Remove Typesafe Config usage and conf files to fix nested property names
With Typesafe Config we had the subtle problem of no longer allowing
nested property names, which are used for a few of our properties:
http://apache-spark-developers-list.1001551.n3.nabble.com/Config-properties-broken-in-master-td208.html
This PR is for branch 0.9 but should be added into master too.
(cherry picked from commit 34e911ce9a)
Signed-off-by: Patrick Wendell <pwendell@gmail.com>
This is useful for the cases when a file needs to be refreshed and downloaded
by the executors periodically.
Signed-off-by: Yinan Li <liyinan926@gmail.com>
SPARK-1024 Remove "-XX:+UseCompressedStrings" option from tuning guide
remove "-XX:+UseCompressedStrings" option from tuning guide since jdk7 no longer supports this.
Removed unnecessary DStream operations and updated docs
Removed StreamingContext.registerInputStream and registerOutputStream - they were useless. InputDStream has been made to register itself, and just registering a DStream as output stream cause RDD objects to be created but the RDDs will not be computed at all.. Also made DStream.register() private[streaming] for the same reasons.
Updated docs, specially added package documentation for streaming package.
Also, changed NetworkWordCount's input storage level to use MEMORY_ONLY, replication on the local machine causes warning messages (as replication fails) which is scary for a new user trying out his/her first example.
Add Naive Bayes to Python MLlib, and some API fixes
- Added a Python wrapper for Naive Bayes
- Updated the Scala Naive Bayes to match the style of our other
algorithms better and in particular make it easier to call from Java
(added builder pattern, removed default value in train method)
- Updated Python MLlib functions to not require a SparkContext; we can
get that from the RDD the user gives
- Added a toString method in LabeledPoint
- Made the Python MLlib tests run as part of run-tests as well (before
they could only be run individually through each file)
GraphX: Unifying Graphs and Tables
GraphX extends Spark's distributed fault-tolerant collections API and interactive console with a new graph API which leverages recent advances in graph systems (e.g., [GraphLab](http://graphlab.org)) to enable users to easily and interactively build, transform, and reason about graph structured data at scale. See http://amplab.github.io/graphx/.
Thanks to @jegonzal, @rxin, @ankurdave, @dcrankshaw, @jianpingjwang, @amatsukawa, @kellrott, and @adamnovak.
Tasks left:
- [x] Graph-level uncache
- [x] Uncache previous iterations in Pregel
- [x] ~~Uncache previous iterations in GraphLab~~ (postponed to post-release)
- [x] - Describe GC issue with GraphLab
- [ ] Write `docs/graphx-programming-guide.md`
- [x] - Mention future Bagel support in docs
- [ ] - Section on caching/uncaching in docs: As with Spark, cache something that is used more than once. In an iterative algorithm, try to cache and force (i.e., materialize) something every iteration, then uncache the cached things that depended on the newly materialized RDD but that won't be referenced again.
- [x] Undo modifications to core collections and instead copy them to org.apache.spark.graphx
- [x] Make Graph serializable to work around capture in Spark shell
- [x] Rename graph -> graphx in package name and subproject
- [x] Remove standalone PageRank
- [x] ~~Fix amplab/graphx#52 by checking `iter.hasNext`~~
Improvements to external sorting
1. Adds the option of compressing outputs.
2. Adds batching to the serialization to prevent OOM on the read side.
3. Slight renaming of config options.
4. Use Spark's buffer size for reads in addition to writes.
1. Adds the option of compressing outputs.
2. Adds batching to the serialization to prevent OOM on the read side.
3. Slight renaming of config options.
4. Use Spark's buffer size for reads in addition to writes.
Moved DStream and PairDSream to org.apache.spark.streaming.dstream
Similar to the package location of `org.apache.spark.rdd.RDD`, `DStream` has been moved from `org.apache.spark.streaming.DStream` to `org.apache.spark.streaming.dstream.DStream`. I know that the package name is a little long, but I think its better to keep it consistent with Spark's structure.
Also fixed persistence of windowed DStream. The RDDs generated generated by windowed DStream are essentially unions of underlying RDDs, and persistent these union RDDs would store numerous copies of the underlying data. Instead setting the persistence level on the windowed DStream is made to set the persistence level of the underlying DStream.
Disable shuffle file consolidation by default
After running various performance tests for the 0.9 release, this still seems to have performance issues even on XFS. So let's keep this off-by-default for 0.9 and users can experiment with it depending on their disk configurations.
`foreachRDD` makes it clear that the granularity of this operator is per-RDD.
As it stands, `foreach` is inconsistent with with `map`, `filter`, and the other
DStream operators which get pushed down to individual records within each RDD.
We've used camel case in other Spark methods so it felt reasonable to
keep using it here and make the code match Scala/Java as much as
possible. Note that parameter names matter in Python because it allows
passing optional parameters by name.
- Added a Python wrapper for Naive Bayes
- Updated the Scala Naive Bayes to match the style of our other
algorithms better and in particular make it easier to call from Java
(added builder pattern, removed default value in train method)
- Updated Python MLlib functions to not require a SparkContext; we can
get that from the RDD the user gives
- Added a toString method in LabeledPoint
- Made the Python MLlib tests run as part of run-tests as well (before
they could only be run individually through each file)
External Sorting for Aggregator and CoGroupedRDDs (Revisited)
(This pull request is re-opened from https://github.com/apache/incubator-spark/pull/303, which was closed because Jenkins / github was misbehaving)
The target issue for this patch is the out-of-memory exceptions triggered by aggregate operations such as reduce, groupBy, join, and cogroup. The existing AppendOnlyMap used by these operations resides purely in memory, and grows with the size of the input data until the amount of allocated memory is exceeded. Under large workloads, this problem is aggravated by the fact that OOM frequently occurs only after a very long (> 1 hour) map phase, in which case the entire job must be restarted.
The solution is to spill the contents of this map to disk once a certain memory threshold is exceeded. This functionality is provided by ExternalAppendOnlyMap, which additionally sorts this buffer before writing it out to disk, and later merges these buffers back in sorted order.
Under normal circumstances in which OOM is not triggered, ExternalAppendOnlyMap is simply a wrapper around AppendOnlyMap and incurs little overhead. Only when the memory usage is expected to exceed the given threshold does ExternalAppendOnlyMap spill to disk.
Aside from trivial formatting changes, use nulls instead of Options for
DiskMapIterator, and add documentation for spark.shuffle.externalSorting
and spark.shuffle.memoryFraction.
Also, set spark.shuffle.memoryFraction to 0.3, and spark.storage.memoryFraction = 0.6.
Yarn client addjar and misc fixes
Fix the addJar functionality in yarn-client mode, add support for the other options supported in yarn-standalone mode, set the application type on yarn in hadoop 2.X, add documentation, change heartbeat interval to be same code as the yarn-standalone so it doesn't take so long to get containers and exit.
Simplify and fix pyspark script.
This patch removes compatibility for IPython < 1.0 but fixes the launch
script and makes it much simpler.
I tested this using the three commands in the PySpark documentation page:
1. IPYTHON=1 ./pyspark
2. IPYTHON_OPTS="notebook" ./pyspark
3. IPYTHON_OPTS="notebook --pylab inline" ./pyspark
There are two changes:
- We rely on PYTHONSTARTUP env var to start PySpark
- Removed the quotes around $IPYTHON_OPTS... having quotes
gloms them together as a single argument passed to `exec` which
seemed to cause ipython to fail (it instead expects them as
multiple arguments).
SPARK-998: Support Launching Driver Inside of Standalone Mode
[NOTE: I need to bring the tests up to date with new changes, so for now they will fail]
This patch provides support for launching driver programs inside of a standalone cluster manager. It also supports monitoring and re-launching of driver programs which is useful for long running, recoverable applications such as Spark Streaming jobs. For those jobs, this patch allows a deployment mode which is resilient to the failure of any worker node, failure of a master node (provided a multi-master setup), and even failures of the applicaiton itself, provided they are recoverable on a restart. Driver information, such as the status and logs from a driver, is displayed in the UI
There are a few small TODO's here, but the code is generally feature-complete. They are:
- Bring tests up to date and add test coverage
- Restarting on failure should be optional and maybe off by default.
- See if we can re-use akka connections to facilitate clients behind a firewall
A sensible place to start for review would be to look at the `DriverClient` class which presents users the ability to launch their driver program. I've also added an example program (`DriverSubmissionTest`) that allows you to test this locally and play around with killing workers, etc. Most of the code is devoted to persisting driver state in the cluster manger, exposing it in the UI, and dealing correctly with various types of failures.
Instructions to test locally:
- `sbt/sbt assembly/assembly examples/assembly`
- start a local version of the standalone cluster manager
```
./spark-class org.apache.spark.deploy.client.DriverClient \
-j -Dspark.test.property=something \
-e SPARK_TEST_KEY=SOMEVALUE \
launch spark://10.99.1.14:7077 \
../path-to-examples-assembly-jar \
org.apache.spark.examples.DriverSubmissionTest 1000 some extra options --some-option-here -X 13
```
- Go in the UI and make sure it started correctly, look at the output etc
- Kill workers, the driver program, masters, etc.
support distributing extra files to worker for yarn client mode
So that user doesn't need to package all dependency into one assemble jar as spark app jar
SPARK-1009 Updated MLlib docs to show how to use it in Python
In addition added detailed examples for regression, clustering and recommendation algorithms in a separate Scala section. Fixed a few minor issues with existing documentation.
This patch removes compatibility for IPython < 1.0 but fixes the launch
script and makes it much simpler.
I tested this using the three commands in the PySpark documentation page:
1. IPYTHON=1 ./pyspark
2. IPYTHON_OPTS="notebook" ./pyspark
3. IPYTHON_OPTS="notebook --pylab inline" ./pyspark
There are two changes:
- We rely on PYTHONSTARTUP env var to start PySpark
- Removed the quotes around $IPYTHON_OPTS... having quotes
gloms them together as a single argument passed to `exec` which
seemed to cause ipython to fail (it instead expects them as
multiple arguments).
Conf improvements
There are two new features.
1. Allow users to set arbitrary akka configurations via spark conf.
2. Allow configuration to be printed in logs for diagnosis.
Add a script to download sbt if not present on the system
As per the discussion on the dev mailing list this script will use the system sbt if present or otherwise attempt to install the sbt launcher. The fall back error message in the event it fails instructs the user to install sbt. While the URLs it fetches from aren't controlled by the spark project directly, they are stable and the current authoritative sources.
For SPARK-527, Support spark-shell when running on YARN
sync to trunk and resubmit here
In current YARN mode approaching, the application is run in the Application Master as a user program thus the whole spark context is on remote.
This approaching won't support application that involve local interaction and need to be run on where it is launched.
So In this pull request I have a YarnClientClusterScheduler and backend added.
With this scheduler, the user application is launched locally,While the executor will be launched by YARN on remote nodes with a thin AM which only launch the executor and monitor the Driver Actor status, so that when client app is done, it can finish the YARN Application as well.
This enables spark-shell to run upon YARN.
This also enable other Spark applications to have the spark context to run locally with a master-url "yarn-client". Thus e.g. SparkPi could have the result output locally on console instead of output in the log of the remote machine where AM is running on.
Docs also updated to show how to use this yarn-client mode.
Add graphite sink for metrics
This adds a metrics sink for graphite. The sink must
be configured with the host and port of a graphite node
and optionally may be configured with a prefix that will
be prepended to all metrics that are sent to graphite.
With this scheduler, the user application is launched locally,
While the executor will be launched by YARN on remote nodes.
This enables spark-shell to run upon YARN.
I've diff'd this patch against my own -- since they were both created
independently, this means that two sets of eyes have gone over all the
merge conflicts that were created, so I'm feeling significantly more
confident in the resulting PR.
@rxin has looked at the changes to the repl and is resoundingly
confident that they are correct.
This adds a metrics sink for graphite. The sink must
be configured with the host and port of a graphite node
and optionally may be configured with a prefix that will
be prepended to all metrics that are sent to graphite.
This patch adds an operator called repartition with more straightforward
semantics than the current `coalesce` operator. There are a few use cases
where this operator is useful:
1. If a user wants to increase the number of partitions in the RDD. This
is more common now with streaming. E.g. a user is ingesting data on one
node but they want to add more partitions to ensure parallelism of
subsequent operations across threads or the cluster.
Right now they have to call rdd.coalesce(numSplits, shuffle=true) - that's
super confusing.
2. If a user has input data where the number of partitions is not known. E.g.
> sc.textFile("some file").coalesce(50)....
This is both vague semantically (am I growing or shrinking this RDD) but also,
may not work correctly if the base RDD has fewer than 50 partitions.
The new operator forces shuffles every time, so it will always produce exactly
the number of new partitions. It also throws an exception rather than silently
not-working if a bad input is passed.
I am currently adding streaming tests (requires refactoring some of the test
suite to allow testing at partition granularity), so this is not ready for
merge yet. But feedback is welcome.
Add classmethod to SparkContext to set system properties.
Add a new classmethod to SparkContext to set system properties like is
possible in Scala/Java. Unlike the Java/Scala implementations, there's
no access to System until the JVM bridge is created. Since
SparkContext handles that, move the initialization of the JVM
connection to a separate classmethod that can safely be called
repeatedly as long as the same instance (or no instance) is provided.
Standalone Scheduler fault tolerance using ZooKeeper
This patch implements full distributed fault tolerance for standalone scheduler Masters.
There is only one master Leader at a time, which is actively serving scheduling
requests. If this Leader crashes, another master will eventually be elected, reconstruct
the state from the first Master, and continue serving scheduling requests.
Leader election is performed using the ZooKeeper leader election pattern. We try to minimize
the use of ZooKeeper and the assumptions about ZooKeeper's behavior, so there is a layer of
retries and session monitoring on top of the ZooKeeper client.
Master failover follows directly from the single-node Master recovery via the file
system (patch d5a96fe), save that the Master state is stored in ZooKeeper instead.
Configuration:
By default, no recovery mechanism is enabled (spark.deploy.recoveryMode = NONE).
By setting spark.deploy.recoveryMode to ZOOKEEPER and setting spark.deploy.zookeeper.url
to an appropriate ZooKeeper URL, ZooKeeper recovery mode is enabled.
By setting spark.deploy.recoveryMode to FILESYSTEM and setting spark.deploy.recoveryDirectory
to an appropriate directory accessible by the Master, we will keep the behavior of from d5a96fe.
Additionally, places where a Master could be specificied by a spark:// url can now take
comma-delimited lists to specify backup masters. Note that this is only used for registration
of NEW Workers and application Clients. Once a Worker or Client has registered with the
Master Leader, it is "in the system" and will never need to register again.
Conflicts:
bagel/pom.xml
core/pom.xml
core/src/test/scala/org/apache/spark/ui/UISuite.scala
examples/pom.xml
mllib/pom.xml
pom.xml
project/SparkBuild.scala
repl/pom.xml
streaming/pom.xml
tools/pom.xml
In scala 2.10, a shorter representation is used for naming artifacts
so changed to shorter scala version for artifacts and made it a property in pom.
This commit makes Spark invocation saner by using an assembly JAR to
find all of Spark's dependencies instead of adding all the JARs in
lib_managed. It also packages the examples into an assembly and uses
that as SPARK_EXAMPLES_JAR. Finally, it replaces the old "run" script
with two better-named scripts: "run-examples" for examples, and
"spark-class" for Spark internal classes (e.g. REPL, master, etc). This
is also designed to minimize the confusion people have in trying to use
"run" to run their own classes; it's not meant to do that, but now at
least if they look at it, they can modify run-examples to do a decent
job for them.
As part of this, Bagel's examples are also now properly moved to the
examples package instead of bagel.
- When a resourceOffers() call has multiple offers, force the TaskSets
to consider them in increasing order of locality levels so that they
get a chance to launch stuff locally across all offers
- Simplify ClusterScheduler.prioritizeContainers
- Add docs on the new configuration options
Adds links to new instructions in:
* The main Spark project README.md
* The docs nav menu called "More"
* The docs Overview page under the "Building" and "Where to Go from Here" sections
