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11174 commits

Author SHA1 Message Date
Davies Liu a8332098ce [SPARK-6216] [PYSPARK] check python version of worker with driver
This PR revert #5404, change to pass the version of python in driver into JVM, check it in worker before deserializing closure, then it can works with different major version of Python.

Author: Davies Liu <davies@databricks.com>

Closes #6203 from davies/py_version and squashes the following commits:

b8fb76e [Davies Liu] fix test
6ce5096 [Davies Liu] use string for version
47c6278 [Davies Liu] check python version of worker with driver

(cherry picked from commit 32fbd297dd)
Signed-off-by: Josh Rosen <joshrosen@databricks.com>
2015-05-18 12:55:37 -07:00
Cheng Lian 39623481fc [SPARK-7673] [SQL] WIP: HadoopFsRelation and ParquetRelation2 performance optimizations
This PR introduces several performance optimizations to `HadoopFsRelation` and `ParquetRelation2`:

1.  Moving `FileStatus` listing from `DataSourceStrategy` into a cache within `HadoopFsRelation`.

    This new cache generalizes and replaces the one used in `ParquetRelation2`.

    This also introduces an interface change: to reuse cached `FileStatus` objects, `HadoopFsRelation.buildScan` methods now receive `Array[FileStatus]` instead of `Array[String]`.

1.  When Parquet task side metadata reading is enabled, skip reading row group information when reading Parquet footers.

    This is basically what PR #5334 does. Also, now we uses `ParquetFileReader.readAllFootersInParallel` to read footers in parallel.

Another optimization in question is, instead of asking `HadoopFsRelation.buildScan` to return an `RDD[Row]` for a single selected partition and then union them all, we ask it to return an `RDD[Row]` for all selected partitions. This optimization is based on the fact that Hadoop configuration broadcasting used in `NewHadoopRDD` takes 34% time in the following microbenchmark.  However, this complicates data source user code because user code must merge partition values manually.

To check the cost of broadcasting in `NewHadoopRDD`, I also did microbenchmark after removing the `broadcast` call in `NewHadoopRDD`.  All results are shown below.

### Microbenchmark

#### Preparation code

Generating a partitioned table with 50k partitions, 1k rows per partition:

```scala
import sqlContext._
import sqlContext.implicits._

for (n <- 0 until 500) {
  val data = for {
    p <- (n * 10) until ((n + 1) * 10)
    i <- 0 until 1000
  } yield (i, f"val_$i%04d", f"$p%04d")

  data.
    toDF("a", "b", "p").
    write.
    partitionBy("p").
    mode("append").
    parquet(path)
}
```

#### Benchmarking code

```scala
import sqlContext._
import sqlContext.implicits._

import org.apache.spark.sql.types._
import com.google.common.base.Stopwatch

val path = "hdfs://localhost:9000/user/lian/5k"

def benchmark(n: Int)(f: => Unit) {
  val stopwatch = new Stopwatch()

  def run() = {
    stopwatch.reset()
    stopwatch.start()
    f
    stopwatch.stop()
    stopwatch.elapsedMillis()
  }

  val records = (0 until n).map(_ => run())

  (0 until n).foreach(i => println(s"Round $i: ${records(i)} ms"))
  println(s"Average: ${records.sum / n.toDouble} ms")
}

benchmark(3) { read.parquet(path).explain(extended = true) }
```

#### Results

Before:

```
Round 0: 72528 ms
Round 1: 68938 ms
Round 2: 65372 ms
Average: 68946.0 ms
```

After:

```
Round 0: 59499 ms
Round 1: 53645 ms
Round 2: 53844 ms
Round 3: 49093 ms
Round 4: 50555 ms
Average: 53327.2 ms
```

Also removing Hadoop configuration broadcasting:

(Note that I was testing on a local laptop, thus network cost is pretty low.)

```
Round 0: 15806 ms
Round 1: 14394 ms
Round 2: 14699 ms
Round 3: 15334 ms
Round 4: 14123 ms
Average: 14871.2 ms
```

Author: Cheng Lian <lian@databricks.com>

Closes #6225 from liancheng/spark-7673 and squashes the following commits:

2d58a2b [Cheng Lian] Skips reading row group information when using task side metadata reading
7aa3748 [Cheng Lian] Optimizes FileStatusCache by introducing a map from parent directories to child files
ba41250 [Cheng Lian] Reuses HadoopFsRelation FileStatusCache in ParquetRelation2
3d278f7 [Cheng Lian] Fixes a bug when reading a single Parquet data file
b84612a [Cheng Lian] Fixes Scala style issue
6a08b02 [Cheng Lian] WIP: Moves file status cache into HadoopFSRelation

(cherry picked from commit 9dadf019b9)
Signed-off-by: Yin Huai <yhuai@databricks.com>
2015-05-18 12:47:19 -07:00
Yin Huai a385f4b8dd [SPARK-7567] [SQL] [follow-up] Use a new flag to set output committer based on mapreduce apis
cc liancheng marmbrus

Author: Yin Huai <yhuai@databricks.com>

Closes #6130 from yhuai/directOutput and squashes the following commits:

312b07d [Yin Huai] A data source can use spark.sql.sources.outputCommitterClass to override the output committer.

(cherry picked from commit 530397ba2f)
Signed-off-by: Michael Armbrust <michael@databricks.com>
2015-05-18 12:17:22 -07:00
Wenchen Fan d6f5f37911 [SPARK-7269] [SQL] Incorrect analysis for aggregation(use semanticEquals)
A modified version of https://github.com/apache/spark/pull/6110, use `semanticEquals` to make it more efficient.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #6173 from cloud-fan/7269 and squashes the following commits:

e4a3cc7 [Wenchen Fan] address comments
cc02045 [Wenchen Fan] consider elements length equal
d7ff8f4 [Wenchen Fan] fix 7269

(cherry picked from commit 103c863c2e)
Signed-off-by: Michael Armbrust <michael@databricks.com>
2015-05-18 12:13:09 -07:00
scwf dbd4ec807b [SPARK-7631] [SQL] treenode argString should not print children
spark-sql>
> explain extended
> select * from (
> select key from src union all
> select key from src) t;

now the spark plan will print children in argString
```
== Physical Plan ==
Union[ HiveTableScan key#1, (MetastoreRelation default, src, None), None,
HiveTableScan key#3, (MetastoreRelation default, src, None), None]
HiveTableScan key#1, (MetastoreRelation default, src, None), None
HiveTableScan key#3, (MetastoreRelation default, src, None), None
```

after this patch:
```
== Physical Plan ==
Union
 HiveTableScan [key#1], (MetastoreRelation default, src, None), None
 HiveTableScan [key#3], (MetastoreRelation default, src, None), None
```

I have tested this locally

Author: scwf <wangfei1@huawei.com>

Closes #6144 from scwf/fix-argString and squashes the following commits:

1a642e0 [scwf] fix treenode argString

(cherry picked from commit fc2480ed13)
Signed-off-by: Michael Armbrust <michael@databricks.com>
2015-05-18 12:05:32 -07:00
Zhan Zhang 65d71bd9fb [SPARK-2883] [SQL] ORC data source for Spark SQL
This PR updates PR #6135 authored by zhzhan from Hortonworks.

----

This PR implements a Spark SQL data source for accessing ORC files.

> **NOTE**
>
> Although ORC is now an Apache TLP, the codebase is still tightly coupled with Hive.  That's why the new ORC data source is under `org.apache.spark.sql.hive` package, and must be used with `HiveContext`.  However, it doesn't require existing Hive installation to access ORC files.

1.  Saving/loading ORC files without contacting Hive metastore

1.  Support for complex data types (i.e. array, map, and struct)

1.  Aware of common optimizations provided by Spark SQL:

    - Column pruning
    - Partitioning pruning
    - Filter push-down

1.  Schema evolution support
1.  Hive metastore table conversion

This PR also include initial work done by scwf from Huawei (PR #3753).

Author: Zhan Zhang <zhazhan@gmail.com>
Author: Cheng Lian <lian@databricks.com>

Closes #6194 from liancheng/polishing-orc and squashes the following commits:

55ecd96 [Cheng Lian] Reorganizes ORC test suites
d4afeed [Cheng Lian] Addresses comments
21ada22 [Cheng Lian] Adds @since and @Experimental annotations
128bd3b [Cheng Lian] ORC filter bug fix
d734496 [Cheng Lian] Polishes the ORC data source
2650a42 [Zhan Zhang] resolve review comments
3c9038e [Zhan Zhang] resolve review comments
7b3c7c5 [Zhan Zhang] save mode fix
f95abfd [Zhan Zhang] reuse test suite
7cc2c64 [Zhan Zhang] predicate fix
4e61c16 [Zhan Zhang] minor change
305418c [Zhan Zhang] orc data source support

(cherry picked from commit aa31e431fc)
Signed-off-by: Michael Armbrust <michael@databricks.com>
2015-05-18 12:03:59 -07:00
Xiangrui Meng cf4e04a0c5 [SPARK-7380] [MLLIB] pipeline stages should be copyable in Python
This PR makes pipeline stages in Python copyable and hence simplifies some implementations. It also includes the following changes:

1. Rename `paramMap` and `defaultParamMap` to `_paramMap` and `_defaultParamMap`, respectively.
2. Accept a list of param maps in `fit`.
3. Use parent uid and name to identify param.

jkbradley

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

Closes #6088 from mengxr/SPARK-7380 and squashes the following commits:

413c463 [Xiangrui Meng] remove unnecessary doc
4159f35 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7380
611c719 [Xiangrui Meng] fix python style
68862b8 [Xiangrui Meng] update _java_obj initialization
927ad19 [Xiangrui Meng] fix ml/tests.py
0138fc3 [Xiangrui Meng] update feature transformers and fix a bug in RegexTokenizer
9ca44fb [Xiangrui Meng] simplify Java wrappers and add tests
c7d84ef [Xiangrui Meng] update ml/tests.py to test copy params
7e0d27f [Xiangrui Meng] merge master
46840fb [Xiangrui Meng] update wrappers
b6db1ed [Xiangrui Meng] update all self.paramMap to self._paramMap
46cb6ed [Xiangrui Meng] merge master
a163413 [Xiangrui Meng] fix style
1042e80 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7380
9630eae [Xiangrui Meng] fix Identifiable._randomUID
13bd70a [Xiangrui Meng] update ml/tests.py
64a536c [Xiangrui Meng] use _fit/_transform/_evaluate to simplify the impl
02abf13 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into copyable-python
66ce18c [Joseph K. Bradley] some cleanups before sending to Xiangrui
7431272 [Joseph K. Bradley] Rebased with master

(cherry picked from commit 9c7e802a5a)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
2015-05-18 12:02:26 -07:00
Wenchen Fan 7d44c01c5e [SQL] [MINOR] [THIS] use private for internal field in ScalaUdf
Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #6235 from cloud-fan/tmp and squashes the following commits:

8f16367 [Wenchen Fan] use private[this]

(cherry picked from commit 56ede88485)
Signed-off-by: Michael Armbrust <michael@databricks.com>
2015-05-18 12:02:10 -07:00
Cheng Lian c7623a20a9 [SPARK-7570] [SQL] Ignores _temporary during partition discovery
<!-- Reviewable:start -->
[<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/6091)
<!-- Reviewable:end -->

Author: Cheng Lian <lian@databricks.com>

Closes #6091 from liancheng/spark-7570 and squashes the following commits:

8ff07e8 [Cheng Lian] Ignores _temporary during partition discovery

(cherry picked from commit 010a1c2780)
Signed-off-by: Michael Armbrust <michael@databricks.com>
2015-05-18 11:59:57 -07:00
Rene Treffer b41301a13f [SPARK-6888] [SQL] Make the jdbc driver handling user-definable
Replace the DriverQuirks with JdbcDialect(s) (and MySQLDialect/PostgresDialect)
and allow developers to change the dialects on the fly (for new JDBCRRDs only).

Some types (like an unsigned 64bit number) can be trivially mapped to java.
The status quo is that the RRD will fail to load.
This patch makes it possible to overwrite the type mapping to read e.g.
64Bit numbers as strings and handle them afterwards in software.

JDBCSuite has an example that maps all types to String, which should always
work (at the cost of extra code afterwards).

As a side effect it should now be possible to develop simple dialects
out-of-tree and even with spark-shell.

Author: Rene Treffer <treffer@measite.de>

Closes #5555 from rtreffer/jdbc-dialects and squashes the following commits:

3cbafd7 [Rene Treffer] [SPARK-6888] ignore classes belonging to changed API in MIMA report
fe7e2e8 [Rene Treffer] [SPARK-6888] Make the jdbc driver handling user-definable
2015-05-18 11:57:06 -07:00
Andrew Or a0ae8ce013 [SPARK-7627] [SPARK-7472] DAG visualization: style skipped stages
This patch fixes two things:

**SPARK-7627.** Cached RDDs no longer light up on the job page. This is a simple fix.
**SPARK-7472.** Display skipped stages differently from normal stages.

The latter is a major UX issue. Because we link the job viz to the stage viz even for skipped stages, the user may inadvertently click into the stage page of a skipped stage, which is empty.

-------------------
<img src="https://cloud.githubusercontent.com/assets/2133137/7675241/de1a3da6-fcea-11e4-8101-88055cef78c5.png" width="300px" />

Author: Andrew Or <andrew@databricks.com>

Closes #6171 from andrewor14/dag-viz-skipped and squashes the following commits:

f261797 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
0eda358 [Andrew Or] Tweak skipped stage border color
c604150 [Andrew Or] Tweak grayscale colors
7010676 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
762b541 [Andrew Or] Use special prefix for stage clusters to avoid collisions
51c95b9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
b928cd4 [Andrew Or] Fix potential leak + write tests for it
7c4c364 [Andrew Or] Show skipped stages differently
7cc34ce [Andrew Or] Merge branch 'master' of github.com:apache/spark into dag-viz-skipped
c121fa2 [Andrew Or] Fix cache color

(cherry picked from commit 563bfcc1ab)
Signed-off-by: Andrew Or <andrew@databricks.com>
2015-05-18 10:59:46 -07:00
Vincenzo Selvaggio a95d4e18f2 [SPARK-7272] [MLLIB] User guide for PMML model export
https://issues.apache.org/jira/browse/SPARK-7272

Author: Vincenzo Selvaggio <vselvaggio@hotmail.it>

Closes #6219 from selvinsource/mllib_pmml_model_export_SPARK-7272 and squashes the following commits:

c866fb8 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
1beda98 [Vincenzo Selvaggio] [SPARK-7272] Initial user guide for pmml export
d670662 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
2731375 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
680dc33 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
2e298b5 [Vincenzo Selvaggio] Update mllib-pmml-model-export.md
a932f51 [Vincenzo Selvaggio] Create mllib-pmml-model-export.md

(cherry picked from commit 814b3dabdf)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
2015-05-18 08:46:40 -07:00
Xiangrui Meng 2c94ffe7e8 [SPARK-6657] [PYSPARK] Fix doc warnings
Fixed the following warnings in `make clean html` under `python/docs`:

~~~
/Users/meng/src/spark/python/pyspark/mllib/evaluation.py:docstring of pyspark.mllib.evaluation.RankingMetrics.ndcgAt:3: ERROR: Unexpected indentation.
/Users/meng/src/spark/python/pyspark/mllib/evaluation.py:docstring of pyspark.mllib.evaluation.RankingMetrics.ndcgAt:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/meng/src/spark/python/pyspark/mllib/fpm.py:docstring of pyspark.mllib.fpm.FPGrowth.train:3: ERROR: Unexpected indentation.
/Users/meng/src/spark/python/pyspark/mllib/fpm.py:docstring of pyspark.mllib.fpm.FPGrowth.train:4: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/meng/src/spark/python/pyspark/sql/__init__.py:docstring of pyspark.sql.DataFrame.replace:16: WARNING: Field list ends without a blank line; unexpected unindent.
/Users/meng/src/spark/python/pyspark/streaming/kafka.py:docstring of pyspark.streaming.kafka.KafkaUtils.createRDD:8: ERROR: Unexpected indentation.
/Users/meng/src/spark/python/pyspark/streaming/kafka.py:docstring of pyspark.streaming.kafka.KafkaUtils.createRDD:9: WARNING: Block quote ends without a blank line; unexpected unindent.
~~~

davies

Author: Xiangrui Meng <meng@databricks.com>

Closes #6221 from mengxr/SPARK-6657 and squashes the following commits:

e3f83fe [Xiangrui Meng] fix sql and streaming doc warnings
2b4371e [Xiangrui Meng] fix mllib python doc warnings

(cherry picked from commit 1ecfac6e38)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
2015-05-18 08:35:24 -07:00
Liang-Chi Hsieh 0e7cd8ff82 [SPARK-7299][SQL] Set precision and scale for Decimal according to JDBC metadata instead of returned BigDecimal
JIRA: https://issues.apache.org/jira/browse/SPARK-7299

When connecting with oracle db through jdbc, the precision and scale of `BigDecimal` object returned by `ResultSet.getBigDecimal` is not correctly matched to the table schema reported by `ResultSetMetaData.getPrecision` and `ResultSetMetaData.getScale`.

So in case you insert a value like `19999` into a column with `NUMBER(12, 2)` type, you get through a `BigDecimal` object with scale as 0. But the dataframe schema has correct type as `DecimalType(12, 2)`. Thus, after you save the dataframe into parquet file and then retrieve it, you will get wrong result `199.99`.

Because it is reported to be problematic on jdbc connection with oracle db. It might be difficult to add test case for it. But according to the user's test on JIRA, it solves this problem.

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

Closes #5833 from viirya/jdbc_decimal_precision and squashes the following commits:

69bc2b5 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into jdbc_decimal_precision
928f864 [Liang-Chi Hsieh] Add comments.
5f9da94 [Liang-Chi Hsieh] Set up Decimal's precision and scale according to table schema instead of returned BigDecimal.

(cherry picked from commit e32c0f69f3)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-18 01:11:10 -07:00
Shuo Xiang 0b6bc8a239 [SPARK-7694] [MLLIB] Use getOrElse for getting the threshold of LR model
The `toString` method of `LogisticRegressionModel` calls `get` method on an Option (threshold) without a safeguard. In spark-shell, the following code `val model = algorithm.run(data).clearThreshold()` in lbfgs code will fail as `toString `method will be called right after `clearThreshold()` to show the results in the REPL.

Author: Shuo Xiang <shuoxiangpub@gmail.com>

Closes #6224 from coderxiang/getorelse and squashes the following commits:

d5f53c9 [Shuo Xiang] use getOrElse for getting the threshold of LR model
5f109b4 [Shuo Xiang] Merge remote-tracking branch 'upstream/master'
c5c5bfe [Shuo Xiang] Merge remote-tracking branch 'upstream/master'
98804c9 [Shuo Xiang] fix bug in topBykey and update test

(cherry picked from commit 775e6f9909)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
2015-05-17 21:16:59 -07:00
zsxwing 2a42d2d8f2 [SPARK-7693][Core] Remove "import scala.concurrent.ExecutionContext.Implicits.global"
Learnt a lesson from SPARK-7655: Spark should avoid to use `scala.concurrent.ExecutionContext.Implicits.global` because the user may submit blocking actions to `scala.concurrent.ExecutionContext.Implicits.global` and exhaust all threads in it. This could crash Spark. So Spark should always use its own thread pools for safety.

This PR removes all usages of `scala.concurrent.ExecutionContext.Implicits.global` and uses proper thread pools to replace them.

Author: zsxwing <zsxwing@gmail.com>

Closes #6223 from zsxwing/SPARK-7693 and squashes the following commits:

a33ff06 [zsxwing] Decrease the max thread number from 1024 to 128
cf4b3fc [zsxwing] Remove "import scala.concurrent.ExecutionContext.Implicits.global"

(cherry picked from commit ff71d34e00)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-17 20:37:27 -07:00
Wenchen Fan be66d1924e [SQL] [MINOR] use catalyst type converter in ScalaUdf
It's a follow-up of https://github.com/apache/spark/pull/5154, we can speed up scala udf evaluation by create type converter in advance.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #6182 from cloud-fan/tmp and squashes the following commits:

241cfe9 [Wenchen Fan] use converter in ScalaUdf

(cherry picked from commit 2f22424e9f)
Signed-off-by: Yin Huai <yhuai@databricks.com>
2015-05-17 16:52:21 -07:00
Tathagata Das e0632ffafd [SPARK-6514] [SPARK-5960] [SPARK-6656] [SPARK-7679] [STREAMING] [KINESIS] Updates to the Kinesis API
SPARK-6514 - Use correct region
SPARK-5960 - Allow AWS Credentials to be directly passed
SPARK-6656 - Specify kinesis application name explicitly
SPARK-7679 - Upgrade to latest KCL and AWS SDK.

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

Closes #6147 from tdas/kinesis-api-update and squashes the following commits:

f23ea77 [Tathagata Das] Updated versions and updated APIs
373b201 [Tathagata Das] Updated Kinesis API

(cherry picked from commit ca4257aec6)
Signed-off-by: Tathagata Das <tathagata.das1565@gmail.com>
2015-05-17 16:49:31 -07:00
Michael Armbrust a8556086d3 [SPARK-7491] [SQL] Allow configuration of classloader isolation for hive
Author: Michael Armbrust <michael@databricks.com>

Closes #6167 from marmbrus/configureIsolation and squashes the following commits:

6147cbe [Michael Armbrust] filter other conf
22cc3bc7 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into configureIsolation
07476ee [Michael Armbrust] filter empty prefixes
dfdf19c [Michael Armbrust] [SPARK-6906][SQL] Allow configuration of classloader isolation for hive

(cherry picked from commit 2ca60ace8f)
Signed-off-by: Michael Armbrust <michael@databricks.com>
2015-05-17 12:43:26 -07:00
Josh Rosen 53d6ab51b2 [SPARK-7686] [SQL] DescribeCommand is assigned wrong output attributes in SparkStrategies
In `SparkStrategies`, `RunnableDescribeCommand` is called with the output attributes of the table being described rather than the attributes for the `describe` command's output.  I discovered this issue because it caused type conversion errors in some UnsafeRow conversion code that I'm writing.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6217 from JoshRosen/SPARK-7686 and squashes the following commits:

953a344 [Josh Rosen] Fix SPARK-7686 with a simple change in SparkStrategies.
a4eec9f [Josh Rosen] Add failing regression test for SPARK-7686

(cherry picked from commit 564562874f)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-17 11:59:35 -07:00
Josh Rosen 6df71eb8c1 [SPARK-7660] Wrap SnappyOutputStream to work around snappy-java bug
This patch wraps `SnappyOutputStream` to ensure that `close()` is idempotent and to guard against write-after-`close()` bugs. This is a workaround for https://github.com/xerial/snappy-java/issues/107, a bug where a non-idempotent `close()` method can lead to stream corruption. We can remove this workaround if we upgrade to a snappy-java version that contains my fix for this bug, but in the meantime this patch offers a backportable Spark fix.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6176 from JoshRosen/SPARK-7660-wrap-snappy and squashes the following commits:

8b77aae [Josh Rosen] Wrap SnappyOutputStream to fix SPARK-7660

(cherry picked from commit f2cc6b5bcc)
Signed-off-by: Josh Rosen <joshrosen@databricks.com>
2015-05-17 09:33:49 -07:00
Steve Loughran 0feb3ded2e [SPARK-7669] Builds against Hadoop 2.6+ get inconsistent curator depend…
This adds a new profile, `hadoop-2.6`, copying over the hadoop-2.4 properties, updating ZK to 3.4.6 and making the curator version a configurable option. That keeps the curator-recipes JAR in sync with that used in hadoop.

There's one more option to consider: making the full curator-client version explicit with its own dependency version. This will pin down the version from hadoop and hive imports

Author: Steve Loughran <stevel@hortonworks.com>

Closes #6191 from steveloughran/stevel/SPARK-7669-hadoop-2.6 and squashes the following commits:

e3e281a [Steve Loughran] SPARK-7669 declare the version of curator-client and curator-framework JARs
2901ea9 [Steve Loughran] SPARK-7669 Builds against Hadoop 2.6+ get inconsistent curator dependencies

(cherry picked from commit 50217667cc)
Signed-off-by: Sean Owen <sowen@cloudera.com>
2015-05-17 17:03:20 +01:00
Liang-Chi Hsieh 898be62489 [SPARK-7447] [SQL] Don't re-merge Parquet schema when the relation is deserialized
JIRA: https://issues.apache.org/jira/browse/SPARK-7447

`MetadataCache` in `ParquetRelation2` is annotated as `transient`. When `ParquetRelation2` is deserialized, we ask `MetadataCache` to refresh and perform schema merging again. It is time-consuming especially for very many parquet files.

With the new `FSBasedParquetRelation`, although `MetadataCache` is not `transient` now, `MetadataCache.refresh()` still performs schema merging again when the relation is deserialized.

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

Closes #6012 from viirya/without_remerge_schema and squashes the following commits:

2663957 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into without_remerge_schema
6ac7d93 [Liang-Chi Hsieh] Merge remote-tracking branch 'upstream/master' into without_remerge_schema
b0fc09b [Liang-Chi Hsieh] Don't generate and merge parquetSchema multiple times.

(cherry picked from commit 3399055787)
Signed-off-by: Cheng Lian <lian@databricks.com>
2015-05-17 15:42:40 +08:00
Shivaram Venkataraman 0ed376afad [MINOR] Add 1.3, 1.3.1 to master branch EC2 scripts
cc pwendell

P.S: I can't believe this was outdated all along ?

Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

Closes #6215 from shivaram/update-ec2-map and squashes the following commits:

ae3937a [Shivaram Venkataraman] Add 1.3, 1.3.1 to master branch EC2 scripts

(cherry picked from commit 1a7b9ce80b)
Signed-off-by: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
2015-05-17 00:12:46 -07:00
Cheng Lian 671a6bca5f [MINOR] [SQL] Removes an unreachable case clause
This case clause is already covered by the one above, and generates a compilation warning.

Author: Cheng Lian <lian@databricks.com>

Closes #6214 from liancheng/remove-unreachable-code and squashes the following commits:

c38ca7c [Cheng Lian] Removes an unreachable case clause

(cherry picked from commit ba4f8ca0d9)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-16 23:20:19 -07:00
Reynold Xin 17e078671e [SPARK-7654][SQL] Move JDBC into DataFrame's reader/writer interface.
Also moved all the deprecated functions into one place for SQLContext and DataFrame, and updated tests to use the new API.

Author: Reynold Xin <rxin@databricks.com>

Closes #6210 from rxin/df-writer-reader-jdbc and squashes the following commits:

7465c2c [Reynold Xin] Fixed unit test.
118e609 [Reynold Xin] Updated tests.
3441b57 [Reynold Xin] Updated javadoc.
13cdd1c [Reynold Xin] [SPARK-7654][SQL] Move JDBC into DataFrame's reader/writer interface.

(cherry picked from commit 517eb37a85)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-16 22:02:00 -07:00
zsxwing 84949104c9 [SPARK-7655][Core] Deserializing value should not hold the TaskSchedulerImpl lock
We should not call `DirectTaskResult.value` when holding the `TaskSchedulerImpl` lock. It may cost dozens of seconds to deserialize a large object.

Author: zsxwing <zsxwing@gmail.com>

Closes #6195 from zsxwing/SPARK-7655 and squashes the following commits:

21f502e [zsxwing] Add more comments
e25fa88 [zsxwing] Add comments
15010b5 [zsxwing] Deserialize value should not hold the TaskSchedulerImpl lock

(cherry picked from commit 3b6ef2c539)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-16 21:03:28 -07:00
Reynold Xin bd057f8b55 [SPARK-7654][MLlib] Migrate MLlib to the DataFrame reader/writer API.
Author: Reynold Xin <rxin@databricks.com>

Closes #6211 from rxin/mllib-reader and squashes the following commits:

79a2cb9 [Reynold Xin] [SPARK-7654][MLlib] Migrate MLlib to the DataFrame reader/writer API.

(cherry picked from commit 161d0b4a41)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-16 15:04:26 -07:00
Matthew Brandyberry 8bde352bd7 [BUILD] update jblas dependency version to 1.2.4
jblas 1.2.4 includes native library support for PPC64LE.

Author: Matthew Brandyberry <mbrandy@us.ibm.com>

Closes #6199 from mtbrandy/jblas-1.2.4 and squashes the following commits:

9df9301 [Matthew Brandyberry] [BUILD] update jblas dependency version to 1.2.4

(cherry picked from commit 1b4e710e5c)
Signed-off-by: Sean Owen <sowen@cloudera.com>
2015-05-16 18:17:59 +01:00
Cheng Lian 856619d485 [HOTFIX] [SQL] Fixes DataFrameWriter.mode(String)
We forgot an assignment there.

/cc rxin

Author: Cheng Lian <lian@databricks.com>

Closes #6212 from liancheng/fix-df-writer and squashes the following commits:

711fbb0 [Cheng Lian] Adds a test case
3b72d78 [Cheng Lian] Fixes DataFrameWriter.mode(String)

(cherry picked from commit ce6391296a)
Signed-off-by: Cheng Lian <lian@databricks.com>
2015-05-16 20:57:26 +08:00
zsxwing ad5b0b1ce2 [SPARK-7655][Core][SQL] Remove 'scala.concurrent.ExecutionContext.Implicits.global' in 'ask' and 'BroadcastHashJoin'
Because both `AkkaRpcEndpointRef.ask` and `BroadcastHashJoin` uses `scala.concurrent.ExecutionContext.Implicits.global`. However, because the tasks in `BroadcastHashJoin` are usually long-running tasks, which will occupy all threads in `global`. Then `ask` cannot get a chance to process the replies.

For `ask`, actually the tasks are very simple, so we can use `MoreExecutors.sameThreadExecutor()`. For `BroadcastHashJoin`, it's better to use `ThreadUtils.newDaemonCachedThreadPool`.

Author: zsxwing <zsxwing@gmail.com>

Closes #6200 from zsxwing/SPARK-7655-2 and squashes the following commits:

cfdc605 [zsxwing] Remove redundant imort and minor doc fix
cf83153 [zsxwing] Add "sameThread" and "newDaemonCachedThreadPool with maxThreadNumber" to ThreadUtils
08ad0ee [zsxwing] Remove 'scala.concurrent.ExecutionContext.Implicits.global' in 'ask' and 'BroadcastHashJoin'

(cherry picked from commit 47e7ffe36b)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-16 00:44:36 -07:00
Nishkam Ravi e7607e5cbc [SPARK-7672] [CORE] Use int conversion in translating kryoserializer.buffer.mb to kryoserializer.buffer
In translating spark.kryoserializer.buffer.mb to spark.kryoserializer.buffer, use of toDouble will lead to "Fractional values not supported" error even when spark.kryoserializer.buffer.mb is an integer.
ilganeli, andrewor14

Author: Nishkam Ravi <nravi@cloudera.com>
Author: nishkamravi2 <nishkamravi@gmail.com>
Author: nravi <nravi@c1704.halxg.cloudera.com>

Closes #6198 from nishkamravi2/master_nravi and squashes the following commits:

171a53c [nishkamravi2] Update SparkConfSuite.scala
5261bf6 [Nishkam Ravi] Add a test for deprecated config spark.kryoserializer.buffer.mb
5190f79 [Nishkam Ravi] In translating from deprecated spark.kryoserializer.buffer.mb to spark.kryoserializer.buffer use int conversion since fractions are not permissible
059ce82 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
eaa13b5 [nishkamravi2] Update Client.scala
981afd2 [Nishkam Ravi] Check for read permission before initiating copy
1b81383 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
0f1abd0 [nishkamravi2] Update Utils.scala
474e3bf [nishkamravi2] Update DiskBlockManager.scala
97c383e [nishkamravi2] Update Utils.scala
8691e0c [Nishkam Ravi] Add a try/catch block around Utils.removeShutdownHook
2be1e76 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
1c13b79 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
bad4349 [nishkamravi2] Update Main.java
36a6f87 [Nishkam Ravi] Minor changes and bug fixes
b7f4ae7 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
4a45d6a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
458af39 [Nishkam Ravi] Locate the jar using getLocation, obviates the need to pass assembly path as an argument
d9658d6 [Nishkam Ravi] Changes for SPARK-6406
ccdc334 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
3faa7a4 [Nishkam Ravi] Launcher library changes (SPARK-6406)
345206a [Nishkam Ravi] spark-class merge Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi
ac58975 [Nishkam Ravi] spark-class changes
06bfeb0 [nishkamravi2] Update spark-class
35af990 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
32c3ab3 [nishkamravi2] Update AbstractCommandBuilder.java
4bd4489 [nishkamravi2] Update AbstractCommandBuilder.java
746f35b [Nishkam Ravi] "hadoop" string in the assembly name should not be mandatory (everywhere else in spark we mandate spark-assembly*hadoop*.jar)
bfe96e0 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
ee902fa [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
d453197 [nishkamravi2] Update NewHadoopRDD.scala
6f41a1d [nishkamravi2] Update NewHadoopRDD.scala
0ce2c32 [nishkamravi2] Update HadoopRDD.scala
f7e33c2 [Nishkam Ravi] Merge branch 'master_nravi' of https://github.com/nishkamravi2/spark into master_nravi
ba1eb8b [Nishkam Ravi] Try-catch block around the two occurrences of removeShutDownHook. Deletion of semi-redundant occurrences of expensive operation inShutDown.
71d0e17 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
494d8c0 [nishkamravi2] Update DiskBlockManager.scala
3c5ddba [nishkamravi2] Update DiskBlockManager.scala
f0d12de [Nishkam Ravi] Workaround for IllegalStateException caused by recent changes to BlockManager.stop
79ea8b4 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
b446edc [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
5c9a4cb [nishkamravi2] Update TaskSetManagerSuite.scala
535295a [nishkamravi2] Update TaskSetManager.scala
3e1b616 [Nishkam Ravi] Modify test for maxResultSize
9f6583e [Nishkam Ravi] Changes to maxResultSize code (improve error message and add condition to check if maxResultSize > 0)
5f8f9ed [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
636a9ff [nishkamravi2] Update YarnAllocator.scala
8f76c8b [Nishkam Ravi] Doc change for yarn memory overhead
35daa64 [Nishkam Ravi] Slight change in the doc for yarn memory overhead
5ac2ec1 [Nishkam Ravi] Remove out
dac1047 [Nishkam Ravi] Additional documentation for yarn memory overhead issue
42c2c3d [Nishkam Ravi] Additional changes for yarn memory overhead issue
362da5e [Nishkam Ravi] Additional changes for yarn memory overhead
c726bd9 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
f00fa31 [Nishkam Ravi] Improving logging for AM memoryOverhead
1cf2d1e [nishkamravi2] Update YarnAllocator.scala
ebcde10 [Nishkam Ravi] Modify default YARN memory_overhead-- from an additive constant to a multiplier (redone to resolve merge conflicts)
2e69f11 [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark into master_nravi
efd688a [Nishkam Ravi] Merge branch 'master' of https://github.com/apache/spark
2b630f9 [nravi] Accept memory input as "30g", "512M" instead of an int value, to be consistent with rest of Spark
3bf8fad [nravi] Merge branch 'master' of https://github.com/apache/spark
5423a03 [nravi] Merge branch 'master' of https://github.com/apache/spark
eb663ca [nravi] Merge branch 'master' of https://github.com/apache/spark
df2aeb1 [nravi] Improved fix for ConcurrentModificationIssue (Spark-1097, Hadoop-10456)
6b840f0 [nravi] Undo the fix for SPARK-1758 (the problem is fixed)
5108700 [nravi] Fix in Spark for the Concurrent thread modification issue (SPARK-1097, HADOOP-10456)
681b36f [nravi] Fix for SPARK-1758: failing test org.apache.spark.JavaAPISuite.wholeTextFiles

(cherry picked from commit 0ac8b01a07)
Signed-off-by: Sean Owen <sowen@cloudera.com>
2015-05-16 08:24:34 +01:00
Sean Owen 1fc35607d7 [SPARK-4556] [BUILD] binary distribution assembly can't run in local mode
Add note on building a runnable distribution with make-distribution.sh

Author: Sean Owen <sowen@cloudera.com>

Closes #6186 from srowen/SPARK-4556 and squashes the following commits:

4002966 [Sean Owen] Add pointer to --help flag
9fa7883 [Sean Owen] Add note on building a runnable distribution with make-distribution.sh

(cherry picked from commit 1fd33815f4)
Signed-off-by: Sean Owen <sowen@cloudera.com>
2015-05-16 08:18:50 +01:00
FavioVazquez 7e3f9fea65 [SPARK-7671] Fix wrong URLs in MLlib Data Types Documentation
There is a mistake in the URL of Matrices in the MLlib Data Types documentation (Local matrix scala section), the URL points to https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Matrices which is a mistake, since Matrices is an object that implements factory methods for Matrix that does not have a companion class. The correct link should point to https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Matrices$

There is another mistake, in the Local Vector section in Scala, Java and Python

In the Scala section the URL of Vectors points to the trait Vector (https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Vector) and not to the factory methods implemented in Vectors.

The correct link should be: https://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.mllib.linalg.Vectors$

In the Java section the URL of Vectors points to the Interface Vector (https://spark.apache.org/docs/latest/api/java/org/apache/spark/mllib/linalg/Vector.html) and not to the Class Vectors

The correct link should be:
https://spark.apache.org/docs/latest/api/java/org/apache/spark/mllib/linalg/Vectors.html

In the Python section the URL of Vectors points to the class Vector (https://spark.apache.org/docs/latest/api/python/pyspark.mllib.html#pyspark.mllib.linalg.Vector) and not the Class Vectors

The correct link should be:
https://spark.apache.org/docs/latest/api/python/pyspark.mllib.html#pyspark.mllib.linalg.Vectors

Author: FavioVazquez <favio.vazquezp@gmail.com>

Closes #6196 from FavioVazquez/fix-typo-matrices-mllib-datatypes and squashes the following commits:

3e9efd5 [FavioVazquez] - Fixed wrong URLs in the MLlib Data Types Documentation
9af7074 [FavioVazquez] Merge remote-tracking branch 'upstream/master'
edab1ef [FavioVazquez] Merge remote-tracking branch 'upstream/master'
b2e2f8c [FavioVazquez] Merge remote-tracking branch 'upstream/master'

(cherry picked from commit d41ae4344c)
Signed-off-by: Sean Owen <sowen@cloudera.com>
2015-05-16 08:07:16 +01:00
Reynold Xin 9da55b5706 [SPARK-7654][SQL] DataFrameReader and DataFrameWriter for input/output API
This patch introduces DataFrameWriter and DataFrameReader.

DataFrameReader interface, accessible through SQLContext.read, contains methods that create DataFrames. These methods used to reside in SQLContext. Example usage:
```scala
sqlContext.read.json("...")
sqlContext.read.parquet("...")
```

DataFrameWriter interface, accessible through DataFrame.write, implements a builder pattern to avoid the proliferation of options in writing DataFrame out. It currently implements:
- mode
- format (e.g. "parquet", "json")
- options (generic options passed down into data sources)
- partitionBy (partitioning columns)
Example usage:
```scala
df.write.mode("append").format("json").partitionBy("date").saveAsTable("myJsonTable")
```

TODO:

- [ ] Documentation update
- [ ] Move JDBC into reader / writer?
- [ ] Deprecate the old interfaces
- [ ] Move the generic load interface into reader.
- [ ] Update example code and documentation

Author: Reynold Xin <rxin@databricks.com>

Closes #6175 from rxin/reader-writer and squashes the following commits:

b146c95 [Reynold Xin] Deprecation of old APIs.
bd8abdf [Reynold Xin] Fixed merge conflict.
26abea2 [Reynold Xin] Added general load methods.
244fbec [Reynold Xin] Added equivalent to example.
4f15d92 [Reynold Xin] Added documentation for partitionBy.
7e91611 [Reynold Xin] [SPARK-7654][SQL] DataFrameReader and DataFrameWriter for input/output API.

(cherry picked from commit 578bfeeff5)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-15 22:09:52 -07:00
AiHe f41be8fb38 [SPARK-7473] [MLLIB] Add reservoir sample in RandomForest
reservoir feature sample by using existing api

Author: AiHe <ai.he@ussuning.com>

Closes #5988 from AiHe/reservoir and squashes the following commits:

e7a41ac [AiHe] remove non-robust testing case
28ffb9a [AiHe] set seed as rng.nextLong
37459e1 [AiHe] set fixed seed
1e98a4c [AiHe] [MLLIB][tree] Add reservoir sample in RandomForest

(cherry picked from commit deb411335a)
Signed-off-by: Joseph K. Bradley <joseph@databricks.com>
2015-05-15 20:42:59 -07:00
Davies Liu 8164fbc255 [SPARK-7543] [SQL] [PySpark] split dataframe.py into multiple files
dataframe.py is splited into column.py, group.py and dataframe.py:
```
   360 column.py
  1223 dataframe.py
   183 group.py
```

Author: Davies Liu <davies@databricks.com>

Closes #6201 from davies/split_df and squashes the following commits:

fc8f5ab [Davies Liu] split dataframe.py into multiple files

(cherry picked from commit d7b69946cb)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-15 20:09:23 -07:00
Davies Liu 61806f6fd1 [SPARK-7073] [SQL] [PySpark] Clean up SQL data type hierarchy in Python
Author: Davies Liu <davies@databricks.com>

Closes #6206 from davies/sql_type and squashes the following commits:

33d6860 [Davies Liu] [SPARK-7073] [SQL] [PySpark] Clean up SQL data type hierarchy in Python

(cherry picked from commit adfd366814)
Signed-off-by: Reynold Xin <rxin@databricks.com>
2015-05-15 20:05:33 -07:00
Ram Sriharsha 04323ba4ab [SPARK-7575] [ML] [DOC] Example code for OneVsRest
Java and Scala examples for OneVsRest. Fixes the base classifier to be Logistic Regression and accepts the configuration parameters of the base classifier.

Author: Ram Sriharsha <rsriharsha@hw11853.local>

Closes #6115 from harsha2010/SPARK-7575 and squashes the following commits:

87ad3c7 [Ram Sriharsha] extra line
f5d9891 [Ram Sriharsha] Merge branch 'master' into SPARK-7575
7076084 [Ram Sriharsha] cleanup
dfd660c [Ram Sriharsha] cleanup
8703e4f [Ram Sriharsha] update doc
cb23995 [Ram Sriharsha] fix commandline options for JavaOneVsRestExample
69e91f8 [Ram Sriharsha] cleanup
7f4e127 [Ram Sriharsha] cleanup
d4c40d0 [Ram Sriharsha] Code Review fixes
461eb38 [Ram Sriharsha] cleanup
e0106d9 [Ram Sriharsha] Fix typo
935cf56 [Ram Sriharsha] Try to match Java and Scala Example Commandline options
5323ff9 [Ram Sriharsha] cleanup
196a59a [Ram Sriharsha] cleanup
6adfa0c [Ram Sriharsha] Style Fix
8cfc5d5 [Ram Sriharsha] [SPARK-7575] Example code for OneVsRest

(cherry picked from commit cc12a86fb0)
Signed-off-by: Joseph K. Bradley <joseph@databricks.com>
2015-05-15 19:33:46 -07:00
Josh Rosen ed75cc02bc [SPARK-7563] OutputCommitCoordinator.stop() should only run on the driver
This fixes a bug where an executor that exits can cause the driver's OutputCommitCoordinator to stop. To fix this, we use an `isDriver` flag and check it in `stop()`.

See https://issues.apache.org/jira/browse/SPARK-7563 for more details.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #6197 from JoshRosen/SPARK-7563 and squashes the following commits:

04b2cc5 [Josh Rosen] [SPARK-7563] OutputCommitCoordinator.stop() should only be executed on the driver

(cherry picked from commit 2c04c8a1ae)
Signed-off-by: Patrick Wendell <patrick@databricks.com>
2015-05-15 18:06:12 -07:00
Kay Ousterhout 6f78d03d2a [SPARK-7676] Bug fix and cleanup of stage timeline view
cc pwendell sarutak

This commit cleans up some unnecessary code, eliminates the feature where when you mouse-over a box in the timeline, the corresponding task is highlighted in the table (because that feature is only useful in the rare case when you have a very small number of tasks, in which case it's easy to figure out the mapping anyway), and fixes a bug where nothing shows up if you try to visualize a stage with only 1 task.

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #6202 from kayousterhout/SPARK-7676 and squashes the following commits:

dfd29d4 [Kay Ousterhout] [SPARK-7676] Bug fix and cleanup of stage timeline view

(cherry picked from commit e745456476)
Signed-off-by: Kay Ousterhout <kayousterhout@gmail.com>
2015-05-15 17:45:23 -07:00
Liang-Chi Hsieh e847d86215 [SPARK-7556] [ML] [DOC] Add user guide for spark.ml Binarizer, including Scala, Java and Python examples
JIRA: https://issues.apache.org/jira/browse/SPARK-7556

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

Closes #6116 from viirya/binarizer_doc and squashes the following commits:

40cb677 [Liang-Chi Hsieh] Better print out.
5b7ef1d [Liang-Chi Hsieh] Make examples more clear.
1bf9c09 [Liang-Chi Hsieh] For comments.
6cf8cba [Liang-Chi Hsieh] Add user guide for Binarizer.

(cherry picked from commit c8696337e2)
Signed-off-by: Joseph K. Bradley <joseph@databricks.com>
2015-05-15 15:05:13 -07:00
Iulian Dragos 31e6404995 [SPARK-7677] [STREAMING] Add Kafka modules to the 2.11 build.
This is somewhat related to [SPARK-6154](https://issues.apache.org/jira/browse/SPARK-6154), though it only touches Kafka, not the jline dependency for thriftserver.

I tested this locally on 2.11 (./run-tests) and everything looked good (I had to disable mima, because `MimaBuild` harcodes 2.10 for the previous version -- that's another PR).

Author: Iulian Dragos <jaguarul@gmail.com>

Closes #6149 from dragos/issue/spark-2.11-kafka and squashes the following commits:

aa15d99 [Iulian Dragos] Add Kafka modules to the 2.11 build.

(cherry picked from commit 6e77105e11)
Signed-off-by: Patrick Wendell <patrick@databricks.com>
2015-05-15 14:57:56 -07:00
qhuang 9ef6d743a6 [SPARK-7226] [SPARKR] Support math functions in R DataFrame
Author: qhuang <qian.huang@intel.com>

Closes #6170 from hqzizania/master and squashes the following commits:

f20c39f [qhuang] add tests units and fixes
2a7d121 [qhuang] use a function name more familiar to R users
07aa72e [qhuang] Support math functions in R DataFrame

(cherry picked from commit 50da9e8916)
Signed-off-by: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
2015-05-15 14:06:39 -07:00
Kousuke Saruta a5f7b3b9c7 [SPARK-7296] Add timeline visualization for stages in the UI.
This PR builds on #2342 by adding a timeline view for the Stage page,
showing how tasks spend their time.

With this timeline, we can understand following things of a Stage.

* When/where each task ran
* Total duration of each task
* Proportion of the time each task spends

Also, this timeline view can scrollable and zoomable.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #5843 from sarutak/stage-page-timeline and squashes the following commits:

4ba9604 [Kousuke Saruta] Fixed the order of legends
16bb552 [Kousuke Saruta] Removed border of legend area
2e5d605 [Kousuke Saruta] Modified warning message
16cb2e6 [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into stage-page-timeline
7ae328f [Kousuke Saruta] Modified code style
d5f794a [Kousuke Saruta] Fixed performance issues more
64e6642 [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into stage-page-timeline
e4a3354 [Kousuke Saruta] minor code style change
878e3b8 [Kousuke Saruta] Fixed a bug that tooltip remains
b9d8f1b [Kousuke Saruta] Fixed performance issue
ac8842b [Kousuke Saruta] Fixed layout
2319739 [Kousuke Saruta] Modified appearances more
81903ab [Kousuke Saruta] Modified appearances
a79dcc3 [Kousuke Saruta] Modified appearance
55a390c [Kousuke Saruta] Ignored scalastyle for a line-comment
29eae3e [Kousuke Saruta] limited to longest 1000 tasks
2a9e376 [Kousuke Saruta] Minor cleanup
385b6d2 [Kousuke Saruta] Added link feature
ba1ac3e [Kousuke Saruta] Fixed style
2ae8520 [Kousuke Saruta] Updated bootstrap-tooltip.js from 2.2.2 to 2.3.2
af430f1 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into stage-page-timeline
e694b8e [Kousuke Saruta] Added timeline view to StagePage
8f6610c [Kousuke Saruta] Fixed conflict
b587cf2 [Kousuke Saruta] initial commit
11fe67d [Kousuke Saruta] Fixed conflict
79ac03d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
a91abd3 [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into timeline-viewer-feature
ef34a5b [Kousuke Saruta] Implement tooltip using bootstrap
b09d0c5 [Kousuke Saruta] Move `stroke` and `fill` attribute of rect elements to css
d3c63c8 [Kousuke Saruta] Fixed a little bit bugs
a36291b [Kousuke Saruta] Merge branch 'master' of https://github.com/apache/spark into timeline-viewer-feature
28714b6 [Kousuke Saruta] Fixed highlight issue
0dc4278 [Kousuke Saruta] Addressed most of Patrics's feedbacks
8110acf [Kousuke Saruta] Added scroll limit to Job timeline
974a64a [Kousuke Saruta] Removed unused function
ee7a7f0 [Kousuke Saruta] Refactored
6a91872 [Kousuke Saruta] Temporary commit
6693f34 [Kousuke Saruta] Added link to job/stage box in the timeline in order to move to corresponding row when we click
8f88222 [Kousuke Saruta] Added job/stage description
aeed4b1 [Kousuke Saruta] Removed stage timeline
fc1696c [Kousuke Saruta] Merge branch 'timeline-viewer-feature' of github.com:sarutak/spark into timeline-viewer-feature
999ccd4 [Kousuke Saruta] Improved scalability
0fc6a31 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
19815ae [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
68b7540 [Kousuke Saruta] Merge branch 'timeline-viewer-feature' of github.com:sarutak/spark into timeline-viewer-feature
52b5f0b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
dec85db [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
fcdab7d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
dab7cc1 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
09cce97 [Kousuke Saruta] Cleanuped
16f82cf [Kousuke Saruta] Cleanuped
9fb522e [Kousuke Saruta] Cleanuped
d05f2c2 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into timeline-viewer-feature
e85e9aa [Kousuke Saruta] Cleanup: Added TimelineViewUtils.scala
a76e569 [Kousuke Saruta] Removed unused setting in timeline-view.css
5ce1b21 [Kousuke Saruta] Added vis.min.js, vis.min.css and vis.map to .rat-exclude
082f709 [Kousuke Saruta] Added Timeline-View feature for Applications, Jobs and Stages

(cherry picked from commit 9b6cf285d0)
Signed-off-by: Kay Ousterhout <kayousterhout@gmail.com>
2015-05-15 13:58:08 -07:00
ehnalis 7dc0ff3f12 [SPARK-7504] [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode
Added a simple checking for SparkContext.
Also added two rational checking against null at AM object.

Author: ehnalis <zoltan.zvara@gmail.com>

Closes #6083 from ehnalis/cluster and squashes the following commits:

926bd96 [ehnalis] Moved check to SparkContext.
7c89b6e [ehnalis] Remove false line.
ea2a5fe [ehnalis] [SPARK-7504] [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode
4924e01 [ehnalis] [SPARK-7504] [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode
39e4fa3 [ehnalis] SPARK-7504 [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode
9f287c5 [ehnalis] [SPARK-7504] [YARN] NullPointerException when initializing SparkContext in YARN-cluster mode

(cherry picked from commit 8e3822a079)
Signed-off-by: Andrew Or <andrew@databricks.com>
2015-05-15 12:16:03 -07:00
Kousuke Saruta e319719e06 [SPARK-7664] [WEBUI] DAG visualization: Fix incorrect link paths of DAG.
In JobPage, we can jump a StagePage when we click corresponding box of DAG viz but the link path is incorrect.

When we click a box like as follows ...
![screenshot_from_2015-05-15 19 24 25](https://cloud.githubusercontent.com/assets/4736016/7651528/5f7ef824-fb3c-11e4-9518-8c9ade2dff7a.png)

We jump to index page.
![screenshot_from_2015-05-15 19 24 45](https://cloud.githubusercontent.com/assets/4736016/7651534/6d666274-fb3c-11e4-971c-c3f2dc2b1da2.png)

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #6184 from sarutak/fix-link-path-of-dag-viz and squashes the following commits:

faba3ba [Kousuke Saruta] Fix a incorrect link

(cherry picked from commit ad92af9dbb)
Signed-off-by: Andrew Or <andrew@databricks.com>
2015-05-15 11:54:40 -07:00
Sean Owen fe3c7340f0 [SPARK-5412] [DEPLOY] Cannot bind Master to a specific hostname as per the documentation
Pass args to start-master.sh through to start-daemon.sh, as other scripts do, so that things like --host have effect on start-master.sh as per docs

Author: Sean Owen <sowen@cloudera.com>

Closes #6185 from srowen/SPARK-5412 and squashes the following commits:

b3ce9da [Sean Owen] Pass args to start-master.sh through to start-daemon.sh, as other scripts do, so that things like --host have effect on start-master.sh as per docs

(cherry picked from commit 8ab1450d39)
Signed-off-by: Andrew Or <andrew@databricks.com>
2015-05-15 11:30:26 -07:00
Tim Ellison 866e4b5204 [CORE] Protect additional test vars from early GC
Fix more places in which some test variables could be collected early by aggressive JVM optimization.
Added a couple of comments to note where existing references are sufficient in the same test pattern.

Author: Tim Ellison <t.p.ellison@gmail.com>

Closes #6187 from tellison/DefeatEarlyGC and squashes the following commits:

27329d9 [Tim Ellison] [CORE] Protect additional test vars from early GC

(cherry picked from commit 270d4b5181)
Signed-off-by: Andrew Or <andrew@databricks.com>
2015-05-15 11:27:35 -07:00
Oleksii Kostyliev c58b9c6167 [SPARK-7233] [CORE] Detect REPL mode once
<h3>Description</h3>
Detect REPL mode once per JVM lifespan.
Previous behavior was to check presence of interpreter mode every time a job was submitted. In the case of execution of multiple short-living jobs this was causing massive mutual blocks between submission threads.

For more details please refer to https://issues.apache.org/jira/browse/SPARK-7233.

<h3>Notes</h3>
* I inverted the return value in case of catching an exception from `true` to `false`. It seems more logical to assume that if the REPL class is not found, we aren't in the interpreter mode.
* I'd personally would call `classForName` with just a Spark classloader (`org.apache.spark.util.Utils#getSparkClassLoader`) but `org.apache.spark.util.Utils#getContextOrSparkClassLoader` is said to be preferable.
* I struggled to come up with a concise, readable and clear unit test. Suggestions are welcome if you feel necessary.

Author: Oleksii Kostyliev <etander@gmail.com>
Author: Oleksii Kostyliev <okostyliev@thunderhead.com>

Closes #5835 from preeze/SPARK-7233 and squashes the following commits:

69bb9e4 [Oleksii Kostyliev] SPARK-7527: fixed explanatory comment to meet style-checker requirements
26dcc24 [Oleksii Kostyliev] SPARK-7527: fixed explanatory comment to meet style-checker requirements
c6f9685 [Oleksii Kostyliev] Merge remote-tracking branch 'remotes/upstream/master' into SPARK-7233
b78a983 [Oleksii Kostyliev] SPARK-7527: revert the fix and let it be addressed separately at a later stage
b64d441 [Oleksii Kostyliev] SPARK-7233: inline inInterpreter parameter into instantiateClass
86e2606 [Oleksii Kostyliev] SPARK-7233, SPARK-7527: Handle interpreter mode properly.
c7ee69c [Oleksii Kostyliev] Merge remote-tracking branch 'upstream/master' into SPARK-7233
d6c07fc [Oleksii Kostyliev] SPARK-7233: properly handle the inverted meaning of isInInterpreter
c319039 [Oleksii Kostyliev] SPARK-7233: move inInterpreter to Utils and make it lazy

(cherry picked from commit b1b9d5802e)
Signed-off-by: Andrew Or <andrew@databricks.com>
2015-05-15 11:21:06 -07:00