Commit graph

13348 commits

Author SHA1 Message Date
Marcelo Vanzin fa6a4fbf08 [SPARK-11134][CORE] Increase LauncherBackendSuite timeout.
This test can take a little while to finish on slow / loaded machines.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #9235 from vanzin/SPARK-11134.
2015-10-22 22:41:21 -07:00
zsxwing a88c66ca87 [SPARK-11098][CORE] Add Outbox to cache the sending messages to resolve the message disorder issue
The current NettyRpc has a message order issue because it uses a thread pool to send messages. E.g., running the following two lines in the same thread,

```
ref.send("A")
ref.send("B")
```

The remote endpoint may see "B" before "A" because sending "A" and "B" are in parallel.
To resolve this issue, this PR added an outbox for each connection, and if we are connecting to the remote node when sending messages, just cache the sending messages in the outbox and send them one by one when the connection is established.

Author: zsxwing <zsxwing@gmail.com>

Closes #9197 from zsxwing/rpc-outbox.
2015-10-22 21:01:01 -07:00
Andrew Or 34e71c6d89 [SPARK-11251] Fix page size calculation in local mode
```
// My machine only has 8 cores
$ bin/spark-shell --master local[32]
scala> val df = sc.parallelize(Seq((1, 1), (2, 2))).toDF("a", "b")
scala> df.as("x").join(df.as("y"), $"x.a" === $"y.a").count()

Caused by: java.io.IOException: Unable to acquire 2097152 bytes of memory
	at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter.acquireNewPage(UnsafeExternalSorter.java:351)
```

Author: Andrew Or <andrew@databricks.com>

Closes #9209 from andrewor14/fix-local-page-size.
2015-10-22 15:58:08 -07:00
Gábor Lipták 163d53e829 [SPARK-7021] Add JUnit output for Python unit tests
WIP

Author: Gábor Lipták <gliptak@gmail.com>

Closes #8323 from gliptak/SPARK-7021.
2015-10-22 15:27:11 -07:00
Michael Armbrust 53e83a3a77 [SPARK-11116][SQL] First Draft of Dataset API
*This PR adds a new experimental API to Spark, tentitively named Datasets.*

A `Dataset` is a strongly-typed collection of objects that can be transformed in parallel using functional or relational operations.  Example usage is as follows:

### Functional
```scala
> val ds: Dataset[Int] = Seq(1, 2, 3).toDS()
> ds.filter(_ % 1 == 0).collect()
res1: Array[Int] = Array(1, 2, 3)
```

### Relational
```scala
scala> ds.toDF().show()
+-----+
|value|
+-----+
|    1|
|    2|
|    3|
+-----+

> ds.select(expr("value + 1").as[Int]).collect()
res11: Array[Int] = Array(2, 3, 4)
```

## Comparison to RDDs
 A `Dataset` differs from an `RDD` in the following ways:
  - The creation of a `Dataset` requires the presence of an explicit `Encoder` that can be
    used to serialize the object into a binary format.  Encoders are also capable of mapping the
    schema of a given object to the Spark SQL type system.  In contrast, RDDs rely on runtime
    reflection based serialization.
  - Internally, a `Dataset` is represented by a Catalyst logical plan and the data is stored
    in the encoded form.  This representation allows for additional logical operations and
    enables many operations (sorting, shuffling, etc.) to be performed without deserializing to
    an object.

A `Dataset` can be converted to an `RDD` by calling the `.rdd` method.

## Comparison to DataFrames

A `Dataset` can be thought of as a specialized DataFrame, where the elements map to a specific
JVM object type, instead of to a generic `Row` container. A DataFrame can be transformed into
specific Dataset by calling `df.as[ElementType]`.  Similarly you can transform a strongly-typed
`Dataset` to a generic DataFrame by calling `ds.toDF()`.

## Implementation Status and TODOs

This is a rough cut at the least controversial parts of the API.  The primary purpose here is to get something committed so that we can better parallelize further work and get early feedback on the API.  The following is being deferred to future PRs:
 - Joins and Aggregations (prototype here f11f91e6f0)
 - Support for Java

Additionally, the responsibility for binding an encoder to a given schema is currently done in a fairly ad-hoc fashion.  This is an internal detail, and what we are doing today works for the cases we care about.  However, as we add more APIs we'll probably need to do this in a more principled way (i.e. separate resolution from binding as we do in DataFrames).

## COMPATIBILITY NOTE
Long term we plan to make `DataFrame` extend `Dataset[Row]`.  However,
making this change to che class hierarchy would break the function signatures for the existing
function operations (map, flatMap, etc).  As such, this class should be considered a preview
of the final API.  Changes will be made to the interface after Spark 1.6.

Author: Michael Armbrust <michael@databricks.com>

Closes #9190 from marmbrus/dataset-infra.
2015-10-22 15:20:17 -07:00
guoxi 188ea348fd [SPARK-11242][SQL] In conf/spark-env.sh.template SPARK_DRIVER_MEMORY is documented incorrectly
Minor fix on the comment

Author: guoxi <guoxi@us.ibm.com>

Closes #9201 from xguo27/SPARK-11242.
2015-10-22 13:56:18 -07:00
Cheng Hao d4950e6be4 [SPARK-9735][SQL] Respect the user specified schema than the infer partition schema for HadoopFsRelation
To enable the unit test of `hadoopFsRelationSuite.Partition column type casting`. It previously threw exception like below, as we treat the auto infer partition schema with higher priority than the user specified one.

```
java.lang.ClassCastException: java.lang.Integer cannot be cast to org.apache.spark.unsafe.types.UTF8String
	at org.apache.spark.sql.catalyst.expressions.BaseGenericInternalRow$class.getUTF8String(rows.scala:45)
	at org.apache.spark.sql.catalyst.expressions.GenericInternalRow.getUTF8String(rows.scala:220)
	at org.apache.spark.sql.catalyst.expressions.JoinedRow.getUTF8String(JoinedRow.scala:102)
	at org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificUnsafeProjection.apply(generated.java:62)
	at org.apache.spark.sql.execution.datasources.DataSourceStrategy$$anonfun$17$$anonfun$apply$9.apply(DataSourceStrategy.scala:212)
	at org.apache.spark.sql.execution.datasources.DataSourceStrategy$$anonfun$17$$anonfun$apply$9.apply(DataSourceStrategy.scala:212)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$12.apply(RDD.scala:903)
	at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$12.apply(RDD.scala:903)
	at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1846)
	at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1846)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
	at org.apache.spark.scheduler.Task.run(Task.scala:88)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
07:44:01.344 ERROR org.apache.spark.executor.Executor: Exception in task 14.0 in stage 3.0 (TID 206)
java.lang.ClassCastException: java.lang.Integer cannot be cast to org.apache.spark.unsafe.types.UTF8String
	at org.apache.spark.sql.catalyst.expressions.BaseGenericInternalRow$class.getUTF8String(rows.scala:45)
	at org.apache.spark.sql.catalyst.expressions.GenericInternalRow.getUTF8String(rows.scala:220)
	at org.apache.spark.sql.catalyst.expressions.JoinedRow.getUTF8String(JoinedRow.scala:102)
	at org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificUnsafeProjection.apply(generated.java:62)
	at org.apache.spark.sql.execution.datasources.DataSourceStrategy$$anonfun$17$$anonfun$apply$9.apply(DataSourceStrategy.scala:212)
	at org.apache.spark.sql.execution.datasources.DataSourceStrategy$$anonfun$17$$anonfun$apply$9.apply(DataSourceStrategy.scala:212)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
	at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
	at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
	at scala.collection.AbstractIterator.to(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
	at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
	at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
	at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
	at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$12.apply(RDD.scala:903)
	at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$12.apply(RDD.scala:903)
	at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1846)
	at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1846)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
	at org.apache.spark.scheduler.Task.run(Task.scala:88)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
```

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

Closes #8026 from chenghao-intel/partition_discovery.
2015-10-22 13:11:37 -07:00
Kay Ousterhout 3535b91ddc [SPARK-11163] Remove unnecessary addPendingTask calls.
This commit removes unnecessary calls to addPendingTask in
TaskSetManager.executorLost. These calls are unnecessary: for
tasks that are still pending and haven't been launched, they're
still in all of the correct pending lists, so calling addPendingTask
has no effect. For tasks that are currently running (which may still be
in the pending lists, depending on how they were scheduled), we call
addPendingTask in handleFailedTask, so the calls at the beginning
of executorLost are redundant.

I think these calls are left over from when we re-computed the locality
levels in addPendingTask; now that we call recomputeLocality separately,
I don't think these are necessary.

Now that those calls are removed, the readding parameter in addPendingTask
is no longer necessary, so this commit also removes that parameter.

markhamstra can you take a look at this?

cc vanzin

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #9154 from kayousterhout/SPARK-11163.
2015-10-22 11:39:06 -07:00
zsxwing 7bb6d31cff [SPARK-11232][CORE] Use 'offer' instead of 'put' to make sure calling send won't be interrupted
The current `NettyRpcEndpointRef.send` can be interrupted because it uses `LinkedBlockingQueue.put`, which may hang the application.

Image the following execution order:

  | thread 1: TaskRunner.kill | thread 2: TaskRunner.run
------------- | ------------- | -------------
1 | killed = true |
2 |  | if (killed) {
3 |  | throw new TaskKilledException
4 |  | case _: TaskKilledException  _: InterruptedException if task.killed =>
5 | task.kill(interruptThread): interruptThread is true |
6 | | execBackend.statusUpdate(taskId, TaskState.KILLED, ser.serialize(TaskKilled))
7 | | localEndpoint.send(StatusUpdate(taskId, state, serializedData)): in LocalBackend

Then `localEndpoint.send(StatusUpdate(taskId, state, serializedData))` will throw `InterruptedException`. This will prevent the executor from updating the task status and hang the application.

An failure caused by the above issue here: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/44062/consoleFull

Since `receivers` is an unbounded `LinkedBlockingQueue`, we can just use `LinkedBlockingQueue.offer` to resolve this issue.

Author: zsxwing <zsxwing@gmail.com>

Closes #9198 from zsxwing/dont-interrupt-send.
2015-10-22 11:31:47 -07:00
Wenchen Fan 42d225f449 [SPARK-11216][SQL][FOLLOW-UP] add encoder/decoder for external row
address comments in https://github.com/apache/spark/pull/9184

Author: Wenchen Fan <wenchen@databricks.com>

Closes #9212 from cloud-fan/encoder.
2015-10-22 10:53:59 -07:00
Josh Rosen f6d06adf05 [SPARK-10708] Consolidate sort shuffle implementations
There's a lot of duplication between SortShuffleManager and UnsafeShuffleManager. Given that these now provide the same set of functionality, now that UnsafeShuffleManager supports large records, I think that we should replace SortShuffleManager's serialized shuffle implementation with UnsafeShuffleManager's and should merge the two managers together.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #8829 from JoshRosen/consolidate-sort-shuffle-implementations.
2015-10-22 09:46:30 -07:00
Forest Fang 94e2064fa1 [SPARK-11244][SPARKR] sparkR.stop() should remove SQLContext
SparkR should remove `.sparkRSQLsc` and `.sparkRHivesc` when `sparkR.stop()` is called. Otherwise even when SparkContext is reinitialized, `sparkRSQL.init` returns the stale copy of the object and complains:

```r
sc <- sparkR.init("local")
sqlContext <- sparkRSQL.init(sc)
sparkR.stop()
sc <- sparkR.init("local")
sqlContext <- sparkRSQL.init(sc)
sqlContext
```
producing
```r
Error in callJMethod(x, "getClass") :
  Invalid jobj 1. If SparkR was restarted, Spark operations need to be re-executed.
```

I have added the check and removal only when SparkContext itself is initialized. I have also added corresponding test for this fix. Let me know if you want me to move the test to SQL test suite instead.

p.s. I tried lint-r but ended up a lots of errors on existing code.

Author: Forest Fang <forest.fang@outlook.com>

Closes #9205 from saurfang/sparkR.stop.
2015-10-22 09:34:07 -07:00
zhichao.li c03b6d1158 [SPARK-11121][CORE] Correct the TaskLocation type
Correct the logic to return `HDFSCacheTaskLocation` instance when the input `str` is a in memory location.

Author: zhichao.li <zhichao.li@intel.com>

Closes #9096 from zhichao-li/uselessBranch.
2015-10-22 03:59:26 -07:00
Davies Liu 1d97332715 [SPARK-11243][SQL] output UnsafeRow from columnar cache
This PR change InMemoryTableScan to output UnsafeRow, and optimize the unrolling and scanning by coping the bytes for var-length types between UnsafeRow and ByteBuffer directly without creating the wrapper objects. When scanning the decimals in TPC-DS store_sales table, it's 80% faster (copy it as long without create Decimal objects).

Author: Davies Liu <davies@databricks.com>

Closes #9203 from davies/unsafe_cache.
2015-10-21 19:20:31 -07:00
Yanbo Liang 40a10d7675 [SPARK-9392][SQL] Dataframe drop should work on unresolved columns
Dataframe drop should work on unresolved columns

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8821 from yanboliang/spark-9392.
2015-10-21 17:50:33 -07:00
Reynold Xin 555b2086a1 Minor cleanup of ShuffleMapStage.outputLocs code.
I was looking at this code and found the documentation to be insufficient. I added more documentation, and refactored some relevant code path slightly to improve encapsulation. There are more that I want to do, but I want to get these changes in before doing more work.

My goal is to reduce exposing internal fields directly in ShuffleMapStage to improve encapsulation. After this change, DAGScheduler no longer directly writes outputLocs. There are still 3 places that reads outputLocs directly, but we can change those later.

Author: Reynold Xin <rxin@databricks.com>

Closes #9175 from rxin/stage-cleanup.
2015-10-21 15:33:13 -07:00
navis.ryu f481090a71 [SPARK-10151][SQL] Support invocation of hive macro
Macro in hive (which is GenericUDFMacro) contains real function inside of it but it's not conveyed to tasks, resulting null-pointer exception.

Author: navis.ryu <navis@apache.org>

Closes #8354 from navis/SPARK-10151.
2015-10-21 15:07:08 -07:00
Dilip Biswal dce2f8c9d7 [SPARK-8654][SQL] Analysis exception when using NULL IN (...) : invalid cast
In the analysis phase , while processing the rules for IN predicate, we
compare the in-list types to the lhs expression type and generate
cast operation if necessary. In the case of NULL [NOT] IN expr1 , we end up
generating cast between in list types to NULL like cast (1 as NULL) which
is not a valid cast.

The fix is to find a common type between LHS and RHS expressions and cast
all the expression to the common type.

Author: Dilip Biswal <dbiswal@us.ibm.com>

This patch had conflicts when merged, resolved by
Committer: Michael Armbrust <michael@databricks.com>

Closes #9036 from dilipbiswal/spark_8654_new.
2015-10-21 14:29:03 -07:00
Shagun Sodhani 19ad18638e [SPARK-11233][SQL] register cosh in function registry
Author: Shagun Sodhani <sshagunsodhani@gmail.com>

Closes #9199 from shagunsodhani/proposed-fix-#11233.
2015-10-21 14:18:06 -07:00
Artem Aliev a37cd87048 [SPARK-11208][SQL] Filter out 'hive.metastore.rawstore.impl' from executionHive temporary config
The executionHive assumed to be a standard meta store located in temporary directory as a derby db. But hive.metastore.rawstore.impl was not filtered out so any custom implementation of the metastore with other storage properties (not JDO) will persist that temporary functions. CassandraHiveMetaStore from DataStax Enterprise is one of examples.

Author: Artem Aliev <artem.aliev@datastax.com>

Closes #9178 from artem-aliev/SPARK-11208.
2015-10-21 14:12:07 -07:00
Yin Huai 3afe448d39 [SPARK-9740][SPARK-9592][SPARK-9210][SQL] Change the default behavior of First/Last to RESPECT NULLS.
I am changing the default behavior of `First`/`Last` to respect null values (the SQL standard default behavior).

https://issues.apache.org/jira/browse/SPARK-9740

Author: Yin Huai <yhuai@databricks.com>

Closes #8113 from yhuai/firstLast.
2015-10-21 13:43:17 -07:00
Davies Liu f8c6bec657 [SPARK-11197][SQL] run SQL on files directly
This PR introduce a new feature to run SQL directly on files without create a table, for example:

```
select id from json.`path/to/json/files` as j
```

Author: Davies Liu <davies@databricks.com>

Closes #9173 from davies/source.
2015-10-21 13:38:30 -07:00
Wenchen Fan 7c74ebca05 [SPARK-10743][SQL] keep the name of expression if possible when do cast
Author: Wenchen Fan <cloud0fan@163.com>

Closes #8859 from cloud-fan/cast.
2015-10-21 13:22:35 -07:00
Dilip Biswal 49ea0e9d7c [SPARK-10534] [SQL] ORDER BY clause allows only columns that are present in the select projection list
Find out the missing attributes by recursively looking
at the sort order expression and rest of the code
takes care of projecting them out.

Added description from cloud-fan

I wanna explain a bit more about this bug.

When we resolve sort ordering, we will use a special method, which only resolves UnresolvedAttributes and UnresolvedExtractValue. However, for something like Floor('a), even the 'a is resolved, the floor expression may still being unresolved as data type mismatch(for example, 'a is string type and Floor need double type), thus can't pass this filter, and we can't push down this missing attribute 'a

Author: Dilip Biswal <dbiswal@us.ibm.com>

Closes #9123 from dilipbiswal/SPARK-10534.
2015-10-21 11:10:32 -07:00
Wenchen Fan ccf536f903 [SPARK-11216] [SQL] add encoder/decoder for external row
Implement encode/decode for external row based on `ClassEncoder`.

TODO:
* code cleanup
* ~~fix corner cases~~
* refactor the encoder interface
* improve test for product codegen, to cover more corner cases.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #9184 from cloud-fan/encoder.
2015-10-21 11:06:34 -07:00
nitin goyal f62e326088 [SPARK-11179] [SQL] Push filters through aggregate
Push conjunctive predicates though Aggregate operators when their references are a subset of the groupingExpressions.

Query plan before optimisation :-
Filter ((c#138L = 2) && (a#0 = 3))
 Aggregate [a#0], [a#0,count(b#1) AS c#138L]
  Project [a#0,b#1]
   LocalRelation [a#0,b#1,c#2]

Query plan after optimisation :-
Filter (c#138L = 2)
 Aggregate [a#0], [a#0,count(b#1) AS c#138L]
  Filter (a#0 = 3)
   Project [a#0,b#1]
    LocalRelation [a#0,b#1,c#2]

Author: nitin goyal <nitin.goyal@guavus.com>
Author: nitin.goyal <nitin.goyal@guavus.com>

Closes #9167 from nitin2goyal/master.
2015-10-21 10:45:21 -07:00
Pravin Gadakh 8e82e59834 [SPARK-11037][SQL] using Option instead of Some in JdbcDialects
Using Option instead of Some in getCatalystType method.

Author: Pravin Gadakh <prgadakh@in.ibm.com>

Closes #9195 from pravingadakh/master.
2015-10-21 10:35:09 -07:00
Jeff Zhang 5cdea7d1e5 [SPARK-11205][PYSPARK] Delegate to scala DataFrame API rather than p…
…rint in python

No test needed. Verify it manually in pyspark shell

Author: Jeff Zhang <zjffdu@apache.org>

Closes #9177 from zjffdu/SPARK-11205.
2015-10-20 23:58:27 -07:00
felixcheung 1107bd958a [SPARK-11221][SPARKR] fix R doc for lit and add examples
Currently the documentation for `lit` is inconsistent with doc format, references "Scala symbol" and has no example. Fixing that.
shivaram

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #9187 from felixcheung/rlit.
2015-10-20 21:40:22 -07:00
Xiangrui Meng 135ade9050 [MINOR][ML] fix doc warnings
Without an empty line, sphinx will treat doctest as docstring. holdenk

~~~
/Users/meng/src/spark/python/pyspark/ml/feature.py:docstring of pyspark.ml.feature.CountVectorizer:3: ERROR: Undefined substitution referenced: "label|raw |vectors | +-----+---------------+-------------------------+ |0 |[a, b, c] |(3,[0,1,2],[1.0,1.0,1.0])".
/Users/meng/src/spark/python/pyspark/ml/feature.py:docstring of pyspark.ml.feature.CountVectorizer:3: ERROR: Undefined substitution referenced: "1 |[a, b, b, c, a]|(3,[0,1,2],[2.0,2.0,1.0])".
~~~

Author: Xiangrui Meng <meng@databricks.com>

Closes #9188 from mengxr/py-count-vec-doc-fix.
2015-10-20 18:38:06 -07:00
Xiangrui Meng 45861693be [SPARK-10082][MLLIB] minor style updates for matrix indexing after #8271
* `>=0` => `>= 0`
* print `i`, `j` in the log message

MechCoder

Author: Xiangrui Meng <meng@databricks.com>

Closes #9189 from mengxr/SPARK-10082.
2015-10-20 18:37:29 -07:00
Cheng Lian 89e6db6150 [SPARK-11153][SQL] Disables Parquet filter push-down for string and binary columns
Due to PARQUET-251, `BINARY` columns in existing Parquet files may be written with corrupted statistics information. This information is used by filter push-down optimization. Since Spark 1.5 turns on Parquet filter push-down by default, we may end up with wrong query results. PARQUET-251 has been fixed in parquet-mr 1.8.1, but Spark 1.5 is still using 1.7.0.

This affects all Spark SQL data types that can be mapped to Parquet {{BINARY}}, namely:

- `StringType`

- `BinaryType`

- `DecimalType`

  (But Spark SQL doesn't support pushing down filters involving `DecimalType` columns for now.)

To avoid wrong query results, we should disable filter push-down for columns of `StringType` and `BinaryType` until we upgrade to parquet-mr 1.8.

Author: Cheng Lian <lian@databricks.com>

Closes #9152 from liancheng/spark-11153.workaround-parquet-251.

(cherry picked from commit 0887e5e878)
Signed-off-by: Cheng Lian <lian@databricks.com>
2015-10-21 09:02:59 +08:00
Holden Karau aea7142c98 [SPARK-10767][PYSPARK] Make pyspark shared params codegen more consistent
Namely "." shows up in some places in the template when using the param docstring and not in others

Author: Holden Karau <holden@pigscanfly.ca>

Closes #9017 from holdenk/SPARK-10767-Make-pyspark-shared-params-codegen-more-consistent.
2015-10-20 16:51:32 -07:00
MechCoder da46b77afd [SPARK-10082][MLLIB] Validate i, j in apply DenseMatrices and SparseMatrices
Given row_ind should be less than the number of rows
Given col_ind should be less than the number of cols.

The current code in master gives unpredictable behavior for such cases.

Author: MechCoder <manojkumarsivaraj334@gmail.com>

Closes #8271 from MechCoder/hash_code_matrices.
2015-10-20 16:35:34 -07:00
noelsmith 04521ea067 [SPARK-10269][PYSPARK][MLLIB] Add @since annotation to pyspark.mllib.classification
Duplicated the since decorator from pyspark.sql into pyspark (also tweaked to handle functions without docstrings).

Added since to methods + "versionadded::" to classes derived from the file history.

Note - some methods are inherited from the regression module (i.e. LinearModel.intercept) so these won't have version numbers in the API docs until that model is updated.

Author: noelsmith <mail@noelsmith.com>

Closes #8626 from noel-smith/SPARK-10269-since-mlib-classification.
2015-10-20 16:14:20 -07:00
Tijo Thomas 9f49895fef [SPARK-10261][DOCUMENTATION, ML] Fixed @Since annotation to ml.evaluation
Author: Tijo Thomas <tijoparacka@gmail.com>
Author: tijo <tijo@ezzoft.com>

Closes #8554 from tijoparacka/SPARK-10261-2.
2015-10-20 16:13:34 -07:00
noelsmith 82e9d9c81b [SPARK-10272][PYSPARK][MLLIB] Added @since tags to pyspark.mllib.evaluation
Duplicated the since decorator from pyspark.sql into pyspark (also tweaked to handle functions without docstrings).

Added since to public methods + "versionadded::" to classes (derived from the git file history in pyspark).

Note - I added also the tags to MultilabelMetrics even though it isn't declared as public in the __all__ statement... if that's incorrect - I'll remove.

Author: noelsmith <mail@noelsmith.com>

Closes #8628 from noel-smith/SPARK-10272-since-mllib-evalutation.
2015-10-20 15:05:02 -07:00
Davies Liu 06e6b765d0 [SPARK-11149] [SQL] Improve cache performance for primitive types
This PR improve the performance by:

1) Generate an Iterator that take Iterator[CachedBatch] as input, and call accessors (unroll the loop for columns), avoid the expensive Iterator.flatMap.

2) Use Unsafe.getInt/getLong/getFloat/getDouble instead of ByteBuffer.getInt/getLong/getFloat/getDouble, the later one actually read byte by byte.

3) Remove the unnecessary copy() in Coalesce(), which is not related to memory cache, found during benchmark.

The following benchmark showed that we can speedup the columnar cache of int by 2x.

```
path = '/opt/tpcds/store_sales/'
int_cols = ['ss_sold_date_sk', 'ss_sold_time_sk', 'ss_item_sk','ss_customer_sk']
df = sqlContext.read.parquet(path).select(int_cols).cache()
df.count()

t = time.time()
print df.select("*")._jdf.queryExecution().toRdd().count()
print time.time() - t
```

Author: Davies Liu <davies@databricks.com>

Closes #9145 from davies/byte_buffer.
2015-10-20 14:01:53 -07:00
Davies Liu 67d468f8d9 [SPARK-11111] [SQL] fast null-safe join
Currently, we use CartesianProduct for join with null-safe-equal condition.
```
scala> sqlContext.sql("select * from t a join t b on (a.i <=> b.i)").explain
== Physical Plan ==
TungstenProject [i#2,j#3,i#7,j#8]
 Filter (i#2 <=> i#7)
  CartesianProduct
   LocalTableScan [i#2,j#3], [[1,1]]
   LocalTableScan [i#7,j#8], [[1,1]]
```
Actually, we can have an equal-join condition as  `coalesce(i, default) = coalesce(b.i, default)`, then an partitioned join algorithm could be used.

After this PR, the plan will become:
```
>>> sqlContext.sql("select * from a join b ON a.id <=> b.id").explain()
TungstenProject [id#0L,id#1L]
 Filter (id#0L <=> id#1L)
  SortMergeJoin [coalesce(id#0L,0)], [coalesce(id#1L,0)]
   TungstenSort [coalesce(id#0L,0) ASC], false, 0
    TungstenExchange hashpartitioning(coalesce(id#0L,0),200)
     ConvertToUnsafe
      Scan PhysicalRDD[id#0L]
   TungstenSort [coalesce(id#1L,0) ASC], false, 0
    TungstenExchange hashpartitioning(coalesce(id#1L,0),200)
     ConvertToUnsafe
      Scan PhysicalRDD[id#1L]
```

Author: Davies Liu <davies@databricks.com>

Closes #9120 from davies/null_safe.
2015-10-20 13:40:24 -07:00
Wenchen Fan 478c7ce862 [SPARK-6740] [SQL] correctly parse NOT operator with comparison operations
We can't parse `NOT` operator with comparison operations like `SELECT NOT TRUE > TRUE`, this PR fixed it.

Takes over https://github.com/apache/spark/pull/6326.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #8617 from cloud-fan/not.
2015-10-20 13:38:25 -07:00
vundela 2f6dd634c1 [SPARK-11105] [YARN] Distribute log4j.properties to executors
Currently log4j.properties file is not uploaded to executor's which is leading them to use the default values. This fix will make sure that file is always uploaded to distributed cache so that executor will use the latest settings.

If user specifies log configurations through --files then executors will be picking configs from --files instead of $SPARK_CONF_DIR/log4j.properties

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

Closes #9118 from vundela/master.
2015-10-20 11:12:28 -07:00
Holden Karau e18b571c33 [SPARK-10447][SPARK-3842][PYSPARK] upgrade pyspark to py4j0.9
Upgrade to Py4j0.9

Author: Holden Karau <holden@pigscanfly.ca>
Author: Holden Karau <holden@us.ibm.com>

Closes #8615 from holdenk/SPARK-10447-upgrade-pyspark-to-py4j0.9.
2015-10-20 10:52:49 -07:00
Daoyuan Wang 94139557c5 [SPARK-10463] [SQL] remove PromotePrecision during optimization
PromotePrecision is not necessary after HiveTypeCoercion done.

Jira:
https://issues.apache.org/jira/browse/SPARK-10463

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

Closes #8621 from adrian-wang/promoterm.
2015-10-20 09:20:35 -07:00
Jakob Odersky 60851bc7bf [SPARK-11110][BUILD] Remove transient annotation for parameters.
`transient` annotations on class parameters (not case class parameters or vals) causes compilation errors during compilation with Scala 2.11.
I understand that transient *parameters* make no sense, however I don't quite understand why the 2.10 compiler accepted them.

Note: in case it is preferred to keep the annotations in case someone would in the future want to redefine them as vals, it would also be possible to just add `val` after the annotation, e.g. `class Foo(transient x: Int)` becomes `class Foo(transient private val x: Int)`.

I chose to remove the annotation as it also reduces needles clutter, however please feel free to tell me if you prefer the second option and I'll update the PR

Author: Jakob Odersky <jodersky@gmail.com>

Closes #9126 from jodersky/sbt-scala-2.11.
2015-10-20 08:54:34 +01:00
Jean-Baptiste Onofré 8f74aa6397 [SPARK-10876] Display total uptime for completed applications
Author: Jean-Baptiste Onofré <jbonofre@apache.org>

Closes #9059 from jbonofre/SPARK-10876.
2015-10-20 08:45:39 +01:00
Cheng Lian 8b877cc4ee [SPARK-11088][SQL] Merges partition values using UnsafeProjection
`DataSourceStrategy.mergeWithPartitionValues` is essentially a projection implemented in a quite inefficient way. This PR optimizes this method with `UnsafeProjection` to avoid unnecessary boxing costs.

Author: Cheng Lian <lian@databricks.com>

Closes #9104 from liancheng/spark-11088.faster-partition-values-merging.
2015-10-19 16:57:20 -07:00
Ryan Williams 16906ef23a [SPARK-11120] Allow sane default number of executor failures when dynamically allocating in YARN
I also added some information to container-failure error msgs about what host they failed on, which would have helped me identify the problem that lead me to this JIRA and PR sooner.

Author: Ryan Williams <ryan.blake.williams@gmail.com>

Closes #9147 from ryan-williams/dyn-exec-failures.
2015-10-19 16:34:15 -07:00
Chris Bannister fc26f32cf1 [SPARK-9708][MESOS] Spark should create local temporary directories in Mesos sandbox when launched with Mesos
This is my own original work and I license this to the project under the project's open source license

Author: Chris Bannister <chris.bannister@swiftkey.com>
Author: Chris Bannister <chris.bannister@swiftkey.net>

Closes #8358 from Zariel/mesos-local-dir.
2015-10-19 16:24:40 -07:00
Davies Liu 232d7f8d42 [SPARK-11114][PYSPARK] add getOrCreate for SparkContext/SQLContext in Python
Also added SQLContext.newSession()

Author: Davies Liu <davies@databricks.com>

Closes #9122 from davies/py_create.
2015-10-19 16:18:20 -07:00
Liang-Chi Hsieh a1413b3662 [SPARK-11051][CORE] Do not allow local checkpointing after the RDD is materialized and checkpointed
JIRA: https://issues.apache.org/jira/browse/SPARK-11051

When a `RDD` is materialized and checkpointed, its partitions and dependencies are cleared. If we allow local checkpointing on it and assign `LocalRDDCheckpointData` to its `checkpointData`. Next time when the RDD is materialized again, the error will be thrown.

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

Closes #9072 from viirya/no-localcheckpoint-after-checkpoint.
2015-10-19 16:16:31 -07:00