Apache Spark - A unified analytics engine for large-scale data processing
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Josh Rosen 29cfab3f15 [SPARK-17110] Fix StreamCorruptionException in BlockManager.getRemoteValues()
## What changes were proposed in this pull request?

This patch fixes a `java.io.StreamCorruptedException` error affecting remote reads of cached values when certain data types are used. The problem stems from #11801 / SPARK-13990, a patch to have Spark automatically pick the "best" serializer when caching RDDs. If PySpark cached a PythonRDD, then this would be cached as an `RDD[Array[Byte]]` and the automatic serializer selection would pick KryoSerializer for replication and block transfer. However, the `getRemoteValues()` / `getRemoteBytes()` code path did not pass proper class tags in order to enable the same serializer to be used during deserialization, causing Java to be inappropriately used instead of Kryo, leading to the StreamCorruptedException.

We already fixed a similar bug in #14311, which dealt with similar issues in block replication. Prior to that patch, it seems that we had no tests to ensure that block replication actually succeeded. Similarly, prior to this bug fix patch it looks like we had no tests to perform remote reads of cached data, which is why this bug was able to remain latent for so long.

This patch addresses the bug by modifying `BlockManager`'s `get()` and  `getRemoteValues()` methods to accept ClassTags, allowing the proper class tag to be threaded in the `getOrElseUpdate` code path (which is used by `rdd.iterator`)

## How was this patch tested?

Extended the caching tests in `DistributedSuite` to exercise the `getRemoteValues` path, plus manual testing to verify that the PySpark bug reproduction in SPARK-17110 is fixed.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #14952 from JoshRosen/SPARK-17110.
2016-09-06 15:07:28 -07:00
.github [MINOR][MAINTENANCE] Fix typo for the pull request template. 2016-02-24 00:45:31 -08:00
assembly [SPARK-16967] move mesos to module 2016-08-26 12:25:22 -07:00
bin [SPARK-16781][PYSPARK] java launched by PySpark as gateway may not be the same java used in the spark environment 2016-08-24 20:04:09 +01:00
build [SPARK-14279][BUILD] Pick the spark version from pom 2016-06-06 09:42:50 -07:00
common [SPARK-17299] TRIM/LTRIM/RTRIM should not strips characters other than spaces 2016-09-06 22:18:28 +01:00
conf [SPARK-13238][CORE] Add ganglia dmax parameter 2016-08-05 13:07:52 -07:00
core [SPARK-17110] Fix StreamCorruptionException in BlockManager.getRemoteValues() 2016-09-06 15:07:28 -07:00
data [SPARK-16421][EXAMPLES][ML] Improve ML Example Outputs 2016-08-05 20:57:46 +01:00
dev [SPARK-17378][BUILD] Upgrade snappy-java to 1.1.2.6 2016-09-06 22:13:25 +01:00
docs [SPARK-16619] Add shuffle service metrics entry in monitoring docs 2016-09-01 17:01:16 -07:00
examples [SPARK-17347][SQL][EXAMPLES] Encoder in Dataset example has incorrect type 2016-09-03 10:03:40 +01:00
external [SPARK-17229][SQL] PostgresDialect shouldn't widen float and short types during reads 2016-08-25 23:22:40 +02:00
graphx [SPARK-16779][TRIVIAL] Avoid using postfix operators where they do not add much and remove whitelisting 2016-08-08 15:54:03 -07:00
launcher [SPARK-17178][SPARKR][SPARKSUBMIT] Allow to set sparkr shell command through --conf 2016-08-31 00:20:41 -07:00
licenses [MINOR][BUILD] Add modernizr MIT license; specify "2014 and onwards" in license copyright 2016-06-04 21:41:27 +01:00
mesos [SPARK-16533][HOTFIX] Fix compilation on Scala 2.10. 2016-09-01 14:02:58 -07:00
mllib [MINOR] Remove unnecessary check in MLSerDe 2016-09-06 14:20:56 -07:00
mllib-local [MINOR][ML][MLLIB] Remove work around for breeze sparse matrix. 2016-09-04 05:38:47 -07:00
project [SPARK-17308] Improved the spark core code by replacing all pattern match on boolean value by if/else block. 2016-09-04 12:39:26 +01:00
python [MINOR][ML] Correct weights doc of MultilayerPerceptronClassificationModel. 2016-09-06 03:30:37 -07:00
R [SPARK-17315][SPARKR] Kolmogorov-Smirnov test SparkR wrapper 2016-09-03 12:26:30 -07:00
repl [SPARK-17318][TESTS] Fix ReplSuite replicating blocks of object with class defined in repl again 2016-08-31 23:25:20 -07:00
sbin [SPARK-16781][PYSPARK] java launched by PySpark as gateway may not be the same java used in the spark environment 2016-08-24 20:04:09 +01:00
sql [SPARK-16922] [SPARK-17211] [SQL] make the address of values portable in LongToUnsafeRowMap 2016-09-06 10:46:31 -07:00
streaming [SPARK-17110] Fix StreamCorruptionException in BlockManager.getRemoteValues() 2016-09-06 15:07:28 -07:00
tools [SPARK-16535][BUILD] In pom.xml, remove groupId which is redundant definition and inherited from the parent 2016-07-19 11:59:46 +01:00
yarn [SPARK-16711] YarnShuffleService doesn't re-init properly on YARN rolling upgrade 2016-09-02 10:42:13 -07:00
.gitattributes [SPARK-3870] EOL character enforcement 2014-10-31 12:39:52 -07:00
.gitignore [SPARKR][BUILD] ignore cran-check.out under R folder 2016-08-25 12:11:27 -07:00
.travis.yml [SPARK-16967] move mesos to module 2016-08-26 12:25:22 -07:00
CONTRIBUTING.md [SPARK-6889] [DOCS] CONTRIBUTING.md updates to accompany contribution doc updates 2015-04-21 22:34:31 -07:00
LICENSE [SPARK-16781][PYSPARK] java launched by PySpark as gateway may not be the same java used in the spark environment 2016-08-24 20:04:09 +01:00
NOTICE [MINOR][BUILD] Add modernizr MIT license; specify "2014 and onwards" in license copyright 2016-06-04 21:41:27 +01:00
pom.xml [SPARK-17378][BUILD] Upgrade snappy-java to 1.1.2.6 2016-09-06 22:13:25 +01:00
README.md [SPARK-15821][DOCS] Include parallel build info 2016-06-14 13:59:01 +01:00
scalastyle-config.xml [SPARK-16877][BUILD] Add rules for preventing to use Java annotations (Deprecated and Override) 2016-08-04 21:43:05 +01:00

Apache Spark

Spark is a fast and general cluster computing system for Big Data. 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 Spark Streaming for stream processing.

http://spark.apache.org/

Online Documentation

You can find the latest Spark documentation, including a programming guide, on the project web page and project wiki. 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.)

You can build Spark using more than one thread by using the -T option with Maven, see "Parallel builds in Maven 3". More detailed documentation is available from the project site, at "Building Spark". For developing Spark using an IDE, see Eclipse and IntelliJ.

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 1000:

scala> sc.parallelize(1 to 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 1000:

>>> sc.parallelize(range(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.

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" 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.