Commit graph

10659 commits

Author SHA1 Message Date
Marcelo Vanzin 5d45e1f600 [SPARK-3090] [CORE] Stop SparkContext if user forgets to.
Set up a shutdown hook to try to stop the Spark context in
case the user forgets to do it. The main effect is that any
open logs files are flushed and closed, which is particularly
interesting for event logs.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5696 from vanzin/SPARK-3090 and squashes the following commits:

3b554b5 [Marcelo Vanzin] [SPARK-3090] [core] Stop SparkContext if user forgets to.
2015-04-27 19:46:17 -04:00
Hong Shen 8e1c00dbf4 [SPARK-6738] [CORE] Improve estimate the size of a large array
Currently, SizeEstimator.visitArray is not correct in the follow case,
```
array size > 200,
elem has the share object
```

when I add a debug log in SizeTracker.scala:
```
 System.err.println(s"numUpdates:$numUpdates, size:$ts, bytesPerUpdate:$bytesPerUpdate, cost time:$b")
```
I get the following log:
```
 numUpdates:1, size:262448, bytesPerUpdate:0.0, cost time:35
 numUpdates:2, size:420698, bytesPerUpdate:158250.0, cost time:35
 numUpdates:4, size:420754, bytesPerUpdate:28.0, cost time:32
 numUpdates:7, size:420754, bytesPerUpdate:0.0, cost time:27
 numUpdates:12, size:420754, bytesPerUpdate:0.0, cost time:28
 numUpdates:20, size:420754, bytesPerUpdate:0.0, cost time:25
 numUpdates:32, size:420754, bytesPerUpdate:0.0, cost time:21
 numUpdates:52, size:420754, bytesPerUpdate:0.0, cost time:20
 numUpdates:84, size:420754, bytesPerUpdate:0.0, cost time:20
 numUpdates:135, size:420754, bytesPerUpdate:0.0, cost time:20
 numUpdates:216, size:420754, bytesPerUpdate:0.0, cost time:11
 numUpdates:346, size:420754, bytesPerUpdate:0.0, cost time:6
 numUpdates:554, size:488911, bytesPerUpdate:327.67788461538464, cost time:8
 numUpdates:887, size:2312259426, bytesPerUpdate:6942253.798798799, cost time:198
15/04/21 14:27:26 INFO collection.ExternalAppendOnlyMap: Thread 51 spilling in-memory map of 3.0 GB to disk (1 time so far)
15/04/21 14:27:26 INFO collection.ExternalAppendOnlyMap: /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc
```
But in fact the file size is only 162K:
```
$ ll -h /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc
-rw-r----- 1 spark users 162K Apr 21 14:27 /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc
```

In order to test case, I change visitArray to:
```
       var size = 0l
         for (i <- 0 until length) {
          val obj = JArray.get(array, i)
          size += SizeEstimator.estimate(obj, state.visited).toLong
        }
       state.size += size
```
I get the following log:
```
...
14895 277016088 566.9046118590662 time:8470
23832 281840544 552.3308270676691 time:8031
38132 289891824 539.8294729775092 time:7897
61012 302803640 563.0265734265735 time:13044
97620 322904416 564.3276223776223 time:13554
15/04/14 11:46:43 INFO collection.ExternalAppendOnlyMap: Thread 51 spilling in-memory map of 314.5 MB to disk (1 time so far)
15/04/14 11:46:43 INFO collection.ExternalAppendOnlyMap: /data1/yarnenv/local/usercache/spark/appcache/application_1426746631567_8477/spark-local-20150414114020-2fcb/14/temp_local_5b6b98d5-5bfa-47e2-8216-059482ccbda0
```
 the file size is 85M.
```
$ ll -h /data1/yarnenv/local/usercache/spark/appcache/application_1426746631567_8477/spark- local-20150414114020-2fcb/14/
total 85M
-rw-r----- 1 spark users 85M Apr 14 11:46 temp_local_5b6b98d5-5bfa-47e2-8216-059482ccbda0
```

The following log is when I use this patch,
```
....
numUpdates:32, size:365484, bytesPerUpdate:0.0, cost time:7
numUpdates:52, size:365484, bytesPerUpdate:0.0, cost time:5
numUpdates:84, size:365484, bytesPerUpdate:0.0, cost time:5
numUpdates:135, size:372208, bytesPerUpdate:131.84313725490196, cost time:86
numUpdates:216, size:379020, bytesPerUpdate:84.09876543209876, cost time:21
numUpdates:346, size:1865208, bytesPerUpdate:11432.215384615385, cost time:23
numUpdates:554, size:2052380, bytesPerUpdate:899.8653846153846, cost time:16
numUpdates:887, size:2142820, bytesPerUpdate:271.59159159159157, cost time:15
..
numUpdates:14895, size:251675500, bytesPerUpdate:438.5263157894737, cost time:13
numUpdates:23832, size:257010268, bytesPerUpdate:596.9305135951662, cost time:14
numUpdates:38132, size:263922396, bytesPerUpdate:483.3655944055944, cost time:15
numUpdates:61012, size:268962596, bytesPerUpdate:220.28846153846155, cost time:24
numUpdates:97620, size:286980644, bytesPerUpdate:492.1888111888112, cost time:22
15/04/21 14:45:12 INFO collection.ExternalAppendOnlyMap: Thread 53 spilling in-memory map of 328.7 MB to disk (1 time so far)
15/04/21 14:45:12 INFO collection.ExternalAppendOnlyMap: /data4/yarnenv/local/usercache/spark/appcache/application_1426746631567_11758/spark-local-20150421144456-a2a5/2a/temp_local_9c109510-af16-4468-8f23-48cad04da88f
```
 the file size is 88M.
```
$ ll -h /data4/yarnenv/local/usercache/spark/appcache/application_1426746631567_11758/spark-local-20150421144456-a2a5/2a/
total 88M
-rw-r----- 1 spark users 88M Apr 21 14:45 temp_local_9c109510-af16-4468-8f23-48cad04da88f
```

Author: Hong Shen <hongshen@tencent.com>

Closes #5608 from shenh062326/my_change5 and squashes the following commits:

5506bae [Hong Shen] Fix compile error
c275dd3 [Hong Shen] Alter code style
fe202a2 [Hong Shen] Change the code style and add documentation.
a9fca84 [Hong Shen] Add test case for SizeEstimator
4877eee [Hong Shen] Improve estimate the size of a large array
a2ea7ac [Hong Shen] Alter code style
4c28e36 [Hong Shen] Improve estimate the size of a large array
2015-04-27 18:59:45 -04:00
Steven She b9de9e040a [SPARK-7103] Fix crash with SparkContext.union when RDD has no partitioner
Added a check to the SparkContext.union method to check that a partitioner is defined on all RDDs when instantiating a PartitionerAwareUnionRDD.

Author: Steven She <steven@canopylabs.com>

Closes #5679 from stevencanopy/SPARK-7103 and squashes the following commits:

5a3d846 [Steven She] SPARK-7103: Fix crash with SparkContext.union when at least one RDD has no partitioner
2015-04-27 18:55:02 -04:00
hlin09 ca9f4ebb8e [SPARK-6991] [SPARKR] Adds support for zipPartitions.
Author: hlin09 <hlin09pu@gmail.com>

Closes #5568 from hlin09/zipPartitions and squashes the following commits:

12c08a5 [hlin09] Fix comments
d2d32db [hlin09] Merge branch 'master' into zipPartitions
ec56d2f [hlin09] Fix test.
27655d3 [hlin09] Adds support for zipPartitions.
2015-04-27 15:04:37 -07:00
tedyu ef82bddc11 SPARK-7107 Add parameter for zookeeper.znode.parent to hbase_inputformat...
....py

Author: tedyu <yuzhihong@gmail.com>

Closes #5673 from tedyu/master and squashes the following commits:

ab7c72b [tedyu] SPARK-7107 Adjust indentation to pass Python style tests
6e25939 [tedyu] Adjust line length to be shorter than 100 characters
18d172a [tedyu] SPARK-7107 Add parameter for zookeeper.znode.parent to hbase_inputformat.py
2015-04-27 14:42:40 -07:00
Jeff Harrison 7078f6028b [SPARK-6856] [R] Make RDD information more useful in SparkR
Author: Jeff Harrison <jeffrharrison@gmail.com>

Closes #5667 from His-name-is-Joof/joofspark and squashes the following commits:

f8814a6 [Jeff Harrison] newline added after RDD show() output
4d9d972 [Jeff Harrison] Merge branch 'master' into joofspark
9d2295e [Jeff Harrison] parallelize with 1:10
878b830 [Jeff Harrison] Merge branch 'master' into joofspark
c8c0b80 [Jeff Harrison] add test for RDD function show()
123be65 [Jeff Harrison] SPARK-6856
2015-04-27 13:38:25 -07:00
Misha Chernetsov 998aac21f0 [SPARK-4925] Publish Spark SQL hive-thriftserver maven artifact
turned on hive-thriftserver profile in release script

Author: Misha Chernetsov <chernetsov@gmail.com>

Closes #5429 from chernetsov/master and squashes the following commits:

9cc36af [Misha Chernetsov] [SPARK-4925] Publish Spark SQL hive-thriftserver maven artifact turned on hive-thriftserver profile in release script for scala 2.10
2015-04-27 11:27:56 -07:00
baishuo 82bb7fd41a [SPARK-6505] [SQL] Remove the reflection call in HiveFunctionWrapper
according liancheng‘s  comment in https://issues.apache.org/jira/browse/SPARK-6505,  this patch remove the  reflection call in HiveFunctionWrapper, and implement the functions named "deserializeObjectByKryo" and "serializeObjectByKryo" according the functions with the save name in
org.apache.hadoop.hive.ql.exec.Utilities.java

Author: baishuo <vc_java@hotmail.com>

Closes #5660 from baishuo/SPARK-6505-20150423 and squashes the following commits:

ae61ec4 [baishuo] modify code style
78d9fa3 [baishuo] modify code style
0b522a7 [baishuo] modify code style
a5ff9c7 [baishuo] Remove the reflection call in HiveFunctionWrapper
2015-04-27 14:08:05 +08:00
wangfei d188b8bad8 [SQL][Minor] rename DataTypeParser.apply to DataTypeParser.parse
rename DataTypeParser.apply to DataTypeParser.parse to make it more clear and readable.
/cc rxin

Author: wangfei <wangfei1@huawei.com>

Closes #5710 from scwf/apply and squashes the following commits:

c319977 [wangfei] rename apply to parse
2015-04-26 21:08:47 -07:00
Reynold Xin ca55dc95b7 [SPARK-7152][SQL] Add a Column expression for partition ID.
Author: Reynold Xin <rxin@databricks.com>

Closes #5705 from rxin/df-pid and squashes the following commits:

401018f [Reynold Xin] [SPARK-7152][SQL] Add a Column expression for partition ID.
2015-04-26 11:46:58 -07:00
Alain 9a5bbe05fc [MINOR] [MLLIB] Refactor toString method in MLLIB
1. predict(predict.toString) has already output prefix “predict” thus it’s duplicated to print ", predict = " again
2. there are some extra spaces

Author: Alain <aihe@usc.edu>

Closes #5687 from AiHe/tree-node-issue-2 and squashes the following commits:

9862b9a [Alain] Pass scala coding style checking
44ba947 [Alain] Minor][MLLIB] Format toString method in MLLIB
bdc402f [Alain] [Minor][MLLIB] Fix a formatting bug in toString method in Node
426eee7 [Alain] [Minor][MLLIB] Fix a formatting bug in toString method in Node.scala
2015-04-26 07:14:24 -04:00
Nishkam Ravi f5473c2bbf [SPARK-6014] [CORE] [HOTFIX] Add try-catch block around ShutDownHook
Add a try/catch block around removeShutDownHook else IllegalStateException thrown in YARN cluster mode (see https://github.com/apache/spark/pull/4690)

cc andrewor14, srowen

Author: Nishkam Ravi <nravi@cloudera.com>
Author: nishkamravi2 <nishkamravi@gmail.com>
Author: nravi <nravi@c1704.halxg.cloudera.com>

Closes #5672 from nishkamravi2/master_nravi and squashes the following commits:

0f1abd0 [nishkamravi2] Update Utils.scala
474e3bf [nishkamravi2] Update DiskBlockManager.scala
97c383e [nishkamravi2] Update Utils.scala
8691e0c [Nishkam Ravi] Add a try/catch block around Utils.removeShutdownHook
2be1e76 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
1c13b79 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
bad4349 [nishkamravi2] Update Main.java
36a6f87 [Nishkam Ravi] Minor changes and bug fixes
b7f4ae7 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
4a45d6a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
458af39 [Nishkam Ravi] Locate the jar using getLocation, obviates the need to pass assembly path as an argument
d9658d6 [Nishkam Ravi] Changes for SPARK-6406
ccdc334 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
3faa7a4 [Nishkam Ravi] Launcher library changes (SPARK-6406)
345206a [Nishkam Ravi] spark-class merge Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi
ac58975 [Nishkam Ravi] spark-class changes
06bfeb0 [nishkamravi2] Update spark-class
35af990 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
32c3ab3 [nishkamravi2] Update AbstractCommandBuilder.java
4bd4489 [nishkamravi2] Update AbstractCommandBuilder.java
746f35b [Nishkam Ravi] "hadoop" string in the assembly name should not be mandatory (everywhere else in spark we mandate spark-assembly*hadoop*.jar)
bfe96e0 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
ee902fa [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
d453197 [nishkamravi2] Update NewHadoopRDD.scala
6f41a1d [nishkamravi2] Update NewHadoopRDD.scala
0ce2c32 [nishkamravi2] Update HadoopRDD.scala
f7e33c2 [Nishkam Ravi] Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi
ba1eb8b [Nishkam Ravi] Try-catch block around the two occurrences of removeShutDownHook. Deletion of semi-redundant occurrences of expensive operation inShutDown.
71d0e17 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
494d8c0 [nishkamravi2] Update DiskBlockManager.scala
3c5ddba [nishkamravi2] Update DiskBlockManager.scala
f0d12de [Nishkam Ravi] Workaround for IllegalStateException caused by recent changes to BlockManager.stop
79ea8b4 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
b446edc [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
5c9a4cb [nishkamravi2] Update TaskSetManagerSuite.scala
535295a [nishkamravi2] Update TaskSetManager.scala
3e1b616 [Nishkam Ravi] Modify test for maxResultSize
9f6583e [Nishkam Ravi] Changes to maxResultSize code (improve error message and add condition to check if maxResultSize > 0)
5f8f9ed [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
636a9ff [nishkamravi2] Update YarnAllocator.scala
8f76c8b [Nishkam Ravi] Doc change for yarn memory overhead
35daa64 [Nishkam Ravi] Slight change in the doc for yarn memory overhead
5ac2ec1 [Nishkam Ravi] Remove out
dac1047 [Nishkam Ravi] Additional documentation for yarn memory overhead issue
42c2c3d [Nishkam Ravi] Additional changes for yarn memory overhead issue
362da5e [Nishkam Ravi] Additional changes for yarn memory overhead
c726bd9 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
f00fa31 [Nishkam Ravi] Improving logging for AM memoryOverhead
1cf2d1e [nishkamravi2] Update YarnAllocator.scala
ebcde10 [Nishkam Ravi] Modify default YARN memory_overhead-- from an additive constant to a multiplier (redone to resolve merge conflicts)
2e69f11 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
efd688a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark
2b630f9 [nravi] Accept memory input as "30g", "512M" instead of an int value, to be consistent with rest of Spark
3bf8fad [nravi] Merge branch 'master' of https://github.com/apache/spark
5423a03 [nravi] Merge branch 'master' of https://github.com/apache/spark
eb663ca [nravi] Merge branch 'master' of https://github.com/apache/spark
df2aeb1 [nravi] Improved fix for ConcurrentModificationIssue (Spark-1097, Hadoop-10456)
6b840f0 [nravi] Undo the fix for SPARK-1758 (the problem is fixed)
5108700 [nravi] Fix in Spark for the Concurrent thread modification issue (SPARK-1097, HADOOP-10456)
681b36f [nravi] Fix for SPARK-1758: failing test org.apache.spark.JavaAPISuite.wholeTextFiles
2015-04-25 20:02:23 -04:00
Prashant Sharma a11c8683c7 [SPARK-7092] Update spark scala version to 2.11.6
Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #5662 from ScrapCodes/SPARK-7092/scala-update-2.11.6 and squashes the following commits:

58cf4f9 [Prashant Sharma] [SPARK-7092] Update spark scala version to 2.11.6
2015-04-25 18:07:34 -04:00
Yin Huai aa6966ff34 [SQL] Update SQL readme to include instructions on generating golden answer files based on Hive 0.13.1.
Author: Yin Huai <yhuai@databricks.com>

Closes #5702 from yhuai/howToGenerateGoldenFiles and squashes the following commits:

9c4a7f8 [Yin Huai] Update readme to include instructions on generating golden answer files based on Hive 0.13.1.
2015-04-25 13:43:39 -07:00
Joseph K. Bradley a7160c4e3a [SPARK-6113] [ML] Tree ensembles for Pipelines API
This is a continuation of [https://github.com/apache/spark/pull/5530] (which was for Decision Trees), but for ensembles: Random Forests and Gradient-Boosted Trees.  Please refer to the JIRA [https://issues.apache.org/jira/browse/SPARK-6113], the design doc linked from the JIRA, and the previous PR linked above for design discussions.

This PR follows the example set by the previous PR for Decision Trees.  It includes a few cleanups to Decision Trees.

Note: There is one issue which will be addressed in a separate PR: Ensembles' component Models have no parent or fittingParamMap.  I plan to submit a separate PR which makes those values in Model be Options.  It does not matter much which PR gets merged first.

CC: mengxr manishamde codedeft chouqin

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #5626 from jkbradley/dt-api-ensembles and squashes the following commits:

729167a [Joseph K. Bradley] small cleanups based on code review
bbae2a2 [Joseph K. Bradley] Updated per all comments in code review
855aa9a [Joseph K. Bradley] scala style fix
ea3d901 [Joseph K. Bradley] Added GBT to spark.ml, with tests and examples
c0f30c1 [Joseph K. Bradley] Added random forests and test suites to spark.ml.  Not tested yet.  Need to add example as well
d045ebd [Joseph K. Bradley] some more updates, but far from done
ee1a10b [Joseph K. Bradley] Added files from old PR and did some initial updates.
2015-04-25 12:27:19 -07:00
Patrick Wendell a61d65fc8b Revert "[SPARK-6752][Streaming] Allow StreamingContext to be recreated from checkpoint and existing SparkContext"
This reverts commit 534f2a4362.
2015-04-25 10:37:34 -07:00
KeheCAI cca9905b93 update the deprecated CountMinSketchMonoid function to TopPctCMS function
http://twitter.github.io/algebird/index.html#com.twitter.algebird.legacy.CountMinSketchMonoid$
The CountMinSketchMonoid has been deprecated since 0.8.1. Newer code should use TopPctCMS.monoid().

![image](https://cloud.githubusercontent.com/assets/1327396/7269619/d8b48b92-e8d5-11e4-8902-087f630e6308.png)

Author: KeheCAI <caikehe@gmail.com>

Closes #5629 from caikehe/master and squashes the following commits:

e8aa06f [KeheCAI] update algebird-core to version 0.9.0 from 0.8.1
5653351 [KeheCAI] change scala code style
4c0dfd1 [KeheCAI] update the deprecated CountMinSketchMonoid function to TopPctCMS function
2015-04-25 08:42:38 -04:00
Deborah Siegel 59b7cfc41b [SPARK-7136][Docs] Spark SQL and DataFrame Guide fix example file and paths
Changes example file for Generic Load/Save Functions to users.parquet rather than people.parquet which doesn't exist unless a later example has already been executed. Also adds filepaths.

Author: Deborah Siegel <deborah.siegel@gmail.com>
Author: DEBORAH SIEGEL <deborahsiegel@d-140-142-0-49.dhcp4.washington.edu>
Author: DEBORAH SIEGEL <deborahsiegel@DEBORAHs-MacBook-Pro.local>
Author: DEBORAH SIEGEL <deborahsiegel@d-69-91-154-197.dhcp4.washington.edu>

Closes #5693 from d3borah/master and squashes the following commits:

4d5e43b [Deborah Siegel] sparkSQL doc change
b15a497 [Deborah Siegel] Revert "sparkSQL doc change"
5a2863c [DEBORAH SIEGEL] Merge remote-tracking branch 'upstream/master'
91972fc [DEBORAH SIEGEL] sparkSQL doc change
f000e59 [DEBORAH SIEGEL] Merge remote-tracking branch 'upstream/master'
db54173 [DEBORAH SIEGEL] fixed aggregateMessages example in graphX doc
2015-04-24 20:25:07 -07:00
linweizhong d874f8b546 [PySpark][Minor] Update sql example, so that can read file correctly
To run Spark, default will read file from HDFS if we don't set the schema.

Author: linweizhong <linweizhong@huawei.com>

Closes #5684 from Sephiroth-Lin/pyspark_example_minor and squashes the following commits:

19fe145 [linweizhong] Update example sql.py, so that can read file correctly
2015-04-24 20:23:19 -07:00
Calvin Jia 438859eb7c [SPARK-6122] [CORE] Upgrade tachyon-client version to 0.6.3
This is a reopening of #4867.
A short summary of the issues resolved from the previous PR:

1. HTTPClient version mismatch: Selenium (used for UI tests) requires version 4.3.x, and Tachyon included 4.2.5 through a transitive dependency of its shaded thrift jar. To address this, Tachyon 0.6.3 will promote the transitive dependencies of the shaded jar so they can be excluded in spark.

2. Jackson-Mapper-ASL version mismatch: In lower versions of hadoop-client (ie. 1.0.4), version 1.0.1 is included. The parquet library used in spark sql requires version 1.8+. Its unclear to me why upgrading tachyon-client would cause this dependency to break. The solution was to exclude jackson-mapper-asl from hadoop-client.

It seems that the dependency management in spark-parent will not work on transitive dependencies, one way to make sure jackson-mapper-asl is included with the correct version is to add it as a top level dependency. The best solution would be to exclude the dependency in the modules which require a higher version, but that did not fix the unit tests. Any suggestions on the best way to solve this would be appreciated!

Author: Calvin Jia <jia.calvin@gmail.com>

Closes #5354 from calvinjia/upgrade_tachyon_0.6.3 and squashes the following commits:

0eefe4d [Calvin Jia] Handle httpclient version in maven dependency management. Remove httpclient version setting from profiles.
7c00dfa [Calvin Jia] Set httpclient version to 4.3.2 for selenium. Specify version of httpclient for sql/hive (previously 4.2.5 transitive dependency of libthrift).
9263097 [Calvin Jia] Merge master to test latest changes
dbfc1bd [Calvin Jia] Use Tachyon 0.6.4 for cleaner dependencies.
e2ff80a [Calvin Jia] Exclude the jetty and curator promoted dependencies from tachyon-client.
a3a29da [Calvin Jia] Update tachyon-client exclusions.
0ae6c97 [Calvin Jia] Change tachyon version to 0.6.3
a204df9 [Calvin Jia] Update make distribution tachyon version.
a93c94f [Calvin Jia] Exclude jackson-mapper-asl from hadoop client since it has a lower version than spark's expected version.
a8a923c [Calvin Jia] Exclude httpcomponents from Tachyon
910fabd [Calvin Jia] Update to master
eed9230 [Calvin Jia] Update tachyon version to 0.6.1.
11907b3 [Calvin Jia] Use TachyonURI for tachyon paths instead of strings.
71bf441 [Calvin Jia] Upgrade Tachyon client version to 0.6.0.
2015-04-24 17:57:41 -04:00
Sun Rui caf0136ec5 [SPARK-6852] [SPARKR] Accept numeric as numPartitions in SparkR.
Author: Sun Rui <rui.sun@intel.com>

Closes #5613 from sun-rui/SPARK-6852 and squashes the following commits:

abaf02e [Sun Rui] Change the type of default numPartitions from integer to numeric in generics.R.
29d67c1 [Sun Rui] [SPARK-6852][SPARKR] Accept numeric as numPartitions in SparkR.
2015-04-24 12:52:07 -07:00
Sun Rui ebb77b2aff [SPARK-7033] [SPARKR] Clean usage of split. Use partition instead where applicable.
Author: Sun Rui <rui.sun@intel.com>

Closes #5628 from sun-rui/SPARK-7033 and squashes the following commits:

046bc9e [Sun Rui] Clean split usage in tests.
d531c86 [Sun Rui] [SPARK-7033][SPARKR] Clean usage of split. Use partition instead where applicable.
2015-04-24 11:00:19 -07:00
Xusen Yin 6e57d57b32 [SPARK-6528] [ML] Add IDF transformer
See [SPARK-6528](https://issues.apache.org/jira/browse/SPARK-6528). Add IDF transformer in ML package.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #5266 from yinxusen/SPARK-6528 and squashes the following commits:

741db31 [Xusen Yin] get param from new paramMap
d169967 [Xusen Yin] add final to param and IDF class
c9c3759 [Xusen Yin] simplify test suite
5867c09 [Xusen Yin] refine IDF transformer with new interfaces
7727cae [Xusen Yin] Merge branch 'master' into SPARK-6528
4338a37 [Xusen Yin] Merge branch 'master' into SPARK-6528
aef2cdf [Xusen Yin] add doc and group for param
5760b49 [Xusen Yin] fix code style
2add691 [Xusen Yin] fix code style and test
03fbecb [Xusen Yin] remove duplicated code
2aa4be0 [Xusen Yin] clean test suite
4802c67 [Xusen Yin] add IDF transformer and test suite
2015-04-24 08:29:49 -07:00
Xiangrui Meng 78b39c7e0d [SPARK-7115] [MLLIB] skip the very first 1 in poly expansion
yinxusen

Author: Xiangrui Meng <meng@databricks.com>

Closes #5681 from mengxr/SPARK-7115 and squashes the following commits:

9ac27cd [Xiangrui Meng] skip the very first 1 in poly expansion
2015-04-24 08:27:48 -07:00
Xusen Yin 8509519d8b [SPARK-5894] [ML] Add polynomial mapper
See [SPARK-5894](https://issues.apache.org/jira/browse/SPARK-5894).

Author: Xusen Yin <yinxusen@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #5245 from yinxusen/SPARK-5894 and squashes the following commits:

dc461a6 [Xusen Yin] merge polynomial expansion v2
6d0c3cc [Xusen Yin] Merge branch 'SPARK-5894' of https://github.com/mengxr/spark into mengxr-SPARK-5894
57bfdd5 [Xusen Yin] Merge branch 'master' into SPARK-5894
3d02a7d [Xusen Yin] Merge branch 'master' into SPARK-5894
a067da2 [Xiangrui Meng] a new approach for poly expansion
0789d81 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5894
4e9aed0 [Xusen Yin] fix test suite
95d8fb9 [Xusen Yin] fix sparse vector indices
8d39674 [Xusen Yin] fix sparse vector expansion error
5998dd6 [Xusen Yin] fix dense vector fillin
fa3ade3 [Xusen Yin] change the functional code into imperative one to speedup
b70e7e1 [Xusen Yin] remove useless case class
6fa236f [Xusen Yin] fix vector slice error
daff601 [Xusen Yin] fix index error of sparse vector
6bd0a10 [Xusen Yin] merge repeated features
419f8a2 [Xusen Yin] need to merge same columns
4ebf34e [Xusen Yin] add test suite of polynomial expansion
372227c [Xusen Yin] add polynomial expansion
2015-04-24 00:39:29 -07:00
Reynold Xin 4c722d77ae Fixed a typo from the previous commit. 2015-04-23 22:39:00 -07:00
Reynold Xin d3a302defc [SQL] Fixed expression data type matching.
Also took the chance to improve documentation for various types.

Author: Reynold Xin <rxin@databricks.com>

Closes #5675 from rxin/data-type-matching-expr and squashes the following commits:

0f31856 [Reynold Xin] One more function documentation.
27c1973 [Reynold Xin] Added more documentation.
336a36d [Reynold Xin] [SQL] Fixed expression data type matching.
2015-04-23 21:21:03 -07:00
Ken Geis 67bccbda1e Update sql-programming-guide.md
fix typo

Author: Ken Geis <geis.ken@gmail.com>

Closes #5674 from kgeis/patch-1 and squashes the following commits:

5ae67de [Ken Geis] Update sql-programming-guide.md
2015-04-23 20:45:33 -07:00
Yin Huai 2d010f7afe [SPARK-7060][SQL] Add alias function to python dataframe
This pr tries to provide a way to let python users workaround https://issues.apache.org/jira/browse/SPARK-6231.

Author: Yin Huai <yhuai@databricks.com>

Closes #5634 from yhuai/pythonDFAlias and squashes the following commits:

8465acd [Yin Huai] Add an alias to a Python DF.
2015-04-23 18:52:55 -07:00
Cheolsoo Park 336f7f5373 [SPARK-7037] [CORE] Inconsistent behavior for non-spark config properties in spark-shell and spark-submit
When specifying non-spark properties (i.e. names don't start with spark.) in the command line and config file, spark-submit and spark-shell behave differently, causing confusion to users.
Here is the summary-
* spark-submit
  * --conf k=v => silently ignored
  * spark-defaults.conf => applied
* spark-shell
  * --conf k=v => show a warning message and ignored
  *  spark-defaults.conf => show a warning message and ignored

I assume that ignoring non-spark properties is intentional. If so, it should always be ignored with a warning message in all cases.

Author: Cheolsoo Park <cheolsoop@netflix.com>

Closes #5617 from piaozhexiu/SPARK-7037 and squashes the following commits:

8957950 [Cheolsoo Park] Add IgnoreNonSparkProperties method
fedd01c [Cheolsoo Park] Ignore non-spark properties with a warning message in all cases
2015-04-23 20:10:55 -04:00
Sun Rui 73db132bf5 [SPARK-6818] [SPARKR] Support column deletion in SparkR DataFrame API.
Author: Sun Rui <rui.sun@intel.com>

Closes #5655 from sun-rui/SPARK-6818 and squashes the following commits:

7c66570 [Sun Rui] [SPARK-6818][SPARKR] Support column deletion in SparkR DataFrame API.
2015-04-23 16:08:14 -07:00
Reynold Xin 6220d933e5 [SQL] Break dataTypes.scala into multiple files.
It was over 1000 lines of code, making it harder to find all the types. Only moved code around, and didn't change any.

Author: Reynold Xin <rxin@databricks.com>

Closes #5670 from rxin/break-types and squashes the following commits:

8c59023 [Reynold Xin] Check in missing files.
dcd5193 [Reynold Xin] [SQL] Break dataTypes.scala into multiple files.
2015-04-23 14:48:19 -07:00
Xiangrui Meng 1ed46a60ad [SPARK-7070] [MLLIB] LDA.setBeta should call setTopicConcentration.
jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #5649 from mengxr/SPARK-7070 and squashes the following commits:

c66023c [Xiangrui Meng] setBeta should call setTopicConcentration
2015-04-23 14:46:54 -07:00
Tijo Thomas 6d0749cae3 [SPARK-7087] [BUILD] Fix path issue change version script
Author: Tijo Thomas <tijoparacka@gmail.com>

Closes #5656 from tijoparacka/FIX_PATHISSUE_CHANGE_VERSION_SCRIPT and squashes the following commits:

ab4f4b1 [Tijo Thomas] removed whitespace
24478c9 [Tijo Thomas] modified to provide the spark base dir while searching for pom and also while changing the vesrion no
7b8e10b [Tijo Thomas] Modified for providing the base directories while finding the list of pom files and also while changing the version no
2015-04-23 17:23:15 -04:00
WangTaoTheTonic baa83a9a67 [SPARK-6879] [HISTORYSERVER] check if app is completed before clean it up
https://issues.apache.org/jira/browse/SPARK-6879

Use `applications` to replace `FileStatus`, and check if the app is completed before clean it up.
If an exception was throwed, add it to `applications` to wait for the next loop.

Author: WangTaoTheTonic <wangtao111@huawei.com>

Closes #5491 from WangTaoTheTonic/SPARK-6879 and squashes the following commits:

4a533eb [WangTaoTheTonic] treat ACE specially
cb45105 [WangTaoTheTonic] rebase
d4d5251 [WangTaoTheTonic] per Marcelo's comments
d7455d8 [WangTaoTheTonic] slightly change when delete file
b0abca5 [WangTaoTheTonic] use global var to store apps to clean
94adfe1 [WangTaoTheTonic] leave expired apps alone to be deleted
9872a9d [WangTaoTheTonic] use the right path
fdef4d6 [WangTaoTheTonic] check if app is completed before clean it up
2015-04-23 17:20:17 -04:00
wizz 3e91cc273d [SPARK-7085][MLlib] Fix miniBatchFraction parameter in train method called with 4 arguments
Author: wizz <wizz@wizz-dev01.kawasaki.flab.fujitsu.com>

Closes #5658 from kuromatsu-nobuyuki/SPARK-7085 and squashes the following commits:

6ec2d21 [wizz] Fix miniBatchFraction parameter in train method called with 4 arguments
2015-04-23 14:00:07 -07:00
Josh Rosen 6afde2c781 [SPARK-7058] Include RDD deserialization time in "task deserialization time" metric
The web UI's "task deserialization time" metric is slightly misleading because it does not capture the time taken to deserialize the broadcasted RDD.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #5635 from JoshRosen/SPARK-7058 and squashes the following commits:

ed90f75 [Josh Rosen] Update UI tooltip
a3743b4 [Josh Rosen] Update comments.
4f52910 [Josh Rosen] Roll back whitespace change
e9cf9f4 [Josh Rosen] Remove unused variable
9f32e55 [Josh Rosen] Expose executorDeserializeTime on Task instead of pushing runtime calculation into Task.
21f5b47 [Josh Rosen] Don't double-count the broadcast deserialization time in task runtime
1752f0e [Josh Rosen] [SPARK-7058] Incorporate RDD deserialization time in task deserialization time metric
2015-04-23 13:19:03 -07:00
Vinod K C c1213e6a92 [SPARK-7055][SQL]Use correct ClassLoader for JDBC Driver in JDBCRDD.getConnector
Author: Vinod K C <vinod.kc@huawei.com>

Closes #5633 from vinodkc/use_correct_classloader_driverload and squashes the following commits:

73c5380 [Vinod K C] Use correct ClassLoader for JDBC Driver
2015-04-23 12:00:23 -07:00
Tathagata Das 534f2a4362 [SPARK-6752][Streaming] Allow StreamingContext to be recreated from checkpoint and existing SparkContext
Currently if you want to create a StreamingContext from checkpoint information, the system will create a new SparkContext. This prevent StreamingContext to be recreated from checkpoints in managed environments where SparkContext is precreated.

The solution in this PR: Introduce the following methods on StreamingContext
1. `new StreamingContext(checkpointDirectory, sparkContext)`
   Recreate StreamingContext from checkpoint using the provided SparkContext
2. `StreamingContext.getOrCreate(checkpointDirectory, sparkContext, createFunction: SparkContext => StreamingContext)`
   If checkpoint file exists, then recreate StreamingContext using the provided SparkContext (that is, call 1.), else create StreamingContext using the provided createFunction

TODO: the corresponding Java and Python API has to be added as well.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5428 from tdas/SPARK-6752 and squashes the following commits:

94db63c [Tathagata Das] Fix long line.
524f519 [Tathagata Das] Many changes based on PR comments.
eabd092 [Tathagata Das] Added Function0, Java API and unit tests for StreamingContext.getOrCreate
36a7823 [Tathagata Das] Minor changes.
204814e [Tathagata Das] Added StreamingContext.getOrCreate with existing SparkContext
2015-04-23 11:29:34 -07:00
Cheng Hao cc48e6387a [SPARK-7044] [SQL] Fix the deadlock in script transformation
Author: Cheng Hao <hao.cheng@intel.com>

Closes #5625 from chenghao-intel/transform and squashes the following commits:

5ec1dd2 [Cheng Hao] fix the deadlock issue in ScriptTransform
2015-04-23 10:35:22 -07:00
Prabeesh K 975f53e4f9 [minor][streaming]fixed scala string interpolation error
Author: Prabeesh K <prabeesh.k@namshi.com>

Closes #5653 from prabeesh/fix and squashes the following commits:

9d7a9f5 [Prabeesh K] fixed scala string interpolation error
2015-04-23 10:33:13 -07:00
Prashant Sharma a7d65d38f9 [HOTFIX] [SQL] Fix compilation for scala 2.11.
Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #5652 from ScrapCodes/hf/compilation-fix-scala-2.11 and squashes the following commits:

819ff06 [Prashant Sharma] [HOTFIX] Fix compilation for scala 2.11.
2015-04-23 16:45:26 +05:30
Reynold Xin f60bece14f [SPARK-7069][SQL] Rename NativeType -> AtomicType.
Also renamed JvmType to InternalType.

Author: Reynold Xin <rxin@databricks.com>

Closes #5651 from rxin/native-to-atomic-type and squashes the following commits:

cbd4028 [Reynold Xin] [SPARK-7069][SQL] Rename NativeType -> AtomicType.
2015-04-23 01:43:40 -07:00
Reynold Xin 29163c5200 [SPARK-7068][SQL] Remove PrimitiveType
Author: Reynold Xin <rxin@databricks.com>

Closes #5646 from rxin/remove-primitive-type and squashes the following commits:

01b673d [Reynold Xin] [SPARK-7068][SQL] Remove PrimitiveType
2015-04-22 23:55:20 -07:00
Reynold Xin 2d33323cad [MLlib] Add support for BooleanType to VectorAssembler.
Author: Reynold Xin <rxin@databricks.com>

Closes #5648 from rxin/vectorAssembler-boolean and squashes the following commits:

1bf3d40 [Reynold Xin] [MLlib] Add support for BooleanType to VectorAssembler.
2015-04-22 23:54:48 -07:00
Liang-Chi Hsieh d9e70f331f [HOTFIX][SQL] Fix broken cached test
Added in #5475. Pointed as broken in #5639.
/cc marmbrus

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #5640 from viirya/fix_cached_test and squashes the following commits:

c0cf69a [Liang-Chi Hsieh] Fix broken cached test.
2015-04-22 22:18:56 -07:00
Kay Ousterhout 03e85b4a11 [SPARK-7046] Remove InputMetrics from BlockResult
This is a code cleanup.

The BlockResult class originally contained an InputMetrics object so that InputMetrics could
directly be used as the InputMetrics for the whole task. Now we copy the fields out of here, and
the presence of this object is confusing because it's only a partial input metrics (it doesn't
include the records read). Because this object is no longer useful (and is confusing), it should
be removed.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #5627 from kayousterhout/SPARK-7046 and squashes the following commits:

bf64bbe [Kay Ousterhout] Import fix
a08ca19 [Kay Ousterhout] [SPARK-7046] Remove InputMetrics from BlockResult
2015-04-22 21:42:09 -07:00
Reynold Xin d20686066e [SPARK-7066][MLlib] VectorAssembler should use NumericType not NativeType.
Author: Reynold Xin <rxin@databricks.com>

Closes #5642 from rxin/mllib-native-type and squashes the following commits:

e23af5b [Reynold Xin] Remove StringType
7cbb205 [Reynold Xin] [SPARK-7066][MLlib] VectorAssembler should use NumericType and StringType, not NativeType.
2015-04-22 21:35:42 -07:00
Reynold Xin 1b85e08509 [MLlib] UnaryTransformer nullability should not depend on PrimitiveType.
Author: Reynold Xin <rxin@databricks.com>

Closes #5644 from rxin/mllib-nullable and squashes the following commits:

a727e5b [Reynold Xin] [MLlib] UnaryTransformer nullability should not depend on primitive types.
2015-04-22 21:35:12 -07:00
Reynold Xin b69c4f9b2e Disable flaky test: ReceiverSuite "block generator throttling". 2015-04-22 21:24:22 -07:00