Commit graph

6433 commits

Author SHA1 Message Date
Marcelo Vanzin c13b60e019 [SPARK-22533][CORE] Handle deprecated names in ConfigEntry.
This change hooks up the config reader to `SparkConf.getDeprecatedConfig`,
so that config constants with deprecated names generate the proper warnings.
It also changes two deprecated configs from the new "alternatives" system to
the old deprecation system, since they're not yet hooked up to each other.

Added a few unit tests to verify the desired behavior.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19760 from vanzin/SPARK-22533.
2017-11-20 12:45:21 +01:00
Kazuaki Ishizaki 3c3eebc873 [SPARK-20101][SQL] Use OffHeapColumnVector when "spark.sql.columnVector.offheap.enable" is set to "true"
This PR enables to use ``OffHeapColumnVector`` when ``spark.sql.columnVector.offheap.enable`` is set to ``true``. While ``ColumnVector`` has two implementations ``OnHeapColumnVector`` and ``OffHeapColumnVector``, only ``OnHeapColumnVector`` is always used.

This PR implements the followings
- Pass ``OffHeapColumnVector`` to ``ColumnarBatch.allocate()`` when ``spark.sql.columnVector.offheap.enable`` is set to ``true``
- Free all of off-heap memory regions by ``OffHeapColumnVector.close()``
- Ensure to call ``OffHeapColumnVector.close()``

Use existing tests

Author: Kazuaki Ishizaki <ishizaki@jp.ibm.com>

Closes #17436 from kiszk/SPARK-20101.
2017-11-20 12:40:26 +01:00
hyukjinkwon 57c5514de9 [SPARK-22554][PYTHON] Add a config to control if PySpark should use daemon or not for workers
## What changes were proposed in this pull request?

This PR proposes to add a flag to control if PySpark should use daemon or not.

Actually, SparkR already has a flag for useDaemon:
478fbc866f/core/src/main/scala/org/apache/spark/api/r/RRunner.scala (L362)

It'd be great if we have this flag too. It makes easier to debug Windows specific issue.

## How was this patch tested?

Manually tested.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #19782 from HyukjinKwon/use-daemon-flag.
2017-11-20 13:34:06 +09:00
Dongjoon Hyun b10837ab1a [SPARK-22557][TEST] Use ThreadSignaler explicitly
## What changes were proposed in this pull request?

ScalaTest 3.0 uses an implicit `Signaler`. This PR makes it sure all Spark tests uses `ThreadSignaler` explicitly which has the same default behavior of interrupting a thread on the JVM like ScalaTest 2.2.x. This will reduce potential flakiness.

## How was this patch tested?

This is testsuite-only update. This should passes the Jenkins tests.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #19784 from dongjoon-hyun/use_thread_signaler.
2017-11-20 13:32:01 +09:00
Li Jin 7d039e0c0a [SPARK-22409] Introduce function type argument in pandas_udf
## What changes were proposed in this pull request?

* Add a "function type" argument to pandas_udf.
* Add a new public enum class `PandasUdfType` in pyspark.sql.functions
* Refactor udf related code from pyspark.sql.functions to pyspark.sql.udf
* Merge "PythonUdfType" and "PythonEvalType" into a single enum class "PythonEvalType"

Example:
```
from pyspark.sql.functions import pandas_udf, PandasUDFType

pandas_udf('double', PandasUDFType.SCALAR):
def plus_one(v):
    return v + 1
```

## Design doc
https://docs.google.com/document/d/1KlLaa-xJ3oz28xlEJqXyCAHU3dwFYkFs_ixcUXrJNTc/edit

## How was this patch tested?

Added PandasUDFTests

## TODO:
* [x] Implement proper enum type for `PandasUDFType`
* [x] Update documentation
* [x] Add more tests in PandasUDFTests

Author: Li Jin <ice.xelloss@gmail.com>

Closes #19630 from icexelloss/spark-22409-pandas-udf-type.
2017-11-17 16:43:08 +01:00
yucai d00b55d4b2 [SPARK-22540][SQL] Ensure HighlyCompressedMapStatus calculates correct avgSize
## What changes were proposed in this pull request?

Ensure HighlyCompressedMapStatus calculates correct avgSize

## How was this patch tested?

New unit test added.

Author: yucai <yucai.yu@intel.com>

Closes #19765 from yucai/avgsize.
2017-11-17 07:53:53 -06:00
Shixiong Zhu 03f2b7bff7 [SPARK-22535][PYSPARK] Sleep before killing the python worker in PythonRunner.MonitorThread
## What changes were proposed in this pull request?

`PythonRunner.MonitorThread` should give the task a little time to finish before forcibly killing the python worker. This will reduce the chance of the race condition a lot. I also improved the log a bit to find out the task to blame when it's stuck.

## How was this patch tested?

Jenkins

Author: Shixiong Zhu <zsxwing@gmail.com>

Closes #19762 from zsxwing/SPARK-22535.
2017-11-16 14:22:25 +09:00
ArtRand 1e82335413 [SPARK-21842][MESOS] Support Kerberos ticket renewal and creation in Mesos
## What changes were proposed in this pull request?
tl;dr: Add a class, `MesosHadoopDelegationTokenManager` that updates delegation tokens on a schedule on the behalf of Spark Drivers. Broadcast renewed credentials to the executors.

## The problem
We recently added Kerberos support to Mesos-based Spark jobs as well as Secrets support to the Mesos Dispatcher (SPARK-16742, SPARK-20812, respectively). However the delegation tokens have a defined expiration. This poses a problem for long running Spark jobs (e.g. Spark Streaming applications). YARN has a solution for this where a thread is scheduled to renew the tokens they reach 75% of their way to expiration. It then writes the tokens to HDFS for the executors to find (uses a monotonically increasing suffix).

## This solution
We replace the current method in `CoarseGrainedSchedulerBackend` which used to discard the token renewal time with a protected method `fetchHadoopDelegationTokens`. Now the individual cluster backends are responsible for overriding this method to fetch and manage token renewal. The delegation tokens themselves, are still part of the `CoarseGrainedSchedulerBackend` as before.
In the case of Mesos renewed Credentials are broadcasted to the executors. This maintains all transfer of Credentials within Spark (as opposed to Spark-to-HDFS). It also does not require any writing of Credentials to disk. It also does not require any GC of old files.

## How was this patch tested?
Manually against a Kerberized HDFS cluster.

Thank you for the reviews.

Author: ArtRand <arand@soe.ucsc.edu>

Closes #19272 from ArtRand/spark-21842-450-kerberos-ticket-renewal.
2017-11-15 15:53:05 -08:00
osatici 2014e7a789 [SPARK-22479][SQL] Exclude credentials from SaveintoDataSourceCommand.simpleString
## What changes were proposed in this pull request?

Do not include jdbc properties which may contain credentials in logging a logical plan with `SaveIntoDataSourceCommand` in it.

## How was this patch tested?

building locally and trying to reproduce (per the steps in https://issues.apache.org/jira/browse/SPARK-22479):
```
== Parsed Logical Plan ==
SaveIntoDataSourceCommand org.apache.spark.sql.execution.datasources.jdbc.JdbcRelationProvider570127fa, Map(dbtable -> test20, driver -> org.postgresql.Driver, url -> *********(redacted), password -> *********(redacted)), ErrorIfExists
   +- Range (0, 100, step=1, splits=Some(8))

== Analyzed Logical Plan ==
SaveIntoDataSourceCommand org.apache.spark.sql.execution.datasources.jdbc.JdbcRelationProvider570127fa, Map(dbtable -> test20, driver -> org.postgresql.Driver, url -> *********(redacted), password -> *********(redacted)), ErrorIfExists
   +- Range (0, 100, step=1, splits=Some(8))

== Optimized Logical Plan ==
SaveIntoDataSourceCommand org.apache.spark.sql.execution.datasources.jdbc.JdbcRelationProvider570127fa, Map(dbtable -> test20, driver -> org.postgresql.Driver, url -> *********(redacted), password -> *********(redacted)), ErrorIfExists
   +- Range (0, 100, step=1, splits=Some(8))

== Physical Plan ==
Execute SaveIntoDataSourceCommand
   +- SaveIntoDataSourceCommand org.apache.spark.sql.execution.datasources.jdbc.JdbcRelationProvider570127fa, Map(dbtable -> test20, driver -> org.postgresql.Driver, url -> *********(redacted), password -> *********(redacted)), ErrorIfExists
         +- Range (0, 100, step=1, splits=Some(8))
```

Author: osatici <osatici@palantir.com>

Closes #19708 from onursatici/os/redact-jdbc-creds.
2017-11-15 14:08:51 -08:00
Marcelo Vanzin 39b3f10dda [SPARK-20649][CORE] Simplify REST API resource structure.
With the new UI store, the API resource classes have a lot less code,
since there's no need for complicated translations between the UI
types and the API types. So the code ended up with a bunch of files
with a single method declared in them.

This change re-structures the API code so that it uses less classes;
mainly, most sub-resources were removed, and the code to deal with
single-attempt and multi-attempt apps was simplified.

The only change was the addition of a method to return a single
attempt's information; that was missing in the old API, so trying
to retrieve "/v1/applications/appId/attemptId" would result in a
404 even if the attempt existed (and URIs under that one would
return valid data).

The streaming API resources also overtook the same treatment, even
though the data is not stored in the new UI store.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19748 from vanzin/SPARK-20649.
2017-11-15 15:41:53 -06:00
Marcelo Vanzin 0ffa7c488f [SPARK-20652][SQL] Store SQL UI data in the new app status store.
This change replaces the SQLListener with a new implementation that
saves the data to the same store used by the SparkContext's status
store. For that, the types used by the old SQLListener had to be
updated a bit so that they're more serialization-friendly.

The interface for getting data from the store was abstracted into
a new class, SQLAppStatusStore (following the convention used in
core).

Another change is the way that the SQL UI hooks up into the core
UI or the SHS. The old "SparkHistoryListenerFactory" was replaced
with a new "AppStatePlugin" that more explicitly differentiates
between the two use cases: processing events, and showing the UI.
Both live apps and the SHS use this new API (previously, it was
restricted to the SHS).

Note on the above: this causes a slight change of behavior for
live apps; the SQL tab will only show up after the first execution
is started.

The metrics gathering code was re-worked a bit so that the types
used are less memory hungry and more serialization-friendly. This
reduces memory usage when using in-memory stores, and reduces load
times when using disk stores.

Tested with existing and added unit tests. Note one unit test was
disabled because it depends on SPARK-20653, which isn't in yet.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19681 from vanzin/SPARK-20652.
2017-11-14 15:28:22 -06:00
Marcelo Vanzin 4741c07809 [SPARK-20648][CORE] Port JobsTab and StageTab to the new UI backend.
This change is a little larger because there's a whole lot of logic
behind these pages, all really tied to internal types and listeners,
and some of that logic had to be implemented in the new listener and
the needed data exposed through the API types.

- Added missing StageData and ExecutorStageSummary fields which are
  used by the UI. Some json golden files needed to be updated to account
  for new fields.

- Save RDD graph data in the store. This tries to re-use existing types as
  much as possible, so that the code doesn't need to be re-written. So it's
  probably not very optimal.

- Some old classes (e.g. JobProgressListener) still remain, since they're used
  in other parts of the code; they're not used by the UI anymore, though, and
  will be cleaned up in a separate change.

- Save information about active pools in the store. This data is not really used
  in the SHS, but it's not a lot of data so it's still recorded when replaying
  applications.

- Because the new store sorts things slightly differently from the previous
  code, some json golden files had some elements within them shuffled around.

- The retention unit test in UISeleniumSuite was disabled because the code
  to throw away old stages / tasks hasn't been added yet.

- The job description field in the API tries to follow the old behavior, which
  makes it be empty most of the time, even though there's information to fill it
  in. For stages, a new field was added to hold the description (which is basically
  the job description), so that the UI can be rendered in the old way.

- A new stage status ("SKIPPED") was added to account for the fact that the API
  couldn't represent that state before. Without this, the stage would show up as
  "PENDING" in the UI, which is now based on API types.

- The API used to expose "executorRunTime" as the value of the task's duration,
  which wasn't really correct (also because that value was easily available
  from the metrics object); this change fixes that by storing the correct duration,
  which also means a few expectation files needed to be updated to account for
  the new durations and sorting differences due to the changed values.

- Added changes to implement SPARK-20713 and SPARK-21922 in the new code.

Tested with existing unit tests (and by using the UI a lot).

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19698 from vanzin/SPARK-20648.
2017-11-14 10:34:32 -06:00
Xianyang Liu 176ae4d53e [MINOR][CORE] Using bufferedInputStream for dataDeserializeStream
## What changes were proposed in this pull request?

Small fix. Using bufferedInputStream for dataDeserializeStream.

## How was this patch tested?

Existing UT.

Author: Xianyang Liu <xianyang.liu@intel.com>

Closes #19735 from ConeyLiu/smallfix.
2017-11-13 06:19:13 -06:00
Xianyang Liu 1c923d7d65 [SPARK-22450][CORE][MLLIB] safely register class for mllib
## What changes were proposed in this pull request?

There are still some algorithms based on mllib, such as KMeans. For now, many mllib common class (such as: Vector, DenseVector, SparseVector, Matrix, DenseMatrix, SparseMatrix) are not registered in Kryo. So there are some performance issues for those object serialization or deserialization.
Previously dicussed: https://github.com/apache/spark/pull/19586

## How was this patch tested?

New test case.

Author: Xianyang Liu <xianyang.liu@intel.com>

Closes #19661 from ConeyLiu/register_vector.
2017-11-10 12:43:29 +01:00
Nathan Kronenfeld b57ed2245c [SPARK-22308][TEST-MAVEN] Support alternative unit testing styles in external applications
Continuation of PR#19528 (https://github.com/apache/spark/pull/19529#issuecomment-340252119)

The problem with the maven build in the previous PR was the new tests.... the creation of a spark session outside the tests meant there was more than one spark session around at a time.
I was using the spark session outside the tests so that the tests could share data; I've changed it so that each test creates the data anew.

Author: Nathan Kronenfeld <nicole.oresme@gmail.com>
Author: Nathan Kronenfeld <nkronenfeld@uncharted.software>

Closes #19705 from nkronenfeld/alternative-style-tests-2.
2017-11-09 19:11:30 -08:00
Srinivasa Reddy Vundela 9eb7096c47 [SPARK-22483][CORE] Exposing java.nio bufferedPool memory metrics to Metric System
## What changes were proposed in this pull request?

Adds java.nio bufferedPool memory metrics to metrics system which includes both direct and mapped memory.

## How was this patch tested?
Manually tested and checked direct and mapped memory metrics too available in metrics system using Console sink.

Here is the sample console output

application_1509655862825_0016.2.jvm.direct.capacity
             value = 19497
application_1509655862825_0016.2.jvm.direct.count
             value = 6
application_1509655862825_0016.2.jvm.direct.used
             value = 19498

application_1509655862825_0016.2.jvm.mapped.capacity
             value = 0
application_1509655862825_0016.2.jvm.mapped.count
             value = 0
application_1509655862825_0016.2.jvm.mapped.used
             value = 0

Author: Srinivasa Reddy Vundela <vsr@cloudera.com>

Closes #19709 from vundela/SPARK-22483.
2017-11-09 16:05:47 -08:00
Marcelo Vanzin 6ae12715c7 [SPARK-20647][CORE] Port StorageTab to the new UI backend.
This required adding information about StreamBlockId to the store,
which is not available yet via the API. So an internal type was added
until there's a need to expose that information in the API.

The UI only lists RDDs that have cached partitions, and that information
wasn't being correctly captured in the listener, so that's also fixed,
along with some minor (internal) API adjustments so that the UI can
get the correct data.

Because of the way partitions are cached, some optimizations w.r.t. how
often the data is flushed to the store could not be applied to this code;
because of that, some different ways to make the code more performant
were added to the data structures tracking RDD blocks, with the goal of
avoiding expensive copies when lots of blocks are being updated.

Tested with existing and updated unit tests.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19679 from vanzin/SPARK-20647.
2017-11-09 15:46:16 -06:00
Srinivasa Reddy Vundela 6b19c0735d [MINOR][CORE] Fix nits in MetricsSystemSuite
## What changes were proposed in this pull request?
Fixing nits in MetricsSystemSuite file
1) Using Sink instead of Source while casting
2) Using meaningful naming for variables, which reflect their usage

## How was this patch tested?
Ran the tests locally and all of them passing

Author: Srinivasa Reddy Vundela <vsr@cloudera.com>

Closes #19699 from vundela/master.
2017-11-09 09:53:41 -08:00
Sean Owen 51debf8b1f [SPARK-14540][BUILD] Support Scala 2.12 closures and Java 8 lambdas in ClosureCleaner (step 0)
## What changes were proposed in this pull request?

Preliminary changes to get ClosureCleaner to work with Scala 2.12. Makes many usages just work, but not all. This does _not_ resolve the JIRA.

## How was this patch tested?

Existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #19675 from srowen/SPARK-14540.0.
2017-11-08 10:24:40 +00:00
Marcelo Vanzin 11eea1a4ce [SPARK-20646][CORE] Port executors page to new UI backend.
The executors page is built on top of the REST API, so the page itself
was easy to hook up to the new code.

Some other pages depend on the `ExecutorListener` class that is being
removed, though, so they needed to be modified to use data from the
new store. Fortunately, all they seemed to need is the map of executor
logs, so that was somewhat easy too.

The executor timeline graph required adding some properties to the
ExecutorSummary API type. Instead of following the previous code,
which stored all the listener events in memory, the timeline is
now created based on the data available from the API.

I had to change some of the test golden files because the old code would
return executors in "random" order (since it used a mutable Map instead
of something that returns a sorted list), and the new code returns executors
in id order.

Tested with existing unit tests.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19678 from vanzin/SPARK-20646.
2017-11-07 23:14:29 -06:00
Marcelo Vanzin 7475a9655c [SPARK-20645][CORE] Port environment page to new UI backend.
This change modifies the status listener to collect the information
needed to render the envionment page, and populates that page and the
API with information collected by the listener.

Tested with existing and added unit tests.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19677 from vanzin/SPARK-20645.
2017-11-07 16:03:24 -06:00
Alexander Istomin 14a32a647a [SPARK-22330][CORE] Linear containsKey operation for serialized maps
…alization.

## What changes were proposed in this pull request?

Use non-linear containsKey operation for serialized maps, lookup into underlying map.

## How was this patch tested?

unit tests

Author: Alexander Istomin <istomin@rutarget.ru>

Closes #19553 from Whoosh/SPARK-22330.
2017-11-07 00:47:16 +01:00
Marcelo Vanzin c7f38e5adb [SPARK-20644][core] Initial ground work for kvstore UI backend.
There are two somewhat unrelated things going on in this patch, but
both are meant to make integration of individual UI pages later on
much easier.

The first part is some tweaking of the code in the listener so that
it does less updates of the kvstore for data that changes fast; for
example, it avoids writing changes down to the store for every
task-related event, since those can arrive very quickly at times.
Instead, for these kinds of events, it chooses to only flush things
if a certain interval has passed. The interval is based on how often
the current spark-shell code updates the progress bar for jobs, so
that users can get reasonably accurate data.

The code also delays as much as possible hitting the underlying kvstore
when replaying apps in the history server. This is to avoid unnecessary
writes to disk.

The second set of changes prepare the history server and SparkUI for
integrating with the kvstore. A new class, AppStatusStore, is used
for translating between the stored data and the types used in the
UI / API. The SHS now populates a kvstore with data loaded from
event logs when an application UI is requested.

Because this store can hold references to disk-based resources, the
code was modified to retrieve data from the store under a read lock.
This allows the SHS to detect when the store is still being used, and
only update it (e.g. because an updated event log was detected) when
there is no other thread using the store.

This change ended up creating a lot of churn in the ApplicationCache
code, which was cleaned up a lot in the process. I also removed some
metrics which don't make too much sense with the new code.

Tested with existing and added unit tests, and by making sure the SHS
still works on a real cluster.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19582 from vanzin/SPARK-20644.
2017-11-06 08:45:40 -06:00
Kazuaki Ishizaki bc1e101039 [SPARK-22254][CORE] Fix the arrayMax in BufferHolder
## What changes were proposed in this pull request?

This PR replaces the old the maximum array size (`Int.MaxValue`) with the new one (`ByteArrayMethods.MAX_ROUNDED_ARRAY_LENGTH`).
This PR also refactor the code to calculate the new array size to easily understand why we have to use `newSize - 2` for allocating a new array.

## How was this patch tested?

Used the existing test

Author: Kazuaki Ishizaki <ishizaki@jp.ibm.com>

Closes #19650 from kiszk/SPARK-22254.
2017-11-03 23:35:57 -07:00
zhoukang 51145f1376 [SPARK-22407][WEB-UI] Add rdd id column on storage page to speed up navigating
## What changes were proposed in this pull request?

Add rdd id column on storage page to speed up navigating.
Example has attached on [SPARK-22407](https://issues.apache.org/jira/browse/SPARK-22407)
An example below:
![add-rddid](https://user-images.githubusercontent.com/26762018/32361127-da0758ac-c097-11e7-9f8c-0ea7ffb87e12.png)
![rdd-cache](https://user-images.githubusercontent.com/26762018/32361128-da3c1574-c097-11e7-8ab1-2def66466f33.png)
## How was this patch tested?

Current unit test and manually deploy an history server for testing

Author: zhoukang <zhoukang199191@gmail.com>

Closes #19625 from caneGuy/zhoukang/add-rddid.
2017-11-03 12:20:17 +00:00
Stavros Kontopoulos b2463fad71 [SPARK-22145][MESOS] fix supervise with checkpointing on mesos
## What changes were proposed in this pull request?

- Fixes the issue with the frameworkId being recovered by checkpointed data overwriting the one sent by the dipatcher.
- Keeps submission driver id as the only index for all data structures in the dispatcher.
Allocates a different task id per driver retry to satisfy the mesos requirements. Check the relevant ticket for the details on that.
## How was this patch tested?

Manually tested this with DC/OS 1.10. Launched a streaming job with checkpointing to hdfs, made the driver fail several times and observed behavior:
![image](https://user-images.githubusercontent.com/7945591/30940500-f7d2a744-a3e9-11e7-8c56-f2ccbb271e80.png)

![image](https://user-images.githubusercontent.com/7945591/30940550-19bc15de-a3ea-11e7-8a11-f48abfe36720.png)

![image](https://user-images.githubusercontent.com/7945591/30940524-083ea308-a3ea-11e7-83ae-00d3fa17b928.png)

![image](https://user-images.githubusercontent.com/7945591/30940579-2f0fb242-a3ea-11e7-82f9-86179da28b8c.png)

![image](https://user-images.githubusercontent.com/7945591/30940591-3b561b0e-a3ea-11e7-9dbd-e71912bb2ef3.png)

![image](https://user-images.githubusercontent.com/7945591/30940605-49c810ca-a3ea-11e7-8af5-67930851fd38.png)

![image](https://user-images.githubusercontent.com/7945591/30940631-59f4a288-a3ea-11e7-88cb-c3741b72bb13.png)

![image](https://user-images.githubusercontent.com/7945591/30940642-62346c9e-a3ea-11e7-8935-82e494925f67.png)

![image](https://user-images.githubusercontent.com/7945591/30940653-6c46d53c-a3ea-11e7-8dd1-5840d484d28c.png)

Author: Stavros Kontopoulos <st.kontopoulos@gmail.com>

Closes #19374 from skonto/fix_retry.
2017-11-02 13:25:48 +00:00
LucaCanali 1ffe03d9e8 [SPARK-22190][CORE] Add Spark executor task metrics to Dropwizard metrics
## What changes were proposed in this pull request?

This proposed patch is about making Spark executor task metrics available as Dropwizard metrics. This is intended to be of aid in monitoring Spark jobs and when drilling down on performance troubleshooting issues.

## How was this patch tested?

Manually tested on a Spark cluster (see JIRA for an example screenshot).

Author: LucaCanali <luca.canali@cern.ch>

Closes #19426 from LucaCanali/SparkTaskMetricsDropWizard.
2017-11-01 15:40:25 +01:00
Sital Kedia 444bce1c98 [SPARK-19112][CORE] Support for ZStandard codec
## What changes were proposed in this pull request?

Using zstd compression for Spark jobs spilling 100s of TBs of data, we could reduce the amount of data written to disk by as much as 50%. This translates to significant latency gain because of reduced disk io operations. There is a degradation CPU time by 2 - 5% because of zstd compression overhead, but for jobs which are bottlenecked by disk IO, this hit can be taken.

## Benchmark
Please note that this benchmark is using real world compute heavy production workload spilling TBs of data to disk

|         | zstd performance as compred to LZ4   |
| ------------- | -----:|
| spill/shuffle bytes    | -48% |
| cpu time    |    + 3% |
| cpu reservation time       |    -40%|
| latency     |     -40% |

## How was this patch tested?

Tested by running few jobs spilling large amount of data on the cluster and amount of intermediate data written to disk reduced by as much as 50%.

Author: Sital Kedia <skedia@fb.com>

Closes #18805 from sitalkedia/skedia/upstream_zstd.
2017-11-01 14:54:08 +01:00
Devaraj K 96798d14f0 [SPARK-22172][CORE] Worker hangs when the external shuffle service port is already in use
## What changes were proposed in this pull request?

Handling the NonFatal exceptions while starting the external shuffle service, if there are any NonFatal exceptions it logs and continues without the external shuffle service.

## How was this patch tested?

I verified it manually, it logs the exception and continues to serve without external shuffle service when BindException occurs.

Author: Devaraj K <devaraj@apache.org>

Closes #19396 from devaraj-kavali/SPARK-22172.
2017-11-01 18:07:39 +08:00
Zheng RuiFeng 556b5d2151 [SPARK-5484][FOLLOWUP] PeriodicRDDCheckpointer doc cleanup
## What changes were proposed in this pull request?
PeriodicRDDCheckpointer was already moved out of mllib in Spark-5484

## How was this patch tested?
existing tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #19618 from zhengruifeng/checkpointer_doc.
2017-11-01 08:45:11 +00:00
Sital Kedia 7986cc09b1 [SPARK-11334][CORE] Fix bug in Executor allocation manager in running tasks calculation
## What changes were proposed in this pull request?

We often see the issue of Spark jobs stuck because the Executor Allocation Manager does not ask for any executor even if there are pending tasks in case dynamic allocation is turned on. Looking at the logic in Executor Allocation Manager, which calculates the running tasks, it can happen that the calculation will be wrong and the number of running tasks can become negative.

## How was this patch tested?

Added unit test

Author: Sital Kedia <skedia@fb.com>

Closes #19580 from sitalkedia/skedia/fix_stuck_job.
2017-10-31 09:49:58 -07:00
Wenchen Fan 079a2609d7 [SPARK-17788][SPARK-21033][SQL] fix the potential OOM in UnsafeExternalSorter and ShuffleExternalSorter
## What changes were proposed in this pull request?

In `UnsafeInMemorySorter`, one record may take 32 bytes: 1 `long` for pointer, 1 `long` for key-prefix, and another 2 `long`s as the temporary buffer for radix sort.

In `UnsafeExternalSorter`, we set the `DEFAULT_NUM_ELEMENTS_FOR_SPILL_THRESHOLD` to be `1024 * 1024 * 1024 / 2`, and hoping the max size of point array to be 8 GB. However this is wrong, `1024 * 1024 * 1024 / 2 * 32` is actually 16 GB, and if we grow the point array before reach this limitation, we may hit the max-page-size error.

Users may see exception like this on large dataset:
```
Caused by: java.lang.IllegalArgumentException: Cannot allocate a page with more than 17179869176 bytes
at org.apache.spark.memory.TaskMemoryManager.allocatePage(TaskMemoryManager.java:241)
at org.apache.spark.memory.MemoryConsumer.allocatePage(MemoryConsumer.java:121)
at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter.acquireNewPageIfNecessary(UnsafeExternalSorter.java:374)
at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter.insertRecord(UnsafeExternalSorter.java:396)
at org.apache.spark.sql.execution.UnsafeExternalRowSorter.insertRow(UnsafeExternalRowSorter.java:94)
...
```

Setting `DEFAULT_NUM_ELEMENTS_FOR_SPILL_THRESHOLD` to a smaller number is not enough, users can still set the config to a big number and trigger the too large page size issue. This PR fixes it by explicitly handling the too large page size exception in the sorter and spill.

This PR also change the type of `spark.shuffle.spill.numElementsForceSpillThreshold` to int, because it's only compared with `numRecords`, which is an int. This is an internal conf so we don't have a serious compatibility issue.

## How was this patch tested?

TODO

Author: Wenchen Fan <wenchen@databricks.com>

Closes #18251 from cloud-fan/sort.
2017-10-30 17:53:06 +01:00
guoxiaolong 3663764254 [WEB-UI] Add count in fair scheduler pool page
## What changes were proposed in this pull request?

Add count in fair scheduler pool page. The purpose is to know the statistics clearly.
For specific reasons, please refer to PR of https://github.com/apache/spark/pull/18525

fix before:
![1](https://user-images.githubusercontent.com/26266482/31641589-4b17b970-b318-11e7-97eb-f5a36db428f6.png)

![2](https://user-images.githubusercontent.com/26266482/31641643-97b6345a-b318-11e7-8c20-4b164ade228d.png)

fix after:
![3](https://user-images.githubusercontent.com/26266482/31641688-e6ceacb6-b318-11e7-8204-6a816c581a29.png)

![4](https://user-images.githubusercontent.com/26266482/31641766-7310b0c0-b319-11e7-871d-a57f874f1e8b.png)

## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)

Please review http://spark.apache.org/contributing.html before opening a pull request.

Author: guoxiaolong <guo.xiaolong1@zte.com.cn>

Closes #19507 from guoxiaolongzte/add_count_in_fair_scheduler_pool_page.
2017-10-30 12:14:38 +00:00
gatorsmile 659acf18da Revert "[SPARK-22308] Support alternative unit testing styles in external applications"
This reverts commit 592cfeab9c.
2017-10-29 10:37:25 -07:00
Liang-Chi Hsieh 4f8dc6b01e [SPARK-22328][CORE] ClosureCleaner should not miss referenced superclass fields
## What changes were proposed in this pull request?

When the given closure uses some fields defined in super class, `ClosureCleaner` can't figure them and don't set it properly. Those fields will be in null values.

## How was this patch tested?

Added test.

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #19556 from viirya/SPARK-22328.
2017-10-26 21:41:45 +01:00
Marcelo Vanzin 0e9a750a8d [SPARK-20643][CORE] Add listener implementation to collect app state.
The initial listener code is based on the existing JobProgressListener (and others),
and tries to mimic their behavior as much as possible. The change also includes
some minor code movement so that some types and methods from the initial history
server code code can be reused.

The code introduces a few mutable versions of public API types, used internally,
to make it easier to update information without ugly copy methods, and also to
make certain updates cheaper.

Note the code here is not 100% correct. This is meant as a building ground for
the UI integration in the next milestones. As different parts of the UI are
ported, fixes will be made to the different parts of this code to account
for the needed behavior.

I also added annotations to API types so that Jackson is able to correctly
deserialize options, sequences and maps that store primitive types.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19383 from vanzin/SPARK-20643.
2017-10-26 11:05:16 -05:00
Marcelo Vanzin 3073344a25 [SPARK-21840][CORE] Add trait that allows conf to be directly set in application.
Currently SparkSubmit uses system properties to propagate configuration to
applications. This makes it hard to implement features such as SPARK-11035,
which would allow multiple applications to be started in the same JVM. The
current code would cause the config data from multiple apps to get mixed
up.

This change introduces a new trait, currently internal to Spark, that allows
the app configuration to be passed directly to the application, without
having to use system properties. The current "call main() method" behavior
is maintained as an implementation of this new trait. This will be useful
to allow multiple cluster mode apps to be submitted from the same JVM.

As part of this, SparkSubmit was modified to collect all configuration
directly into a SparkConf instance. Most of the changes are to tests so
they use SparkConf instead of an opaque map.

Tested with existing and added unit tests.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19519 from vanzin/SPARK-21840.
2017-10-26 15:50:27 +08:00
Nathan Kronenfeld 592cfeab9c [SPARK-22308] Support alternative unit testing styles in external applications
## What changes were proposed in this pull request?
Support unit tests of external code (i.e., applications that use spark) using scalatest that don't want to use FunSuite.  SharedSparkContext already supports this, but SharedSQLContext does not.

I've introduced SharedSparkSession as a parent to SharedSQLContext, written in a way that it does support all scalatest styles.

## How was this patch tested?
There are three new unit test suites added that just test using FunSpec, FlatSpec, and WordSpec.

Author: Nathan Kronenfeld <nicole.oresme@gmail.com>

Closes #19529 from nkronenfeld/alternative-style-tests-2.
2017-10-26 00:29:49 -07:00
Sergei Lebedev b377ef133c [SPARK-22227][CORE] DiskBlockManager.getAllBlocks now tolerates temp files
## What changes were proposed in this pull request?

Prior to this commit getAllBlocks implicitly assumed that the directories
managed by the DiskBlockManager contain only the files corresponding to
valid block IDs. In reality, this assumption was violated during shuffle,
which produces temporary files in the same directory as the resulting
blocks. As a result, calls to getAllBlocks during shuffle were unreliable.

The fix could be made more efficient, but this is probably good enough.

## How was this patch tested?

`DiskBlockManagerSuite`

Author: Sergei Lebedev <s.lebedev@criteo.com>

Closes #19458 from superbobry/block-id-option.
2017-10-25 22:15:44 +01:00
Sean Owen 6c6950839d [SPARK-22322][CORE] Update FutureAction for compatibility with Scala 2.12 Future
## What changes were proposed in this pull request?

Scala 2.12's `Future` defines two new methods to implement, `transform` and `transformWith`. These can be implemented naturally in Spark's `FutureAction` extension and subclasses, but, only in terms of the new methods that don't exist in Scala 2.11. To support both at the same time, reflection is used to implement these.

## How was this patch tested?

Existing tests.

Author: Sean Owen <sowen@cloudera.com>

Closes #19561 from srowen/SPARK-22322.
2017-10-25 12:51:20 +01:00
Steven Rand 57accf6e39 [SPARK-22319][CORE] call loginUserFromKeytab before accessing hdfs
In `SparkSubmit`, call `loginUserFromKeytab` before attempting to make RPC calls to the NameNode.

I manually tested this patch by:

1. Confirming that my Spark application failed to launch with the error reported in https://issues.apache.org/jira/browse/SPARK-22319.
2. Applying this patch and confirming that the app no longer fails to launch, even when I have not manually run `kinit` on the host.

Presumably we also want integration tests for secure clusters so that we catch this sort of thing. I'm happy to take a shot at this if it's feasible and someone can point me in the right direction.

Author: Steven Rand <srand@palantir.com>

Closes #19540 from sjrand/SPARK-22319.

Change-Id: Ic306bfe7181107fbcf92f61d75856afcb5b6f761
2017-10-23 09:43:45 +08:00
Takuya UESHIN b8624b06e5 [SPARK-20396][SQL][PYSPARK][FOLLOW-UP] groupby().apply() with pandas udf
## What changes were proposed in this pull request?

This is a follow-up of #18732.
This pr modifies `GroupedData.apply()` method to convert pandas udf to grouped udf implicitly.

## How was this patch tested?

Exisiting tests.

Author: Takuya UESHIN <ueshin@databricks.com>

Closes #19517 from ueshin/issues/SPARK-20396/fup2.
2017-10-20 12:44:30 -07:00
Andrew Ash 7fae7995ba [SPARK-22268][BUILD] Fix lint-java
## What changes were proposed in this pull request?

Fix java style issues

## How was this patch tested?

Run `./dev/lint-java` locally since it's not run on Jenkins

Author: Andrew Ash <andrew@andrewash.com>

Closes #19486 from ash211/aash/fix-lint-java.
2017-10-20 09:40:00 +09:00
krishna-pandey 5a07aca4d4 [SPARK-22188][CORE] Adding security headers for preventing XSS, MitM and MIME sniffing
## What changes were proposed in this pull request?

The HTTP Strict-Transport-Security response header (often abbreviated as HSTS) is a security feature that lets a web site tell browsers that it should only be communicated with using HTTPS, instead of using HTTP.

Note: The Strict-Transport-Security header is ignored by the browser when your site is accessed using HTTP; this is because an attacker may intercept HTTP connections and inject the header or remove it. When your site is accessed over HTTPS with no certificate errors, the browser knows your site is HTTPS capable and will honor the Strict-Transport-Security header.

The HTTP X-XSS-Protection response header is a feature of Internet Explorer, Chrome and Safari that stops pages from loading when they detect reflected cross-site scripting (XSS) attacks.

The HTTP X-Content-Type-Options response header is used to protect against MIME sniffing vulnerabilities.

## How was this patch tested?
Checked on my system locally.

<img width="750" alt="screen shot 2017-10-03 at 6 49 20 pm" src="https://user-images.githubusercontent.com/6433184/31127234-eadf7c0c-a86b-11e7-8e5d-f6ea3f97b210.png">

Author: krishna-pandey <krish.pandey21@gmail.com>
Author: Krishna Pandey <krish.pandey21@gmail.com>

Closes #19419 from krishna-pandey/SPARK-22188.
2017-10-19 08:33:14 +01:00
Marcelo Vanzin dc2714da50 [SPARK-22290][CORE] Avoid creating Hive delegation tokens when not necessary.
Hive delegation tokens are only needed when the Spark driver has no access
to the kerberos TGT. That happens only in two situations:

- when using a proxy user
- when using cluster mode without a keytab

This change modifies the Hive provider so that it only generates delegation
tokens in those situations, and tweaks the YARN AM so that it makes the proper
user visible to the Hive code when running with keytabs, so that the TGT
can be used instead of a delegation token.

The effect of this change is that now it's possible to initialize multiple,
non-concurrent SparkContext instances in the same JVM. Before, the second
invocation would fail to fetch a new Hive delegation token, which then could
make the second (or third or...) application fail once the token expired.
With this change, the TGT will be used to authenticate to the HMS instead.

This change also avoids polluting the current logged in user's credentials
when launching applications. The credentials are copied only when running
applications as a proxy user. This makes it possible to implement SPARK-11035
later, where multiple threads might be launching applications, and each app
should have its own set of credentials.

Tested by verifying HDFS and Hive access in following scenarios:
- client and cluster mode
- client and cluster mode with proxy user
- client and cluster mode with principal / keytab
- long-running cluster app with principal / keytab
- pyspark app that creates (and stops) multiple SparkContext instances
  through its lifetime

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #19509 from vanzin/SPARK-22290.
2017-10-19 14:56:48 +08:00
Michael Mior 1437e344ec [SPARK-22050][CORE] Allow BlockUpdated events to be optionally logged to the event log
## What changes were proposed in this pull request?

I see that block updates are not logged to the event log.
This makes sense as a default for performance reasons.
However, I find it helpful when trying to get a better understanding of caching for a job to be able to log these updates.
This PR adds a configuration setting `spark.eventLog.blockUpdates` (defaulting to false) which allows block updates to be recorded in the log.
This contribution is original work which is licensed to the Apache Spark project.

## How was this patch tested?

Current and additional unit tests.

Author: Michael Mior <mmior@uwaterloo.ca>

Closes #19263 from michaelmior/log-block-updates.
2017-10-17 14:30:52 -07:00
jerryshao e1960c3d6f [SPARK-22062][CORE] Spill large block to disk in BlockManager's remote fetch to avoid OOM
## What changes were proposed in this pull request?

In the current BlockManager's `getRemoteBytes`, it will call `BlockTransferService#fetchBlockSync` to get remote block. In the `fetchBlockSync`, Spark will allocate a temporary `ByteBuffer` to store the whole fetched block. This will potentially lead to OOM if block size is too big or several blocks are fetched simultaneously in this executor.

So here leveraging the idea of shuffle fetch, to spill the large block to local disk before consumed by upstream code. The behavior is controlled by newly added configuration, if block size is smaller than the threshold, then this block will be persisted in memory; otherwise it will first spill to disk, and then read from disk file.

To achieve this feature, what I did is:

1. Rename `TempShuffleFileManager` to `TempFileManager`, since now it is not only used by shuffle.
2. Add a new `TempFileManager` to manage the files of fetched remote blocks, the files are tracked by weak reference, will be deleted when no use at all.

## How was this patch tested?

This was tested by adding UT, also manual verification in local test to perform GC to clean the files.

Author: jerryshao <sshao@hortonworks.com>

Closes #19476 from jerryshao/SPARK-22062.
2017-10-17 22:54:38 +08:00
Xingbo Jiang 0fa10666cf [SPARK-22233][CORE][FOLLOW-UP] Allow user to filter out empty split in HadoopRDD
## What changes were proposed in this pull request?

Update the config `spark.files.ignoreEmptySplits`, rename it and make it internal.

This is followup of #19464

## How was this patch tested?

Exsiting tests.

Author: Xingbo Jiang <xingbo.jiang@databricks.com>

Closes #19504 from jiangxb1987/partitionsplit.
2017-10-16 22:15:50 +08:00
Mridul Muralidharan 13c1559587 [SPARK-21549][CORE] Respect OutputFormats with no/invalid output directory provided
## What changes were proposed in this pull request?

PR #19294 added support for null's - but spark 2.1 handled other error cases where path argument can be invalid.
Namely:

* empty string
* URI parse exception while creating Path

This is resubmission of PR #19487, which I messed up while updating my repo.

## How was this patch tested?

Enhanced test to cover new support added.

Author: Mridul Muralidharan <mridul@gmail.com>

Closes #19497 from mridulm/master.
2017-10-15 18:40:53 -07:00
liulijia 014dc84712 [SPARK-22233][CORE] Allow user to filter out empty split in HadoopRDD
## What changes were proposed in this pull request?
Add a flag spark.files.ignoreEmptySplits. When true, methods like that use HadoopRDD and NewHadoopRDD such as SparkContext.textFiles will not create a partition for input splits that are empty.

Author: liulijia <liulijia@meituan.com>

Closes #19464 from liutang123/SPARK-22233.
2017-10-14 17:37:33 +09:00