/deploy/PythonRunner.scala#L41) to determine the python executable for a python script.

Author: Sun Rui <rui.sun@intel.com>

Closes #9179 from sun-rui/SPARK-10971.
2015-10-23 21:38:04 -07:00
Xusen Yin 03ccb22080 [SPARK-10382] Make example code in user guide testable
A POC code for making example code in user guide testable.

mengxr We still need to talk about the labels in code.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9109 from yinxusen/SPARK-10382.
2015-10-23 08:31:01 -07:00
Rohan Bhanderi 16dc9f344c Fix typo "Received" to "Receiver" in streaming-kafka-integration.md
Removed typo on line 8 in markdown : "Received" -> "Receiver"

Author: Rohan Bhanderi <rohan.bhanderi@sjsu.edu>

Closes #9242 from RohanBhanderi/patch-1.
2015-10-23 01:10:46 -07:00
Josh Rosen f6d06adf05 [SPARK-10708] Consolidate sort shuffle implementations
There's a lot of duplication between SortShuffleManager and UnsafeShuffleManager. Given that these now provide the same set of functionality, now that UnsafeShuffleManager supports large records, I think that we should replace SortShuffleManager's serialized shuffle implementation with UnsafeShuffleManager's and should merge the two managers together.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #8829 from JoshRosen/consolidate-sort-shuffle-implementations.
2015-10-22 09:46:30 -07:00
vundela 2f6dd634c1 [SPARK-11105] [YARN] Distribute log4j.properties to executors
Currently log4j.properties file is not uploaded to executor's which is leading them to use the default values. This fix will make sure that file is always uploaded to distributed cache so that executor will use the latest settings.

If user specifies log configurations through --files then executors will be picking configs from --files instead of $SPARK_CONF_DIR/log4j.properties

Author: vundela <vsr@cloudera.com>
Author: Srinivasa Reddy Vundela <vsr@cloudera.com>

Closes #9118 from vundela/master.
2015-10-20 11:12:28 -07:00
Lukasz Piepiora a112d69fdc [SPARK-11174] [DOCS] Fix typo in the GraphX programming guide
This patch fixes a small typo in the GraphX programming guide

Author: Lukasz Piepiora <lpiepiora@gmail.com>

Closes #9160 from lpiepiora/11174-fix-typo-in-graphx-programming-guide.
2015-10-18 14:25:57 +01:00
Britta Weber 723aa75a9d fix typo bellow -> below
Author: Britta Weber <britta.weber@elasticsearch.com>

Closes #9136 from brwe/typo-bellow.
2015-10-15 14:47:11 -07:00
Nick Pritchard b591de7c07 [SPARK-11039][Documentation][Web UI] Document additional ui configurations
Add documentation for configuration:
- spark.sql.ui.retainedExecutions
- spark.streaming.ui.retainedBatches

Author: Nick Pritchard <nicholas.pritchard@falkonry.com>

Closes #9052 from pnpritchard/SPARK-11039.
2015-10-15 12:45:37 -07:00
Andrew Or b3ffac5178 [SPARK-10983] Unified memory manager
This patch unifies the memory management of the storage and execution regions such that either side can borrow memory from each other. When memory pressure arises, storage will be evicted in favor of execution. To avoid regressions in cases where storage is crucial, we dynamically allocate a fraction of space for storage that execution cannot evict. Several configurations are introduced:

- **spark.memory.fraction (default 0.75)**: ​fraction of the heap space used for execution and storage. The lower this is, the more frequently spills and cached data eviction occur. The purpose of this config is to set aside memory for internal metadata, user data structures, and imprecise size estimation in the case of sparse, unusually large records.

- **spark.memory.storageFraction (default 0.5)**: size of the storage region within the space set aside by `s​park.memory.fraction`. ​Cached data may only be evicted if total storage exceeds this region.

- **spark.memory.useLegacyMode (default false)**: whether to use the memory management that existed in Spark 1.5 and before. This is mainly for backward compatibility.

For a detailed description of the design, see [SPARK-10000](https://issues.apache.org/jira/browse/SPARK-10000). This patch builds on top of the `MemoryManager` interface introduced in #9000.

Author: Andrew Or <andrew@databricks.com>

Closes #9084 from andrewor14/unified-memory-manager.
2015-10-13 13:49:59 -07:00
jerryshao f97e9323b5 [SPARK-10739] [YARN] Add application attempt window for Spark on Yarn
Add application attempt window for Spark on Yarn to ignore old out of window failures, this is useful for long running applications to recover from failures.

Author: jerryshao <sshao@hortonworks.com>

Closes #8857 from jerryshao/SPARK-10739 and squashes the following commits:

36eabdc [jerryshao] change the doc
7f9b77d [jerryshao] Style change
1c9afd0 [jerryshao] Address the comments
caca695 [jerryshao] Add application attempt window for Spark on Yarn
2015-10-12 18:18:19 -07:00
Kay Ousterhout 091c2c3ecd [SPARK-11056] Improve documentation of SBT build.
This commit improves the documentation around building Spark to
(1) recommend using SBT interactive mode to avoid the overhead of
launching SBT and (2) refer to the wiki page that documents using
SPARK_PREPEND_CLASSES to avoid creating the assembly jar for each
compile.

cc srowen

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #9068 from kayousterhout/SPARK-11056.
2015-10-12 14:23:29 -07:00
Jean-Baptiste Onofré 60150cf00a [SPARK-10883] Add a note about how to build Spark sub-modules (reactor)
Author: Jean-Baptiste Onofré <jbonofre@apache.org>

Closes #8993 from jbonofre/SPARK-10883-2.
2015-10-08 11:38:39 +01:00
admackin cd28139c9b Akka framesize units should be specified
1.4 docs noted that the units were MB - i have assumed this is still the case

Author: admackin <admackin@users.noreply.github.com>

Closes #9025 from admackin/master.
2015-10-08 00:01:23 -07:00
Xin Ren 27cdde2ff8 [SPARK-10669] [DOCS] Link to each language's API in codetabs in ML docs: spark.mllib
In the Markdown docs for the spark.mllib Programming Guide, we have code examples with codetabs for each language. We should link to each language's API docs within the corresponding codetab, but we are inconsistent about this. For an example of what we want to do, see the "ChiSqSelector" section in 64743870f2/docs/mllib-feature-extraction.md
This JIRA is just for spark.mllib, not spark.ml.

Please let me know if more work is needed, thanks a lot.

Author: Xin Ren <iamshrek@126.com>

Closes #8977 from keypointt/SPARK-10669.
2015-10-07 15:00:19 +01:00