Commit graph

5688 commits

Author SHA1 Message Date
Marcelo Vanzin 59f9c1bd1a [SPARK-16385][CORE] Catch correct exception when calling method via reflection.
Using "Method.invoke" causes an exception to be thrown, not an error, so
Utils.waitForProcess() was always throwing an exception when run on Java 7.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #14056 from vanzin/SPARK-16385.
2016-07-05 16:55:22 -07:00
Sean Owen 18fb57f58a [MINOR][DOCS] Remove unused images; crush PNGs that could use it for good measure
## What changes were proposed in this pull request?

Coincidentally, I discovered that a couple images were unused in `docs/`, and then searched and found more, and then realized some PNGs were pretty big and could be crushed, and before I knew it, had done the same for the ASF site (not committed yet).

No functional change at all, just less superfluous image data.

## How was this patch tested?

`jekyll serve`

Author: Sean Owen <sowen@cloudera.com>

Closes #14029 from srowen/RemoveCompressImages.
2016-07-04 09:21:58 +01:00
Dongjoon Hyun 3000b4b29f [MINOR][BUILD] Fix Java linter errors
## What changes were proposed in this pull request?

This PR fixes the minor Java linter errors like the following.
```
-    public int read(char cbuf[], int off, int len) throws IOException {
+    public int read(char[] cbuf, int off, int len) throws IOException {
```

## How was this patch tested?

Manual.
```
$ build/mvn -T 4 -q -DskipTests -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install
$ dev/lint-java
Using `mvn` from path: /usr/local/bin/mvn
Checkstyle checks passed.
```

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #14017 from dongjoon-hyun/minor_build_java_linter_error.
2016-07-02 16:31:06 +01:00
Reynold Xin d601894c04 [SPARK-16335][SQL] Structured streaming should fail if source directory does not exist
## What changes were proposed in this pull request?
In structured streaming, Spark does not report errors when the specified directory does not exist. This is a behavior different from the batch mode. This patch changes the behavior to fail if the directory does not exist (when the path is not a glob pattern).

## How was this patch tested?
Updated unit tests to reflect the new behavior.

Author: Reynold Xin <rxin@databricks.com>

Closes #14002 from rxin/SPARK-16335.
2016-07-01 15:16:04 -07:00
Sean Owen 2075bf8ef6 [SPARK-16182][CORE] Utils.scala -- terminateProcess() should call Process.destroyForcibly() if and only if Process.destroy() fails
## What changes were proposed in this pull request?

Utils.terminateProcess should `destroy()` first and only fall back to `destroyForcibly()` if it fails. It's kind of bad that we're force-killing executors -- and only in Java 8. See JIRA for an example of the impact: no shutdown

While here: `Utils.waitForProcess` should use the Java 8 method if available instead of a custom implementation.

## How was this patch tested?

Existing tests, which cover the force-kill case, and Amplab tests, which will cover both Java 7 and Java 8 eventually. However I tested locally on Java 8 and the PR builder will try Java 7 here.

Author: Sean Owen <sowen@cloudera.com>

Closes #13973 from srowen/SPARK-16182.
2016-07-01 09:22:27 +01:00
Imran Rashid fdf9f94f8c [SPARK-15865][CORE] Blacklist should not result in job hanging with less than 4 executors
## What changes were proposed in this pull request?

Before this change, when you turn on blacklisting with `spark.scheduler.executorTaskBlacklistTime`, but you have fewer than `spark.task.maxFailures` executors, you can end with a job "hung" after some task failures.

Whenever a taskset is unable to schedule anything on resourceOfferSingleTaskSet, we check whether the last pending task can be scheduled on *any* known executor.  If not, the taskset (and any corresponding jobs) are failed.
* Worst case, this is O(maxTaskFailures + numTasks).  But unless many executors are bad, this should be small
* This does not fail as fast as possible -- when a task becomes unschedulable, we keep scheduling other tasks.  This is to avoid an O(numPendingTasks * numExecutors) operation
* Also, it is conceivable this fails too quickly.  You may be 1 millisecond away from unblacklisting a place for a task to run, or acquiring a new executor.

## How was this patch tested?

Added unit test which failed before the change, ran new test 5k times manually, ran all scheduler tests manually, and the full suite via jenkins.

Author: Imran Rashid <irashid@cloudera.com>

Closes #13603 from squito/progress_w_few_execs_and_blacklist.
2016-06-30 13:36:06 -05:00
Sital Kedia 07f46afc73 [SPARK-13850] Force the sorter to Spill when number of elements in th…
## What changes were proposed in this pull request?

Force the sorter to Spill when number of elements in the pointer array reach a certain size. This is to workaround the issue of timSort failing on large buffer size.

## How was this patch tested?

Tested by running a job which was failing without this change due to TimSort bug.

Author: Sital Kedia <skedia@fb.com>

Closes #13107 from sitalkedia/fix_TimSort.
2016-06-30 10:53:18 -07:00
Eric Liang 23c58653f9 [SPARK-16238] Metrics for generated method and class bytecode size
## What changes were proposed in this pull request?

This extends SPARK-15860 to include metrics for the actual bytecode size of janino-generated methods. They can be accessed in the same way as any other codahale metric, e.g.

```
scala> org.apache.spark.metrics.source.CodegenMetrics.METRIC_GENERATED_CLASS_BYTECODE_SIZE.getSnapshot().getValues()
res7: Array[Long] = Array(532, 532, 532, 542, 1479, 2670, 3585, 3585)

scala> org.apache.spark.metrics.source.CodegenMetrics.METRIC_GENERATED_METHOD_BYTECODE_SIZE.getSnapshot().getValues()
res8: Array[Long] = Array(5, 5, 5, 5, 10, 10, 10, 10, 15, 15, 15, 38, 63, 79, 88, 94, 94, 94, 132, 132, 165, 165, 220, 220)
```

## How was this patch tested?

Small unit test, also verified manually that the performance impact is minimal (<10%). hvanhovell

Author: Eric Liang <ekl@databricks.com>

Closes #13934 from ericl/spark-16238.
2016-06-29 15:07:32 -07:00
Tom Magrino ae14f36235 [SPARK-16148][SCHEDULER] Allow for underscores in TaskLocation in the Executor ID
## What changes were proposed in this pull request?

Previously, the TaskLocation implementation would not allow for executor ids which include underscores.  This tweaks the string split used to get the hostname and executor id, allowing for underscores in the executor id.

This addresses the JIRA found here: https://issues.apache.org/jira/browse/SPARK-16148

This is moved over from a previous PR against branch-1.6: https://github.com/apache/spark/pull/13857

## How was this patch tested?

Ran existing unit tests for core and streaming.  Manually ran a simple streaming job with an executor whose id contained underscores and confirmed that the job ran successfully.

This is my original work and I license the work to the project under the project's open source license.

Author: Tom Magrino <tmagrino@fb.com>

Closes #13858 from tmagrino/fixtasklocation.
2016-06-28 13:36:41 -07:00
Imran Rashid c15b552dd5 [SPARK-16106][CORE] TaskSchedulerImpl should properly track executors added to existing hosts
## What changes were proposed in this pull request?

TaskSchedulerImpl used to only set `newExecAvailable` when a new *host* was added, not when a new executor was added to an existing host.  It also didn't update some internal state tracking live executors until a task was scheduled on the executor.  This patch changes it to properly update as soon as it knows about a new executor.

## How was this patch tested?

added a unit test, ran everything via jenkins.

Author: Imran Rashid <irashid@cloudera.com>

Closes #13826 from squito/SPARK-16106_executorByHosts.
2016-06-27 16:38:03 -05:00
Imran Rashid 282158914d [SPARK-16136][CORE] Fix flaky TaskManagerSuite
## What changes were proposed in this pull request?

TaskManagerSuite "Kill other task attempts when one attempt belonging to the same task succeeds" was flaky.  When checking whether a task is speculatable, at least one millisecond must pass since the task was submitted.  Use a manual clock to avoid the problem.

I noticed these tests were leaving lots of threads lying around as well (which prevented me from running the test repeatedly), so I fixed that too.

## How was this patch tested?

Ran the test 1k times on my laptop, passed every time (it failed about 20% of the time before this).

Author: Imran Rashid <irashid@cloudera.com>

Closes #13848 from squito/fix_flaky_taskmanagersuite.
2016-06-27 16:28:59 -05:00
jerryshao 52d4fe0579 [MINOR][CORE] Fix display wrong free memory size in the log
## What changes were proposed in this pull request?

Free memory size displayed in the log is wrong (used memory), fix to make it correct.

## How was this patch tested?

N/A

Author: jerryshao <sshao@hortonworks.com>

Closes #13804 from jerryshao/memory-log-fix.
2016-06-27 09:23:58 +01:00
Sean Owen e87741589a [SPARK-16193][TESTS] Address flaky ExternalAppendOnlyMapSuite spilling tests
## What changes were proposed in this pull request?

Make spill tests wait until job has completed before returning the number of stages that spilled

## How was this patch tested?

Existing Jenkins tests.

Author: Sean Owen <sowen@cloudera.com>

Closes #13896 from srowen/SPARK-16193.
2016-06-25 12:14:14 +01:00
Alex Bozarth 3ee9695d1f [SPARK-1301][WEB UI] Added anchor links to Accumulators and Tasks on StagePage
## What changes were proposed in this pull request?

Sometimes the "Aggregated Metrics by Executor" table on the Stage page can get very long so actor links to the Accumulators and Tasks tables below it have been added to the summary at the top of the page. This has been done in the same way as the Jobs and Stages pages. Note: the Accumulators link only displays when the table exists.

## How was this patch tested?

Manually Tested and dev/run-tests

![justtasks](https://cloud.githubusercontent.com/assets/13952758/15165269/6e8efe8c-16c9-11e6-9784-cffe966fdcf0.png)
![withaccumulators](https://cloud.githubusercontent.com/assets/13952758/15165270/7019ec9e-16c9-11e6-8649-db69ed7a317d.png)

Author: Alex Bozarth <ajbozart@us.ibm.com>

Closes #13037 from ajbozarth/spark1301.
2016-06-25 09:27:22 +01:00
Sital Kedia bf665a9586 [SPARK-15958] Make initial buffer size for the Sorter configurable
## What changes were proposed in this pull request?

Currently the initial buffer size in the sorter is hard coded inside the code and is too small for large workload. As a result, the sorter spends significant time expanding the buffer size and copying the data. It would be useful to have it configurable.

## How was this patch tested?

Tested by running a job on the cluster.

Author: Sital Kedia <skedia@fb.com>

Closes #13699 from sitalkedia/config_sort_buffer_upstream.
2016-06-25 09:13:39 +01:00
Liwei Lin a4851ed050 [SPARK-15963][CORE] Catch TaskKilledException correctly in Executor.TaskRunner
## The problem

Before this change, if either of the following cases happened to a task , the task would be marked as `FAILED` instead of `KILLED`:
- the task was killed before it was deserialized
- `executor.kill()` marked `taskRunner.killed`, but before calling `task.killed()` the worker thread threw the `TaskKilledException`

The reason is, in the `catch` block of the current [Executor.TaskRunner](https://github.com/apache/spark/blob/master/core/src/main/scala/org/apache/spark/executor/Executor.scala#L362)'s implementation, we are mistakenly catching:
```scala
case _: TaskKilledException | _: InterruptedException if task.killed => ...
```
the semantics of which is:
- **(**`TaskKilledException` **OR** `InterruptedException`**)** **AND** `task.killed`

Then when `TaskKilledException` is thrown but `task.killed` is not marked, we would mark the task as `FAILED` (which should really be `KILLED`).

## What changes were proposed in this pull request?

This patch alters the catch condition's semantics from:
- **(**`TaskKilledException` **OR** `InterruptedException`**)** **AND** `task.killed`

to

- `TaskKilledException` **OR** **(**`InterruptedException` **AND** `task.killed`**)**

so that we can catch `TaskKilledException` correctly and mark the task as `KILLED` correctly.

## How was this patch tested?

Added unit test which failed before the change, ran new test 1000 times manually

Author: Liwei Lin <lwlin7@gmail.com>

Closes #13685 from lw-lin/fix-task-killed.
2016-06-24 10:09:04 -05:00
Sean Owen 158af162ea [SPARK-16129][CORE][SQL] Eliminate direct use of commons-lang classes in favor of commons-lang3
## What changes were proposed in this pull request?

Replace use of `commons-lang` in favor of `commons-lang3` and forbid the former via scalastyle; remove `NotImplementedException` from `comons-lang` in favor of JDK `UnsupportedOperationException`

## How was this patch tested?

Jenkins tests

Author: Sean Owen <sowen@cloudera.com>

Closes #13843 from srowen/SPARK-16129.
2016-06-24 10:35:54 +01:00
peng.zhang f4fd7432fb [SPARK-16125][YARN] Fix not test yarn cluster mode correctly in YarnClusterSuite
## What changes were proposed in this pull request?

Since SPARK-13220(Deprecate "yarn-client" and "yarn-cluster"), YarnClusterSuite doesn't test "yarn cluster" mode correctly.
This pull request fixes it.

## How was this patch tested?
Unit test

(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

Author: peng.zhang <peng.zhang@xiaomi.com>

Closes #13836 from renozhang/SPARK-16125-test-yarn-cluster-mode.
2016-06-24 08:28:32 +01:00
Ryan Blue 738f134bf4 [SPARK-13723][YARN] Change behavior of --num-executors with dynamic allocation.
## What changes were proposed in this pull request?

This changes the behavior of --num-executors and spark.executor.instances when using dynamic allocation. Instead of turning dynamic allocation off, it uses the value for the initial number of executors.

This changes was discussed on [SPARK-13723](https://issues.apache.org/jira/browse/SPARK-13723). I highly recommend using it while we can change the behavior for 2.0.0. In practice, the 1.x behavior causes unexpected behavior for users (it is not clear that it disables dynamic allocation) and wastes cluster resources because users rarely notice the log message.

## How was this patch tested?

This patch updates tests and adds a test for Utils.getDynamicAllocationInitialExecutors.

Author: Ryan Blue <blue@apache.org>

Closes #13338 from rdblue/SPARK-13723-num-executors-with-dynamic-allocation.
2016-06-23 14:03:46 -05:00
Dongjoon Hyun 5eef1e6c6a [SPARK-15660][CORE] Update RDD variance/stdev description and add popVariance/popStdev
## What changes were proposed in this pull request?

In Spark-11490, `variance/stdev` are redefined as the **sample** `variance/stdev` instead of population ones. This PR updates the other old documentations to prevent users from misunderstanding. This will update the following Scala/Java API docs.

- http://spark.apache.org/docs/2.0.0-preview/api/scala/index.html#org.apache.spark.api.java.JavaDoubleRDD
- http://spark.apache.org/docs/2.0.0-preview/api/scala/index.html#org.apache.spark.rdd.DoubleRDDFunctions
- http://spark.apache.org/docs/2.0.0-preview/api/scala/index.html#org.apache.spark.util.StatCounter
- http://spark.apache.org/docs/2.0.0-preview/api/java/org/apache/spark/api/java/JavaDoubleRDD.html
- http://spark.apache.org/docs/2.0.0-preview/api/java/org/apache/spark/rdd/DoubleRDDFunctions.html
- http://spark.apache.org/docs/2.0.0-preview/api/java/org/apache/spark/util/StatCounter.html

Also, this PR adds them `popVariance` and `popStdev` functions clearly.

## How was this patch tested?

Pass the updated Jenkins tests.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #13403 from dongjoon-hyun/SPARK-15660.
2016-06-23 11:07:34 +01:00
Prajwal Tuladhar 044971eca0 [SPARK-16131] initialize internal logger lazily in Scala preferred way
## What changes were proposed in this pull request?

Initialize logger instance lazily in Scala preferred way

## How was this patch tested?

By running `./build/mvn clean test` locally

Author: Prajwal Tuladhar <praj@infynyxx.com>

Closes #13842 from infynyxx/spark_internal_logger.
2016-06-22 16:30:10 -07:00
Eric Liang 6f915c9ec2 [SPARK-16003] SerializationDebugger runs into infinite loop
## What changes were proposed in this pull request?

This fixes SerializationDebugger to not recurse forever when `writeReplace` returns an object of the same class, which is the case for at least the `SQLMetrics` class.

See also the OpenJDK unit tests on the behavior of recursive `writeReplace()`:
f4d80957e8/test/java/io/Serializable/nestedReplace/NestedReplace.java

cc davies cloud-fan

## How was this patch tested?

Unit tests for SerializationDebugger.

Author: Eric Liang <ekl@databricks.com>

Closes #13814 from ericl/spark-16003.
2016-06-22 12:12:34 -07:00
Imran Rashid cf1995a976 [SPARK-15783][CORE] Fix Flakiness in BlacklistIntegrationSuite
## What changes were proposed in this pull request?

Three changes here -- first two were causing failures w/ BlacklistIntegrationSuite

1. The testing framework didn't include the reviveOffers thread, so the test which involved delay scheduling might never submit offers late enough for the delay scheduling to kick in.  So added in the periodic revive offers, just like the real scheduler.

2. `assertEmptyDataStructures` would occasionally fail, because it appeared there was still an active job.  This is because in DAGScheduler, the jobWaiter is notified of the job completion before the data structures are cleaned up.  Most of the time the test code that is waiting on the jobWaiter won't become active until after the data structures are cleared, but occasionally the race goes the other way, and the assertions fail.

3. `DAGSchedulerSuite` was not stopping all the inner parts it was setting up, so each test was leaking a number of threads.  So we stop those parts too.

4. Turns out that `assertMapOutputAvailable` is not terribly useful in this framework -- most of the places I was trying to use it suffer from some race.

5. When there is an exception in the backend, try to improve the error msg a little bit.  Before the exception was printed to the console, but the test would fail w/ a timeout, and the logs wouldn't show anything.

## How was this patch tested?

I ran all the tests in `BlacklistIntegrationSuite` 5k times and everything in `DAGSchedulerSuite` 1k times on my laptop.  Also I ran a full jenkins build with `BlacklistIntegrationSuite` 500 times and `DAGSchedulerSuite` 50 times, see https://github.com/apache/spark/pull/13548.  (I tried more times but jenkins timed out.)

To check for more leaked threads, I added some code to dump the list of all threads at the end of each test in DAGSchedulerSuite, which is how I discovered the mapOutputTracker and eventLoop were leaking threads.  (I removed that code from the final pr, just part of the testing.)

And I'll run Jenkins on this a couple of times to do one more check.

Author: Imran Rashid <irashid@cloudera.com>

Closes #13565 from squito/blacklist_extra_tests.
2016-06-22 08:35:41 -05:00
Shixiong Zhu c399c7f0e4 [SPARK-16002][SQL] Sleep when no new data arrives to avoid 100% CPU usage
## What changes were proposed in this pull request?

Add a configuration to allow people to set a minimum polling delay when no new data arrives (default is 10ms). This PR also cleans up some INFO logs.

## How was this patch tested?

Existing unit tests.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #13718 from zsxwing/SPARK-16002.
2016-06-21 12:42:49 -07:00
hyukjinkwon 4f7f1c4362 [SPARK-16044][SQL] input_file_name() returns empty strings in data sources based on NewHadoopRDD
## What changes were proposed in this pull request?

This PR makes `input_file_name()` function return the file paths not empty strings for external data sources based on `NewHadoopRDD`, such as [spark-redshift](cba5eee1ab/src/main/scala/com/databricks/spark/redshift/RedshiftRelation.scala (L149)) and [spark-xml](https://github.com/databricks/spark-xml/blob/master/src/main/scala/com/databricks/spark/xml/util/XmlFile.scala#L39-L47).

The codes with the external data sources below:

```scala
df.select(input_file_name).show()
```

will produce

- **Before**
  ```
+-----------------+
|input_file_name()|
+-----------------+
|                 |
+-----------------+
```

- **After**
  ```
+--------------------+
|   input_file_name()|
+--------------------+
|file:/private/var...|
+--------------------+
```

## How was this patch tested?

Unit tests in `ColumnExpressionSuite`.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #13759 from HyukjinKwon/SPARK-16044.
2016-06-20 21:55:34 -07:00
Shixiong Zhu 62d8fe2089 [SPARK-16017][CORE] Send hostname from CoarseGrainedExecutorBackend to driver
## What changes were proposed in this pull request?

[SPARK-15395](https://issues.apache.org/jira/browse/SPARK-15395) changes the behavior that how the driver gets the executor host and the driver will get the executor IP address instead of the host name. This PR just sends the hostname from executors to driver so that driver can pass it to TaskScheduler.

## How was this patch tested?

Existing unit tests.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #13741 from zsxwing/SPARK-16017.
2016-06-17 15:48:17 -07:00
Kay Ousterhout c8809db5a5 [SPARK-15926] Improve readability of DAGScheduler stage creation methods
## What changes were proposed in this pull request?

This pull request refactors parts of the DAGScheduler to improve readability, focusing on the code around stage creation.  One goal of this change it to make it clearer which functions may create new stages (as opposed to looking up stages that already exist).  There are no functionality changes in this pull request.  In more detail:

* shuffleToMapStage was renamed to shuffleIdToMapStage (when reading the existing code I have sometimes struggled to remember what the key is -- is it a stage? A stage id? This change is intended to avoid that confusion)
* Cleaned up the code to create shuffle map stages.  Previously, creating a shuffle map stage involved 3 different functions (newOrUsedShuffleStage, newShuffleMapStage, and getShuffleMapStage), and it wasn't clear what the purpose of each function was.  With the new code, a single function (getOrCreateShuffleMapStage) is responsible for getting a stage (if it already exists) or creating new shuffle map stages and any missing ancestor stages, and it delegates to createShuffleMapStage when new stages need to be created.  There's some remaining confusion here because the getOrCreateParentStages call in createShuffleMapStage may recursively create ancestor stages; this is an issue I plan to fix in a future pull request, because it's trickier to fix and involves a slight functionality change.
* newResultStage was renamed to createResultStage, for consistency with naming around shuffle map stages.
* getParentStages has been renamed to getOrCreateParentStages, to make it clear that this function will sometimes create missing ancestor stages.
* The only *slight* functionality change is that on line 478, updateJobIdStageIdMaps now uses a stage's parents instance variable rather than re-calculating them (I couldn't see any reason why they'd need to be re-calculated, and suspect this is just leftover from older code).
* getAncestorShuffleDependencies was renamed to getMissingAncestorShuffleDependencies, to make it clear that this only returns dependencies that have not yet been run.

cc squito markhamstra JoshRosen (who requested more DAG scheduler commenting long ago -- an issue this pull request tries, in part, to address)

FYI rxin

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #13677 from kayousterhout/SPARK-15926.
2016-06-17 12:12:46 -07:00
Nezih Yigitbasi 63470afc99 [SPARK-15782][YARN] Fix spark.jars and spark.yarn.dist.jars handling
When `--packages` is specified with spark-shell the classes from those packages cannot be found, which I think is due to some of the changes in SPARK-12343.

Tested manually with both scala 2.10 and 2.11 repls.

vanzin davies can you guys please review?

Author: Marcelo Vanzin <vanzin@cloudera.com>
Author: Nezih Yigitbasi <nyigitbasi@netflix.com>

Closes #13709 from nezihyigitbasi/SPARK-15782.
2016-06-16 18:20:16 -07:00
Alex Bozarth e849285df0 [SPARK-15868][WEB UI] Executors table in Executors tab should sort Executor IDs in numerical order
## What changes were proposed in this pull request?

Currently the Executors table sorts by id using a string sort (since that's what it is stored as). Since  the id is a number (other than the driver) we should be sorting numerically. I have changed both the initial sort on page load as well as the table sort to sort on id numerically, treating non-numeric strings (like the driver) as "-1"

## How was this patch tested?

Manually tested and dev/run-tests

![pageload](https://cloud.githubusercontent.com/assets/13952758/16027882/d32edd0a-318e-11e6-9faf-fc972b7c36ab.png)
![sorted](https://cloud.githubusercontent.com/assets/13952758/16027883/d34541c6-318e-11e6-9ed7-6bfc0cd4152e.png)

Author: Alex Bozarth <ajbozart@us.ibm.com>

Closes #13654 from ajbozarth/spark15868.
2016-06-16 14:29:11 -07:00
Sean Owen 457126e420 [SPARK-15796][CORE] Reduce spark.memory.fraction default to avoid overrunning old gen in JVM default config
## What changes were proposed in this pull request?

Reduce `spark.memory.fraction` default to 0.6 in order to make it fit within default JVM old generation size (2/3 heap). See JIRA discussion. This means a full cache doesn't spill into the new gen. CC andrewor14

## How was this patch tested?

Jenkins tests.

Author: Sean Owen <sowen@cloudera.com>

Closes #13618 from srowen/SPARK-15796.
2016-06-16 23:04:10 +02:00
Narine Kokhlikyan 7c6c692637 [SPARK-12922][SPARKR][WIP] Implement gapply() on DataFrame in SparkR
## What changes were proposed in this pull request?

gapply() applies an R function on groups grouped by one or more columns of a DataFrame, and returns a DataFrame. It is like GroupedDataSet.flatMapGroups() in the Dataset API.

Please, let me know what do you think and if you have any ideas to improve it.

Thank you!

## How was this patch tested?
Unit tests.
1. Primitive test with different column types
2. Add a boolean column
3. Compute average by a group

Author: Narine Kokhlikyan <narine.kokhlikyan@gmail.com>
Author: NarineK <narine.kokhlikyan@us.ibm.com>

Closes #12836 from NarineK/gapply2.
2016-06-15 21:42:05 -07:00
Reynold Xin 5a52ba0f95 [SPARK-15851][BUILD] Fix the call of the bash script to enable proper run in Windows
## What changes were proposed in this pull request?
The way bash script `build/spark-build-info` is called from core/pom.xml prevents Spark building on Windows. Instead of calling the script directly we call bash and pass the script as an argument. This enables running it on Windows with bash installed which typically comes with Git.

This brings https://github.com/apache/spark/pull/13612 up-to-date and also addresses comments from the code review.

Closes #13612

## How was this patch tested?
I built manually (on a Mac) to verify it didn't break Mac compilation.

Author: Reynold Xin <rxin@databricks.com>
Author: avulanov <nashb@yandex.ru>

Closes #13691 from rxin/SPARK-15851.
2016-06-15 20:11:23 -07:00
Davies Liu a153e41c08 Revert "[SPARK-15782][YARN] Set spark.jars system property in client mode"
This reverts commit 4df8df5c2e.
2016-06-15 15:55:07 -07:00
Imran Rashid cafc696d09 [HOTFIX][CORE] fix flaky BasicSchedulerIntegrationTest
## What changes were proposed in this pull request?

SPARK-15927 exacerbated a race in BasicSchedulerIntegrationTest, so it went from very unlikely to fairly frequent.  The issue is that stage numbering is not completely deterministic, but these tests treated it like it was.  So turn off the tests.

## How was this patch tested?

on my laptop the test failed abotu 10% of the time before this change, and didn't fail in 500 runs after the change.

Author: Imran Rashid <irashid@cloudera.com>

Closes #13688 from squito/hotfix_basic_scheduler.
2016-06-15 16:44:18 -05:00
Nezih Yigitbasi 4df8df5c2e [SPARK-15782][YARN] Set spark.jars system property in client mode
## What changes were proposed in this pull request?

When `--packages` is specified with `spark-shell` the classes from those packages cannot be found, which I think is due to some of the changes in `SPARK-12343`. In particular `SPARK-12343` removes a line that sets the `spark.jars` system property in client mode, which is used by the repl main class to set the classpath.

## How was this patch tested?

Tested manually.

This system property is used by the repl to populate its classpath. If
this is not set properly the classes for external packages cannot be
found.

tgravescs vanzin as you may be familiar with this part of the code.

Author: Nezih Yigitbasi <nyigitbasi@netflix.com>

Closes #13527 from nezihyigitbasi/repl-fix.
2016-06-15 14:07:36 -07:00
Tejas Patil 279bd4aa5f [SPARK-15826][CORE] PipedRDD to allow configurable char encoding
## What changes were proposed in this pull request?

Link to jira which describes the problem: https://issues.apache.org/jira/browse/SPARK-15826

The fix in this PR is to allow users specify encoding in the pipe() operation. For backward compatibility,
keeping the default value to be system default.

## How was this patch tested?

Ran existing unit tests

Author: Tejas Patil <tejasp@fb.com>

Closes #13563 from tejasapatil/pipedrdd_utf8.
2016-06-15 12:03:00 -07:00
Liwei Lin 9b234b55d1 [SPARK-15518][CORE][FOLLOW-UP] Rename LocalSchedulerBackendEndpoint -> LocalSchedulerBackend
## What changes were proposed in this pull request?

This patch is a follow-up to https://github.com/apache/spark/pull/13288 completing the renaming:
 - LocalScheduler -> LocalSchedulerBackend~~Endpoint~~

## How was this patch tested?

Updated test cases to reflect the name change.

Author: Liwei Lin <lwlin7@gmail.com>

Closes #13683 from lw-lin/rename-backend.
2016-06-15 11:52:36 -07:00
Marcelo Vanzin 40eeef9525 [SPARK-15046][YARN] Parse value of token renewal interval correctly.
Use the config variable definition both to set and parse the value,
avoiding issues with code expecting the value in a different format.

Tested by running spark-submit with --principal / --keytab.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #13669 from vanzin/SPARK-15046.
2016-06-15 09:09:21 -05:00
Kay Ousterhout 5d50d4f0f9 [SPARK-15927] Eliminate redundant DAGScheduler code.
To try to eliminate redundant code to traverse the RDD dependency graph,
this PR creates a new function getShuffleDependencies that returns
shuffle dependencies that are immediate parents of a given RDD.  This
new function is used by getParentStages and
getAncestorShuffleDependencies.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #13646 from kayousterhout/SPARK-15927.
2016-06-14 17:27:01 -07:00
Sean Owen 6151d2641f [MINOR] Clean up several build warnings, mostly due to internal use of old accumulators
## What changes were proposed in this pull request?

Another PR to clean up recent build warnings. This particularly cleans up several instances of the old accumulator API usage in tests that are straightforward to update. I think this qualifies as "minor".

## How was this patch tested?

Jenkins

Author: Sean Owen <sowen@cloudera.com>

Closes #13642 from srowen/BuildWarnings.
2016-06-14 09:40:07 -07:00
Dongjoon Hyun 938434dc78 [SPARK-15913][CORE] Dispatcher.stopped should be enclosed by synchronized block.
## What changes were proposed in this pull request?

`Dispatcher.stopped` is guarded by `this`, but it is used without synchronization in `postMessage` function. This PR fixes this and also the exception message became more accurate.

## How was this patch tested?

Pass the existing Jenkins tests.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #13634 from dongjoon-hyun/SPARK-15913.
2016-06-13 10:30:17 -07:00
Sean Owen 0a6f090837 [SPARK-15876][CORE] Remove support for "zk://" master URL
## What changes were proposed in this pull request?

Remove deprecated support for `zk://` master (`mesos://zk//` remains supported)

## How was this patch tested?

Jenkins

Author: Sean Owen <sowen@cloudera.com>

Closes #13625 from srowen/SPARK-15876.
2016-06-12 11:46:33 -07:00
Sean Owen f51dfe616b [SPARK-15086][CORE][STREAMING] Deprecate old Java accumulator API
## What changes were proposed in this pull request?

- Deprecate old Java accumulator API; should use Scala now
- Update Java tests and examples
- Don't bother testing old accumulator API in Java 8 (too)
- (fix a misspelling too)

## How was this patch tested?

Jenkins tests

Author: Sean Owen <sowen@cloudera.com>

Closes #13606 from srowen/SPARK-15086.
2016-06-12 11:44:33 -07:00
bomeng 50248dcfff [SPARK-15806][DOCUMENTATION] update doc for SPARK_MASTER_IP
## What changes were proposed in this pull request?

SPARK_MASTER_IP is a deprecated environment variable. It is replaced by SPARK_MASTER_HOST according to MasterArguments.scala.

## How was this patch tested?

Manually verified.

Author: bomeng <bmeng@us.ibm.com>

Closes #13543 from bomeng/SPARK-15806.
2016-06-12 14:25:48 +01:00
Imran Rashid 8cc22b0085 [SPARK-15878][CORE][TEST] fix cleanup in EventLoggingListenerSuite and ReplayListenerSuite
## What changes were proposed in this pull request?

These tests weren't properly using `LocalSparkContext` so weren't cleaning up correctly when tests failed.

## How was this patch tested?

Jenkins.

Author: Imran Rashid <irashid@cloudera.com>

Closes #13602 from squito/SPARK-15878_cleanup_replaylistener.
2016-06-12 12:54:57 +01:00
Eric Liang e1f986c7a3 [SPARK-15860] Metrics for codegen size and perf
## What changes were proposed in this pull request?

Adds codahale metrics for the codegen source text size and how long it takes to compile. The size is particularly interesting, since the JVM does have hard limits on how large methods can get.

To simplify, I added the metrics under a statically-initialized source that is always registered with SparkEnv.

## How was this patch tested?

Unit tests

Author: Eric Liang <ekl@databricks.com>

Closes #13586 from ericl/spark-15860.
2016-06-11 23:16:21 -07:00
Eric Liang c06c58bbbb [SPARK-14851][CORE] Support radix sort with nullable longs
## What changes were proposed in this pull request?

This adds support for radix sort of nullable long fields. When a sort field is null and radix sort is enabled, we keep nulls in a separate region of the sort buffer so that radix sort does not need to deal with them. This also has performance benefits when sorting smaller integer types, since the current representation of nulls in two's complement (Long.MIN_VALUE) otherwise forces a full-width radix sort.

This strategy for nulls does mean the sort is no longer stable. cc davies

## How was this patch tested?

Existing randomized sort tests for correctness. I also tested some TPCDS queries and there does not seem to be any significant regression for non-null sorts.

Some test queries (best of 5 runs each).
Before change:
scala> val start = System.nanoTime; spark.range(5000000).selectExpr("if(id > 5, cast(hash(id) as long), NULL) as h").coalesce(1).orderBy("h").collect(); (System.nanoTime - start) / 1e6
start: Long = 3190437233227987
res3: Double = 4716.471091

After change:
scala> val start = System.nanoTime; spark.range(5000000).selectExpr("if(id > 5, cast(hash(id) as long), NULL) as h").coalesce(1).orderBy("h").collect(); (System.nanoTime - start) / 1e6
start: Long = 3190367870952791
res4: Double = 2981.143045

Author: Eric Liang <ekl@databricks.com>

Closes #13161 from ericl/sc-2998.
2016-06-11 15:42:58 -07:00
Sean Owen 3761330dd0 [SPARK-15879][DOCS][UI] Update logo in UI and docs to add "Apache"
## What changes were proposed in this pull request?

Use new Spark logo including "Apache" (now, with crushed PNGs). Remove old unreferenced logo files.

## How was this patch tested?

Manual check of generated HTML site and Spark UI. I searched for references to the deleted files to make sure they were not used.

Author: Sean Owen <sowen@cloudera.com>

Closes #13609 from srowen/SPARK-15879.
2016-06-11 12:46:07 +01:00
wangyang 026eb90644 [SPARK-15875] Try to use Seq.isEmpty and Seq.nonEmpty instead of Seq.length == 0 and Seq.length > 0
## What changes were proposed in this pull request?

In scala, immutable.List.length is an expensive operation so we should
avoid using Seq.length == 0 or Seq.lenth > 0, and use Seq.isEmpty and Seq.nonEmpty instead.

## How was this patch tested?
existing tests

Author: wangyang <wangyang@haizhi.com>

Closes #13601 from yangw1234/isEmpty.
2016-06-10 13:10:03 -07:00
Kay Ousterhout 5c16ad0d52 Revert [SPARK-14485][CORE] ignore task finished for executor lost
This reverts commit 695dbc816a.

This change is being reverted because it hurts performance of some jobs, and
only helps in a narrow set of cases.  For more discussion, refer to the JIRA.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #13580 from kayousterhout/revert-SPARK-14485.
2016-06-10 12:50:50 -07:00