## What changes were proposed in this pull request?
1, There are two `[Graph.partitionBy]` in `graphx-programming-guide.md`, the first one had no effert.
2, `DataFrame`, `Transformer`, `Pipeline` and `Parameter` in `ml-pipeline.md` were linked to `ml-guide.html` by mistake.
3, `PythonMLLibAPI` in `mllib-linear-methods.md` was not accessable, because class `PythonMLLibAPI` is private.
4, Other link updates.
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#15912 from zhengruifeng/md_fix.
## What changes were proposed in this pull request?
Remove `spark.driver.memory`, `spark.executor.memory`, `spark.driver.cores`, and `spark.executor.cores` from `running-on-yarn.md` as they are not Yarn-specific, and they are also defined in`configuration.md`.
## How was this patch tested?
Build passed & Manually check.
Author: Weiqing Yang <yangweiqing001@gmail.com>
Closes#15869 from weiqingy/yarnDoc.
## What changes were proposed in this pull request?
Suggest users to increase `NodeManager's` heap size if `External Shuffle Service` is enabled as
`NM` can spend a lot of time doing GC resulting in shuffle operations being a bottleneck due to `Shuffle Read blocked time` bumped up.
Also because of GC `NodeManager` can use an enormous amount of CPU and cluster performance will suffer.
I have seen NodeManager using 5-13G RAM and up to 2700% CPU with `spark_shuffle` service on.
## How was this patch tested?
#### Added step 5:
Author: Artur Sukhenko <artur.sukhenko@gmail.com>
Closes#15906 from Devian-ua/nmHeapSize.
## What changes were proposed in this pull request?
This PR aims to provide a pip installable PySpark package. This does a bunch of work to copy the jars over and package them with the Python code (to prevent challenges from trying to use different versions of the Python code with different versions of the JAR). It does not currently publish to PyPI but that is the natural follow up (SPARK-18129).
Done:
- pip installable on conda [manual tested]
- setup.py installed on a non-pip managed system (RHEL) with YARN [manual tested]
- Automated testing of this (virtualenv)
- packaging and signing with release-build*
Possible follow up work:
- release-build update to publish to PyPI (SPARK-18128)
- figure out who owns the pyspark package name on prod PyPI (is it someone with in the project or should we ask PyPI or should we choose a different name to publish with like ApachePySpark?)
- Windows support and or testing ( SPARK-18136 )
- investigate details of wheel caching and see if we can avoid cleaning the wheel cache during our test
- consider how we want to number our dev/snapshot versions
Explicitly out of scope:
- Using pip installed PySpark to start a standalone cluster
- Using pip installed PySpark for non-Python Spark programs
*I've done some work to test release-build locally but as a non-committer I've just done local testing.
## How was this patch tested?
Automated testing with virtualenv, manual testing with conda, a system wide install, and YARN integration.
release-build changes tested locally as a non-committer (no testing of upload artifacts to Apache staging websites)
Author: Holden Karau <holden@us.ibm.com>
Author: Juliet Hougland <juliet@cloudera.com>
Author: Juliet Hougland <not@myemail.com>
Closes#15659 from holdenk/SPARK-1267-pip-install-pyspark.
## What changes were proposed in this pull request?
Add links to API docs for ML algos
## How was this patch tested?
Manual checking for the API links
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#15890 from zhengruifeng/algo_link.
## What changes were proposed in this pull request?
Fix typos in the 'configuration', 'monitoring' and 'sql-programming-guide' documentation.
## How was this patch tested?
Manually.
Author: Weiqing Yang <yangweiqing001@gmail.com>
Closes#15886 from weiqingy/fixTypo.
## What changes were proposed in this pull request?
1,Remove `runs` from docs of mllib.KMeans
2,Add notes for `k` according to comments in sources
## How was this patch tested?
existing tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#15873 from zhengruifeng/update_doc_mllib_kmeans.
## What changes were proposed in this pull request?
Adds support for CNI-isolated containers
## How was this patch tested?
I launched SparkPi both with and without `spark.mesos.network.name`, and verified the job completed successfully.
Author: Michael Gummelt <mgummelt@mesosphere.io>
Closes#15740 from mgummelt/spark-342-cni.
## What changes were proposed in this pull request?
1, Add link of `VertexRDD` and `EdgeRDD`
2, Notify in `Vertex and Edge RDDs` that not all methods are listed
3, `VertexID` -> `VertexId`
## How was this patch tested?
No tests, only docs is modified
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#15875 from zhengruifeng/update_graphop_doc.
## What changes were proposed in this pull request?
Update the python section of the Structured Streaming Guide from .builder() to .builder
## How was this patch tested?
Validated documentation and successfully running the test example.
Please review https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark before opening a pull request.
'Builder' object is not callable object hence changed .builder() to
.builder
Author: Denny Lee <dennylee@gallifrey.local>
Closes#15872 from dennyglee/master.
## What changes were proposed in this pull request?
Many applications take Spark as a computing engine and run on it. This PR adds a configuration property `spark.log.callerContext` that can be used by Spark's upstream applications (e.g. Oozie) to set up their caller contexts into Spark. In the end, Spark will combine its own caller context with the caller contexts of its upstream applications, and write them into Yarn RM log and HDFS audit log.
The audit log has a config to truncate the caller contexts passed in (default 128). The caller contexts will be sent over rpc, so it should be concise. The call context written into HDFS log and Yarn log consists of two parts: the information `A` specified by Spark itself and the value `B` of `spark.log.callerContext` property. Currently `A` typically takes 64 to 74 characters, so `B` can have up to 50 characters (mentioned in the doc `running-on-yarn.md`)
## How was this patch tested?
Manual tests. I have run some Spark applications with `spark.log.callerContext` configuration in Yarn client/cluster mode, and verified that the caller contexts were written into Yarn RM log and HDFS audit log correctly.
The ways to configure `spark.log.callerContext` property:
- In spark-defaults.conf:
```
spark.log.callerContext infoSpecifiedByUpstreamApp
```
- In app's source code:
```
val spark = SparkSession
.builder
.appName("SparkKMeans")
.config("spark.log.callerContext", "infoSpecifiedByUpstreamApp")
.getOrCreate()
```
When running on Spark Yarn cluster mode, the driver is unable to pass 'spark.log.callerContext' to Yarn client and AM since Yarn client and AM have already started before the driver performs `.config("spark.log.callerContext", "infoSpecifiedByUpstreamApp")`.
The following example shows the command line used to submit a SparkKMeans application and the corresponding records in Yarn RM log and HDFS audit log.
Command:
```
./bin/spark-submit --verbose --executor-cores 3 --num-executors 1 --master yarn --deploy-mode client --class org.apache.spark.examples.SparkKMeans examples/target/original-spark-examples_2.11-2.1.0-SNAPSHOT.jar hdfs://localhost:9000/lr_big.txt 2 5
```
Yarn RM log:
<img width="1440" alt="screen shot 2016-10-19 at 9 12 03 pm" src="https://cloud.githubusercontent.com/assets/8546874/19547050/7d2f278c-9649-11e6-9df8-8d5ff12609f0.png">
HDFS audit log:
<img width="1400" alt="screen shot 2016-10-19 at 10 18 14 pm" src="https://cloud.githubusercontent.com/assets/8546874/19547102/096060ae-964a-11e6-981a-cb28efd5a058.png">
Author: Weiqing Yang <yangweiqing001@gmail.com>
Closes#15563 from weiqingy/SPARK-16759.
## What changes were proposed in this pull request?
DIGEST-MD5 mechanism is used for SASL authentication and secure communication. DIGEST-MD5 mechanism supports 3DES, DES, and RC4 ciphers. However, 3DES, DES and RC4 are slow relatively.
AES provide better performance and security by design and is a replacement for 3DES according to NIST. Apache Common Crypto is a cryptographic library optimized with AES-NI, this patch employ Apache Common Crypto as enc/dec backend for SASL authentication and secure channel to improve spark RPC.
## How was this patch tested?
Unit tests and Integration test.
Author: Junjie Chen <junjie.j.chen@intel.com>
Closes#15172 from cjjnjust/shuffle_rpc_encrypt.
## What changes were proposed in this pull request?
1, `**Example**` => `**Examples**`, because more algos use `**Examples**`.
2, delete `### Examples` in `Isotonic regression`, because it's not that special in http://spark.apache.org/docs/latest/ml-classification-regression.html
3, add missing marks for `LDA` and other algos.
## How was this patch tested?
No tests for it only modify doc
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#15783 from zhengruifeng/doc_fix.
## What changes were proposed in this pull request?
This Pull request comprises of the critical bug SPARK-16575 changes. This change rectifies the issue with BinaryFileRDD partition calculations as upon creating an RDD with sc.binaryFiles, the resulting RDD always just consisted of two partitions only.
## How was this patch tested?
The original issue ie. getNumPartitions on binary Files RDD (always having two partitions) was first replicated and then tested upon the changes. Also the unit tests have been checked and passed.
This contribution is my original work and I licence the work to the project under the project's open source license
srowen hvanhovell rxin vanzin skyluc kmader zsxwing datafarmer Please have a look .
Author: fidato <fidato.july13@gmail.com>
Closes#15327 from fidato13/SPARK-16575.
## What changes were proposed in this pull request?
Document that Java 7, Python 2.6, Scala 2.10, Hadoop < 2.6 are deprecated in Spark 2.1.0. This does not actually implement any of the change in SPARK-18138, just peppers the documentation with notices about it.
## How was this patch tested?
Doc build
Author: Sean Owen <sowen@cloudera.com>
Closes#15733 from srowen/SPARK-18138.
## What changes were proposed in this pull request?
This patch uses `{% highlight lang %}...{% endhighlight %}` to highlight code snippets in the `Structured Streaming Kafka010 integration doc` and the `Spark Streaming Kafka010 integration doc`.
This patch consists of two commits:
- the first commit fixes only the leading spaces -- this is large
- the second commit adds the highlight instructions -- this is much simpler and easier to review
## How was this patch tested?
SKIP_API=1 jekyll build
## Screenshots
**Before**
**After**
Author: Liwei Lin <lwlin7@gmail.com>
Closes#15715 from lw-lin/doc-highlight-code-snippet.
## What changes were proposed in this pull request?
- Renamed kbest to numTopFeatures
- Renamed alpha to fpr
- Added missing Since annotations
- Doc cleanups
## How was this patch tested?
Added new standardized unit tests for spark.ml.
Improved existing unit test coverage a bit.
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#15647 from jkbradley/chisqselector-follow-ups.
In SPARK-4761 / #3621 (December 2014) we enabled Kryo serialization by default in the Spark Thrift Server. However, I don't think that the original rationale for doing this still holds now that most Spark SQL serialization is now performed via encoders and our UnsafeRow format.
In addition, the use of Kryo as the default serializer can introduce performance problems because the creation of new KryoSerializer instances is expensive and we haven't performed instance-reuse optimizations in several code paths (including DirectTaskResult deserialization).
Given all of this, I propose to revert back to using JavaSerializer as the default serializer in the Thrift Server.
/cc liancheng
Author: Josh Rosen <joshrosen@databricks.com>
Closes#14906 from JoshRosen/disable-kryo-in-thriftserver.
Mesos 0.23.0 introduces a Fetch Cache feature http://mesos.apache.org/documentation/latest/fetcher/ which allows caching of resources specified in command URIs.
This patch:
- Updates the Mesos shaded protobuf dependency to 0.23.0
- Allows setting `spark.mesos.fetcherCache.enable` to enable the fetch cache for all specified URIs. (URIs must be specified for the setting to have any affect)
- Updates documentation for Mesos configuration with the new setting.
This patch does NOT:
- Allow for per-URI caching configuration. The cache setting is global to ALL URIs for the command.
Author: Charles Allen <charles@allen-net.com>
Closes#13713 from drcrallen/SPARK15994.
## What changes were proposed in this pull request?
This PR merges multiple lines enumerating items in order to remove the redundant spaces following slashes in [Structured Streaming Programming Guide in 2.0.2-rc1](http://people.apache.org/~pwendell/spark-releases/spark-2.0.2-rc1-docs/structured-streaming-programming-guide.html).
- Before: `Scala/ Java/ Python`
- After: `Scala/Java/Python`
## How was this patch tested?
Manual by the followings because this is documentation update.
```
cd docs
SKIP_API=1 jekyll build
```
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes#15686 from dongjoon-hyun/minor_doc_space.
## What changes were proposed in this pull request?
This patch makes RBackend connection timeout configurable by user.
## How was this patch tested?
N/A
Author: Hossein <hossein@databricks.com>
Closes#15471 from falaki/SPARK-17919.
## What changes were proposed in this pull request?
This PR is an enhancement of PR with commit ID:57dc326bd00cf0a49da971e9c573c48ae28acaa2.
NaN is a special type of value which is commonly seen as invalid. But We find that there are certain cases where NaN are also valuable, thus need special handling. We provided user when dealing NaN values with 3 options, to either reserve an extra bucket for NaN values, or remove the NaN values, or report an error, by setting handleNaN "keep", "skip", or "error"(default) respectively.
'''Before:
val bucketizer: Bucketizer = new Bucketizer()
.setInputCol("feature")
.setOutputCol("result")
.setSplits(splits)
'''After:
val bucketizer: Bucketizer = new Bucketizer()
.setInputCol("feature")
.setOutputCol("result")
.setSplits(splits)
.setHandleNaN("keep")
## How was this patch tested?
Tests added in QuantileDiscretizerSuite, BucketizerSuite and DataFrameStatSuite
Signed-off-by: VinceShieh <vincent.xieintel.com>
Author: VinceShieh <vincent.xie@intel.com>
Author: Vincent Xie <vincent.xie@intel.com>
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#15428 from VinceShieh/spark-17219_followup.
## What changes were proposed in this pull request?
maxOffsetsPerTrigger option for rate limiting, proportionally based on volume of different topicpartitions.
## How was this patch tested?
Added unit test
Author: cody koeninger <cody@koeninger.org>
Closes#15527 from koeninger/SPARK-17813.
## What changes were proposed in this pull request?
API and programming guide doc changes for Scala, Python and R.
## How was this patch tested?
manual test
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#15629 from felixcheung/jsondoc.
## What changes were proposed in this pull request?
Currently users can kill stages via the web ui but not jobs directly (jobs are killed if one of their stages is). I've added the ability to kill jobs via the web ui. This code change is based on #4823 by lianhuiwang and updated to work with the latest code matching how stages are currently killed. In general I've copied the kill stage code warning and note comments and all. I also updated applicable tests and documentation.
## How was this patch tested?
Manually tested and dev/run-tests
Author: Alex Bozarth <ajbozart@us.ibm.com>
Author: Lianhui Wang <lianhuiwang09@gmail.com>
Closes#15441 from ajbozarth/spark4411.
## What changes were proposed in this pull request?
Always resolve spark.sql.warehouse.dir as a local path, and as relative to working dir not home dir
## How was this patch tested?
Existing tests.
Author: Sean Owen <sowen@cloudera.com>
Closes#15382 from srowen/SPARK-17810.
## What changes were proposed in this pull request?
Document `user:password` syntax as possible means of specifying credentials for password-protected `--repositories`
## How was this patch tested?
Doc build
Author: Sean Owen <sowen@cloudera.com>
Closes#15584 from srowen/SPARK-17898.
## What changes were proposed in this pull request?
Minor doc change to mention kafka configuration for larger spark batches.
## How was this patch tested?
Doc change only, confirmed via jekyll.
The configuration issue was discussed / confirmed with users on the mailing list.
Author: cody koeninger <cody@koeninger.org>
Closes#15570 from koeninger/kafka-doc-heartbeat.
## What changes were proposed in this pull request?
startingOffsets takes specific per-topicpartition offsets as a json argument, usable with any consumer strategy
assign with specific topicpartitions as a consumer strategy
## How was this patch tested?
Unit tests
Author: cody koeninger <cody@koeninger.org>
Closes#15504 from koeninger/SPARK-17812.
## What changes were proposed in this pull request?
Add crossJoin and do not default to cross join if joinExpr is left out
## How was this patch tested?
unit test
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#15559 from felixcheung/rcrossjoin.
## What changes were proposed in this pull request?
Update docs to not suggest to package Spark before running tests.
## How was this patch tested?
Not creating a JIRA since this pretty small. We haven't had the need to run mvn package before mvn test since 1.6 at least, or so I am told. So, updating the docs to not be misguiding.
Author: Mark Grover <mark@apache.org>
Closes#15572 from markgrover/doc_update.
## What changes were proposed in this pull request?
`SerializationUtils.clone()` of commons-lang3 (<3.5) has a bug that breaks thread safety, which gets stack sometimes caused by race condition of initializing hash map.
See https://issues.apache.org/jira/browse/LANG-1251.
## How was this patch tested?
Existing tests.
Author: Takuya UESHIN <ueshin@happy-camper.st>
Closes#15548 from ueshin/issues/SPARK-17985.
## What changes were proposed in this pull request?
In http://spark.apache.org/docs/latest/sql-programming-guide.html, Section "Untyped Dataset Operations (aka DataFrame Operations)"
Link to R DataFrame doesn't work that return
The requested URL /docs/latest/api/R/DataFrame.html was not found on this server.
Correct link is SparkDataFrame.html for spark 2.0
## How was this patch tested?
Manual checked.
Author: Tommy YU <tummyyu@163.com>
Closes#15543 from Wenpei/spark-18001.
This reverts commit bfe7885aee.
The commit caused build failures on Hadoop 2.2 profile:
```
[error] /scratch/rxin/spark/core/src/main/scala/org/apache/spark/util/Utils.scala:1489: value read is not a member of object org.apache.commons.io.IOUtils
[error] var numBytes = IOUtils.read(gzInputStream, buf)
[error] ^
[error] /scratch/rxin/spark/core/src/main/scala/org/apache/spark/util/Utils.scala:1492: value read is not a member of object org.apache.commons.io.IOUtils
[error] numBytes = IOUtils.read(gzInputStream, buf)
[error] ^
```
## What changes were proposed in this pull request?
Add more built-in sources in sql-programming-guide.md.
## How was this patch tested?
Manually.
Author: Weiqing Yang <yangweiqing001@gmail.com>
Closes#15522 from weiqingy/dsDoc.
## What changes were proposed in this pull request?
`SerializationUtils.clone()` of commons-lang3 (<3.5) has a bug that breaks thread safety, which gets stack sometimes caused by race condition of initializing hash map.
See https://issues.apache.org/jira/browse/LANG-1251.
## How was this patch tested?
Existing tests.
Author: Takuya UESHIN <ueshin@happy-camper.st>
Closes#15525 from ueshin/issues/SPARK-17985.
## What changes were proposed in this pull request?
This PR adds support for executor log compression.
## How was this patch tested?
Unit tests
cc: yhuai tdas mengxr
Author: Yu Peng <loneknightpy@gmail.com>
Closes#15285 from loneknightpy/compress-executor-log.
This reverts commit ed14633414.
The patch merged had obvious quality and documentation issue. The idea is useful, and we should work towards improving its quality and merging it in again.
## What changes were proposed in this pull request?
Restructure the code and implement two new task assigner.
PackedAssigner: try to allocate tasks to the executors with least available cores, so that spark can release reserved executors when dynamic allocation is enabled.
BalancedAssigner: try to allocate tasks to the executors with more available cores in order to balance the workload across all executors.
By default, the original round robin assigner is used.
We test a pipeline, and new PackedAssigner save around 45% regarding the reserved cpu and memory with dynamic allocation enabled.
## How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Both unit test in TaskSchedulerImplSuite and manual tests in production pipeline.
Author: Zhan Zhang <zhanzhang@fb.com>
Closes#15218 from zhzhan/packed-scheduler.
## What changes were proposed in this pull request?
This is a step along the way to SPARK-8425.
To enable incremental review, the first step proposed here is to expand the blacklisting within tasksets. In particular, this will enable blacklisting for
* (task, executor) pairs (this already exists via an undocumented config)
* (task, node)
* (taskset, executor)
* (taskset, node)
Adding (task, node) is critical to making spark fault-tolerant of one-bad disk in a cluster, without requiring careful tuning of "spark.task.maxFailures". The other additions are also important to avoid many misleading task failures and long scheduling delays when there is one bad node on a large cluster.
Note that some of the code changes here aren't really required for just this -- they put pieces in place for SPARK-8425 even though they are not used yet (eg. the `BlacklistTracker` helper is a little out of place, `TaskSetBlacklist` holds onto a little more info than it needs to for just this change, and `ExecutorFailuresInTaskSet` is more complex than it needs to be).
## How was this patch tested?
Added unit tests, run tests via jenkins.
Author: Imran Rashid <irashid@cloudera.com>
Author: mwws <wei.mao@intel.com>
Closes#15249 from squito/taskset_blacklist_only.
## What changes were proposed in this pull request?
Documentation fix to make it clear that reusing group id for different streams is super duper bad, just like it is with the underlying Kafka consumer.
## How was this patch tested?
I built jekyll doc and made sure it looked ok.
Author: cody koeninger <cody@koeninger.org>
Closes#15442 from koeninger/SPARK-17853.
## What changes were proposed in this pull request?
In `programming-guide.md`, the url which links to `AccumulatorV2` says `api/scala/index.html#org.apache.spark.AccumulatorV2` but `api/scala/index.html#org.apache.spark.util.AccumulatorV2` is correct.
## How was this patch tested?
manual test.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#15439 from sarutak/SPARK-17880.
