spark-instrumented-optimizer/docs
Aaron Staple ff637c9380 [SPARK-1484][MLLIB] Warn when running an iterative algorithm on uncached data.
Add warnings to KMeans, GeneralizedLinearAlgorithm, and computeSVD when called with input data that is not cached. KMeans is implemented iteratively, and I believe that GeneralizedLinearAlgorithm’s current optimizers are iterative and its future optimizers are also likely to be iterative. RowMatrix’s computeSVD is iterative against an RDD when run in DistARPACK mode. ALS and DecisionTree are iterative as well, but they implement RDD caching internally so do not require a warning.

I added a warning to GeneralizedLinearAlgorithm rather than inside its optimizers, where the iteration actually occurs, because internally GeneralizedLinearAlgorithm maps its input data to an uncached RDD before passing it to an optimizer. (In other words, the warning would be printed for every GeneralizedLinearAlgorithm run, regardless of whether its input is cached, if the warning were in GradientDescent or other optimizer.) I assume that use of an uncached RDD by GeneralizedLinearAlgorithm is intentional, and that the mapping there (adding label, intercepts and scaling) is a lightweight operation. Arguably a user calling an optimizer such as GradientDescent will be knowledgable enough to cache their data without needing a log warning, so lack of a warning in the optimizers may be ok.

Some of the documentation examples making use of these iterative algorithms did not cache their training RDDs (while others did). I updated the examples to always cache. I also fixed some (unrelated) minor errors in the documentation examples.

Author: Aaron Staple <aaron.staple@gmail.com>

Closes #2347 from staple/SPARK-1484 and squashes the following commits:

bd49701 [Aaron Staple] Address review comments.
ab2d4a4 [Aaron Staple] Disable warnings on python code path.
a7a0f99 [Aaron Staple] Change code comments per review comments.
7cca1dc [Aaron Staple] Change warning message text.
c77e939 [Aaron Staple] [SPARK-1484][MLLIB] Warn when running an iterative algorithm on uncached data.
3b6c511 [Aaron Staple] Minor doc example fixes.
2014-09-25 16:11:00 -07:00
..
_layouts Add a Community Projects page 2014-09-16 13:46:06 -07:00
_plugins [SPARK-1981][Streaming][Hotfix] Fixed docs related to kinesis 2014-09-02 19:02:48 -07:00
css [SPARK-1566] consolidate programming guide, and general doc updates 2014-05-30 00:34:33 -07:00
img [SPARK-2419][Streaming][Docs] More updates to the streaming programming guide 2014-09-06 14:46:43 -07:00
js [SPARK-1566] consolidate programming guide, and general doc updates 2014-05-30 00:34:33 -07:00
_config.yml SPARK-3579 Jekyll doc generation is different across environments. 2014-09-18 10:30:17 -07:00
api.md [SPARK-1439, SPARK-1440] Generate unified Scaladoc across projects and Javadocs 2014-04-21 21:57:40 -07:00
bagel-programming-guide.md SPARK-2363. Clean MLlib's sample data files 2014-07-13 19:27:43 -07:00
building-spark.md SPARK-3069 [DOCS] Build instructions in README are outdated 2014-09-16 09:18:03 -07:00
cluster-overview.md [SPARK-1566] consolidate programming guide, and general doc updates 2014-05-30 00:34:33 -07:00
configuration.md [SPARK-3565]Fix configuration item not consistent with document 2014-09-17 21:59:23 -07:00
contributing-to-spark.md Work in progress: 2013-09-08 00:29:11 -07:00
ec2-scripts.md [SPARK-787] Add S3 configuration parameters to the EC2 deploy scripts 2014-09-16 13:40:16 -07:00
graphx-programming-guide.md [SPARK-1566] consolidate programming guide, and general doc updates 2014-05-30 00:34:33 -07:00
hadoop-third-party-distributions.md SPARK-3069 [DOCS] Build instructions in README are outdated 2014-09-16 09:18:03 -07:00
hardware-provisioning.md Change port from 3030 to 4040 2013-09-11 10:01:38 -07:00
index.md Add a Community Projects page 2014-09-16 13:46:06 -07:00
java-programming-guide.md [SPARK-1566] consolidate programming guide, and general doc updates 2014-05-30 00:34:33 -07:00
job-scheduling.md SPARK-1183. Don't use "worker" to mean executor 2014-03-13 12:11:33 -07:00
mllib-classification-regression.md SPARK-2830 [MLlib]: re-organize mllib documentation 2014-08-12 17:15:21 -07:00
mllib-clustering.md [SPARK-1484][MLLIB] Warn when running an iterative algorithm on uncached data. 2014-09-25 16:11:00 -07:00
mllib-collaborative-filtering.md [SPARK-2843][MLLIB] add a section about regularization parameter in ALS 2014-08-20 17:47:39 -07:00
mllib-data-types.md [SPARK-2830][MLLIB] doc update for 1.1 2014-08-27 01:19:48 -07:00
mllib-decision-tree.md [SPARK-3443][MLLIB] update default values of tree: 2014-09-08 18:59:57 -07:00
mllib-dimensionality-reduction.md [SPARK-2830][MLLIB] doc update for 1.1 2014-08-27 01:19:48 -07:00
mllib-feature-extraction.md [MLLib] Fix example code variable name misspelling in MLLib Feature Extraction guide 2014-09-22 09:10:41 -07:00
mllib-guide.md [SPARK-3227] [mllib] Added migration guide for v1.0 to v1.1 2014-08-27 01:45:59 -07:00
mllib-linear-methods.md [SPARK-1484][MLLIB] Warn when running an iterative algorithm on uncached data. 2014-09-25 16:11:00 -07:00
mllib-naive-bayes.md [SPARK-3130][MLLIB] detect negative values in naive Bayes 2014-08-19 21:01:23 -07:00
mllib-optimization.md [SPARK-1484][MLLIB] Warn when running an iterative algorithm on uncached data. 2014-09-25 16:11:00 -07:00
mllib-statistics.md [SPARK-2830][MLLIB] doc update for 1.1 2014-08-27 01:19:48 -07:00
monitoring.md Docs: monitoring, streaming programming guide 2014-07-31 14:58:52 -07:00
programming-guide.md [SPARK-546] Add full outer join to RDD and DStream. 2014-09-24 20:39:09 -07:00
python-programming-guide.md [SPARK-1566] consolidate programming guide, and general doc updates 2014-05-30 00:34:33 -07:00
quick-start.md SPARK-1996. Remove use of special Maven repo for Akka 2014-06-21 23:29:57 -07:00
README.md SPARK-3579 Jekyll doc generation is different across environments. 2014-09-18 10:30:17 -07:00
running-on-mesos.md [SPARK-3240] Adding known issue for MESOS-1688 2014-08-26 18:30:45 -07:00
running-on-yarn.md [YARN] SPARK-2668: Add variable of yarn log directory for reference from the log4j configuration 2014-09-23 08:45:56 -05:00
scala-programming-guide.md [SPARK-1566] consolidate programming guide, and general doc updates 2014-05-30 00:34:33 -07:00
security.md [SPARK-2157] Enable tight firewall rules for Spark 2014-08-06 00:07:40 -07:00
spark-standalone.md [Docs] Fix outdated docs for standalone cluster 2014-09-19 16:02:38 -07:00
sql-programming-guide.md Update docs to use jsonRDD instead of wrong jsonRdd. 2014-09-22 10:13:44 -07:00
storage-openstack-swift.md [SPARK-938][doc] Add OpenStack Swift support 2014-09-07 20:56:04 -07:00
streaming-custom-receivers.md [DOCS] Fixed wrong links 2014-08-19 22:43:22 -07:00
streaming-flume-integration.md [SPARK-2419][Streaming][Docs] Updates to the streaming programming guide 2014-09-03 17:38:01 -07:00
streaming-kafka-integration.md [SPARK-2419][Streaming][Docs] Updates to the streaming programming guide 2014-09-03 17:38:01 -07:00
streaming-kinesis-integration.md SPARK-3069 [DOCS] Build instructions in README are outdated 2014-09-16 09:18:03 -07:00
streaming-programming-guide.md Fix Java example in Streaming Programming Guide 2014-09-20 15:05:03 -07:00
submitting-applications.md SPARK-2310. Support arbitrary Spark properties on the command line with ... 2014-07-23 23:11:26 -07:00
tuning.md [SPARK-2859] Update url of Kryo project in related docs 2014-08-05 11:50:08 -07:00

Welcome to the Spark documentation!

This readme will walk you through navigating and building the Spark documentation, which is included here with the Spark source code. You can also find documentation specific to release versions of Spark at http://spark.apache.org/documentation.html.

Read on to learn more about viewing documentation in plain text (i.e., markdown) or building the documentation yourself. Why build it yourself? So that you have the docs that corresponds to whichever version of Spark you currently have checked out of revision control.

Generating the Documentation HTML

We include the Spark documentation as part of the source (as opposed to using a hosted wiki, such as the github wiki, as the definitive documentation) to enable the documentation to evolve along with the source code and be captured by revision control (currently git). This way the code automatically includes the version of the documentation that is relevant regardless of which version or release you have checked out or downloaded.

In this directory you will find textfiles formatted using Markdown, with an ".md" suffix. You can read those text files directly if you want. Start with index.md.

The markdown code can be compiled to HTML using the Jekyll tool. Jekyll and a few dependencies must be installed for this to work. We recommend installing via the Ruby Gem dependency manager. Since the exact HTML output varies between versions of Jekyll and its dependencies, we list specific versions here in some cases:

$ sudo gem install jekyll -v 1.4.3
$ sudo gem uninstall kramdown -v 1.4.1
$ sudo gem install jekyll-redirect-from

Execute jekyll from the docs/ directory. Compiling the site with Jekyll will create a directory called _site containing index.html as well as the rest of the compiled files.

You can modify the default Jekyll build as follows:

# Skip generating API docs (which takes a while)
$ SKIP_API=1 jekyll build
# Serve content locally on port 4000
$ jekyll serve --watch
# Build the site with extra features used on the live page
$ PRODUCTION=1 jekyll build

Pygments

We also use pygments (http://pygments.org) for syntax highlighting in documentation markdown pages, so you will also need to install that (it requires Python) by running sudo easy_install Pygments.

To mark a block of code in your markdown to be syntax highlighted by jekyll during the compile phase, use the following sytax:

{% highlight scala %}
// Your scala code goes here, you can replace scala with many other
// supported languages too.
{% endhighlight %}

API Docs (Scaladoc and Epydoc)

You can build just the Spark scaladoc by running sbt/sbt doc from the SPARK_PROJECT_ROOT directory.

Similarly, you can build just the PySpark epydoc by running epydoc --config epydoc.conf from the SPARK_PROJECT_ROOT/pyspark directory. Documentation is only generated for classes that are listed as public in __init__.py.

When you run jekyll in the docs directory, it will also copy over the scaladoc for the various Spark subprojects into the docs directory (and then also into the _site directory). We use a jekyll plugin to run sbt/sbt doc before building the site so if you haven't run it (recently) it may take some time as it generates all of the scaladoc. The jekyll plugin also generates the PySpark docs using epydoc.

NOTE: To skip the step of building and copying over the Scala and Python API docs, run SKIP_API=1 jekyll.