Commit graph

10723 commits

Author SHA1 Message Date
Josh Rosen 6afde2c781 [SPARK-7058] Include RDD deserialization time in "task deserialization time" metric
The web UI's "task deserialization time" metric is slightly misleading because it does not capture the time taken to deserialize the broadcasted RDD.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #5635 from JoshRosen/SPARK-7058 and squashes the following commits:

ed90f75 [Josh Rosen] Update UI tooltip
a3743b4 [Josh Rosen] Update comments.
4f52910 [Josh Rosen] Roll back whitespace change
e9cf9f4 [Josh Rosen] Remove unused variable
9f32e55 [Josh Rosen] Expose executorDeserializeTime on Task instead of pushing runtime calculation into Task.
21f5b47 [Josh Rosen] Don't double-count the broadcast deserialization time in task runtime
1752f0e [Josh Rosen] [SPARK-7058] Incorporate RDD deserialization time in task deserialization time metric
2015-04-23 13:19:03 -07:00
Vinod K C c1213e6a92 [SPARK-7055][SQL]Use correct ClassLoader for JDBC Driver in JDBCRDD.getConnector
Author: Vinod K C <vinod.kc@huawei.com>

Closes #5633 from vinodkc/use_correct_classloader_driverload and squashes the following commits:

73c5380 [Vinod K C] Use correct ClassLoader for JDBC Driver
2015-04-23 12:00:23 -07:00
Tathagata Das 534f2a4362 [SPARK-6752][Streaming] Allow StreamingContext to be recreated from checkpoint and existing SparkContext
Currently if you want to create a StreamingContext from checkpoint information, the system will create a new SparkContext. This prevent StreamingContext to be recreated from checkpoints in managed environments where SparkContext is precreated.

The solution in this PR: Introduce the following methods on StreamingContext
1. `new StreamingContext(checkpointDirectory, sparkContext)`
   Recreate StreamingContext from checkpoint using the provided SparkContext
2. `StreamingContext.getOrCreate(checkpointDirectory, sparkContext, createFunction: SparkContext => StreamingContext)`
   If checkpoint file exists, then recreate StreamingContext using the provided SparkContext (that is, call 1.), else create StreamingContext using the provided createFunction

TODO: the corresponding Java and Python API has to be added as well.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5428 from tdas/SPARK-6752 and squashes the following commits:

94db63c [Tathagata Das] Fix long line.
524f519 [Tathagata Das] Many changes based on PR comments.
eabd092 [Tathagata Das] Added Function0, Java API and unit tests for StreamingContext.getOrCreate
36a7823 [Tathagata Das] Minor changes.
204814e [Tathagata Das] Added StreamingContext.getOrCreate with existing SparkContext
2015-04-23 11:29:34 -07:00
Cheng Hao cc48e6387a [SPARK-7044] [SQL] Fix the deadlock in script transformation
Author: Cheng Hao <hao.cheng@intel.com>

Closes #5625 from chenghao-intel/transform and squashes the following commits:

5ec1dd2 [Cheng Hao] fix the deadlock issue in ScriptTransform
2015-04-23 10:35:22 -07:00
Prabeesh K 975f53e4f9 [minor][streaming]fixed scala string interpolation error
Author: Prabeesh K <prabeesh.k@namshi.com>

Closes #5653 from prabeesh/fix and squashes the following commits:

9d7a9f5 [Prabeesh K] fixed scala string interpolation error
2015-04-23 10:33:13 -07:00
Prashant Sharma a7d65d38f9 [HOTFIX] [SQL] Fix compilation for scala 2.11.
Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #5652 from ScrapCodes/hf/compilation-fix-scala-2.11 and squashes the following commits:

819ff06 [Prashant Sharma] [HOTFIX] Fix compilation for scala 2.11.
2015-04-23 16:45:26 +05:30
Reynold Xin f60bece14f [SPARK-7069][SQL] Rename NativeType -> AtomicType.
Also renamed JvmType to InternalType.

Author: Reynold Xin <rxin@databricks.com>

Closes #5651 from rxin/native-to-atomic-type and squashes the following commits:

cbd4028 [Reynold Xin] [SPARK-7069][SQL] Rename NativeType -> AtomicType.
2015-04-23 01:43:40 -07:00
Reynold Xin 29163c5200 [SPARK-7068][SQL] Remove PrimitiveType
Author: Reynold Xin <rxin@databricks.com>

Closes #5646 from rxin/remove-primitive-type and squashes the following commits:

01b673d [Reynold Xin] [SPARK-7068][SQL] Remove PrimitiveType
2015-04-22 23:55:20 -07:00
Reynold Xin 2d33323cad [MLlib] Add support for BooleanType to VectorAssembler.
Author: Reynold Xin <rxin@databricks.com>

Closes #5648 from rxin/vectorAssembler-boolean and squashes the following commits:

1bf3d40 [Reynold Xin] [MLlib] Add support for BooleanType to VectorAssembler.
2015-04-22 23:54:48 -07:00
Liang-Chi Hsieh d9e70f331f [HOTFIX][SQL] Fix broken cached test
Added in #5475. Pointed as broken in #5639.
/cc marmbrus

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

Closes #5640 from viirya/fix_cached_test and squashes the following commits:

c0cf69a [Liang-Chi Hsieh] Fix broken cached test.
2015-04-22 22:18:56 -07:00
Kay Ousterhout 03e85b4a11 [SPARK-7046] Remove InputMetrics from BlockResult
This is a code cleanup.

The BlockResult class originally contained an InputMetrics object so that InputMetrics could
directly be used as the InputMetrics for the whole task. Now we copy the fields out of here, and
the presence of this object is confusing because it's only a partial input metrics (it doesn't
include the records read). Because this object is no longer useful (and is confusing), it should
be removed.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #5627 from kayousterhout/SPARK-7046 and squashes the following commits:

bf64bbe [Kay Ousterhout] Import fix
a08ca19 [Kay Ousterhout] [SPARK-7046] Remove InputMetrics from BlockResult
2015-04-22 21:42:09 -07:00
Reynold Xin d20686066e [SPARK-7066][MLlib] VectorAssembler should use NumericType not NativeType.
Author: Reynold Xin <rxin@databricks.com>

Closes #5642 from rxin/mllib-native-type and squashes the following commits:

e23af5b [Reynold Xin] Remove StringType
7cbb205 [Reynold Xin] [SPARK-7066][MLlib] VectorAssembler should use NumericType and StringType, not NativeType.
2015-04-22 21:35:42 -07:00
Reynold Xin 1b85e08509 [MLlib] UnaryTransformer nullability should not depend on PrimitiveType.
Author: Reynold Xin <rxin@databricks.com>

Closes #5644 from rxin/mllib-nullable and squashes the following commits:

a727e5b [Reynold Xin] [MLlib] UnaryTransformer nullability should not depend on primitive types.
2015-04-22 21:35:12 -07:00
Reynold Xin b69c4f9b2e Disable flaky test: ReceiverSuite "block generator throttling". 2015-04-22 21:24:22 -07:00
Daoyuan Wang 04525c077c [SPARK-6967] [SQL] fix date type convertion in jdbcrdd
This pr convert java.sql.Date type into Int for JDBCRDD.

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #5590 from adrian-wang/datebug and squashes the following commits:

f897b81 [Daoyuan Wang] add a test case
3c9184c [Daoyuan Wang] fix date type convertion in jdbcrdd
2015-04-22 19:14:28 -07:00
Yanbo Liang f4f39981f4 [SPARK-6827] [MLLIB] Wrap FPGrowthModel.freqItemsets and make it consistent with Java API
Make PySpark ```FPGrowthModel.freqItemsets``` consistent with Java/Scala API like ```MatrixFactorizationModel.userFeatures```
It return a RDD with each tuple is composed of an array and a long value.
I think it's difficult to implement namedtuples to wrap the output because items of freqItemsets can be any type with arbitrary length which is tedious to impelement corresponding SerDe function.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #5614 from yanboliang/spark-6827 and squashes the following commits:

da8c404 [Yanbo Liang] use namedtuple
5532e78 [Yanbo Liang] Wrap FPGrowthModel.freqItemsets and make it consistent with Java API
2015-04-22 17:22:26 -07:00
Reynold Xin baf865ddc2 [SPARK-7059][SQL] Create a DataFrame join API to facilitate equijoin.
Author: Reynold Xin <rxin@databricks.com>

Closes #5638 from rxin/joinUsing and squashes the following commits:

13e9cc9 [Reynold Xin] Code review + Python.
b1bd914 [Reynold Xin] [SPARK-7059][SQL] Create a DataFrame join API to facilitate equijoin and self join.
2015-04-22 15:26:58 -07:00
szheng79 fbe7106d75 [SPARK-7039][SQL]JDBCRDD: Add support on type NVARCHAR
Issue:

https://issues.apache.org/jira/browse/SPARK-7039

Add support to column type NVARCHAR in Sql Server

java.sql.Types:
http://docs.oracle.com/javase/7/docs/api/java/sql/Types.html

Author: szheng79 <szheng.code@gmail.com>

Closes #5618 from szheng79/patch-1 and squashes the following commits:

10da99c [szheng79] Update JDBCRDD.scala
eab0bd8 [szheng79] Add support on type NVARCHAR
2015-04-22 13:02:55 -07:00
Reynold Xin cdf0328684 [SQL] Rename some apply functions.
I was looking at the code gen code and got confused by a few of use cases of apply, in particular apply on objects. So I went ahead and changed a few of them. Hopefully slightly more clear with a proper verb.

Author: Reynold Xin <rxin@databricks.com>

Closes #5624 from rxin/apply-rename and squashes the following commits:

ee45034 [Reynold Xin] [SQL] Rename some apply functions.
2015-04-22 11:18:01 -07:00
zsxwing 33b85620f9 [SPARK-7052][Core] Add ThreadUtils and move thread methods from Utils to ThreadUtils
As per rxin 's suggestion in https://github.com/apache/spark/pull/5392/files#r28757176

What's more, there is a race condition in the global shared `daemonThreadFactoryBuilder`. `daemonThreadFactoryBuilder` may be modified by multiple threads. This PR removed the global `daemonThreadFactoryBuilder` and created a new `ThreadFactoryBuilder` every time.

Author: zsxwing <zsxwing@gmail.com>

Closes #5631 from zsxwing/thread-utils and squashes the following commits:

9fe5b0e [zsxwing] Add ThreadUtils and move thread methods from Utils to ThreadUtils
2015-04-22 11:08:59 -07:00
Sean Owen bdc5c16e76 [SPARK-6889] [DOCS] CONTRIBUTING.md updates to accompany contribution doc updates
Part of the SPARK-6889 doc updates, to accompany wiki updates at https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark

See draft text at https://docs.google.com/document/d/1tB9-f9lmxhC32QlOo4E8Z7eGDwHx1_Q3O8uCmRXQTo8/edit#

Author: Sean Owen <sowen@cloudera.com>

Closes #5623 from srowen/SPARK-6889 and squashes the following commits:

03773b1 [Sean Owen] Part of the SPARK-6889 doc updates, to accompany wiki updates at https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark
2015-04-21 22:34:31 -07:00
Joseph K. Bradley 607eff0edf [SPARK-6113] [ML] Small cleanups after original tree API PR
This does a few clean-ups.  With this PR, all spark.ml tree components have ```private[ml]``` constructors.

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #5567 from jkbradley/dt-api-dt2 and squashes the following commits:

2263b5b [Joseph K. Bradley] Added note about tree example issue.
bb9f610 [Joseph K. Bradley] Small cleanups after original tree API PR
2015-04-21 21:44:44 -07:00
Patrick Wendell 70f9f8ff38 [MINOR] Comment improvements in ExternalSorter.
1. Clearly specifies the contract/interactions for users of this class.
2. Minor fix in one doc to avoid ambiguity.

Author: Patrick Wendell <patrick@databricks.com>

Closes #5620 from pwendell/cleanup and squashes the following commits:

8d8f44f [Patrick Wendell] [Minor] Comment improvements in ExternalSorter.
2015-04-21 21:04:04 -07:00
zsxwing 3a3f7100f4 [SPARK-6490][Docs] Add docs for rpc configurations
Added docs for rpc configurations and also fixed two places that should have been fixed in #5595.

Author: zsxwing <zsxwing@gmail.com>

Closes #5607 from zsxwing/SPARK-6490-docs and squashes the following commits:

25a6736 [zsxwing] Increase the default timeout to 120s
6e37c30 [zsxwing] Update docs
5577540 [zsxwing] Use spark.network.timeout as the default timeout if it presents
4f07174 [zsxwing] Fix unit tests
1c2cf26 [zsxwing] Add docs for rpc configurations
2015-04-21 18:37:53 -07:00
texasmichelle a0761ec706 [SPARK-1684] [PROJECT INFRA] Merge script should standardize SPARK-XXX prefix
Cleans up the pull request title in the merge script to follow conventions outlined in the wiki under Contributing Code.
https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark#ContributingtoSpark-ContributingCode

[MODULE] SPARK-XXXX: Description

Author: texasmichelle <texasmichelle@gmail.com>

Closes #5149 from texasmichelle/master and squashes the following commits:

9b6b0a7 [texasmichelle] resolved variable scope issue
7d5fa20 [texasmichelle] only prompt if title has been modified
8c195bb [texasmichelle] removed erroneous line
4f1ed46 [texasmichelle] Deque removal, logic simplifications, & prompt user to pick a title (orig or modified)
df73f6a [texasmichelle] reworked regex's to enforce brackets around JIRA ref
43b5aed [texasmichelle] Merge remote-tracking branch 'apache/master'
25229c6 [texasmichelle] Merge remote-tracking branch 'apache/master'
aa20a6e [texasmichelle] Move code into main() and add doctest for new text parsing method
48520ba [texasmichelle] SPARK-1684: Corrected import statement
042099d [texasmichelle] SPARK-1684 Merge script should standardize SPARK-XXX prefix
8f4a7d1 [texasmichelle] SPARK-1684 Merge script should standardize SPARK-XXX prefix
2015-04-21 18:08:29 -07:00
Reynold Xin 41ef78a941 Closes #5427 2015-04-21 17:52:52 -07:00
Reynold Xin 3134c3fe49 [SPARK-6953] [PySpark] speed up python tests
This PR try to speed up some python tests:

```
tests.py                       144s -> 103s      -41s
mllib/classification.py         24s -> 17s        -7s
mllib/regression.py             27s -> 15s       -12s
mllib/tree.py                   27s -> 13s       -14s
mllib/tests.py                  64s -> 31s       -33s
streaming/tests.py             185s -> 84s      -101s
```
Considering python3, the total saving will be 558s (almost 10 minutes) (core, and streaming run three times, mllib runs twice).

During testing, it will show used time for each test file:
```
Run core tests ...
Running test: pyspark/rdd.py ... ok (22s)
Running test: pyspark/context.py ... ok (16s)
Running test: pyspark/conf.py ... ok (4s)
Running test: pyspark/broadcast.py ... ok (4s)
Running test: pyspark/accumulators.py ... ok (4s)
Running test: pyspark/serializers.py ... ok (6s)
Running test: pyspark/profiler.py ... ok (5s)
Running test: pyspark/shuffle.py ... ok (1s)
Running test: pyspark/tests.py ... ok (103s)   144s
```

Author: Reynold Xin <rxin@databricks.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #5605 from rxin/python-tests-speed and squashes the following commits:

d08542d [Reynold Xin] Merge pull request #14 from mengxr/SPARK-6953
89321ee [Xiangrui Meng] fix seed in tests
3ad2387 [Reynold Xin] Merge pull request #5427 from davies/python_tests
2015-04-21 17:49:55 -07:00
Marcelo Vanzin e72c16e30d [SPARK-6014] [core] Revamp Spark shutdown hooks, fix shutdown races.
This change adds some new utility code to handle shutdown hooks in
Spark. The main goal is to take advantage of Hadoop 2.x's API for
shutdown hooks, which allows Spark to register a hook that will
run before the one that cleans up HDFS clients, and thus avoids
some races that would cause exceptions to show up and other issues
such as failure to properly close event logs.

Unfortunately, Hadoop 1.x does not have such APIs, so in that case
correctness is still left to chance.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5560 from vanzin/SPARK-6014 and squashes the following commits:

edfafb1 [Marcelo Vanzin] Better scaladoc.
fcaeedd [Marcelo Vanzin] Merge branch 'master' into SPARK-6014
e7039dc [Marcelo Vanzin] [SPARK-6014] [core] Revamp Spark shutdown hooks, fix shutdown races.
2015-04-21 20:33:57 -04:00
mweindel b063a61b98 Avoid warning message about invalid refuse_seconds value in Mesos >=0.21...
Starting with version 0.21.0, Apache Mesos is very noisy if the filter parameter refuse_seconds is set to an invalid value like `-1`.
I have seen systems with millions of log lines like
```
W0420 18:00:48.773059 32352 hierarchical_allocator_process.hpp:589] Using the default value of 'refuse_seconds' to create the refused resources filter because the input value is negative
```
in the Mesos master INFO and WARNING log files.
Therefore the CoarseMesosSchedulerBackend should set the default value for refuse seconds (i.e. 5 seconds) directly.
This is no problem for the fine-grained MesosSchedulerBackend, as it uses the value 1 second for this parameter.

Author: mweindel <m.weindel@usu-software.de>

Closes #5597 from MartinWeindel/master and squashes the following commits:

2f99ffd [mweindel] Avoid warning message about invalid refuse_seconds value in Mesos >=0.21.
2015-04-21 20:19:33 -04:00
Alain ae036d0817 [Minor][MLLIB] Fix a minor formatting bug in toString method in Node.scala
add missing comma and space

Author: Alain <aihe@usc.edu>

Closes #5621 from AiHe/tree-node-issue and squashes the following commits:

159a7bb [Alain] [Minor][MLLIB] Fix a minor formatting bug in toString methods in Node.scala

(cherry picked from commit 4508f01890a723f80d631424ff8eda166a13a727)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
2015-04-21 16:48:05 -07:00
Xiangrui Meng 686dd742e1 [SPARK-7036][MLLIB] ALS.train should support DataFrames in PySpark
SchemaRDD works with ALS.train in 1.2, so we should continue support DataFrames for compatibility. coderxiang

Author: Xiangrui Meng <meng@databricks.com>

Closes #5619 from mengxr/SPARK-7036 and squashes the following commits:

dfcaf5a [Xiangrui Meng] ALS.train should support DataFrames in PySpark
2015-04-21 16:44:52 -07:00
MechCoder 7fe6142cd3 [SPARK-6065] [MLlib] Optimize word2vec.findSynonyms using blas calls
1. Use blas calls to find the dot product between two vectors.
2. Prevent re-computing the L2 norm of the given vector for each word in model.

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #5467 from MechCoder/spark-6065 and squashes the following commits:

dd0b0b2 [MechCoder] Preallocate wordVectors
ffc9240 [MechCoder] Minor
6b74c81 [MechCoder] Switch back to native blas calls
da1642d [MechCoder] Explicit types and indexing
64575b0 [MechCoder] Save indexedmap and a wordvecmat instead of matrix
fbe0108 [MechCoder] Made the following changes 1. Calculate norms during initialization. 2. Use Blas calls from linalg.blas
1350cf3 [MechCoder] [SPARK-6065] Optimize word2vec.findSynonynms using blas calls
2015-04-21 16:42:45 -07:00
Marcelo Vanzin a70e849c7f [minor] [build] Set java options when generating mima ignores.
The default java options make the call to GenerateMIMAIgnore take
forever to run since it's gc'ing all the time. Improve things by
setting the perm gen size / max heap size to larger values.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5615 from vanzin/gen-mima-fix and squashes the following commits:

f44e921 [Marcelo Vanzin] [minor] [build] Set java options when generating mima ignores.
2015-04-21 16:35:37 -07:00
Josh Rosen f83c0f112d [SPARK-3386] Share and reuse SerializerInstances in shuffle paths
This patch modifies several shuffle-related code paths to share and re-use SerializerInstances instead of creating new ones.  Some serializers, such as KryoSerializer or SqlSerializer, can be fairly expensive to create or may consume moderate amounts of memory, so it's probably best to avoid unnecessary serializer creation in hot code paths.

The key change in this patch is modifying `getDiskWriter()` / `DiskBlockObjectWriter` to accept `SerializerInstance`s instead of `Serializer`s (which are factories for instances).  This allows the disk writer's creator to decide whether the serializer instance can be shared or re-used.

The rest of the patch modifies several write and read paths to use shared serializers.  One big win is in `ShuffleBlockFetcherIterator`, where we used to create a new serializer per received block.  Similarly, the shuffle write path used to create a new serializer per file even though in many cases only a single thread would be writing to a file at a time.

I made a small serializer reuse optimization in CoarseGrainedExecutorBackend as well, since it seemed like a small and obvious improvement.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #5606 from JoshRosen/SPARK-3386 and squashes the following commits:

f661ce7 [Josh Rosen] Remove thread local; add comment instead
64f8398 [Josh Rosen] Use ThreadLocal for serializer instance in CoarseGrainedExecutorBackend
aeb680e [Josh Rosen] [SPARK-3386] Reuse SerializerInstance in shuffle code paths
2015-04-21 16:24:15 -07:00
Cheng Hao 7662ec23bb [SPARK-5817] [SQL] Fix bug of udtf with column names
It's a bug while do query like:
```sql
select d from (select explode(array(1,1)) d from src limit 1) t
```
And it will throws exception like:
```
org.apache.spark.sql.AnalysisException: cannot resolve 'd' given input columns _c0; line 1 pos 7
at org.apache.spark.sql.catalyst.analysis.package$AnalysisErrorAt.failAnalysis(package.scala:42)
at org.apache.spark.sql.catalyst.analysis.CheckAnalysis$$anonfun$apply$3$$anonfun$apply$1.applyOrElse(CheckAnalysis.scala:48)
at org.apache.spark.sql.catalyst.analysis.CheckAnalysis$$anonfun$apply$3$$anonfun$apply$1.applyOrElse(CheckAnalysis.scala:45)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$transformUp$1.apply(TreeNode.scala:250)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$transformUp$1.apply(TreeNode.scala:250)
at org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(TreeNode.scala:50)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:249)
at org.apache.spark.sql.catalyst.plans.QueryPlan.org$apache$spark$sql$catalyst$plans$QueryPlan$$transformExpressionUp$1(QueryPlan.scala:103)
at org.apache.spark.sql.catalyst.plans.QueryPlan$$anonfun$2$$anonfun$apply$2.apply(QueryPlan.scala:117)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
at scala.collection.AbstractTraversable.map(Traversable.scala:105)
at org.apache.spark.sql.catalyst.plans.QueryPlan$$anonfun$2.apply(QueryPlan.scala:116)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
```

To solve the bug, it requires code refactoring for UDTF
The major changes are about:
* Simplifying the UDTF development, UDTF will manage the output attribute names any more, instead, the `logical.Generate` will handle that properly.
* UDTF will be asked for the output schema (data types) during the logical plan analyzing.

Author: Cheng Hao <hao.cheng@intel.com>

Closes #4602 from chenghao-intel/explode_bug and squashes the following commits:

c2a5132 [Cheng Hao] add back resolved for Alias
556e982 [Cheng Hao] revert the unncessary change
002c361 [Cheng Hao] change the rule of resolved for Generate
04ae500 [Cheng Hao] add qualifier only for generator output
5ee5d2c [Cheng Hao] prepend the new qualifier
d2e8b43 [Cheng Hao] Update the code as feedback
ca5e7f4 [Cheng Hao] shrink the commits
2015-04-21 15:11:15 -07:00
Punya Biswal 2a24bf92e6 [SPARK-6996][SQL] Support map types in java beans
liancheng mengxr this is similar to #5146.

Author: Punya Biswal <pbiswal@palantir.com>

Closes #5578 from punya/feature/SPARK-6996 and squashes the following commits:

d56c3e0 [Punya Biswal] Fix imports
c7e308b [Punya Biswal] Support java iterable types in POJOs
5e00685 [Punya Biswal] Support map types in java beans
2015-04-21 14:50:02 -07:00
Yin Huai 6265cba00f [SPARK-6969][SQL] Refresh the cached table when REFRESH TABLE is used
https://issues.apache.org/jira/browse/SPARK-6969

Author: Yin Huai <yhuai@databricks.com>

Closes #5583 from yhuai/refreshTableRefreshDataCache and squashes the following commits:

1e5142b [Yin Huai] Add todo.
92b2498 [Yin Huai] Minor updates.
367df92 [Yin Huai] Recache data in the command of REFRESH TABLE.
2015-04-21 14:48:42 -07:00
Wenchen Fan 03fd921671 [SQL][minor] make it more clear that we only need to re-throw GetField exception for UnresolvedAttribute
For `GetField` outside `UnresolvedAttribute`, we will throw exception in `Analyzer`.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #5588 from cloud-fan/tmp and squashes the following commits:

7ac74d2 [Wenchen Fan] small refactor
2015-04-21 14:48:02 -07:00
vidmantas zemleris 2e8c6ca47d [SPARK-6994] Allow to fetch field values by name in sql.Row
It looked weird that up to now there was no way in Spark's Scala API to access fields of `DataFrame/sql.Row` by name, only by their index.

This tries to solve this issue.

Author: vidmantas zemleris <vidmantas@vinted.com>

Closes #5573 from vidma/features/row-with-named-fields and squashes the following commits:

6145ae3 [vidmantas zemleris] [SPARK-6994][SQL] Allow to fetch field values by name on Row
9564ebb [vidmantas zemleris] [SPARK-6994][SQL] Add fieldIndex to schema (StructType)
2015-04-21 14:47:09 -07:00
Prashant Sharma 04bf34e34f [SPARK-7011] Build(compilation) fails with scala 2.11 option, because a protected[sql] type is accessed in ml package.
[This](https://github.com/apache/spark/blob/master/mllib/src/main/scala/org/apache/spark/ml/feature/VectorAssembler.scala#L58) is where it is used and fails compilations at.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #5593 from ScrapCodes/SPARK-7011/build-fix and squashes the following commits:

e6d57a3 [Prashant Sharma] [SPARK-7011] Build fails with scala 2.11 option, because a protected[sql] type is accessed in ml package.
2015-04-21 14:43:46 -07:00
MechCoder 45c47fa417 [SPARK-6845] [MLlib] [PySpark] Add isTranposed flag to DenseMatrix
Since sparse matrices now support a isTransposed flag for row major data, DenseMatrices should do the same.

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #5455 from MechCoder/spark-6845 and squashes the following commits:

525c370 [MechCoder] minor
004a37f [MechCoder] Cast boolean to int
151f3b6 [MechCoder] [WIP] Add isTransposed to pickle DenseMatrix
cc0b90a [MechCoder] [SPARK-6845] Add isTranposed flag to DenseMatrix
2015-04-21 14:36:50 -07:00
emres c25ca7c5a1 SPARK-3276 Added a new configuration spark.streaming.minRememberDuration
SPARK-3276 Added a new configuration parameter ``spark.streaming.minRememberDuration``, with a default value of 1 minute.

So that when a Spark Streaming application is started, an arbitrary number of minutes can be taken as threshold for remembering.

Author: emres <emre.sevinc@gmail.com>

Closes #5438 from emres/SPARK-3276 and squashes the following commits:

766f938 [emres] SPARK-3276 Switched to using newly added getTimeAsSeconds method.
affee1d [emres] SPARK-3276 Changed the property name and variable name for minRememberDuration
c9d58ca [emres] SPARK-3276 Minor code re-formatting.
1c53ba9 [emres] SPARK-3276 Started to use ssc.conf rather than ssc.sparkContext.getConf,  and also getLong method directly.
bfe0acb [emres] SPARK-3276 Moved the minRememberDurationMin to the class
daccc82 [emres] SPARK-3276 Changed the property name to reflect the unit of value and reduced number of fields.
43cc1ce [emres] SPARK-3276 Added a new configuration parameter spark.streaming.minRemember duration, with a default value of 1 minute.
2015-04-21 16:39:56 -04:00
Kay Ousterhout c035c0f2d7 [SPARK-5360] [SPARK-6606] Eliminate duplicate objects in serialized CoGroupedRDD
CoGroupPartition, part of CoGroupedRDD, includes references to each RDD that the CoGroupedRDD narrowly depends on, and a reference to the ShuffleHandle. The partition is serialized separately from the RDD, so when the RDD and partition arrive on the worker, the references in the partition and in the RDD no longer point to the same object.

This is a relatively minor performance issue (the closure can be 2x larger than it needs to be because the rdds and partitions are serialized twice; see numbers below) but is more annoying as a developer issue (this is where I ran into): if any state is stored in the RDD or ShuffleHandle on the worker side, subtle bugs can appear due to the fact that the references to the RDD / ShuffleHandle in the RDD and in the partition point to separate objects. I'm not sure if this is enough of a potential future problem to fix this old and central part of the code, so hoping to get input from others here.

I did some simple experiments to see how much this effects closure size. For this example:
$ val a = sc.parallelize(1 to 10).map((_, 1))
$ val b = sc.parallelize(1 to 2).map(x => (x, 2*x))
$ a.cogroup(b).collect()
the closure was 1902 bytes with current Spark, and 1129 bytes after my change. The difference comes from eliminating duplicate serialization of the shuffle handle.

For this example:
$ val sortedA = a.sortByKey()
$ val sortedB = b.sortByKey()
$ sortedA.cogroup(sortedB).collect()
the closure was 3491 bytes with current Spark, and 1333 bytes after my change. Here, the difference comes from eliminating duplicate serialization of the two RDDs for the narrow dependencies.

The ShuffleHandle includes the ShuffleDependency, so this difference will get larger if a ShuffleDependency includes a serializer, a key ordering, or an aggregator (all set to None by default). It would also get bigger for a big RDD -- although I can't think of any examples where the RDD object gets large.  The difference is not affected by the size of the function the user specifies, which (based on my understanding) is typically the source of large task closures.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #4145 from kayousterhout/SPARK-5360 and squashes the following commits:

85156c3 [Kay Ousterhout] Better comment the narrowDeps parameter
cff0209 [Kay Ousterhout] Fixed spelling issue
658e1af [Kay Ousterhout] [SPARK-5360] Eliminate duplicate objects in serialized CoGroupedRDD
2015-04-21 11:01:18 -07:00
David McGuire 5fea3e5c36 [SPARK-6985][streaming] Receiver maxRate over 1000 causes a StackOverflowError
A simple truncation in integer division (on rates over 1000 messages / second) causes the existing implementation to sleep for 0 milliseconds, then call itself recursively; this causes what is essentially an infinite recursion, since the base case of the calculated amount of time having elapsed can't be reached before available stack space is exhausted. A fix to this truncation error is included in this patch.

However, even with the defect patched, the accuracy of the existing implementation is abysmal (the error bounds of the original test were effectively [-30%, +10%], although this fact was obscured by hard-coded error margins); as such, when the error bounds were tightened down to [-5%, +5%], the existing implementation failed to meet the new, tightened, requirements. Therefore, an industry-vetted solution (from Guava) was used to get the adapted tests to pass.

Author: David McGuire <david.mcguire2@nike.com>

Closes #5559 from dmcguire81/master and squashes the following commits:

d29d2e0 [David McGuire] Back out to +/-5% error margins, for flexibility in timing
8be6934 [David McGuire] Fix spacing per code review
90e98b9 [David McGuire] Address scalastyle errors
29011bd [David McGuire] Further ratchet down the error margins
b33b796 [David McGuire] Eliminate dependency on even distribution by BlockGenerator
8f2934b [David McGuire] Remove arbitrary thread timing / cooperation code
70ee310 [David McGuire] Use Thread.yield(), since Thread.sleep(0) is system-dependent
82ee46d [David McGuire] Replace guard clause with nested conditional
2794717 [David McGuire] Replace the RateLimiter with the Guava implementation
38f3ca8 [David McGuire] Ratchet down the error rate to +/- 5%; tests fail
24b1bc0 [David McGuire] Fix truncation in integer division causing infinite recursion
d6e1079 [David McGuire] Stack overflow error in RateLimiter on rates over 1000/s
2015-04-21 07:21:10 -04:00
Yanbo Liang 1f2f723b0d [SPARK-5990] [MLLIB] Model import/export for IsotonicRegression
Model import/export for IsotonicRegression

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #5270 from yanboliang/spark-5990 and squashes the following commits:

872028d [Yanbo Liang] fix code style
f80ec1b [Yanbo Liang] address comments
49600cc [Yanbo Liang] address comments
429ff7d [Yanbo Liang] store each interval as a record
2b2f5a1 [Yanbo Liang] Model import/export for IsotonicRegression
2015-04-21 00:14:16 -07:00
Davies Liu ab9128fb7e [SPARK-6949] [SQL] [PySpark] Support Date/Timestamp in Column expression
This PR enable auto_convert in JavaGateway, then we could register a converter for a given types, for example, date and datetime.

There are two bugs related to auto_convert, see [1] and [2], we workaround it in this PR.

[1]  https://github.com/bartdag/py4j/issues/160
[2] https://github.com/bartdag/py4j/issues/161

cc rxin JoshRosen

Author: Davies Liu <davies@databricks.com>

Closes #5570 from davies/py4j_date and squashes the following commits:

eb4fa53 [Davies Liu] fix tests in python 3
d17d634 [Davies Liu] rollback changes in mllib
2e7566d [Davies Liu] convert tuple into ArrayList
ceb3779 [Davies Liu] Update rdd.py
3c373f3 [Davies Liu] support date and datetime by auto_convert
cb094ff [Davies Liu] enable auto convert
2015-04-21 00:08:18 -07:00
zsxwing 8136810dfa [SPARK-6490][Core] Add spark.rpc.* and deprecate spark.akka.*
Deprecated `spark.akka.num.retries`, `spark.akka.retry.wait`, `spark.akka.askTimeout`,  `spark.akka.lookupTimeout`, and added `spark.rpc.num.retries`, `spark.rpc.retry.wait`, `spark.rpc.askTimeout`, `spark.rpc.lookupTimeout`.

Author: zsxwing <zsxwing@gmail.com>

Closes #5595 from zsxwing/SPARK-6490 and squashes the following commits:

e0d80a9 [zsxwing] Use getTimeAsMs and getTimeAsSeconds and other minor fixes
31dbe69 [zsxwing] Add spark.rpc.* and deprecate spark.akka.*
2015-04-20 23:18:42 -07:00
Liang-Chi Hsieh c736220dac [SPARK-6635][SQL] DataFrame.withColumn should replace columns with identical column names
JIRA https://issues.apache.org/jira/browse/SPARK-6635

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

Closes #5541 from viirya/replace_with_column and squashes the following commits:

b539c7b [Liang-Chi Hsieh] For comment.
72f35b1 [Liang-Chi Hsieh] DataFrame.withColumn can replace original column with identical column name.
2015-04-20 18:54:01 -07:00
Yin Huai ce7ddabbcd [SPARK-6368][SQL] Build a specialized serializer for Exchange operator.
JIRA: https://issues.apache.org/jira/browse/SPARK-6368

Author: Yin Huai <yhuai@databricks.com>

Closes #5497 from yhuai/serializer2 and squashes the following commits:

da562c5 [Yin Huai] Merge remote-tracking branch 'upstream/master' into serializer2
50e0c3d [Yin Huai] When no filed is emitted to shuffle, use SparkSqlSerializer for now.
9f1ed92 [Yin Huai] Merge remote-tracking branch 'upstream/master' into serializer2
6d07678 [Yin Huai] Address comments.
4273b8c [Yin Huai] Enabled SparkSqlSerializer2.
09e587a [Yin Huai] Remove TODO.
791b96a [Yin Huai] Use UTF8String.
60a1487 [Yin Huai] Merge remote-tracking branch 'upstream/master' into serializer2
3e09655 [Yin Huai] Use getAs for Date column.
43b9fb4 [Yin Huai] Test.
8297732 [Yin Huai] Fix test.
c9373c8 [Yin Huai] Support DecimalType.
2379eeb [Yin Huai] ASF header.
39704ab [Yin Huai] Specialized serializer for Exchange.
2015-04-20 18:42:50 -07:00
BenFradet 517bdf36ae [doc][streaming] Fixed broken link in mllib section
The commit message is pretty self-explanatory.

Author: BenFradet <benjamin.fradet@gmail.com>

Closes #5600 from BenFradet/master and squashes the following commits:

108492d [BenFradet] [doc][streaming] Fixed broken link in mllib section
2015-04-20 13:46:55 -07:00