Apache Spark - A unified analytics engine for large-scale data processing
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Gabor Somogyi 0bb911d979 [SPARK-33143][PYTHON] Add configurable timeout to python server and client
### What changes were proposed in this pull request?
Spark creates local server to serialize several type of data for python. The python code tries to connect to the server, immediately after it's created but there are several system calls in between (this may change in each Spark version):
* getaddrinfo
* socket
* settimeout
* connect

Under some circumstances in heavy user environments these calls can be super slow (more than 15 seconds). These issues must be analyzed one-by-one but since these are system calls the underlying OS and/or DNS servers must be debugged and fixed. This is not trivial task and at the same time data processing must work somehow. In this PR I'm only intended to add a configuration possibility to increase the mentioned timeouts in order to be able to provide temporary workaround. The rootcause analysis is ongoing but I think this can vary in each case.

Because the server part doesn't contain huge amount of log entries to with one can measure time, I've added some.

### Why are the changes needed?
Provide workaround when localhost python server connection timeout appears.

### Does this PR introduce _any_ user-facing change?
Yes, new configuration added.

### How was this patch tested?
Existing unit tests + manual test.
```
#Compile Spark

echo "spark.io.encryption.enabled true" >> conf/spark-defaults.conf
echo "spark.python.authenticate.socketTimeout 10" >> conf/spark-defaults.conf

$ ./bin/pyspark
Python 3.8.5 (default, Jul 21 2020, 10:48:26)
[Clang 11.0.3 (clang-1103.0.32.62)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
20/11/20 10:17:03 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
20/11/20 10:17:03 WARN SparkEnv: I/O encryption enabled without RPC encryption: keys will be visible on the wire.
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /__ / .__/\_,_/_/ /_/\_\   version 3.1.0-SNAPSHOT
      /_/

Using Python version 3.8.5 (default, Jul 21 2020 10:48:26)
Spark context Web UI available at http://192.168.0.189:4040
Spark context available as 'sc' (master = local[*], app id = local-1605863824276).
SparkSession available as 'spark'.
>>> sc.setLogLevel("TRACE")
>>> sc.parallelize([0, 2, 3, 4, 6], 5).glom().collect()
20/11/20 10:17:09 TRACE PythonParallelizeServer: Creating listening socket
20/11/20 10:17:09 TRACE PythonParallelizeServer: Setting timeout to 10 sec
20/11/20 10:17:09 TRACE PythonParallelizeServer: Waiting for connection on port 59726
20/11/20 10:17:09 TRACE PythonParallelizeServer: Connection accepted from address /127.0.0.1:59727
20/11/20 10:17:09 TRACE PythonParallelizeServer: Client authenticated
20/11/20 10:17:09 TRACE PythonParallelizeServer: Closing server
...
20/11/20 10:17:10 TRACE SocketFuncServer: Creating listening socket
20/11/20 10:17:10 TRACE SocketFuncServer: Setting timeout to 10 sec
20/11/20 10:17:10 TRACE SocketFuncServer: Waiting for connection on port 59735
20/11/20 10:17:10 TRACE SocketFuncServer: Connection accepted from address /127.0.0.1:59736
20/11/20 10:17:10 TRACE SocketFuncServer: Client authenticated
20/11/20 10:17:10 TRACE SocketFuncServer: Closing server
[[0], [2], [3], [4], [6]]
>>>
```

Closes #30389 from gaborgsomogyi/SPARK-33143.

Lead-authored-by: Gabor Somogyi <gabor.g.somogyi@gmail.com>
Co-authored-by: Hyukjin Kwon <gurwls223@gmail.com>
Co-authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
2020-11-23 15:19:34 +09:00
.github [SPARK-33464][INFRA] Add/remove (un)necessary cache and restructure GitHub Actions yaml 2020-11-18 15:13:43 -08:00
assembly [SPARK-30950][BUILD] Setting version to 3.1.0-SNAPSHOT 2020-02-25 19:44:31 -08:00
bin [SPARK-32839][WINDOWS] Make Spark scripts working with the spaces in paths on Windows 2020-09-14 13:15:14 +09:00
binder [SPARK-32204][SPARK-32182][DOCS] Add a quickstart page with Binder integration in PySpark documentation 2020-08-26 12:23:24 +09:00
build [SPARK-32998][BUILD] Add ability to override default remote repos with internal one 2020-10-22 16:35:55 -07:00
common [SPARK-31069][CORE] Avoid repeat compute chunksBeingTransferred cause hight cpu cost in external shuffle service when maxChunksBeingTransferred use default value 2020-11-17 20:52:58 -06:00
conf [SPARK-32004][ALL] Drop references to slave 2020-07-13 14:05:33 -07:00
core [SPARK-33143][PYTHON] Add configurable timeout to python server and client 2020-11-23 15:19:34 +09:00
data [SPARK-22666][ML][SQL] Spark datasource for image format 2018-09-05 11:59:00 -07:00
dev [MINOR][INFRA] Suppress warning in check-license 2020-11-23 10:38:40 +09:00
docs [SPARK-31962][SQL] Provide modifiedAfter and modifiedBefore options when filtering from a batch-based file data source 2020-11-23 08:30:41 +09:00
examples [SPARK-31962][SQL] Provide modifiedAfter and modifiedBefore options when filtering from a batch-based file data source 2020-11-23 08:30:41 +09:00
external [MINOR][TESTS][DOCS] Use fully-qualified class name in docker integration test 2020-11-20 10:14:37 -08:00
graphx [MINOR][GRAPHX] Correct typos in the sub-modules: graphx, external, and examples 2020-11-12 08:29:22 +09:00
hadoop-cloud [SPARK-33212][BUILD] Move to shaded clients for Hadoop 3.x profile 2020-10-22 03:21:34 +00:00
launcher [SPARK-33212][BUILD] Move to shaded clients for Hadoop 3.x profile 2020-10-22 03:21:34 +00:00
licenses [SPARK-32435][PYTHON] Remove heapq3 port from Python 3 2020-07-27 20:10:13 +09:00
licenses-binary [SPARK-32435][PYTHON] Remove heapq3 port from Python 3 2020-07-27 20:10:13 +09:00
mllib [SPARK-33466][ML][PYTHON] Imputer support mode(most_frequent) strategy 2020-11-20 11:35:34 -06:00
mllib-local [SPARK-32907][ML] adaptively blockify instances - revert blockify gmm 2020-09-23 15:54:56 +08:00
project [SPARK-33441][BUILD][FOLLOWUP] Make unused-imports check for SBT specific 2020-11-20 21:27:41 +09:00
python [SPARK-33143][PYTHON] Add configurable timeout to python server and client 2020-11-23 15:19:34 +09:00
R [SPARK-33304][R][SQL] Add from_avro and to_avro functions to SparkR 2020-11-19 09:52:29 +09:00
repl [SPARK-33441][BUILD] Add unused-imports compilation check and remove all unused-imports 2020-11-19 14:20:39 +09:00
resource-managers [SPARK-32919][SHUFFLE][TEST-MAVEN][TEST-HADOOP2.7] Driver side changes for coordinating push based shuffle by selecting external shuffle services for merging partitions 2020-11-20 06:00:30 -06:00
sbin [MINOR][DOCS] fix typo for docs,log message and comments 2020-08-22 06:45:35 +09:00
sql [SPARK-33427][SQL][FOLLOWUP] Put key and value into IdentityHashMap sequantially 2020-11-23 10:42:28 +09:00
streaming [SPARK-33441][BUILD] Add unused-imports compilation check and remove all unused-imports 2020-11-19 14:20:39 +09:00
tools [SPARK-21708][BUILD] Migrate build to sbt 1.x 2020-10-07 15:28:00 -07:00
.asf.yaml [SPARK-31352] Add .asf.yaml to control Github settings 2020-04-06 09:06:01 -05:00
.gitattributes [SPARK-30653][INFRA][SQL] EOL character enforcement for java/scala/xml/py/R files 2020-01-27 10:20:51 -08:00
.gitignore [SPARK-33269][INFRA] Ignore ".bsp/" directory in Git 2020-10-28 21:32:09 +09:00
.sbtopts [SPARK-21708][BUILD] Migrate build to sbt 1.x 2020-10-07 15:28:00 -07:00
appveyor.yml [SPARK-32647][INFRA] Report SparkR test results with JUnit reporter 2020-08-18 19:35:15 +09:00
CONTRIBUTING.md [MINOR][DOCS] Tighten up some key links to the project and download pages to use HTTPS 2019-05-21 10:56:42 -07:00
LICENSE [SPARK-32435][PYTHON] Remove heapq3 port from Python 3 2020-07-27 20:10:13 +09:00
LICENSE-binary [SPARK-32435][PYTHON] Remove heapq3 port from Python 3 2020-07-27 20:10:13 +09:00
NOTICE [SPARK-29674][CORE] Update dropwizard metrics to 4.1.x for JDK 9+ 2019-11-03 15:13:06 -08:00
NOTICE-binary [SPARK-29674][CORE] Update dropwizard metrics to 4.1.x for JDK 9+ 2019-11-03 15:13:06 -08:00
pom.xml [SPARK-33512][BUILD] Upgrade test libraries 2020-11-22 16:40:54 -08:00
README.md [MINOR][DOCS] Fix Jenkins build image and link in README.md 2020-01-20 23:08:24 -08:00
scalastyle-config.xml [SPARK-32539][INFRA] Disallow FileSystem.get(Configuration conf) in style check by default 2020-08-06 05:56:59 +00:00

Apache Spark

Spark is a unified analytics engine for large-scale data processing. It provides high-level APIs in Scala, Java, Python, and R, and an optimized engine that supports general computation graphs for data analysis. It also supports a rich set of higher-level tools including Spark SQL for SQL and DataFrames, MLlib for machine learning, GraphX for graph processing, and Structured Streaming for stream processing.

https://spark.apache.org/

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Online Documentation

You can find the latest Spark documentation, including a programming guide, on the project web page. This README file only contains basic setup instructions.

Building Spark

Spark is built using Apache Maven. To build Spark and its example programs, run:

./build/mvn -DskipTests clean package

(You do not need to do this if you downloaded a pre-built package.)

More detailed documentation is available from the project site, at "Building Spark".

For general development tips, including info on developing Spark using an IDE, see "Useful Developer Tools".

Interactive Scala Shell

The easiest way to start using Spark is through the Scala shell:

./bin/spark-shell

Try the following command, which should return 1,000,000,000:

scala> spark.range(1000 * 1000 * 1000).count()

Interactive Python Shell

Alternatively, if you prefer Python, you can use the Python shell:

./bin/pyspark

And run the following command, which should also return 1,000,000,000:

>>> spark.range(1000 * 1000 * 1000).count()

Example Programs

Spark also comes with several sample programs in the examples directory. To run one of them, use ./bin/run-example <class> [params]. For example:

./bin/run-example SparkPi

will run the Pi example locally.

You can set the MASTER environment variable when running examples to submit examples to a cluster. This can be a mesos:// or spark:// URL, "yarn" to run on YARN, and "local" to run locally with one thread, or "local[N]" to run locally with N threads. You can also use an abbreviated class name if the class is in the examples package. For instance:

MASTER=spark://host:7077 ./bin/run-example SparkPi

Many of the example programs print usage help if no params are given.

Running Tests

Testing first requires building Spark. Once Spark is built, tests can be run using:

./dev/run-tests

Please see the guidance on how to run tests for a module, or individual tests.

There is also a Kubernetes integration test, see resource-managers/kubernetes/integration-tests/README.md

A Note About Hadoop Versions

Spark uses the Hadoop core library to talk to HDFS and other Hadoop-supported storage systems. Because the protocols have changed in different versions of Hadoop, you must build Spark against the same version that your cluster runs.

Please refer to the build documentation at "Specifying the Hadoop Version and Enabling YARN" for detailed guidance on building for a particular distribution of Hadoop, including building for particular Hive and Hive Thriftserver distributions.

Configuration

Please refer to the Configuration Guide in the online documentation for an overview on how to configure Spark.

Contributing

Please review the Contribution to Spark guide for information on how to get started contributing to the project.