aboutsummaryrefslogtreecommitdiff
Commit message (Collapse)AuthorAgeFilesLines
* [SPARK-7156][SQL] support RandomSplit in DataFramesBurak Yavuz2015-04-2910-22/+130
| | | | | | | | | | | | | | | | | This is built on top of kaka1992 's PR #5711 using Logical plans. Author: Burak Yavuz <brkyvz@gmail.com> Closes #5761 from brkyvz/random-sample and squashes the following commits: a1fb0aa [Burak Yavuz] remove unrelated file 69669c3 [Burak Yavuz] fix broken test 1ddb3da [Burak Yavuz] copy base 6000328 [Burak Yavuz] added python api and fixed test 3c11d1b [Burak Yavuz] fixed broken test f400ade [Burak Yavuz] fix build errors 2384266 [Burak Yavuz] addressed comments v0.1 e98ebac [Burak Yavuz] [SPARK-7156][SQL] support RandomSplit in DataFrames
* [SPARK-6529] [ML] Add Word2Vec transformerXusen Yin2015-04-294-1/+267
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | See JIRA issue [here](https://issues.apache.org/jira/browse/SPARK-6529). There are some notes: 1. I add `learningRate` in sharedParams since it is a common parameter for ML algorithms. 2. We will not support transform of finding synonyms from a `Vector`, which will support in further JIRA issues. 3. Word2Vec is different with other ML models that its training set and transformed set are different. Its training set is an `RDD[Iterable[String]]` which represents documents, but the transformed set we want is an `RDD[String]` that represents unique words. So you have to switch your `inputCol` in these two stages. Author: Xusen Yin <yinxusen@gmail.com> Closes #5596 from yinxusen/SPARK-6529 and squashes the following commits: ee2b37a [Xusen Yin] merge with former HEAD 4945462 [Xusen Yin] merge with #5626 3bc2cbd [Xusen Yin] change foldLeft to for loop and use blas 5dd4ee7 [Xusen Yin] fix scala style 743e0d5 [Xusen Yin] fix comments and code style 04c48e9 [Xusen Yin] ensure the functionality a190f2c [Xusen Yin] fix code style and refine the transform function of word2vec 02848fa [Xusen Yin] refine comments 34a55c0 [Xusen Yin] fix errors 109d124 [Xusen Yin] add test suite and pass it 04dde06 [Xusen Yin] add shared params c594095 [Xusen Yin] add word2vec transformer 23d77fa [Xusen Yin] merge with #5626 e8cfaf7 [Xusen Yin] fix conflict with master 66e7bd3 [Xusen Yin] change foldLeft to for loop and use blas 566ec20 [Xusen Yin] fix scala style b54399f [Xusen Yin] fix comments and code style 1211e86 [Xusen Yin] ensure the functionality 6b97ec8 [Xusen Yin] fix code style and refine the transform function of word2vec 7cde18f [Xusen Yin] rm sharedParams 618abd0 [Xusen Yin] refine comments e29680a [Xusen Yin] fix errors fe3afe9 [Xusen Yin] add test suite and pass it 02767fb [Xusen Yin] add shared params 6a514f1 [Xusen Yin] add word2vec transformer
* [SPARK-7222] [ML] Added mathematical derivation in comment and compressed ↵DB Tsai2015-04-293-37/+101
| | | | | | | | | | | | | | | | | | | | the model, removed the correction terms in LinearRegression with ElasticNet Added detailed mathematical derivation of how scaling and LeastSquaresAggregator work. Refactored the code so the model is compressed based on the storage. We may try compression based on the prediction time. Also, I found that diffSum will be always zero mathematically, so no corrections are required. Author: DB Tsai <dbt@netflix.com> Closes #5767 from dbtsai/lir-doc and squashes the following commits: 5e346c9 [DB Tsai] refactoring fc9f582 [DB Tsai] doc 58456d8 [DB Tsai] address feedback 69757b8 [DB Tsai] actually diffSum is mathematically zero! No correction is needed. 5929e49 [DB Tsai] typo 63f7d1e [DB Tsai] Added compression to the model based on storage 203a295 [DB Tsai] Add more documentation to LinearRegression in new ML framework.
* [SPARK-6629] cancelJobGroup() may not work for jobs whose job groups are ↵Josh Rosen2015-04-293-5/+91
| | | | | | | | | | | | | | | | | | | | | inherited from parent threads When a job is submitted with a job group and that job group is inherited from a parent thread, there are multiple bugs that may prevent this job from being cancelable via `SparkContext.cancelJobGroup()`: - When filtering jobs based on their job group properties, DAGScheduler calls `get()` instead of `getProperty()`, which does not respect inheritance, so it will skip over jobs whose job group properties were inherited. - `Properties` objects are mutable, but we do not make defensive copies / snapshots, so modifications of the parent thread's job group will cause running jobs' groups to change; this also breaks cancelation. Both of these issues are easy to fix: use `getProperty()` and perform defensive copying. Author: Josh Rosen <joshrosen@databricks.com> Closes #5288 from JoshRosen/localProperties-mutability-race and squashes the following commits: 9e29654 [Josh Rosen] Fix style issue 5d90750 [Josh Rosen] Merge remote-tracking branch 'origin/master' into localProperties-mutability-race 3f7b9e8 [Josh Rosen] Add JIRA reference; move clone into DAGScheduler 707e417 [Josh Rosen] Clone local properties to prevent mutations from breaking job cancellation. b376114 [Josh Rosen] Fix bug that prevented jobs with inherited job group properties from being cancelled.
* [SPARK-6752] [STREAMING] [REOPENED] Allow StreamingContext to be recreated ↵Tathagata Das2015-04-297-61/+503
| | | | | | | | | | | | | | | | | | | | from checkpoint and existing SparkContext Original PR #5428 got reverted due to issues between MutableBoolean and Hadoop 1.0.4 (see JIRA). This replaces MutableBoolean with AtomicBoolean. srowen pwendell Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #5773 from tdas/SPARK-6752 and squashes the following commits: a0c0ead [Tathagata Das] Fix for hadoop 1.0.4 70ae85b [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into SPARK-6752 94db63c [Tathagata Das] Fix long line. 524f519 [Tathagata Das] Many changes based on PR comments. eabd092 [Tathagata Das] Added Function0, Java API and unit tests for StreamingContext.getOrCreate 36a7823 [Tathagata Das] Minor changes. 204814e [Tathagata Das] Added StreamingContext.getOrCreate with existing SparkContext
* [SPARK-7056] [STREAMING] Make the Write Ahead Log pluggableTathagata Das2015-04-2922-207/+686
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Users may want the WAL data to be written to non-HDFS data storage systems. To allow that, we have to make the WAL pluggable. The following design doc outlines the plan. https://docs.google.com/a/databricks.com/document/d/1A2XaOLRFzvIZSi18i_luNw5Rmm9j2j4AigktXxIYxmY/edit?usp=sharing Things to add. * Unit tests for WriteAheadLogUtils Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #5645 from tdas/wal-pluggable and squashes the following commits: 2c431fd [Tathagata Das] Minor fixes. c2bc7384 [Tathagata Das] More changes based on PR comments. 569a416 [Tathagata Das] fixed long line bde26b1 [Tathagata Das] Renamed segment to record handle everywhere b65e155 [Tathagata Das] More changes based on PR comments. d7cd15b [Tathagata Das] Fixed test 1a32a4b [Tathagata Das] Fixed test e0d19fb [Tathagata Das] Fixed defaults 9310cbf [Tathagata Das] style fix. 86abcb1 [Tathagata Das] Refactored WriteAheadLogUtils, and consolidated all WAL related configuration into it. 84ce469 [Tathagata Das] Added unit test and fixed compilation error. bce5e75 [Tathagata Das] Fixed long lines. 837c4f5 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into wal-pluggable 754fbf8 [Tathagata Das] Added license and docs. 09bc6fe [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into wal-pluggable 7dd2d4b [Tathagata Das] Added pluggable WriteAheadLog interface, and refactored all code along with it
* Fix a typo of "threshold"Xusen Yin2015-04-291-2/+2
| | | | | | | | | | | mengxr Author: Xusen Yin <yinxusen@gmail.com> Closes #5769 from yinxusen/patch-1 and squashes the following commits: 43235f4 [Xusen Yin] Update PearsonCorrelation.scala f7287ee [Xusen Yin] Fix a typo of "threshold"
* [SQL][Minor] fix java doc for DataFrame.aggWenchen Fan2015-04-291-11/+6
| | | | | | | | Author: Wenchen Fan <cloud0fan@outlook.com> Closes #5712 from cloud-fan/minor and squashes the following commits: be23064 [Wenchen Fan] fix java doc for DataFrame.agg
* Better error message on access to non-existing attributeksonj2015-04-291-1/+2
| | | | | | | | | | I believe column access via `__getattr__` is bad and shouldn't be implicitly encouraged by the error message when accessing a non-existing attribute on DataFrame. This patch changes the error message from 'no such column' to the more generic 'no such attribute', which is also what Pandas DFs will throw. Author: ksonj <kson@siberie.de> Closes #5771 from ksonj/master and squashes the following commits: bcc2220 [ksonj] Better error message on access to non-existing attribute
* [SPARK-7223] Rename RPC askWithReply -> askWithReply, sendWithReply -> ask.Reynold Xin2015-04-2920-331/+394
| | | | | | | | | | The old naming scheme was very confusing between askWithReply and sendWithReply. I also divided RpcEnv.scala into multiple files. Author: Reynold Xin <rxin@databricks.com> Closes #5768 from rxin/rpc-rename and squashes the following commits: a84058e [Reynold Xin] [SPARK-7223] Rename RPC askWithReply -> askWithReply, sendWithReply -> ask.
* [SPARK-6918] [YARN] Secure HBase support.Dean Chen2015-04-291-1/+37
| | | | | | | | | | | | | | Obtain HBase security token with Kerberos credentials locally to be sent to executors. Tested on eBay's secure HBase cluster. Similar to obtainTokenForNamenodes and fails gracefully if HBase classes are not included in path. Requires hbase-site.xml to be in the classpath(typically via conf dir) for the zookeeper configuration. Should that go in the docs somewhere? Did not see an HBase section. Author: Dean Chen <deanchen5@gmail.com> Closes #5586 from deanchen/master and squashes the following commits: 0c190ef [Dean Chen] [SPARK-6918][YARN] Secure HBase support.
* [SPARK-7076][SPARK-7077][SPARK-7080][SQL] Use managed memory for aggregationsJosh Rosen2015-04-2947-18/+3675
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch adds managed-memory-based aggregation to Spark SQL / DataFrames. Instead of working with Java objects, this new aggregation path uses `sun.misc.Unsafe` to manipulate raw memory. This reduces the memory footprint for aggregations, resulting in fewer spills, OutOfMemoryErrors, and garbage collection pauses. As a result, this allows for higher memory utilization. It can also result in better cache locality since objects will be stored closer together in memory. This feature can be eanbled by setting `spark.sql.unsafe.enabled=true`. For now, this feature is only supported when codegen is enabled and only supports aggregations for which the grouping columns are primitive numeric types or strings and aggregated values are numeric. ### Managing memory with sun.misc.Unsafe This patch supports both on- and off-heap managed memory. - In on-heap mode, memory addresses are identified by the combination of a base Object and an offset within that object. - In off-heap mode, memory is addressed directly with 64-bit long addresses. To support both modes, functions that manipulate memory accept both `baseObject` and `baseOffset` fields. In off-heap mode, we simply pass `null` as `baseObject`. We allocate memory in large chunks, so memory fragmentation and allocation speed are not significant bottlenecks. By default, we use on-heap mode. To enable off-heap mode, set `spark.unsafe.offHeap=true`. To track allocated memory, this patch extends `SparkEnv` with an `ExecutorMemoryManager` and supplies each `TaskContext` with a `TaskMemoryManager`. These classes work together to track allocations and detect memory leaks. ### Compact tuple format This patch introduces `UnsafeRow`, a compact row layout. In this format, each tuple has three parts: a null bit set, fixed length values, and variable-length values: ![image](https://cloud.githubusercontent.com/assets/50748/7328538/2fdb65ce-ea8b-11e4-9743-6c0f02bb7d1f.png) - Rows are always 8-byte word aligned (so their sizes will always be a multiple of 8 bytes) - The bit set is used for null tracking: - Position _i_ is set if and only if field _i_ is null - The bit set is aligned to an 8-byte word boundary. - Every field appears as an 8-byte word in the fixed-length values part: - If a field is null, we zero out the values. - If a field is variable-length, the word stores a relative offset (w.r.t. the base of the tuple) that points to the beginning of the field's data in the variable-length part. - Each variable-length data type can have its own encoding: - For strings, the first word stores the length of the string and is followed by UTF-8 encoded bytes. If necessary, the end of the string is padded with empty bytes in order to ensure word-alignment. For example, a tuple that consists 3 fields of type (int, string, string), with value (null, “data”, “bricks”) would look like this: ![image](https://cloud.githubusercontent.com/assets/50748/7328526/1e21959c-ea8b-11e4-9a28-a4350fe4a7b5.png) This format allows us to compare tuples for equality by directly comparing their raw bytes. This also enables fast hashing of tuples. ### Hash map for performing aggregations This patch introduces `UnsafeFixedWidthAggregationMap`, a hash map for performing aggregations where the aggregation result columns are fixed-with. This map's keys and values are `Row` objects. `UnsafeFixedWidthAggregationMap` is implemented on top of `BytesToBytesMap`, an append-only map which supports byte-array keys and values. `BytesToBytesMap` stores pointers to key and value tuples. For each record with a new key, we copy the key and create the aggregation value buffer for that key and put them in a buffer. The hash table then simply stores pointers to the key and value. For each record with an existing key, we simply run the aggregation function to update the values in place. This map is implemented using open hashing with triangular sequence probing. Each entry stores two words in a long array: the first word stores the address of the key and the second word stores the relative offset from the key tuple to the value tuple, as well as the key's 32-bit hashcode. By storing the full hashcode, we reduce the number of equality checks that need to be performed to handle position collisions ()since the chance of hashcode collision is much lower than position collision). `UnsafeFixedWidthAggregationMap` allows regular Spark SQL `Row` objects to be used when probing the map. Internally, it encodes these rows into `UnsafeRow` format using `UnsafeRowConverter`. This conversion has a small overhead that can be eliminated in the future once we use UnsafeRows in other operators. <!-- Reviewable:start --> [<img src="https://reviewable.io/review_button.png" height=40 alt="Review on Reviewable"/>](https://reviewable.io/reviews/apache/spark/5725) <!-- Reviewable:end --> Author: Josh Rosen <joshrosen@databricks.com> Closes #5725 from JoshRosen/unsafe and squashes the following commits: eeee512 [Josh Rosen] Add converters for Null, Boolean, Byte, and Short columns. 81f34f8 [Josh Rosen] Follow 'place children last' convention for GeneratedAggregate 1bc36cc [Josh Rosen] Refactor UnsafeRowConverter to avoid unnecessary boxing. 017b2dc [Josh Rosen] Remove BytesToBytesMap.finalize() 50e9671 [Josh Rosen] Throw memory leak warning even in case of error; add warning about code duplication 70a39e4 [Josh Rosen] Split MemoryManager into ExecutorMemoryManager and TaskMemoryManager: 6e4b192 [Josh Rosen] Remove an unused method from ByteArrayMethods. de5e001 [Josh Rosen] Fix debug vs. trace in logging message. a19e066 [Josh Rosen] Rename unsafe Java test suites to match Scala test naming convention. 78a5b84 [Josh Rosen] Add logging to MemoryManager ce3c565 [Josh Rosen] More comments, formatting, and code cleanup. 529e571 [Josh Rosen] Measure timeSpentResizing in nanoseconds instead of milliseconds. 3ca84b2 [Josh Rosen] Only zero the used portion of groupingKeyConversionScratchSpace 162caf7 [Josh Rosen] Fix test compilation b45f070 [Josh Rosen] Don't redundantly store the offset from key to value, since we can compute this from the key size. a8e4a3f [Josh Rosen] Introduce MemoryManager interface; add to SparkEnv. 0925847 [Josh Rosen] Disable MiMa checks for new unsafe module cde4132 [Josh Rosen] Add missing pom.xml 9c19fc0 [Josh Rosen] Add configuration options for heap vs. offheap 6ffdaa1 [Josh Rosen] Null handling improvements in UnsafeRow. 31eaabc [Josh Rosen] Lots of TODO and doc cleanup. a95291e [Josh Rosen] Cleanups to string handling code afe8dca [Josh Rosen] Some Javadoc cleanup f3dcbfe [Josh Rosen] More mod replacement 854201a [Josh Rosen] Import and comment cleanup 06e929d [Josh Rosen] More warning cleanup ef6b3d3 [Josh Rosen] Fix a bunch of FindBugs and IntelliJ inspections 29a7575 [Josh Rosen] Remove debug logging 49aed30 [Josh Rosen] More long -> int conversion. b26f1d3 [Josh Rosen] Fix bug in murmur hash implementation. 765243d [Josh Rosen] Enable optional performance metrics for hash map. 23a440a [Josh Rosen] Bump up default hash map size 628f936 [Josh Rosen] Use ints intead of longs for indexing. 92d5a06 [Josh Rosen] Address a number of minor code review comments. 1f4b716 [Josh Rosen] Merge Unsafe code into the regular GeneratedAggregate, guarded by a configuration flag; integrate planner support and re-enable all tests. d85eeff [Josh Rosen] Add basic sanity test for UnsafeFixedWidthAggregationMap bade966 [Josh Rosen] Comment update (bumping to refresh GitHub cache...) b3eaccd [Josh Rosen] Extract aggregation map into its own class. d2bb986 [Josh Rosen] Update to implement new Row methods added upstream 58ac393 [Josh Rosen] Use UNSAFE allocator in GeneratedAggregate (TODO: make this configurable) 7df6008 [Josh Rosen] Optimizations related to zeroing out memory: c1b3813 [Josh Rosen] Fix bug in UnsafeMemoryAllocator.free(): 738fa33 [Josh Rosen] Add feature flag to guard UnsafeGeneratedAggregate c55bf66 [Josh Rosen] Free buffer once iterator has been fully consumed. 62ab054 [Josh Rosen] Optimize for fact that get() is only called on String columns. c7f0b56 [Josh Rosen] Reuse UnsafeRow pointer in UnsafeRowConverter ae39694 [Josh Rosen] Add finalizer as "cleanup method of last resort" c754ae1 [Josh Rosen] Now that the store*() contract has been stregthened, we can remove an extra lookup f764d13 [Josh Rosen] Simplify address + length calculation in Location. 079f1bf [Josh Rosen] Some clarification of the BytesToBytesMap.lookup() / set() contract. 1a483c5 [Josh Rosen] First version that passes some aggregation tests: fc4c3a8 [Josh Rosen] Sketch how the converters will be used in UnsafeGeneratedAggregate 53ba9b7 [Josh Rosen] Start prototyping Java Row -> UnsafeRow converters 1ff814d [Josh Rosen] Add reminder to free memory on iterator completion 8a8f9df [Josh Rosen] Add skeleton for GeneratedAggregate integration. 5d55cef [Josh Rosen] Add skeleton for Row implementation. f03e9c1 [Josh Rosen] Play around with Unsafe implementations of more string methods. ab68e08 [Josh Rosen] Begin merging the UTF8String implementations. 480a74a [Josh Rosen] Initial import of code from Databricks unsafe utils repo.
* [SPARK-7204] [SQL] Fix callSite for Dataframe and SQL operationsPatrick Wendell2015-04-292-10/+21
| | | | | | | | | | | | | | | | | | | | | | | | | This patch adds SQL to the set of excluded libraries when generating a callSite. This makes the callSite mechanism work properly for the data frame API. I also added a small improvement for JDBC queries where we just use the string "Spark JDBC Server Query" instead of trying to give a callsite that doesn't make any sense to the user. Before (DF): ![screen shot 2015-04-28 at 1 29 26 pm](https://cloud.githubusercontent.com/assets/320616/7380170/ef63bfb0-edae-11e4-989c-f88a5ba6bbee.png) After (DF): ![screen shot 2015-04-28 at 1 34 58 pm](https://cloud.githubusercontent.com/assets/320616/7380181/fa7f6d90-edae-11e4-9559-26f163ed63b8.png) After (JDBC): ![screen shot 2015-04-28 at 2 00 10 pm](https://cloud.githubusercontent.com/assets/320616/7380185/02f5b2a4-edaf-11e4-8e5b-99bdc3df66dd.png) Author: Patrick Wendell <patrick@databricks.com> Closes #5757 from pwendell/dataframes and squashes the following commits: 0d931a4 [Patrick Wendell] Attempting to fix PySpark tests 85bf740 [Patrick Wendell] [SPARK-7204] Fix callsite for dataframe operations.
* [SPARK-7188] added python support for math DataFrame functionsBurak Yavuz2015-04-298-423/+276
| | | | | | | | | | | | | | | | | | | Adds support for the math functions for DataFrames in PySpark. rxin I love Davies. Author: Burak Yavuz <brkyvz@gmail.com> Closes #5750 from brkyvz/python-math-udfs and squashes the following commits: 7c4f563 [Burak Yavuz] removed is_math 3c4adde [Burak Yavuz] cleanup imports d5dca3f [Burak Yavuz] moved math functions to mathfunctions 25e6534 [Burak Yavuz] addressed comments v2.0 d3f7e0f [Burak Yavuz] addressed comments and added tests 7b7d7c4 [Burak Yavuz] remove tests for removed methods 33c2c15 [Burak Yavuz] fixed python style 3ee0c05 [Burak Yavuz] added python functions
* MAINTENANCE: Automated closing of pull requests.Patrick Wendell2015-04-280-0/+0
| | | | | | | | | | | | This commit exists to close the following pull requests on Github: Closes #3205 (close requested by 'srowen') Closes #5478 (close requested by 'andrewor14') Closes #4910 (close requested by 'srowen') Closes #5080 (close requested by 'marmbrus') Closes #537 (close requested by 'srowen') Closes #5691 (close requested by 'srowen') Closes #5469 (close requested by 'marmbrus')
* [SPARK-7205] Support `.ivy2/local` and `.m2/repositories/` in --packagesBurak Yavuz2015-04-282-21/+40
| | | | | | | | | | | | In addition, I made a small change that will allow users to import 2 different artifacts with the same name. That change is made in `[organization]_[artifact]-[revision].[ext]`. This used to be only `[artifact].[ext]` which might have caused collisions between artifacts with the same artifactId, but different groupId's. cc pwendell Author: Burak Yavuz <brkyvz@gmail.com> Closes #5755 from brkyvz/local-caches and squashes the following commits: c47c9c5 [Burak Yavuz] Small fixes to --packages
* [SPARK-7215] made coalesce and repartition a part of the query planBurak Yavuz2015-04-286-13/+40
| | | | | | | | | | | | | | | | | Coalesce and repartition now show up as part of the query plan, rather than resulting in a new `DataFrame`. cc rxin Author: Burak Yavuz <brkyvz@gmail.com> Closes #5762 from brkyvz/df-repartition and squashes the following commits: b1e76dd [Burak Yavuz] added documentation on repartitions 5807e35 [Burak Yavuz] renamed coalescepartitions fa4509f [Burak Yavuz] rename coalesce 2c349b5 [Burak Yavuz] address comments f2e6af1 [Burak Yavuz] add ticks 686c90b [Burak Yavuz] made coalesce and repartition a part of the query plan
* [SPARK-6756] [MLLIB] add toSparse, toDense, numActives, numNonzeros, and ↵Xiangrui Meng2015-04-283-0/+149
| | | | | | | | | | | | | compressed to Vector Add `compressed` to `Vector` with some other methods: `numActives`, `numNonzeros`, `toSparse`, and `toDense`. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #5756 from mengxr/SPARK-6756 and squashes the following commits: 8d4ecbd [Xiangrui Meng] address comment and add mima excludes da54179 [Xiangrui Meng] add toSparse, toDense, numActives, numNonzeros, and compressed to Vector
* [SPARK-7208] [ML] [PYTHON] Added Matrix, SparseMatrix to __all__ list in ↵Joseph K. Bradley2015-04-281-1/+2
| | | | | | | | | | | | | | linalg.py Added Matrix, SparseMatrix to __all__ list in linalg.py CC: mengxr Author: Joseph K. Bradley <joseph@databricks.com> Closes #5759 from jkbradley/SPARK-7208 and squashes the following commits: deb51a2 [Joseph K. Bradley] Added Matrix, SparseMatrix to __all__ list in linalg.py
* [SPARK-7138] [STREAMING] Add method to BlockGenerator to add multiple ↵Tathagata Das2015-04-281-0/+14
| | | | | | | | | | | | | records to BlockGenerator with single callback This is to ensure that receivers that receive data in small batches (like Kinesis) and want to add them but want the callback function to be called only once. This is for internal use only for improvement to Kinesis Receiver that we are planning to do. Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #5695 from tdas/SPARK-7138 and squashes the following commits: a35cf7d [Tathagata Das] Fixed style. a7a4cb9 [Tathagata Das] Added extra method to BlockGenerator.
* [SPARK-6965] [MLLIB] StringIndexer handles numeric input.Xiangrui Meng2015-04-282-5/+31
| | | | | | | | | | | Cast numeric types to String for indexing. Boolean type is not handled in this PR. jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #5753 from mengxr/SPARK-6965 and squashes the following commits: 2e34f3c [Xiangrui Meng] add actual type in the error message ad938bf [Xiangrui Meng] StringIndexer handles numeric input.
* Closes #4807Xiangrui Meng2015-04-280-0/+0
| | | | | Closes #5055 Closes #3583
* [SPARK-7201] [MLLIB] move Identifiable to ml.utilXiangrui Meng2015-04-283-2/+3
| | | | | | | | | | It shouldn't live directly under `spark.ml`. Author: Xiangrui Meng <meng@databricks.com> Closes #5749 from mengxr/SPARK-7201 and squashes the following commits: 53847f9 [Xiangrui Meng] move Identifiable to ml.util
* [MINOR] [CORE] Warn users who try to cache RDDs with dynamic allocation on.Marcelo Vanzin2015-04-281-0/+5
| | | | | | | | | Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5751 from vanzin/cached-rdd-warning and squashes the following commits: 554cc07 [Marcelo Vanzin] Change message. 9efb9da [Marcelo Vanzin] [minor] [core] Warn users who try to cache RDDs with dynamic allocation on.
* [SPARK-5338] [MESOS] Add cluster mode support for MesosTimothy Chen2015-04-2830-493/+2147
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch adds the support for cluster mode to run on Mesos. It introduces a new Mesos framework dedicated to launch new apps/drivers, and can be called with the spark-submit script and specifying --master flag to the cluster mode REST interface instead of Mesos master. Example: ./bin/spark-submit --deploy-mode cluster --class org.apache.spark.examples.SparkPi --master mesos://10.0.0.206:8077 --executor-memory 1G --total-executor-cores 100 examples/target/spark-examples_2.10-1.3.0-SNAPSHOT.jar 30 Part of this patch is also to abstract the StandaloneRestServer so it can have different implementations of the REST endpoints. Features of the cluster mode in this PR: - Supports supervise mode where scheduler will keep trying to reschedule exited job. - Adds a new UI for the cluster mode scheduler to see all the running jobs, finished jobs, and supervise jobs waiting to be retried - Supports state persistence to ZK, so when the cluster scheduler fails over it can pick up all the queued and running jobs Author: Timothy Chen <tnachen@gmail.com> Author: Luc Bourlier <luc.bourlier@typesafe.com> Closes #5144 from tnachen/mesos_cluster_mode and squashes the following commits: 069e946 [Timothy Chen] Fix rebase. e24b512 [Timothy Chen] Persist submitted driver. 390c491 [Timothy Chen] Fix zk conf key for mesos zk engine. e324ac1 [Timothy Chen] Fix merge. fd5259d [Timothy Chen] Address review comments. 1553230 [Timothy Chen] Address review comments. c6c6b73 [Timothy Chen] Pass spark properties to mesos cluster tasks. f7d8046 [Timothy Chen] Change app name to spark cluster. 17f93a2 [Timothy Chen] Fix head of line blocking in scheduling drivers. 6ff8e5c [Timothy Chen] Address comments and add logging. df355cd [Timothy Chen] Add metrics to mesos cluster scheduler. 20f7284 [Timothy Chen] Address review comments 7252612 [Timothy Chen] Fix tests. a46ad66 [Timothy Chen] Allow zk cli param override. 920fc4b [Timothy Chen] Fix scala style issues. 862b5b5 [Timothy Chen] Support asking driver status when it's retrying. 7f214c2 [Timothy Chen] Fix RetryState visibility e0f33f7 [Timothy Chen] Add supervise support and persist retries. 371ce65 [Timothy Chen] Handle cluster mode recovery and state persistence. 3d4dfa1 [Luc Bourlier] Adds support to kill submissions febfaba [Timothy Chen] Bound the finished drivers in memory 543a98d [Timothy Chen] Schedule multiple jobs 6887e5e [Timothy Chen] Support looking at SPARK_EXECUTOR_URI env variable in schedulers 8ec76bc [Timothy Chen] Fix Mesos dispatcher UI. d57d77d [Timothy Chen] Add documentation 825afa0 [Luc Bourlier] Supports more spark-submit parameters b8e7181 [Luc Bourlier] Adds a shutdown latch to keep the deamon running 0fa7780 [Luc Bourlier] Launch task through the mesos scheduler 5b7a12b [Timothy Chen] WIP: Making a cluster mode a mesos framework. 4b2f5ef [Timothy Chen] Specify user jar in command to be replaced with local. e775001 [Timothy Chen] Support fetching remote uris in driver runner. 7179495 [Timothy Chen] Change Driver page output and add logging 880bc27 [Timothy Chen] Add Mesos Cluster UI to display driver results 9986731 [Timothy Chen] Kill drivers when shutdown 67cbc18 [Timothy Chen] Rename StandaloneRestClient to RestClient and add sbin scripts e3facdd [Timothy Chen] Add Mesos Cluster dispatcher
* [SPARK-6314] [CORE] handle JsonParseException for history serverZhang, Liye2015-04-281-2/+3
| | | | | | | | | | This is handled in the same way with [SPARK-6197](https://issues.apache.org/jira/browse/SPARK-6197). The result of this PR is that exception showed in history server log will be replaced by a warning, and the application that with un-complete history log file will be listed on history server webUI Author: Zhang, Liye <liye.zhang@intel.com> Closes #5736 from liyezhang556520/SPARK-6314 and squashes the following commits: b8d2d88 [Zhang, Liye] handle JsonParseException for history server
* [SPARK-5932] [CORE] Use consistent naming for size propertiesIlya Ganelin2015-04-2823-81/+488
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | I've added an interface to JavaUtils to do byte conversion and added hooks within Utils.scala to handle conversion within Spark code (like for time strings). I've added matching tests for size conversion, and then updated all deprecated configs and documentation as per SPARK-5933. Author: Ilya Ganelin <ilya.ganelin@capitalone.com> Closes #5574 from ilganeli/SPARK-5932 and squashes the following commits: 11f6999 [Ilya Ganelin] Nit fixes 49a8720 [Ilya Ganelin] Whitespace fix 2ab886b [Ilya Ganelin] Scala style fc85733 [Ilya Ganelin] Got rid of floating point math 852a407 [Ilya Ganelin] [SPARK-5932] Added much improved overflow handling. Can now handle sizes up to Long.MAX_VALUE Petabytes instead of being capped at Long.MAX_VALUE Bytes 9ee779c [Ilya Ganelin] Simplified fraction matches 22413b1 [Ilya Ganelin] Made MAX private 3dfae96 [Ilya Ganelin] Fixed some nits. Added automatic conversion of old paramter for kryoserializer.mb to new values. e428049 [Ilya Ganelin] resolving merge conflict 8b43748 [Ilya Ganelin] Fixed error in pattern matching for doubles 84a2581 [Ilya Ganelin] Added smoother handling of fractional values for size parameters. This now throws an exception and added a warning for old spark.kryoserializer.buffer d3d09b6 [Ilya Ganelin] [SPARK-5932] Fixing error in KryoSerializer fe286b4 [Ilya Ganelin] Resolved merge conflict c7803cd [Ilya Ganelin] Empty lines 54b78b4 [Ilya Ganelin] Simplified byteUnit class 69e2f20 [Ilya Ganelin] Updates to code f32bc01 [Ilya Ganelin] [SPARK-5932] Fixed error in API in SparkConf.scala where Kb conversion wasn't being done properly (was Mb). Added test cases for both timeUnit and ByteUnit conversion f15f209 [Ilya Ganelin] Fixed conversion of kryo buffer size 0f4443e [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-5932 35a7fa7 [Ilya Ganelin] Minor formatting 928469e [Ilya Ganelin] [SPARK-5932] Converted some longs to ints 5d29f90 [Ilya Ganelin] [SPARK-5932] Finished documentation updates 7a6c847 [Ilya Ganelin] [SPARK-5932] Updated spark.shuffle.file.buffer afc9a38 [Ilya Ganelin] [SPARK-5932] Updated spark.broadcast.blockSize and spark.storage.memoryMapThreshold ae7e9f6 [Ilya Ganelin] [SPARK-5932] Updated spark.io.compression.snappy.block.size 2d15681 [Ilya Ganelin] [SPARK-5932] Updated spark.executor.logs.rolling.size.maxBytes 1fbd435 [Ilya Ganelin] [SPARK-5932] Updated spark.broadcast.blockSize eba4de6 [Ilya Ganelin] [SPARK-5932] Updated spark.shuffle.file.buffer.kb b809a78 [Ilya Ganelin] [SPARK-5932] Updated spark.kryoserializer.buffer.max 0cdff35 [Ilya Ganelin] [SPARK-5932] Updated to use bibibytes in method names. Updated spark.kryoserializer.buffer.mb and spark.reducer.maxMbInFlight 475370a [Ilya Ganelin] [SPARK-5932] Simplified ByteUnit code, switched to using longs. Updated docs to clarify that we use kibi, mebi etc instead of kilo, mega 851d691 [Ilya Ganelin] [SPARK-5932] Updated memoryStringToMb to use new interfaces a9f4fcf [Ilya Ganelin] [SPARK-5932] Added unit tests for unit conversion 747393a [Ilya Ganelin] [SPARK-5932] Added unit tests for ByteString conversion 09ea450 [Ilya Ganelin] [SPARK-5932] Added byte string conversion to Jav utils 5390fd9 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-5932 db9a963 [Ilya Ganelin] Closing second spark context 1dc0444 [Ilya Ganelin] Added ref equality check 8c884fa [Ilya Ganelin] Made getOrCreate synchronized cb0c6b7 [Ilya Ganelin] Doc updates and code cleanup 270cfe3 [Ilya Ganelin] [SPARK-6703] Documentation fixes 15e8dea [Ilya Ganelin] Updated comments and added MiMa Exclude 0e1567c [Ilya Ganelin] Got rid of unecessary option for AtomicReference dfec4da [Ilya Ganelin] Changed activeContext to AtomicReference 733ec9f [Ilya Ganelin] Fixed some bugs in test code 8be2f83 [Ilya Ganelin] Replaced match with if e92caf7 [Ilya Ganelin] [SPARK-6703] Added test to ensure that getOrCreate both allows creation, retrieval, and a second context if desired a99032f [Ilya Ganelin] Spacing fix d7a06b8 [Ilya Ganelin] Updated SparkConf class to add getOrCreate method. Started test suite implementation
* [SPARK-4286] Add an external shuffle service that can be run as a daemon.Iulian Dragos2015-04-287-15/+124
| | | | | | | | | | | | | | | | | | | | This allows Mesos deployments to use the shuffle service (and implicitly dynamic allocation). It does so by adding a new "main" class and two corresponding scripts in `sbin`: - `sbin/start-shuffle-service.sh` - `sbin/stop-shuffle-service.sh` Specific options can be passed in `SPARK_SHUFFLE_OPTS`. This is picking up work from #3861 /cc tnachen Author: Iulian Dragos <jaguarul@gmail.com> Closes #4990 from dragos/feature/external-shuffle-service and squashes the following commits: 6c2b148 [Iulian Dragos] Import order and wrong name fixup. 07804ad [Iulian Dragos] Moved ExternalShuffleService to the `deploy` package + other minor tweaks. 4dc1f91 [Iulian Dragos] Reviewer’s comments: 8145429 [Iulian Dragos] Add an external shuffle service that can be run as a daemon.
* [Core][test][minor] replace try finally block with tryWithSafeFinallyZhang, Liye2015-04-281-2/+2
| | | | | | | | Author: Zhang, Liye <liye.zhang@intel.com> Closes #5739 from liyezhang556520/trySafeFinally and squashes the following commits: 55683e5 [Zhang, Liye] replace try finally block with tryWithSafeFinally
* [SPARK-7140] [MLLIB] only scan the first 16 entries in Vector.hashCodeXiangrui Meng2015-04-281-21/+67
| | | | | | | | | | | | The Python SerDe calls `Object.hashCode`, which is very expensive for Vectors. It is not necessary to scan the whole vector, especially for large ones. In this PR, we only scan the first 16 nonzeros. srowen Author: Xiangrui Meng <meng@databricks.com> Closes #5697 from mengxr/SPARK-7140 and squashes the following commits: 2abc86d [Xiangrui Meng] typo 8fb7d74 [Xiangrui Meng] update impl 1ebad60 [Xiangrui Meng] only scan the first 16 nonzeros in Vector.hashCode
* [SPARK-5253] [ML] LinearRegression with L1/L2 (ElasticNet) using OWLQNDB Tsai2015-04-288-64/+508
| | | | | | | | | | | | | | Author: DB Tsai <dbt@netflix.com> Author: DB Tsai <dbtsai@alpinenow.com> Closes #4259 from dbtsai/lir and squashes the following commits: a81c201 [DB Tsai] add import org.apache.spark.util.Utils back 9fc48ed [DB Tsai] rebase 2178b63 [DB Tsai] add comments 9988ca8 [DB Tsai] addressed feedback and fixed a bug. TODO: documentation and build another synthetic dataset which can catch the bug fixed in this commit. fcbaefe [DB Tsai] Refactoring 4eb078d [DB Tsai] first commit
* [SPARK-6435] spark-shell --jars option does not add all jars to classpathMasayoshi TSUZUKI2015-04-284-12/+13
| | | | | | | | | | | | | | | Modified to accept double-quotated args properly in spark-shell.cmd. Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp> Closes #5227 from tsudukim/feature/SPARK-6435-2 and squashes the following commits: ac55787 [Masayoshi TSUZUKI] removed unnecessary argument. 60789a7 [Masayoshi TSUZUKI] Merge branch 'master' of https://github.com/apache/spark into feature/SPARK-6435-2 1fee420 [Masayoshi TSUZUKI] fixed test code for escaping '='. 0d4dc41 [Masayoshi TSUZUKI] - escaped comman and semicolon in CommandBuilderUtils.java - added random string to the temporary filename - double-quotation followed by `cmd /c` did not worked properly - no need to escape `=` by `^` - if double-quoted string ended with `\` like classpath, the last `\` is parsed as the escape charactor and the closing `"` didn't work properly 2a332e5 [Masayoshi TSUZUKI] Merge branch 'master' into feature/SPARK-6435-2 04f4291 [Masayoshi TSUZUKI] [SPARK-6435] spark-shell --jars option does not add all jars to classpath
* [SPARK-7100] [MLLIB] Fix persisted RDD leak in GradientBoostTreesJim Carroll2015-04-281-2/+6
| | | | | | | | | | | | | | This fixes a leak of a persisted RDD where GradientBoostTrees can call persist but never unpersists. Jira: https://issues.apache.org/jira/browse/SPARK-7100 Discussion: http://apache-spark-developers-list.1001551.n3.nabble.com/GradientBoostTrees-leaks-a-persisted-RDD-td11750.html Author: Jim Carroll <jim@dontcallme.com> Closes #5669 from jimfcarroll/gb-unpersist-fix and squashes the following commits: 45f4b03 [Jim Carroll] [SPARK-7100][MLLib] Fix persisted RDD leak in GradientBoostTrees
* [SPARK-7168] [BUILD] Update plugin versions in Maven build and centralize ↵Sean Owen2015-04-285-16/+32
| | | | | | | | | | | | | versions Update Maven build plugin versions and centralize plugin version management Author: Sean Owen <sowen@cloudera.com> Closes #5720 from srowen/SPARK-7168 and squashes the following commits: 98a8947 [Sean Owen] Make install, deploy plugin versions explicit 4ecf3b2 [Sean Owen] Update Maven build plugin versions and centralize plugin version management
* [SPARK-6352] [SQL] Custom parquet output committerPei-Lun Lee2015-04-283-0/+116
| | | | | | | | | | | | | | | | | | | | | | | | Add new config "spark.sql.parquet.output.committer.class" to allow custom parquet output committer and an output committer class specific to use on s3. Fix compilation error introduced by https://github.com/apache/spark/pull/5042. Respect ParquetOutputFormat.ENABLE_JOB_SUMMARY flag. Author: Pei-Lun Lee <pllee@appier.com> Closes #5525 from ypcat/spark-6352 and squashes the following commits: 54c6b15 [Pei-Lun Lee] error handling 472870e [Pei-Lun Lee] add back custom parquet output committer ddd0f69 [Pei-Lun Lee] Merge branch 'master' of https://github.com/apache/spark into spark-6352 9ece5c5 [Pei-Lun Lee] compatibility with hadoop 1.x 8413fcd [Pei-Lun Lee] Merge branch 'master' of https://github.com/apache/spark into spark-6352 fe65915 [Pei-Lun Lee] add support for parquet config parquet.enable.summary-metadata e17bf47 [Pei-Lun Lee] Merge branch 'master' of https://github.com/apache/spark into spark-6352 9ae7545 [Pei-Lun Lee] [SPARL-6352] [SQL] Change to allow custom parquet output committer. 0d540b9 [Pei-Lun Lee] [SPARK-6352] [SQL] add license c42468c [Pei-Lun Lee] [SPARK-6352] [SQL] add test case 0fc03ca [Pei-Lun Lee] [SPARK-6532] [SQL] hide class DirectParquetOutputCommitter 769bd67 [Pei-Lun Lee] DirectParquetOutputCommitter f75e261 [Pei-Lun Lee] DirectParquetOutputCommitter
* [SPARK-7135][SQL] DataFrame expression for monotonically increasing IDs.Reynold Xin2015-04-285-5/+103
| | | | | | | | | | | Author: Reynold Xin <rxin@databricks.com> Closes #5709 from rxin/inc-id and squashes the following commits: 7853611 [Reynold Xin] private sql. a9fda0d [Reynold Xin] Missed a few numbers. 343d896 [Reynold Xin] Self review feedback. a7136cb [Reynold Xin] [SPARK-7135][SQL] DataFrame expression for monotonically increasing IDs.
* [SPARK-7187] SerializationDebugger should not crash user codeAndrew Or2015-04-281-2/+10
| | | | | | | | | | | rxin Author: Andrew Or <andrew@databricks.com> Closes #5734 from andrewor14/ser-deb and squashes the following commits: e8aad6c [Andrew Or] NonFatal 57d0ef4 [Andrew Or] try catch improveException
* [SPARK-5946] [STREAMING] Add Python API for direct Kafka streamjerryshao2015-04-274-15/+383
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Currently only added `createDirectStream` API, I'm not sure if `createRDD` is also needed, since some Java object needs to be wrapped in Python. Please help to review, thanks a lot. Author: jerryshao <saisai.shao@intel.com> Author: Saisai Shao <saisai.shao@intel.com> Closes #4723 from jerryshao/direct-kafka-python-api and squashes the following commits: a1fe97c [jerryshao] Fix rebase issue eebf333 [jerryshao] Address the comments da40f4e [jerryshao] Fix Python 2.6 Syntax error issue 5c0ee85 [jerryshao] Style fix 4aeac18 [jerryshao] Fix bug in example code 7146d86 [jerryshao] Add unit test bf3bdd6 [jerryshao] Add more APIs and address the comments f5b3801 [jerryshao] Small style fix 8641835 [Saisai Shao] Rebase and update the code 589c05b [Saisai Shao] Fix the style d6fcb6a [Saisai Shao] Address the comments dfda902 [Saisai Shao] Style fix 0f7d168 [Saisai Shao] Add the doc and fix some style issues 67e6880 [Saisai Shao] Fix test bug 917b0db [Saisai Shao] Add Python createRDD API for Kakfa direct stream c3fc11d [jerryshao] Modify the docs 2c00936 [Saisai Shao] address the comments 3360f44 [jerryshao] Fix code style e0e0f0d [jerryshao] Code clean and bug fix 338c41f [Saisai Shao] Add python API and example for direct kafka stream
* [SPARK-6829] Added math functions for DataFramesBurak Yavuz2015-04-279-1/+1259
| | | | | | | | | | | | | | | | | | | | | | | | Implemented almost all math functions found in scala.math (max, min and abs were already present). cc mengxr marmbrus Author: Burak Yavuz <brkyvz@gmail.com> Closes #5616 from brkyvz/math-udfs and squashes the following commits: fb27153 [Burak Yavuz] reverted exception message 836a098 [Burak Yavuz] fixed test and addressed small comment e5f0d13 [Burak Yavuz] addressed code review v2.2 b26c5fb [Burak Yavuz] addressed review v2.1 2761f08 [Burak Yavuz] addressed review v2 6588a5b [Burak Yavuz] fixed merge conflicts b084e10 [Burak Yavuz] Addressed code review 029e739 [Burak Yavuz] fixed atan2 test 534cc11 [Burak Yavuz] added more tests, addressed comments fa68dbe [Burak Yavuz] added double specific test data 937d5a5 [Burak Yavuz] use doubles instead of ints 8e28fff [Burak Yavuz] Added apache header 7ec8f7f [Burak Yavuz] Added math functions for DataFrames
* [SPARK-7174][Core] Move calling `TaskScheduler.executorHeartbeatReceived` to ↵zsxwing2015-04-271-9/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | another thread `HeartbeatReceiver` will call `TaskScheduler.executorHeartbeatReceived`, which is a blocking operation because `TaskScheduler.executorHeartbeatReceived` will call ```Scala blockManagerMaster.driverEndpoint.askWithReply[Boolean]( BlockManagerHeartbeat(blockManagerId), 600 seconds) ``` finally. Even if it asks from a local Actor, it may block the current Akka thread. E.g., the reply may be dispatched to the same thread of the ask operation. So the reply cannot be processed. An extreme case is setting the thread number of Akka dispatch thread pool to 1. jstack log: ``` "sparkDriver-akka.actor.default-dispatcher-14" daemon prio=10 tid=0x00007f2a8c02d000 nid=0x725 waiting on condition [0x00007f2b1d6d0000] java.lang.Thread.State: TIMED_WAITING (parking) at sun.misc.Unsafe.park(Native Method) - parking to wait for <0x00000006197a0868> (a scala.concurrent.impl.Promise$CompletionLatch) at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:226) at java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireSharedNanos(AbstractQueuedSynchronizer.java:1033) at java.util.concurrent.locks.AbstractQueuedSynchronizer.tryAcquireSharedNanos(AbstractQueuedSynchronizer.java:1326) at scala.concurrent.impl.Promise$DefaultPromise.tryAwait(Promise.scala:208) at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:218) at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:223) at scala.concurrent.Await$$anonfun$result$1.apply(package.scala:107) at akka.dispatch.MonitorableThreadFactory$AkkaForkJoinWorkerThread$$anon$3.block(ThreadPoolBuilder.scala:169) at scala.concurrent.forkjoin.ForkJoinPool.managedBlock(ForkJoinPool.java:3640) at akka.dispatch.MonitorableThreadFactory$AkkaForkJoinWorkerThread.blockOn(ThreadPoolBuilder.scala:167) at scala.concurrent.Await$.result(package.scala:107) at org.apache.spark.rpc.RpcEndpointRef.askWithReply(RpcEnv.scala:355) at org.apache.spark.scheduler.DAGScheduler.executorHeartbeatReceived(DAGScheduler.scala:169) at org.apache.spark.scheduler.TaskSchedulerImpl.executorHeartbeatReceived(TaskSchedulerImpl.scala:367) at org.apache.spark.HeartbeatReceiver$$anonfun$receiveAndReply$1.applyOrElse(HeartbeatReceiver.scala:103) at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$processMessage(AkkaRpcEnv.scala:182) at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1$$anonfun$applyOrElse$4.apply$mcV$sp(AkkaRpcEnv.scala:128) at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$safelyCall(AkkaRpcEnv.scala:203) at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1.applyOrElse(AkkaRpcEnv.scala:127) at scala.runtime.AbstractPartialFunction$mcVL$sp.apply$mcVL$sp(AbstractPartialFunction.scala:33) at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:33) at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:25) at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:59) at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:42) at scala.PartialFunction$class.applyOrElse(PartialFunction.scala:118) at org.apache.spark.util.ActorLogReceive$$anon$1.applyOrElse(ActorLogReceive.scala:42) at akka.actor.Actor$class.aroundReceive(Actor.scala:465) at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1.aroundReceive(AkkaRpcEnv.scala:94) at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516) at akka.actor.ActorCell.invoke(ActorCell.scala:487) at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238) at akka.dispatch.Mailbox.run(Mailbox.scala:220) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:393) at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) ``` This PR moved this blocking operation to a separated thread. Author: zsxwing <zsxwing@gmail.com> Closes #5723 from zsxwing/SPARK-7174 and squashes the following commits: 98bfe48 [zsxwing] Use a single thread for checking timeout and reporting executorHeartbeatReceived 5b3b545 [zsxwing] Move calling `TaskScheduler.executorHeartbeatReceived` to another thread to avoid blocking the Akka thread pool
* [SPARK-7090] [MLLIB] Introduce LDAOptimizer to LDA to further improve ↵Yuhao Yang2015-04-278-151/+256
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | extensibility jira: https://issues.apache.org/jira/browse/SPARK-7090 LDA was implemented with extensibility in mind. And with the development of OnlineLDA and Gibbs Sampling, we are collecting more detailed requirements from different algorithms. As Joseph Bradley jkbradley proposed in https://github.com/apache/spark/pull/4807 and with some further discussion, we'd like to adjust the code structure a little to present the common interface and extension point clearly. Basically class LDA would be a common entrance for LDA computing. And each LDA object will refer to a LDAOptimizer for the concrete algorithm implementation. Users can customize LDAOptimizer with specific parameters and assign it to LDA. Concrete changes: 1. Add a trait `LDAOptimizer`, which defines the common iterface for concrete implementations. Each subClass is a wrapper for a specific LDA algorithm. 2. Move EMOptimizer to file LDAOptimizer and inherits from LDAOptimizer, rename to EMLDAOptimizer. (in case a more generic EMOptimizer comes in the future) -adjust the constructor of EMOptimizer, since all the parameters should be passed in through initialState method. This can avoid unwanted confusion or overwrite. -move the code from LDA.initalState to initalState of EMLDAOptimizer 3. Add property ldaOptimizer to LDA and its getter/setter, and EMLDAOptimizer is the default Optimizer. 4. Change the return type of LDA.run from DistributedLDAModel to LDAModel. Further work: add OnlineLDAOptimizer and other possible Optimizers once ready. Author: Yuhao Yang <hhbyyh@gmail.com> Closes #5661 from hhbyyh/ldaRefactor and squashes the following commits: 0e2e006 [Yuhao Yang] respond to review comments 08a45da [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaRefactor e756ce4 [Yuhao Yang] solve mima exception d74fd8f [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaRefactor 0bb8400 [Yuhao Yang] refactor LDA with Optimizer ec2f857 [Yuhao Yang] protoptype for discussion
* [SPARK-7162] [YARN] Launcher error in yarn-clientGuoQiang Li2015-04-271-1/+1
| | | | | | | | | | jira: https://issues.apache.org/jira/browse/SPARK-7162 Author: GuoQiang Li <witgo@qq.com> Closes #5716 from witgo/SPARK-7162 and squashes the following commits: b64564c [GuoQiang Li] Launcher error in yarn-client
* [SPARK-7145] [CORE] commons-lang (2.x) classes used instead of commons-lang3 ↵Sean Owen2015-04-2710-27/+35
| | | | | | | | | | | | (3.x); commons-io used without dependency Remove use of commons-lang in favor of commons-lang3 classes; remove commons-io use in favor of Guava Author: Sean Owen <sowen@cloudera.com> Closes #5703 from srowen/SPARK-7145 and squashes the following commits: 21fbe03 [Sean Owen] Remove use of commons-lang in favor of commons-lang3 classes; remove commons-io use in favor of Guava
* [SPARK-3090] [CORE] Stop SparkContext if user forgets to.Marcelo Vanzin2015-04-273-23/+35
| | | | | | | | | | | | | Set up a shutdown hook to try to stop the Spark context in case the user forgets to do it. The main effect is that any open logs files are flushed and closed, which is particularly interesting for event logs. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #5696 from vanzin/SPARK-3090 and squashes the following commits: 3b554b5 [Marcelo Vanzin] [SPARK-3090] [core] Stop SparkContext if user forgets to.
* [SPARK-6738] [CORE] Improve estimate the size of a large arrayHong Shen2015-04-272-15/+48
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Currently, SizeEstimator.visitArray is not correct in the follow case, ``` array size > 200, elem has the share object ``` when I add a debug log in SizeTracker.scala: ``` System.err.println(s"numUpdates:$numUpdates, size:$ts, bytesPerUpdate:$bytesPerUpdate, cost time:$b") ``` I get the following log: ``` numUpdates:1, size:262448, bytesPerUpdate:0.0, cost time:35 numUpdates:2, size:420698, bytesPerUpdate:158250.0, cost time:35 numUpdates:4, size:420754, bytesPerUpdate:28.0, cost time:32 numUpdates:7, size:420754, bytesPerUpdate:0.0, cost time:27 numUpdates:12, size:420754, bytesPerUpdate:0.0, cost time:28 numUpdates:20, size:420754, bytesPerUpdate:0.0, cost time:25 numUpdates:32, size:420754, bytesPerUpdate:0.0, cost time:21 numUpdates:52, size:420754, bytesPerUpdate:0.0, cost time:20 numUpdates:84, size:420754, bytesPerUpdate:0.0, cost time:20 numUpdates:135, size:420754, bytesPerUpdate:0.0, cost time:20 numUpdates:216, size:420754, bytesPerUpdate:0.0, cost time:11 numUpdates:346, size:420754, bytesPerUpdate:0.0, cost time:6 numUpdates:554, size:488911, bytesPerUpdate:327.67788461538464, cost time:8 numUpdates:887, size:2312259426, bytesPerUpdate:6942253.798798799, cost time:198 15/04/21 14:27:26 INFO collection.ExternalAppendOnlyMap: Thread 51 spilling in-memory map of 3.0 GB to disk (1 time so far) 15/04/21 14:27:26 INFO collection.ExternalAppendOnlyMap: /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc ``` But in fact the file size is only 162K: ``` $ ll -h /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc -rw-r----- 1 spark users 162K Apr 21 14:27 /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc ``` In order to test case, I change visitArray to: ``` var size = 0l for (i <- 0 until length) { val obj = JArray.get(array, i) size += SizeEstimator.estimate(obj, state.visited).toLong } state.size += size ``` I get the following log: ``` ... 14895 277016088 566.9046118590662 time:8470 23832 281840544 552.3308270676691 time:8031 38132 289891824 539.8294729775092 time:7897 61012 302803640 563.0265734265735 time:13044 97620 322904416 564.3276223776223 time:13554 15/04/14 11:46:43 INFO collection.ExternalAppendOnlyMap: Thread 51 spilling in-memory map of 314.5 MB to disk (1 time so far) 15/04/14 11:46:43 INFO collection.ExternalAppendOnlyMap: /data1/yarnenv/local/usercache/spark/appcache/application_1426746631567_8477/spark-local-20150414114020-2fcb/14/temp_local_5b6b98d5-5bfa-47e2-8216-059482ccbda0 ``` the file size is 85M. ``` $ ll -h /data1/yarnenv/local/usercache/spark/appcache/application_1426746631567_8477/spark- local-20150414114020-2fcb/14/ total 85M -rw-r----- 1 spark users 85M Apr 14 11:46 temp_local_5b6b98d5-5bfa-47e2-8216-059482ccbda0 ``` The following log is when I use this patch, ``` .... numUpdates:32, size:365484, bytesPerUpdate:0.0, cost time:7 numUpdates:52, size:365484, bytesPerUpdate:0.0, cost time:5 numUpdates:84, size:365484, bytesPerUpdate:0.0, cost time:5 numUpdates:135, size:372208, bytesPerUpdate:131.84313725490196, cost time:86 numUpdates:216, size:379020, bytesPerUpdate:84.09876543209876, cost time:21 numUpdates:346, size:1865208, bytesPerUpdate:11432.215384615385, cost time:23 numUpdates:554, size:2052380, bytesPerUpdate:899.8653846153846, cost time:16 numUpdates:887, size:2142820, bytesPerUpdate:271.59159159159157, cost time:15 .. numUpdates:14895, size:251675500, bytesPerUpdate:438.5263157894737, cost time:13 numUpdates:23832, size:257010268, bytesPerUpdate:596.9305135951662, cost time:14 numUpdates:38132, size:263922396, bytesPerUpdate:483.3655944055944, cost time:15 numUpdates:61012, size:268962596, bytesPerUpdate:220.28846153846155, cost time:24 numUpdates:97620, size:286980644, bytesPerUpdate:492.1888111888112, cost time:22 15/04/21 14:45:12 INFO collection.ExternalAppendOnlyMap: Thread 53 spilling in-memory map of 328.7 MB to disk (1 time so far) 15/04/21 14:45:12 INFO collection.ExternalAppendOnlyMap: /data4/yarnenv/local/usercache/spark/appcache/application_1426746631567_11758/spark-local-20150421144456-a2a5/2a/temp_local_9c109510-af16-4468-8f23-48cad04da88f ``` the file size is 88M. ``` $ ll -h /data4/yarnenv/local/usercache/spark/appcache/application_1426746631567_11758/spark-local-20150421144456-a2a5/2a/ total 88M -rw-r----- 1 spark users 88M Apr 21 14:45 temp_local_9c109510-af16-4468-8f23-48cad04da88f ``` Author: Hong Shen <hongshen@tencent.com> Closes #5608 from shenh062326/my_change5 and squashes the following commits: 5506bae [Hong Shen] Fix compile error c275dd3 [Hong Shen] Alter code style fe202a2 [Hong Shen] Change the code style and add documentation. a9fca84 [Hong Shen] Add test case for SizeEstimator 4877eee [Hong Shen] Improve estimate the size of a large array a2ea7ac [Hong Shen] Alter code style 4c28e36 [Hong Shen] Improve estimate the size of a large array
* [SPARK-7103] Fix crash with SparkContext.union when RDD has no partitionerSteven She2015-04-273-1/+23
| | | | | | | | | | Added a check to the SparkContext.union method to check that a partitioner is defined on all RDDs when instantiating a PartitionerAwareUnionRDD. Author: Steven She <steven@canopylabs.com> Closes #5679 from stevencanopy/SPARK-7103 and squashes the following commits: 5a3d846 [Steven She] SPARK-7103: Fix crash with SparkContext.union when at least one RDD has no partitioner
* [SPARK-6991] [SPARKR] Adds support for zipPartitions.hlin092015-04-274-0/+85
| | | | | | | | | | | Author: hlin09 <hlin09pu@gmail.com> Closes #5568 from hlin09/zipPartitions and squashes the following commits: 12c08a5 [hlin09] Fix comments d2d32db [hlin09] Merge branch 'master' into zipPartitions ec56d2f [hlin09] Fix test. 27655d3 [hlin09] Adds support for zipPartitions.
* SPARK-7107 Add parameter for zookeeper.znode.parent to hbase_inputformat...tedyu2015-04-271-1/+5
| | | | | | | | | | | | ....py Author: tedyu <yuzhihong@gmail.com> Closes #5673 from tedyu/master and squashes the following commits: ab7c72b [tedyu] SPARK-7107 Adjust indentation to pass Python style tests 6e25939 [tedyu] Adjust line length to be shorter than 100 characters 18d172a [tedyu] SPARK-7107 Add parameter for zookeeper.znode.parent to hbase_inputformat.py
* [SPARK-6856] [R] Make RDD information more useful in SparkRJeff Harrison2015-04-272-0/+10
| | | | | | | | | | | | | Author: Jeff Harrison <jeffrharrison@gmail.com> Closes #5667 from His-name-is-Joof/joofspark and squashes the following commits: f8814a6 [Jeff Harrison] newline added after RDD show() output 4d9d972 [Jeff Harrison] Merge branch 'master' into joofspark 9d2295e [Jeff Harrison] parallelize with 1:10 878b830 [Jeff Harrison] Merge branch 'master' into joofspark c8c0b80 [Jeff Harrison] add test for RDD function show() 123be65 [Jeff Harrison] SPARK-6856
* [SPARK-4925] Publish Spark SQL hive-thriftserver maven artifactMisha Chernetsov2015-04-271-1/+1
| | | | | | | | | | turned on hive-thriftserver profile in release script Author: Misha Chernetsov <chernetsov@gmail.com> Closes #5429 from chernetsov/master and squashes the following commits: 9cc36af [Misha Chernetsov] [SPARK-4925] Publish Spark SQL hive-thriftserver maven artifact turned on hive-thriftserver profile in release script for scala 2.10
generated by cgit v1.2.3 (git 2.39.1) at 2024-08-15 23:38:43 +0000