The test was timing out on some slow EC2 workers.
Author: Ankur Dave <ankurdave@gmail.com>
Closes#1037 from ankurdave/bagel-test-time-limit and squashes the following commits:
67fd487 [Ankur Dave] Increase time limit for Bagel test
Author: Patrick Wendell <pwendell@gmail.com>
Closes#1036 from pwendell/jenkins-test and squashes the following commits:
9c99856 [Patrick Wendell] Better output during tests
71e7b74 [Patrick Wendell] Removing incorrect python path
74984db [Patrick Wendell] HOTFIX: Allow PySpark tests to run on Jenkins.
As the rule described in https://cwiki.apache.org/confluence/display/Hive/OuterJoinBehavior, we can optimize the SQL Join by pushing down the Join predicate and Where predicate.
Author: Cheng Hao <hao.cheng@intel.com>
Closes#1015 from chenghao-intel/join_predicate_push_down and squashes the following commits:
10feff9 [Cheng Hao] fix bug of changing the join type in PredicatePushDownThroughJoin
44c6700 [Cheng Hao] Add logical to support pushdown the join filter
0bce426 [Cheng Hao] Pushdown the join filter & predicate for outer join
Author: witgo <witgo@qq.com>
Closes#921 from witgo/allocateExecutors and squashes the following commits:
bc3aa66 [witgo] review commit
8800eba [witgo] Merge branch 'master' of https://github.com/apache/spark into allocateExecutors
32ac7af [witgo] review commit
056b8c7 [witgo] Merge branch 'master' of https://github.com/apache/spark into allocateExecutors
04c6f7e [witgo] Merge branch 'master' into allocateExecutors
aff827c [witgo] review commit
5c376e0 [witgo] Merge branch 'master' of https://github.com/apache/spark into allocateExecutors
1faf4f4 [witgo] Merge branch 'master' into allocateExecutors
3c464bd [witgo] add time limit to allocateExecutors
e00b656 [witgo] In some cases, yarn does not automatically restart the container
The package is `org.apache.spark.sql.hive.execution`, while the file was placed under `sql/hive/src/main/scala/org/apache/spark/sql/hive/`.
Author: Cheng Lian <lian.cs.zju@gmail.com>
Closes#1029 from liancheng/moveHiveOperators and squashes the following commits:
d632eb8 [Cheng Lian] Moved hiveOperators.scala to the right package folder
This PR (1) introduces a new class SQLConf that stores key-value properties for a SQLContext (2) clean up the semantics of various forms of SET commands.
The SQLConf class unlocks user-controllable optimization opportunities; for example, user can now override the number of partitions used during an Exchange. A SQLConf can be accessed and modified programmatically through its getters and setters. It can also be modified through SET commands executed by `sql()` or `hql()`. Note that users now have the ability to change a particular property for different queries inside the same Spark job, unlike settings configured in SparkConf.
For SET commands: "SET" will return all properties currently set in a SQLConf, "SET key" will return the key-value pair (if set) or an undefined message, and "SET key=value" will call the setter on SQLConf, and if a HiveContext is used, it will be executed in Hive as well.
Author: Zongheng Yang <zongheng.y@gmail.com>
Closes#956 from concretevitamin/sqlconf and squashes the following commits:
4968c11 [Zongheng Yang] Very minor cleanup.
d74dde5 [Zongheng Yang] Remove the redundant mkQueryExecution() method.
c129b86 [Zongheng Yang] Merge remote-tracking branch 'upstream/master' into sqlconf
26c40eb [Zongheng Yang] Make SQLConf a trait and have SQLContext mix it in.
dd19666 [Zongheng Yang] Update a comment.
baa5d29 [Zongheng Yang] Remove default param for shuffle partitions accessor.
5f7e6d8 [Zongheng Yang] Add default num partitions.
22d9ed7 [Zongheng Yang] Fix output() of Set physical. Add SQLConf param accessor method.
e9856c4 [Zongheng Yang] Use java.util.Collections.synchronizedMap on a Java HashMap.
88dd0c8 [Zongheng Yang] Remove redundant SET Keyword.
271f0b1 [Zongheng Yang] Minor change.
f8983d1 [Zongheng Yang] Minor changes per review comments.
1ce8a5e [Zongheng Yang] Invoke runSqlHive() in SQLConf#get for the HiveContext case.
b766af9 [Zongheng Yang] Remove a test.
d52e1bd [Zongheng Yang] De-hardcode number of shuffle partitions for BasicOperators (read from SQLConf).
555599c [Zongheng Yang] Bullet-proof (relatively) parsing SET per review comment.
c2067e8 [Zongheng Yang] Mark SQLContext transient and put it in a second param list.
2ea8cdc [Zongheng Yang] Wrap long line.
41d7f09 [Zongheng Yang] Fix imports.
13279e6 [Zongheng Yang] Refactor the logic of eagerly processing SET commands.
b14b83e [Zongheng Yang] In a HiveContext, make SQLConf a subset of HiveConf.
6983180 [Zongheng Yang] Move a SET test to SQLQuerySuite and make it complete.
5b67985 [Zongheng Yang] New line at EOF.
c651797 [Zongheng Yang] Add commands.scala.
efd82db [Zongheng Yang] Clean up semantics of several cases of SET.
c1017c2 [Zongheng Yang] WIP in changing SetCommand to take two Options (for different semantics of SETs).
0f00d86 [Zongheng Yang] Add a test for singleton set command in SQL.
41acd75 [Zongheng Yang] Add a test for hql() in HiveQuerySuite.
2276929 [Zongheng Yang] Fix default hive result for set commands in HiveComparisonTest.
3b0c71b [Zongheng Yang] Remove Parser for set commands. A few other fixes.
d0c4578 [Zongheng Yang] Tmux typo.
0ecea46 [Zongheng Yang] Changes for HiveQl and HiveContext.
ce22d80 [Zongheng Yang] Fix parsing issues.
cb722c1 [Zongheng Yang] Finish up SQLConf patch.
4ebf362 [Zongheng Yang] First cut at SQLConf inside SQLContext.
So I finally resurrected this PR. It seems the old one against the incubator mirror is no longer available, so I cannot reference it.
This adds initial support for reading Hadoop ```SequenceFile```s, as well as arbitrary Hadoop ```InputFormat```s, in PySpark.
# Overview
The basics are as follows:
1. ```PythonRDD``` object contains the relevant methods, that are in turn invoked by ```SparkContext``` in PySpark
2. The SequenceFile or InputFormat is read on the Scala side and converted from ```Writable``` instances to the relevant Scala classes (in the case of primitives)
3. Pyrolite is used to serialize Java objects. If this fails, the fallback is ```toString```
4. ```PickleSerializer``` on the Python side deserializes.
This works "out the box" for simple ```Writable```s:
* ```Text```
* ```IntWritable```, ```DoubleWritable```, ```FloatWritable```
* ```NullWritable```
* ```BooleanWritable```
* ```BytesWritable```
* ```MapWritable```
It also works for simple, "struct-like" classes. Due to the way Pyrolite works, this requires that the classes satisfy the JavaBeans convenstions (i.e. with fields and a no-arg constructor and getters/setters). (Perhaps in future some sugar for case classes and reflection could be added).
I've tested it out with ```ESInputFormat``` as an example and it works very nicely:
```python
conf = {"es.resource" : "index/type" }
rdd = sc.newAPIHadoopRDD("org.elasticsearch.hadoop.mr.EsInputFormat", "org.apache.hadoop.io.NullWritable", "org.elasticsearch.hadoop.mr.LinkedMapWritable", conf=conf)
rdd.first()
```
I suspect for things like HBase/Cassandra it will be a bit trickier to get it to work out the box.
# Some things still outstanding:
1. ~~Requires ```msgpack-python``` and will fail without it. As originally discussed with Josh, add a ```as_strings``` argument that defaults to ```False```, that can be used if ```msgpack-python``` is not available~~
2. ~~I see from https://github.com/apache/spark/pull/363 that Pyrolite is being used there for SerDe between Scala and Python. @ahirreddy @mateiz what is the plan behind this - is Pyrolite preferred? It seems from a cursory glance that adapting the ```msgpack```-based SerDe here to use Pyrolite wouldn't be too hard~~
3. ~~Support the key and value "wrapper" that would allow a Scala/Java function to be plugged in that would transform whatever the key/value Writable class is into something that can be serialized (e.g. convert some custom Writable to a JavaBean or ```java.util.Map``` that can be easily serialized)~~
4. Support ```saveAsSequenceFile``` and ```saveAsHadoopFile``` etc. This would require SerDe in the reverse direction, that can be handled by Pyrolite. Will work on this as a separate PR
Author: Nick Pentreath <nick.pentreath@gmail.com>
Closes#455 from MLnick/pyspark-inputformats and squashes the following commits:
268df7e [Nick Pentreath] Documentation changes mer @pwendell comments
761269b [Nick Pentreath] Address @pwendell comments, simplify default writable conversions and remove registry.
4c972d8 [Nick Pentreath] Add license headers
d150431 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
cde6af9 [Nick Pentreath] Parameterize converter trait
5ebacfa [Nick Pentreath] Update docs for PySpark input formats
a985492 [Nick Pentreath] Move Converter examples to own package
365d0be [Nick Pentreath] Make classes private[python]. Add docs and @Experimental annotation to Converter interface.
eeb8205 [Nick Pentreath] Fix path relative to SPARK_HOME in tests
1eaa08b [Nick Pentreath] HBase -> Cassandra app name oversight
3f90c3e [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
2c18513 [Nick Pentreath] Add examples for reading HBase and Cassandra InputFormats from Python
b65606f [Nick Pentreath] Add converter interface
5757f6e [Nick Pentreath] Default key/value classes for sequenceFile asre None
085b55f [Nick Pentreath] Move input format tests to tests.py and clean up docs
43eb728 [Nick Pentreath] PySpark InputFormats docs into programming guide
94beedc [Nick Pentreath] Clean up args in PythonRDD. Set key/value converter defaults to None for PySpark context.py methods
1a4a1d6 [Nick Pentreath] Address @mateiz style comments
01e0813 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
15a7d07 [Nick Pentreath] Remove default args for key/value classes. Arg names to camelCase
9fe6bd5 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
84fe8e3 [Nick Pentreath] Python programming guide space formatting
d0f52b6 [Nick Pentreath] Python programming guide
7caa73a [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
93ef995 [Nick Pentreath] Add back context.py changes
9ef1896 [Nick Pentreath] Recover earlier changes lost in previous merge for serializers.py
077ecb2 [Nick Pentreath] Recover earlier changes lost in previous merge for context.py
5af4770 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
35b8e3a [Nick Pentreath] Another fix for test ordering
bef3afb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
e001b94 [Nick Pentreath] Fix test failures due to ordering
78978d9 [Nick Pentreath] Add doc for SequenceFile and InputFormat support to Python programming guide
64eb051 [Nick Pentreath] Scalastyle fix
e7552fa [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
44f2857 [Nick Pentreath] Remove msgpack dependency and switch serialization to Pyrolite, plus some clean up and refactoring
c0ebfb6 [Nick Pentreath] Change sequencefile test data generator to easily be called from PySpark tests
1d7c17c [Nick Pentreath] Amend tests to auto-generate sequencefile data in temp dir
17a656b [Nick Pentreath] remove binary sequencefile for tests
f60959e [Nick Pentreath] Remove msgpack dependency and serializer from PySpark
450e0a2 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
31a2fff [Nick Pentreath] Scalastyle fixes
fc5099e [Nick Pentreath] Add Apache license headers
4e08983 [Nick Pentreath] Clean up docs for PySpark context methods
b20ec7e [Nick Pentreath] Clean up merge duplicate dependencies
951c117 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
f6aac55 [Nick Pentreath] Bring back msgpack
9d2256e [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
1bbbfb0 [Nick Pentreath] Clean up SparkBuild from merge
a67dfad [Nick Pentreath] Clean up Msgpack serialization and registering
7237263 [Nick Pentreath] Add back msgpack serializer and hadoop file code lost during merging
25da1ca [Nick Pentreath] Add generator for nulls, bools, bytes and maps
65360d5 [Nick Pentreath] Adding test SequenceFiles
0c612e5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
d72bf18 [Nick Pentreath] msgpack
dd57922 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
e67212a [Nick Pentreath] Add back msgpack dependency
f2d76a0 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
41856a5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
97ef708 [Nick Pentreath] Remove old writeToStream
2beeedb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
795a763 [Nick Pentreath] Change name to WriteInputFormatTestDataGenerator. Cleanup some var names. Use SPARK_HOME in path for writing test sequencefile data.
174f520 [Nick Pentreath] Add back graphx settings
703ee65 [Nick Pentreath] Add back msgpack
619c0fa [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
1c8efbc [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
eb40036 [Nick Pentreath] Remove unused comment lines
4d7ef2e [Nick Pentreath] Fix indentation
f1d73e3 [Nick Pentreath] mergeConfs returns a copy rather than mutating one of the input arguments
0f5cd84 [Nick Pentreath] Remove unused pair UTF8 class. Add comments to msgpack deserializer
4294cbb [Nick Pentreath] Add old Hadoop api methods. Clean up and expand comments. Clean up argument names
818a1e6 [Nick Pentreath] Add seqencefile and Hadoop InputFormat support to PythonRDD
4e7c9e3 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
c304cc8 [Nick Pentreath] Adding supporting sequncefiles for tests. Cleaning up
4b0a43f [Nick Pentreath] Refactoring utils into own objects. Cleaning up old commented-out code
d86325f [Nick Pentreath] Initial WIP of PySpark support for SequenceFile and arbitrary Hadoop InputFormat
Author: DB Tsai <dbtsai@dbtsai.com>
Closes#1027 from dbtsai/dbtsai-classloader and squashes the following commits:
9ac6be3 [DB Tsai] Fixed line too long
c9c7ad7 [DB Tsai] Make sure that empty string is filtered out when we get the secondary jars from conf.
This PR attempts to resolve [SPARK-1704](https://issues.apache.org/jira/browse/SPARK-1704) by introducing a physical plan for EXPLAIN commands, which just prints out the debug string (containing various SparkSQL's plans) of the corresponding QueryExecution for the actual query.
Author: Zongheng Yang <zongheng.y@gmail.com>
Closes#1003 from concretevitamin/explain-cmd and squashes the following commits:
5b7911f [Zongheng Yang] Add a regression test.
1bfa379 [Zongheng Yang] Modify output().
719ada9 [Zongheng Yang] Override otherCopyArgs for ExplainCommandPhysical.
4318fd7 [Zongheng Yang] Make all output one Row.
439c6ab [Zongheng Yang] Minor cleanups.
408f574 [Zongheng Yang] SPARK-1704: Add CommandStrategy and ExplainCommandPhysical.
The current implementation of ClientBase.getDefaultYarnApplicationClasspath inspects
the MRJobConfig class for the field DEFAULT_YARN_APPLICATION_CLASSPATH when it should
be really looking into YarnConfiguration. If the Application Configuration has no
yarn.application.classpath defined a NPE exception will be thrown.
Additional Changes include:
* Test Suite for ClientBase added
[ticket: SPARK-1522] : https://issues.apache.org/jira/browse/SPARK-1522
Author : bernardo.gomezpalacio@gmail.com
Testing : SPARK_HADOOP_VERSION=2.3.0 SPARK_YARN=true ./sbt/sbt test
Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com>
Closes#433 from berngp/feature/SPARK-1522 and squashes the following commits:
2c2e118 [Bernardo Gomez Palacio] [SPARK-1522]: YARN ClientBase throws a NPE if there is no YARN Application specific CP
This test ensures that when there are no
alive executors that satisfy a particular locality level,
the TaskSetManager doesn't ever use that as the maximum
allowed locality level (this optimization ensures that a
job doesn't wait extra time in an attempt to satisfy
a scheduling locality level that is impossible).
@mateiz and @lirui-intel this unit test illustrates an issue
with #892 (it fails with that patch).
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#1024 from kayousterhout/scheduler_unit_test and squashes the following commits:
de6a08f [Kay Ousterhout] Added a TaskSetManager unit test.
Just submit another solution for #395
Author: Daoyuan <daoyuan.wang@intel.com>
Author: Michael Armbrust <michael@databricks.com>
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#837 from adrian-wang/left-semi-join-support and squashes the following commits:
d39cd12 [Daoyuan Wang] Merge pull request #1 from marmbrus/pr/837
6713c09 [Michael Armbrust] Better debugging for failed query tests.
035b73e [Michael Armbrust] Add test for left semi that can't be done with a hash join.
5ec6fa4 [Michael Armbrust] Add left semi to SQL Parser.
4c726e5 [Daoyuan] improvement according to Michael
8d4a121 [Daoyuan] add golden files for leftsemijoin
83a3c8a [Daoyuan] scala style fix
14cff80 [Daoyuan] add support for left semi join
https://issues.apache.org/jira/browse/SPARK-1944
Author: Andrew Ash <andrew@andrewash.com>
Closes#1020 from ash211/SPARK-1944 and squashes the following commits:
a831c4d [Andrew Ash] SPARK-1944 Document --verbose in spark-shell -h
Add getNumPartitions to pyspark RDD to provide an intuitive way to get number of partitions in RDD like we can do in scala today.
Author: Syed Hashmi <shashmi@cloudera.com>
Closes#995 from syedhashmi/master and squashes the following commits:
de0ed5e [Syed Hashmi] [SPARK-1308] Add getNumPartitions to pyspark RDD
Author: Andrew Ash <andrew@andrewash.com>
Closes#1016 from ash211/patch-6 and squashes the following commits:
e3865c8 [Andrew Ash] Grammar: read -> reads
Author: Neville Li <neville@spotify.com>
Closes#1006 from nevillelyh/gh/SPARK-2067 and squashes the following commits:
9ee64cf [Neville Li] [SPARK-2067] use relative path for Spark logo in UI
Adding a paragraph clarifying a weird behavior in RangePartitioner.
See also #549.
Author: Reynold Xin <rxin@apache.org>
Closes#1012 from rxin/partitioner-doc and squashes the following commits:
6f0109e [Reynold Xin] SPARK-1628 follow up: Improve RangePartitioner's documentation.
Old code can only be ran under spark_home and use "bin/run-example".
Error "./run-example: line 55: ./bin/spark-submit: No such file or directory" appears when running in other place. So change this
Author: maji2014 <maji3@asiainfo-linkage.com>
Closes#1011 from maji2014/master and squashes the following commits:
2cc1af6 [maji2014] Update run-example
Closes#988.
JIRA: https://issues.apache.org/jira/browse/SPARK-1628
Added `hashCode` in HashPartitioner, RangePartitioner, PythonPartitioner and PageRankUtils.CustomPartitioner.
Author: zsxwing <zsxwing@gmail.com>
Closes#549 from zsxwing/SPARK-1628 and squashes the following commits:
2620936 [zsxwing] SPARK-1628: Add missing hashCode methods in Partitioner subclasses
https://issues.apache.org/jira/browse/SPARK-1898
Author: Colin Patrick McCabe <cmccabe@cloudera.com>
Closes#850 from cmccabe/master and squashes the following commits:
d66eddc [Colin Patrick McCabe] SPARK-1898: In deploy.yarn.Client, use YarnClient rather than YarnClientImpl
The Maven Profiles that refer to hadoopX, e.g. `hadoop2.4`, should set the expected
`hadoop.version` and `yarn.version`.
e.g.
```
<profile>
<id>hadoop-2.4</id>
<properties>
<hadoop.version>2.4.0</hadoop.version>
<yarn.version>${hadoop.version}</yarn.version>
<protobuf.version>2.5.0</protobuf.version>
<jets3t.version>0.9.0</jets3t.version>
</properties>
</profile>
```
Builds can still define the `-Dhadoop.version` option but this will correctly default the
Hadoop Version to the one that is expected according the profile that is selected.
e.g.
```$ mvn -P hadoop-2.4,yarn clean install```
or
```$ mvn -P hadoop-0.23,yarn clean install```
[ticket] : https://issues.apache.org/jira/browse/SPARK-2026
Author : berngp
Reviewer : ?
Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com>
Closes#998 from berngp/feature/SPARK-2026 and squashes the following commits:
07ba4f7 [Bernardo Gomez Palacio] SPARK-2026: Maven Hadoop Profiles Should Set The Hadoop Version
Author: Neville Li <neville@spotify.com>
Closes#992 from nevillelyh/master and squashes the following commits:
3011739 [Neville Li] [SPARK-2056] Set RDD name to input path
Discovered in #992
Author: Patrick Wendell <pwendell@gmail.com>
Closes#1007 from pwendell/hotfix and squashes the following commits:
af90aa0 [Patrick Wendell] HOTFIX: Support empty body in merge script
Basically there is a race condition (possibly a scala bug?) when these values are recomputed on all of the slaves that results in an incorrect projection being generated (possibly because the GUID uniqueness contract is broken?).
In general we should probably enforce that all expression planing occurs on the driver, as is now occurring here.
Author: Michael Armbrust <michael@databricks.com>
Closes#1004 from marmbrus/fixAggBug and squashes the following commits:
e0c116c [Michael Armbrust] Compute aggregate expression during planning instead of lazily on workers.
Followup: #989
Author: Michael Armbrust <michael@databricks.com>
Closes#994 from marmbrus/caseSensitiveFunctions2 and squashes the following commits:
9d9c8ed [Michael Armbrust] Fix DIV and BETWEEN.
In GraphImpl, mapVertices and outerJoinVertices use a more efficient implementation when the map function conserves vertex attribute types. This is implemented by comparing the ClassTags of the old and new vertex attribute types. However, ClassTags store erased types, so the comparison will return a false positive for types with different type parameters, such as Option[Int] and Option[Double].
This PR resolves the problem by requesting that the compiler generate evidence of equality between the old and new vertex attribute types, and providing a default value for the evidence parameter if the two types are not equal. The methods can then check the value of the evidence parameter to see whether the types are equal.
It also adds a test called "mapVertices changing type with same erased type" that failed before the PR and succeeds now.
Callers of mapVertices and outerJoinVertices can no longer use a wildcard for a graph's VD type. To avoid "Error occurred in an application involving default arguments," they must bind VD to a type parameter, as this PR does for ShortestPaths and LabelPropagation.
Author: Ankur Dave <ankurdave@gmail.com>
Closes#967 from ankurdave/SPARK-1552 and squashes the following commits:
68a4fff [Ankur Dave] Undo conserve naming
7388705 [Ankur Dave] Remove unnecessary ClassTag for VD parameters
a704e5f [Ankur Dave] Use type equality constraint with default argument
29a5ab7 [Ankur Dave] Add failing test
f458c83 [Ankur Dave] Revert "[SPARK-1552] Fix type comparison bug in mapVertices and outerJoinVertices"
16d6af8 [Ankur Dave] [SPARK-1552] Fix type comparison bug in mapVertices and outerJoinVertices
Author: Michael Armbrust <michael@databricks.com>
Closes#989 from marmbrus/caseSensitiveFuncitons and squashes the following commits:
681de54 [Michael Armbrust] LIKE, RLIKE and IN in HQL should not be case sensitive.
The current implementation reads one key with the next hash code as it finishes reading the keys with the current hash code, which may cause it to miss some matches of the next key. This can cause operations like join to give the wrong result when reduce tasks spill to disk and there are hash collisions, as values won't be matched together. This PR fixes it by not reading in that next key, using a peeking iterator instead.
Author: Matei Zaharia <matei@databricks.com>
Closes#986 from mateiz/spark-2043 and squashes the following commits:
0959514 [Matei Zaharia] Added unit test for having many hash collisions
892debb [Matei Zaharia] SPARK-2043: don't read a key with the next hash code in ExternalAppendOnlyMap, instead use a buffered iterator to only read values with the current hash code.
Due to a bug introduced by apache/spark#497, Pregel does not unpersist replicated vertices from previous iterations. As a result, they stay cached until memory is full, wasting GC time.
This PR corrects the problem by unpersisting both the edges and the replicated vertices of previous iterations. This is safe because the edges and replicated vertices of the current iteration are cached by the call to `g.cache()` and then materialized by the call to `messages.count()`. Therefore no unmaterialized RDDs depend on `prevG.edges`. I verified that no recomputation occurs by running PageRank with a custom patch to Spark that warns when a partition is recomputed.
Thanks to Tim Weninger for reporting this bug.
Author: Ankur Dave <ankurdave@gmail.com>
Closes#972 from ankurdave/SPARK-2025 and squashes the following commits:
13d5b07 [Ankur Dave] Unpersist edges of previous graph in Pregel
DAGScheduler supports pluggable clock like what TaskSetManager does.
Author: CrazyJvm <crazyjvm@gmail.com>
Closes#976 from CrazyJvm/clock and squashes the following commits:
6779a4c [CrazyJvm] Use pluggable clock in DAGSheduler
Author: Michael Armbrust <michael@databricks.com>
Closes#985 from marmbrus/tableName and squashes the following commits:
3caaa27 [Michael Armbrust] Correctly analyze queries where columnName == tableName.
This avoids having junit classes showing up in the assembly jar.
I verified that only test classes in the jtransforms package
use junit.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#794 from vanzin/junit-dep-exclusion and squashes the following commits:
274e1c2 [Marcelo Vanzin] Remove junit from assembly in sbt build also.
ad950be [Marcelo Vanzin] Remove compile-scoped junit dependency.
https://github.com/sbt/sbt-assembly/blob/master/README.md
Author: Kalpit Shah <shahkalpit84@gmail.com>
Closes#555 from kalpit/upgrade/sbtassembly and squashes the following commits:
1fa7324 [Kalpit Shah] sbt 0.13.X should be using sbt-assembly 0.11.X
This has been causing some false failures on PR's that don't merge
correctly.
Author: Patrick Wendell <pwendell@gmail.com>
Closes#971 from pwendell/mima and squashes the following commits:
1dc80aa [Patrick Wendell] HOTFIX: Remove generated-mima-excludes file after runing MIMA.
`CaseConversionExpression` should check if the evaluated value is `null`.
Author: Takuya UESHIN <ueshin@happy-camper.st>
Closes#982 from ueshin/issues/SPARK-2036 and squashes the following commits:
61e1c54 [Takuya UESHIN] Add check if the evaluated value is null.
https://issues.apache.org/jira/browse/SPARK-1677
For compatibility with older versions of Spark it would be nice to have an option `spark.hadoop.validateOutputSpecs` (default true) for the user to disable the output directory existence checking
Author: CodingCat <zhunansjtu@gmail.com>
Closes#947 from CodingCat/SPARK-1677 and squashes the following commits:
7930f83 [CodingCat] miao
c0c0e03 [CodingCat] bug fix and doc update
5318562 [CodingCat] bug fix
13219b5 [CodingCat] allow user to disable output dir existence checking
Author: Takuya UESHIN <ueshin@happy-camper.st>
Closes#974 from ueshin/issues/SPARK-2029 and squashes the following commits:
e19e8f4 [Takuya UESHIN] Bump version number to 1.1.0-SNAPSHOT.
When building the assembly with the maven "hadoop-provided"
profile, the executors were failing to come up because Hadoop classes
were not found in the classpath anymore; so add them explicitly to
the classpath using spark.executor.extraClassPath. This is only
needed for the local-cluster mode, but doesn't affect other tests,
so it's added for all of them to keep the code simpler.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#781 from vanzin/repl-test-fix and squashes the following commits:
4f0a3b0 [Marcelo Vanzin] Fix issue in ReplSuite with hadoop-provided profile.
Author: Ankur Dave <ankurdave@gmail.com>
Closes#970 from ankurdave/SPARK-1991_docfix and squashes the following commits:
6d07343 [Ankur Dave] Minor: Fix documentation error from apache/spark#946
Author: Varakhedi Sujeet <svarakhedi@gopivotal.com>
Closes#960 from sujeetv/ec2-r3 and squashes the following commits:
3cb9fd5 [Varakhedi Sujeet] SPARK-1790: Update EC2 scripts to support r3 instance
In Hadoop trunk (currently Hadoop 3.0.0), the deprecated
FSDataOutputStream#sync() method has been removed. Instead, we should
call FSDataOutputStream#hflush, which does the same thing as the
deprecated method used to do.
Author: Colin McCabe <cmccabe@cloudera.com>
Closes#898 from cmccabe/SPARK-1518 and squashes the following commits:
752b9d7 [Colin McCabe] FileLogger: Fix compile against Hadoop trunk
We should standardize the text format used to represent vectors and labeled points. The proposed formats are the following:
1. dense vector: `[v0,v1,..]`
2. sparse vector: `(size,[i0,i1],[v0,v1])`
3. labeled point: `(label,vector)`
where "(..)" indicates a tuple and "[...]" indicate an array. `loadLabeledPoints` is added to pyspark's `MLUtils`. I didn't add `loadVectors` to pyspark because `RDD.saveAsTextFile` cannot stringify dense vectors in the proposed format automatically.
`MLUtils#saveLabeledData` and `MLUtils#loadLabeledData` are deprecated. Users should use `RDD#saveAsTextFile` and `MLUtils#loadLabeledPoints` instead. In Scala, `MLUtils#loadLabeledPoints` is compatible with the format used by `MLUtils#loadLabeledData`.
CC: @mateiz, @srowen
Author: Xiangrui Meng <meng@databricks.com>
Closes#685 from mengxr/labeled-io and squashes the following commits:
2d1116a [Xiangrui Meng] make loadLabeledData/saveLabeledData deprecated since 1.0.1
297be75 [Xiangrui Meng] change LabeledPoint.parse to LabeledPointParser.parse to maintain binary compatibility
d6b1473 [Xiangrui Meng] Merge branch 'master' into labeled-io
56746ea [Xiangrui Meng] replace # by .
623a5f0 [Xiangrui Meng] merge master
f06d5ba [Xiangrui Meng] add docs and minor updates
640fe0c [Xiangrui Meng] throw SparkException
5bcfbc4 [Xiangrui Meng] update test to add scientific notations
e86bf38 [Xiangrui Meng] remove NumericTokenizer
050fca4 [Xiangrui Meng] use StringTokenizer
6155b75 [Xiangrui Meng] merge master
f644438 [Xiangrui Meng] remove parse methods based on eval from pyspark
a41675a [Xiangrui Meng] python loadLabeledPoint uses Scala's implementation
ce9a475 [Xiangrui Meng] add deserialize_labeled_point to pyspark with tests
e9fcd49 [Xiangrui Meng] add serializeLabeledPoint and tests
aea4ae3 [Xiangrui Meng] minor updates
810d6df [Xiangrui Meng] update tokenizer/parser implementation
7aac03a [Xiangrui Meng] remove Scala parsers
c1885c1 [Xiangrui Meng] add headers and minor changes
b0c50cb [Xiangrui Meng] add customized parser
d731817 [Xiangrui Meng] style update
63dc396 [Xiangrui Meng] add loadLabeledPoints to pyspark
ea122b5 [Xiangrui Meng] Merge branch 'master' into labeled-io
cd6c78f [Xiangrui Meng] add __str__ and parse to LabeledPoint
a7a178e [Xiangrui Meng] add stringify to pyspark's Vectors
5c2dbfa [Xiangrui Meng] add parse to pyspark's Vectors
7853f88 [Xiangrui Meng] update pyspark's SparseVector.__str__
e761d32 [Xiangrui Meng] make LabelPoint.parse compatible with the dense format used before v1.0 and deprecate loadLabeledData and saveLabeledData
9e63a02 [Xiangrui Meng] add loadVectors and loadLabeledPoints
19aa523 [Xiangrui Meng] update toString and add parsers for Vectors and LabeledPoint
I'd like to use randomSplit through the Java API, and would like to add a convenience wrapper for this method to JavaRDD. This is fairly trivial. (In fact, is the intent that JavaRDD not wrap every RDD method? and that sometimes users should just use JavaRDD.wrapRDD()?)
Along the way, I added tests for it, and also touched up the Java API test style and behavior. This is maybe the more useful part of this small change.
Author: Sean Owen <sowen@cloudera.com>
Author: Xiangrui Meng <meng@databricks.com>
This patch had conflicts when merged, resolved by
Committer: Xiangrui Meng <meng@databricks.com>
Closes#919 from srowen/SPARK-1973 and squashes the following commits:
148cb7b [Sean Owen] Some final Java test polish, while we are at it
1fc3f3e [Xiangrui Meng] more cleaning on Java 8 tests
9ebc57f [Sean Owen] Use accumulator instead of temp files to test foreach
5efb0be [Sean Owen] Add Java randomSplit, and unit tests (including for sample)
5dcc158 [Sean Owen] Simplified Java 8 test with new language features, and fixed the name of MLB's greatest team
91a1769 [Sean Owen] Touch up minor style issues in existing Java API suite test
This is very useful when debugging & fine tuning jobs with large data sets.
Author: Neville Li <neville@spotify.com>
Closes#966 from nevillelyh/master and squashes the following commits:
6747764 [Neville Li] [MLLIB] use string interpolation for RDD names
3b15d34 [Neville Li] [MLLIB] set RDD names in ALS
RDD.zip() will throw an exception if it finds partition sizes are not the same.
Author: Kan Zhang <kzhang@apache.org>
Closes#944 from kanzhang/SPARK-1817 and squashes the following commits:
c073848 [Kan Zhang] [SPARK-1817] Cosmetic updates
524c670 [Kan Zhang] [SPARK-1817] RDD.zip() should verify partition sizes for each partition
The update to Mesos 0.18 caused some deprecation warnings in the build. The change to the non-deprecated version is straightforward as it emulates what the Mesos driver does with the deprecated method anyway (c5aa1dd221/src/sched/sched.cpp (L1354))
Author: Sean Owen <sowen@cloudera.com>
Closes#920 from srowen/SPARK-1806 and squashes the following commits:
8d76b6a [Sean Owen] Use non-deprecated methods in Mesos 0.18
The change was previously committed only to branch-1.0 as part of a34e6fda1d
Author: Aaron Davidson <aaron@databricks.com>
This patch had conflicts when merged, resolved by
Committer: Patrick Wendell <pwendell@gmail.com>
Closes#938 from aarondav/sparkec2 and squashes the following commits:
067cc31 [Aaron Davidson] Update spark-ec2 scripts for 1.0.0 on master
It is currently very difficult to repartition a graph over a different number of partitions. This PR adds an additional `partitionBy` function that takes the number of partitions.
Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>
Closes#719 from jegonzal/graph_partitioning_options and squashes the following commits:
730b405 [Joseph E. Gonzalez] adding an additional number of partitions option to partitionBy
