This PR adds a new SparkR programming guide at the top-level. This will be useful for R users as our APIs don't directly match the Scala/Python APIs and as we need to explain SparkR without using RDDs as examples etc.
cc rxin davies pwendell
cc cafreeman -- Would be great if you could also take a look at this !
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#6490 from shivaram/sparkr-guide and squashes the following commits:
d5ff360 [Shivaram Venkataraman] Add a section on HiveContext, HQL queries
408dce5 [Shivaram Venkataraman] Fix link
dbb86e3 [Shivaram Venkataraman] Fix minor typo
9aff5e0 [Shivaram Venkataraman] Address comments, use dplyr-like syntax in example
d09703c [Shivaram Venkataraman] Fix default argument in read.df
ea816a1 [Shivaram Venkataraman] Add a new SparkR programming guide Also update write.df, read.df to handle defaults better
(cherry picked from commit 5f48e5c33b)
Signed-off-by: Davies Liu <davies@databricks.com>
Author: MechCoder <manojkumarsivaraj334@gmail.com>
Closes#6497 from MechCoder/spark-7946 and squashes the following commits:
2fdd0a3 [MechCoder] Add non-regression test
8c988c6 [MechCoder] [SPARK-7946] DecayFactor wrongly set in StreamingKMeans
(cherry picked from commit 6181937f31)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
The `HiveThriftServer2Test` relies on proper logging behavior to assert whether the Thrift server daemon process is started successfully. However, some other jar files listed in the classpath may potentially contain an unexpected Log4J configuration file which overrides the logging behavior.
This PR writes a temporary `log4j.properties` and prepend it to driver classpath before starting the testing Thrift server process to ensure proper logging behavior.
cc andrewor14 yhuai
Author: Cheng Lian <lian@databricks.com>
Closes#6493 from liancheng/override-log4j and squashes the following commits:
c489e0e [Cheng Lian] Fixes minor Scala styling issue
b46ef0d [Cheng Lian] Uses a temporary log4j.properties in HiveThriftServer2Test to ensure expected logging behavior
(cherry picked from commit 4782e13040)
Signed-off-by: Andrew Or <andrew@databricks.com>
When starting `HiveThriftServer2` via `startWithContext`, property `spark.sql.hive.version` isn't set. This causes Simba ODBC driver 1.0.8.1006 behaves differently and fails simple queries.
Hive2 JDBC driver works fine in this case. Also, when starting the server with `start-thriftserver.sh`, both Hive2 JDBC driver and Simba ODBC driver works fine.
Please refer to [SPARK-7950] [1] for details.
[1]: https://issues.apache.org/jira/browse/SPARK-7950
Author: Cheng Lian <lian@databricks.com>
Closes#6500 from liancheng/odbc-bugfix and squashes the following commits:
051e3a3 [Cheng Lian] Fixes import order
3a97376 [Cheng Lian] Sets spark.sql.hive.version in HiveThriftServer2.startWithContext()
(cherry picked from commit e7b6177557)
Signed-off-by: Yin Huai <yhuai@databricks.com>
Add alias names for supported cipher suites to the sample SSL configuration.
The IBM JSSE provider reports its cipher suite with an SSL_ prefix, but accepts TLS_ prefixed suite names as an alias. However, Jetty filters the requested ciphers based on the provider's reported supported suites, so the TLS_ versions are never passed through to JSSE causing an SSL handshake failure.
Author: Tim Ellison <t.p.ellison@gmail.com>
Closes#6282 from tellison/SSLFailure and squashes the following commits:
8de8a3e [Tim Ellison] Update SecurityManagerSuite with new expected suite names
96158b2 [Tim Ellison] Update the sample configs to use ciphers that are common to both the Oracle and IBM security providers.
705421b [Tim Ellison] Merge branch 'master' of github.com:tellison/spark into SSLFailure
68b9425 [Tim Ellison] Merge branch 'master' of https://github.com/apache/spark into SSLFailure
b0c35f6 [Tim Ellison] [CORE] Add aliases used for cipher suites in IBM provider
(cherry picked from commit bf46580708)
Signed-off-by: Sean Owen <sowen@cloudera.com>
This PR contains two major changes to `OneHotEncoder`:
1. more robust handling of ML attributes. If the input attribute is unknown, we look at the values to get the max category index
2. change `includeFirst` to `dropLast` and leave the default to `true`. There are couple benefits:
a. consistent with other tutorials of one-hot encoding (or dummy coding) (e.g., http://www.ats.ucla.edu/stat/mult_pkg/faq/general/dummy.htm)
b. keep the indices unmodified in the output vector. If we drop the first, all indices will be shifted by 1.
c. If users use `StringIndex`, the last element is the least frequent one.
Sorry for including two changes in one PR! I'll update the user guide in another PR.
jkbradley sryza
Author: Xiangrui Meng <meng@databricks.com>
Closes#6466 from mengxr/SPARK-7912 and squashes the following commits:
a280dca [Xiangrui Meng] fix tests
d8f234d [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-7912
171b276 [Xiangrui Meng] mention the difference between our impl vs sklearn's
00dfd96 [Xiangrui Meng] update OneHotEncoder in Python
208ddad [Xiangrui Meng] update OneHotEncoder to handle ML attributes and change includeFirst to dropLast
(cherry picked from commit 23452be944)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
Attempts to restart the socket receiver when it is supposed to be stopped causes undesirable error messages.
Author: Tathagata Das <tathagata.das1565@gmail.com>
Closes#6483 from tdas/SPARK-7931 and squashes the following commits:
09aeee1 [Tathagata Das] Do not restart receiver when stopped
Expose user/item factors in DataFrames. This is to be more consistent with the pipeline API. It also helps maintain consistent APIs across languages. This PR also removed fitting params from `ALSModel`.
coderxiang
Author: Xiangrui Meng <meng@databricks.com>
Closes#6468 from mengxr/SPARK-7922 and squashes the following commits:
7bfb1d5 [Xiangrui Meng] update ALSModel in PySpark
1ba5607 [Xiangrui Meng] use DataFrames for user/item factors in ALS
(cherry picked from commit db95137897)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
Shutdown hook for temp directories had priority 100 while SparkContext was 50. So the local root directory was deleted before SparkContext was shutdown. This leads to scary errors on running jobs, at the time of shutdown. This is especially a problem when running streaming examples, where Ctrl-C is the only way to shutdown.
The fix in this PR is to make the temp directory shutdown priority lower than SparkContext, so that the temp dirs are the last thing to get deleted, after the SparkContext has been shut down. Also, the DiskBlockManager shutdown priority is change from default 100 to temp_dir_prio + 1, so that it gets invoked just before all temp dirs are cleared.
Author: Tathagata Das <tathagata.das1565@gmail.com>
Closes#6482 from tdas/SPARK-7930 and squashes the following commits:
d7cbeb5 [Tathagata Das] Removed unnecessary line
1514d0b [Tathagata Das] Fixed shutdown hook priorities
(cherry picked from commit cd3d9a5c0c)
Signed-off-by: Patrick Wendell <patrick@databricks.com>
The existing code rounds down to the nearest percent when computing the proportion
of a task's time that was spent on each phase of execution, and then computes
the scheduler delay proportion as 100 - sum(all other proportions). As a result,
a few extra percent can end up in the scheduler delay. This commit eliminates
the rounding so that the time visualizations correspond properly to the real times.
sarutak If you could take a look at this, that would be great! Not sure if there's a good
reason to round here that I missed.
cc shivaram
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#6484 from kayousterhout/SPARK-7932 and squashes the following commits:
1723cc4 [Kay Ousterhout] [SPARK-7932] Fix misleading scheduler delay visualization
(cherry picked from commit 04ddcd4db7)
Signed-off-by: Kay Ousterhout <kayousterhout@gmail.com>
`make clean html` under `python/doc` returns
~~~
/Users/meng/src/spark/python/pyspark/ml/evaluation.py:docstring of pyspark.ml.evaluation.RegressionEvaluator.setParams:3: WARNING: Definition list ends without a blank line; unexpected unindent.
~~~
harsha2010
Author: Xiangrui Meng <meng@databricks.com>
Closes#6469 from mengxr/fix-regression-evaluator-doc and squashes the following commits:
91e2dad [Xiangrui Meng] fix RegressionEvaluator doc
(cherry picked from commit 834e699524)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
Switch to the official Pyrolite release from the one published under `org.spark-project`. Thanks irmen for making the releases on Maven Central. We didn't upgrade to 4.6 because we don't have enough time for QA. I excludes `serpent` from its dependencies because we don't use it in Spark.
~~~
[info] +-net.jpountz.lz4:lz4:1.3.0
[info] +-net.razorvine:pyrolite:4.4
[info] +-net.sf.py4j:py4j:0.8.2.1
~~~
davies
Author: Xiangrui Meng <meng@databricks.com>
Closes#6472 from mengxr/SPARK-7926 and squashes the following commits:
7b3c6bf [Xiangrui Meng] use the official Pyrolite release
(cherry picked from commit c45d58c143)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
So we can enable a whitespace enforcement rule in the style checker to save code review time.
Author: Reynold Xin <rxin@databricks.com>
Closes#6474 from rxin/whitespace-graphx and squashes the following commits:
4d3cd26 [Reynold Xin] Fixed tests.
869dde4 [Reynold Xin] [SPARK-7927] whitespace fixes for GraphX.
(cherry picked from commit b069ad23d9)
Signed-off-by: Reynold Xin <rxin@databricks.com>
So we can enable a whitespace enforcement rule in the style checker to save code review time.
Author: Reynold Xin <rxin@databricks.com>
Closes#6473 from rxin/whitespace-core and squashes the following commits:
058195d [Reynold Xin] Fixed tests.
fce11e9 [Reynold Xin] [SPARK-7927] whitespace fixes for core.
(cherry picked from commit 7f7505d8db)
Signed-off-by: Reynold Xin <rxin@databricks.com>
So we can enable a whitespace enforcement rule in the style checker to save code review time.
Author: Reynold Xin <rxin@databricks.com>
Closes#6476 from rxin/whitespace-catalyst and squashes the following commits:
650409d [Reynold Xin] Fixed tests.
51a9e5d [Reynold Xin] [SPARK-7927] whitespace fixes for Catalyst module.
(cherry picked from commit 8da560d7de)
Signed-off-by: Reynold Xin <rxin@databricks.com>
Conflicts:
sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/expressions/windowExpressions.scala
So we can enable a whitespace enforcement rule in the style checker to save code review time.
Author: Reynold Xin <rxin@databricks.com>
Closes#6477 from rxin/whitespace-sql-core and squashes the following commits:
ce6e369 [Reynold Xin] Fixed tests.
6095fed [Reynold Xin] [SPARK-7927] whitespace fixes for SQL core.
(cherry picked from commit ff44c711ab)
Signed-off-by: Reynold Xin <rxin@databricks.com>
Looks like this was added by accident when pwendell merged a commit back in September: fe2b1d6a20
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#6485 from kayousterhout/SPARK-7933 and squashes the following commits:
7c6164a [Kay Ousterhout] [SPARK-7933] Remove Patrick's username/pw from merge script
(cherry picked from commit 66c49ed60d)
Signed-off-by: Patrick Wendell <patrick@databricks.com>
So we can enable a whitespace enforcement rule in the style checker to save code review time.
Author: Reynold Xin <rxin@databricks.com>
Closes#6478 from rxin/whitespace-hive and squashes the following commits:
e01b0e0 [Reynold Xin] Fixed tests.
a3bba22 [Reynold Xin] [SPARK-7927] whitespace fixes for Hive and ThriftServer.
(cherry picked from commit ee6a0e12fb)
Signed-off-by: Reynold Xin <rxin@databricks.com>
So we can enable a whitespace enforcement rule in the style checker to save code review time.
Author: Reynold Xin <rxin@databricks.com>
Closes#6475 from rxin/whitespace-streaming and squashes the following commits:
810dae4 [Reynold Xin] Fixed tests.
89068ad [Reynold Xin] [SPARK-7927] whitespace fixes for streaming.
(cherry picked from commit 3af0b3136e)
Signed-off-by: Reynold Xin <rxin@databricks.com>
CC jkbradley
Author: Xusen Yin <yinxusen@gmail.com>
Closes#6451 from yinxusen/SPARK-7577 and squashes the following commits:
e2dc32e [Xusen Yin] rename colums
e350e49 [Xusen Yin] add all demos
006ddf1 [Xusen Yin] add java test
3238481 [Xusen Yin] add bucketizer
(cherry picked from commit 1bd63e82fd)
Signed-off-by: Joseph K. Bradley <joseph@databricks.com>
https://issues.apache.org/jira/browse/SPARK-7853
This fixes the problem introduced by my change in https://github.com/apache/spark/pull/6435, which causes that Hive Context fails to create in spark shell because of the class loader issue.
Author: Yin Huai <yhuai@databricks.com>
Closes#6459 from yhuai/SPARK-7853 and squashes the following commits:
37ad33e [Yin Huai] Do not use hiveQlTable at all.
47cdb6d [Yin Huai] Move hiveconf.set to the end of setConf.
005649b [Yin Huai] Update comment.
35d86f3 [Yin Huai] Access TTable directly to make sure Hive will not internally use any metastore utility functions.
3737766 [Yin Huai] Recursively find all jars.
(cherry picked from commit 572b62cafe)
Signed-off-by: Yin Huai <yhuai@databricks.com>
See comments on https://github.com/apache/spark/pull/3913
Author: Reynold Xin <rxin@databricks.com>
Closes#6471 from rxin/sizeestimator and squashes the following commits:
c057095 [Reynold Xin] Fixed import.
2da478b [Reynold Xin] Remove SizeEstimator from o.a.spark package.
(cherry picked from commit 0077af22ca)
Signed-off-by: Reynold Xin <rxin@databricks.com>
`VectorAssembler` should carry over ML attributes. For unknown attributes, we assume numeric values. This PR handles the following cases:
1. DoubleType with ML attribute: carry over
2. DoubleType without ML attribute: numeric value
3. Scalar type: numeric value
4. VectorType with all ML attributes: carry over and update names
5. VectorType with number of ML attributes: assume all numeric
6. VectorType without ML attributes: check the first row and get the number of attributes
jkbradley
Author: Xiangrui Meng <meng@databricks.com>
Closes#6452 from mengxr/SPARK-7198 and squashes the following commits:
a9d2469 [Xiangrui Meng] add space
facdb1f [Xiangrui Meng] VectorAssembler should output ML attributes
(cherry picked from commit 7859ab659e)
Signed-off-by: Joseph K. Bradley <joseph@databricks.com>
The location of the IDE setup information has changed, so this just updates the link on the Building Spark page.
Author: Mike Dusenberry <dusenberrymw@gmail.com>
Closes#6467 from dusenberrymw/Fix_Broken_Link_On_Building_Spark_Doc and squashes the following commits:
75c533a [Mike Dusenberry] Fixing broken "IDE setup" link in the Building Spark documentation by pointing to new location.
(cherry picked from commit 3e312a5ed0)
Signed-off-by: Sean Owen <sowen@cloudera.com>
Fix the bug that entering only 1 arg will cause array out of bounds exception in PageRank example.
Author: Li Yao <hnkfliyao@gmail.com>
Closes#6455 from lastland/patch-1 and squashes the following commits:
de06128 [Li Yao] Fix the bug that entering only 1 arg will cause array out of bounds exception.
(cherry picked from commit c771589c96)
Signed-off-by: Andrew Or <andrew@databricks.com>
~~A PythonUDT shouldn't be serialized into external Scala types in PythonRDD. I'm not sure whether this should fix one of the bugs related to SQL UDT/UDF in PySpark.~~
The fix above didn't work. So I added a workaround for this. If a Python UDF is applied to a Python UDT. This will put the Python SQL types as inputs. Still incorrect, but at least it doesn't throw exceptions on the Scala side. davies harsha2010
Author: Xiangrui Meng <meng@databricks.com>
Closes#6442 from mengxr/SPARK-7903 and squashes the following commits:
c257d2a [Xiangrui Meng] add a workaround for VectorUDT
(cherry picked from commit 530efe3e80)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
Since `spark-streaming-kafka` now is published for both Scala 2.10 and 2.11, we can move `KafkaWordCount` and `DirectKafkaWordCount` from `examples/scala-2.10/src/` to `examples/src/` so that they will appear in `spark-examples-***-jar` for Scala 2.11.
Author: zsxwing <zsxwing@gmail.com>
Closes#6436 from zsxwing/SPARK-7895 and squashes the following commits:
c6052f1 [zsxwing] Update examples/pom.xml
0bcfa87 [zsxwing] Fix the sleep time
b9d1256 [zsxwing] Move Kafka examples from scala-2.10/src to src
(cherry picked from commit 000df2f0d6)
Signed-off-by: Patrick Wendell <patrick@databricks.com>
This contribution is my original work and I license the work to the project under the project's open source license
Author: Matt Wise <mwise@quixey.com>
Closes#6447 from wisematthew/fix-typo-in-java-udf-registration-doc and squashes the following commits:
e7ef5f7 [Matt Wise] Fix typo in documentation for Java UDF registration
(cherry picked from commit 35410614de)
Signed-off-by: Reynold Xin <rxin@databricks.com>
Author: Sandy Ryza <sandy@cloudera.com>
Closes#6440 from sryza/sandy-spark-7896 and squashes the following commits:
49d8a0d [Sandy Ryza] Fix bug introduced when reading over record boundaries
6006856 [Sandy Ryza] Fix overflow issues
006b4b2 [Sandy Ryza] Fix scalastyle by removing non ascii characters
8b000ca [Sandy Ryza] Add ascii art to describe layout of data in metaBuffer
f2053c0 [Sandy Ryza] Fix negative overflow issue
0368c78 [Sandy Ryza] Initialize size as 0
a5a4820 [Sandy Ryza] Use explicit types for all numbers in ChainedBuffer
b7e0213 [Sandy Ryza] SPARK-7896. Allow ChainedBuffer to store more than 2 GB
(cherry picked from commit bd11b01eba)
Signed-off-by: Patrick Wendell <patrick@databricks.com>
This is a somewhat obscure bug, but I think that it will seriously impact KryoSerializer users who use custom registrators which disabled auto-reset. When auto-reset is disabled, then this breaks things in some of our shuffle paths which actually end up creating multiple OutputStreams from the same shared SerializerInstance (which is unsafe).
This was introduced by a patch (SPARK-3386) which enables serializer re-use in some of the shuffle paths, since constructing new serializer instances is actually pretty costly for KryoSerializer. We had already fixed another corner-case (SPARK-7766) bug related to this, but missed this one.
I think that the root problem here is that KryoSerializerInstance can be used in a way which is unsafe even within a single thread, e.g. by creating multiple open OutputStreams from the same instance or by interleaving deserialize and deserializeStream calls. I considered a smaller patch which adds assertions to guard against this type of "misuse" but abandoned that approach after I realized how convoluted the Scaladoc became.
This patch fixes this bug by making it legal to create multiple streams from the same KryoSerializerInstance. Internally, KryoSerializerInstance now implements a `borrowKryo()` / `releaseKryo()` API that's backed by a "pool" of capacity 1. Each call to a KryoSerializerInstance method will borrow the Kryo, do its work, then release the serializer instance back to the pool. If the pool is empty and we need an instance, it will allocate a new Kryo on-demand. This makes it safe for multiple OutputStreams to be opened from the same serializer. If we try to release a Kryo back to the pool but the pool already contains a Kryo, then we'll just discard the new Kryo. I don't think there's a clear benefit to having a larger pool since our usages tend to fall into two cases, a) where we only create a single OutputStream and b) where we create a huge number of OutputStreams with the same lifecycle, then destroy the KryoSerializerInstance (this is what's happening in the bypassMergeSort code path that my regression test hits).
Author: Josh Rosen <joshrosen@databricks.com>
Closes#6415 from JoshRosen/SPARK-7873 and squashes the following commits:
00b402e [Josh Rosen] Initialize eagerly to fix a failing test
ba55d20 [Josh Rosen] Add explanatory comments
3f1da96 [Josh Rosen] Guard against duplicate close()
ab457ca [Josh Rosen] Sketch a loan/release based solution.
9816e8f [Josh Rosen] Add a failing test showing how deserialize() and deserializeStream() can interfere.
7350886 [Josh Rosen] Add failing regression test for SPARK-7873
(cherry picked from commit 852f4de2d3)
Signed-off-by: Patrick Wendell <patrick@databricks.com>
This PR has three changes:
1. Renaming the table of `ThriftServer` to `SQL`;
2. Renaming the title of the tab from `ThriftServer` to `JDBC/ODBC Server`; and
3. Renaming the title of the session page from `ThriftServer` to `JDBC/ODBC Session`.
https://issues.apache.org/jira/browse/SPARK-7907
Author: Yin Huai <yhuai@databricks.com>
Closes#6448 from yhuai/JDBCServer and squashes the following commits:
eadcc3d [Yin Huai] Update test.
9168005 [Yin Huai] Use SQL as the tab name.
221831e [Yin Huai] Rename ThriftServer to JDBCServer.
(cherry picked from commit 3c1f1baaf0)
Signed-off-by: Yin Huai <yhuai@databricks.com>
