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This pull requests integrates SparkR, an R frontend for Spark. The SparkR package contains both RDD and DataFrame APIs in R and is integrated with Spark's submission scripts to work on different cluster managers.
Some integration points that would be great to get feedback on:
1. Build procedure: SparkR requires R to be installed on the machine to be built. Right now we have a new Maven profile `-PsparkR` that can be used to enable SparkR builds
2. YARN cluster mode: The R package that is built needs to be present on the driver and all the worker nodes during execution. The R package location is currently set using SPARK_HOME, but this might not work on YARN cluster mode.
The SparkR package represents the work of many contributors and attached below is a list of people along with areas they worked on
edwardt (edwart) - Documentation improvements
Felix Cheung (felixcheung) - Documentation improvements
Hossein Falaki (falaki) - Documentation improvements
Chris Freeman (cafreeman) - DataFrame API, Programming Guide
Todd Gao (7c00) - R worker Internals
Ryan Hafen (hafen) - SparkR Internals
Qian Huang (hqzizania) - RDD API
Hao Lin (hlin09) - RDD API, Closure cleaner
Evert Lammerts (evertlammerts) - DataFrame API
Davies Liu (davies) - DataFrame API, R worker internals, Merging with Spark
Yi Lu (lythesia) - RDD API, Worker internals
Matt Massie (massie) - Jenkins build
Harihar Nahak (hnahak87) - SparkR examples
Oscar Olmedo (oscaroboto) - Spark configuration
Antonio Piccolboni (piccolbo) - SparkR examples, Namespace bug fixes
Dan Putler (dputler) - Dataframe API, SparkR Install Guide
Ashutosh Raina (ashutoshraina) - Build improvements
Josh Rosen (joshrosen) - Travis CI build
Sun Rui (sun-rui)- RDD API, JVM Backend, Shuffle improvements
Shivaram Venkataraman (shivaram) - RDD API, JVM Backend, Worker Internals
Zongheng Yang (concretevitamin) - RDD API, Pipelined RDDs, Examples and EC2 guide
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Author: Shivaram Venkataraman <shivaram.venkataraman@gmail.com>
Author: Zongheng Yang <zongheng.y@gmail.com>
Author: cafreeman <cfreeman@alteryx.com>
Author: Shivaram Venkataraman <shivaram@eecs.berkeley.edu>
Author: Davies Liu <davies@databricks.com>
Author: Davies Liu <davies.liu@gmail.com>
Author: hlin09 <hlin09pu@gmail.com>
Author: Sun Rui <rui.sun@intel.com>
Author: lythesia <iranaikimi@gmail.com>
Author: oscaroboto <oscarjr@gmail.com>
Author: Antonio Piccolboni <antonio@piccolboni.info>
Author: root <edward>
Author: edwardt <edwardt.tril@gmail.com>
Author: hqzizania <qian.huang@intel.com>
Author: dputler <dan.putler@gmail.com>
Author: Todd Gao <todd.gao.2013@gmail.com>
Author: Chris Freeman <cfreeman@alteryx.com>
Author: Felix Cheung <fcheung@AVVOMAC-119.local>
Author: Hossein <hossein@databricks.com>
Author: Evert Lammerts <evert@apache.org>
Author: Felix Cheung <fcheung@avvomac-119.t-mobile.com>
Author: felixcheung <felixcheung_m@hotmail.com>
Author: Ryan Hafen <rhafen@gmail.com>
Author: Ashutosh Raina <ashutoshraina@users.noreply.github.com>
Author: Oscar Olmedo <oscarjr@gmail.com>
Author: Josh Rosen <rosenville@gmail.com>
Author: Yi Lu <iranaikimi@gmail.com>
Author: Harihar Nahak <hnahak87@users.noreply.github.com>
Closes #5096 from shivaram/R and squashes the following commits:
da64742 [Davies Liu] fix Date serialization
59266d1 [Davies Liu] check exclusive of primary-py-file and primary-r-file
55808e4 [Davies Liu] fix tests
5581c75 [Davies Liu] update author of SparkR
f731b48 [Shivaram Venkataraman] Only run SparkR tests if R is installed
64eda24 [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R
d7c3f22 [Shivaram Venkataraman] Address code review comments Changes include 1. Adding SparkR docs to API docs generated 2. Style fixes in SparkR scala files 3. Clean up of shell scripts and explanation of install-dev.sh
377151f [Shivaram Venkataraman] Merge remote-tracking branch 'apache/master' into R
eb5da53 [Shivaram Venkataraman] Merge pull request #3 from davies/R2
a18ff5c [Davies Liu] Update sparkR.R
5133f3a [Shivaram Venkataraman] Merge pull request #7 from hqzizania/R3
940b631 [hqzizania] [SPARKR-92] Phase 2: implement sum(rdd)
0e788c0 [Shivaram Venkataraman] Merge pull request #5 from hlin09/doc-fix
3487461 [hlin09] Add tests log in .gitignore.
1d1802e [Shivaram Venkataraman] Merge pull request #4 from felixcheung/r-require
11981b7 [felixcheung] Update R to fail early if SparkR package is missing
c300e08 [Davies Liu] remove duplicated file
b045701 [Davies Liu] Merge branch 'remote_r' into R
19c9368 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into remote_r
f8fa8af [Davies Liu] mute logging when start/stop context
e7104b6 [Davies Liu] remove ::: in SparkR
a1777eb [Davies Liu] move rules into R/.gitignore
e88b649 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
6e20e71 [Davies Liu] address comments
b433817 [Davies Liu] Merge branch 'master' of github.com:apache/spark into R
a1cedad [Shivaram Venkataraman] Merge pull request #228 from felixcheung/doc
e089151 [Davies Liu] Merge pull request #225 from sun-rui/SPARKR-154_2
463e28c [Davies Liu] Merge pull request #2 from shivaram/doc-fixes
bc2d6d8 [Shivaram Venkataraman] Remove arg from sparkR.stop and update docs
d425363 [Shivaram Venkataraman] Some doc fixes for column, generics, group
1f1a7e0 [Shivaram Venkataraman] Some fixes to DataFrame, RDD, SQLContext docs
104ad4e [Shivaram Venkataraman] Check the right env in exists
cf5cd99 [Shivaram Venkataraman] Remove unused numCols argument
85a50ec [Shivaram Venkataraman] Merge pull request #226 from RevolutionAnalytics/master
3eacfc0 [Davies Liu] fix flaky test
733380d [Davies Liu] update R examples (remove master from args)
b21a0da [Davies Liu] Merge pull request #1 from shivaram/log4j-tests
a1493d7 [Shivaram Venkataraman] Address comments
e1f83ab [Shivaram Venkataraman] Send Spark INFO logs to a file in SparkR tests
58276f5 [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R
52cc92d [Shivaram Venkataraman] Add license to create-docs.sh
6ff5ea2 [Shivaram Venkataraman] Add instructions to generate docs
1f478c5 [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R
02b4833 [Shivaram Venkataraman] Add a script to generate R docs (Rd, html) Also fix some issues with our documentation
d6d3729 [Davies Liu] enable spark and pyspark tests
0e5a83f [Davies Liu] fix code style
afd8a77 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
d87a181 [Davies Liu] fix flaky tests
7100fb9 [Shivaram Venkataraman] Fix libPaths in README
bdf3a14 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
05e7375 [Davies Liu] sort generics
b44e371 [Shivaram Venkataraman] Include RStudio instructions in README
855537f [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
9fb6af3 [Davies Liu] mark R classes/objects are private
423ea3c [Shivaram Venkataraman] Ignore unknown jobj in cleanup
974e4ea [Davies Liu] fix flaky test
410ec18 [Davies Liu] fix zipRDD() tests
d8b24fc [Davies Liu] disable spark and python tests temporary
ce3ca62 [Davies Liu] fix license check
7da0049 [Davies Liu] fix build
2892e29 [Davies Liu] support R in YARN cluster
ebd4d07 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
38cbf59 [Davies Liu] fix test of zipRDD()
756ece0 [Shivaram Venkataraman] Update README remove outdated TODO
d436f26 [Davies Liu] add missing files
40d193a [Shivaram Venkataraman] Merge pull request #224 from sun-rui/SPARKR-224-new
1a16cd6 [Davies Liu] rm PROJECT_HOME
56670ef [Davies Liu] rm man page
ba4b80b [Davies Liu] Merge branch 'remote_r' into R
f04080c [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into remote_r
028cbfb [Davies Liu] fix exit code of sparkr unit test
42d8b4c [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
ef26015 [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
a1870e8 [Shivaram Venkataraman] Merge pull request #214 from sun-rui/SPARKR-156_3
cb6e5e3 [Shivaram Venkataraman] Add scripts to start SparkR on windows
8030847 [Shivaram Venkataraman] Set windows file separators, install dirs
05afef0 [Shivaram Venkataraman] Only stop backend JVM if R launched it
95d2de3 [Davies Liu] fix spark-submit with R scripot
baefd9e [Shivaram Venkataraman] Make bin/sparkR use spark-submit As a part of this move the R initialization functions into first.R and first-submit.R
d6f2bdd [Shivaram Venkataraman] Fix run-tests path
ea90fab [Davies Liu] fix spark-submit with R path and sparkR -h
0e2412c [Davies Liu] fix bin/sparkR
9f6aa1f [Davies Liu] Merge branch 'R' of github.com:amplab-extras/spark into R
479e3fe [Davies Liu] change println() to logging
52ca6e5 [Shivaram Venkataraman] Add missing comma
716b16f [Shivaram Venkataraman] Merge branch 'R' of https://github.com/amplab-extras/spark into R
2d235d4 [Shivaram Venkataraman] Build SparkR with Maven profile
aae881b [Davies Liu] fix rat
ff776aa [Shivaram Venkataraman] Fix style
e4f1937 [Shivaram Venkataraman] Remove DFC example
f7b6936 [Davies Liu] remove Spark prefix for class
043959e [Davies Liu] cleanup
ba53b09 [Davies Liu] support R in spark-submit
f403b4a [Davies Liu] rm .travis.yml
c4a5bdf [Davies Liu] run sparkr tests in Spark
e8fc7ca [Davies Liu] fix .gitignore
35e5755 [Davies Liu] reduce size of example data
50bff63 [Davies Liu] add LICENSE header for R sources
facb6e0 [Davies Liu] add .gitignore for .o, .so, .Rd
18e5eed [Davies Liu] update docs
0a0e632 [Davies Liu] move sparkR into bin/
a76472f [Davies Liu] fix path of assembly jar
df3eeea [Davies Liu] move R/examples into examples/src/main/r
3415cc7 [Davies Liu] move Scala source into core/ and sql/
180fc9c [Davies Liu] move scala
014d253 [Davies Liu] delete man pages
49a8133 [Davies Liu] Merge branch 'remote_r' into R
44994c2 [Davies Liu] Moved files to R/
2fc553f [Shivaram Venkataraman] Merge pull request #222 from davies/column2
b043876 [Davies Liu] fix test
5e610cb [Davies Liu] add more API for Column
6f95d49 [Shivaram Venkataraman] Merge pull request #221 from shivaram/sparkr-stop-start
3214c6d [Shivaram Venkataraman] Merge pull request #217 from hlin09/cleanClosureFix
f5d3355 [Shivaram Venkataraman] Merge pull request #218 from davies/merge
70f620c [Davies Liu] address comments
4b1628d [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into merge
3139325 [Shivaram Venkataraman] Merge pull request #212 from davies/toDF
6122e0e [Davies Liu] handle NULL
bc2ff38 [Davies Liu] handle NULL
7f5e70c [Davies Liu] Update SerDe.scala
46454e4 [Davies Liu] address comments
dd52cbc [Shivaram Venkataraman] Merge pull request #220 from shivaram/sparkr-utils-include
662938a [Shivaram Venkataraman] Include utils before SparkR for `head` to work Before this change calling `head` on a DataFrame would not work from the sparkR script as utils would be loaded after SparkR and placed ahead in the search list. This change requires utils to be loaded before SparkR
1bc2998 [Shivaram Venkataraman] Merge pull request #179 from evertlammerts/sparkr-sql
7695d36 [Evert Lammerts] added tests
8190127 [Evert Lammerts] fixed parquetFile signature
d8c8fcc [Shivaram Venkataraman] Merge pull request #219 from shivaram/sparkr-build-final
963c7ee [Davies Liu] Merge branch 'master' into merge
8bff523 [Shivaram Venkataraman] Remove staging repo now that 1.3 is released
e52258f [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into toDF
05b9126 [Shivaram Venkataraman] Merge pull request #215 from davies/agg
8e1497d [Davies Liu] Update DataFrame.R
72adb14 [Davies Liu] Update SQLContext.R
66cc92a [Davies Liu] address commets
55c38bc [Shivaram Venkataraman] Merge pull request #216 from davies/select2
3e0555d [Shivaram Venkataraman] Merge pull request #193 from davies/daemon
0467474 [Davies Liu] add more selecter for DataFrame
9a6be74 [Davies Liu] include grouping columns in agg()
e87bb98 [Davies Liu] improve comment and logging
a6dc435 [Davies Liu] remove dependency of jsonlite
26a3621 [Davies Liu] support date.frame and Date/Time
4e4908a [Davies Liu] createDataFrame from rdd
5757b95 [Shivaram Venkataraman] Merge pull request #196 from davies/die
90f2692 [Shivaram Venkataraman] Merge pull request #211 from hlin09/generics
8583968 [Davies Liu] readFully()
46cea3d [Davies Liu] retry
01aa5ee [Davies Liu] add config for using daemon, refactor
ff948db [hlin09] Remove missingOrInteger.
ecdfda1 [hlin09] Remove duplication.
411b751 [Davies Liu] make RStudio happy
8f8813f [Davies Liu] switch back to use parallel
6bccbbf [hlin09] Move roxygen doc back to implementation.
ffd6e8e [Shivaram Venkataraman] Merge pull request #210 from hlin09/hlin09
471c794 [hlin09] Move getJRDD and broadcast's value to 00-generic.R.
89b886d [hlin09] Move setGeneric() to 00-generics.R.
97dde1a [hlin09] Add a test for access operators.
09ff163 [Shivaram Venkataraman] Merge pull request #204 from cafreeman/sparkr-sql
15a713f [cafreeman] Fix example for `dropTempTable`
dc1291b [hlin09] Add checks for namespace access operators in cleanClosure.
b4c0b2e [Davies Liu] use fork package
3db5649 [cafreeman] Merge branch 'sparkr-sql' of https://github.com/amplab-extras/SparkR-pkg into sparkr-sql
789be97 [Shivaram Venkataraman] Merge pull request #207 from shivaram/err-remove
e60578a [cafreeman] update tests to guarantee row order
5eec6fc [Shivaram Venkataraman] Merge pull request #206 from sun-rui/SPARKR-156_2
3f7aed6 [Sun Rui] Fix minor typos in the function description.
a8cebf0 [Shivaram Venkataraman] Remove print statement in SparkRBackendHandler This print statement is noisy for SQL methods which have multiple APIs (like loadDF). We already have a better error message when no valid methods are found
5e3a576 [Sun Rui] Fix indentation.
f3d99a6 [Sun Rui] [SPARKR-156] phase 2: implement zipWithIndex() of the RDD class.
a582810 [cafreeman] Merge branch 'dfMethods' into sparkr-sql
7a5d6fd [cafreeman] `withColumn` and `withColumnRenamed`
c5fa3b9 [cafreeman] New `select` method
bcb0bf5 [Shivaram Venkataraman] Merge pull request #180 from davies/group
9dd6a5a [Davies Liu] Update SparkRBackendHandler.scala
e6fb8d8 [Davies Liu] improve logging
428a99a [Davies Liu] remove test, catch exception
fef99de [cafreeman] `intersect`, `subtract`, `unionAll`
befbd32 [cafreeman] `insertInto`
9d01bcd [cafreeman] `dropTempTable`
d8c1c09 [Davies Liu] add test to start and stop context multiple times
18c6004 [Shivaram Venkataraman] Merge pull request #201 from sun-rui/SPARKR-156_1
dfb399a [Davies Liu] address comments
f06ccec [Sun Rui] Use mapply() instead of for statement.
3c7674f [Davies Liu] Merge branch 'die' of github.com:davies/SparkR-pkg into die
ac8a852 [Davies Liu] close monitor connection in sparkR.stop()
4d0fb56 [Shivaram Venkataraman] Merge pull request #203 from shivaram/sparkr-hive-fix
62b0760 [Shivaram Venkataraman] Fix test hive context package name
47a613f [Shivaram Venkataraman] Fix HiveContext package name
fb3b139 [Davies Liu] fix tests
d0d4626 [Shivaram Venkataraman] Merge pull request #199 from davies/load
8b7fb67 [Davies Liu] fix HiveContext
bb46832 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into load
e9e2a03 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into group
b875b4f [Davies Liu] fix style
de2abfa [Shivaram Venkataraman] Merge pull request #202 from cafreeman/sparkr-sql
3675fcf [cafreeman] Update `explain` and fixed doc for `toJSON`
5fd9575 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into load
6fac596 [Davies Liu] support Column expression in agg()
f10a24e [Davies Liu] address comments
ff8b005 [cafreeman] 'saveAsParquetFile`
a5c2887 [cafreeman] fix test
3fab0f8 [cafreeman] `showDF`
779c102 [cafreeman] `isLocal`
68b11cf [cafreeman] `toJSON`
0ac4abc [cafreeman] 'explain`
20242c4 [cafreeman] clean up docs
6a1fe64 [Shivaram Venkataraman] Merge pull request #198 from cafreeman/sparkr-sql
198c130 [Shivaram Venkataraman] Merge pull request #200 from shivaram/sparkr-sql-build
870acd4 [Shivaram Venkataraman] Use rc2 explicitly
8b9a963 [cafreeman] Merge branch 'sparkr-sql' of https://github.com/amplab-extras/SparkR-pkg into sparkr-sql
bc90115 [cafreeman] Fixed docs
3865f39 [Sun Rui] [SPARKR-156] phase 1: implement zipWithUniqueId() of the RDD class.
a37fd80 [Davies Liu] Update sparkR.R
d18f9d3 [Shivaram Venkataraman] Remove SparkR snapshot build We now have 1.3.0 RC2 on Apache Staging
8de958d [Davies Liu] Update SparkRBackend.scala
4e0becc [Shivaram Venkataraman] Merge pull request #194 from davies/api
197a79b [Davies Liu] add HiveContext (commented)
32aa01d [Shivaram Venkataraman] Merge pull request #191 from felixcheung/doc
5073e07 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into load
7918634 [cafreeman] Fix test
acea146 [cafreeman] remove extra line
74269f3 [cafreeman] Merge branch 'dfMethods' into sparkr-sql
cd7ac8a [Shivaram Venkataraman] Merge pull request #197 from cafreeman/sparkr-sql
494a4dd [cafreeman] update export
e14c328 [cafreeman] `selectExpr`
32b37d1 [cafreeman] Fixed indent in `join` test.
2e7b190 [Felix Cheung] small update on yarn deploy mode.
8ff29d6 [Davies Liu] fix tests
12a6db2 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into api
294ca4a [cafreeman] `join`, `sort`, and `filter`
4fa6343 [cafreeman] Refactor `join` generic for use with `DataFrame`
3f22c8d [Shivaram Venkataraman] Merge pull request #195 from cafreeman/sparkr-sql
2b6f980 [Davies Liu] shutdown the JVM after R process die
e8639c3 [cafreeman] New 1.3 repo and updates to `column.R`
ed9a89f [Davies Liu] address comments
03bcf20 [Davies Liu] Merge branch 'group' of github.com:davies/SparkR-pkg into group
39c253d [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into group
98cc97a [Davies Liu] fix test and docs
e2d144a [Felix Cheung] Fixed small typos
3beadcf [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into api
06cbc2d [Davies Liu] launch R worker by a daemon
8a676b1 [Shivaram Venkataraman] Merge pull request #188 from davies/column
524c122 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into column
f798402 [Davies Liu] Update column.R
1d0f2ae [Davies Liu] Update DataFrame.R
03402eb [Felix Cheung] Updates as per feedback on sparkR-submit
76cf2e0 [Shivaram Venkataraman] Merge pull request #192 from cafreeman/sparkr-sql
1955a09 [cafreeman] return object instead of a list of one object
f585929 [cafreeman] Fix brackets
e998356 [cafreeman] define generic for 'first' in RDD API
71d66a1 [Davies Liu] fix first(0
8ec21af [Davies Liu] fix signature
acae527 [Davies Liu] refactor
d7b17a4 [Davies Liu] fix approxCountDistinct
7dfe27d [Davies Liu] fix cyclic namespace dependency
8caf5bb [Davies Liu] use S4 methods
5c0bb24 [Felix Cheung] Doc updates: build and running on YARN
773baf0 [Zongheng Yang] Merge pull request #178 from davies/random
862f07c [Shivaram Venkataraman] Merge pull request #190 from shivaram/SPARKR-79
b457833 [Shivaram Venkataraman] Merge pull request #189 from shivaram/stdErrFix
f7caeb8 [Davies Liu] Update SparkRBackend.scala
8c4deae [Shivaram Venkataraman] Remove unused function
6e51c7f [Shivaram Venkataraman] Fix stderr redirection on executors
7afa4c9 [Shivaram Venkataraman] Merge pull request #186 from hlin09/funcDep3
4d36ab1 [hlin09] Add tests for broadcast variables.
3f57e56 [hlin09] Fix comments.
7b72487 [hlin09] Fix comments.
ae05bf1 [Davies Liu] Merge branch 'sparkr-sql' of github.com:amplab-extras/SparkR-pkg into column
abb4bb9 [Davies Liu] add Column and expression
eb8ac11 [Shivaram Venkataraman] Set Spark version 1.3.0 in Windows build
5c72e73 [Davies Liu] wait atmost 100 seconds
e425437 [Shivaram Venkataraman] Merge pull request #177 from lythesia/master
a00f502 [lythesia] fix indents
0346e5f [Davies Liu] address comment
6134649 [Shivaram Venkataraman] Merge pull request #187 from cafreeman/sparkr-sql
ad0935e [lythesia] minor fixes
b0e7f73 [cafreeman] Update `sampleDF` test
7b0d070 [lythesia] keep partitions check
889c265 [cafreeman] numToInt utility function
27dd3a0 [lythesia] modify tests for repartition
cad0f0c [cafreeman] Fix docs and indents
2808dcf [cafreeman] Three more DataFrame methods
5ef66fb [Davies Liu] send back the port via temporary file
3b46429 [Davies Liu] Merge branch 'master' of github.com:amplab-extras/SparkR-pkg into random
798f453 [cafreeman] Merge branch 'sparkr-sql' into dev
9aa4acf [Shivaram Venkataraman] Merge pull request #184 from davies/socket
020bce8 [Shivaram Venkataraman] Merge pull request #183 from cafreeman/sparkr-sql
222e06b [cafreeman] Lazy evaluation and formatting changes
e776324 [Davies Liu] fix import
211cc15 [cafreeman] Merge branch 'sparkr-sql' into dev
3351afd [hlin09] Replaces getDependencies with cleanClosure, to serialize UDFs to workers.
e7c56d6 [lythesia] fix random partition key
50c74b1 [Davies Liu] address comments
083c89f [cafreeman] Remove commented lines an unused import
dfa119b [hlin09] Improve the coverage of processClosure.
a41c9b9 [cafreeman] Merge branch 'wrapper' into sparkr-sql
1cd714f [cafreeman] Wrapper function docs.
db0cd9e [cafreeman] Clean up for wrapper functions
818c19f [cafreeman] Update schema-related functions
a57884e [cafreeman] Remove unused import
d72e830 [cafreeman] Add wrapper for `StructField` and `StructType`
2ea2ecf [lythesia] use generic arg
09b9512 [hlin09] add docs
f4f077c [hlin09] Add recursive cleanClosure for function access.
f84ad27 [hlin09] Merge remote-tracking branch 'upstream/master' into funcDep2
5300766 [Shivaram Venkataraman] Merge pull request #185 from hlin09/hlin09
07aa7c0 [hlin09] Unifies the implementation of lapply with lapplyParitionsWithIndex.
f4dbb0b [Davies Liu] use socket in worker
8282c59 [Davies Liu] Update DataFrame.R
ba495a8 [Davies Liu] Update NAMESPACE
36dffb3 [cafreeman] Add 'head` and `first`
534a95f [cafreeman] Schema-related methods
64f488d [cafreeman] Cache and Persist Methods
30d71fd [cafreeman] Standardize method arguments for DataFrame methods
785898b [Shivaram Venkataraman] Merge pull request #182 from cafreeman/sparkr-sql
2619003 [Shivaram Venkataraman] Merge pull request #181 from cafreeman/master
a9bbe0b [cafreeman] Update existing SparkSQL functions
8c241a3 [cafreeman] Merge with master, include changes to method args
68d6de4 [cafreeman] Fix typos
8d2ec6e [Davies Liu] add sum/max/min/avg/mean
774e687 [Davies Liu] add missing API in SQLContext
1e72b4b [Davies Liu] missing API in SQLContext
3294949 [Chris Freeman] Restore `rdd` argument to `getJRDD`
3a58ebc [Davies Liu] rm unrelated file
8bd93b5 [Davies Liu] fix signature
c652b4c [cafreeman] Update method signatures to use generic arg
48c8827 [Davies Liu] update NAMESPACE
84e2d8c [Davies Liu] groupBy and agg()
7c3ddbd [Davies Liu] create jmode in JVM
9465426 [Davies Liu] load and save
982f342 [lythesia] fix numeric issue
7651d84 [lythesia] fix coalesce
4e712e1 [Davies Liu] use random port in backend
041d22b [Shivaram Venkataraman] Merge pull request #172 from cafreeman/sparkr-sql
0d07770 [cafreeman] Added `limit` and updated `take`
301d8e5 [cafreeman] Remove extraneous map functions
0387db2 [cafreeman] Remove colNames
04c4b65 [lythesia] add repartition/coalesce
231deab [cafreeman] Change reserialize to serializeToBytes
acf7e1a [cafreeman] Rework the Scala to R DataFrame Conversion
481ae37 [cafreeman] Updated stale comments and standardized arg names
21d4a97 [hlin09] Adds cleanClosure to capture the function closures.
d24ffb4 [hlin09] Merge remote-tracking branch 'upstream/master' into funcDep2
8be02de [hlin09] Revert "loop 1-12 test pass."
fddb9cc [hlin09] Revert "add docs"
f8ef0ab [hlin09] Revert "More docs"
8e4b3da [hlin09] Revert "More docs"
57e005b [hlin09] Revert "fix tests."
c10148e [Shivaram Venkataraman] Merge pull request #174 from shivaram/sparkr-runner
910e3be [Shivaram Venkataraman] Add a timeout for initialization Also move sparkRBackend.stop into a finally block
bf52b17 [Shivaram Venkataraman] Merge remote-tracking branch 'amplab-sparkr/master' into sparkr-runner
08102b0 [Shivaram Venkataraman] Merge pull request #176 from lythesia/master
9c77b20 [Chris Freeman] Merge pull request #2 from shivaram/sparkr-sql
179ab38 [lythesia] add try counts and increase time interval
71a73b2 [Shivaram Venkataraman] Use a getter for serialization mode This change encapsulates the semantics of serialization mode for RDDs inside a getter function. For PipelinedRDDs if a backing JavaRDD is available we use that else we fall back to a default serialization mode
06bf250 [Shivaram Venkataraman] Merge pull request #173 from shivaram/windows-space-fix
88bf97f [Shivaram Venkataraman] Create SparkContext for R shell launch
f9268d9 [Shivaram Venkataraman] Fix code review comments
e6ad12d [Shivaram Venkataraman] Update comment describing sparkR-submit
17eda4c [Shivaram Venkataraman] Merge pull request #175 from falaki/docfix
ba2b72b [Hossein] Spark 1.1.0 is default
4cd7d3f [lythesia] retry backend connection
749e2d0 [Hossein] Updated README
bc04cf4 [Shivaram Venkataraman] Use SPARKR_BACKEND_PORT in sparkR.R as default Change SparkRRunner to use EXISTING_SPARKR_BACKEND_PORT to differentiate between the two
22a19ac [Shivaram Venkataraman] Use a semaphore to wait for backend to initalize Also pick a random port to avoid collisions
7f1f0f8 [cafreeman] Move comments to fit 100 char line length
8b84e4e [cafreeman] Make if statements more explicit
ce5d5ab [cafreeman] New tests for Union and Object File
b063320 [cafreeman] Changed 'serialized' to 'serializedMode'
0981dff [Zongheng Yang] Merge pull request #168 from sun-rui/SPARKR-153_2
86fc639 [Shivaram Venkataraman] Move sparkR-submit into pkg/inst
fd8f8a9 [Shivaram Venkataraman] Merge branch 'hqzizania-master'
a33dbea [Shivaram Venkataraman] Merge branch 'master' of https://github.com/hqzizania/SparkR-pkg into hqzizania-master
384e6e2 [Shivaram Venkataraman] Merge pull request #171 from hlin09/hlin09
1f5a6ac [hlin09] fixed comments
7f7596a [cafreeman] Additional handling for "row" serialization
8c3b8c5 [cafreeman] Add test for UnionRDD on "row" serialization
b1141f8 [cafreeman] Fixed formatting issues.
5db30bf [cafreeman] Changed serialized from bool to string
2f0c0b8 [cafreeman] Add check for serialized type
d243dfb [cafreeman] Clean up code
5ff63a2 [cafreeman] Change test from boolean to string
77fec1a [cafreeman] Updated .Rd files
9224989 [cafreeman] Various updates for DataFrame to RRDD
26af62b [cafreeman] DataFrame to RRDD
e004481 [cafreeman] Update UnionRDD test
5292be7 [hlin09] Adds support of pipeRDD().
e2a7560 [Shivaram Venkataraman] Merge pull request #170 from cafreeman/sparkr-sql
5d537f4 [cafreeman] Add pairRDD to Description
b6fa88e [cafreeman] Updating to current master
0cda231 [Sun Rui] [SPARKR-153] phase 2: implement aggregateByKey() and foldByKey().
95ee6b4 [Shivaram Venkataraman] Merge remote-tracking branch 'amplab-sparkr/master' into sparkr-runner
67fbc60 [Shivaram Venkataraman] Add support for SparkR shell to use spark-submit This ensures that SparkConf options are read in both in batch and interactive modes
2271030 [Shivaram Venkataraman] Merge pull request #167 from sun-rui/removePartionByInRDD
7fcb46a [Sun Rui] Remove partitionBy() in RDD.
52f94c4 [Shivaram Venkataraman] Merge pull request #160 from lythesia/master
59e2d54 [lythesia] merge with upstream
5836650 [Zongheng Yang] Merge pull request #163 from sun-rui/SPARKR-153_1
141723e [Sun Rui] fix comments.
f73a07e [Shivaram Venkataraman] Merge pull request #165 from shivaram/sparkr-sql-build
10ffc6d [Shivaram Venkataraman] Set Spark version to 1.3 using staging dependency Also fix the maven build
c91ede2 [Shivaram Venkataraman] Merge pull request #164 from hlin09/hlin09
9d335a9 [hlin09] Makes git to ignore Eclipse meta files.
94066bf [Sun Rui] [SPARKR-153] phase 1: implement fold() and aggregate().
9c391c7 [hqzizania] Merge remote-tracking branch 'upstream/master'
5f29551 [hqzizania] modified: pkg/R/RDD.R modified: pkg/R/context.R
d968664 [lythesia] fix comment
7972858 [Shivaram Venkataraman] Merge pull request #159 from sun-rui/SPARKR-150_2
7690878 [lythesia] separate out pair RDD functions
f4573c1 [Sun Rui] Use reduce() instead of sortBy().take() to get the ordered elements.
63e62ed [Sun Rui] [SPARKR-150] phase 2: implement takeOrdered() and top().
050390b [Shivaram Venkataraman] Fix bugs in inferring R file
8398f2e [Shivaram Venkataraman] Add sparkR-submit helper script Also adjust R file path for YARN cluster mode
bd6705b [Zongheng Yang] Merge pull request #154 from sun-rui/SPARKR-150
c7964c9 [Sun Rui] Merge with upstream master.
7feac38 [Sun Rui] Use default arguments for sortBy() and sortKeyBy().
de2bfb3 [Sun Rui] Fix minor comments and add more test cases.
0c6e071 [Zongheng Yang] Merge pull request #157 from lythesia/master
f5038c0 [lythesia] pull out anonymous functions in groupByKey
ba6f044 [lythesia] fixes for reduceByKeyLocally
343b6ab [Oscar Olmedo] Export sparkR.stop Closes #156 from oscaroboto/master
25639cf [Shivaram Venkataraman] Replace tabs with spaces
bb25920 [Shivaram Venkataraman] Merge branch 'dputler-master'
fd836db [hlin09] fix tests.
24a7f13 [hlin09] More docs
a465165 [hlin09] More docs
6ad4fc3 [hlin09] add docs
b082a35 [lythesia] add reduceByKeyLocally
7ca6512 [Shivaram Venkataraman] First cut of SparkRRunner
193f5fe [hlin09] loop 1-12 test pass.
345f1b8 [dputler] [SPARKR-195] Implemented project style guidelines for if-else statements
8043559 [Sun Rui] Add a TODO to use binary search in the range partitioner.
91b2fd6 [Sun Rui] Add more test cases.
e8ebbe4 [Shivaram Venkataraman] Merge pull request #152 from cafreeman/sparkr-sql
0c53d6c [dputler] Data frames now coerced to lists, and messages issued for a data frame or matrix on how they are parallelized
6d57ec0 [cafreeman] Remove json test file since we're using a temp
ac1ef09 [cafreeman] Update registerTempTable test
d9da451 [Sun Rui] [SPARKR-150] phase 1: implement sortBy() and sortByKey().
08ff30b [Shivaram Venkataraman] Merge pull request #153 from hqzizania/master
9767e8e [hqzizania] modified: pkg/man/collect-methods.Rd
5d69f0a [hqzizania] modified: pkg/R/RDD.R
4914091 [hqzizania] modified: pkg/inst/tests/test_rdd.R
742a68b [cafreeman] Update test_sparkRSQL.R
a95823e [hqzizania] modified: pkg/R/RDD.R
2d04526 [cafreeman] Formatting
fae9bdd [cafreeman] Renamed to SQLUtils.scala
39888ea [Chris Freeman] Update test_sparkSQL.R
fce2453 [cafreeman] Updated documentation for SQLContext
13fbf12 [cafreeman] Regenerated .Rd files
51ecf41 [cafreeman] Updated Scala object
30d7337 [cafreeman] Added SparkSQL test
74b3ed6 [cafreeman] Incorporate code feedback
554bda0 [Zongheng Yang] Merge pull request #147 from shivaram/sparkr-ec2-fixes
a5f4f8f [cafreeman] Squashed commit of the following:
f34bb88 [Shivaram Venkataraman] Remove profiling information from this PR
c662f29 [Zongheng Yang] Merge pull request #146 from shivaram/spark-1.2-build
21e9b74 [Zongheng Yang] Merge pull request #145 from lythesia/master
76f6b9e [Shivaram Venkataraman] Merge pull request #149 from hqzizania/master
1c2dbec [lythesia] minor fix for refactoring join code
5b380d3 [hqzizania] modified: pkg/man/combineByKey.Rd modified: pkg/man/groupByKey.Rd modified: pkg/man/partitionBy.Rd modified: pkg/man/reduceByKey.Rd
98794fe [hqzizania] modified: pkg/R/RDD.R
b66534d [Zongheng Yang] Merge pull request #144 from shivaram/fix-rd-files
60da1df [Shivaram Venkataraman] Initialize timing variables
179aa75 [Shivaram Venkataraman] Bunch of fixes for longer running jobs 1. Increase the timeout for socket connection to wait for long jobs 2. Add some profiling information in worker.R 3. Put temp file writes before stdin writes in RRDD.scala
06d99f0 [Shivaram Venkataraman] Fix URI to have right number of slashes
add97f5 [Shivaram Venkataraman] Use URL encode to create valid URIs for jars
4eec962 [lythesia] refactor join functions
73430c6 [Shivaram Venkataraman] Make SparkR work on paths with spaces on Windows
aaf8f47 [Shivaram Venkataraman] Exclude hadoop client from Spark dependency
227ee42 [Zongheng Yang] Merge pull request #141 from shivaram/SPARKR-140
ac5ceb1 [Shivaram Venkataraman] Fix code review comments
32394de [Shivaram Venkataraman] Regenerate Rd files for SparkR This fixes a number of issues in SparkR man pages. The main changes are 1. Don't export or generate docs for PipelineRDD 2. Fix variable names for Filter, count to match base methods 3. Document missing arguments for sparkR.init, print.jobj etc.
e157bf6 [Shivaram Venkataraman] Use prev_serialized to track if JRDD is serialized This changes introduces a new variable in PipelineRDD environment to track if the prev_jrdd is serialized or not.
7428a7e [Zongheng Yang] Merge pull request #143 from shivaram/SPARKR-181
7dd1797 [Shivaram Venkataraman] Address code review comments
8f81c45 [Shivaram Venkataraman] Remove roxygen export for PipelinedRDD
0cb90f1 [Zongheng Yang] Merge pull request #142 from shivaram/SPARKR-169
d1c6e6c [Shivaram Venkataraman] Buffer stderr from R and return it on Exception This change buffers the last 100 lines from R process and passes these lines back to the driver if we have an exception. This will help users debug why their tasks failed on the cluster
d6c1393 [Shivaram Venkataraman] Suppress warnings from normalizePath
a382835 [Shivaram Venkataraman] Fix serialization tracking in pipelined RDDs When creating a pipeline RDD, we need to check if the JavaRDD belonging to the parent is serialized.
da39529 [Zongheng Yang] Merge pull request #140 from sun-rui/SPARKR-183
2814caa [Sun Rui] Merge with upstream master.
cd2a5b3 [Sun Rui] Add reference to Nagle's algorithm and clean code.
52356b6 [Shivaram Venkataraman] Merge pull request #139 from shivaram/fix-backend-exit
97e5a1f [Sun Rui] [SPARKR-183] Fix the issue that parallelize collect tests are slow.
a9f8e8e [Shivaram Venkataraman] Merge pull request #138 from concretevitamin/fix-collect-test
125ae43 [Shivaram Venkataraman] Fix SparkR backend to exit in more cases This change has two fixes 1. When the workspace is saved (from R or RStudio) the backend connection seems to be closed before the finalizer is run. In such cases we reopen the connection and stop the backend 2. With RStudio when R is restarted, there are port-conflicts which appear due to a race condition between the JVM and rsession restart. This change adds a 1 sec sleep to avoid this race.
12c102a [Zongheng Yang] Simplify a unit test.
9c0637a [Zongheng Yang] Merge pull request #137 from shivaram/fix-docs
0df0e18 [Shivaram Venkataraman] Fix documentation for includePackage
7549f88 [Zongheng Yang] Merge pull request #136 from shivaram/man-updates
7edbe46 [Shivaram Venkataraman] Add missing man pages
9cb9567 [Shivaram Venkataraman] Merge pull request #131 from shivaram/rJavaExpt
1fa722e [Shivaram Venkataraman] Rename to SerDe now
2fcb051 [Shivaram Venkataraman] Rename to SerDeJVMR
d112cf0 [Shivaram Venkataraman] Style fixes
9fd01cc [Shivaram Venkataraman] Remove unnecessary braces
0881931 [Shivaram Venkataraman] Some more style fixes
f00b531 [Shivaram Venkataraman] Address code review comments. Big changes include style fixes throughout for named arguments
c09ba05 [Shivaram Venkataraman] Change jobj id to be just an integer Add a new print.jobj that gets the class name and prints it Also add a utility function isInstanceOf
be05b16 [Shivaram Venkataraman] Check if context, connection exist before stopping
d596a23 [Shivaram Venkataraman] Address code review comments
396e7ac [Shivaram Venkataraman] Changes to make new backend work on Windows This change uses file.path to construct the Java binary path in a OS agnostic way and uses system2 to handle quoting binary paths correctly. Tests pass on Mac OSX and a Windows EC2 instance.
e7a4e03 [Shivaram Venkataraman] Remove unused file BACKEND.md
62f380b [Shivaram Venkataraman] Update worker.R to use new deserialization call
8b9c4e6 [Shivaram Venkataraman] Change RDD name, setName to use new backend
6dcd5c5 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into rJavaExpt
0873397 [Shivaram Venkataraman] Refactor java object tracking into a new singleton. Also add comments describing each class
95db964 [Shivaram Venkataraman] Add comments, cleanup new R code
bcd4258 [Zongheng Yang] Merge pull request #130 from lythesia/master
74dbc5e [Sun Rui] Match method using parameter types.
7ad4a4d [Sun Rui] Use 1 char to represent types on the backend->client direction.
bace887 [Sun Rui] Use an integer count for the backend java object ID because Uniqueness isn't guaranteed by System.identityHashCode().
b38d04f [Sun Rui] Use 1 char to represent types on the client -> backend direction.
f88bc68 [lythesia] Merge branch 'master' of github.com:lythesia/SparkR-pkg
71d41f5 [lythesia] add test case for fullOuterJoin
eb4f423 [lythesia] --amend
cffecc5 [lythesia] add test case for fullOuterJoin
a547dd2 [Shivaram Venkataraman] Move classTag, rddRef into newJObject call This avoids them getting eagerly garbage collected
1255391 [Shivaram Venkataraman] Add a finalizer for jobj objects This enables Java objects to be garbage collected on the backend when they are no longer referenced in R. Also rename newJava to newJObject to be more consistent with callJMethod
70fa409 [Sun Rui] Add YARN Conf Dir to the class path when launching the backend.
a1108ca [lythesia] add fullOuterJoin in RDD.R
2152727 [Shivaram Venkataraman] Remove empty file
cd08bee [Shivaram Venkataraman] Update all functions to use new backend All unit tests pass.
9de49b7 [Shivaram Venkataraman] Add high level calls for methods, constructors Also update BACKEND.md
5a97ea4 [Shivaram Venkataraman] Add jobj S3 class that holds backend refs
e071d3e [Shivaram Venkataraman] Change SparkRBackend to use general method calls This change uses a custom protocl + JNI to invoke any method on a given object type. Also update serializers, deserializers to make code more concise
49f0404 [Shivaram Venkataraman] Merge pull request #129 from lythesia/master
7f8cd82 [lythesia] update man
4715ed2 [Yi Lu] Update RDD.R
5a53801 [lythesia] fix name,setName
4f3870b [lythesia] add name,setName in RDD.R
1c25700 [Shivaram Venkataraman] Merge pull request #128 from sun-rui/SPARKR-165
c8507d8 [Sun Rui] [SPARKR-165] IS_SCALAR is not present in R before 3.1
2cff2bd [Sun Rui] Add function to invoke Java method.
7a31da1 [Shivaram Venkataraman] Merge branch 'dputler-master'. Closes #119
0ceba82 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/dputler/SparkR-pkg into dputler-master
735f70c [Shivaram Venkataraman] Merge pull request #125 from 7c00/rawcon
fccfe6c [Shivaram Venkataraman] Merge pull request #127 from sun-rui/SPARKR-164
387bd57 [Sun Rui] [SPARKR-164] Temporary files used by SparkR accumulat as time goes on.
5f2268f [Shivaram Venkataraman] Add support to stop backend
5f745c0 [Shivaram Venkataraman] Update notes in backend
22015c1 [Shivaram Venkataraman] Add first cut of SparkR Backend
52821da [Todd Gao] switch the order of packages and function deps
d7b0007 [Todd Gao] remove memCompress
cb6873e [Shivaram Venkataraman] Merge pull request #126 from sun-rui/SPARKR-147
c5962eb [Todd Gao] further optimize using rawConnection
f04c6e0 [Sun Rui] [SPARKR-147] Support multiple directories as input to textFile.
b7de604 [Todd Gao] optimize execFunctionDeps loading in worker.R
4d4fc30 [Shivaram Venkataraman] Merge pull request #122 from cafreeman/master
b508877 [cafreeman] Update SparkR_IDE_Setup.sh
21ed9d7 [cafreeman] Update build.sbt
f73ec16 [cafreeman] Delete SparkR_IDE_Setup_Guide.md
d63b026 [cafreeman] Delete SparkR_Quick_Start_Guide.md
6e6cb62 [cafreeman] Update SparkR_IDE_Setup.sh
bc6042b [cafreeman] Update build.sbt
a8197d5 [cafreeman] Merge remote-tracking branch 'upstream/master'
d671564 [Zongheng Yang] Merge pull request #123 from shivaram/jcheck-void
76b8d00 [Zongheng Yang] Merge pull request #124 from shivaram/master
b690d58 [Shivaram Venkataraman] Specify how to change Spark versions in README
0fb003d [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into jcheck-void
1c227b4 [Shivaram Venkataraman] Also add a check in context.R
96812b6 [Shivaram Venkataraman] Check for exceptions after void method calls
f5c216d [cafreeman] Merge remote-tracking branch 'upstream/master'
90c8933 [Zongheng Yang] Merge pull request #121 from shivaram/fix-sort-order
bd0e3b4 [Shivaram Venkataraman] Fix saveAsTextFile test case
2e55f67 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into fix-sort-order
f10c607 [Shivaram Venkataraman] Merge pull request #118 from sun-rui/saveAsTextFile
6c9bfc0 [Sun Rui] Merge remote-tracking branch 'SparkR_upstream/master' into saveAsTextFile
6faedbe [cafreeman] Update SparkR_IDE_Setup_Guide.md
57008bc [cafreeman] Update SparkR_IDE_Setup.sh
bb1c17d [cafreeman] Update SparkR_IDE_Setup.sh
538bfdb [cafreeman] Update SparkR_Quick_Start_Guide.md
31322c6 [cafreeman] Update SparkR_IDE_Setup.sh
ca3f593 [Sun Rui] Refactor RRDD code.
df58d95 [cafreeman] Update SparkR_Quick_Start_Guide.md
b488c88 [cafreeman] Rename Spark_IDE_Setup.sh to SparkR_IDE_Setup.sh
b2545a4 [cafreeman] Added IDE Setup Guide
0ffb5de [cafreeman] Merge branch 'master' of https://github.com/cafreeman/SparkR-pkg
bd8fbfb [cafreeman] Merge remote-tracking branch 'upstream/master'
98efa5b [cafreeman] Added Quick Start Guide
3cf88f2 [Shivaram Venkataraman] Sort lists before comparing in unit tests Since Spark doesn't guarantee that shuffle results will always be in the same order, we need to sort the results before comparing for deterministic behavior
d621dbc [Shivaram Venkataraman] Merge pull request #120 from sun-rui/objectFile
c4a44d7 [Sun Rui] Add @seealso in comments and extract some common code into a function.
724e3a4 [cafreeman] Update Spark_IDE_Setup.sh
8153e5a [Sun Rui] [SPARKR-146] Support read/save object files in SparkR.
17f9909 [cafreeman] Update Spark_IDE_Setup.sh
a9eb080 [cafreeman] IDE Shell Script
64d800c [dputler] Merge remote branch 'upstream/master'
1fbdb2e [dputler] Added the ability for the user to specify a text file location throught the use of tilde expansion or just the file name if it is in the working directory.
d83c017 [Shivaram Venkataraman] Merge pull request #113 from sun-rui/stringHashCodeInC
a7d9cdb [Sun Rui] Fix build on Windows.
7d81b05 [Shivaram Venkataraman] Merge pull request #114 from hlin09/hlin09
47c4bb7 [hlin09] fix reviews
a457f7f [Shivaram Venkataraman] Merge pull request #116 from dputler/master
0fa48d1 [Shivaram Venkataraman] Merge pull request #117 from sun-rui/keyBy
85cfeb4 [Sun Rui] [SPARKR-144] Implement saveAsTextFile() in the RDD class.
09083d9 [Sun Rui] Add keyBy() to the RDD class.
caad5d7 [dputler] Adding the script to install software on the Cloudera Quick Start VM.
dca3d05 [hlin09] Minor fix.
ece5f7d [hlin09] Merge remote-tracking branch 'upstream/master' into hlin09
a40874b [hlin09] Use extendible accumulators aggregate the cogroup values.
d0347ce [Zongheng Yang] Merge pull request #112 from sun-rui/outer_join
492f76e [Sun Rui] Refine code and add description.
ba01358 [Shivaram Venkataraman] Merge pull request #115 from sun-rui/SPARKR-130
5c8e46e [Sun Rui] Fix per the review comments.
7190a2c [Sun Rui] Update comment to add a reference to storage levels.
1da705e [hlin09] Fix the review comments.
c4b77be [Sun Rui] [SPARKR-130] Add persist(storageLevel) API to RDD.
b424a1a [hlin09] Add function cogroup().
9770312 [Shivaram Venkataraman] Merge pull request #111 from hlin09/hlin09
cead7df [hlin09] fix review comments.
54f712e [Sun Rui] Implement string hash code in C.
425f0c6 [Sun Rui] Add leftOuterJoin() and rightOuterJoin() to the RDD class.
39509c7 [hlin09] add Rd file for foreach and foreachPartition.
63d6ac7 [hlin09] Adds function foreach() and foreachPartition().
9c954df [Zongheng Yang] Merge pull request #105 from sun-rui/join
c71228d [Sun Rui] Pre-allocate list with fixed length. Add test case for join() using string key.
bc3e9f6 [Shivaram Venkataraman] Merge pull request #108 from concretevitamin/take-optimize
c06fc90 [Zongheng Yang] Fix: only optimize for unserialized dataset case.
d399aeb [Zongheng Yang] Apply size-capping on logical representation instead of physical.
e4217dd [Zongheng Yang] Merge pull request #107 from shivaram/master
7952180 [Shivaram Venkataraman] Copy, use getLocalDirs from Spark Utils.scala
08e24c3 [Zongheng Yang] Merge pull request #109 from hlin09/hlin09
97d4e02 [Zongheng Yang] Min() upper-bound size with actual size.
bb779bf [hlin09] Rename the filter function to filterRDD to follow the API consistency. Filter() is also kept.
ce1661f [Zongheng Yang] Fix slow take(): deserialize only up to necessary # of elements.
4dca9b1 [Shivaram Venkataraman] Merge pull request #106 from hlin09/hlin09
1220d92 [hlin09] Adds function numPartitions().
2326a65 [Shivaram Venkataraman] Use SPARK_LOCAL_DIRS to create tmp files
e119757 [hlin09] Minor fix.
9c24c8b [hlin09] Adds function countByKey().
48fce67 [hlin09] Adds countByValue().
6679eef [Sun Rui] Update documentation for join().
70586b4 [Sun Rui] Add join() to the RDD class.
e6fb999 [Zongheng Yang] Merge pull request #103 from shivaram/rlibdir-fix
a21f146 [Shivaram Venkataraman] Merge pull request #102 from hlin09/hlin09
32eb619 [Shivaram Venkataraman] Merge pull request #104 from sun-rui/add_keys_values
d8692e9 [Sun Rui] Add keys() and values() for the RDD class.
18b9be1 [Shivaram Venkataraman] Allow users to set where SparkR is installed This also adds a warning if somebody tries to call sparkR.init multiple times.
a17f135 [hlin09] Adds tests for flatMap and flatMapValues.
4bcf59b [hlin09] Adds function flatMapValues.
4a193ef [Zongheng Yang] Merge pull request #101 from ashutoshraina/master
60d22f2 [Ashutosh Raina] changed sbt version
5400793 [Zongheng Yang] Merge pull request #98 from shivaram/windows-fixes-build
36d61a7 [Shivaram Venkataraman] Merge pull request #97 from hlin09/hlin09
f7d7d89 [hlin09] Remove redundant code in test.
6bbe823 [hlin09] minor style fix.
9b47f3a [Shivaram Venkataraman] Merge pull request #100 from hnahak87/patch-1
7f6e4ea [Harihar Nahak] Update logistic_regression.R
a605047 [Shivaram Venkataraman] Merge pull request #99 from hlin09/makefile
323151d [hlin09] Fix yar flag in Makefile to remove build error in Maven.
8911897 [hlin09] Make reserialize() private function in package.
79aee73 [Shivaram Venkataraman] Add notes on how to build SparkR on windows
49a99e7 [Shivaram Venkataraman] Clean up some commented code
ddc271b [Shivaram Venkataraman] Only append file:/// to non empty jar paths
a53952e [Shivaram Venkataraman] Add windows build scripts
325b179 [hlin09] Merge remote-tracking branch 'upstream/master' into hlin09
daf5040 [hlin09] Add reserialize() before union if two RDDs are not both serialized.
536afb1 [hlin09] Add new function of union().
7044677 [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into windows-fixes
d22a02d [Zongheng Yang] Merge pull request #94 from shivaram/windows-fixes-stdin
51924f7 [Shivaram Venkataraman] Merge pull request #90 from oscaroboto/master
eb97d85 [Shivaram Venkataraman] Merge pull request #96 from sun-rui/add_clarification_readme
5a128f4 [Sun Rui] Add clarification on setting Spark master when launching the SparkR shell.
187526a [oscaroboto] Update sparkR.R
32c567b [Shivaram Venkataraman] Merge pull request #95 from concretevitamin/master
4cd2d5e [Zongheng Yang] Notes about spark-ec2.
1c28e3b [Shivaram Venkataraman] Merge branch 'master' of https://github.com/amplab-extras/SparkR-pkg into windows-fixes
8e8a029 [Zongheng Yang] Merge pull request #92 from shivaram/sparkr-yarn
721043b [Zongheng Yang] Update README.md with YARN instructions.
1681f58 [Shivaram Venkataraman] Use temporary files for input instead of stdin This fixes a bug for Windows where stdin would get truncated
b084314 [oscaroboto] removed ... from example
44c93d4 [oscaroboto] Added example to SparkR.R
be82dcc [Shivaram Venkataraman] Merge pull request #93 from hlin09/hlin09
868554d [oscaroboto] Update sparkR.R
488ac47 [hlin09] Add generated Rd file of previous added functions, distinct() and mapValues().
b2740ad [hlin09] Add test for filter all elements. Add filter() as alias.
08d3631 [hlin09] Minor style fixes.
2c0e34f [hlin09] Adds function Filter(), which extracts the elements that satisfy a predicate.
5951d3b [Shivaram Venkataraman] Remove SBT plugin
4e70ced [oscaroboto] changed ExecutorEnv to sparkExecutorEnvMap, to make it consistent with sparkEnvirMap
903d18a [oscaroboto] changed executorEnv to sparkExecutorEnvMap, will do the same in R
f97346e [oscaroboto] executorEnv to lower-case e
88a524e [oscaroboto] Added LD_LIBRARY_PATH to the ExecutorEnv. This is need so that the nodes can find libjvm.so, or if the master has a different LD_LIBRARY_PATH then the nodes. Make sure to export LD_LIBRARY_PATH that includes the path to libjvm.so in the nodes.
1d208ae [oscaroboto] added the YARN_CONF_DIR to the classpath
8a9b75c [oscaroboto] forgot to change hm and ee inside the for loops
579db58 [Shivaram Venkataraman] Merge pull request #91 from sun-rui/add_max_min
4381efa [Sun Rui] use reduce() to implemement max() and min().
a5459c5 [Shivaram Venkataraman] Consolidate yarn flags
86b04eb [Shivaram Venkataraman] Don't use quotes around yarn
bf0797f [Shivaram Venkataraman] Add dependency on spark yarn module
af5fe77 [Shivaram Venkataraman] Fix SBT build, add dependency tree plugin
4917607 [Sun Rui] Add maximum() and minimum() API to RDD.
51bbbe4 [Shivaram Venkataraman] Changes to make SparkR work with YARN
9d5e3ab [oscaroboto] a few stylistic changes. Also change vars to sparkEnvirMap and eevars to ExecutorEnv, to match sparkR.R
578f545 [oscaroboto] a few stylistic changes
39eea2f [oscaroboto] Modification to dynamically create a sparkContext with YARN. Added .setExecutorEnv to the sparkConf in createSparkContext within the RRDD object. This modification was made together with sparkR.R
17ec42e [oscaroboto] A modification to dynamically create a sparkContext with YARN. sparkR.R modified to pass custom Jar file names and EnvironmentEnv to the sparkConf. RRDD.scala was also modified to accept the new inputs to creatSparkContext.
624ac9d [Shivaram Venkataraman] Merge pull request #87 from sun-rui/SPARKR-125
4f213db [Shivaram Venkataraman] Merge pull request #89 from sun-rui/SPARKR-108
eb833c5 [Shivaram Venkataraman] Merge pull request #88 from hlin09/hlin09
07bf971 [Sun Rui] [SPARKR-108] Implement map-side reduction for reduceByKey().
4accba1 [hlin09] Fixes style and adds an optional param 'numPartition' in distinct().
80d303a [hlin09] typo fixed.
e37a9b5 [hlin09] Adds function distinct() and mapValues().
08dac06 [Sun Rui] [SPARKR-125] Get the iterator of the parent RDD before launching a R worker process in compute() of RRDD/PairwiseRRDD
c4ba53c [Shivaram Venkataraman] Merge pull request #85 from edwardt/master
72a9d27 [root] reorder to keep relative ordering the same
f3fcb10 [root] fix up build.sbt also to match pom.xml
5ecbe3e [root] Make spark verison configurable in build script per ISSUE122
a44e63d [Shivaram Venkataraman] Merge pull request #84 from sun-rui/SPARKR-94
fbb5663 [Sun Rui] Add {} to one-line functions and add a test case for lookup where no match is found.
95beb4e [Shivaram Venkataraman] Merge pull request #82 from edwardt/master
36776c5 [edwardt] missed one 0.9.0 revert
b26deec [Sun Rui] [SPARKR-94] Add a method to get an element of a pair RDD object by key.
1ba256e [edwardt] Keep 0.9.0 and says uses 1.1.0 by default
5380c43 [root] missed one version
21f74da [root] upgrade to spark version 1.1.0 to match lastest merge list
ddfcde9 [root] merge
67d067a [Shivaram Venkataraman] Merge pull request #81 from sun-rui/SparkR-117
993868f [Sun Rui] [SPARKR-117] Update Spark dependency to 1.1.0
d20661a [Zongheng Yang] Merge pull request #80 from sun-rui/master
0b2da9f [Sun Rui] Update Rd file and add a test case for mapPartitions.
5879648 [Sun Rui] Add mapPartitions() method to RDD for API consistency.
c033461 [Shivaram Venkataraman] Merge pull request #79 from sun-rui/fix-kmeans
f62b77e [Sun Rui] Adjust coding style.
b40911d [Sun Rui] Fix syntax error in examples/kmeans.R.
5304451 [Shivaram Venkataraman] Merge pull request #78 from sun-rui/master
70ffbfb [Sun Rui] Fix a bug that modifications to build.sbt won't trigger rebuilding.
a25696c [Shivaram Venkataraman] Merge pull request #76 from edwardt/addjira
b8bbd93 [edwardt] Update README.md
615d930 [edwardt] Update README.md
e522e69 [edwardt] Update README.md
03e6ced [edwardt] Update README.md
3007015 [root] don't check in gedit buffer file'
c35c9a6 [root] Add where to enter bugs ad feeback
469eae3 [edwardt] Update README.md
61b4a43 [edwardt] Update Makefile (style uniformity)
ce3337d [edwardt] Update README.md
7ff68fc [root] Merge branch 'master' of https://github.com/edwardt/SparkR-pkg
16353f5 [root] add links to devtools and install_github
513b9e5 [Shivaram Venkataraman] Merge pull request #72 from edwardt/master
31608a4 [edwardt] Update Makefile (style uniformity)
4ffe146 [root] Makefile: factor out SPARKR_VERSION to reduce potential copy&paste error; cp & rm called with -f in build/clean phase; .gitignore includes checkpoints and unit test log generated by run-tests.sh
715275f [Zongheng Yang] Merge pull request #68 from shivaram/master
90e2083 [Shivaram Venkataraman] Add return type to hasNext
8eb983d [Shivaram Venkataraman] Fix up comment
2206164 [Shivaram Venkataraman] Delete temporary files after they are read This change deletes temporary files used for communication between Rscript and the JVM once they have been completely read.
5881da7 [Zongheng Yang] Merge pull request #67 from shivaram/improve-shuffle
81251e2 [Shivaram Venkataraman] Address code review comments
a5f573f [Shivaram Venkataraman] Use a better list append in shuffles This is helpful in scenarios where we have a large number of values in a bucket
388e64d [Shivaram Venkataraman] Merge pull request #55 from RevolutionAnalytics/master
e1f95b6 [Zongheng Yang] Merge pull request #65 from concretevitamin/parallelize-fix
fc1a71a [Zongheng Yang] Fix that collect(parallelize(sc,1:72,15)) drops elements.
b8204c5 [Zongheng Yang] Minor: update a URL in README.
86f30c3 [Antonio Piccolboni] better fix for amplab-extras/SparkR-pkg#53
b3c318d [Antonio Piccolboni] delayed loading to have all namespaces available.
f323e97 [Antonio Piccolboni] tentative fix for amplab-extras/SparkR-pkg#53
6f82269 [Zongheng Yang] Merge pull request #48 from shivaram/master
8f433e5 [Shivaram Venkataraman] Move up Hadoop in pom.xml and add back protobufs As Hadoop 1.0.4 doesn't use protobufs, we can't exclude protobufs from Spark always. This change tries to order the dependencies so that the shader first picks up Hadoop's protobufs over Mesos.
bfe7e26 [Shivaram Venkataraman] Merge pull request #36 from RevolutionAnalytics/vectorize-examples
059ae41 [Antonio Piccolboni] and more formatting
9dbd531 [Antonio Piccolboni] more formatting per committer request
948738a [Antonio Piccolboni] converted tabs to spaces per project request
49f5f5a [Shivaram Venkataraman] Merge pull request #35 from shivaram/master
3eb5ad3 [Shivaram Venkataraman] on_failure -> after_failure in travis.yml
139bdee [Shivaram Venkataraman] Cache sbt, maven, ivy dependencies
4ebced2 [Shivaram Venkataraman] Merge pull request #34 from shivaram/master
8437061 [Shivaram Venkataraman] Exclude protobuf from Spark dependency in Maven This avoids pulling in multiple versions of protobuf from Mesos and Hadoop.
91aa527 [Antonio Piccolboni] vectorized version, 36s 10 slices 10^6 per slice. The older version takes 30 sec on 1/10th of data.
f137a57 [Antonio Piccolboni] for rstudio users
1f7ffb0 [Antonio Piccolboni] implemented using matrices and vectorized calls wherever possible
46b23df [Antonio Piccolboni] replace require with library
b15d7db [Antonio Piccolboni] faster parsing
8b7aeb3 [Antonio Piccolboni] 22x speed improvement, 3X mem impovement
c5bce07 [Zongheng Yang] Merge pull request #30 from shivaram/string-tests
21fa2d8 [Shivaram Venkataraman] Fix bug where serialized was not changed for RRRD Reason: When an RRDD is created in getJRDD we have converted any possibly unserialized RDD to a serialized RDD.
9d1ea20 [Shivaram Venkataraman] Merge branch 'master' of github.com:amplab/SparkR-pkg into string-tests
7b9348c [Shivaram Venkataraman] Add tests for partition with string keys Add two tests one with a string array and one from a textFile to test both codepaths
aacd726 [Shivaram Venkataraman] Update README with maven proxy instructions
803e62c [Shivaram Venkataraman] Merge pull request #28 from concretevitamin/master
7c093e6 [Zongheng Yang] Use inherits() to test an object's class.
061c591 [Shivaram Venkataraman] Merge pull request #26 from hafen/master
90f9fda [Ryan Hafen] Fix isRdd() to properly check for class
5b10cc7 [Zongheng Yang] Merge pull request #24 from shivaram/master
7014f83 [Shivaram Venkataraman] Remove unused transformers in maven's pom.xml
b00cea5 [Shivaram Venkataraman] Add support for a Maven build
11ec9b2 [Shivaram Venkataraman] Merge pull request #12 from concretevitamin/pipelined
6b18a90 [Zongheng Yang] Merge branch 'master' into pipelined
57127b8 [Zongheng Yang] Merge pull request #23 from shivaram/master
1ac3940 [Zongheng Yang] Review feedback.
a06fb34 [Zongheng Yang] Remove outdated comment.
0a1fc13 [Shivaram Venkataraman] Fixes for using SparkR with Hadoop2. 1. Exclude ASM, Netty from Hadoop similar to Spark. 2. Concat services files to ensure HDFS filesystems work. 3. Update README with an example
9a1db44 [Zongheng Yang] Merge pull request #22 from shivaram/master
e462448 [Shivaram Venkataraman] Use `$` for calling `put` instead of .jrcall
ed4559a [Shivaram Venkataraman] Add support for passing Spark environment vars This change creates a new `createSparkContext` method in RRDD as we can't pass Map<String, String> through rJava. Also use SPARK_MEM in local mode to increase heap size and update the README with some examples.
10228fb [Shivaram Venkataraman] Merge pull request #20 from concretevitamin/digit-ex
1398d9f [Zongheng Yang] Add linear_solver_mnist to examples/.
d484c2a [Zongheng Yang] Add tests for actions on PipelinedRDD.
d9cb95c [Zongheng Yang] Add setCheckpointDir() to context.R; comment fix.
f8bc8a9 [Zongheng Yang] Minor edits per Shivaram's comments.
8cd67f7 [Shivaram Venkataraman] Merge pull request #15 from shivaram/master
d4468a9 [Shivaram Venkataraman] Remove trailing comma
e2714b8 [Shivaram Venkataraman] Remove Apache Staging repo and update README
334eace [Zongheng Yang] Add a multi-transformation test to benchmark on pipelining.
5650ad7 [Zongheng Yang] Put serialized field inside env for both RDD and PipelinedRDD.
0b9e8bb [Zongheng Yang] First cut at PipelinedRDD.
a4c431e [Zongheng Yang] Add `isCheckpointed` field and checkpoint().
dac0795 [Zongheng Yang] Minor inline comment style fix.
bfb8e26 [Zongheng Yang] Add isCached field (inside an env) and unpersist().
295bff6 [Zongheng Yang] Merge pull request #11 from shivaram/master
4cb209c [Shivaram Venkataraman] Search rLibDir in worker before libPaths This ensures we pick up the SparkR intended and not an older version installed on the same machine
ef198ff [Zongheng Yang] Merge pull request #10 from shivaram/unit-tests
e0557a8 [Shivaram Venkataraman] Update travis to install plyr
8b18bc1 [Shivaram Venkataraman] Merge branch 'master' of github.com:amplab/SparkR-pkg into unit-tests
4a9ca31 [Shivaram Venkataraman] Use smaller broadcast and plyr instead of Matrix Matrix package takes around 2s to load and slows down unit tests.
21c6a61 [Zongheng Yang] Merge pull request #8 from shivaram/master
08c2947 [Shivaram Venkataraman] Move dev install directory to front of libPaths
bda42ee [Shivaram Venkataraman] Merge pull request #7 from JoshRosen/travis
cc5f5c0 [Josh Rosen] Add Travis CI integration (using craigcitro/r-travis)
b6c864b [Shivaram Venkataraman] Merge pull request #6 from concretevitamin/env-style-fix
4fcef22 [Zongheng Yang] Use one style ($) for accessing names in environments.
8a948c6 [Shivaram Venkataraman] Merge pull request #4 from shivaram/master
24978eb [Shivaram Venkataraman] Update README to use install_github
8899db4 [Shivaram Venkataraman] Update TODO.md
91792de [Shivaram Venkataraman] Update Spark requirements
f34f4bf [Shivaram Venkataraman] Check tests for failures and output error msg
cd750d3 [Shivaram Venkataraman] Update run-tests to use new path
1877b7c [Shivaram Venkataraman] Unset R_TESTS to make tests work with R CMD check Also silence Akka remoting logs and update Makefile to build on log4j changes
e60e18a [Shivaram Venkataraman] Update README to remove Spark installation notes
4450189 [Shivaram Venkataraman] Add Spark 0.9 dependency from Apache Staging Also clean up assembly jar from inst on make clean
5eb2131 [Shivaram Venkataraman] Update repo path in README
ec8210e [Shivaram Venkataraman] Remove broadcastId hack as it is public in Spark
9f0e080 [Shivaram Venkataraman] Merge branch 'install-github'
5c88fbd [Shivaram Venkataraman] Add helper script to run tests
77450a1 [Shivaram Venkataraman] Remove dependency on Spark Logging
6cb00d1 [Shivaram Venkataraman] Update README and add helper script install-dev.sh
28346ca [Shivaram Venkataraman] Only normalize if SPARK_HOME is not empty
0fd6571 [Shivaram Venkataraman] Normalize SPARK_HOME before passing it
ff96d5c [Shivaram Venkataraman] Pass in SPARK_HOME and jar file path
34c4dce [Shivaram Venkataraman] Move src into pkg and update Makefile This enables the package to be installed using install_github using devtools and automates the build procedure.
b25afed [Shivaram Venkataraman] Change package name to edu.berkeley.cs.amplab
c691464 [Shivaram Venkataraman] Add Apache 2.0 License file
27a4a4b [Shivaram Venkataraman] Add notes on how to compile roxygen2 docs
ca63844 [Shivaram Venkataraman] Add broadcast documentation Also generate documentation for sample, takeSample etc.
e4dd976 [Shivaram Venkataraman] Update TODO.md
e42d435 [Shivaram Venkataraman] Add support for broadcast variables
6b638e7 [Shivaram Venkataraman] Add the assembly jar to SparkContext
bf24e32 [Shivaram Venkataraman] Merge branch 'master' of github.com:amplab/SparkR-pkg
43c05ce [Zongheng Yang] Fix a flaky/incorrect test for sampleRDD().
c6a9dfc [Zongheng Yang] Initial port of the kmeans example.
6885581 [Zongheng Yang] Implement element-level sampleRDD() and takeSample() with tests.
d3a4987 [Zongheng Yang] Add a test for lapplyPartitionsWithIndex on pairwise RDD.
c7899c1 [Zongheng Yang] Add lapplyPartitionsWithIndex, with a test and an alias function.
a9a7436 [Shivaram Venkataraman] Add DFC example from Tselil, Benjamin and Jonah
fbc5a95 [Zongheng Yang] Implement take() and takeSample().
c4a3409 [Shivaram Venkataraman] Use RDD instead of RRDD
dfad3f5 [Zongheng Yang] Add test_utils.R: a unit test for convertJListToRList().
a45227d [Zongheng Yang] Update .gitignore.
238fe6e [Zongheng Yang] Add a unit test for textFile().
a88898b [Zongheng Yang] Rename test_rrd to test_rrdd
10c8baa [Shivaram Venkataraman] Make SparkR work as a standalone package. Changes include: 1. Adding a new `sbt` project that builds RRDD.scala 2. Change the onLoad functions to load the assembly jar for SparkR 3. Set rLibDir in RRDD.scala and worker.R to load things correctly
78adcd8 [Shivaram Venkataraman] Add a gitignore
ca6108f [Shivaram Venkataraman] Merge branch 'SparkR-scalacode' of ../SparkR
999bd61 [Shivaram Venkataraman] Update collectPartition in R and use ClassTag
c58f63e [Shivaram Venkataraman] Update collectPartition in R and use ClassTag
48265fd [Shivaram Venkataraman] Use new version of collectPartitions in take
d4fe086 [Shivaram Venkataraman] Move collectPartitions to JavaRDDLike Also remove numPartitions in JavaRDD and update R code
bfecd7b [Shivaram Venkataraman] Scala 2.10 changes 1. Update sparkR script 2. Use classTag instead of classManifest
092a4b3 [Shivaram Venkataraman] Add combineByKey, update TODO
ac0d81d [Shivaram Venkataraman] Add more documentation
d1dc3fa [Shivaram Venkataraman] Add more documentation
c515e3a [Shivaram Venkataraman] Update TODO
db56a34 [Shivaram Venkataraman] Add a test case for include package
41cea51 [Shivaram Venkataraman] Ensure all parent environments are serialized. Also add a test case with an inline function
a978e84 [Shivaram Venkataraman] Add support to include packages in the worker
12bf8ce [Shivaram Venkataraman] Add support to include packages in the worker
fb7e72c [Shivaram Venkataraman] Cleanup TODO
16ac314 [Shivaram Venkataraman] Add documentation for functions in context, sparkR
85b1d25 [Shivaram Venkataraman] Set license to Apache
88f1101 [Shivaram Venkataraman] Add unit test running instructions
c40768e [Shivaram Venkataraman] Update TODO
0c7efbf [Shivaram Venkataraman] Refactor RRDD.scala and add comments to functions
5880d42 [Shivaram Venkataraman] Refactor RRDD.scala and add comments to functions
2dee36c [Shivaram Venkataraman] Remove empty test file
a82219b [Shivaram Venkataraman] Update TODOs
5db00dc [Shivaram Venkataraman] Add reduceByKey, groupByKey and refactor shuffle Other changes include 1. Adding unit tests for basic RDD functions and shuffle 2. Add a word count example 3. Change the dependency serialization to handle double loading of SparkR package 4. Allow partitionBy to operate on any RDDs to create pair-wise RDD.
f196479 [Shivaram Venkataraman] Add reduceByKey, groupByKey and refactor shuffle Other changes include 1. Adding unit tests for basic RDD functions and shuffle 2. Add a word count example 3. Change the dependency serialization to handle double loading of SparkR package 4. Allow partitionBy to operate on any RDDs to create pair-wise RDD.
987e36f [Shivaram Venkataraman] Add perf todo
0b03265 [Shivaram Venkataraman] Update TODO with testing, docs todo
685aaad [Zongheng Yang] First cut at refactoring worker.R. Remove pairwiseWorker.R.
95b9ddc [Zongheng Yang] First cut at refactoring worker.R. Remove pairwiseWorker.R.
4f00895 [Zongheng Yang] Remove the unnecessary `pairwise' flag in RRDD class. Reasons:
75d36d9 [Zongheng Yang] Working versions: partitionBy() and collectPartition() for RRDD.
e3fbd9d [Zongheng Yang] Working versions: partitionBy() and collectPartition() for RRDD.
67a4335 [Zongheng Yang] Add unit test for parallelize() and collect() pairwise data.
100ae65 [Zongheng Yang] Properly parallelize() and collect() pairwise data.
cd0a5e2 [Zongheng Yang] Properly parallelize() and collect() pairwise data.
aea16c3 [Zongheng Yang] WIP: second cut at partitionBy. Running into R/Scala communication issues.
45eb943 [Zongheng Yang] WIP: second cut at partitionBy. Running into R/Scala communication issues.
11c893b [Zongheng Yang] WIP: need to figure out the logic of (whether or not) shipping a hash func
82c201a [Zongheng Yang] WIP: need to figure out the logic of (whether or not) shipping a hash func
b3bfad2 [Zongheng Yang] Update TODO: take() done.
0e45293 [Zongheng Yang] Add ability to parallelize key-val collections in R.
f60406a [Zongheng Yang] Add ability to parallelize key-val collections in R.
7d7fe3b [Zongheng Yang] Re-implement take(): take a partition at a time and append.
a054e55 [Zongheng Yang] Fix take() tests(): mode difference.
9de0935 [Zongheng Yang] Implement take() for RRDD.
1e4427e [Zongheng Yang] Implement take() for RRDD.
ec3cd67 [Shivaram Venkataraman] Use temp file in Spark to pipe output
417aaed [Shivaram Venkataraman] Use temp file in Spark to pipe output
bb0a3c3 [Shivaram Venkataraman] Add conf directory to classpath
9594d8a [Shivaram Venkataraman] Clean up LR example
3b26b58 [Shivaram Venkataraman] Add a list of things to do.
cabce68 [Shivaram Venkataraman] Fix warnings from package check
fde3f9c [Shivaram Venkataraman] Flatten by default and disable recursive unlist
ab2e061 [Shivaram Venkataraman] Create LIB_DIR before installing SparkR package
555220a [Shivaram Venkataraman] Add readme and update Makefile
1319cda [Shivaram Venkataraman] Make standalone programs run with sparkR
ae19fa8 [Shivaram Venkataraman] Add support for cache and use `tempfile`
4e89ca4 [Shivaram Venkataraman] Add support for apply, reduce, count Also serialize closures using `save` and add two examples
25a0bea [Shivaram Venkataraman] Add support for apply, reduce, count Also serialize closures using `save` and add two examples
f50223f [Zongheng Yang] Make parallelize() and collect() use lists. Add a few more tests for them.
fc7693f [Zongheng Yang] Refactor and enhance the previously added unit test a little bit.
6de9b81 [Zongheng Yang] Add a simple unit test for parallelize().
8b95155 [Zongheng Yang] Add testthat skeleton infrastructure
ef305bf [Zongheng Yang] parallelize() followed by collect() now work for vectors/lists of strings and numerics (should work for other primitives as well).
dc16af4 [Zongheng Yang] Comment: toArray() allocates memory for a copy
f50121e [Zongheng Yang] Make parallelize() return JavaRDD[Array[Byte]]. Add RRDD.scala with a helper function in the singleton object.
46eb063 [Zongheng Yang] Make parallelize() return JavaRDD[Array[Byte]]. Add RRDD.scala with a helper function in the singleton object.
6b4938a [Zongheng Yang] parallelize(): a raw can be parallelized by JavaSparkContext and get back JavaRDD
978aa0f [Zongheng Yang] Add parallelize() skeleton: only return serialized slices now
84c1fd2 [Zongheng Yang] Use .jsimplify() to get around generic List's get() type erasure problem
f16b891 [Zongheng Yang] Convert a few reflectionc alls to .jcall
1284c13 [Zongheng Yang] WIP on collect(): JavaListToRList() failed with errors.
4c2e516 [Zongheng Yang] Add simple prototype of S4 class RRDD. Make TextFile() returns an RRDD.
82aa17a [Zongheng Yang] Add textFile()
83ce63f [Zongheng Yang] Create a JavaSparkContext and save it in .sparkEnv using sparkR.init()
01cdf0e [Zongheng Yang] Add Makefile for SparkR
fc9cae2 [Shivaram Venkataraman] Add skeleton R package
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Prior to this change, the unit test for SPARK-3426 did not clone the
original SparkConf, which meant that that test did not use the options
set by suites that subclass ShuffleSuite.scala. This commit fixes that
problem.
JoshRosen would be great if you could take a look at this, since you wrote this
test originally.
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes #5401 from kayousterhout/SPARK-6753 and squashes the following commits:
368c540 [Kay Ousterhout] [SPARK-6753] Clone SparkConf in ShuffleSuite tests
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The TaskContextHelper was originally necessary because TaskContext was written in Java, which does
not have a way to specify that classes are package-private, so TaskContextHelper existed to work
around this. Now that TaskContext has been re-written in Scala, this class is no longer necessary.
rxin can you look at this? It looks like you missed this bit of cleanup when you moved TaskContext from Java to Scala in #4324
cc ScrapCodes and pwendell who added this originally.
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes #5402 from kayousterhout/SPARK-6754 and squashes the following commits:
f089800 [Kay Ousterhout] [SPARK-6754] Remove unnecessary TaskContextHelper
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This patch fixes a memory leak in the DAGScheduler, which caused us to leak a map entry per submitted stage. The problem is that the OutputCommitCoordinator needs to be informed when stages end in order to remove entries from its `authorizedCommitters` map, but the DAGScheduler only called it in one of the four code paths that are used to mark stages as completed.
This patch fixes this issue by consolidating the processing of stage completion into a new `markStageAsFinished` method and updates DAGSchedulerSuite's `assertDataStructuresEmpty` assertion to also check the OutputCommitCoordinator data structures. I've also added a comment at the top of DAGScheduler so that we remember to update this test when adding new data structures.
Author: Josh Rosen <joshrosen@databricks.com>
Closes #5397 from JoshRosen/SPARK-6737 and squashes the following commits:
af3b02f [Josh Rosen] Consolidate stage completion handling code in a single method.
e96ce3a [Josh Rosen] Consolidate stage completion handling code in a single method.
3052aea [Josh Rosen] Comment update
7896899 [Josh Rosen] Fix SPARK-6737 by informing OutputCommitCoordinator of all stage end events.
4ead1dc [Josh Rosen] Add regression tests for SPARK-6737
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that has space in its path"
This reverts commit 596ba77c5fdca79486396989e549632153055caf.
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space in its path
escape spaces in the arguments.
Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>
Closes #5347 from tsudukim/feature/SPARK-6568 and squashes the following commits:
9180aaf [Masayoshi TSUZUKI] [SPARK-6568] spark-shell.cmd --jars option does not accept the jar that has space in its path
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Invoking .size on arrays is valid, but requires an implicit conversion to SeqLike. This incurs a compile time overhead and more importantly a runtime overhead, as the Array must be wrapped before the method can be invoked. For example, the difference in generated byte code is:
public int withSize();
Code:
0: getstatic #23 // Field scala/Predef$.MODULE$:Lscala/Predef$;
3: aload_0
4: invokevirtual #25 // Method array:()[I
7: invokevirtual #29 // Method scala/Predef$.intArrayOps:([I)Lscala/collection/mutable/ArrayOps;
10: invokeinterface #34, 1 // InterfaceMethod scala/collection/mutable/ArrayOps.size:()I
15: ireturn
public int withLength();
Code:
0: aload_0
1: invokevirtual #25 // Method array:()[I
4: arraylength
5: ireturn
Author: sksamuel <sam@sksamuel.com>
Closes #5376 from sksamuel/master and squashes the following commits:
77ec261 [sksamuel] Replace use of .size with .length for Arrays.
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Author: Vinod K C <vinod.kc@huawei.com>
Closes #5384 from vinodkc/Suppression_Scala_existential_code and squashes the following commits:
82a3a1f [Vinod K C] Added scala.language.existentials
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https://issues.apache.org/jira/browse/SPARK-3591
The output after this patch:
>doggie153:/opt/oss/spark-1.3.0-bin-hadoop2.4/bin # ./spark-submit --class org.apache.spark.examples.SparkPi --master yarn-cluster ../lib/spark-examples*.jar
15/03/31 21:15:25 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
15/03/31 21:15:25 INFO RMProxy: Connecting to ResourceManager at doggie153/10.177.112.153:8032
15/03/31 21:15:25 INFO Client: Requesting a new application from cluster with 4 NodeManagers
15/03/31 21:15:25 INFO Client: Verifying our application has not requested more than the maximum memory capability of the cluster (8192 MB per container)
15/03/31 21:15:25 INFO Client: Will allocate AM container, with 896 MB memory including 384 MB overhead
15/03/31 21:15:25 INFO Client: Setting up container launch context for our AM
15/03/31 21:15:25 INFO Client: Preparing resources for our AM container
15/03/31 21:15:26 INFO Client: Uploading resource file:/opt/oss/spark-1.3.0-bin-hadoop2.4/lib/spark-assembly-1.4.0-SNAPSHOT-hadoop2.4.1.jar -> hdfs://doggie153:9000/user/root/.sparkStaging/application_1427257505534_0016/spark-assembly-1.4.0-SNAPSHOT-hadoop2.4.1.jar
15/03/31 21:15:27 INFO Client: Uploading resource file:/opt/oss/spark-1.3.0-bin-hadoop2.4/lib/spark-examples-1.3.0-hadoop2.4.0.jar -> hdfs://doggie153:9000/user/root/.sparkStaging/application_1427257505534_0016/spark-examples-1.3.0-hadoop2.4.0.jar
15/03/31 21:15:28 INFO Client: Setting up the launch environment for our AM container
15/03/31 21:15:28 INFO SecurityManager: Changing view acls to: root
15/03/31 21:15:28 INFO SecurityManager: Changing modify acls to: root
15/03/31 21:15:28 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(root); users with modify permissions: Set(root)
15/03/31 21:15:28 INFO Client: Submitting application 16 to ResourceManager
15/03/31 21:15:28 INFO YarnClientImpl: Submitted application application_1427257505534_0016
15/03/31 21:15:28 INFO Client: ... waiting before polling ResourceManager for application state
15/03/31 21:15:33 INFO Client: ... polling ResourceManager for application state
15/03/31 21:15:33 INFO Client: Application report for application_1427257505534_0016 (state: RUNNING)
15/03/31 21:15:33 INFO Client:
client token: N/A
diagnostics: N/A
ApplicationMaster host: doggie157
ApplicationMaster RPC port: 0
queue: default
start time: 1427807728307
final status: UNDEFINED
tracking URL: http://doggie153:8088/proxy/application_1427257505534_0016/
user: root
/cc andrewor14
Author: WangTaoTheTonic <wangtao111@huawei.com>
Closes #5297 from WangTaoTheTonic/SPARK-3591 and squashes the following commits:
c76d232 [WangTaoTheTonic] wrap lines
16c90a8 [WangTaoTheTonic] move up lines to avoid duplicate
fea390d [WangTaoTheTonic] log failed/killed report, style and comment
be1cc2e [WangTaoTheTonic] reword
f0bc54f [WangTaoTheTonic] minor: expose appid in excepiton messages
ba9b22b [WangTaoTheTonic] wrong config name
e1a4013 [WangTaoTheTonic] revert to the old version and do some robust
19706c0 [WangTaoTheTonic] add a config to control whether to forget
0cbdce8 [WangTaoTheTonic] fire and forget for YARN cluster mode
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Currently, the driver's executorId is set to `<driver>`. This choice of ID was present in older Spark versions, but it has started to cause problems now that executorIds are used in more contexts, such as Ganglia metric names or driver thread-dump links the web UI. The angle brackets must be escaped when embedding this ID in XML or as part of URLs and this has led to multiple problems:
- https://issues.apache.org/jira/browse/SPARK-6484
- https://issues.apache.org/jira/browse/SPARK-4313
The simplest solution seems to be to change this id to something that does not contain any special characters, such as `driver`.
I'm not sure whether we can perform this change in a patch release, since this ID may be considered a stable API by metrics users, but it's probably okay to do this in a major release as long as we document it in the release notes.
Author: Josh Rosen <joshrosen@databricks.com>
Closes #5372 from JoshRosen/driver-id-fix and squashes the following commits:
42d3c10 [Josh Rosen] Clarify comment
0c5d04b [Josh Rosen] Add backwards-compatibility in BlockManagerId.isDriver
7ff12e0 [Josh Rosen] Change SparkContext.DRIVER_IDENTIFIER from <driver> to driver
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MapOutputTrackerMasterEndpoint
This is the second PR for [SPARK-6602]. It updated MapOutputTrackerMasterActor and its unit tests.
cc rxin
Author: zsxwing <zsxwing@gmail.com>
Closes #5371 from zsxwing/rpc-rewrite-part2 and squashes the following commits:
fcf3816 [zsxwing] Fix the code style
4013a22 [zsxwing] Add doc for uncaught exceptions in RpcEnv
93c6c20 [zsxwing] Add an example of UnserializableException and add ErrorMonitor to monitor errors from Akka
134fe7b [zsxwing] Update MapOutputTrackerMasterActor to MapOutputTrackerMasterEndpoint
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This PR replaced the following `Actor`s to `RpcEndpoint`:
1. HeartbeatReceiver
1. ExecutorActor
1. BlockManagerMasterActor
1. BlockManagerSlaveActor
1. CoarseGrainedExecutorBackend and subclasses
1. CoarseGrainedSchedulerBackend.DriverActor
This is the first PR. I will split the work of SPARK-6602 to several PRs for code review.
Author: zsxwing <zsxwing@gmail.com>
Closes #5268 from zsxwing/rpc-rewrite and squashes the following commits:
287e9f8 [zsxwing] Fix the code style
26c56b7 [zsxwing] Merge branch 'master' into rpc-rewrite
9cc825a [zsxwing] Rmove setupThreadSafeEndpoint and add ThreadSafeRpcEndpoint
30a9036 [zsxwing] Make self return null after stopping RpcEndpointRef; fix docs and error messages
705245d [zsxwing] Fix some bugs after rebasing the changes on the master
003cf80 [zsxwing] Update CoarseGrainedExecutorBackend and CoarseGrainedSchedulerBackend to use RpcEndpoint
7d0e6dc [zsxwing] Update BlockManagerSlaveActor to use RpcEndpoint
f5d6543 [zsxwing] Update BlockManagerMaster to use RpcEndpoint
30e3f9f [zsxwing] Update ExecutorActor to use RpcEndpoint
478b443 [zsxwing] Update HeartbeatReceiver to use RpcEndpoint
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Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes #5340 from vanzin/SPARK-6688 and squashes the following commits:
ccfddd9 [Marcelo Vanzin] Resolve at the source.
20d2a34 [Marcelo Vanzin] [SPARK-6688] [core] Always use resolved URIs in EventLoggingListener.
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retrieving HeartbeatReceiver
This PR moved the code of creating `HeartbeatReceiver` above the code of creating `schedulerBackend` to resolve the race condition.
Author: zsxwing <zsxwing@gmail.com>
Closes #5306 from zsxwing/SPARK-6640 and squashes the following commits:
840399d [zsxwing] Don't send TaskScheduler through Akka
a90616a [zsxwing] Fix docs
dd202c7 [zsxwing] Fix typo
d7c250d [zsxwing] Fix the race condition of creating HeartbeatReceiver and retrieving HeartbeatReceiver
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DAGSchedulerEventProcessLoop dies
I've added a timeout and retry loop around the SparkContext shutdown code that should fix this deadlock. If a SparkContext shutdown is in progress when another thread comes knocking, it will wait for 10 seconds for the lock, then fall through where the outer loop will re-submit the request.
Author: Ilya Ganelin <ilya.ganelin@capitalone.com>
Closes #5277 from ilganeli/SPARK-6492 and squashes the following commits:
8617a7e [Ilya Ganelin] Resolved merge conflict
2fbab66 [Ilya Ganelin] Added MIMA Exclude
a0e2c70 [Ilya Ganelin] Deleted stale imports
fa28ce7 [Ilya Ganelin] reverted to just having a single stopped
76fc825 [Ilya Ganelin] Updated to use atomic booleans instead of the synchronized vars
6e8a7f7 [Ilya Ganelin] Removing unecessary null check for now since i'm not fixing stop ordering yet
cdf7073 [Ilya Ganelin] [SPARK-6492] Moved stopped=true back to the start of the shutdown sequence so this can be addressed in a seperate PR
7fb795b [Ilya Ganelin] Spacing
b7a0c5c [Ilya Ganelin] Import ordering
df8224f [Ilya Ganelin] Added comment for added lock
343cb94 [Ilya Ganelin] [SPARK-6492] Added timeout/retry logic to fix a deadlock in SparkContext shutdown
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If there is a failure in the Hadoop backend while calling
writer.write, we should remember this original exception,
and try to call writer.close(), but if that fails as well,
still report the original exception.
Note that, if writer.write fails, it is likely that writer
was left in an invalid state, and so actually makes it more
likely that writer.close will also fail. Which just increases
the chances for writer.write's exception to be suppressed.
This patch introduces an admittedly potentially too cute
Utils.tryWithSafeFinally method to handle the try/finally
gyrations.
Author: Stephen Haberman <stephen@exigencecorp.com>
Closes #5223 from stephenh/do_not_suppress_writer_exception and squashes the following commits:
c7ad53f [Stephen Haberman] [SPARK-6560][CORE] Do not suppress exceptions from writer.write.
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This builds on my earlier pull requests and turns on the explicit type checking in scalastyle.
Author: Reynold Xin <rxin@databricks.com>
Closes #5342 from rxin/SPARK-6428 and squashes the following commits:
7b531ab [Reynold Xin] import ordering
2d9a8a5 [Reynold Xin] jl
e668b1c [Reynold Xin] override
9b9e119 [Reynold Xin] Parenthesis.
82e0cf5 [Reynold Xin] [SPARK-6428] Turn on explicit type checking for public methods.
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EventLoop.onReceive/onError/onStart doesn't call onStop
Author: zsxwing <zsxwing@gmail.com>
Closes #5280 from zsxwing/SPARK-6621 and squashes the following commits:
521125e [zsxwing] Fix the bug that calling EventLoop.stop in EventLoop.onReceive and EventLoop.onError doesn't call onStop
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spark.history.fs.logDirectory
The config option is spark.history.fs.logDirectory, not spark.fs.history.logDirectory. So the descriptionof should be changed. Thanks.
Author: KaiXinXiaoLei <huleilei1@huawei.com>
Closes #5332 from KaiXinXiaoLei/historyConfig and squashes the following commits:
5ffbfb5 [KaiXinXiaoLei] the describe of jobHistory config is error
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This fixes the thread leak. I also changed the unit test to keep track
of allocated contexts and make sure they're closed after tests are
run; this is needed since some tests use this pattern:
val sc = createContext()
doSomethingThatMayThrow()
sc.stop()
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes #5311 from vanzin/SPARK-6650 and squashes the following commits:
652c73b [Marcelo Vanzin] Nits.
5711512 [Marcelo Vanzin] More exception safety.
cc5a744 [Marcelo Vanzin] Stop alloc manager before scheduler.
9886f69 [Marcelo Vanzin] [SPARK-6650] [core] Stop ExecutorAllocationManager when context stops.
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Use Option for ActiveJob.properties to avoid NPE bug
Author: Hung Lin <hung.lin@gmail.com>
Closes #5124 from hunglin/SPARK-6414 and squashes the following commits:
2290b6b [Hung Lin] [SPARK-6414][core] Fix NPE in SparkContext.cancelJobGroup()
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The reused address on server side had caused the server can not acknowledge the connected connections, remove it.
This PR will retry once after timeout, it also add a timeout at client side.
Author: Davies Liu <davies@databricks.com>
Closes #5324 from davies/collect_hang and squashes the following commits:
e5a51a2 [Davies Liu] remove setReuseAddress
7977c2f [Davies Liu] do retry on client side
b838f35 [Davies Liu] retry after timeout
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Before diving into review #4450 I did a look through the existing shuffle
code to learn how it works. Unfortunately, there are some very
confusing things in this code. This patch makes a few small changes
to simplify things. It is not easily to concisely describe the changes
because of how convoluted the issues were, but they are fairly small
logically:
1. There is a trait named `ShuffleBlockManager` that only deals with
one logical function which is retrieving shuffle block data given shuffle
block coordinates. This trait has two implementors FileShuffleBlockManager
and IndexShuffleBlockManager. Confusingly the vast majority of those
implementations have nothing to do with this particular functionality.
So I've renamed the trait to ShuffleBlockResolver and documented it.
2. The aforementioned trait had two almost identical methods, for no good
reason. I removed one method (getBytes) and modified callers to use the
other one. I think the behavior is preserved in all cases.
3. The sort shuffle code uses an identifier "0" in the reduce slot of a
BlockID as a placeholder. I made it into a constant since it needs to
be consistent across multiple places.
I think for (3) there is actually a better solution that would avoid the
need to do this type of workaround/hack in the first place, but it's more
complex so I'm punting it for now.
Author: Patrick Wendell <patrick@databricks.com>
Closes #5286 from pwendell/cleanup and squashes the following commits:
c71fbc7 [Patrick Wendell] Open interface back up for testing
f36edd5 [Patrick Wendell] Code review feedback
d1c0494 [Patrick Wendell] Style fix
a406079 [Patrick Wendell] [HOTFIX] Some clean-up in shuffle code.
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in additional-metrics.js
In additional-metrics.js, there are some selector notation like `input:checkbox` but JQuery's official document says `input[type="checkbox"]` is better.
https://api.jquery.com/checkbox-selector/
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes #5254 from sarutak/SPARK-6597 and squashes the following commits:
a253bc4 [Kousuke Saruta] Replaced input:checkbox with input[type="checkbox"]
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Hi all - this patch changes the Stage class to an abstract class and introduces two new classes that extend it: ShuffleMapStage and ResultStage - with the goal of increasing readability of the DAGScheduler class. Their usage is updated within DAGScheduler.
Author: Ilya Ganelin <ilya.ganelin@capitalone.com>
Author: Ilya Ganelin <ilganeli@gmail.com>
Closes #4708 from ilganeli/SPARK-4655 and squashes the following commits:
c248924 [Ilya Ganelin] Merge branch 'SPARK-4655' of github.com:ilganeli/spark into SPARK-4655
d930385 [Ilya Ganelin] Fixed merge conflict from
a9a765f [Ilya Ganelin] Update DAGScheduler.scala
c03563c [Ilya Ganelin] Minor fixeS
c39e971 [Ilya Ganelin] Added return typing for public methods
845bc87 [Ilya Ganelin] Merge branch 'SPARK-4655' of github.com:ilganeli/spark into SPARK-4655
e8031d8 [Ilya Ganelin] Minor string fixes
4ec53ac [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-4655
c004f62 [Ilya Ganelin] Update DAGScheduler.scala
a2cb03f [Ilya Ganelin] [SPARK-4655] Replaced usages of Nil and eliminated some code reuse
3d5cf20 [Ilya Ganelin] [SPARK-4655] Moved mima exclude to 1.4
6912c55 [Ilya Ganelin] Resolved merge conflict
4bff208 [Ilya Ganelin] Minor stylistic fixes
c6fffbb [Ilya Ganelin] newline
41402ad [Ilya Ganelin] Style fixes
02c6981 [Ilya Ganelin] Merge branch 'SPARK-4655' of github.com:ilganeli/spark into SPARK-4655
c755a09 [Ilya Ganelin] Some more stylistic updates and minor refactoring
b6257a0 [Ilya Ganelin] Update MimaExcludes.scala
0f0c624 [Ilya Ganelin] Fixed merge conflict
2eba262 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-4655
6b43d7b [Ilya Ganelin] Got rid of some spaces
6f1a5db [Ilya Ganelin] Revert "More minor formatting and refactoring"
1b3471b [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-4655
c9288e2 [Ilya Ganelin] More minor formatting and refactoring
d548caf [Ilya Ganelin] Formatting fix
c3ae5c2 [Ilya Ganelin] Explicit typing
0dacaf3 [Ilya Ganelin] Got rid of stale import
6da3a71 [Ilya Ganelin] Trailing whitespace
b85c5fe [Ilya Ganelin] Added minor fixes
a57dfcd [Ilya Ganelin] Added MiMA exclusion to get around binary compatibility check
83ed849 [Ilya Ganelin] moved braces for consistency
96dd161 [Ilya Ganelin] Fixed minor style error
cfd6f10 [Ilya Ganelin] Updated DAGScheduler to use new ResultStage and ShuffleMapStage classes
83494e9 [Ilya Ganelin] Added new Stage classes
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after authorized committer fails, not after any failure
In OutputCommitCoordinator, there is some logic to clear the authorized committer's lock on committing in case that task fails. However, it looks like the current code also clears this lock if other non-authorized tasks fail, which is an obvious bug.
In theory, it's possible that this could allow a new committer to start, run to completion, and commit output before the authorized committer finished, but it's unlikely that this race occurs often in practice due to the complex combination of failure and timing conditions that would be required to expose it.
This patch addresses this issue and adds a regression test.
Thanks to aarondav for spotting this issue.
Author: Josh Rosen <joshrosen@databricks.com>
Closes #5276 from JoshRosen/SPARK-6614 and squashes the following commits:
d532ba7 [Josh Rosen] Check whether failed task was authorized committer
cbb3784 [Josh Rosen] Add regression test for SPARK-6614
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not require a reply
Hotfix for #4588
cc rxin
Author: zsxwing <zsxwing@gmail.com>
Closes #5283 from zsxwing/hotfix and squashes the following commits:
cf3e5a7 [zsxwing] Move StopCoordinator to the receive method since it does not require a reply
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Parquet tables
This PR leverages the output commit coordinator introduced in #4066 to help committing Hive and Parquet tables.
This PR extracts output commit code in `SparkHadoopWriter.commit` to `SparkHadoopMapRedUtil.commitTask`, and reuses it for committing Parquet and Hive tables on executor side.
TODO
- [ ] Add tests
<!-- Reviewable:start -->
[<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/5139)
<!-- Reviewable:end -->
Author: Cheng Lian <lian@databricks.com>
Closes #5139 from liancheng/spark-6369 and squashes the following commits:
72eb628 [Cheng Lian] Fixes typo in javadoc
9a4b82b [Cheng Lian] Adds javadoc and addresses @aarondav's comments
dfdf3ef [Cheng Lian] Uses commit coordinator to help committing Hive and Parquet tables
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Error log before fixed
<code>15/03/29 10:07:25 ERROR YarnScheduler: Lost an executor 24 (already removed): Executor heartbeat timed out after ${now - lastSeenMs} ms</code>
Author: Li Zhihui <zhihui.li@intel.com>
Closes #5255 from li-zhihui/fixstringinterpolator and squashes the following commits:
c93f2b7 [Li Zhihui] Fix string interpolator error in HeartbeatReceiver
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This PR added a standard internal RPC interface for Spark and an Akka implementation. See [the design document](https://issues.apache.org/jira/secure/attachment/12698710/Pluggable%20RPC%20-%20draft%202.pdf) for more details.
I will split the whole work into multiple PRs to make it easier for code review. This is the first PR and avoid to touch too many files.
Author: zsxwing <zsxwing@gmail.com>
Closes #4588 from zsxwing/rpc-part1 and squashes the following commits:
fe3df4c [zsxwing] Move registerEndpoint and use actorSystem.dispatcher in asyncSetupEndpointRefByURI
f6f3287 [zsxwing] Remove RpcEndpointRef.toURI
8bd1097 [zsxwing] Fix docs and the code style
f459380 [zsxwing] Add RpcAddress.fromURI and rename urls to uris
b221398 [zsxwing] Move send methods above ask methods
15cfd7b [zsxwing] Merge branch 'master' into rpc-part1
9ffa997 [zsxwing] Fix MiMa tests
78a1733 [zsxwing] Merge remote-tracking branch 'origin/master' into rpc-part1
385b9c3 [zsxwing] Fix the code style and add docs
2cc3f78 [zsxwing] Add an asynchronous version of setupEndpointRefByUrl
e8dfec3 [zsxwing] Remove 'sendWithReply(message: Any, sender: RpcEndpointRef): Unit'
08564ae [zsxwing] Add RpcEnvFactory to create RpcEnv
e5df4ca [zsxwing] Handle AkkaFailure(e) in Actor
ec7c5b0 [zsxwing] Fix docs
7fc95e1 [zsxwing] Implement askWithReply in RpcEndpointRef
9288406 [zsxwing] Document thread-safety for setupThreadSafeEndpoint
3007c09 [zsxwing] Move setupDriverEndpointRef to RpcUtils and rename to makeDriverRef
c425022 [zsxwing] Fix the code style
5f87700 [zsxwing] Move the logical of processing message to a private function
3e56123 [zsxwing] Use lazy to eliminate CountDownLatch
07f128f [zsxwing] Remove ActionScheduler.scala
4d34191 [zsxwing] Remove scheduler from RpcEnv
7cdd95e [zsxwing] Add docs for RpcEnv
51e6667 [zsxwing] Add 'sender' to RpcCallContext and rename the parameter of receiveAndReply to 'context'
ffc1280 [zsxwing] Rename 'fail' to 'sendFailure' and other minor code style changes
28e6d0f [zsxwing] Add onXXX for network events and remove the companion objects of network events
3751c97 [zsxwing] Rename RpcResponse to RpcCallContext
fe7d1ff [zsxwing] Add explicit reply in rpc
7b9e0c9 [zsxwing] Fix the indentation
04a106e [zsxwing] Remove NopCancellable and add a const NOP in object SettableCancellable
2a579f4 [zsxwing] Remove RpcEnv.systemName
155b987 [zsxwing] Change newURI to uriOf and add some comments
45b2317 [zsxwing] A standard RPC interface and An Akka implementation
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Change FileServerSuite.test("HttpFileServer should not work with SSL when the server is untrusted") catch SSLException
Author: June.He <jun.hejun@huawei.com>
Closes #5239 from sisihj/SPARK-6585 and squashes the following commits:
cb19ae3 [June.He] Change FileServerSuite.test("HttpFileServer should not work with SSL when the server is untrusted") catch SSLException
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instead of login name
Utils.getCurrentUserName returns UserGroupInformation.getCurrentUser().getUserName() when SPARK_USER isn't set. It should return UserGroupInformation.getCurrentUser().getShortUserName()
getUserName() returns the users full principal name (ie user1CORP.COM). getShortUserName() returns just the users login name (user1).
This just happens to work on YARN because the Client code sets:
env("SPARK_USER") = UserGroupInformation.getCurrentUser().getShortUserName()
Author: Thomas Graves <tgraves@apache.org>
Closes #5229 from tgravescs/SPARK-6558 and squashes the following commits:
24830bf [Thomas Graves] Utils.getCurrentUserName returns the full principal name instead of login name
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checkTimeoutIntervalMs in HeartbeatReceiver
The current reading logic of `executorTimeoutMs` is:
```Scala
private val executorTimeoutMs = sc.conf.getLong("spark.network.timeout",
sc.conf.getLong("spark.storage.blockManagerSlaveTimeoutMs", 120)) * 1000
```
So if `spark.storage.blockManagerSlaveTimeoutMs` is 10000 and `spark.network.timeout` is not set, executorTimeoutMs will be 10000 * 1000. But the correct value should have been 10000.
`checkTimeoutIntervalMs` has the same issue.
This PR fixes them.
Author: zsxwing <zsxwing@gmail.com>
Closes #5209 from zsxwing/SPARK-6556 and squashes the following commits:
6a0a411 [zsxwing] Fix docs
c7d5422 [zsxwing] Add comments for executorTimeoutMs and checkTimeoutIntervalMs
ccd5147 [zsxwing] Fix wrong parsing logic of executorTimeoutMs and checkTimeoutIntervalMs in HeartbeatReceiver
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Kryo buffers are backed by byte arrays, but primitive arrays can only be
up to 2GB in size. It is misleading to allow users to set buffers past
this size.
Author: mcheah <mcheah@palantir.com>
Closes #5218 from mccheah/feature/limit-kryo-buffer and squashes the following commits:
1d6d1be [mcheah] Fixing numeric typo
e2e30ce [mcheah] Removing explicit int and double type to match style
09fd80b [mcheah] Should be >= not >. Slightly more consistent error message.
60634f9 [mcheah] [SPARK-6405] Limiting the maximum Kryo buffer size to be 2GB.
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Fix fastBucketFunction for histogram() to handle edge conditions more correctly. Add a test, and fix existing one accordingly
Author: Sean Owen <sowen@cloudera.com>
Closes #5148 from srowen/SPARK-6480 and squashes the following commits:
974a0a0 [Sean Owen] Additional test of huge ranges, and a few more comments (and comment fixes)
23ec01e [Sean Owen] Fix fastBucketFunction for histogram() to handle edge conditions more correctly. Add a test, and fix existing one accordingly
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DiskBlockManager
There are two race conditions of `subDirs` in `DiskBlockManager`:
1. `getAllFiles` does not use correct locks to read the contents in `subDirs`. Although it's designed for testing, it's still worth to add correct locks to eliminate the race condition.
2. The double-check has a race condition in `getFile(filename: String)`. If a thread finds `subDirs(dirId)(subDirId)` is not null out of the `synchronized` block, it may not be able to see the correct content of the File instance pointed by `subDirs(dirId)(subDirId)` according to the Java memory model (there is no volatile variable here).
This PR fixed the above race conditions.
Author: zsxwing <zsxwing@gmail.com>
Closes #5136 from zsxwing/SPARK-6468 and squashes the following commits:
cbb872b [zsxwing] Fix the race condition of subDirs in DiskBlockManager
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`StatusTracker.getJobIdsForGroup()` is implemented via a linear scan over a HashMap rather than using an index, which might be an expensive operation if there are many (e.g. thousands) of retained jobs.
This patch adds a new map to `JobProgressListener` in order to speed up these lookups.
Author: Josh Rosen <joshrosen@databricks.com>
Closes #4830 from JoshRosen/statustracker-job-group-indexing and squashes the following commits:
e39c5c7 [Josh Rosen] Address review feedback
6709fb2 [Josh Rosen] Merge remote-tracking branch 'origin/master' into statustracker-job-group-indexing
2c49614 [Josh Rosen] getOrElse
97275a7 [Josh Rosen] Add jobGroup to jobId index to JobProgressListener
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If the user calls `sc.stop()`, then the number of cores under "Completed Applications" will be 0. If the user does not call `sc.stop()`, then the number of cores will be however many cores were being used before the application exited. This PR makes both cases have the behavior of the latter.
Note that there have been a series of PR that attempted to fix this. For the full discussion, please refer to #4841. The unregister event is necessary because of a subtle race condition explained in that PR.
Tested this locally with and without calling `sc.stop()`.
Author: Andrew Or <andrew@databricks.com>
Closes #5177 from andrewor14/master-ui-cores and squashes the following commits:
62449d1 [Andrew Or] Freeze application state before finishing it
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SparkContext until all jobs finish
The main thread of UIWorkloadGenerator spawn sub threads to launch jobs but the main thread stop SparkContext without waiting for finishing those threads.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes #5187 from sarutak/SPARK-6537 and squashes the following commits:
4e9307a [Kousuke Saruta] Fixed UIWorkloadGenerator so that the main thread stop SparkContext after all jobs finish
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MEMORY_AND_DISK_SER
In https://github.com/apache/spark/blob/dcd1e42d6b6ac08d2c0736bf61a15f515a1f222b/core/src/main/scala/org/apache/spark/storage/BlockManager.scala#L538 , when StorageLevel is `MEMORY_AND_DISK_SER`, it will copy the content from file into memory, then put it into MemoryStore.
```scala
val copyForMemory = ByteBuffer.allocate(bytes.limit)
copyForMemory.put(bytes)
memoryStore.putBytes(blockId, copyForMemory, level)
bytes.rewind()
```
However, if the file is bigger than the free memory, OOM will happen. A better approach is testing if there is enough memory. If not, copyForMemory should not be created, since this is an optional operation.
Author: zsxwing <zsxwing@gmail.com>
Closes #4827 from zsxwing/SPARK-6076 and squashes the following commits:
7d25545 [zsxwing] Add alias for tryToPut and dropFromMemory
1100a54 [zsxwing] Replace call-by-name with () => T
0cc0257 [zsxwing] Fix a potential OOM issue when StorageLevel is MEMORY_AND_DISK_SER
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Though I don't see any bug in the existing code, the update in this PR makes it read better. rxin
Author: Xiangrui Meng <meng@databricks.com>
Closes #5176 from mengxr/SPARK-6515 and squashes the following commits:
134494d [Xiangrui Meng] update OpenHashSet impl
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Add `contains` to test whether a key exists in an OpenHashMap. rxin
Author: Xiangrui Meng <meng@databricks.com>
Closes #5171 from mengxr/openhashmap-contains and squashes the following commits:
d6e6f1f [Xiangrui Meng] add contains to primitivekeyopenhashmap
748a69b [Xiangrui Meng] add contains to OpenHashMap
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Master Web Page always be 0 if sc.stop() is called"
This reverts commit dd077abf2e2949fdfec31074b760b587f00efcf2.
Conflicts:
core/src/main/scala/org/apache/spark/deploy/master/ApplicationInfo.scala
core/src/main/scala/org/apache/spark/deploy/master/ui/MasterPage.scala
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cores is not set"
This reverts commit 12135e90549f957962899487cd5eb95badd8976d.
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Opening shuffle files can be very significant when the disk is
contended, especially when using ext3. While writing data to
a file can avoid hitting disk (and instead hit the buffer
cache), opening a file always involves writing some metadata
about the file to disk, so the open time can be a very significant
portion of the shuffle write time. In one job I ran recently, the time to
write shuffle data to the file was only 4ms for each task, but
the time to open the file was about 100x as long (~400ms).
When we add metrics about spilled data (#2504), we should ensure
that the file open time is also included there.
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes #4550 from kayousterhout/SPARK-3570 and squashes the following commits:
ea3a4ae [Kay Ousterhout] Added comment about excluded open time
fdc5185 [Kay Ousterhout] Improved comment
42b7e43 [Kay Ousterhout] Fixed parens for nanotime
2423555 [Kay Ousterhout] [SPARK-3570] Include time to open files in shuffle write time.
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It would be great to fix this for 1.3. since the fix is surgical and it helps understandability for users.
cc shivaram pwendell
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes #4839 from kayousterhout/SPARK-6088 and squashes the following commits:
3ab012c [Kay Ousterhout] Update getting result time incrementally, correctly set GET_RESULT status
f346b49 [Kay Ousterhout] Typos
748ea6b [Kay Ousterhout] Fixed build failure
84d617c [Kay Ousterhout] [SPARK-6088] Correct how tasks that get remote results are shown in the UI.
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running FlumeStreamSuite
When we run FlumeStreamSuite on Jenkins, sometimes we get error like as follows.
sbt.ForkMain$ForkError: The code passed to eventually never returned normally. Attempted 52 times over 10.094849836 seconds. Last failure message: Error connecting to localhost/127.0.0.1:23456.
at org.scalatest.concurrent.Eventually$class.tryTryAgain$1(Eventually.scala:420)
at org.scalatest.concurrent.Eventually$class.eventually(Eventually.scala:438)
at org.scalatest.concurrent.Eventually$.eventually(Eventually.scala:478)
at org.scalatest.concurrent.Eventually$class.eventually(Eventually.scala:307)
at org.scalatest.concurrent.Eventually$.eventually(Eventually.scala:478)
at org.apache.spark.streaming.flume.FlumeStreamSuite.writeAndVerify(FlumeStreamSuite.scala:116)
at org.apache.spark.streaming.flume.FlumeStreamSuite.org$apache$spark$streaming$flume$FlumeStreamSuite$$testFlumeStream(FlumeStreamSuite.scala:74)
at org.apache.spark.streaming.flume.FlumeStreamSuite$$anonfun$3.apply$mcV$sp(FlumeStreamSuite.scala:66)
at org.apache.spark.streaming.flume.FlumeStreamSuite$$anonfun$3.apply(FlumeStreamSuite.scala:66)
at org.apache.spark.streaming.flume.FlumeStreamSuite$$anonfun$3.apply(FlumeStreamSuite.scala:66)
at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
at org.scalatest.Transformer.apply(Transformer.scala:22)
at org.scalatest.Transformer.apply(Transformer.scala:20)
at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
at org.scalatest.Suite$class.withFixture(Suite.scala:1122)
at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
This error is caused by check-then-act logic when it find free-port .
/** Find a free port */
private def findFreePort(): Int = {
Utils.startServiceOnPort(23456, (trialPort: Int) => {
val socket = new ServerSocket(trialPort)
socket.close()
(null, trialPort)
}, conf)._2
}
Removing the check-then-act is not easy but we can reduce the chance of having the error by choosing random value for initial port instead of 23456.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes #4337 from sarutak/SPARK-5559 and squashes the following commits:
16f109f [Kousuke Saruta] Added `require` to Utils#startServiceOnPort
c39d8b6 [Kousuke Saruta] Merge branch 'SPARK-5559' of github.com:sarutak/spark into SPARK-5559
1610ba2 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-5559
33357e3 [Kousuke Saruta] Changed "findFreePort" method in MQTTStreamSuite and FlumeStreamSuite so that it can choose valid random port
a9029fe [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-5559
9489ef9 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-5559
8212e42 [Kousuke Saruta] Modified default port used in FlumeStreamSuite from 23456 to random value
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Author: Reynold Xin <rxin@databricks.com>
Closes #5125 from rxin/core-explicit-type and squashes the following commits:
f471415 [Reynold Xin] Revert style checker changes.
81b66e4 [Reynold Xin] Code review feedback.
a7533e3 [Reynold Xin] Mima excludes.
1d795f5 [Reynold Xin] [SPARK-6428] Added explicit types for all public methods in core.
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This reverts commit a41b9c6004cfee84bd56dfa1faf5a0cf084551ae.
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Changes the Tachyon client version from 0.5 to 0.6 in spark core and distribution script.
New dependencies in Tachyon 0.6.0 include
commons-codec:commons-codec:jar:1.5:compile
io.netty:netty-all:jar:4.0.23.Final:compile
These are already in spark core.
Author: Calvin Jia <jia.calvin@gmail.com>
Closes #4867 from calvinjia/upgrade_tachyon_0.6.0 and squashes the following commits:
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.
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