This is a reopening of #4867.
A short summary of the issues resolved from the previous PR:
1. HTTPClient version mismatch: Selenium (used for UI tests) requires version 4.3.x, and Tachyon included 4.2.5 through a transitive dependency of its shaded thrift jar. To address this, Tachyon 0.6.3 will promote the transitive dependencies of the shaded jar so they can be excluded in spark.
2. Jackson-Mapper-ASL version mismatch: In lower versions of hadoop-client (ie. 1.0.4), version 1.0.1 is included. The parquet library used in spark sql requires version 1.8+. Its unclear to me why upgrading tachyon-client would cause this dependency to break. The solution was to exclude jackson-mapper-asl from hadoop-client.
It seems that the dependency management in spark-parent will not work on transitive dependencies, one way to make sure jackson-mapper-asl is included with the correct version is to add it as a top level dependency. The best solution would be to exclude the dependency in the modules which require a higher version, but that did not fix the unit tests. Any suggestions on the best way to solve this would be appreciated!
Author: Calvin Jia <jia.calvin@gmail.com>
Closes#5354 from calvinjia/upgrade_tachyon_0.6.3 and squashes the following commits:
0eefe4d [Calvin Jia] Handle httpclient version in maven dependency management. Remove httpclient version setting from profiles.
7c00dfa [Calvin Jia] Set httpclient version to 4.3.2 for selenium. Specify version of httpclient for sql/hive (previously 4.2.5 transitive dependency of libthrift).
9263097 [Calvin Jia] Merge master to test latest changes
dbfc1bd [Calvin Jia] Use Tachyon 0.6.4 for cleaner dependencies.
e2ff80a [Calvin Jia] Exclude the jetty and curator promoted dependencies from tachyon-client.
a3a29da [Calvin Jia] Update tachyon-client exclusions.
0ae6c97 [Calvin Jia] Change tachyon version to 0.6.3
a204df9 [Calvin Jia] Update make distribution tachyon version.
a93c94f [Calvin Jia] Exclude jackson-mapper-asl from hadoop client since it has a lower version than spark's expected version.
a8a923c [Calvin Jia] Exclude httpcomponents from Tachyon
910fabd [Calvin Jia] Update to master
eed9230 [Calvin Jia] Update tachyon version to 0.6.1.
11907b3 [Calvin Jia] Use TachyonURI for tachyon paths instead of strings.
71bf441 [Calvin Jia] Upgrade Tachyon client version to 0.6.0.
Move scalastyle-config.xml to dev/ (SBT config still doesn't work) to fix running mvn targets from subdirs; make scalastyle a verify stage target again in Maven; output results in target not project root; update to scalastyle 0.7.0
Author: Sean Owen <sowen@cloudera.com>
Closes#5471 from srowen/SPARK-6861 and squashes the following commits:
acac637 [Sean Owen] Oops, add back execution but leave it at the default verify phase
35a4fd2 [Sean Owen] Revert change to scalastyle-config.xml location, but return scalastyle Maven check to verify phase instead of package to get it farther out of the way, since the Maven invocation is optional
c4fb42c [Sean Owen] Move scalastyle-config.xml to dev/ (SBT config still doesn't work) to fix running mvn targets from subdirs; make scalastyle a verify stage target again in Maven; output results in target not project root; update to scalastyle 0.7.0
We should upgrade our snappy-java dependency to 1.1.1.7 in order to include a fix for a bug that results in worse compression in SnappyOutputStream (see https://github.com/xerial/snappy-java/issues/100).
Author: Josh Rosen <joshrosen@databricks.com>
Closes#5512 from JoshRosen/snappy-1.1.1.7 and squashes the following commits:
f1ac0f8 [Josh Rosen] Upgrade to snappy-java 1.1.1.7.
Version 3.1.1 is two years old and the newer version includes
approximate percentile statistics (among other things).
Author: Punyashloka Biswal <punya.biswal@gmail.com>
Closes#5380 from punya/patch-1 and squashes the following commits:
226622b [Punyashloka Biswal] Bump version of apache commons-math3
This is needed at least for YARN integration tests, since `$JAVA_HOME` is used to launch the executors.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#5441 from vanzin/yarn-test-test and squashes the following commits:
3eeec30 [Marcelo Vanzin] Use JAVA_HOME when available, java.home otherwise.
d71f1bb [Marcelo Vanzin] And sbt too.
6bda399 [Marcelo Vanzin] WIP: Testing to see whether this fixes the yarn test issue.
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
1. Test JARs are built & published
1. log4j.resources is explicitly excluded. Without this, downstream test run logging depends on the order the JARs are listed/loaded
1. sql/hive pulls in spark-sql &...spark-catalyst for its test runs
1. The copied in test classes were rm'd, and a test edited to remove its now duplicate assert method
1. Spark streaming is now build with the same plugin/phase as the rest, but its shade plugin declaration is kept in (so different from the rest of the test plugins). Due to (#2), this means the test JAR no longer includes its log4j file.
Outstanding issues:
* should the JARs be shaded? `spark-streaming-test.jar` does, but given these are test jars for developers only, especially in the same spark source tree, it's hard to justify.
* `maven-jar-plugin` v 2.6 was explicitly selected; without this the apache-1.4 parent template JAR version (2.4) chosen.
* Are there any other resources to exclude?
Author: Steve Loughran <stevel@hortonworks.com>
Closes#5119 from steveloughran/stevel/patches/SPARK-6433-test-jars and squashes the following commits:
81ceb01 [Steve Loughran] SPARK-6433 add a clearer comment explaining what the plugin is doing & why
a6dca33 [Steve Loughran] SPARK-6433 : pull configuration section form archive plugin
c2b5f89 [Steve Loughran] SPARK-6433 omit "jar" goal from jar plugin
fdac51b [Steve Loughran] SPARK-6433 -002; indentation & delegate plugin version to parent
650f442 [Steve Loughran] SPARK-6433 patch 001: test JARs are built; sql/hive pulls in spark-sql & spark-catalyst for its test runs
Use standard UTF-8 source / report encoding for scalastyle
Author: Sean Owen <sowen@cloudera.com>
Closes#5211 from srowen/SPARK-6532 and squashes the following commits:
16a33e5 [Sean Owen] Use standard UTF-8 source / report encoding for scalastyle
Bump default Hadoop version to 2.2.0. (This is already the dependency version reported by published Maven artifacts.) See JIRA for further discussion.
Author: Sean Owen <sowen@cloudera.com>
Closes#5027 from srowen/SPARK-5134 and squashes the following commits:
acbee14 [Sean Owen] Bump default Hadoop version to 2.2.0. (This is already the dependency version reported by published Maven artifacts.)
The issue is discussed in https://issues.apache.org/jira/browse/SPARK-5669. Replacing all JBLAS usage by netlib-java gives us a simpler dependency tree and less license issues to worry about. I didn't touch the test scope in this PR. The user guide is not modified to avoid merge conflicts with branch-1.3. srowen ankurdave pwendell
Author: Xiangrui Meng <meng@databricks.com>
Closes#4699 from mengxr/SPARK-5814 and squashes the following commits:
48635c6 [Xiangrui Meng] move netlib-java version to parent pom
ca21c74 [Xiangrui Meng] remove jblas from ml-guide
5f7767a [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5814
c5c4183 [Xiangrui Meng] merge master
0f20cad [Xiangrui Meng] add mima excludes
e53e9f4 [Xiangrui Meng] remove jblas from mllib runtime
ceaa14d [Xiangrui Meng] replace jblas by netlib-java in graphx
fa7c2ca [Xiangrui Meng] move jblas to test scope
This change encapsulates all the logic involved in launching a Spark job
into a small Java library that can be easily embedded into other applications.
The overall goal of this change is twofold, as described in the bug:
- Provide a public API for launching Spark processes. This is a common request
from users and currently there's no good answer for it.
- Remove a lot of the duplicated code and other coupling that exists in the
different parts of Spark that deal with launching processes.
A lot of the duplication was due to different code needed to build an
application's classpath (and the bootstrapper needed to run the driver in
certain situations), and also different code needed to parse spark-submit
command line options in different contexts. The change centralizes those
as much as possible so that all code paths can rely on the library for
handling those appropriately.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#3916 from vanzin/SPARK-4924 and squashes the following commits:
18c7e4d [Marcelo Vanzin] Fix make-distribution.sh.
2ce741f [Marcelo Vanzin] Add lots of quotes.
3b28a75 [Marcelo Vanzin] Update new pom.
a1b8af1 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
897141f [Marcelo Vanzin] Review feedback.
e2367d2 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
28cd35e [Marcelo Vanzin] Remove stale comment.
b1d86b0 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
00505f9 [Marcelo Vanzin] Add blurb about new API in the programming guide.
5f4ddcc [Marcelo Vanzin] Better usage messages.
92a9cfb [Marcelo Vanzin] Fix Win32 launcher, usage.
6184c07 [Marcelo Vanzin] Rename field.
4c19196 [Marcelo Vanzin] Update comment.
7e66c18 [Marcelo Vanzin] Fix pyspark tests.
0031a8e [Marcelo Vanzin] Review feedback.
c12d84b [Marcelo Vanzin] Review feedback. And fix spark-submit on Windows.
e2d4d71 [Marcelo Vanzin] Simplify some code used to launch pyspark.
43008a7 [Marcelo Vanzin] Don't make builder extend SparkLauncher.
b4d6912 [Marcelo Vanzin] Use spark-submit script in SparkLauncher.
28b1434 [Marcelo Vanzin] Add a comment.
304333a [Marcelo Vanzin] Fix propagation of properties file arg.
bb67b93 [Marcelo Vanzin] Remove unrelated Yarn change (that is also wrong).
8ec0243 [Marcelo Vanzin] Add missing newline.
95ddfa8 [Marcelo Vanzin] Fix handling of --help for spark-class command builder.
72da7ec [Marcelo Vanzin] Rename SparkClassLauncher.
62978e4 [Marcelo Vanzin] Minor cleanup of Windows code path.
9cd5b44 [Marcelo Vanzin] Make all non-public APIs package-private.
e4c80b6 [Marcelo Vanzin] Reorganize the code so that only SparkLauncher is public.
e50dc5e [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
de81da2 [Marcelo Vanzin] Fix CommandUtils.
86a87bf [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
2061967 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
46d46da [Marcelo Vanzin] Clean up a test and make it more future-proof.
b93692a [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
ad03c48 [Marcelo Vanzin] Revert "Fix a thread-safety issue in "local" mode."
0b509d0 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
23aa2a9 [Marcelo Vanzin] Read java-opts from conf dir, not spark home.
7cff919 [Marcelo Vanzin] Javadoc updates.
eae4d8e [Marcelo Vanzin] Fix new unit tests on Windows.
e570fb5 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
44cd5f7 [Marcelo Vanzin] Add package-info.java, clean up javadocs.
f7cacff [Marcelo Vanzin] Remove "launch Spark in new thread" feature.
7ed8859 [Marcelo Vanzin] Some more feedback.
54cd4fd [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
61919df [Marcelo Vanzin] Clean leftover debug statement.
aae5897 [Marcelo Vanzin] Use launcher classes instead of jars in non-release mode.
e584fc3 [Marcelo Vanzin] Rework command building a little bit.
525ef5b [Marcelo Vanzin] Rework Unix spark-class to handle argument with newlines.
8ac4e92 [Marcelo Vanzin] Minor test cleanup.
e946a99 [Marcelo Vanzin] Merge PySparkLauncher into SparkSubmitCliLauncher.
c617539 [Marcelo Vanzin] Review feedback round 1.
fc6a3e2 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
f26556b [Marcelo Vanzin] Fix a thread-safety issue in "local" mode.
2f4e8b4 [Marcelo Vanzin] Changes needed to make this work with SPARK-4048.
799fc20 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
bb5d324 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
53faef1 [Marcelo Vanzin] Merge branch 'master' into SPARK-4924
a7936ef [Marcelo Vanzin] Fix pyspark tests.
656374e [Marcelo Vanzin] Mima fixes.
4d511e7 [Marcelo Vanzin] Fix tools search code.
7a01e4a [Marcelo Vanzin] Fix pyspark on Yarn.
1b3f6e9 [Marcelo Vanzin] Call SparkSubmit from spark-class launcher for unknown classes.
25c5ae6 [Marcelo Vanzin] Centralize SparkSubmit command line parsing.
27be98a [Marcelo Vanzin] Modify Spark to use launcher lib.
6f70eea [Marcelo Vanzin] [SPARK-4924] Add a library for launching Spark jobs programatically.
Add xml-apis to core test deps to work aroudn UISeleniumSuite classpath issue
Author: Sean Owen <sowen@cloudera.com>
Closes#4933 from srowen/SPARK-6205 and squashes the following commits:
ddd4d32 [Sean Owen] Add xml-apis to core test deps to work aroudn UISeleniumSuite classpath issue
Option 1 of 2: Convert spark-parent module name to spark-parent_2.10 / spark-parent_2.11
Author: Sean Owen <sowen@cloudera.com>
Closes#4912 from srowen/SPARK-6182.1 and squashes the following commits:
eff60de [Sean Owen] Convert spark-parent module name to spark-parent_2.10 / spark-parent_2.11
This PR excludes Guava 15.0 from the SBT build, to make Spark SQL CLI (`bin/spark-sql`) work when compiled against Hive 0.12.0.
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Author: Cheng Lian <lian@databricks.com>
Closes#4890 from liancheng/exclude-guava-15 and squashes the following commits:
91ae9fa [Cheng Lian] Moves Guava 15 exclusion from SBT build to POM
282bd2a [Cheng Lian] Excludes Guava 15 referenced by jackson-module-scala_2.10
Resolves https://issues.apache.org/jira/browse/SPARK-5357
In commons-codec 1.5, Base64 instances are not thread safe. That was only true from 1.4-1.6.
Author: Matt Whelan <mwhelan@perka.com>
Closes#4153 from MattWhelan/depsUpdate and squashes the following commits:
b4a91f4 [Matt Whelan] SPARK-5357: Update commons-codec version to 1.10 (current)
When import the whole project into eclipse as maven project, found that the
src/main/scala & src/test/scala can not be set as source folder as default
behavior, so add a "add-source" goal in scala-maven-plugin to let this work.
Author: gli <gli@redhat.com>
Closes#4531 from ligangty/addsource and squashes the following commits:
4e4db4c [gli] [IDE] cannot import src/main/scala & src/test/scala into eclipse as source folder
This patch replaces all uses of EasyMock with Mockito. There are two motivations for this:
1. We should use a single mocking framework in our tests in order to keep things consistent.
2. EasyMock may be responsible for non-deterministic unit test failures due to its Objensis dependency (see SPARK-5626 for more details).
Most of these changes are fairly mechanical translations of Mockito code to EasyMock, although I made a small change that strengthens the assertions in one test in KinesisReceiverSuite.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#4578 from JoshRosen/SPARK-5735-remove-easymock and squashes the following commits:
0ab192b [Josh Rosen] Import sorting plus two minor changes to more closely match old semantics.
977565b [Josh Rosen] Remove EasyMock from build.
fae1d8f [Josh Rosen] Remove EasyMock usage in KinesisReceiverSuite.
7cca486 [Josh Rosen] Remove EasyMock usage in MesosSchedulerBackendSuite
fc5e94d [Josh Rosen] Remove EasyMock in CacheManagerSuite
This is a follow-up PR for #4454 and #4484. JetS3t 0.9.2 contains a log4j.properties file inside the artifact and breaks our tests (see SPARK-5696). This is fixed in 0.9.3.
This PR also reverts hotfix changes introduced in #4484. The reason is that asking users to configure HiveThriftServer2 logging configurations in hive-log4j.properties can be unintuitive.
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Author: Cheng Lian <lian@databricks.com>
Closes#4499 from liancheng/spark-5700 and squashes the following commits:
4f020c7 [Cheng Lian] Bumps jets3t to 0.9.3 for hadoop-2.3 and hadoop-2.4 profiles
Yarn's config option `spark.yarn.user.classpath.first` does not work the same way as
`spark.files.userClassPathFirst`; Yarn's version is a lot more dangerous, in that it
modifies the system classpath, instead of restricting the changes to the user's class
loader. So this change implements the behavior of the latter for Yarn, and deprecates
the more dangerous choice.
To be able to achieve feature-parity, I also implemented the option for drivers (the existing
option only applies to executors). So now there are two options, each controlling whether
to apply userClassPathFirst to the driver or executors. The old option was deprecated, and
aliased to the new one (`spark.executor.userClassPathFirst`).
The existing "child-first" class loader also had to be fixed. It didn't handle resources, and it
was also doing some things that ended up causing JVM errors depending on how things
were being called.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#3233 from vanzin/SPARK-2996 and squashes the following commits:
9cf9cf1 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
a1499e2 [Marcelo Vanzin] Remove SPARK_HOME propagation.
fa7df88 [Marcelo Vanzin] Remove 'test.resource' file, create it dynamically.
a8c69f1 [Marcelo Vanzin] Review feedback.
cabf962 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
a1b8d7e [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
3f768e3 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
2ce3c7a [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
0e6d6be [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
70d4044 [Marcelo Vanzin] Fix pyspark/yarn-cluster test.
0fe7777 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
0e6ef19 [Marcelo Vanzin] Move class loaders around and make names more meaninful.
fe970a7 [Marcelo Vanzin] Review feedback.
25d4fed [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
3cb6498 [Marcelo Vanzin] Call the right loadClass() method on the parent.
fbb8ab5 [Marcelo Vanzin] Add locking in loadClass() to avoid deadlocks.
2e6c4b7 [Marcelo Vanzin] Mention new setting in documentation.
b6497f9 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
a10f379 [Marcelo Vanzin] Some feedback.
3730151 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
f513871 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
44010b6 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
7b57cba [Marcelo Vanzin] Remove now outdated message.
5304d64 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
35949c8 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
54e1a98 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
d1273b2 [Marcelo Vanzin] Add test file to rat exclude.
fa1aafa [Marcelo Vanzin] Remove write check on user jars.
89d8072 [Marcelo Vanzin] Cleanups.
a963ea3 [Marcelo Vanzin] Implement spark.driver.userClassPathFirst for standalone cluster mode.
50afa5f [Marcelo Vanzin] Fix Yarn executor command line.
7d14397 [Marcelo Vanzin] Register user jars in executor up front.
7f8603c [Marcelo Vanzin] Fix yarn-cluster mode without userClassPathFirst.
20373f5 [Marcelo Vanzin] Fix ClientBaseSuite.
55c88fa [Marcelo Vanzin] Run all Yarn integration tests via spark-submit.
0b64d92 [Marcelo Vanzin] Add deprecation warning to yarn option.
4a84d87 [Marcelo Vanzin] Fix the child-first class loader.
d0394b8 [Marcelo Vanzin] Add "deprecated configs" to SparkConf.
46d8cf2 [Marcelo Vanzin] Update doc with new option, change name to "userClassPathFirst".
a314f2d [Marcelo Vanzin] Enable driver class path isolation in SparkSubmit.
91f7e54 [Marcelo Vanzin] [yarn] Enable executor class path isolation.
a853e74 [Marcelo Vanzin] Re-work CoarseGrainedExecutorBackend command line arguments.
89522ef [Marcelo Vanzin] Add class path isolation support for Yarn cluster mode.
...ns avro-mapred for
hadoop 1 API had been marked as resolved but did not work for at least some
builds due to version conflicts using avro-mapred-1.7.5.jar and
avro-mapred-1.7.6-hadoop2.jar (the correct version) when building for hadoop2.
sql/hive/pom.xml org.spark-project.hive:hive-exec's depends on 1.7.5:
Building Spark Project Hive 1.2.0
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-dependency-plugin:2.4:tree (default-cli) spark-hive_2.10 ---
[INFO] org.apache.spark:spark-hive_2.10🫙1.2.0
[INFO] +- org.spark-project.hive:hive-exec:jar:0.13.1a:compile
[INFO] | \- org.apache.avro:avro-mapred:jar:1.7.5:compile
[INFO] \- org.apache.avro:avro-mapred:jar:hadoop2:1.7.6:compile
[INFO]
Excluding this dependency allows the explicitly listed avro-mapred dependency
to be picked up.
Author: medale <medale94@yahoo.com>
Closes#4315 from medale/avro-hadoop2 and squashes the following commits:
1ab4fa3 [medale] Merge branch 'master' into avro-hadoop2
9d85e2a [medale] Merge remote-tracking branch 'upstream/master' into avro-hadoop2
51b9c2a [medale] [SPARK-3039] [BUILD] Spark assembly for new hadoop API (hadoop 2) contains avro-mapred for hadoop 1 API had been marked as resolved but did not work for at least some builds due to version conflicts using avro-mapred-1.7.5.jar and avro-mapred-1.7.6-hadoop2.jar (the correct version) when building for hadoop2.
Upgrading from jets3t 0.9.0 to 0.9.2 fixes a dependency issue that was
causing UISeleniumSuite to fail with ClassNotFoundExceptions when run
the hadoop-2.3 or hadoop-2.4 profiles.
The jets3t release notes can be found at http://www.jets3t.org/RELEASE_NOTES.html
Author: Josh Rosen <joshrosen@databricks.com>
Closes#4454 from JoshRosen/SPARK-5671 and squashes the following commits:
fa6cb3e [Josh Rosen] [SPARK-5671] Upgrade jets3t to 0.9.2 in hadoop-2.3 and 2.4 profiles
There is dependency compatibility issue. Currently hadoop-2.6.0 use 1.9.13 for jackson. Upgrade to the same version to make it consistent.
Author: Zhan Zhang <zhazhan@gmail.com>
Closes#3938 from zhzhan/spark5108 and squashes the following commits:
0080a84 [Zhan Zhang] change to upgrade jackson version only in hadoop-2.x
0b9bad6 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark into spark5108
917600a [Zhan Zhang] solve conflicts
f7064d0 [Zhan Zhang] hadoop2.6 dependency management fix
fc56b25 [Zhan Zhang] squash all commits
3bf966c [Zhan Zhang] test
The goal is to provide a stable, REST-based application submission gateway that is not inherently based on Akka, which is unstable across versions. This PR targets standalone cluster mode, but is implemented in a general enough manner that can be potentially extended to other modes in the future. Client mode is currently not included in the changes here because there are many more Akka messages exchanged there.
As of the changes here, the Master will advertise two ports, 7077 and 6066. We need to keep around the old one (7077) for client mode and older versions of Spark submit. However, all new versions of Spark submit will use the REST gateway (6066).
By the way this includes ~700 lines of tests and ~200 lines of license.
Author: Andrew Or <andrew@databricks.com>
Closes#4216 from andrewor14/rest and squashes the following commits:
8d7ce07 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
6f0c597 [Andrew Or] Use nullable fields for integer and boolean values
dfe4bd7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
b9e2a08 [Andrew Or] Minor comments
02b5cea [Andrew Or] Fix tests
d2b1ef8 [Andrew Or] Comment changes + minor code refactoring across the board
9c82a36 [Andrew Or] Minor comment and wording updates
b4695e7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
c9a8ad7 [Andrew Or] Do not include appResource and mainClass as properties
6fc7670 [Andrew Or] Report REST server response back to the user
40e6095 [Andrew Or] Pass submit parameters through system properties
cbd670b [Andrew Or] Include unknown fields, if any, in server response
9fee16f [Andrew Or] Include server protocol version on mismatch
09f873a [Andrew Or] Fix style
8188e61 [Andrew Or] Upgrade Jackson from 2.3.0 to 2.4.4
37538e0 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
9165ae8 [Andrew Or] Fall back to Akka if endpoint was not REST
252d53c [Andrew Or] Clean up server error handling behavior further
c643f64 [Andrew Or] Fix style
bbbd329 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
792e112 [Andrew Or] Use specific HTTP response codes on error
f98660b [Andrew Or] Version the protocol and include it in REST URL
721819f [Andrew Or] Provide more REST-like interface for submit/kill/status
581f7bf [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
9e0d1af [Andrew Or] Move some classes around to reduce number of files (minor)
42e5de4 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
1f1c03f [Andrew Or] Use Jackson's DefaultScalaModule to simplify messages
9229433 [Andrew Or] Reduce duplicate naming in REST field
ade28fd [Andrew Or] Clean up REST response output in Spark submit
b2fef8b [Andrew Or] Abstract the success field to the general response
6c57b4b [Andrew Or] Increase timeout in end-to-end tests
bf696ff [Andrew Or] Add checks for enabling REST when using kill/status
7ee6737 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
e2f7f5f [Andrew Or] Provide more safeguard against missing fields
9581df7 [Andrew Or] Clean up uses of exceptions
914fdff [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
e2104e6 [Andrew Or] stable -> rest
3db7379 [Andrew Or] Fix comments and name fields for better error messages
8d43486 [Andrew Or] Replace SubmitRestProtocolAction with class name
df90e8b [Andrew Or] Use Jackson for JSON de/serialization
d7a1f9f [Andrew Or] Fix local cluster tests
efa5e18 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
e42c131 [Andrew Or] Add end-to-end tests for standalone REST protocol
837475b [Andrew Or] Show the REST port on the Master UI
d8d3717 [Andrew Or] Use a daemon thread pool for REST server
6568ca5 [Andrew Or] Merge branch 'master' of github.com:apache/spark into rest
77774ba [Andrew Or] Minor fixes
206cae4 [Andrew Or] Refactor and add tests for the REST protocol
63c05b3 [Andrew Or] Remove MASTER as a field (minor)
9e21b72 [Andrew Or] Action -> SparkSubmitAction (minor)
51c5ca6 [Andrew Or] Distinguish client and server side Spark versions
b44e103 [Andrew Or] Implement status requests + fix validation behavior
120ab9d [Andrew Or] Support kill and request driver status through SparkSubmit
544de1d [Andrew Or] Major clean ups in code and comments
e958cae [Andrew Or] Supported nested values in messages
484bd21 [Andrew Or] Specify an ordering for fields in SubmitDriverRequestMessage
6ff088d [Andrew Or] Rename classes to generalize REST protocol
af9d9cb [Andrew Or] Integrate REST protocol in standalone mode
53e7c0e [Andrew Or] Initial client, server, and all the messages
Because of the way we shade jetty, we lose its dependency orbit
in the assembly jar, which includes the javax servlet API's. This
adds back orbit explicitly, using the version that matches
our jetty version.
Author: Patrick Wendell <patrick@databricks.com>
Closes#4411 from pwendell/servlet-api and squashes the following commits:
445f868 [Patrick Wendell] SPARK-5557: Explicitly include servlet API in dependencies.
Our existing Kryo version actually embeds objenesis 1.2 classes in
its jar, causing dependency conflicts during tests. This updates us to
Kryo 2.24.0 (which was changed to not embed objenesis) to avoid this
behavior. See the JIRA for more detail.
Author: Patrick Wendell <patrick@databricks.com>
Closes#4383 from pwendell/SPARK-5607 and squashes the following commits:
c3b8d27 [Patrick Wendell] SPARK-5607: Update to Kryo 2.24.0 to avoid including objenesis 1.2.
This PR adds support for using maven coordinates as dependencies to spark-shell.
Coordinates can be provided as a comma-delimited string after the flag `--packages`.
Additional remote repositories (like SonaType) can be supplied as a comma-delimited string after the flag
`--repositories`.
Uses the Ivy library to resolve dependencies. Unfortunately the library has no decent documentation, therefore solving more complex dependency issues can be a problem.
pwendell, mateiz, mengxr
**Note: This is still a WIP. The following need to be handled:**
- [x] add docs for the methods
- [x] take local ivy cache path as an argument
- [x] add tests
- [x] add Windows compatibility
- [x] exclude unused Ivy dependencies
Author: Burak Yavuz <brkyvz@gmail.com>
Closes#4215 from brkyvz/SPARK-5341ivy and squashes the following commits:
9215851 [Burak Yavuz] ready to merge
db2a5cc [Burak Yavuz] changed logging to printStream
9dae87f [Burak Yavuz] file separators changed
71c374d [Burak Yavuz] merge conflicts fixed
c08dc9f [Burak Yavuz] fixed merge conflicts
3ada19a [Burak Yavuz] fixed Jenkins error (hopefully) and added comment on oro
43c2290 [Burak Yavuz] fixed that ONE line
231f72f [Burak Yavuz] addressed code review
2cd6562 [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into SPARK-5341ivy
85ec5a3 [Burak Yavuz] added oro as a dependency explicitly
ea44ca4 [Burak Yavuz] add oro back to dependencies
cef0e24 [Burak Yavuz] IntelliJ is just messing things up
97c4a92 [Burak Yavuz] fix more weird IntelliJ formatting
9cf077d [Burak Yavuz] fix weird IntelliJ formatting
dcf5e13 [Burak Yavuz] fix windows command line flags
3a23f21 [Burak Yavuz] excluded ivy dependencies
53423e0 [Burak Yavuz] tests added
3705907 [Burak Yavuz] remove ivy-repo as a command line argument. Use global ivy cache as default
c04d885 [Burak Yavuz] take path to ivy cache as a conf
2edc9b5 [Burak Yavuz] managed to exclude Spark and it's dependencies
a0870af [Burak Yavuz] add docs. remove unnecesary new lines
6645af4 [Burak Yavuz] [SPARK-5341] added base implementation
882c4c8 [Burak Yavuz] added maven dependency download
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#3820 from adrian-wang/parquettimestamp and squashes the following commits:
b1e2a0d [Daoyuan Wang] fix for nanos
4dadef1 [Daoyuan Wang] fix wrong read
93f438d [Daoyuan Wang] parquet timestamp support
These are needed transitively from the other Jetty libraries
we include. It was not picked up by unit tests because we
disable the UI.
Author: Patrick Wendell <patrick@databricks.com>
Closes#4323 from pwendell/jetty and squashes the following commits:
d8669da [Patrick Wendell] SPARK-3996: Add jetty servlet and continuations.
This PR brings the Python API for Spark Streaming Kafka data source.
```
class KafkaUtils(__builtin__.object)
| Static methods defined here:
|
| createStream(ssc, zkQuorum, groupId, topics, storageLevel=StorageLevel(True, True, False, False,
2), keyDecoder=<function utf8_decoder>, valueDecoder=<function utf8_decoder>)
| Create an input stream that pulls messages from a Kafka Broker.
|
| :param ssc: StreamingContext object
| :param zkQuorum: Zookeeper quorum (hostname:port,hostname:port,..).
| :param groupId: The group id for this consumer.
| :param topics: Dict of (topic_name -> numPartitions) to consume.
| Each partition is consumed in its own thread.
| :param storageLevel: RDD storage level.
| :param keyDecoder: A function used to decode key
| :param valueDecoder: A function used to decode value
| :return: A DStream object
```
run the example:
```
bin/spark-submit --driver-class-path external/kafka-assembly/target/scala-*/spark-streaming-kafka-assembly-*.jar examples/src/main/python/streaming/kafka_wordcount.py localhost:2181 test
```
Author: Davies Liu <davies@databricks.com>
Author: Tathagata Das <tdas@databricks.com>
Closes#3715 from davies/kafka and squashes the following commits:
d93bfe0 [Davies Liu] Update make-distribution.sh
4280d04 [Davies Liu] address comments
e6d0427 [Davies Liu] Merge branch 'master' of github.com:apache/spark into kafka
f257071 [Davies Liu] add tests for null in RDD
23b039a [Davies Liu] address comments
9af51c4 [Davies Liu] Merge branch 'kafka' of github.com:davies/spark into kafka
a74da87 [Davies Liu] address comments
dc1eed0 [Davies Liu] Update kafka_wordcount.py
31e2317 [Davies Liu] Update kafka_wordcount.py
370ba61 [Davies Liu] Update kafka.py
97386b3 [Davies Liu] address comment
2c567a5 [Davies Liu] update logging and comment
33730d1 [Davies Liu] Merge branch 'master' of github.com:apache/spark into kafka
adeeb38 [Davies Liu] Merge pull request #3 from tdas/kafka-python-api
aea8953 [Tathagata Das] Kafka-assembly for Python API
eea16a7 [Davies Liu] refactor
f6ce899 [Davies Liu] add example and fix bugs
98c8d17 [Davies Liu] fix python style
5697a01 [Davies Liu] bypass decoder in scala
048dbe6 [Davies Liu] fix python style
75d485e [Davies Liu] add mqtt
07923c4 [Davies Liu] support kafka in Python
(v2 of this patch with a fix that was only relevant for the maven build).
This patch piggy-back's on vanzin's work to simplify the Guava shading,
and adds Jetty as a shaded library in Spark. Other than adding Jetty,
it consilidates the <artifactSet>'s into the root pom. I found it was
a bit easier to follow that way, since you don't need to look into
child pom's to find out specific artifact sets included in shading.
Author: Patrick Wendell <patrick@databricks.com>
Closes#4285 from pwendell/jetty and squashes the following commits:
d3e7f4e [Patrick Wendell] Fix for shaded deps causing compile errors
19f0710 [Patrick Wendell] More code review feedback
961452d [Patrick Wendell] Responding to feedback from Marcello
6df25ca [Patrick Wendell] [WIP] [SPARK-3996]: Shade Jetty in Spark deliverables
Depends on [SPARK-5413](https://issues.apache.org/jira/browse/SPARK-5413) / #4209, included here, will rebase once the latter's merged.
Author: Ryan Williams <ryan.blake.williams@gmail.com>
Closes#4218 from ryan-williams/udp and squashes the following commits:
ebae393 [Ryan Williams] Add support for sending Graphite metrics via UDP
cb58262 [Ryan Williams] bump metrics dependency to v3.1.0
This patch piggy-back's on vanzin's work to simplify the Guava shading,
and adds Jetty as a shaded library in Spark. Other than adding Jetty,
it consilidates the \<artifactSet\>'s into the root pom. I found it was
a bit easier to follow that way, since you don't need to look into
child pom's to find out specific artifact sets included in shading.
Author: Patrick Wendell <patrick@databricks.com>
Closes#4252 from pwendell/jetty and squashes the following commits:
19f0710 [Patrick Wendell] More code review feedback
961452d [Patrick Wendell] Responding to feedback from Marcello
6df25ca [Patrick Wendell] [WIP] [SPARK-3996]: Shade Jetty in Spark deliverables
The current way of shading Guava is a little problematic. Code that
depends on "spark-core" does not see the transitive dependency, yet
classes in "spark-core" actually depend on Guava. So it's a little
tricky to run unit tests that use spark-core classes, since you need
a compatible version of Guava in your dependencies when running the
tests. This can become a little tricky, and is kind of a bad user
experience.
This change modifies the way Guava is shaded so that it's applied
uniformly across the Spark build. This means Guava is shaded inside
spark-core itself, so that the dependency issues above are solved.
Aside from that, all Spark sub-modules have their Guava references
relocated, so that they refer to the relocated classes now packaged
inside spark-core. Before, this was only done by the time the assembly
was built, so projects that did not end up inside the assembly (such
as streaming backends) could still reference the original location
of Guava classes.
The Guava classes are added to the "first" artifact Spark generates
(network-common), so that all downstream modules have the needed
classes available. Since "network-common" is a dependency of spark-core,
all Spark apps should get the relocated classes automatically.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#3658 from vanzin/SPARK-4809 and squashes the following commits:
3c93e42 [Marcelo Vanzin] Shade Guava in the network-common artifact.
5d69ec9 [Marcelo Vanzin] Merge branch 'master' into SPARK-4809
b3104fc [Marcelo Vanzin] Add comment.
941848f [Marcelo Vanzin] Merge branch 'master' into SPARK-4809
f78c48a [Marcelo Vanzin] Merge branch 'master' into SPARK-4809
8053dd4 [Marcelo Vanzin] Merge branch 'master' into SPARK-4809
107d7da [Marcelo Vanzin] Add fix for SPARK-5052 (PR #3874).
40b8723 [Marcelo Vanzin] Merge branch 'master' into SPARK-4809
4a4ed42 [Marcelo Vanzin] [SPARK-4809] Rework Guava library shading.
Although the underlying issue can I think be solved by having user code use slf4j 1.7.6+, it might be helpful and consistent to update Spark's slf4j too. I see no reason to believe it would be incompatible with other 1.7.x releases: http://www.slf4j.org/news.html Lots of different version of slf4j are in use in the wild and anecdotally I have never seen an issue mixing them.
Author: Sean Owen <sowen@cloudera.com>
Closes#4184 from srowen/SPARK-3782 and squashes the following commits:
5608d28 [Sean Owen] Update slf4j to 1.7.10
Author: Kannan Rajah <rkannan82@gmail.com>
Closes#4108 from rkannan82/master and squashes the following commits:
eca095b [Kannan Rajah] Update pom.xml to pull MapR's Hadoop version 2.4.1.
In addition to the `hadoop-2.x` profiles in the parent POM, there is actually another set of profiles in `examples` that has to be activated differently to get the right Hadoop 1 vs 2 flavor of HBase. This wasn't actually used in making Hadoop 2 distributions, hence the problem.
To reduce complexity, I suggest merging them with the parent POM profiles, which is possible now.
You'll see this changes appears to update the HBase version, but actually, the default 0.94 version was not being used. HBase is only used in examples, and the examples POM always chose one profile or the other that updated the version to 0.98.x anyway.
Author: Sean Owen <sowen@cloudera.com>
Closes#3992 from srowen/SPARK-5172 and squashes the following commits:
17830d9 [Sean Owen] Control hbase hadoop1/2 flavor in the parent POM with existing hadoop-2.x profiles
https://issues.apache.org/jira/browse/SPARK-4159 was resolved but as Sandy points out, the guidance in https://cwiki.apache.org/confluence/display/SPARK/Useful+Developer+Tools under "Running Individual Tests" no longer quite works, not optimally.
This minor change is not really the important change, which is an update to the wiki text. The correct way to run one Scala test suite in Maven is now:
```
mvn test -DwildcardSuites=org.apache.spark.io.CompressionCodecSuite -Dtests=none
```
The correct way to run one Java test is
```
mvn test -DwildcardSuites=none -Dtests=org.apache.spark.streaming.JavaAPISuite
```
Basically, you have to set two properties in order to suppress all of one type of test (with a non-existent test name like 'none') and all but one test of the other type.
The change in the PR just prevents Surefire from barfing when it finds no "none" test.
Author: Sean Owen <sowen@cloudera.com>
Closes#3993 from srowen/SPARK-4159 and squashes the following commits:
83106d7 [Sean Owen] Default failIfNoTests to false to enable the -DwildcardSuites=... -Dtests=... syntax for running one test to work
- update version from 0.18.1 to 0.21.0
- I'm doing some tests in order to verify some spark jobs work fine on mesos 0.21.0 environment.
Author: Jongyoul Lee <jongyoul@gmail.com>
Closes#3934 from jongyoul/SPARK-3619 and squashes the following commits:
ab994fa [Jongyoul Lee] [SPARK-3619] Upgrade to Mesos 0.21 to work around MESOS-1688 - update version from 0.18.1 to 0.21.0
This change does a few things to make the hadoop-provided profile more useful:
- Create new profiles for other libraries / services that might be provided by the infrastructure
- Simplify and fix the poms so that the profiles are only activated while building assemblies.
- Fix tests so that they're able to run when the profiles are activated
- Add a new env variable to be used by distributions that use these profiles to provide the runtime
classpath for Spark jobs and daemons.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#2982 from vanzin/SPARK-4048 and squashes the following commits:
82eb688 [Marcelo Vanzin] Add a comment.
eb228c0 [Marcelo Vanzin] Fix borked merge.
4e38f4e [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
9ef79a3 [Marcelo Vanzin] Alternative way to propagate test classpath to child processes.
371ebee [Marcelo Vanzin] Review feedback.
52f366d [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
83099fc [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
7377e7b [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
322f882 [Marcelo Vanzin] Fix merge fail.
f24e9e7 [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
8b00b6a [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
9640503 [Marcelo Vanzin] Cleanup child process log message.
115fde5 [Marcelo Vanzin] Simplify a comment (and make it consistent with another pom).
e3ab2da [Marcelo Vanzin] Fix hive-thriftserver profile.
7820d58 [Marcelo Vanzin] Fix CliSuite with provided profiles.
1be73d4 [Marcelo Vanzin] Restore flume-provided profile.
d1399ed [Marcelo Vanzin] Restore jetty dependency.
82a54b9 [Marcelo Vanzin] Remove unused profile.
5c54a25 [Marcelo Vanzin] Fix HiveThriftServer2Suite with *-provided profiles.
1fc4d0b [Marcelo Vanzin] Update dependencies for hive-thriftserver.
f7b3bbe [Marcelo Vanzin] Add snappy to hadoop-provided list.
9e4e001 [Marcelo Vanzin] Remove duplicate hive profile.
d928d62 [Marcelo Vanzin] Redirect child stderr to parent's log.
4d67469 [Marcelo Vanzin] Propagate SPARK_DIST_CLASSPATH on Yarn.
417d90e [Marcelo Vanzin] Introduce "SPARK_DIST_CLASSPATH".
2f95f0d [Marcelo Vanzin] Propagate classpath to child processes during testing.
1adf91c [Marcelo Vanzin] Re-enable maven-install-plugin for a few projects.
284dda6 [Marcelo Vanzin] Rework the "hadoop-provided" profile, add new ones.
This PR:
- Reenables `surefire`, and copies config from `scalatest` (which is itself an old fork of `surefire`, so similar)
- Tells `surefire` to test only Java tests
- Enables `surefire` and `scalatest` for all children, and in turn eliminates some duplication.
For me this causes the Scala and Java tests to be run once each, it seems, as desired. It doesn't affect the SBT build but works for Maven. I still need to verify that all of the Scala tests and Java tests are being run.
Author: Sean Owen <sowen@cloudera.com>
Closes#3651 from srowen/SPARK-4159 and squashes the following commits:
2e8a0af [Sean Owen] Remove specialized SPARK_HOME setting for REPL, YARN tests as it appears to be obsolete
12e4558 [Sean Owen] Append to unit-test.log instead of overwriting, so that both surefire and scalatest output is preserved. Also standardize/correct comments a bit.
e6f8601 [Sean Owen] Reenable Java tests by reenabling surefire with config cloned from scalatest; centralize test config in the parent
pwendell 2483c1efb6 didn't actually add a reference to `jackson-core-asl` as intended, but a second redundant reference to `jackson-mapper-asl`, as markhamstra picked up on (https://github.com/apache/spark/pull/3716#issuecomment-68180192) This just rectifies the typo. I missed it as well; the original PR https://github.com/apache/spark/pull/2818 had it correct and I also didn't see the problem.
Author: Sean Owen <sowen@cloudera.com>
Closes#3829 from srowen/SPARK-3955 and squashes the following commits:
6cfdc4e [Sean Owen] Actually refer to jackson-core-asl
...ore-asl
- set the same version to jackson-mapper-asl and jackson-core-asl
- It's related with #2818
- coded a same patch from a latest master
Author: Jongyoul Lee <jongyoul@gmail.com>
Closes#3716 from jongyoul/SPARK-3955 and squashes the following commits:
efa29aa [Jongyoul Lee] [SPARK-3955] Different versions between jackson-mapper-asl and jackson-core-asl - set the same version to jackson-mapper-asl and jackson-core-asl
This PR tries to fix the Hive tests failure encountered in PR #3157 by cleaning `lib_managed` before building assembly jar against Hive 0.13.1 in `dev/run-tests`. Otherwise two sets of datanucleus jars would be left in `lib_managed` and may mess up class paths while executing Hive test suites. Please refer to [this thread] [1] for details. A clean build would be even safer, but we only clean `lib_managed` here to save build time.
This PR also takes the chance to clean up some minor typos and formatting issues in the comments.
[1]: https://github.com/apache/spark/pull/3157#issuecomment-67656488
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Author: Cheng Lian <lian@databricks.com>
Closes#3756 from liancheng/clean-lib-managed and squashes the following commits:
e2bd21d [Cheng Lian] Adds lib_managed to clean set
c9f2f3e [Cheng Lian] Cleans lib_managed before compiling with Hive 0.13.1
This enables assertions for the Maven and SBT build, but overrides the Hive module to not enable assertions.
Author: Sean Owen <sowen@cloudera.com>
Closes#3692 from srowen/SPARK-4814 and squashes the following commits:
caca704 [Sean Owen] Disable assertions just for Hive
f71e783 [Sean Owen] Enable assertions for SBT and Maven build
Sorry if this is a little premature with 1.2 still not out the door, but it will make other work like SPARK-4136 and SPARK-2089 a lot easier.
Author: Sandy Ryza <sandy@cloudera.com>
Closes#3215 from sryza/sandy-spark-4338 and squashes the following commits:
1c5ac08 [Sandy Ryza] Update building Spark docs and remove unnecessary newline
9c1421c [Sandy Ryza] SPARK-4338. Ditch yarn-alpha.
The old location will return a 404.
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#3504 from adrian-wang/repo and squashes the following commits:
f604e05 [Daoyuan Wang] already in maven central, remove at all
f494fac [Daoyuan Wang] spark staging repo outdated
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#3277 from vanzin/version-1.3 and squashes the following commits:
7c3c396 [Marcelo Vanzin] Added temp repo to sbt build.
5f404ff [Marcelo Vanzin] Add another exclusion.
19457e7 [Marcelo Vanzin] Update old version to 1.2, add temporary 1.2 repo.
3c8d705 [Marcelo Vanzin] Workaround for MIMA checks.
e940810 [Marcelo Vanzin] Bumping version to 1.3.0-SNAPSHOT.
The progress bar will look like this:
In the right corner, the numbers are: finished tasks, running tasks, total tasks.
After the stage has finished, it will disappear.
The progress bar is only showed if logging level is WARN or higher (but progress in title is still showed), it can be turned off by spark.driver.showConsoleProgress.
Author: Davies Liu <davies@databricks.com>
Closes#3029 from davies/progress and squashes the following commits:
95336d5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
fc49ac8 [Davies Liu] address commentse
2e90f75 [Davies Liu] show multiple stages in same time
0081bcc [Davies Liu] address comments
38c42f1 [Davies Liu] fix tests
ab87958 [Davies Liu] disable progress bar during tests
30ac852 [Davies Liu] re-implement progress bar
b3f34e5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
6fd30ff [Davies Liu] show progress bar if no task finished in 500ms
e4e7344 [Davies Liu] refactor
e1f524d [Davies Liu] revert unnecessary change
a60477c [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
5cae3f2 [Davies Liu] fix style
ea49fe0 [Davies Liu] address comments
bc53d99 [Davies Liu] refactor
e6bb189 [Davies Liu] fix logging in sparkshell
7e7d4e7 [Davies Liu] address commments
5df26bb [Davies Liu] fix style
9e42208 [Davies Liu] show progress bar in console and title
This patch adds error-detection logic to throw an exception when attempting to create multiple active SparkContexts in the same JVM, since this is currently unsupported and has been known to cause confusing behavior (see SPARK-2243 for more details).
**The solution implemented here is only a partial fix.** A complete fix would have the following properties:
1. Only one SparkContext may ever be under construction at any given time.
2. Once a SparkContext has been successfully constructed, any subsequent construction attempts should fail until the active SparkContext is stopped.
3. If the SparkContext constructor throws an exception, then all resources created in the constructor should be cleaned up (SPARK-4194).
4. If a user attempts to create a SparkContext but the creation fails, then the user should be able to create new SparkContexts.
This PR only provides 2) and 4); we should be able to provide all of these properties, but the correct fix will involve larger changes to SparkContext's construction / initialization, so we'll target it for a different Spark release.
### The correct solution:
I think that the correct way to do this would be to move the construction of SparkContext's dependencies into a static method in the SparkContext companion object. Specifically, we could make the default SparkContext constructor `private` and change it to accept a `SparkContextDependencies` object that contains all of SparkContext's dependencies (e.g. DAGScheduler, ContextCleaner, etc.). Secondary constructors could call a method on the SparkContext companion object to create the `SparkContextDependencies` and pass the result to the primary SparkContext constructor. For example:
```scala
class SparkContext private (deps: SparkContextDependencies) {
def this(conf: SparkConf) {
this(SparkContext.getDeps(conf))
}
}
object SparkContext(
private[spark] def getDeps(conf: SparkConf): SparkContextDependencies = synchronized {
if (anotherSparkContextIsActive) { throw Exception(...) }
var dagScheduler: DAGScheduler = null
try {
dagScheduler = new DAGScheduler(...)
[...]
} catch {
case e: Exception =>
Option(dagScheduler).foreach(_.stop())
[...]
}
SparkContextDependencies(dagScheduler, ....)
}
}
```
This gives us mutual exclusion and ensures that any resources created during the failed SparkContext initialization are properly cleaned up.
This indirection is necessary to maintain binary compatibility. In retrospect, it would have been nice if SparkContext had no private constructors and could only be created through builder / factory methods on its companion object, since this buys us lots of flexibility and makes dependency injection easier.
### Alternative solutions:
As an alternative solution, we could refactor SparkContext's primary constructor to perform all object creation in a giant `try-finally` block. Unfortunately, this will require us to turn a bunch of `vals` into `vars` so that they can be assigned from the `try` block. If we still want `vals`, we could wrap each `val` in its own `try` block (since the try block can return a value), but this will lead to extremely messy code and won't guard against the introduction of future code which doesn't properly handle failures.
The more complex approach outlined above gives us some nice dependency injection benefits, so I think that might be preferable to a `var`-ification.
### This PR's solution:
- At the start of the constructor, check whether some other SparkContext is active; if so, throw an exception.
- If another SparkContext might be under construction (or has thrown an exception during construction), allow the new SparkContext to begin construction but log a warning (since resources might have been leaked from a failed creation attempt).
- At the end of the SparkContext constructor, check whether some other SparkContext constructor has raced and successfully created an active context. If so, throw an exception.
This guarantees that no two SparkContexts will ever be active and exposed to users (since we check at the very end of the constructor). If two threads race to construct SparkContexts, then one of them will win and another will throw an exception.
This exception can be turned into a warning by setting `spark.driver.allowMultipleContexts = true`. The exception is disabled in unit tests, since there are some suites (such as Hive) that may require more significant refactoring to clean up their SparkContexts. I've made a few changes to other suites' test fixtures to properly clean up SparkContexts so that the unit test logs contain fewer warnings.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#3121 from JoshRosen/SPARK-4180 and squashes the following commits:
23c7123 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4180
d38251b [Josh Rosen] Address latest round of feedback.
c0987d3 [Josh Rosen] Accept boolean instead of SparkConf in methods.
85a424a [Josh Rosen] Incorporate more review feedback.
372d0d3 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4180
f5bb78c [Josh Rosen] Update mvn build, too.
d809cb4 [Josh Rosen] Improve handling of failed SparkContext creation attempts.
79a7e6f [Josh Rosen] Fix commented out test
a1cba65 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4180
7ba6db8 [Josh Rosen] Add utility to set system properties in tests.
4629d5c [Josh Rosen] Set spark.driver.allowMultipleContexts=true in tests.
ed17e14 [Josh Rosen] Address review feedback; expose hack workaround for existing unit tests.
1c66070 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4180
06c5c54 [Josh Rosen] Add / improve SparkContext cleanup in streaming BasicOperationsSuite
d0437eb [Josh Rosen] StreamingContext.stop() should stop SparkContext even if StreamingContext has not been started yet.
c4d35a2 [Josh Rosen] Log long form of creation site to aid debugging.
918e878 [Josh Rosen] Document "one SparkContext per JVM" limitation.
afaa7e3 [Josh Rosen] [SPARK-4180] Prevent creations of multiple active SparkContexts.
This upgrades snappy-java to 1.1.1.6, which includes a patch that improves error messages when attempting to deserialize empty inputs using SnappyInputStream (see xerial/snappy-java#89).
We previously tried up upgrade to 1.1.1.5 in #2911 but reverted that patch after discovering a memory leak in snappy-java. This should leak have been fixed in 1.1.1.6, though (see xerial/snappy-java#92).
Author: Josh Rosen <joshrosen@databricks.com>
Closes#3287 from JoshRosen/SPARK-4419 and squashes the following commits:
5d6f4cc [Josh Rosen] [SPARK-4419] Upgrade snappy-java to 1.1.1.6.
It seems like the winds might have moved away from this approach, but wanted to post the PR anyway because I got it working and to show what it would look like.
Author: Sandy Ryza <sandy@cloudera.com>
Closes#3239 from sryza/sandy-spark-4375 and squashes the following commits:
0ffbe95 [Sandy Ryza] Enable -Dscala-2.11 in sbt
cd42d94 [Sandy Ryza] Update doc
f6644c3 [Sandy Ryza] SPARK-4375 take 2
Let's give this another go using a version of Hive that shades its JLine dependency.
Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Patrick Wendell <pwendell@gmail.com>
Closes#3159 from pwendell/scala-2.11-prashant and squashes the following commits:
e93aa3e [Patrick Wendell] Restoring -Phive-thriftserver profile and cleaning up build script.
f65d17d [Patrick Wendell] Fixing build issue due to merge conflict
a8c41eb [Patrick Wendell] Reverting dev/run-tests back to master state.
7a6eb18 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into scala-2.11-prashant
583aa07 [Prashant Sharma] REVERT ME: removed hive thirftserver
3680e58 [Prashant Sharma] Revert "REVERT ME: Temporarily removing some Cli tests."
935fb47 [Prashant Sharma] Revert "Fixed by disabling a few tests temporarily."
925e90f [Prashant Sharma] Fixed by disabling a few tests temporarily.
2fffed3 [Prashant Sharma] Exclude groovy from sbt build, and also provide a way for such instances in future.
8bd4e40 [Prashant Sharma] Switched to gmaven plus, it fixes random failures observer with its predecessor gmaven.
5272ce5 [Prashant Sharma] SPARK_SCALA_VERSION related bugs.
2121071 [Patrick Wendell] Migrating version detection to PySpark
b1ed44d [Patrick Wendell] REVERT ME: Temporarily removing some Cli tests.
1743a73 [Patrick Wendell] Removing decimal test that doesn't work with Scala 2.11
f5cad4e [Patrick Wendell] Add Scala 2.11 docs
210d7e1 [Patrick Wendell] Revert "Testing new Hive version with shaded jline"
48518ce [Patrick Wendell] Remove association of Hive and Thriftserver profiles.
e9d0a06 [Patrick Wendell] Revert "Enable thritfserver for Scala 2.10 only"
67ec364 [Patrick Wendell] Guard building of thriftserver around Scala 2.10 check
8502c23 [Patrick Wendell] Enable thritfserver for Scala 2.10 only
e22b104 [Patrick Wendell] Small fix in pom file
ec402ab [Patrick Wendell] Various fixes
0be5a9d [Patrick Wendell] Testing new Hive version with shaded jline
4eaec65 [Prashant Sharma] Changed scripts to ignore target.
5167bea [Prashant Sharma] small correction
a4fcac6 [Prashant Sharma] Run against scala 2.11 on jenkins.
80285f4 [Prashant Sharma] MAven equivalent of setting spark.executor.extraClasspath during tests.
034b369 [Prashant Sharma] Setting test jars on executor classpath during tests from sbt.
d4874cb [Prashant Sharma] Fixed Python Runner suite. null check should be first case in scala 2.11.
6f50f13 [Prashant Sharma] Fixed build after rebasing with master. We should use ${scala.binary.version} instead of just 2.10
e56ca9d [Prashant Sharma] Print an error if build for 2.10 and 2.11 is spotted.
937c0b8 [Prashant Sharma] SCALA_VERSION -> SPARK_SCALA_VERSION
cb059b0 [Prashant Sharma] Code review
0476e5e [Prashant Sharma] Scala 2.11 support with repl and all build changes.
SPARK-3797 introduced the `network/yarn` module, but its YARN code depends on YARN APIs not present in older versions covered by the `yarn-alpha` profile. As a result builds like `mvn -Pyarn-alpha -Phadoop-0.23 -Dhadoop.version=0.23.7 -DskipTests clean package` fail.
The solution is just to not build `network/yarn` with profile `yarn-alpha`.
Author: Sean Owen <sowen@cloudera.com>
Closes#3167 from srowen/SPARK-4305 and squashes the following commits:
88938cb [Sean Owen] Don't build network/yarn in yarn-alpha profile as it won't compile
This creates a new module `network/yarn` that depends on `network/shuffle` recently created in #3001. This PR introduces a custom Yarn auxiliary service that runs the external shuffle service. As of the changes here this shuffle service is required for using dynamic allocation with Spark.
This is still WIP mainly because it doesn't handle security yet. I have tested this on a stable Yarn cluster.
Author: Andrew Or <andrew@databricks.com>
Closes#3082 from andrewor14/yarn-shuffle-service and squashes the following commits:
ef3ddae [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
0ee67a2 [Andrew Or] Minor wording suggestions
1c66046 [Andrew Or] Remove unused provided dependencies
0eb6233 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
6489db5 [Andrew Or] Try catch at the right places
7b71d8f [Andrew Or] Add detailed java docs + reword a few comments
d1124e4 [Andrew Or] Add security to shuffle service (INCOMPLETE)
5f8a96f [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
9b6e058 [Andrew Or] Address various feedback
f48b20c [Andrew Or] Fix tests again
f39daa6 [Andrew Or] Do not make network-yarn an assembly module
761f58a [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-shuffle-service
15a5b37 [Andrew Or] Fix build for Hadoop 1.x
baff916 [Andrew Or] Fix tests
5bf9b7e [Andrew Or] Address a few minor comments
5b419b8 [Andrew Or] Add missing license header
804e7ff [Andrew Or] Include the Yarn shuffle service jar in the distribution
cd076a4 [Andrew Or] Require external shuffle service for dynamic allocation
ea764e0 [Andrew Or] Connect to Yarn shuffle service only if it's enabled
1bf5109 [Andrew Or] Use the shuffle service port specified through hadoop config
b4b1f0c [Andrew Or] 4 tabs -> 2 tabs
43dcb96 [Andrew Or] First cut integration of shuffle service with Yarn aux service
b54a0c4 [Andrew Or] Initial skeleton for Yarn shuffle service
instead of `hive.version=0.13.1`.
e.g. mvn -Phive -Phive=0.13.1
Note: `hive.version=0.13.1a` is the default property value. However, when explicitly specifying the `hive-0.13.1` maven profile, the wrong one would be selected.
References: PR #2685, which resolved a package incompatibility issue with Hive-0.13.1 by introducing a special version Hive-0.13.1a
Author: fi <coderfi@gmail.com>
Closes#3072 from coderfi/master and squashes the following commits:
7ca4b1e [fi] Fixes the `hive-0.13.1` maven profile referencing `hive.version=0.13.1` instead of the Spark compatible `hive.version=0.13.1a` Note: `hive.version=0.13.1a` is the default version. However, when explicitly specifying the `hive-0.13.1` maven profile, the wrong one would be selected. e.g. mvn -Phive -Phive=0.13.1 See PR #2685
In #2928 , we shade commons-math3 to prevent future conflicts with hadoop. It caused problems with our Jenkins master build with maven. Some tests used local-cluster mode, where the assembly jar contains relocated math3 classes, while mllib test code still compiles with core and the untouched math3 classes.
This PR sets commons-math3 version based on hadoop profiles.
pwendell JoshRosen srowen
Author: Xiangrui Meng <meng@databricks.com>
Closes#3023 from mengxr/SPARK-4121-alt and squashes the following commits:
580f6d9 [Xiangrui Meng] replace tab by spaces
7f71f08 [Xiangrui Meng] revert changes to PoissonSampler to avoid conflicts
d3353d9 [Xiangrui Meng] do not shade commons-math3
b4180dc [Xiangrui Meng] temp work
This patch introduces the tooling necessary to construct an external shuffle service which is independent of Spark executors, and then use this service inside Spark. An example (just for the sake of this PR) of the service creation can be found in Worker, and the service itself is used by plugging in the StandaloneShuffleClient as Spark's ShuffleClient (setup in BlockManager).
This PR continues the work from #2753, which extracted out the transport layer of Spark's block transfer into an independent package within Spark. A new package was created which contains the Spark business logic necessary to retrieve the actual shuffle data, which is completely independent of the transport layer introduced in the previous patch. Similar to the transport layer, this package must not depend on Spark as we anticipate plugging this service as a lightweight process within, say, the YARN NodeManager, and do not wish to include Spark's dependencies (including Scala itself).
There are several outstanding tasks which must be complete before this PR can be merged:
- [x] Complete unit testing of network/shuffle package.
- [x] Performance and correctness testing on a real cluster.
- [x] Remove example service instantiation from Worker.scala.
There are even more shortcomings of this PR which should be addressed in followup patches:
- Don't use Java serializer for RPC layer! It is not cross-version compatible.
- Handle shuffle file cleanup for dead executors once the application terminates or the ContextCleaner triggers.
- Documentation of the feature in the Spark docs.
- Improve behavior if the shuffle service itself goes down (right now we don't blacklist it, and new executors cannot spawn on that machine).
- SSL and SASL integration
- Nice to have: Handle shuffle file consolidation (this would requires changes to Spark's implementation).
Author: Aaron Davidson <aaron@databricks.com>
Closes#3001 from aarondav/shuffle-service and squashes the following commits:
4d1f8c1 [Aaron Davidson] Remove changes to Worker
705748f [Aaron Davidson] Rename Standalone* to External*
fd3928b [Aaron Davidson] Do not unregister executor outputs unduly
9883918 [Aaron Davidson] Make suggested build changes
3d62679 [Aaron Davidson] Add Spark integration test
7fe51d5 [Aaron Davidson] Fix SBT integration
56caa50 [Aaron Davidson] Address comments
c8d1ac3 [Aaron Davidson] Add unit tests
2f70c0c [Aaron Davidson] Fix unit tests
5483e96 [Aaron Davidson] Fix unit tests
46a70bf [Aaron Davidson] Whoops, bracket
5ea4df6 [Aaron Davidson] [SPARK-3796] Create external service which can serve shuffle files
I recommend upgrading roaring to 0.4.5 as it fixes a rarely occurring bug in iterators (that would otherwise throw an unwarranted exception). The upgrade should have no other consequence.
Author: Daniel Lemire <lemire@gmail.com>
Closes#3044 from lemire/master and squashes the following commits:
54018c5 [Daniel Lemire] Recommended update to roaring 0.4.5 (bug fix release)
048933e [Daniel Lemire] Merge remote-tracking branch 'upstream/master'
431f3a0 [Daniel Lemire] Recommended bug fix release
In #2241 hive-thriftserver is not enabled. This patch enable hive-thriftserver to support hive-0.13.1 by using a shim layer refer to #2241.
1 A light shim layer(code in sql/hive-thriftserver/hive-version) for each different hive version to handle api compatibility
2 New pom profiles "hive-default" and "hive-versions"(copy from #2241) to activate different hive version
3 SBT cmd for different version as follows:
hive-0.12.0 --- sbt/sbt -Phive,hadoop-2.3 -Phive-0.12.0 assembly
hive-0.13.1 --- sbt/sbt -Phive,hadoop-2.3 -Phive-0.13.1 assembly
4 Since hive-thriftserver depend on hive subproject, this patch should be merged with #2241 to enable hive-0.13.1 for hive-thriftserver
Author: wangfei <wangfei1@huawei.com>
Author: scwf <wangfei1@huawei.com>
Closes#2685 from scwf/shim-thriftserver1 and squashes the following commits:
f26f3be [wangfei] remove clean to save time
f5cac74 [wangfei] remove local hivecontext test
578234d [wangfei] use new shaded hive
18fb1ff [wangfei] exclude kryo in hive pom
fa21d09 [wangfei] clean package assembly/assembly
8a4daf2 [wangfei] minor fix
0d7f6cf [wangfei] address comments
f7c93ae [wangfei] adding build with hive 0.13 before running tests
bcf943f [wangfei] Merge branch 'master' of https://github.com/apache/spark into shim-thriftserver1
c359822 [wangfei] reuse getCommandProcessor in hiveshim
52674a4 [scwf] sql/hive included since examples depend on it
3529e98 [scwf] move hive module to hive profile
f51ff4e [wangfei] update and fix conflicts
f48d3a5 [scwf] Merge branch 'master' of https://github.com/apache/spark into shim-thriftserver1
41f727b [scwf] revert pom changes
13afde0 [scwf] fix small bug
4b681f4 [scwf] enable thriftserver in profile hive-0.13.1
0bc53aa [scwf] fixed when result filed is null
dfd1c63 [scwf] update run-tests to run hive-0.12.0 default now
c6da3ce [scwf] Merge branch 'master' of https://github.com/apache/spark into shim-thriftserver
7c66b8e [scwf] update pom according spark-2706
ae47489 [scwf] update and fix conflicts
The parquet-mr project has introduced a new filter api (https://github.com/apache/incubator-parquet-mr/pull/4), along with several fixes . It can also eliminate entire RowGroups depending on certain statistics like min/max
We can leverage that to further improve performance of queries with filters.
Also filter2 api introduces ability to create custom filters. We can create a custom filter for the optimized In clause (InSet) , so that elimination happens in the ParquetRecordReader itself
Author: Yash Datta <Yash.Datta@guavus.com>
Closes#2841 from saucam/master and squashes the following commits:
8282ba0 [Yash Datta] SPARK-3968: fix scala code style and add some more tests for filtering on optional columns
515df1c [Yash Datta] SPARK-3968: Add a test case for filter pushdown on optional column
5f4530e [Yash Datta] SPARK-3968: Fix scala code style
f304667 [Yash Datta] SPARK-3968: Using task metadata strategy for row group filtering
ec53e92 [Yash Datta] SPARK-3968: No push down should result in case we are unable to create a record filter
48163c3 [Yash Datta] SPARK-3968: Code cleanup
cc7b596 [Yash Datta] SPARK-3968: 1. Fix RowGroupFiltering not working 2. Use the serialization/deserialization from Parquet library for filter pushdown
caed851 [Yash Datta] Revert "SPARK-3968: Not pushing the filters in case of OPTIONAL columns" since filtering on optional columns is now supported in filter2 api
49703c9 [Yash Datta] SPARK-3968: Not pushing the filters in case of OPTIONAL columns
9d09741 [Yash Datta] SPARK-3968: Change parquet filter pushdown to use filter2 api of parquet-mr
This PR encapsulates #2330, which is itself a continuation of #2240. The first goal of this PR is to provide an alternate, simpler implementation of the ConnectionManager which is based on Netty.
In addition to this goal, however, we want to resolve [SPARK-3796](https://issues.apache.org/jira/browse/SPARK-3796), which calls for a standalone shuffle service which can be integrated into the YARN NodeManager, Standalone Worker, or on its own. This PR makes the first step in this direction by ensuring that the actual Netty service is as small as possible and extracted from Spark core. Given this, we should be able to construct this standalone jar which can be included in other JVMs without incurring significant dependency or runtime issues. The actual work to ensure that such a standalone shuffle service would work in Spark will be left for a future PR, however.
In order to minimize dependencies and allow for the service to be long-running (possibly much longer-running than Spark, and possibly having to support multiple version of Spark simultaneously), the entire service has been ported to Java, where we have full control over the binary compatibility of the components and do not depend on the Scala runtime or version.
These issues: have been addressed by folding in #2330:
SPARK-3453: Refactor Netty module to use BlockTransferService interface
SPARK-3018: Release all buffers upon task completion/failure
SPARK-3002: Create a connection pool and reuse clients across different threads
SPARK-3017: Integration tests and unit tests for connection failures
SPARK-3049: Make sure client doesn't block when server/connection has error(s)
SPARK-3502: SO_RCVBUF and SO_SNDBUF should be bootstrap childOption, not option
SPARK-3503: Disable thread local cache in PooledByteBufAllocator
TODO before mergeable:
- [x] Implement uploadBlock()
- [x] Unit tests for RPC side of code
- [x] Performance testing (see comments [here](https://github.com/apache/spark/pull/2753#issuecomment-59475022))
- [x] Turn OFF by default (currently on for unit testing)
Author: Reynold Xin <rxin@apache.org>
Author: Aaron Davidson <aaron@databricks.com>
Author: cocoatomo <cocoatomo77@gmail.com>
Author: Patrick Wendell <pwendell@gmail.com>
Author: Prashant Sharma <prashant.s@imaginea.com>
Author: Davies Liu <davies.liu@gmail.com>
Author: Anand Avati <avati@redhat.com>
Closes#2753 from aarondav/netty and squashes the following commits:
cadfd28 [Aaron Davidson] Turn netty off by default
d7be11b [Aaron Davidson] Turn netty on by default
4a204b8 [Aaron Davidson] Fail block fetches if client connection fails
2b0d1c0 [Aaron Davidson] 100ch
0c5bca2 [Aaron Davidson] Merge branch 'master' of https://github.com/apache/spark into netty
14e37f7 [Aaron Davidson] Address Reynold's comments
8dfcceb [Aaron Davidson] Merge branch 'master' of https://github.com/apache/spark into netty
322dfc1 [Aaron Davidson] Address Reynold's comments, including major rename
e5675a4 [Aaron Davidson] Fail outstanding RPCs as well
ccd4959 [Aaron Davidson] Don't throw exception if client immediately fails
9da0bc1 [Aaron Davidson] Add RPC unit tests
d236dfd [Aaron Davidson] Remove no-op serializer :)
7b7a26c [Aaron Davidson] Fix Nio compile issue
dd420fd [Aaron Davidson] Merge branch 'master' of https://github.com/apache/spark into netty-test
939f276 [Aaron Davidson] Attempt to make comm. bidirectional
aa58f67 [cocoatomo] [SPARK-3909][PySpark][Doc] A corrupted format in Sphinx documents and building warnings
8dc1ded [cocoatomo] [SPARK-3867][PySpark] ./python/run-tests failed when it run with Python 2.6 and unittest2 is not installed
5b5dbe6 [Prashant Sharma] [SPARK-2924] Required by scala 2.11, only one fun/ctor amongst overriden alternatives, can have default argument(s).
2c5d9dc [Patrick Wendell] HOTFIX: Fix build issue with Akka 2.3.4 upgrade.
020691e [Davies Liu] [SPARK-3886] [PySpark] use AutoBatchedSerializer by default
ae4083a [Anand Avati] [SPARK-2805] Upgrade Akka to 2.3.4
29c6dcf [Aaron Davidson] [SPARK-3453] Netty-based BlockTransferService, extracted from Spark core
f7e7568 [Reynold Xin] Fixed spark.shuffle.io.receiveBuffer setting.
5d98ce3 [Reynold Xin] Flip buffer.
f6c220d [Reynold Xin] Merge with latest master.
407e59a [Reynold Xin] Fix style violation.
a0518c7 [Reynold Xin] Implemented block uploads.
4b18db2 [Reynold Xin] Copy the buffer in fetchBlockSync.
bec4ea2 [Reynold Xin] Removed OIO and added num threads settings.
1bdd7ee [Reynold Xin] Fixed tests.
d68f328 [Reynold Xin] Logging close() in case close() fails.
f63fb4c [Reynold Xin] Add more debug message.
6afc435 [Reynold Xin] Added logging.
c066309 [Reynold Xin] Implement java.io.Closeable interface.
519d64d [Reynold Xin] Mark private package visibility and MimaExcludes.
f0a16e9 [Reynold Xin] Fixed test hanging.
14323a5 [Reynold Xin] Removed BlockManager.getLocalShuffleFromDisk.
b2f3281 [Reynold Xin] Added connection pooling.
d23ed7b [Reynold Xin] Incorporated feedback from Norman: - use same pool for boss and worker - remove ioratio - disable caching of byte buf allocator - childoption sendbuf/receivebuf - fire exception through pipeline
9e0cb87 [Reynold Xin] Fixed BlockClientHandlerSuite
5cd33d7 [Reynold Xin] Fixed style violation.
cb589ec [Reynold Xin] Added more test cases covering cleanup when fault happens in ShuffleBlockFetcherIteratorSuite
1be4e8e [Reynold Xin] Shorten NioManagedBuffer and NettyManagedBuffer class names.
108c9ed [Reynold Xin] Forgot to add TestSerializer to the commit list.
b5c8d1f [Reynold Xin] Fixed ShuffleBlockFetcherIteratorSuite.
064747b [Reynold Xin] Reference count buffers and clean them up properly.
2b44cf1 [Reynold Xin] Added more documentation.
1760d32 [Reynold Xin] Use Epoll.isAvailable in BlockServer as well.
165eab1 [Reynold Xin] [SPARK-3453] Refactor Netty module to use BlockTransferService.
This change replaces usages of colt with commons-math3 equivalents, and makes some minor necessary adjustments to related code and tests to match.
Author: Sean Owen <sowen@cloudera.com>
Closes#2928 from srowen/SPARK-4022 and squashes the following commits:
61a232f [Sean Owen] Fix failure due to different sampling in JavaAPISuite.sample()
16d66b8 [Sean Owen] Simplify seeding with call to reseedRandomGenerator
a1a78e0 [Sean Owen] Use Well19937c
31c7641 [Sean Owen] Fix Python Poisson test by choosing a different seed; about 88% of seeds should work but 1 didn't, it seems
5c9c67f [Sean Owen] Additional test fixes from review
d8f88e0 [Sean Owen] Replace colt with commons-math3. Some tests do not pass yet.
This patch adds Selenium tests for Spark's web UI. To avoid adding extra
dependencies to the test environment, the tests use Selenium's HtmlUnitDriver,
which is pure-Java, instead of, say, ChromeDriver.
I added new tests to try to reproduce a few UI bugs reported on JIRA, namely
SPARK-3021, SPARK-2105, and SPARK-2527. I wasn't able to reproduce these bugs;
I suspect that the older ones might have been fixed by other patches.
In order to use HtmlUnitDriver, I added an explicit dependency on the
org.apache.httpcomponents version of httpclient in order to prevent jets3t's
older version from taking precedence on the classpath.
I also upgraded ScalaTest to 2.2.1.
Author: Josh Rosen <joshrosen@apache.org>
Author: Josh Rosen <joshrosen@databricks.com>
Closes#2474 from JoshRosen/webui-selenium-tests and squashes the following commits:
fcc9e83 [Josh Rosen] scalautils -> scalactic package rename
510e54a [Josh Rosen] [SPARK-3616] Add basic Selenium tests to WebUISuite.
Roaring has been updated to version 0.4.3. We fixed a rarely occurring bug with serialization. No API or format changes were made.
Author: Daniel Lemire <lemire@gmail.com>
Closes#2938 from lemire/master and squashes the following commits:
431f3a0 [Daniel Lemire] Recommended bug fix release
This upgrades snappy-java to 1.1.1.5, which improves error messages when attempting to deserialize empty inputs using SnappyInputStream (see https://github.com/xerial/snappy-java/issues/89).
Author: Josh Rosen <rosenville@gmail.com>
Author: Josh Rosen <joshrosen@databricks.com>
Closes#2911 from JoshRosen/upgrade-snappy-java and squashes the following commits:
adec96c [Josh Rosen] Use snappy-java 1.1.1.5
cc953d6 [Josh Rosen] [SPARK-4056] Upgrade snappy-java to 1.1.1.4
Given that a lot of users are trying to use hive 0.13 in spark, and the incompatibility between hive-0.12 and hive-0.13 on the API level I want to propose following approach, which has no or minimum impact on existing hive-0.12 support, but be able to jumpstart the development of hive-0.13 and future version support.
Approach: Introduce “hive-version” property, and manipulate pom.xml files to support different hive version at compiling time through shim layer, e.g., hive-0.12.0 and hive-0.13.1. More specifically,
1. For each different hive version, there is a very light layer of shim code to handle API differences, sitting in sql/hive/hive-version, e.g., sql/hive/v0.12.0 or sql/hive/v0.13.1
2. Add a new profile hive-default active by default, which picks up all existing configuration and hive-0.12.0 shim (v0.12.0) if no hive.version is specified.
3. If user specifies different version (currently only 0.13.1 by -Dhive.version = 0.13.1), hive-versions profile will be activated, which pick up hive-version specific shim layer and configuration, mainly the hive jars and hive-version shim, e.g., v0.13.1.
4. With this approach, nothing is changed with current hive-0.12 support.
No change by default: sbt/sbt -Phive
For example: sbt/sbt -Phive -Pyarn -Phadoop-2.4 -Dhadoop.version=2.4.0 assembly
To enable hive-0.13: sbt/sbt -Dhive.version=0.13.1
For example: sbt/sbt -Dhive.version=0.13.1 -Pyarn -Phadoop-2.4 -Dhadoop.version=2.4.0 assembly
Note that in hive-0.13, hive-thriftserver is not enabled, which should be fixed by other Jira, and we don’t need -Phive with -Dhive.version in building (probably we should use -Phive -Dhive.version=xxx instead after thrift server is also supported in hive-0.13.1).
Author: Zhan Zhang <zhazhan@gmail.com>
Author: zhzhan <zhazhan@gmail.com>
Author: Patrick Wendell <pwendell@gmail.com>
Closes#2241 from zhzhan/spark-2706 and squashes the following commits:
3ece905 [Zhan Zhang] minor fix
410b668 [Zhan Zhang] solve review comments
cbb4691 [Zhan Zhang] change run-test for new options
0d4d2ed [Zhan Zhang] rebase
497b0f4 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
8fad1cf [Zhan Zhang] change the pom file and make hive-0.13.1 as the default
ab028d1 [Zhan Zhang] rebase
4a2e36d [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
4cb1b93 [zhzhan] Merge pull request #1 from pwendell/pr-2241
b0478c0 [Patrick Wendell] Changes to simplify the build of SPARK-2706
2b50502 [Zhan Zhang] rebase
a72c0d4 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
cb22863 [Zhan Zhang] correct the typo
20f6cf7 [Zhan Zhang] solve compatability issue
f7912a9 [Zhan Zhang] rebase and solve review feedback
301eb4a [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
10c3565 [Zhan Zhang] address review comments
6bc9204 [Zhan Zhang] rebase and remove temparory repo
d3aa3f2 [Zhan Zhang] Merge branch 'master' into spark-2706
cedcc6f [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
3ced0d7 [Zhan Zhang] rebase
d9b981d [Zhan Zhang] rebase and fix error due to rollback
adf4924 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
3dd50e8 [Zhan Zhang] solve conflicts and remove unnecessary implicts
d10bf00 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
dc7bdb3 [Zhan Zhang] solve conflicts
7e0cc36 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
d7c3e1e [Zhan Zhang] Merge branch 'master' into spark-2706
68deb11 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
d48bd18 [Zhan Zhang] address review comments
3ee3b2b [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
57ea52e [Zhan Zhang] Merge branch 'master' into spark-2706
2b0d513 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
9412d24 [Zhan Zhang] address review comments
f4af934 [Zhan Zhang] rebase
1ccd7cc [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
128b60b [Zhan Zhang] ignore 0.12.0 test cases for the time being
af9feb9 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
5f5619f [Zhan Zhang] restructure the directory and different hive version support
05d3683 [Zhan Zhang] solve conflicts
e4c1982 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
94b4fdc [Zhan Zhang] Spark-2706: hive-0.13.1 support on spark
87ebf3b [Zhan Zhang] Merge branch 'master' into spark-2706
921e914 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
f896b2a [Zhan Zhang] Merge branch 'master' into spark-2706
789ea21 [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
cb53a2c [Zhan Zhang] Merge branch 'master' of https://github.com/apache/spark
f6a8a40 [Zhan Zhang] revert
ba14f28 [Zhan Zhang] test
dbedff3 [Zhan Zhang] Merge remote-tracking branch 'upstream/master'
70964fe [Zhan Zhang] revert
fe0f379 [Zhan Zhang] Merge branch 'master' of https://github.com/zhzhan/spark
70ffd93 [Zhan Zhang] revert
42585ec [Zhan Zhang] test
7d5fce2 [Zhan Zhang] test
Author: Prashant Sharma <prashant.s@imaginea.com>
Closes#2921 from ScrapCodes/build-changes-effective-pom and squashes the following commits:
8841491 [Prashant Sharma] Fixed broken maven build.
aa7b91d [Prashant Sharma] used an unused dep.
0300dac [Prashant Sharma] improved comment messages..
28f891e [Prashant Sharma] Added a useless dependency, so that we can shade it. And realized fake shading works for us.
553d96b [Prashant Sharma] Shaded some unused class of an unused dep, to generate effective pom(s)
This commit fixes a bug in MapStatus that could cause jobs to wrongly return
empty results if those jobs contained stages with more than 2000 partitions
where most of those partitions were empty.
For jobs with > 2000 partitions, MapStatus uses HighlyCompressedMapStatus,
which only stores the average size of blocks. If the average block size is
zero, then this will cause all blocks to be reported as empty, causing
BlockFetcherIterator to mistakenly skip them.
For example, this would return an empty result:
sc.makeRDD(0 until 10, 1000).repartition(2001).collect()
This can also lead to deserialization errors (e.g. Snappy decoding errors)
for jobs with > 2000 partitions where the average block size is non-zero but
there is at least one empty block. In this case, the BlockFetcher attempts to
fetch empty blocks and fails when trying to deserialize them.
The root problem here is that MapStatus has a (previously undocumented)
correctness property that was violated by HighlyCompressedMapStatus:
If a block is non-empty, then getSizeForBlock must be non-zero.
I fixed this by modifying HighlyCompressedMapStatus to store the average size
of _non-empty_ blocks and to use a compressed bitmap to track which blocks are
empty.
I also removed a test which was broken as originally written: it attempted
to check that HighlyCompressedMapStatus's size estimation error was < 10%,
but this was broken because HighlyCompressedMapStatus is only used for map
statuses with > 2000 partitions, but the test only created 50.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#2866 from JoshRosen/spark-4019 and squashes the following commits:
fc8b490 [Josh Rosen] Roll back hashset change, which didn't improve performance.
5faa0a4 [Josh Rosen] Incorporate review feedback
c8b8cae [Josh Rosen] Two performance fixes:
3b892dd [Josh Rosen] Address Reynold's review comments
ba2e71c [Josh Rosen] Add missing newline
609407d [Josh Rosen] Use Roaring Bitmap to track non-empty blocks.
c23897a [Josh Rosen] Use sets when comparing collect() results
91276a3 [Josh Rosen] [SPARK-4019] Fix MapStatus compression bug that could lead to empty results.
I have tried maven help plugin first but that published all projects in top level pom. So I was left with no choice but to roll my own trivial plugin. This patch basically installs an effective pom after maven install is finished.
The problem it fixes is described as follows:
If you install using maven
` mvn install -DskipTests -Dhadoop.version=2.2.0 -Phadoop-2.2 `
Then without this patch the published pom(s) will have hadoop version as 1.0.4. This can be a problem at some point.
Author: Prashant Sharma <prashant.s@imaginea.com>
Closes#2673 from ScrapCodes/build-changes-effective-pom and squashes the following commits:
aa7b91d [Prashant Sharma] used an unused dep.
0300dac [Prashant Sharma] improved comment messages..
28f891e [Prashant Sharma] Added a useless dependency, so that we can shade it. And realized fake shading works for us.
553d96b [Prashant Sharma] Shaded some unused class of an unused dep, to generate effective pom(s)
We had to upgrade our Hive 0.12 version as well to deal with a protobuf
conflict (both hive and akka have been using a shaded protobuf version).
This is testing a correctly patched version of Hive 0.12.
Author: Patrick Wendell <pwendell@gmail.com>
Closes#2756 from pwendell/hotfix and squashes the following commits:
cc979d0 [Patrick Wendell] HOTFIX: Fix build issue with Akka 2.3.4 upgrade.
This is a second rev of the Akka upgrade (earlier merged, but reverted). I made a slight modification which is that I also upgrade Hive to deal with a compatibility issue related to the protocol buffers library.
Author: Anand Avati <avati@redhat.com>
Author: Patrick Wendell <pwendell@gmail.com>
Closes#2752 from pwendell/akka-upgrade and squashes the following commits:
4c7ca3f [Patrick Wendell] Upgrading to new hive->protobuf version
57a2315 [Anand Avati] SPARK-1812: streaming - remove tests which depend on akka.actor.IO
2a551d3 [Anand Avati] SPARK-1812: core - upgrade to akka 2.3.4
Upgrade to akka 2.3.4
Author: Anand Avati <avati@redhat.com>
Closes#1685 from avati/SPARK-1812-akka-2.3 and squashes the following commits:
57a2315 [Anand Avati] SPARK-1812: streaming - remove tests which depend on akka.actor.IO
2a551d3 [Anand Avati] SPARK-1812: core - upgrade to akka 2.3.4
This patch forces use of commons http client 4.2 in Kinesis-asl profile so that the AWS SDK does not run into dependency conflicts
Author: aniketbhatnagar <aniket.bhatnagar@gmail.com>
Closes#2535 from aniketbhatnagar/Kinesis-HttpClient-Dep-Fix and squashes the following commits:
aa2079f [aniketbhatnagar] Merge branch 'Kinesis-HttpClient-Dep-Fix' of https://github.com/aniketbhatnagar/spark into Kinesis-HttpClient-Dep-Fix
73f55f6 [aniketbhatnagar] SPARK-3638 | Forced a compatible version of http client in kinesis-asl profile
70cc75b [aniketbhatnagar] deleted merge files
725dbc9 [aniketbhatnagar] Merge remote-tracking branch 'origin/Kinesis-HttpClient-Dep-Fix' into Kinesis-HttpClient-Dep-Fix
4ed61d8 [aniketbhatnagar] SPARK-3638 | Forced a compatible version of http client in kinesis-asl profile
9cd6103 [aniketbhatnagar] SPARK-3638 | Forced a compatible version of http client in kinesis-asl profile
Since 1.1.0 has published, remove spark-staging-1030.
Author: wangfei <wangfei1@huawei.com>
Closes#2532 from scwf/patch-2 and squashes the following commits:
bc9e00b [wangfei] remove spark-staging-1030
This patch adds a couple of, currently, very simple integration tests
to make sure both client and cluster modes are working. The tests don't
do much yet other than run a simple job, but the plan is to enhance
them after we get the framework in.
The cluster tests are noisy, so redirect all log output to a file
like other tests do. Copying the conf around sucks but it's less
work than messing with maven/sbt and having to clean up other
projects.
Note the test is only added for yarn-stable. The code compiles
against yarn-alpha but there are two issues I ran into that I
could not overcome:
- an old netty dependency kept creeping into the classpath and
causing akka to not work, when using sbt; the old netty was
correctly suppressed under maven.
- MiniYARNCluster kept failing to execute containers because it
did not create the NM's local dir itself; this is apparently
a known behavior, but I'm not sure how to work around it.
None of those issues are present with the stable Yarn.
Also, these tests are a little slow to run. Apparently Spark doesn't
yet tag tests (so that these could be isolated in a "slow" batch),
so this is something to keep in mind.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#2257 from vanzin/yarn-tests and squashes the following commits:
6d5b84e [Marcelo Vanzin] Fix wrong system property being set.
8b0933d [Marcelo Vanzin] Merge branch 'master' into yarn-tests
5c2b56f [Marcelo Vanzin] Use custom log4j conf for Yarn containers.
ec73f17 [Marcelo Vanzin] More review feedback.
67f5b02 [Marcelo Vanzin] Review feedback.
f01517c [Marcelo Vanzin] Review feedback.
68fbbbf [Marcelo Vanzin] Use older constructor available in older Hadoop releases.
d07ef9a [Marcelo Vanzin] Merge branch 'master' into yarn-tests
add8416 [Marcelo Vanzin] [SPARK-2778] [yarn] Add yarn integration tests.
SPARK-3039: Adds the maven property "avro.mapred.classifier" to build spark-assembly with avro-mapred with support for the new Hadoop API. Sets this property to hadoop2 for Hadoop 2 profiles.
I am not very familiar with maven, nor do I know whether this potentially breaks something in the hive part of spark. There might be a more elegant way of doing this.
Author: Bertrand Bossy <bertrandbossy@gmail.com>
Closes#1945 from bbossy/SPARK-3039 and squashes the following commits:
c32ce59 [Bertrand Bossy] SPARK-3039: Allow spark to be built using avro-mapred for hadoop2
At the same time, import the `scala.language.postfixOps` and ` org.scalatest.time.SpanSugar._` cause `scala.language.postfixOps` doesn't work
Author: witgo <witgo@qq.com>
Closes#1330 from witgo/sbt_warnings3 and squashes the following commits:
179ba61 [witgo] Resolve sbt warnings during build
We currently open many ephemeral ports during the tests, and as a result we occasionally can't bind to new ones. This has caused the `DriverSuite` and the `SparkSubmitSuite` to fail intermittently.
By disabling the `SparkUI` when it's not needed, we already cut down on the number of ports opened significantly, on the order of the number of `SparkContexts` ever created. We must keep it enabled for a few tests for the UI itself, however.
Author: Andrew Or <andrewor14@gmail.com>
Closes#2363 from andrewor14/disable-ui-for-tests and squashes the following commits:
332a7d5 [Andrew Or] No need to set spark.ui.port to 0 anymore
30c93a2 [Andrew Or] Simplify streaming UISuite
a431b84 [Andrew Or] Fix streaming test failures
8f5ae53 [Andrew Or] Fix no new line at the end
29c9b5b [Andrew Or] Disable SparkUI for tests
This fixes the `SparkSubmitSuite` failure by setting `<spark.ui.port>0</spark.ui.port>` in the Maven build, to match the SBT build. This avoids a port conflict which causes failures.
(This also updates the `scalatest` plugin off of a release candidate, to the identical final release.)
Author: Sean Owen <sowen@cloudera.com>
Closes#2328 from srowen/SPARK-3404 and squashes the following commits:
512d782 [Sean Owen] Set spark.ui.port=0 in Maven scalatest config to match SBT build and avoid SparkSubmitSuite failure due to port conflict
By merging #2268, which bumped the Spark version to 1.2.0-SNAPSHOT, I inadvertently broke the Mima binary compatibility tests. The issue is that we were comparing 1.2.0-SNAPSHOT against Spark 1.0.0 without using any Mima excludes. The right long-term fix for this is probably to publish nightly snapshots on Maven central and change the master branch to test binary compatibility against the current release candidate branch's snapshots until that release is finalized.
As a short-term fix until 1.1.0 is published on Maven central, I've configured the build to test the master branch for binary compatibility against the 1.1.0-RC4 jars. I'll loop back and remove the Apache staging repo as soon as 1.1.0 final is available.
Author: Josh Rosen <joshrosen@apache.org>
Closes#2315 from JoshRosen/mima-fix and squashes the following commits:
776bc2c [Josh Rosen] Add two excludes to workaround Mima annotation issues.
ec90e21 [Josh Rosen] Add deploy and graphx to 1.2 MiMa excludes.
57569be [Josh Rosen] Fix MiMa tests in master branch; test against 1.1.0 RC.
Author: GuoQiang Li <witgo@qq.com>
Closes#2268 from witgo/SPARK-3397 and squashes the following commits:
eaf913f [GuoQiang Li] Bump pom.xml version number of master branch to 1.2.0-SNAPSHOT
The Maven build was failing on Windows because it tried to call the unix `unzip` utility to extract the Py4J files into core's build directory. I've fixed this issue by using the `maven-antrun-plugin` to perform the unzipping.
I also fixed an issue that prevented tests from running under Windows:
In the Maven ScalaTest plugin, the filename listed in <filereports> is placed under the <reportsDirectory>; the current code places it in a subdirectory of reportsDirectory, e.g.
```
${project.build.directory}/surefire-reports/${project.build.directory}/SparkTestSuite.txt
```
This caused problems under Windows because it would try to create a subdirectory named "c:\\".
Note that the tests still fail under Windows (for other reasons); this PR just allows them to run and fail rather than crash when trying to create the test reports directory.
Author: Josh Rosen <joshrosen@apache.org>
Author: Josh Rosen <rosenville@gmail.com>
Author: Josh Rosen <joshrosen@databricks.com>
Closes#2165 from JoshRosen/windows-support and squashes the following commits:
651d210 [Josh Rosen] Unzip to python/build instead of core/build
fbf3e61 [Josh Rosen] 4 spaces -> 2 spaces
e347668 [Josh Rosen] Fix Maven scalatest filereports path:
4994af1 [Josh Rosen] [SPARK-3061] Use maven-antrun-plugin to unzip Py4J.
(EDIT) Since the scalatest issue was since resolved, this is now about a few small problems in the Flume Sink `pom.xml`
- `scalatest` is not declared as a test-scope dependency
- Its Avro version doesn't match the rest of the build
- Its Flume version is not synced with the other Flume module
- The other Flume module declares its dependency on Flume Sink slightly incorrectly, hard-coding the Scala 2.10 version
- It depends on Scala Lang directly, which it shouldn't
Author: Sean Owen <sowen@cloudera.com>
Closes#1726 from srowen/SPARK-2798 and squashes the following commits:
a46e2c6 [Sean Owen] scalatest to test scope, harmonize Avro and Flume versions, remove direct Scala dependency, fix '2.10' in Flume dependency
For further discussion, please check the JIRA entry.
This change moves Guava classes to a different package so that they don't conflict with the user-provided Guava (or the Hadoop-provided one). Since one class (Optional) was exposed through Spark's public API, that class was forked from Guava at the current dependency version (14.0.1) so that it can be kept going forward (until the API is cleaned).
Note this change has a few implications:
- *all* classes in the final jars will reference the relocated classes. If Hadoop classes are included (i.e. "-Phadoop-provided" is not activated), those will also reference the Guava 14 classes (instead of the Guava 11 classes from the Hadoop classpath).
- if the Guava version in Spark is ever changed, the new Guava will still reference the forked Optional class; this may or may not be a problem, but in the long term it's better to think about removing Optional from the public API.
For the end user, there are two visible implications:
- Guava is not provided as a transitive dependency anymore (since it's "provided" in Spark)
- At runtime, unless they provide their own, they'll either have no Guava or Hadoop's version of Guava (11), depending on how they set up their classpath.
Note that this patch does not change the sbt deliverables; those will still contain guava in its original package, and provide guava as a compile-time dependency. This assumes that maven is the canonical build, and sbt-built artifacts are not (officially) published.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#1813 from vanzin/SPARK-2848 and squashes the following commits:
9bdffb0 [Marcelo Vanzin] Undo sbt build changes.
819b445 [Marcelo Vanzin] Review feedback.
05e0a3d [Marcelo Vanzin] Merge branch 'master' into SPARK-2848
fef4370 [Marcelo Vanzin] Unfork Optional.java.
d3ea8e1 [Marcelo Vanzin] Exclude asm classes from final jar.
637189b [Marcelo Vanzin] Add hacky filter to prefer Spark's copy of Optional.
2fec990 [Marcelo Vanzin] Shade Guava in the sbt build.
616998e [Marcelo Vanzin] Shade Guava in the maven build, fork Guava's Optional.java.
Currently we have a separate profile called hive-thriftserver. I originally suggested this in case users did not want to bundle the thriftserver, but it's ultimately lead to a lot of confusion. Since the thriftserver is only a few classes, I don't see a really good reason to isolate it from the rest of Hive. So let's go ahead and just include it in the same profile to simplify things.
This has been suggested in the past by liancheng.
Author: Patrick Wendell <pwendell@gmail.com>
Closes#2006 from pwendell/hiveserver and squashes the following commits:
742ea40 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into hiveserver
034ad47 [Patrick Wendell] SPARK-3092: Always include the thriftserver when -Phive is enabled.
Previous pull request (#1907) was reverted. This brings it back. Still looking into the hang.
Author: Reynold Xin <rxin@apache.org>
Closes#1971 from rxin/netty1 and squashes the following commits:
b0be96f [Reynold Xin] Added test to make sure outstandingRequests are cleaned after firing the events.
4c6d0ee [Reynold Xin] Pass callbacks cleanly.
603dce7 [Reynold Xin] Upgrade Netty to 4.0.23 to fix the DefaultFileRegion bug.
88be1d4 [Reynold Xin] Downgrade to 4.0.21 to work around a bug in writing DefaultFileRegion.
002626a [Reynold Xin] Remove netty-test-file.txt.
db6e6e0 [Reynold Xin] Revert "Revert "[SPARK-2468] Netty based block server / client module""
This upgrades snappy-java which fixes the issue reported in SPARK-2881.
This is the master branch equivalent to #1994 which provides a different
work-around for the 1.1 branch.
Author: Patrick Wendell <pwendell@gmail.com>
Closes#1995 from pwendell/snappy-1.1 and squashes the following commits:
0c7c4c2 [Patrick Wendell] SPARK-2881. Upgrade snappy-java to 1.1.1.3.
Calvin Jia
Sean Owen
Josh Rosen
Punyashloka Biswal
Marcelo Vanzin
Shivaram Venkataraman
Steve Loughran
Dean Chen
Xiangrui Meng
Cheng Lian
Patrick Wendell
Matt Whelan
gli
medale
Zhan Zhang
Andrew Or
Burak Yavuz
Daoyuan Wang
Davies Liu
Ryan Williams
Kannan Rajah
Jongyoul Lee
scwf
Sandy Ryza
Takuya UESHIN
Prashant Sharma
fi
Aaron Davidson
Daniel Lemire
Yash Datta
Reynold Xin
Josh Rosen
Josh Rosen
Patrick Wendell
Anand Avati
aniketbhatnagar
Bertrand Bossy
witgo
Andrew Or
