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* [SPARK-3573][MLLIB] Make MLlib's Vector compatible with SQL's SchemaRDDXiangrui Meng2014-11-038-6/+353
| | | | | | | | | | | | | | | Register MLlib's Vector as a SQL user-defined type (UDT) in both Scala and Python. With this PR, we can easily map a RDD[LabeledPoint] to a SchemaRDD, and then select columns or save to a Parquet file. Examples in Scala/Python are attached. The Scala code was copied from jkbradley. ~~This PR contains the changes from #3068 . I will rebase after #3068 is merged.~~ marmbrus jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #3070 from mengxr/SPARK-3573 and squashes the following commits: 3a0b6e5 [Xiangrui Meng] organize imports 236f0a0 [Xiangrui Meng] register vector as UDT and provide dataset examples
* [SPARK-4192][SQL] Internal API for Python UDTXiangrui Meng2014-11-037-5/+375
| | | | | | | | | | | | | | | | | | | | | Following #2919, this PR adds Python UDT (for internal use only) with tests under "pyspark.tests". Before `SQLContext.applySchema`, we check whether we need to convert user-type instances into SQL recognizable data. In the current implementation, a Python UDT must be paired with a Scala UDT for serialization on the JVM side. A following PR will add VectorUDT in MLlib for both Scala and Python. marmbrus jkbradley davies Author: Xiangrui Meng <meng@databricks.com> Closes #3068 from mengxr/SPARK-4192-sql and squashes the following commits: acff637 [Xiangrui Meng] merge master dba5ea7 [Xiangrui Meng] only use pyClass for Python UDT output sqlType as well 2c9d7e4 [Xiangrui Meng] move import to global setup; update needsConversion 7c4a6a9 [Xiangrui Meng] address comments 75223db [Xiangrui Meng] minor update f740379 [Xiangrui Meng] remove UDT from default imports e98d9d0 [Xiangrui Meng] fix py style 4e84fce [Xiangrui Meng] remove local hive tests and add more tests 39f19e0 [Xiangrui Meng] add tests b7f666d [Xiangrui Meng] add Python UDT
* [FIX][MLLIB] fix seed in BaggedPointSuiteXiangrui Meng2014-11-031-5/+5
| | | | | | | | | | | | Saw Jenkins test failures due to random seeds. jkbradley manishamde Author: Xiangrui Meng <meng@databricks.com> Closes #3084 from mengxr/fix-baggedpoint-suite and squashes the following commits: f735a43 [Xiangrui Meng] fix seed in BaggedPointSuite
* [SPARK-611] Display executor thread dumps in web UIJosh Rosen2014-11-0313-7/+247
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch allows executor thread dumps to be collected on-demand and viewed in the Spark web UI. The thread dumps are collected using Thread.getAllStackTraces(). To allow remote thread dumps to be triggered from the web UI, I added a new `ExecutorActor` that runs inside of the Executor actor system and responds to RPCs from the driver. The driver's mechanism for obtaining a reference to this actor is a little bit hacky: it uses the block manager master actor to determine the host/port of the executor actor systems in order to construct ActorRefs to ExecutorActor. Unfortunately, I couldn't find a much cleaner way to do this without a big refactoring of the executor -> driver communication. Screenshots: ![image](https://cloud.githubusercontent.com/assets/50748/4781793/7e7a0776-5cbf-11e4-874d-a91cd04620bd.png) ![image](https://cloud.githubusercontent.com/assets/50748/4781794/8bce76aa-5cbf-11e4-8d13-8477748c9f7e.png) ![image](https://cloud.githubusercontent.com/assets/50748/4781797/bd11a8b8-5cbf-11e4-9ad7-a7459467ec8e.png) Author: Josh Rosen <joshrosen@databricks.com> Closes #2944 from JoshRosen/jstack-in-web-ui and squashes the following commits: 3c21a5d [Josh Rosen] Address review comments: 880f7f7 [Josh Rosen] Merge remote-tracking branch 'origin/master' into jstack-in-web-ui f719266 [Josh Rosen] Merge remote-tracking branch 'origin/master' into jstack-in-web-ui 19707b0 [Josh Rosen] Add one comment. 127a130 [Josh Rosen] Update to use SparkContext.DRIVER_IDENTIFIER b8e69aa [Josh Rosen] Merge remote-tracking branch 'origin/master' into jstack-in-web-ui 3dfc2d4 [Josh Rosen] Add missing file. bc1e675 [Josh Rosen] Undo some leftover changes from the earlier approach. f4ac1c1 [Josh Rosen] Switch to on-demand collection of thread dumps dfec08b [Josh Rosen] Add option to disable thread dumps in UI. 4c87d7f [Josh Rosen] Use separate RPC for sending thread dumps. 2b8bdf3 [Josh Rosen] Enable thread dumps from the driver when running in non-local mode. cc3e6b3 [Josh Rosen] Fix test code in DAGSchedulerSuite. 87b8b65 [Josh Rosen] Add new listener event for thread dumps. 8c10216 [Josh Rosen] Add missing file. 0f198ac [Josh Rosen] [SPARK-611] Display executor thread dumps in web UI
* [SPARK-4168][WebUI] web statges number should show correctly when stages are ↵Zhang, Liye2014-11-032-4/+15
| | | | | | | | | | | | | | more than 1000 The number of completed stages and failed stages showed on webUI will always be less than 1000. This is really misleading when there are already thousands of stages completed or failed. The number should be correct even when only partial stages listed on the webUI (stage info will be removed if the number is too large). Author: Zhang, Liye <liye.zhang@intel.com> Closes #3035 from liyezhang556520/webStageNum and squashes the following commits: d9e29fb [Zhang, Liye] add detailed comments for variables 4ea8fd1 [Zhang, Liye] change variable name accroding to comments f4c404d [Zhang, Liye] [SPARK-4168][WebUI] web statges number should show correctly when stages are more than 1000
* [SQL] Convert arguments to Scala UDFsMichael Armbrust2014-11-032-262/+316
| | | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #3077 from marmbrus/udfsWithUdts and squashes the following commits: 34b5f27 [Michael Armbrust] style 504adef [Michael Armbrust] Convert arguments to Scala UDFs
* SPARK-4178. Hadoop input metrics ignore bytes read in RecordReader insta...Sandy Ryza2014-11-033-25/+53
| | | | | | | | | | | ...ntiation Author: Sandy Ryza <sandy@cloudera.com> Closes #3045 from sryza/sandy-spark-4178 and squashes the following commits: 8d2e70e [Sandy Ryza] Kostas's review feedback e5b27c0 [Sandy Ryza] SPARK-4178. Hadoop input metrics ignore bytes read in RecordReader instantiation
* [SQL] More aggressive defaultsMichael Armbrust2014-11-034-14/+22
| | | | | | | | | | | | | | | | | | | | - Turns on compression for in-memory cached data by default - Changes the default parquet compression format back to gzip (we have seen more OOMs with production workloads due to the way Snappy allocates memory) - Ups the batch size to 10,000 rows - Increases the broadcast threshold to 10mb. - Uses our parquet implementation instead of the hive one by default. - Cache parquet metadata by default. Author: Michael Armbrust <michael@databricks.com> Closes #3064 from marmbrus/fasterDefaults and squashes the following commits: 97ee9f8 [Michael Armbrust] parquet codec docs e641694 [Michael Armbrust] Remote also a12866a [Michael Armbrust] Cache metadata. 2d73acc [Michael Armbrust] Update docs defaults. d63d2d5 [Michael Armbrust] document parquet option da373f9 [Michael Armbrust] More aggressive defaults
* [SPARK-4152] [SQL] Avoid data change in CTAS while table already existedCheng Hao2014-11-034-3/+46
| | | | | | | | | | | | CREATE TABLE t1 (a String); CREATE TABLE t1 AS SELECT key FROM src; – throw exception CREATE TABLE if not exists t1 AS SELECT key FROM src; – expect do nothing, currently it will overwrite the t1, which is incorrect. Author: Cheng Hao <hao.cheng@intel.com> Closes #3013 from chenghao-intel/ctas_unittest and squashes the following commits: 194113e [Cheng Hao] fix bug in CTAS when table already existed
* [SPARK-4202][SQL] Simple DSL support for Scala UDFCheng Lian2014-11-032-4/+72
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This feature is based on an offline discussion with mengxr, hopefully can be useful for the new MLlib pipeline API. For the following test snippet ```scala case class KeyValue(key: Int, value: String) val testData = sc.parallelize(1 to 10).map(i => KeyValue(i, i.toString)).toSchemaRDD def foo(a: Int, b: String) => a.toString + b ``` the newly introduced DSL enables the following syntax ```scala import org.apache.spark.sql.catalyst.dsl._ testData.select(Star(None), foo.call('key, 'value) as 'result) ``` which is equivalent to ```scala testData.registerTempTable("testData") sqlContext.registerFunction("foo", foo) sql("SELECT *, foo(key, value) AS result FROM testData") ``` Author: Cheng Lian <lian@databricks.com> Closes #3067 from liancheng/udf-dsl and squashes the following commits: f132818 [Cheng Lian] Adds DSL support for Scala UDF
* [SPARK-3594] [PySpark] [SQL] take more rows to infer schema or samplingDavies Liu2014-11-033-69/+148
| | | | | | | | | | | | | | | | | | | | | | | | This patch will try to infer schema for RDD which has empty value (None, [], {}) in the first row. It will try first 100 rows and merge the types into schema, also merge fields of StructType together. If there is still NullType in schema, then it will show an warning, tell user to try with sampling. If sampling is presented, it will infer schema from all the rows after sampling. Also, add samplingRatio for jsonFile() and jsonRDD() Author: Davies Liu <davies.liu@gmail.com> Author: Davies Liu <davies@databricks.com> Closes #2716 from davies/infer and squashes the following commits: e678f6d [Davies Liu] Merge branch 'master' of github.com:apache/spark into infer 34b5c63 [Davies Liu] Merge branch 'master' of github.com:apache/spark into infer 567dc60 [Davies Liu] update docs 9767b27 [Davies Liu] Merge branch 'master' into infer e48d7fb [Davies Liu] fix tests 29e94d5 [Davies Liu] let NullType inherit from PrimitiveType ee5d524 [Davies Liu] Merge branch 'master' of github.com:apache/spark into infer 540d1d5 [Davies Liu] merge fields for StructType f93fd84 [Davies Liu] add more tests 3603e00 [Davies Liu] take more rows to infer schema, or infer the schema by sampling the RDD
* [SPARK-4207][SQL] Query which has syntax like 'not like' is not working in ↵ravipesala2014-11-032-0/+6
| | | | | | | | | | | | | | | Spark SQL Queries which has 'not like' is not working spark sql. sql("SELECT * FROM records where value not like 'val%'") same query works in Spark HiveQL Author: ravipesala <ravindra.pesala@huawei.com> Closes #3075 from ravipesala/SPARK-4207 and squashes the following commits: 35c11e7 [ravipesala] Supported 'not like' syntax in sql
* [SPARK-4211][Build] Fixes hive.version in Maven profile hive-0.13.1fi2014-11-031-1/+1
| | | | | | | | | | | | | | instead of `hive.version=0.13.1`. e.g. mvn -Phive -Phive=0.13.1 Note: `hive.version=0.13.1a` is the default property value. However, when explicitly specifying the `hive-0.13.1` maven profile, the wrong one would be selected. References: PR #2685, which resolved a package incompatibility issue with Hive-0.13.1 by introducing a special version Hive-0.13.1a Author: fi <coderfi@gmail.com> Closes #3072 from coderfi/master and squashes the following commits: 7ca4b1e [fi] Fixes the `hive-0.13.1` maven profile referencing `hive.version=0.13.1` instead of the Spark compatible `hive.version=0.13.1a` Note: `hive.version=0.13.1a` is the default version. However, when explicitly specifying the `hive-0.13.1` maven profile, the wrong one would be selected. e.g. mvn -Phive -Phive=0.13.1 See PR #2685
* [SPARK-4148][PySpark] fix seed distribution and add some tests for rdd.sampleXiangrui Meng2014-11-033-9/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The current way of seed distribution makes the random sequences from partition i and i+1 offset by 1. ~~~ In [14]: import random In [15]: r1 = random.Random(10) In [16]: r1.randint(0, 1) Out[16]: 1 In [17]: r1.random() Out[17]: 0.4288890546751146 In [18]: r1.random() Out[18]: 0.5780913011344704 In [19]: r2 = random.Random(10) In [20]: r2.randint(0, 1) Out[20]: 1 In [21]: r2.randint(0, 1) Out[21]: 0 In [22]: r2.random() Out[22]: 0.5780913011344704 ~~~ Note: The new tests are not for this bug fix. Author: Xiangrui Meng <meng@databricks.com> Closes #3010 from mengxr/SPARK-4148 and squashes the following commits: 869ae4b [Xiangrui Meng] move tests tests.py c1bacd9 [Xiangrui Meng] fix seed distribution and add some tests for rdd.sample
* [EC2] Factor out Mesos spark-ec2 branchNicholas Chammas2014-11-031-2/+9
| | | | | | | | | | We reference a specific branch in two places. This patch makes it one place. Author: Nicholas Chammas <nicholas.chammas@gmail.com> Closes #3008 from nchammas/mesos-spark-ec2-branch and squashes the following commits: 10a6089 [Nicholas Chammas] factor out mess spark-ec2 branch
* [SPARK-4163][Core][WebUI] Send the fetch failure message back to Web UIzsxwing2014-11-0212-65/+92
| | | | | | | | | | | | | | | | | | | | | | | | This is a PR to send the fetch failure message back to Web UI. Before: ![f1](https://cloud.githubusercontent.com/assets/1000778/4856595/1f036c80-60be-11e4-956f-335147fbccb7.png) ![f2](https://cloud.githubusercontent.com/assets/1000778/4856596/1f11cbea-60be-11e4-8fe9-9f9b2b35c884.png) After (Please ignore the meaning of exception, I threw it in the code directly because it's hard to simulate a fetch failure): ![e1](https://cloud.githubusercontent.com/assets/1000778/4856600/2657ea38-60be-11e4-9f2d-d56c5f900f10.png) ![e2](https://cloud.githubusercontent.com/assets/1000778/4856601/26595008-60be-11e4-912b-2744af786991.png) Author: zsxwing <zsxwing@gmail.com> Closes #3032 from zsxwing/SPARK-4163 and squashes the following commits: f7e1faf [zsxwing] Discard changes for FetchFailedException and minor modification 4e946f7 [zsxwing] Add e as the cause of SparkException 316767d [zsxwing] Add private[storage] to FetchResult d51b0b6 [zsxwing] Set e as the cause of FetchFailedException b88c919 [zsxwing] Use 'private[storage]' for case classes instead of 'sealed' 62103fd [zsxwing] Update as per review 0c07d1f [zsxwing] Backward-compatible support a3bca65 [zsxwing] Send the fetch failure message back to Web UI
* [SPARK-4177][Doc]update build doc since JDBC/CLI support hive 13 nowwangfei2014-11-021-10/+7
| | | | | | | | | Author: wangfei <wangfei1@huawei.com> Closes #3042 from scwf/patch-9 and squashes the following commits: 3784ed1 [wangfei] remove 'TODO' 1891553 [wangfei] update build doc since JDBC/CLI support hive 13
* Close #2971.Reynold Xin2014-11-020-0/+0
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* [SPARK-4183] Enable NettyBlockTransferService by defaultAaron Davidson2014-11-021-0/+10
| | | | | | | | | | Note that we're turning this on for at least the first part of the QA period as a trial. We want to enable this (and deprecate the NioBlockTransferService) as soon as possible in the hopes that NettyBlockTransferService will be more stable and easier to maintain. We will turn it off if we run into major issues. Author: Aaron Davidson <aaron@databricks.com> Closes #3049 from aarondav/enable-netty and squashes the following commits: bb981cc [Aaron Davidson] [SPARK-4183] Enable NettyBlockTransferService by default
* [SPARK-3572] [SQL] Internal API for User-Defined TypesJoseph K. Bradley2014-11-0224-146/+620
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR adds User-Defined Types (UDTs) to SQL. It is a precursor to using SchemaRDD as a Dataset for the new MLlib API. Currently, the UDT API is private since there is incomplete support (e.g., no Java or Python support yet). Author: Joseph K. Bradley <joseph@databricks.com> Author: Michael Armbrust <michael@databricks.com> Author: Xiangrui Meng <meng@databricks.com> Closes #3063 from marmbrus/udts and squashes the following commits: 7ccfc0d [Michael Armbrust] remove println 46a3aee [Michael Armbrust] Slightly easier to read test output. 6cc434d [Michael Armbrust] Recursively convert rows. e369b91 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into udts 15c10a6 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into sql-udt2 f3c72fe [Joseph K. Bradley] Fixing merge e13cd8a [Joseph K. Bradley] Removed Vector UDTs 5817b2b [Joseph K. Bradley] style edits 30ce5b2 [Joseph K. Bradley] updates based on code review d063380 [Joseph K. Bradley] Cleaned up Java UDT Suite, and added warning about element ordering when creating schema from Java Bean a571bb6 [Joseph K. Bradley] Removed old UDT code (registry and Java UDTs). Cleaned up other code. Extended JavaUserDefinedTypeSuite 6fddc1c [Joseph K. Bradley] Made MyLabeledPoint into a Java Bean 20630bc [Joseph K. Bradley] fixed scalastyle fa86b20 [Joseph K. Bradley] Removed Java UserDefinedType, and made UDTs private[spark] for now 8de957c [Joseph K. Bradley] Modified UserDefinedType to store Java class of user type so that registerUDT takes only the udt argument. 8b242ea [Joseph K. Bradley] Fixed merge error after last merge. Note: Last merge commit also removed SQL UDT examples from mllib. 7f29656 [Joseph K. Bradley] Moved udt case to top of all matches. Small cleanups b028675 [Xiangrui Meng] allow any type in UDT 4500d8a [Xiangrui Meng] update example code 87264a5 [Xiangrui Meng] remove debug code 3143ac3 [Xiangrui Meng] remove unnecessary changes cfbc321 [Xiangrui Meng] support UDT in parquet db16139 [Joseph K. Bradley] Added more doc for UserDefinedType. Removed unused code in Suite 759af7a [Joseph K. Bradley] Added more doc to UserDefineType 63626a4 [Joseph K. Bradley] Updated ScalaReflectionsSuite per @marmbrus suggestions 51e5282 [Joseph K. Bradley] fixed 1 test f025035 [Joseph K. Bradley] Cleanups before PR. Added new tests 85872f6 [Michael Armbrust] Allow schema calculation to be lazy, but ensure its available on executors. dff99d6 [Joseph K. Bradley] Added UDTs for Vectors in MLlib, plus DatasetExample using the UDTs cd60cb4 [Joseph K. Bradley] Trying to get other SQL tests to run 34a5831 [Joseph K. Bradley] Added MLlib dependency on SQL. e1f7b9c [Joseph K. Bradley] blah 2f40c02 [Joseph K. Bradley] renamed UDT types 3579035 [Joseph K. Bradley] udt annotation now working b226b9e [Joseph K. Bradley] Changing UDT to annotation fea04af [Joseph K. Bradley] more cleanups 964b32e [Joseph K. Bradley] some cleanups 893ee4c [Joseph K. Bradley] udt finallly working 50f9726 [Joseph K. Bradley] udts 04303c9 [Joseph K. Bradley] udts 39f8707 [Joseph K. Bradley] removed old udt suite 273ac96 [Joseph K. Bradley] basic UDT is working, but deserialization has yet to be done 8bebf24 [Joseph K. Bradley] commented out convertRowToScala for debugging 53de70f [Joseph K. Bradley] more udts... 982c035 [Joseph K. Bradley] still working on UDTs 19b2f60 [Joseph K. Bradley] still working on UDTs 0eaeb81 [Joseph K. Bradley] Still working on UDTs 105c5a3 [Joseph K. Bradley] Adding UserDefinedType to SQL, not done yet.
* [SPARK-4183] Close transport-related resources between SparkContextsAaron Davidson2014-11-0212-32/+78
| | | | | | | | | | | | A leak of event loops may be causing test failures. Author: Aaron Davidson <aaron@databricks.com> Closes #3053 from aarondav/leak and squashes the following commits: e676d18 [Aaron Davidson] Typo! 8f96475 [Aaron Davidson] Keep original ssc semantics 7e49f10 [Aaron Davidson] A leak of event loops may be causing test failures.
* [SPARK-2189][SQL] Adds dropTempTable APICheng Lian2014-11-023-0/+46
| | | | | | | | | | | | | This PR adds an API for unregistering temporary tables. If a temporary table has been cached before, it's unpersisted as well. Author: Cheng Lian <lian.cs.zju@gmail.com> Closes #3039 from liancheng/unregister-temp-table and squashes the following commits: 54ae99f [Cheng Lian] Fixes Scala styling issue 1948c14 [Cheng Lian] Removes the unpersist argument aca41d3 [Cheng Lian] Ensures thread safety 7d4fb2b [Cheng Lian] Adds unregisterTempTable API
* [SPARK-4185][SQL] JSON schema inference failed when dealing with type ↵Yin Huai2014-11-023-9/+20
| | | | | | | | | | | | | | conflicts in arrays JIRA: https://issues.apache.org/jira/browse/SPARK-4185. This PR also has the fix of #3052. Author: Yin Huai <huai@cse.ohio-state.edu> Closes #3056 from yhuai/SPARK-4185 and squashes the following commits: ed3a5a8 [Yin Huai] Correctly handle type conflicts between structs and primitive types in an array.
* [SPARK-4191][SQL]move wrapperFor to HiveInspectors to reuse itwangfei2014-11-022-43/+48
| | | | | | | | | | | | | | Move wrapperFor in InsertIntoHiveTable to HiveInspectors to reuse them, this method can be reused when writing date with ObjectInspector(such as orc support) Author: wangfei <wangfei1@huawei.com> Author: scwf <wangfei1@huawei.com> Closes #3057 from scwf/reuse-wraperfor and squashes the following commits: 7ccf932 [scwf] fix conflicts d44f4da [wangfei] fix imports 9bf1b50 [wangfei] revert no related change 9a5276a [wangfei] move wrapfor to hiveinspector to reuse them
* [SPARK-3791][SQL] Provides Spark version and Hive version in HiveThriftServer2Cheng Lian2014-11-027-112/+173
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR overrides the `GetInfo` Hive Thrift API to provide correct version information. Another property `spark.sql.hive.version` is added to reveal the underlying Hive version. These are generally useful for Spark SQL ODBC driver providers. The Spark version information is extracted from the jar manifest. Also took the chance to remove the `SET -v` hack, which was a workaround for Simba ODBC driver connectivity. TODO - [x] Find a general way to figure out Hive (or even any dependency) version. This [blog post](http://blog.soebes.de/blog/2014/01/02/version-information-into-your-appas-with-maven/) suggests several methods to inspect application version. In the case of Spark, this can be tricky because the chosen method: 1. must applies to both Maven build and SBT build For Maven builds, we can retrieve the version information from the META-INF/maven directory within the assembly jar. But this doesn't work for SBT builds. 2. must not rely on the original jars of dependencies to extract specific dependency version, because Spark uses assembly jar. This implies we can't read Hive version from Hive jar files since standard Spark distribution doesn't include them. 3. should play well with `SPARK_PREPEND_CLASSES` to ease local testing during development. `SPARK_PREPEND_CLASSES` prevents classes to be loaded from the assembly jar, thus we can't locate the jar file and read its manifest. Given these, maybe the only reliable method is to generate a source file containing version information at build time. pwendell Do you have any suggestions from the perspective of the build process? **Update** Hive version is now retrieved from the newly introduced `HiveShim` object. Author: Cheng Lian <lian.cs.zju@gmail.com> Author: Cheng Lian <lian@databricks.com> Closes #2843 from liancheng/get-info and squashes the following commits: a873d0f [Cheng Lian] Updates test case 53f43cd [Cheng Lian] Retrieves underlying Hive verson via HiveShim 1d282b8 [Cheng Lian] Removes the Simba ODBC "SET -v" hack f857fce [Cheng Lian] Overrides Hive GetInfo Thrift API and adds Hive version property
* [SQL] Fixes race condition in CliSuiteCheng Lian2014-11-021-20/+15
| | | | | | | | | | `CliSuite` has been flaky for a while, this PR tries to improve this situation by fixing a race condition in `CliSuite`. The `captureOutput` function is used to capture both stdout and stderr output of the forked external process in two background threads and search for expected strings, but wasn't been properly synchronized before. Author: Cheng Lian <lian@databricks.com> Closes #3060 from liancheng/fix-cli-suite and squashes the following commits: a70569c [Cheng Lian] Fixes race condition in CliSuite
* [SPARK-4182][SQL] Fixes ColumnStats classes for boolean, binary and complex ↵Cheng Lian2014-11-026-19/+82
| | | | | | | | | | | | | | | data types `NoopColumnStats` was once used for binary, boolean and complex data types. This `ColumnStats` doesn't return properly shaped column statistics and causes caching failure if a table contains columns of the aforementioned types. This PR adds `BooleanColumnStats`, `BinaryColumnStats` and `GenericColumnStats`, used for boolean, binary and all complex data types respectively. In addition, `NoopColumnStats` returns properly shaped column statistics containing null count and row count, but this class is now used for testing purpose only. Author: Cheng Lian <lian@databricks.com> Closes #3059 from liancheng/spark-4182 and squashes the following commits: b398cfd [Cheng Lian] Fixes failed test case fb3ee85 [Cheng Lian] Fixes SPARK-4182
* [SPARK-3247][SQL] An API for adding data sources to Spark SQLMichael Armbrust2014-11-0226-42/+1074
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR introduces a new set of APIs to Spark SQL to allow other developers to add support for reading data from new sources in `org.apache.spark.sql.sources`. New sources must implement the interface `BaseRelation`, which is responsible for describing the schema of the data. BaseRelations have three `Scan` subclasses, which are responsible for producing an RDD containing row objects. The [various Scan interfaces](https://github.com/marmbrus/spark/blob/foreign/sql/core/src/main/scala/org/apache/spark/sql/sources/package.scala#L50) allow for optimizations such as column pruning and filter push down, when the underlying data source can handle these operations. By implementing a class that inherits from RelationProvider these data sources can be accessed using using pure SQL. I've used the functionality to update the JSON support so it can now be used in this way as follows: ```sql CREATE TEMPORARY TABLE jsonTableSQL USING org.apache.spark.sql.json OPTIONS ( path '/home/michael/data.json' ) ``` Further example usage can be found in the test cases: https://github.com/marmbrus/spark/tree/foreign/sql/core/src/test/scala/org/apache/spark/sql/sources There is also a library that uses this new API to read avro data available here: https://github.com/marmbrus/sql-avro Author: Michael Armbrust <michael@databricks.com> Closes #2475 from marmbrus/foreign and squashes the following commits: 1ed6010 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into foreign ab2c31f [Michael Armbrust] fix test 1d41bb5 [Michael Armbrust] unify argument names 5b47901 [Michael Armbrust] Remove sealed, more filter types fab154a [Michael Armbrust] Merge remote-tracking branch 'origin/master' into foreign e3e690e [Michael Armbrust] Add hook for extraStrategies a70d602 [Michael Armbrust] Fix style, more tests, FilteredSuite => PrunedFilteredSuite 70da6d9 [Michael Armbrust] Modify API to ease binary compatibility and interop with Java 7d948ae [Michael Armbrust] Fix equality of AttributeReference. 5545491 [Michael Armbrust] Address comments 5031ac3 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into foreign 22963ef [Michael Armbrust] package objects compile wierdly... b069146 [Michael Armbrust] traits => abstract classes 34f836a [Michael Armbrust] Make @DeveloperApi 0d74bcf [Michael Armbrust] Add documention on object life cycle 3e06776 [Michael Armbrust] remove line wraps de3b68c [Michael Armbrust] Remove empty file 360cb30 [Michael Armbrust] style and java api 2957875 [Michael Armbrust] add override 0fd3a07 [Michael Armbrust] Draft of data sources API
* [HOTFIX][SQL] hive test missing some golden fileswangfei2014-11-0215-0/+8
| | | | | | | | | | cc marmbrus Author: wangfei <wangfei1@huawei.com> Closes #3055 from scwf/hotfix and squashes the following commits: d881bd7 [wangfei] miss golden files
* [SPARK-4166][Core][WebUI] Display the executor ID in the Web UI when ↵zsxwing2014-11-025-8/+13
| | | | | | | | | | | | | ExecutorLostFailure happens Now when ExecutorLostFailure happens, it only displays `ExecutorLostFailure (executor lost)`. Adding the executor id will help locate the faulted executor. Author: zsxwing <zsxwing@gmail.com> Closes #3033 from zsxwing/SPARK-4166 and squashes the following commits: ff4664c [zsxwing] Backward-compatible support c5c4cf2 [zsxwing] Display the executor ID in the Web UI when ExecutorLostFailure happens
* [SPARK-3466] Limit size of results that a driver collects for each actionDavies Liu2014-11-028-22/+104
| | | | | | | | | | | | | | | | | | | | | | | | | | Right now, operations like collect() and take() can crash the driver with an OOM if they bring back too many data. This PR will introduce spark.driver.maxResultSize, after setting it, the driver will abort a job if its result is bigger than it. By default, it's 1g (for backward compatibility for most the cases). In local mode, the driver and executor share the same JVM, the default setting can not protect JVM from OOM. cc mateiz Author: Davies Liu <davies@databricks.com> Closes #3003 from davies/collect and squashes the following commits: 248ed5e [Davies Liu] fix compile 272522e [Davies Liu] address comments 2c35773 [Davies Liu] add sizes in message of abort() 5d62303 [Davies Liu] address comments bc3c077 [Davies Liu] Merge branch 'master' of github.com:apache/spark into collect 11f97c5 [Davies Liu] address comments 47b144f [Davies Liu] check the size of result before send and fetch 3d81af2 [Davies Liu] address comments ca8267d [Davies Liu] limit the size of data by collect
* [SPARK-3930] [SPARK-3933] Support fixed-precision decimal in SQL, and some ↵Matei Zaharia2014-11-0155-232/+1636
| | | | | | | | | | | | | | | | | | | | | | | | | optimizations - Adds optional precision and scale to Spark SQL's decimal type, which behave similarly to those in Hive 13 (https://cwiki.apache.org/confluence/download/attachments/27362075/Hive_Decimal_Precision_Scale_Support.pdf) - Replaces our internal representation of decimals with a Decimal class that can store small values in a mutable Long, saving memory in this situation and letting some operations happen directly on Longs This is still marked WIP because there are a few TODOs, but I'll remove that tag when done. Author: Matei Zaharia <matei@databricks.com> Closes #2983 from mateiz/decimal-1 and squashes the following commits: 35e6b02 [Matei Zaharia] Fix issues after merge 227f24a [Matei Zaharia] Review comments 31f915e [Matei Zaharia] Implement Davies's suggestions in Python eb84820 [Matei Zaharia] Support reading/writing decimals as fixed-length binary in Parquet 4dc6bae [Matei Zaharia] Fix decimal support in PySpark d1d9d68 [Matei Zaharia] Fix compile error and test issues after rebase b28933d [Matei Zaharia] Support decimal precision/scale in Hive metastore 2118c0d [Matei Zaharia] Some test and bug fixes 81db9cb [Matei Zaharia] Added mutable Decimal that will be more efficient for small precisions 7af0c3b [Matei Zaharia] Add optional precision and scale to DecimalType, but use Unlimited for now ec0a947 [Matei Zaharia] Make the result of AVG on Decimals be Decimal, not Double
* [SPARK-3161][MLLIB] Adding a node Id caching mechanism for training deci...Sung Chung2014-11-016-41/+405
| | | | | | | | | | ...sion trees. jkbradley mengxr chouqin Please review this. Author: Sung Chung <schung@alpinenow.com> Closes #2868 from codedeft/SPARK-3161 and squashes the following commits: 5f5a156 [Sung Chung] [SPARK-3161][MLLIB] Adding a node Id caching mechanism for training decision trees.
* [SPARK-4121] Set commons-math3 version based on hadoop profiles, instead of ↵Xiangrui Meng2014-11-013-5/+12
| | | | | | | | | | | | | | | | | | | shading In #2928 , we shade commons-math3 to prevent future conflicts with hadoop. It caused problems with our Jenkins master build with maven. Some tests used local-cluster mode, where the assembly jar contains relocated math3 classes, while mllib test code still compiles with core and the untouched math3 classes. This PR sets commons-math3 version based on hadoop profiles. pwendell JoshRosen srowen Author: Xiangrui Meng <meng@databricks.com> Closes #3023 from mengxr/SPARK-4121-alt and squashes the following commits: 580f6d9 [Xiangrui Meng] replace tab by spaces 7f71f08 [Xiangrui Meng] revert changes to PoissonSampler to avoid conflicts d3353d9 [Xiangrui Meng] do not shade commons-math3 b4180dc [Xiangrui Meng] temp work
* Revert "[SPARK-4183] Enable NettyBlockTransferService by default"Patrick Wendell2014-11-012-11/+1
| | | | This reverts commit 59e626c701227634336110e1bc23afd94c535ede.
* [SPARK-4037][SQL] Removes the SessionState instance created in HiveThriftServer2Cheng Lian2014-11-014-45/+44
| | | | | | | | | | | | | | | `HiveThriftServer2` creates a global singleton `SessionState` instance and overrides `HiveContext` to inject the `SessionState` object. This messes up `SessionState` initialization and causes problems. This PR replaces the global `SessionState` with `HiveContext.sessionState` to avoid the initialization conflict. Also `HiveContext` reuses existing started `SessionState` if any (this is required by `SparkSQLCLIDriver`, which uses specialized `CliSessionState`). Author: Cheng Lian <lian@databricks.com> Closes #2887 from liancheng/spark-4037 and squashes the following commits: 8446675 [Cheng Lian] Removes redundant Driver initialization a28fef5 [Cheng Lian] Avoid starting HiveContext.sessionState multiple times 49b1c5b [Cheng Lian] Reuses existing started SessionState if any 3cd6fab [Cheng Lian] Fixes SPARK-4037
* [SPARK-3796] Create external service which can serve shuffle filesAaron Davidson2014-11-0165-312/+2216
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch introduces the tooling necessary to construct an external shuffle service which is independent of Spark executors, and then use this service inside Spark. An example (just for the sake of this PR) of the service creation can be found in Worker, and the service itself is used by plugging in the StandaloneShuffleClient as Spark's ShuffleClient (setup in BlockManager). This PR continues the work from #2753, which extracted out the transport layer of Spark's block transfer into an independent package within Spark. A new package was created which contains the Spark business logic necessary to retrieve the actual shuffle data, which is completely independent of the transport layer introduced in the previous patch. Similar to the transport layer, this package must not depend on Spark as we anticipate plugging this service as a lightweight process within, say, the YARN NodeManager, and do not wish to include Spark's dependencies (including Scala itself). There are several outstanding tasks which must be complete before this PR can be merged: - [x] Complete unit testing of network/shuffle package. - [x] Performance and correctness testing on a real cluster. - [x] Remove example service instantiation from Worker.scala. There are even more shortcomings of this PR which should be addressed in followup patches: - Don't use Java serializer for RPC layer! It is not cross-version compatible. - Handle shuffle file cleanup for dead executors once the application terminates or the ContextCleaner triggers. - Documentation of the feature in the Spark docs. - Improve behavior if the shuffle service itself goes down (right now we don't blacklist it, and new executors cannot spawn on that machine). - SSL and SASL integration - Nice to have: Handle shuffle file consolidation (this would requires changes to Spark's implementation). Author: Aaron Davidson <aaron@databricks.com> Closes #3001 from aarondav/shuffle-service and squashes the following commits: 4d1f8c1 [Aaron Davidson] Remove changes to Worker 705748f [Aaron Davidson] Rename Standalone* to External* fd3928b [Aaron Davidson] Do not unregister executor outputs unduly 9883918 [Aaron Davidson] Make suggested build changes 3d62679 [Aaron Davidson] Add Spark integration test 7fe51d5 [Aaron Davidson] Fix SBT integration 56caa50 [Aaron Davidson] Address comments c8d1ac3 [Aaron Davidson] Add unit tests 2f70c0c [Aaron Davidson] Fix unit tests 5483e96 [Aaron Davidson] Fix unit tests 46a70bf [Aaron Davidson] Whoops, bracket 5ea4df6 [Aaron Davidson] [SPARK-3796] Create external service which can serve shuffle files
* [SPARK-3569][SQL] Add metadata field to StructFieldXiangrui Meng2014-11-0120-56/+573
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add `metadata: Metadata` to `StructField` to store extra information of columns. `Metadata` is a simple wrapper over `Map[String, Any]` with value types restricted to Boolean, Long, Double, String, Metadata, and arrays of those types. SerDe is via JSON. Metadata is preserved through simple operations like `SELECT`. marmbrus liancheng Author: Xiangrui Meng <meng@databricks.com> Author: Michael Armbrust <michael@databricks.com> Closes #2701 from mengxr/structfield-metadata and squashes the following commits: dedda56 [Xiangrui Meng] merge remote 5ef930a [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata c35203f [Xiangrui Meng] Merge pull request #1 from marmbrus/pr/2701 886b85c [Michael Armbrust] Expose Metadata and MetadataBuilder through the public scala and java packages. 589f314 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata 1e2abcf [Xiangrui Meng] change default value of metadata to None in python 611d3c2 [Xiangrui Meng] move metadata from Expr to NamedExpr ddfcfad [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata a438440 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata 4266f4d [Xiangrui Meng] add StructField.toString back for backward compatibility 3f49aab [Xiangrui Meng] remove StructField.toString 24a9f80 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into structfield-metadata 473a7c5 [Xiangrui Meng] merge master c9d7301 [Xiangrui Meng] organize imports 1fcbf13 [Xiangrui Meng] change metadata type in StructField for Scala/Java 60cc131 [Xiangrui Meng] add doc and header 60614c7 [Xiangrui Meng] add metadata e42c452 [Xiangrui Meng] merge master 93518fb [Xiangrui Meng] support metadata in python 905bb89 [Xiangrui Meng] java conversions 618e349 [Xiangrui Meng] make tests work in scala 61b8e0f [Xiangrui Meng] merge master 7e5a322 [Xiangrui Meng] do not output metadata in StructField.toString c41a664 [Xiangrui Meng] merge master d8af0ed [Xiangrui Meng] move tests to SQLQuerySuite 67fdebb [Xiangrui Meng] add test on join d65072e [Xiangrui Meng] remove Map.empty 367d237 [Xiangrui Meng] add test c194d5e [Xiangrui Meng] add metadata field to StructField and Attribute
* [SPARK-4183] Enable NettyBlockTransferService by defaultAaron Davidson2014-11-012-1/+11
| | | | | | | | | | Note that we're turning this on for at least the first part of the QA period as a trial. We want to enable this (and deprecate the NioBlockTransferService) as soon as possible in the hopes that NettyBlockTransferService will be more stable and easier to maintain. We will turn it off if we run into major issues. Author: Aaron Davidson <aaron@databricks.com> Closes #3049 from aarondav/enable-netty and squashes the following commits: bb981cc [Aaron Davidson] [SPARK-4183] Enable NettyBlockTransferService by default
* [SPARK-2759][CORE] Generic Binary File Support in SparkKevin Mader2014-11-0110-5/+892
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The additions add the abstract BinaryFileInputFormat and BinaryRecordReader classes for reading in data as a byte stream and converting it to another format using the ```def parseByteArray(inArray: Array[Byte]): T``` function. As a trivial example ```ByteInputFormat``` and ```ByteRecordReader``` are included which just return the Array[Byte] from a given file. Finally a RDD for ```BinaryFileInputFormat``` (to allow for easier partitioning changes as was done for WholeFileInput) was added and the appropriate byteFiles to the ```SparkContext``` so the functions can be easily used by others. A common use case might be to read in a folder ``` sc.byteFiles("s3://mydrive/tif/*.tif").map(rawData => ReadTiffFromByteArray(rawData)) ``` Author: Kevin Mader <kevinmader@gmail.com> Author: Kevin Mader <kmader@users.noreply.github.com> Closes #1658 from kmader/master and squashes the following commits: 3c49a30 [Kevin Mader] fixing wholetextfileinput to it has the same setMinPartitions function as in BinaryData files 359a096 [Kevin Mader] making the final corrections suggested by @mateiz and renaming a few functions to make their usage clearer 6379be4 [Kevin Mader] reorganizing code 7b9d181 [Kevin Mader] removing developer API, cleaning up imports 8ac288b [Kevin Mader] fixed a single slightly over 100 character line 92bda0d [Kevin Mader] added new tests, renamed files, fixed several of the javaapi functions, formatted code more nicely a32fef7 [Kevin Mader] removed unneeded classes added DeveloperApi note to portabledatastreams since the implementation might change 49174d9 [Kevin Mader] removed unneeded classes added DeveloperApi note to portabledatastreams since the implementation might change c27a8f1 [Kevin Mader] jenkins crashed before running anything last time, so making minor change b348ce1 [Kevin Mader] fixed order in check (prefix only appears on jenkins not when I run unit tests locally) 0588737 [Kevin Mader] filename check in "binary file input as byte array" test now ignores prefixes and suffixes which might get added by Hadoop 4163e38 [Kevin Mader] fixing line length and output from FSDataInputStream to DataInputStream to minimize sensitivity to Hadoop API changes 19812a8 [Kevin Mader] Fixed the serialization issue with PortableDataStream since neither CombineFileSplit nor TaskAttemptContext implement the Serializable interface, by using ByteArrays for storing both and then recreating the objects from these bytearrays as needed. 238c83c [Kevin Mader] fixed several scala-style issues, changed structure of binaryFiles, removed excessive classes added new tests. The caching tests still have a serialization issue, but that should be easily fixed as well. 932a206 [Kevin Mader] Update RawFileInput.scala a01c9cf [Kevin Mader] Update RawFileInput.scala 441f79a [Kevin Mader] fixed a few small comments and dependency 12e7be1 [Kevin Mader] removing imglib from maven (definitely not ready yet) 5deb79e [Kevin Mader] added new portabledatastream to code so that it can be serialized correctly f032bc0 [Kevin Mader] fixed bug in path name, renamed tests bc5c0b9 [Kevin Mader] made minor stylistic adjustments from mateiz df8e528 [Kevin Mader] fixed line lengths and changed java test 9a313d5 [Kevin Mader] making classes that needn't be public private, adding automatic file closure, adding new tests edf5829 [Kevin Mader] fixing line lengths, adding new lines f4841dc [Kevin Mader] un-optimizing imports, silly intellij eacfaa6 [Kevin Mader] Added FixedLengthBinaryInputFormat and RecordReader from freeman-lab and added them to both the JavaSparkContext and the SparkContext as fixedLengthBinaryFile 1622935 [Kevin Mader] changing the line lengths to make jenkins happy 1cfa38a [Kevin Mader] added apache headers, added datainputstream directly as an output option for more complicated readers (HDF5 perhaps), and renamed several of the functions and files to be more consistent. Also added parallel functions to the java api 84035f1 [Kevin Mader] adding binary and byte file support spark 81c5f12 [Kevin Mader] Merge pull request #1 from apache/master
* [SPARK-4115][GraphX] Add overrided count for edge counting of EdgeRDD.luluorta2014-11-011-1/+6
| | | | | | | | | | Accumulate sizes of all the EdgePartitions just like the VertexRDD. Author: luluorta <luluorta@gmail.com> Closes #2975 from luluorta/graph-edge-count and squashes the following commits: 86ef0e5 [luluorta] Add overrided count for edge counting of EdgeRDD.
* [SPARK-4142][GraphX] Default numEdgePartitionsJoseph E. Gonzalez2014-11-012-6/+12
| | | | | | | | | | Changing the default number of edge partitions to match spark parallelism. Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Closes #3006 from jegonzal/default_partitions and squashes the following commits: a9a5c4f [Joseph E. Gonzalez] Changing the default number of edge partitions to match spark parallelism
* Upgrading to roaring 0.4.5 (bug fix release)Daniel Lemire2014-11-011-1/+1
| | | | | | | | | | | | I recommend upgrading roaring to 0.4.5 as it fixes a rarely occurring bug in iterators (that would otherwise throw an unwarranted exception). The upgrade should have no other consequence. Author: Daniel Lemire <lemire@gmail.com> Closes #3044 from lemire/master and squashes the following commits: 54018c5 [Daniel Lemire] Recommended update to roaring 0.4.5 (bug fix release) 048933e [Daniel Lemire] Merge remote-tracking branch 'upstream/master' 431f3a0 [Daniel Lemire] Recommended bug fix release
* Streaming KMeans [MLLIB][SPARK-3254]freeman2014-10-314-1/+597
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This adds a Streaming KMeans algorithm to MLlib. It uses an update rule that generalizes the mini-batch KMeans update to incorporate a decay factor, which allows past data to be forgotten. The decay factor can be specified explicitly, or via a more intuitive "fractional decay" setting, in units of either data points or batches. The PR includes: - StreamingKMeans algorithm with decay factor settings - Usage example - Additions to documentation clustering page - Unit tests of basic behavior and decay behaviors tdas mengxr rezazadeh Author: freeman <the.freeman.lab@gmail.com> Author: Jeremy Freeman <the.freeman.lab@gmail.com> Author: Xiangrui Meng <meng@databricks.com> Closes #2942 from freeman-lab/streaming-kmeans and squashes the following commits: b2e5b4a [freeman] Fixes to docs / examples 078617c [Jeremy Freeman] Merge pull request #1 from mengxr/SPARK-3254 2e682c0 [Xiangrui Meng] take discount on previous weights; use BLAS; detect dying clusters 0411bf5 [freeman] Change decay parameterization 9f7aea9 [freeman] Style fixes 374a706 [freeman] Formatting ad9bdc2 [freeman] Use labeled points and predictOnValues in examples 77dbd3f [freeman] Make initialization check an assertion 9cfc301 [freeman] Make random seed an argument 44050a9 [freeman] Simpler constructor c7050d5 [freeman] Fix spacing 2899623 [freeman] Use pattern matching for clarity a4a316b [freeman] Use collect 1472ec5 [freeman] Doc formatting ea22ec8 [freeman] Fix imports 2086bdc [freeman] Log cluster center updates ea9877c [freeman] More documentation 9facbe3 [freeman] Bug fix 5db7074 [freeman] Example usage for StreamingKMeans f33684b [freeman] Add explanation and example to docs b5b5f8d [freeman] Add better documentation a0fd790 [freeman] Merge remote-tracking branch 'upstream/master' into streaming-kmeans 9fd9c15 [freeman] Merge remote-tracking branch 'upstream/master' into streaming-kmeans b93350f [freeman] Streaming KMeans with decay
* [MLLIB] SPARK-1547: Add Gradient Boosting to MLlibManish Amde2014-10-3120-267/+1331
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Given the popular demand for gradient boosting and AdaBoost in MLlib, I am creating a WIP branch for early feedback on gradient boosting with AdaBoost to follow soon after this PR is accepted. This is based on work done along with hirakendu that was pending due to decision tree optimizations and random forests work. Ideally, boosting algorithms should work with any base learners. This will soon be possible once the MLlib API is finalized -- we want to ensure we use a consistent interface for the underlying base learners. In the meantime, this PR uses decision trees as base learners for the gradient boosting algorithm. The current PR allows "pluggable" loss functions and provides least squares error and least absolute error by default. Here is the task list: - [x] Gradient boosting support - [x] Pluggable loss functions - [x] Stochastic gradient boosting support – Re-use the BaggedPoint approach used for RandomForest. - [x] Binary classification support - [x] Support configurable checkpointing – This approach will avoid long lineage chains. - [x] Create classification and regression APIs - [x] Weighted Ensemble Model -- created a WeightedEnsembleModel class that can be used by ensemble algorithms such as random forests and boosting. - [x] Unit Tests Future work: + Multi-class classification is currently not supported by this PR since it requires discussion on the best way to support "deviance" as a loss function. + BaggedRDD caching -- Avoid repeating feature to bin mapping for each tree estimator after standard API work is completed. cc: jkbradley hirakendu mengxr etrain atalwalkar chouqin Author: Manish Amde <manish9ue@gmail.com> Author: manishamde <manish9ue@gmail.com> Closes #2607 from manishamde/gbt and squashes the following commits: 991c7b5 [Manish Amde] public api ff2a796 [Manish Amde] addressing comments b4c1318 [Manish Amde] removing spaces 8476b6b [Manish Amde] fixing line length 0183cb9 [Manish Amde] fixed naming and formatting issues 1c40c33 [Manish Amde] add newline, removed spaces e33ab61 [Manish Amde] minor comment eadbf09 [Manish Amde] parameter renaming 035a2ed [Manish Amde] jkbradley formatting suggestions 9f7359d [Manish Amde] simplified gbt logic and added more tests 49ba107 [Manish Amde] merged from master eff21fe [Manish Amde] Added gradient boosting tests 3fd0528 [Manish Amde] moved helper methods to new class a32a5ab [Manish Amde] added test for subsampling without replacement 781542a [Manish Amde] added support for fractional subsampling with replacement 3a18cc1 [Manish Amde] cleaned up api for conversion to bagged point and moved tests to it's own test suite 0e81906 [Manish Amde] improving caching unpersisting logic d971f73 [Manish Amde] moved RF code to use WeightedEnsembleModel class fee06d3 [Manish Amde] added weighted ensemble model 1b01943 [Manish Amde] add weights for base learners 9bc6e74 [Manish Amde] adding random seed as parameter d2c8323 [Manish Amde] Merge branch 'master' into gbt 2ae97b7 [Manish Amde] added documentation for the loss classes 9366b8f [Manish Amde] minor: using numTrees instead of trees.size 3b43896 [Manish Amde] added learning rate for prediction 9b2e35e [Manish Amde] Merge branch 'master' into gbt 6a11c02 [manishamde] fixing formatting 823691b [Manish Amde] fixing RF test 1f47941 [Manish Amde] changing access modifier 5b67102 [Manish Amde] shortened parameter list 5ab3796 [Manish Amde] minor reformatting 9155a9d [Manish Amde] consolidated boosting configuration and added public API 631baea [Manish Amde] Merge branch 'master' into gbt 2cb1258 [Manish Amde] public API support 3b8ffc0 [Manish Amde] added documentation 8e10c63 [Manish Amde] modified unpersist strategy f62bc48 [Manish Amde] added unpersist bdca43a [Manish Amde] added timing parameters 2fbc9c7 [Manish Amde] fixing binomial classification prediction 6dd4dd8 [Manish Amde] added support for log loss 9af0231 [Manish Amde] classification attempt 62cc000 [Manish Amde] basic checkpointing 4784091 [Manish Amde] formatting 78ed452 [Manish Amde] added newline and fixed if statement 3973dd1 [Manish Amde] minor indicating subsample is double during comparison aa8fae7 [Manish Amde] minor refactoring 1a8031c [Manish Amde] sampling with replacement f1c9ef7 [Manish Amde] Merge branch 'master' into gbt cdceeef [Manish Amde] added documentation 6251fd5 [Manish Amde] modified method name 5538521 [Manish Amde] disable checkpointing for now 0ae1c0a [Manish Amde] basic gradient boosting code from earlier branches
* [SPARK-3838][examples][mllib][python] Word2Vec example in pythonAnant2014-10-312-0/+67
| | | | | | | | | | | | | | | | | | | | This pull request refers to issue: https://issues.apache.org/jira/browse/SPARK-3838 Python example for word2vec mengxr Author: Anant <anant.asty@gmail.com> Closes #2952 from anantasty/SPARK-3838 and squashes the following commits: 87bd723 [Anant] remove stop line 4bd439e [Anant] Changes as per code review. Fized error in word2vec python example, simplified example in docs. 3d3c9ee [Anant] Added empty line after python imports 0c90c31 [Anant] Fixed erroneous code. I was still treating each line to be a single word instead of 16 words ee4f5f6 [Anant] Fixes from code review comments c637bcf [Anant] Added word2vec python example to docs 269f31f [Anant] added example in docs c015b14 [Anant] Added python example for word2vec
* [MLLIB] SPARK-2329 Add multi-label evaluation metricsAlexander Ulanov2014-10-312-0/+260
| | | | | | | | | | | | | | | | | | | | | | Implementation of various multi-label classification measures, including: Hamming-loss, strict and default Accuracy, macro-averaged Precision, Recall and F1-measure based on documents and labels, micro-averaged measures: https://issues.apache.org/jira/browse/SPARK-2329 Multi-class measures are currently in the following pull request: https://github.com/apache/spark/pull/1155 Author: Alexander Ulanov <nashb@yandex.ru> Author: avulanov <nashb@yandex.ru> Closes #1270 from avulanov/multilabelmetrics and squashes the following commits: fc8175e [Alexander Ulanov] Merge with previous updates 43a613e [Alexander Ulanov] Addressing reviewers comments: change Set to Array 517a594 [avulanov] Addressing reviewers comments: Scala style cf4222bc [avulanov] Addressing reviewers comments: renaming. Added label method that returns the list of labels 1843f73 [Alexander Ulanov] Scala style fix 79e8476 [Alexander Ulanov] Replacing fold(_ + _) with sum as suggested by srowen ca46765 [Alexander Ulanov] Cosmetic changes: Apache header and parameter explanation 40593f5 [Alexander Ulanov] Multi-label metrics: Hamming-loss, strict and normal accuracy, fix to macro measures, bunch of tests ad62df0 [Alexander Ulanov] Comments and scala style check 154164b [Alexander Ulanov] Multilabel evaluation metics and tests: macro precision and recall averaged by docs, micro and per-class precision and recall averaged by class
* SPARK-4175. Exception on stage pageSandy Ryza2014-10-311-1/+1
| | | | | | | | Author: Sandy Ryza <sandy@cloudera.com> Closes #3043 from sryza/sandy-spark-4175 and squashes the following commits: e327340 [Sandy Ryza] SPARK-4175. Exception on stage page
* [HOT FIX] Yarn stable tests don't compileandrewor142014-10-312-15/+19
| | | | | | | | | | | | This is caused by this commit: acd4ac7c9a503445e27739708cf36e19119b8ddc Author: andrewor14 <andrew@databricks.com> Author: Andrew Or <andrew@databricks.com> Closes #3041 from andrewor14/yarn-hot-fix and squashes the following commits: e5deba1 [andrewor14] Add new line at the end (minor) aa998e8 [Andrew Or] Compilation hot fix
* [SPARK-3870] EOL character enforcementKousuke Saruta2014-10-315-366/+369
| | | | | | | | | | | | | | | | | | | We have shell scripts and Windows batch files, so we should enforce proper EOL character. Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp> Closes #2726 from sarutak/eol-enforcement and squashes the following commits: 9748c3f [Kousuke Saruta] Fixed make.bat 252de89 [Kousuke Saruta] Removed extra characters from make.bat 5b81c00 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into eol-enforcement 8633ed2 [Kousuke Saruta] merge branch 'master' of git://git.apache.org/spark into eol-enforcement 5d630d8 [Kousuke Saruta] Merged ba10797 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into eol-enforcement 7407515 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into eol-enforcement 772fd4e [Kousuke Saruta] Normized EOL character in make.bat and compute-classpath.cmd ac7f873 [Kousuke Saruta] Added an entry for .gitattributes to .rat-excludes 1570e77 [Kousuke Saruta] Added .gitattributes
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