(Updated version of [PR-9457](https://github.com/apache/spark/pull/9457), rebased on latest Spark master, and using mllib-local).
This implements a parallel version of personalized pagerank, which runs all propagations for a list of source vertices in parallel.
I ran a few benchmarks on the full [DBpedia](http://dbpedia.org/) graph. When running personalized pagerank for only one source node, the existing implementation is twice as fast as the parallel one (because of the SparseVector overhead). However for 10 source nodes, the parallel implementation is four times as fast. When increasing the number of source nodes, this difference becomes even greater.
Author: Yves Raimond <yraimond@netflix.com>
Closes#14998 from moustaki/parallel-ppr.
## What changes were proposed in this pull request?
Avoid using postfix operation for command execution in SQLQuerySuite where it wasn't whitelisted and audit existing whitelistings removing postfix operators from most places. Some notable places where postfix operation remains is in the XML parsing & time units (seconds, millis, etc.) where it arguably can improve readability.
## How was this patch tested?
Existing tests.
Author: Holden Karau <holden@us.ibm.com>
Closes#14407 from holdenk/SPARK-16779.
## What changes were proposed in this pull request?
Use foreach/for instead of map where operation requires execution of body, not actually defining a transformation
## How was this patch tested?
Jenkins
Author: Sean Owen <sowen@cloudera.com>
Closes#14332 from srowen/SPARK-16694.
## What changes were proposed in this pull request?
I added caching in every iteration for sccGraph that is returned in strongly connected components. Without this cache strongly connected components returned graph that needed to be computed from scratch when some intermediary caches didn't existed anymore.
## How was this patch tested?
I tested it by running code similar to the one [on databrics](https://databricks-prod-cloudfront.cloud.databricks.com/public/4027ec902e239c93eaaa8714f173bcfc/4889410027417133/3634650767364730/3117184429335832/latest.html). Basically I generated large graph and computed strongly connected components with changed code, than simply run count on vertices and edges. Count after this update takes few seconds instead 20 minutes.
# statement
contribution is my original work and I license the work to the project under the project's open source license.
Author: Michał Wesołowski <michal.wesolowski@bzwbk.pl>
Closes#14137 from wesolowskim/SPARK-16478.
https://issues.apache.org/jira/browse/SPARK-16535
## What changes were proposed in this pull request?
When I scan through the pom.xml of sub projects, I found this warning as below and attached screenshot
```
Definition of groupId is redundant, because it's inherited from the parent
```
I've tried to remove some of the lines with groupId definition, and the build on my local machine is still ok.
```
<groupId>org.apache.spark</groupId>
```
As I just find now `<maven.version>3.3.9</maven.version>` is being used in Spark 2.x, and Maven-3 supports versionless parent elements: Maven 3 will remove the need to specify the parent version in sub modules. THIS is great (in Maven 3.1).
ref: http://stackoverflow.com/questions/3157240/maven-3-worth-it/3166762#3166762
## How was this patch tested?
I've tested by re-building the project, and build succeeded.
Author: Xin Ren <iamshrek@126.com>
Closes#14189 from keypointt/SPARK-16535.
## What changes were proposed in this pull request?
These are yet more changes that resolve problems with unidoc/genjavadoc and Java 8. It does not fully resolve the problem, but gets rid of as many errors as we can from this end.
## How was this patch tested?
Jenkins build of docs
Author: Sean Owen <sowen@cloudera.com>
Closes#14221 from srowen/SPARK-3359.3.
## What changes were proposed in this pull request?
After SPARK-16476 (committed earlier today as #14128), we can finally bump the version number.
## How was this patch tested?
N/A
Author: Reynold Xin <rxin@databricks.com>
Closes#14130 from rxin/SPARK-16477.
## What changes were proposed in this pull request?
There are two test data files used for graphx examples existing in directory "graphx/data"
I move it into "data/" directory because the "graphx" directory is used for code files and other test data files (such as mllib, streaming test data) are all in there.
I also update the graphx document where reference the data files which I move place.
## How was this patch tested?
N/A
Author: WeichenXu <WeichenXu123@outlook.com>
Closes#14010 from WeichenXu123/move_graphx_data_dir.
## What changes were proposed in this pull request?
`an -> a`
Use cmds like `find . -name '*.R' | xargs -i sh -c "grep -in ' an [^aeiou]' {} && echo {}"` to generate candidates, and review them one by one.
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#13515 from zhengruifeng/an_a.
## What changes were proposed in this pull request?
(See https://github.com/apache/spark/pull/12416 where most of this was already reviewed and committed; this is just the module structure and move part. This change does not move the annotations into test scope, which was the apparently problem last time.)
Rename `spark-test-tags` -> `spark-tags`; move common annotations like `Since` to `spark-tags`
## How was this patch tested?
Jenkins tests.
Author: Sean Owen <sowen@cloudera.com>
Closes#13074 from srowen/SPARK-15290.
## What changes were proposed in this pull request?
This PR removes a stale TODO comment in `GraphGenerators.scala`
## How was this patch tested?
Just comment removed.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12839 from dongjoon-hyun/SPARK-15057.
## What changes were proposed in this pull request?
This PR adds `since` tag into the matrix and vector classes in spark-mllib-local.
## How was this patch tested?
Scala-style checks passed.
Author: Pravin Gadakh <prgadakh@in.ibm.com>
Closes#12416 from pravingadakh/SPARK-14613.
## What changes were proposed in this pull request?
Minor typo fixes (too minor to deserve separate a JIRA)
## How was this patch tested?
local build
Author: Jacek Laskowski <jacek@japila.pl>
Closes#12469 from jaceklaskowski/minor-typo-fixes.
## What changes were proposed in this pull request?
Spark uses `NewLineAtEofChecker` rule in Scala by ScalaStyle. And, most Java code also comply with the rule. This PR aims to enforce the same rule `NewlineAtEndOfFile` by CheckStyle explicitly. Also, this fixes lint-java errors since SPARK-14465. The followings are the items.
- Adds a new line at the end of the files (19 files)
- Fixes 25 lint-java errors (12 RedundantModifier, 6 **ArrayTypeStyle**, 2 LineLength, 2 UnusedImports, 2 RegexpSingleline, 1 ModifierOrder)
## How was this patch tested?
After the Jenkins test succeeds, `dev/lint-java` should pass. (Currently, Jenkins dose not run lint-java.)
```bash
$ dev/lint-java
Using `mvn` from path: /usr/local/bin/mvn
Checkstyle checks passed.
```
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12632 from dongjoon-hyun/SPARK-14868.
The current package name uses a dash, which is a little weird but seemed
to work. That is, until a new test tried to mock a class that references
one of those shaded types, and then things started failing.
Most changes are just noise to fix the logging configs.
For reference, SPARK-8815 also raised this issue, although at the time it
did not cause any issues in Spark, so it was not addressed.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#11941 from vanzin/SPARK-14134.
## What changes were proposed in this pull request?
Added an omitted word in the error message displayed by the Graphx Pregel API when `maxIterations <= 0`
## How was this patch tested?
Manual test
Author: Victor Chima <blazy2k9@gmail.com>
Closes#12205 from blazy2k9/hotfix/pregel-error-message.
## What changes were proposed in this pull request?
This PR aims to fix all Scala-Style multiline comments into Java-Style multiline comments in Scala codes.
(All comment-only changes over 77 files: +786 lines, −747 lines)
## How was this patch tested?
Manual.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12130 from dongjoon-hyun/use_multiine_javadoc_comments.
## What changes were proposed in this pull request?
Currently, `GraphOps.pickRandomVertex()` falls into infinite loops for graphs having only one vertex. This PR fixes it by modifying the following termination-checking condition.
```scala
- if (selectedVertices.count > 1) {
+ if (selectedVertices.count > 0) {
```
## How was this patch tested?
Pass the Jenkins tests (including new test case).
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#12018 from dongjoon-hyun/SPARK-14219.
## What changes were proposed in this pull request?
This PR fixes some newly added java-lint errors(unused-imports, line-lengsth).
## How was this patch tested?
Pass the Jenkins tests.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11968 from dongjoon-hyun/SPARK-14167.
## What changes were proposed in this pull request?
Logging was made private in Spark 2.0. If we move it, then users would be able to create a Logging trait themselves to avoid changing their own code.
## How was this patch tested?
existing tests.
Author: Wenchen Fan <wenchen@databricks.com>
Closes#11764 from cloud-fan/logger.
JIRA: https://issues.apache.org/jira/browse/SPARK-13816
## What changes were proposed in this pull request?
Add parameter checks for algorithms in Graphx: Pregel,LabelPropagation,PageRank,SVDPlusPlus
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11655 from zhengruifeng/graphx_param_check.
## What changes were proposed in this pull request?
This PR fixes 135 typos over 107 files:
* 121 typos in comments
* 11 typos in testcase name
* 3 typos in log messages
## How was this patch tested?
Manual.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11689 from dongjoon-hyun/fix_more_typos.
## What changes were proposed in this pull request?
- Fixes calls to `new String(byte[])` or `String.getBytes()` that rely on platform default encoding, to use UTF-8
- Same for `InputStreamReader` and `OutputStreamWriter` constructors
- Standardizes on UTF-8 everywhere
- Standardizes specifying the encoding with `StandardCharsets.UTF-8`, not the Guava constant or "UTF-8" (which means handling `UnuspportedEncodingException`)
- (also addresses the other remaining Coverity scan issues, which are pretty trivial; these are separated into commit 1deecd8d9c )
## How was this patch tested?
Jenkins tests
Author: Sean Owen <sowen@cloudera.com>
Closes#11657 from srowen/SPARK-13823.
## What changes were proposed in this pull request?
This PR fixes typos in comments and testcase name of code.
## How was this patch tested?
manual.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11481 from dongjoon-hyun/minor_fix_typos_in_code.
## What changes were proposed in this pull request?
After SPARK-6990, `dev/lint-java` keeps Java code healthy and helps PR review by saving much time.
This issue aims remove unused imports from Java/Scala code and add `UnusedImports` checkstyle rule to help developers.
## How was this patch tested?
```
./dev/lint-java
./build/sbt compile
```
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11438 from dongjoon-hyun/SPARK-13583.
## What changes were proposed in this pull request?
Make some cross-cutting code improvements according to static analysis. These are individually up for discussion since they exist in separate commits that can be reverted. The changes are broadly:
- Inner class should be static
- Mismatched hashCode/equals
- Overflow in compareTo
- Unchecked warnings
- Misuse of assert, vs junit.assert
- get(a) + getOrElse(b) -> getOrElse(a,b)
- Array/String .size -> .length (occasionally, -> .isEmpty / .nonEmpty) to avoid implicit conversions
- Dead code
- tailrec
- exists(_ == ) -> contains find + nonEmpty -> exists filter + size -> count
- reduce(_+_) -> sum map + flatten -> map
The most controversial may be .size -> .length simply because of its size. It is intended to avoid implicits that might be expensive in some places.
## How was the this patch tested?
Existing Jenkins unit tests.
Author: Sean Owen <sowen@cloudera.com>
Closes#11292 from srowen/SPARK-13423.
## What changes were proposed in this pull request?
This PR tries to fix all typos in all markdown files under `docs` module,
and fixes similar typos in other comments, too.
## How was the this patch tested?
manual tests.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#11300 from dongjoon-hyun/minor_fix_typos.
jegonzal ankurdave please could you review
## What changes were proposed in this pull request?
Reworking of jegonzal PR #2495 to address the issue identified in SPARK-3650. Code amended to use the convertToCanonicalEdges method.
## How was the this patch tested?
Patch was tested using the unit tests created in PR #2495
Author: Robin East <robin.east@xense.co.uk>
Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>
Closes#11290 from insidedctm/spark-3650.
JIRA: https://issues.apache.org/jira/browse/SPARK-13416
## What changes were proposed in this pull request?
The output of StronglyConnectedComponents with numIter no greater than 1 may make no sense. So I just add require check in it.
## How was the this patch tested?
unit tests passed
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11284 from zhengruifeng/scccheck.
JIRA: https://issues.apache.org/jira/browse/SPARK-13386
## What changes were proposed in this pull request?
add maxIteration option for ConnectedComponents algorithm
## How was the this patch tested?
unit tests passed
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11268 from zhengruifeng/ccwithmax.
This patch changes Spark's build to make Scala 2.11 the default Scala version. To be clear, this does not mean that Spark will stop supporting Scala 2.10: users will still be able to compile Spark for Scala 2.10 by following the instructions on the "Building Spark" page; however, it does mean that Scala 2.11 will be the default Scala version used by our CI builds (including pull request builds).
The Scala 2.11 compiler is faster than 2.10, so I think we'll be able to look forward to a slight speedup in our CI builds (it looks like it's about 2X faster for the Maven compile-only builds, for instance).
After this patch is merged, I'll update Jenkins to add new compile-only jobs to ensure that Scala 2.10 compilation doesn't break.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#10608 from JoshRosen/SPARK-6363.
Some VertexRDD and EdgeRDD are created during the intermediate step of g.connectedComponents() but unnecessarily left cached after the method is done. The fix is to unpersist these RDDs once they are no longer in use.
A test case is added to confirm the fix for the reported bug.
Author: Jason Lee <cjlee@us.ibm.com>
Closes#10713 from jasoncl/SPARK-12655.
Fix the style violation (space before `,` and `:`).
This PR is a followup for #10643.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#10683 from sarutak/SPARK-12692-followup-graphx.
Whole code of Vector.scala, VectorSuite.scala and GraphKryoRegistrator.scala are no longer used so it's time to remove them in Spark 2.0.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#10613 from sarutak/SPARK-12665.
We should upgrade to SBT 0.13.9, since this is a requirement in order to use SBT's new Maven-style resolution features (which will be done in a separate patch, because it's blocked by some binary compatibility issues in the POM reader plugin).
I also upgraded Scalastyle to version 0.8.0, which was necessary in order to fix a Scala 2.10.5 compatibility issue (see https://github.com/scalastyle/scalastyle/issues/156). The newer Scalastyle is slightly stricter about whitespace surrounding tokens, so I fixed the new style violations.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#10112 from JoshRosen/upgrade-to-sbt-0.13.9.
The code convertToCanonicalEdges is such that srcIds are smaller than dstIds but the scaladoc suggested otherwise. Have fixed the same.
Author: Gaurav Kumar <gauravkumar37@gmail.com>
Closes#9666 from gauravkumar37/patch-1.
This patch modifies Spark's closure cleaner (and a few other places) to use ASM 5, which is necessary in order to support cleaning of closures that were compiled by Java 8.
In order to avoid ASM dependency conflicts, Spark excludes ASM from all of its dependencies and uses a shaded version of ASM 4 that comes from `reflectasm` (see [SPARK-782](https://issues.apache.org/jira/browse/SPARK-782) and #232). This patch updates Spark to use a shaded version of ASM 5.0.4 that was published by the Apache XBean project; the POM used to create the shaded artifact can be found at https://github.com/apache/geronimo-xbean/blob/xbean-4.4/xbean-asm5-shaded/pom.xml.
http://movingfulcrum.tumblr.com/post/80826553604/asm-framework-50-the-missing-migration-guide was a useful resource while upgrading the code to use the new ASM5 opcodes.
I also added a new regression tests in the `java8-tests` subproject; the existing tests were insufficient to catch this bug, which only affected Scala 2.11 user code which was compiled targeting Java 8.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#9512 from JoshRosen/SPARK-6152.
Changes the personalized pagerank initialization to be non-uniform.
Author: Yves Raimond <yraimond@netflix.com>
Closes#9386 from moustaki/personalized-pagerank-init.
Comments preceding toMessage method state: "The edge partition is encoded in the lower
* 30 bytes of the Int, and the position is encoded in the upper 2 bytes of the Int.". References to bytes should be changed to bits.
This contribution is my original work and I license the work to the Spark project under it's open source license.
Author: Robin East <robin.east@xense.co.uk>
Closes#8756 from insidedctm/master.
Move .java files in `src/main/scala` to `src/main/java` root, except for `package-info.java` (to stay next to package.scala)
Author: Sean Owen <sowen@cloudera.com>
Closes#8736 from srowen/SPARK-10576.
The bulk of the changes are on `transient` annotation on class parameter. Often the compiler doesn't generate a field for this parameters, so the the transient annotation would be unnecessary.
But if the class parameter are used in methods, then fields are created. So it is safer to keep the annotations.
The remainder are some potential bugs, and deprecated syntax.
Author: Luc Bourlier <luc.bourlier@typesafe.com>
Closes#8433 from skyluc/issue/sbt-2.11.
