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* [SPARK-4062][Streaming]Add ReliableKafkaReceiver in Spark Streaming Kafka ↵jerryshao2014-11-141-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | connector Add ReliableKafkaReceiver in Kafka connector to prevent data loss if WAL in Spark Streaming is enabled. Details and design doc can be seen in [SPARK-4062](https://issues.apache.org/jira/browse/SPARK-4062). Author: jerryshao <saisai.shao@intel.com> Author: Tathagata Das <tathagata.das1565@gmail.com> Author: Saisai Shao <saisai.shao@intel.com> Closes #2991 from jerryshao/kafka-refactor and squashes the following commits: 5461f1c [Saisai Shao] Merge pull request #8 from tdas/kafka-refactor3 eae4ad6 [Tathagata Das] Refectored KafkaStreamSuiteBased to eliminate KafkaTestUtils and made Java more robust. fab14c7 [Tathagata Das] minor update. 149948b [Tathagata Das] Fixed mistake 14630aa [Tathagata Das] Minor updates. d9a452c [Tathagata Das] Minor updates. ec2e95e [Tathagata Das] Removed the receiver's locks and essentially reverted to Saisai's original design. 2a20a01 [jerryshao] Address some comments 9f636b3 [Saisai Shao] Merge pull request #5 from tdas/kafka-refactor b2b2f84 [Tathagata Das] Refactored Kafka receiver logic and Kafka testsuites e501b3c [jerryshao] Add Mima excludes b798535 [jerryshao] Fix the missed issue e5e21c1 [jerryshao] Change to while loop ea873e4 [jerryshao] Further address the comments 98f3d07 [jerryshao] Fix comment style 4854ee9 [jerryshao] Address all the comments 96c7a1d [jerryshao] Update the ReliableKafkaReceiver unit test 8135d31 [jerryshao] Fix flaky test a949741 [jerryshao] Address the comments 16bfe78 [jerryshao] Change the ordering of imports 0894aef [jerryshao] Add some comments 77c3e50 [jerryshao] Code refactor and add some unit tests dd9aeeb [jerryshao] Initial commit for reliable Kafka receiver (cherry picked from commit 5930f64bf0d2516304b21bd49eac361a54caabdd) Signed-off-by: Tathagata Das <tathagata.das1565@gmail.com>
* SPARK-1209 [CORE] (Take 2) SparkHadoop{MapRed,MapReduce}Util should not use ↵Sean Owen2014-11-091-0/+8
| | | | | | | | | | | | | | | | | | | | | | | package org.apache.hadoop andrewor14 Another try at SPARK-1209, to address https://github.com/apache/spark/pull/2814#issuecomment-61197619 I successfully tested with `mvn -Dhadoop.version=1.0.4 -DskipTests clean package; mvn -Dhadoop.version=1.0.4 test` I assume that is what failed Jenkins last time. I also tried `-Dhadoop.version1.2.1` and `-Phadoop-2.4 -Pyarn -Phive` for more coverage. So this is why the class was put in `org.apache.hadoop` to begin with, I assume. One option is to leave this as-is for now and move it only when Hadoop 1.0.x support goes away. This is the other option, which adds a call to force the constructor to be public at run-time. It's probably less surprising than putting Spark code in `org.apache.hadoop`, but, does involve reflection. A `SecurityManager` might forbid this, but it would forbid a lot of stuff Spark does. This would also only affect Hadoop 1.0.x it seems. Author: Sean Owen <sowen@cloudera.com> Closes #3048 from srowen/SPARK-1209 and squashes the following commits: 0d48f4b [Sean Owen] For Hadoop 1.0.x, make certain constructors public, which were public in later versions 466e179 [Sean Owen] Disable MIMA warnings resulting from moving the class -- this was also part of the PairRDDFunctions type hierarchy though? eb61820 [Sean Owen] Move SparkHadoopMapRedUtil / SparkHadoopMapReduceUtil from org.apache.hadoop to org.apache.spark (cherry picked from commit f8e5732307dcb1482d9bcf1162a1090ef9a7b913) Signed-off-by: Patrick Wendell <pwendell@gmail.com>
* Revert "SPARK-1209 [CORE] SparkHadoop{MapRed,MapReduce}Util should not use ↵Andrew Or2014-10-301-8/+0
| | | | | | package org.apache.hadoop" This reverts commit 68cb69daf3022e973422e496ccf827ca3806ff30.
* SPARK-1209 [CORE] SparkHadoop{MapRed,MapReduce}Util should not use package ↵Sean Owen2014-10-301-0/+8
| | | | | | | | | | | | | org.apache.hadoop (This is just a look at what completely moving the classes would look like. I know Patrick flagged that as maybe not OK, although, it's private?) Author: Sean Owen <sowen@cloudera.com> Closes #2814 from srowen/SPARK-1209 and squashes the following commits: ead1115 [Sean Owen] Disable MIMA warnings resulting from moving the class -- this was also part of the PairRDDFunctions type hierarchy though? 2d42c1d [Sean Owen] Move SparkHadoopMapRedUtil / SparkHadoopMapReduceUtil from org.apache.hadoop to org.apache.spark
* [SPARK-3822] Executor scaling mechanism for YarnAndrew Or2014-10-291-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is part of a broader effort to enable dynamic scaling of executors ([SPARK-3174](https://issues.apache.org/jira/browse/SPARK-3174)). This is intended to work alongside SPARK-3795 (#2746), SPARK-3796 and SPARK-3797, but is functionally independently of these other issues. The logic is built on top of PraveenSeluka's changes at #2798. This is different from the changes there in a few major ways: (1) the mechanism is implemented within the existing scheduler backend framework rather than in new `Actor` classes. This also introduces a parent abstract class `YarnSchedulerBackend` to encapsulate common logic to communicate with the Yarn `ApplicationMaster`. (2) The interface of requesting executors exposed to the `SparkContext` is the same, but the communication between the scheduler backend and the AM uses total number executors desired instead of an incremental number. This is discussed in #2746 and explained in the comments in the code. I have tested this significantly on a stable Yarn cluster. ------------ A remaining task for this issue is to tone down the error messages emitted when an executor is removed. Currently, `SparkContext` and its components react as if the executor has failed, resulting in many scary error messages and eventual timeouts. While it's not strictly necessary to fix this as of the first-cut implementation of this mechanism, it would be good to add logic to distinguish this case. I prefer to address this in a separate PR. I have filed a separate JIRA for this task at SPARK-4134. Author: Andrew Or <andrew@databricks.com> Author: Andrew Or <andrewor14@gmail.com> Closes #2840 from andrewor14/yarn-scaling-mechanism and squashes the following commits: 485863e [Andrew Or] Minor log message changes 4920be8 [Andrew Or] Clarify that public API is only for Yarn mode for now 1c57804 [Andrew Or] Reword a few comments + other review comments 6321140 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism 02836c0 [Andrew Or] Limit scope of synchronization 4e2ed7f [Andrew Or] Fix bug: keep track of removed executors properly 73ade46 [Andrew Or] Wording changes (minor) 2a7a6da [Andrew Or] Add `sc.killExecutor` as a shorthand (minor) 665f229 [Andrew Or] Mima excludes 79aa2df [Andrew Or] Simplify the request interface by asking for a total 04f625b [Andrew Or] Fix race condition that causes over-allocation of executors f4783f8 [Andrew Or] Change the semantics of requesting executors 005a124 [Andrew Or] Fix tests 4628b16 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism db4a679 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism 572f5c5 [Andrew Or] Unused import (minor) f30261c [Andrew Or] Kill multiple executors rather than one at a time de260d9 [Andrew Or] Simplify by skipping useless null check 9c52542 [Andrew Or] Simplify by skipping the TaskSchedulerImpl 97dd1a8 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-scaling-mechanism d987b3e [Andrew Or] Move addWebUIFilters to Yarn scheduler backend 7b76d0a [Andrew Or] Expose mechanism in SparkContext as developer API 47466cd [Andrew Or] Refactor common Yarn scheduler backend logic c4dfaac [Andrew Or] Avoid thrashing when removing executors 53e8145 [Andrew Or] Start yarn actor early to listen for AM registration message bbee669 [Andrew Or] Add mechanism in yarn client mode
* [SPARK-3453] Netty-based BlockTransferService, extracted from Spark coreReynold Xin2014-10-291-0/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR encapsulates #2330, which is itself a continuation of #2240. The first goal of this PR is to provide an alternate, simpler implementation of the ConnectionManager which is based on Netty. In addition to this goal, however, we want to resolve [SPARK-3796](https://issues.apache.org/jira/browse/SPARK-3796), which calls for a standalone shuffle service which can be integrated into the YARN NodeManager, Standalone Worker, or on its own. This PR makes the first step in this direction by ensuring that the actual Netty service is as small as possible and extracted from Spark core. Given this, we should be able to construct this standalone jar which can be included in other JVMs without incurring significant dependency or runtime issues. The actual work to ensure that such a standalone shuffle service would work in Spark will be left for a future PR, however. In order to minimize dependencies and allow for the service to be long-running (possibly much longer-running than Spark, and possibly having to support multiple version of Spark simultaneously), the entire service has been ported to Java, where we have full control over the binary compatibility of the components and do not depend on the Scala runtime or version. These issues: have been addressed by folding in #2330: SPARK-3453: Refactor Netty module to use BlockTransferService interface SPARK-3018: Release all buffers upon task completion/failure SPARK-3002: Create a connection pool and reuse clients across different threads SPARK-3017: Integration tests and unit tests for connection failures SPARK-3049: Make sure client doesn't block when server/connection has error(s) SPARK-3502: SO_RCVBUF and SO_SNDBUF should be bootstrap childOption, not option SPARK-3503: Disable thread local cache in PooledByteBufAllocator TODO before mergeable: - [x] Implement uploadBlock() - [x] Unit tests for RPC side of code - [x] Performance testing (see comments [here](https://github.com/apache/spark/pull/2753#issuecomment-59475022)) - [x] Turn OFF by default (currently on for unit testing) Author: Reynold Xin <rxin@apache.org> Author: Aaron Davidson <aaron@databricks.com> Author: cocoatomo <cocoatomo77@gmail.com> Author: Patrick Wendell <pwendell@gmail.com> Author: Prashant Sharma <prashant.s@imaginea.com> Author: Davies Liu <davies.liu@gmail.com> Author: Anand Avati <avati@redhat.com> Closes #2753 from aarondav/netty and squashes the following commits: cadfd28 [Aaron Davidson] Turn netty off by default d7be11b [Aaron Davidson] Turn netty on by default 4a204b8 [Aaron Davidson] Fail block fetches if client connection fails 2b0d1c0 [Aaron Davidson] 100ch 0c5bca2 [Aaron Davidson] Merge branch 'master' of https://github.com/apache/spark into netty 14e37f7 [Aaron Davidson] Address Reynold's comments 8dfcceb [Aaron Davidson] Merge branch 'master' of https://github.com/apache/spark into netty 322dfc1 [Aaron Davidson] Address Reynold's comments, including major rename e5675a4 [Aaron Davidson] Fail outstanding RPCs as well ccd4959 [Aaron Davidson] Don't throw exception if client immediately fails 9da0bc1 [Aaron Davidson] Add RPC unit tests d236dfd [Aaron Davidson] Remove no-op serializer :) 7b7a26c [Aaron Davidson] Fix Nio compile issue dd420fd [Aaron Davidson] Merge branch 'master' of https://github.com/apache/spark into netty-test 939f276 [Aaron Davidson] Attempt to make comm. bidirectional aa58f67 [cocoatomo] [SPARK-3909][PySpark][Doc] A corrupted format in Sphinx documents and building warnings 8dc1ded [cocoatomo] [SPARK-3867][PySpark] ./python/run-tests failed when it run with Python 2.6 and unittest2 is not installed 5b5dbe6 [Prashant Sharma] [SPARK-2924] Required by scala 2.11, only one fun/ctor amongst overriden alternatives, can have default argument(s). 2c5d9dc [Patrick Wendell] HOTFIX: Fix build issue with Akka 2.3.4 upgrade. 020691e [Davies Liu] [SPARK-3886] [PySpark] use AutoBatchedSerializer by default ae4083a [Anand Avati] [SPARK-2805] Upgrade Akka to 2.3.4 29c6dcf [Aaron Davidson] [SPARK-3453] Netty-based BlockTransferService, extracted from Spark core f7e7568 [Reynold Xin] Fixed spark.shuffle.io.receiveBuffer setting. 5d98ce3 [Reynold Xin] Flip buffer. f6c220d [Reynold Xin] Merge with latest master. 407e59a [Reynold Xin] Fix style violation. a0518c7 [Reynold Xin] Implemented block uploads. 4b18db2 [Reynold Xin] Copy the buffer in fetchBlockSync. bec4ea2 [Reynold Xin] Removed OIO and added num threads settings. 1bdd7ee [Reynold Xin] Fixed tests. d68f328 [Reynold Xin] Logging close() in case close() fails. f63fb4c [Reynold Xin] Add more debug message. 6afc435 [Reynold Xin] Added logging. c066309 [Reynold Xin] Implement java.io.Closeable interface. 519d64d [Reynold Xin] Mark private package visibility and MimaExcludes. f0a16e9 [Reynold Xin] Fixed test hanging. 14323a5 [Reynold Xin] Removed BlockManager.getLocalShuffleFromDisk. b2f3281 [Reynold Xin] Added connection pooling. d23ed7b [Reynold Xin] Incorporated feedback from Norman: - use same pool for boss and worker - remove ioratio - disable caching of byte buf allocator - childoption sendbuf/receivebuf - fire exception through pipeline 9e0cb87 [Reynold Xin] Fixed BlockClientHandlerSuite 5cd33d7 [Reynold Xin] Fixed style violation. cb589ec [Reynold Xin] Added more test cases covering cleanup when fault happens in ShuffleBlockFetcherIteratorSuite 1be4e8e [Reynold Xin] Shorten NioManagedBuffer and NettyManagedBuffer class names. 108c9ed [Reynold Xin] Forgot to add TestSerializer to the commit list. b5c8d1f [Reynold Xin] Fixed ShuffleBlockFetcherIteratorSuite. 064747b [Reynold Xin] Reference count buffers and clean them up properly. 2b44cf1 [Reynold Xin] Added more documentation. 1760d32 [Reynold Xin] Use Epoll.isAvailable in BlockServer as well. 165eab1 [Reynold Xin] [SPARK-3453] Refactor Netty module to use BlockTransferService.
* [SPARK-4084] Reuse sort key in SorterXiangrui Meng2014-10-281-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Sorter uses generic-typed key for sorting. When data is large, it creates lots of key objects, which is not efficient. We should reuse the key in Sorter for memory efficiency. This change is part of the petabyte sort implementation from rxin . The `Sorter` class was written in Java and marked package private. So it is only available to `org.apache.spark.util.collection`. I renamed it to `TimSort` and add a simple wrapper of it, still called `Sorter`, in Scala, which is `private[spark]`. The benchmark code is updated, which now resets the array before each run. Here is the result on sorting primitive Int arrays of size 25 million using Sorter: ~~~ [info] - Sorter benchmark for key-value pairs !!! IGNORED !!! Java Arrays.sort() on non-primitive int array: Took 13237 ms Java Arrays.sort() on non-primitive int array: Took 13320 ms Java Arrays.sort() on non-primitive int array: Took 15718 ms Java Arrays.sort() on non-primitive int array: Took 13283 ms Java Arrays.sort() on non-primitive int array: Took 13267 ms Java Arrays.sort() on non-primitive int array: Took 15122 ms Java Arrays.sort() on non-primitive int array: Took 15495 ms Java Arrays.sort() on non-primitive int array: Took 14877 ms Java Arrays.sort() on non-primitive int array: Took 16429 ms Java Arrays.sort() on non-primitive int array: Took 14250 ms Java Arrays.sort() on non-primitive int array: (13878 ms first try, 14499 ms average) Java Arrays.sort() on primitive int array: Took 2683 ms Java Arrays.sort() on primitive int array: Took 2683 ms Java Arrays.sort() on primitive int array: Took 2701 ms Java Arrays.sort() on primitive int array: Took 2746 ms Java Arrays.sort() on primitive int array: Took 2685 ms Java Arrays.sort() on primitive int array: Took 2735 ms Java Arrays.sort() on primitive int array: Took 2669 ms Java Arrays.sort() on primitive int array: Took 2693 ms Java Arrays.sort() on primitive int array: Took 2680 ms Java Arrays.sort() on primitive int array: Took 2642 ms Java Arrays.sort() on primitive int array: (2948 ms first try, 2691 ms average) Sorter without key reuse on primitive int array: Took 10732 ms Sorter without key reuse on primitive int array: Took 12482 ms Sorter without key reuse on primitive int array: Took 10718 ms Sorter without key reuse on primitive int array: Took 12650 ms Sorter without key reuse on primitive int array: Took 10747 ms Sorter without key reuse on primitive int array: Took 10783 ms Sorter without key reuse on primitive int array: Took 12721 ms Sorter without key reuse on primitive int array: Took 10604 ms Sorter without key reuse on primitive int array: Took 10622 ms Sorter without key reuse on primitive int array: Took 11843 ms Sorter without key reuse on primitive int array: (11089 ms first try, 11390 ms average) Sorter with key reuse on primitive int array: Took 5141 ms Sorter with key reuse on primitive int array: Took 5298 ms Sorter with key reuse on primitive int array: Took 5066 ms Sorter with key reuse on primitive int array: Took 5164 ms Sorter with key reuse on primitive int array: Took 5203 ms Sorter with key reuse on primitive int array: Took 5274 ms Sorter with key reuse on primitive int array: Took 5186 ms Sorter with key reuse on primitive int array: Took 5159 ms Sorter with key reuse on primitive int array: Took 5164 ms Sorter with key reuse on primitive int array: Took 5078 ms Sorter with key reuse on primitive int array: (5311 ms first try, 5173 ms average) ~~~ So with key reuse, it is faster and less likely to trigger GC. Author: Xiangrui Meng <meng@databricks.com> Author: Reynold Xin <rxin@apache.org> Closes #2937 from mengxr/SPARK-4084 and squashes the following commits: d73c3d0 [Xiangrui Meng] address comments 0b7b682 [Xiangrui Meng] fix mima a72f53c [Xiangrui Meng] update timeIt 38ba50c [Xiangrui Meng] update timeIt 720f731 [Xiangrui Meng] add doc about JIT specialization 78f2879 [Xiangrui Meng] update tests 7de2efd [Xiangrui Meng] update the Sorter benchmark code to be correct 8626356 [Xiangrui Meng] add prepare to timeIt and update testsin SorterSuite 5f0d530 [Xiangrui Meng] update method modifiers of SortDataFormat 6ffbe66 [Xiangrui Meng] rename Sorter to TimSort and add a Scala wrapper that is private[spark] b00db4d [Xiangrui Meng] doc and tests cf94e8a [Xiangrui Meng] renaming 464ddce [Reynold Xin] cherry-pick rxin's commit
* [SPARK-3902] [SPARK-3590] Stabilize AsynRDDActions and add Java APIJosh Rosen2014-10-191-1/+12
| | | | | | | | | | | | | | | | | | This PR adds a Java API for AsyncRDDActions and promotes the API from `Experimental` to stable. Author: Josh Rosen <joshrosen@apache.org> Author: Josh Rosen <joshrosen@databricks.com> Closes #2760 from JoshRosen/async-rdd-actions-in-java and squashes the following commits: 0d45fbc [Josh Rosen] Whitespace fix. ad3ae53 [Josh Rosen] Merge remote-tracking branch 'origin/master' into async-rdd-actions-in-java c0153a5 [Josh Rosen] Remove unused variable. e8e2867 [Josh Rosen] Updates based on Marcelo's review feedback 7a1417f [Josh Rosen] Removed unnecessary java.util import. 6f8f6ac [Josh Rosen] Fix import ordering. ff28e49 [Josh Rosen] Add MiMa excludes and fix a scalastyle error. 346e46e [Josh Rosen] [SPARK-3902] Stabilize AsyncRDDActions; add Java API.
* SPARK-3874: Provide stable TaskContext APIPrashant Sharma2014-10-161-1/+5
| | | | | | | | | | | | | | | | | | This is a small number of clean-up changes on top of #2782. Closes #2782. Author: Prashant Sharma <prashant.s@imaginea.com> Author: Patrick Wendell <pwendell@gmail.com> Closes #2803 from pwendell/pr-2782 and squashes the following commits: 56d5b7a [Patrick Wendell] Minor clean-up 44089ec [Patrick Wendell] Clean-up the TaskContext API. ed551ce [Prashant Sharma] Fixed a typo df261d0 [Prashant Sharma] Josh's suggestion facf3b1 [Prashant Sharma] Fixed the mima issue. 7ecc2fe [Prashant Sharma] CR, Moved implementations to TaskContextImpl bbd9e05 [Prashant Sharma] adding missed out files to git. ef633f5 [Prashant Sharma] SPARK-3874, Provide stable TaskContext API
* SPARK-1767: Prefer HDFS-cached replicas when scheduling data-local tasksColin Patrick Mccabe2014-10-021-0/+2
| | | | | | | | | | | | | | This change reorders the replicas returned by HadoopRDD#getPreferredLocations so that replicas cached by HDFS are at the start of the list. This requires Hadoop 2.5 or higher; previous versions of Hadoop do not expose the information needed to determine whether a replica is cached. Author: Colin Patrick Mccabe <cmccabe@cloudera.com> Closes #1486 from cmccabe/SPARK-1767 and squashes the following commits: 338d4f8 [Colin Patrick Mccabe] SPARK-1767: Prefer HDFS-cached replicas when scheduling data-local tasks
* [SPARK-3613] Record only average block size in MapStatus for large stagesReynold Xin2014-09-291-1/+4
| | | | | | | | | | | | | | | This changes the way we send MapStatus from executors back to driver for large stages (>2000 tasks). For large stages, we no longer send one byte per block. Instead, we just send the average block size. This makes large jobs (tens of thousands of tasks) much more reliable since the driver no longer sends huge amount of data. Author: Reynold Xin <rxin@apache.org> Closes #2470 from rxin/mapstatus and squashes the following commits: 822ff54 [Reynold Xin] Code review feedback. 3b86f56 [Reynold Xin] Added MimaExclude. f89d182 [Reynold Xin] Fixed a bug in MapStatus 6a0401c [Reynold Xin] [SPARK-3613] Record only average block size in MapStatus for large stages.
* [MLlib] [SPARK-2885] DIMSUM: All-pairs similarityReza Zadeh2014-09-291-1/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | # All-pairs similarity via DIMSUM Compute all pairs of similar vectors using brute force approach, and also DIMSUM sampling approach. Laying down some notation: we are looking for all pairs of similar columns in an m x n RowMatrix whose entries are denoted a_ij, with the i’th row denoted r_i and the j’th column denoted c_j. There is an oversampling parameter labeled ɣ that should be set to 4 log(n)/s to get provably correct results (with high probability), where s is the similarity threshold. The algorithm is stated with a Map and Reduce, with proofs of correctness and efficiency in published papers [1] [2]. The reducer is simply the summation reducer. The mapper is more interesting, and is also the heart of the scheme. As an exercise, you should try to see why in expectation, the map-reduce below outputs cosine similarities. ![dimsumv2](https://cloud.githubusercontent.com/assets/3220351/3807272/d1d9514e-1c62-11e4-9f12-3cfdb1d78b3a.png) [1] Bosagh-Zadeh, Reza and Carlsson, Gunnar (2013), Dimension Independent Matrix Square using MapReduce, arXiv:1304.1467 http://arxiv.org/abs/1304.1467 [2] Bosagh-Zadeh, Reza and Goel, Ashish (2012), Dimension Independent Similarity Computation, arXiv:1206.2082 http://arxiv.org/abs/1206.2082 # Testing Tests for all invocations included. Added L1 and L2 norm computation to MultivariateStatisticalSummary since it was needed. Added tests for both of them. Author: Reza Zadeh <rizlar@gmail.com> Author: Xiangrui Meng <meng@databricks.com> Closes #1778 from rezazadeh/dimsumv2 and squashes the following commits: 404c64c [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2 4eb71c6 [Reza Zadeh] Add excludes for normL1 and normL2 ee8bd65 [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2 976ddd4 [Reza Zadeh] Broadcast colMags. Avoid div by zero. 3467cff [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2 aea0247 [Reza Zadeh] Allow large thresholds to promote sparsity 9fe17c0 [Xiangrui Meng] organize imports 2196ba5 [Xiangrui Meng] Merge branch 'rezazadeh-dimsumv2' into dimsumv2 254ca08 [Reza Zadeh] Merge remote-tracking branch 'upstream/master' into dimsumv2 f2947e4 [Xiangrui Meng] some optimization 3c4cf41 [Xiangrui Meng] Merge branch 'master' into rezazadeh-dimsumv2 0e4eda4 [Reza Zadeh] Use partition index for RNG 251bb9c [Reza Zadeh] Documentation 25e9d0d [Reza Zadeh] Line length for style fb296f6 [Reza Zadeh] renamed to normL1 and normL2 3764983 [Reza Zadeh] Documentation e9c6791 [Reza Zadeh] New interface and documentation 613f261 [Reza Zadeh] Column magnitude summary 75a0b51 [Reza Zadeh] Use Ints instead of Longs in the shuffle 0f12ade [Reza Zadeh] Style changes eb1dc20 [Reza Zadeh] Use Double.PositiveInfinity instead of Double.Max f56a882 [Reza Zadeh] Remove changes to MultivariateOnlineSummarizer dbc55ba [Reza Zadeh] Make colMagnitudes a method in RowMatrix 41e8ece [Reza Zadeh] style changes 139c8e1 [Reza Zadeh] Syntax changes 029aa9c [Reza Zadeh] javadoc and new test 75edb25 [Reza Zadeh] All tests passing! 05e59b8 [Reza Zadeh] Add test 502ce52 [Reza Zadeh] new interface 654c4fb [Reza Zadeh] default methods 3726ca9 [Reza Zadeh] Remove MatrixAlgebra 6bebabb [Reza Zadeh] remove changes to MatrixSuite 5b8cd7d [Reza Zadeh] Initial files
* [SPARK-3418] Sparse Matrix support (CCS) and additional native BLAS ↵Burak2014-09-181-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | operations added Local `SparseMatrix` support added in Compressed Column Storage (CCS) format in addition to Level-2 and Level-3 BLAS operations such as dgemv and dgemm respectively. BLAS doesn't support sparse matrix operations, therefore support for `SparseMatrix`-`DenseMatrix` multiplication and `SparseMatrix`-`DenseVector` implementations have been added. I will post performance comparisons in the comments momentarily. Author: Burak <brkyvz@gmail.com> Closes #2294 from brkyvz/SPARK-3418 and squashes the following commits: 88814ed [Burak] Hopefully fixed MiMa this time 47e49d5 [Burak] really fixed MiMa issue f0bae57 [Burak] [SPARK-3418] Fixed MiMa compatibility issues (excluded from check) 4b7dbec [Burak] 9/17 comments addressed 7af2f83 [Burak] sealed traits Vector and Matrix d3a8a16 [Burak] [SPARK-3418] Squashed missing alpha bug. 421045f [Burak] [SPARK-3418] New code review comments addressed f35a161 [Burak] [SPARK-3418] Code review comments addressed and multiplication further optimized 2508577 [Burak] [SPARK-3418] Fixed one more style issue d16e8a0 [Burak] [SPARK-3418] Fixed style issues and added documentation for methods 204a3f7 [Burak] [SPARK-3418] Fixed failing Matrix unit test 6025297 [Burak] [SPARK-3418] Fixed Scala-style errors dc7be71 [Burak] [SPARK-3418][MLlib] Matrix unit tests expanded with indexing and updating d2d5851 [Burak] [SPARK-3418][MLlib] Sparse Matrix support and additional native BLAS operations added
* [SPARK-3433][BUILD] Fix for Mima false-positives with @DeveloperAPI and ↵Prashant Sharma2014-09-151-7/+1
| | | | | | | | | | | | | | | @Experimental annotations. Actually false positive reported was due to mima generator not picking up the new jars in presence of old jars(theoretically this should not have happened.). So as a workaround, ran them both separately and just append them together. Author: Prashant Sharma <prashant@apache.org> Author: Prashant Sharma <prashant.s@imaginea.com> Closes #2285 from ScrapCodes/mima-fix and squashes the following commits: 093c76f [Prashant Sharma] Update mima 59012a8 [Prashant Sharma] Update mima 35b6c71 [Prashant Sharma] SPARK-3433 Fix for Mima false-positives with @DeveloperAPI and @Experimental annotations.
* [HOTFIX] Fix broken Mima tests on the master branchJosh Rosen2014-09-071-0/+12
| | | | | | | | | | | | | | By merging #2268, which bumped the Spark version to 1.2.0-SNAPSHOT, I inadvertently broke the Mima binary compatibility tests. The issue is that we were comparing 1.2.0-SNAPSHOT against Spark 1.0.0 without using any Mima excludes. The right long-term fix for this is probably to publish nightly snapshots on Maven central and change the master branch to test binary compatibility against the current release candidate branch's snapshots until that release is finalized. As a short-term fix until 1.1.0 is published on Maven central, I've configured the build to test the master branch for binary compatibility against the 1.1.0-RC4 jars. I'll loop back and remove the Apache staging repo as soon as 1.1.0 final is available. Author: Josh Rosen <joshrosen@apache.org> Closes #2315 from JoshRosen/mima-fix and squashes the following commits: 776bc2c [Josh Rosen] Add two excludes to workaround Mima annotation issues. ec90e21 [Josh Rosen] Add deploy and graphx to 1.2 MiMa excludes. 57569be [Josh Rosen] Fix MiMa tests in master branch; test against 1.1.0 RC.
* [SPARK-3388] Expose aplication ID in ApplicationStart event, use it in ↵Marcelo Vanzin2014-09-031-2/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | history server. This change exposes the application ID generated by the Spark Master, Mesos or Yarn via the SparkListenerApplicationStart event. It then uses that information to expose the application via its ID in the history server, instead of using the internal directory name generated by the event logger as an application id. This allows someone who knows the application ID to easily figure out the URL for the application's entry in the HS, aside from looking better. In Yarn mode, this is used to generate a direct link from the RM application list to the Spark history server entry (thus providing a fix for SPARK-2150). Note this sort of assumes that the different managers will generate app ids that are sufficiently different from each other that clashes will not occur. Author: Marcelo Vanzin <vanzin@cloudera.com> This patch had conflicts when merged, resolved by Committer: Andrew Or <andrewor14@gmail.com> Closes #1218 from vanzin/yarn-hs-link-2 and squashes the following commits: 2d19f3c [Marcelo Vanzin] Review feedback. 6706d3a [Marcelo Vanzin] Implement applicationId() in base classes. 56fe42e [Marcelo Vanzin] Fix cluster mode history address, plus a cleanup. 44112a8 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2 8278316 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2 a86bbcf [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2 a0056e6 [Marcelo Vanzin] Unbreak test. 4b10cfd [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2 cb0cab2 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2 25f2826 [Marcelo Vanzin] Add MIMA excludes. f0ba90f [Marcelo Vanzin] Use BufferedIterator. c90a08d [Marcelo Vanzin] Remove unused code. 3f8ec66 [Marcelo Vanzin] Review feedback. 21aa71b [Marcelo Vanzin] Fix JSON test. b022bae [Marcelo Vanzin] Undo SparkContext cleanup. c6d7478 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2 4e3483f [Marcelo Vanzin] Fix test. 57517b8 [Marcelo Vanzin] Review feedback. Mostly, more consistent use of Scala's Option. 311e49d [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2 d35d86f [Marcelo Vanzin] Fix yarn backend after rebase. 36dc362 [Marcelo Vanzin] Don't use Iterator::takeWhile(). 0afd696 [Marcelo Vanzin] Wait until master responds before returning from start(). abc4697 [Marcelo Vanzin] Make FsHistoryProvider keep a map of applications by id. 26b266e [Marcelo Vanzin] Use Mesos framework ID as Spark application ID. b3f3664 [Marcelo Vanzin] [yarn] Make the RM link point to the app direcly in the HS. 2fb7de4 [Marcelo Vanzin] Expose the application ID in the ApplicationStart event. ed10348 [Marcelo Vanzin] Expose application id to spark context.
* SPARK-2636: Expose job ID in JobWaiter APIlirui2014-09-011-0/+3
| | | | | | | | | | | | | | | | | | | | | This PR adds the async actions to the Java API. User can call these async actions to get the FutureAction and use JobWaiter (for SimpleFutureAction) to retrieve job Id. Author: lirui <rui.li@intel.com> Closes #2176 from lirui-intel/SPARK-2636 and squashes the following commits: ccaafb7 [lirui] SPARK-2636: fix java doc 5536d55 [lirui] SPARK-2636: mark the async API as experimental e2e01d5 [lirui] SPARK-2636: add mima exclude 0ca320d [lirui] SPARK-2636: fix method name & javadoc 3fa39f7 [lirui] SPARK-2636: refine the patch af4f5d9 [lirui] SPARK-2636: remove unused imports 843276c [lirui] SPARK-2636: only keep foreachAsync in the java API fbf5744 [lirui] SPARK-2636: add more async actions for java api 1b25abc [lirui] SPARK-2636: expose some fields in JobWaiter d09f732 [lirui] SPARK-2636: fix build eb1ee79 [lirui] SPARK-2636: change some parameters in SimpleFutureAction to member field 6e2b87b [lirui] SPARK-2636: add java API for async actions
* [SPARK-2288] Hide ShuffleBlockManager behind ShuffleManagerRaymond Liu2014-08-291-0/+2
| | | | | | | | | | By Hiding the shuffleblockmanager behind Shufflemanager, we decouple the shuffle data's block mapping management work from Diskblockmananger. This give a more clear interface and more easy for other shuffle manager to implement their own block management logic. the jira ticket have more details. Author: Raymond Liu <raymond.liu@intel.com> Closes #1241 from colorant/shuffle and squashes the following commits: 0e01ae3 [Raymond Liu] Move ShuffleBlockmanager behind shuffleManager
* [SPARK-3048][MLLIB] add LabeledPoint.parse and remove loadStreamingLabeledPointsXiangrui Meng2014-08-161-0/+5
| | | | | | | | | | | | | | | | | Move `parse()` from `LabeledPointParser` to `LabeledPoint` and make it public. This breaks binary compatibility only when a user uses synthesized methods like `tupled` and `curried`, which is rare. `LabeledPoint.parse` is more consistent with `Vectors.parse`, which is why `LabeledPointParser` is not preferred. freeman-lab tdas Author: Xiangrui Meng <meng@databricks.com> Closes #1952 from mengxr/labelparser and squashes the following commits: c818fb2 [Xiangrui Meng] merge master ce20e6f [Xiangrui Meng] update mima excludes b386b8d [Xiangrui Meng] fix tests 2436b3d [Xiangrui Meng] add parse() to LabeledPoint
* [SPARK-3045] Make Serializer interface Java friendlyReynold Xin2014-08-151-0/+11
| | | | | | | | | | | | | | | | Author: Reynold Xin <rxin@apache.org> Closes #1948 from rxin/kryo and squashes the following commits: a3a80d8 [Reynold Xin] [SPARK-3046] use executor's class loader as the default serializer classloader 3d13277 [Reynold Xin] Reverted that in TestJavaSerializerImpl too. 196f3dc [Reynold Xin] Ok one more commit to revert the classloader change. c49b50c [Reynold Xin] Removed JavaSerializer change. afbf37d [Reynold Xin] Moved the test case also. a2e693e [Reynold Xin] Removed the Kryo bug fix from this pull request. c81bd6c [Reynold Xin] Use defaultClassLoader when executing user specified custom registrator. 68f261e [Reynold Xin] Added license check excludes. 0c28179 [Reynold Xin] [SPARK-3045] Make Serializer interface Java friendly [SPARK-3046] Set executor's class loader as the default serializer class loader
* [SPARK-2924] remove default args to overloaded methodsAnand Avati2014-08-151-0/+3
| | | | | | | | | | | | Not supported in Scala 2.11. Split them into separate methods instead. Author: Anand Avati <avati@redhat.com> Closes #1704 from avati/SPARK-1812-default-args and squashes the following commits: 3e3924a [Anand Avati] SPARK-1812: Add Mima excludes for the broken ABI 901dfc7 [Anand Avati] SPARK-1812: core - Fix overloaded methods with default arguments 07f00af [Anand Avati] SPARK-1812: streaming - Fix overloaded methods with default arguments
* [SPARK-2923][MLLIB] Implement some basic BLAS routinesXiangrui Meng2014-08-111-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Having some basic BLAS operations implemented in MLlib can help simplify the current implementation and improve some performance. Tested on my local machine: ~~~ bin/spark-submit --class org.apache.spark.examples.mllib.BinaryClassification \ examples/target/scala-*/spark-examples-*.jar --algorithm LR --regType L2 \ --regParam 1.0 --numIterations 1000 ~/share/data/rcv1.binary/rcv1_train.binary ~~~ 1. before: ~1m 2. after: ~30s CC: jkbradley Author: Xiangrui Meng <meng@databricks.com> Closes #1849 from mengxr/ml-blas and squashes the following commits: ba583a2 [Xiangrui Meng] exclude Vector.copy a4d7d2f [Xiangrui Meng] Merge branch 'master' into ml-blas 6edeab9 [Xiangrui Meng] address comments 940bdeb [Xiangrui Meng] rename MLlibBLAS to BLAS c2a38bc [Xiangrui Meng] enhance dot tests 4cfaac4 [Xiangrui Meng] add apache header 48d01d2 [Xiangrui Meng] add tests for zeros and copy 3b882b1 [Xiangrui Meng] use blas.scal in gradient 735eb23 [Xiangrui Meng] remove d from BLAS routines d2d7d3c [Xiangrui Meng] update gradient and lbfgs 7f78186 [Xiangrui Meng] add zeros to Vectors; add dscal and dcopy to BLAS 14e6645 [Xiangrui Meng] add ddot cbb8273 [Xiangrui Meng] add daxpy test 07db0bb [Xiangrui Meng] Merge branch 'master' into ml-blas e8c326d [Xiangrui Meng] axpy
* [SPARK-1997][MLLIB] update breeze to 0.9Xiangrui Meng2014-08-081-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 0.9 dependences (this version doesn't depend on scalalogging and I excluded commons-math3 from its transitive dependencies): ~~~ +-org.scalanlp:breeze_2.10:0.9 [S] +-com.github.fommil.netlib:core:1.1.2 +-com.github.rwl:jtransforms:2.4.0 +-net.sf.opencsv:opencsv:2.3 +-net.sourceforge.f2j:arpack_combined_all:0.1 +-org.scalanlp:breeze-macros_2.10:0.3.1 [S] | +-org.scalamacros:quasiquotes_2.10:2.0.0 [S] | +-org.slf4j:slf4j-api:1.7.5 +-org.spire-math:spire_2.10:0.7.4 [S] +-org.scalamacros:quasiquotes_2.10:2.0.0 [S] | +-org.spire-math:spire-macros_2.10:0.7.4 [S] +-org.scalamacros:quasiquotes_2.10:2.0.0 [S] ~~~ Closes #1749 CC: witgo avati Author: Xiangrui Meng <meng@databricks.com> Closes #1857 from mengxr/breeze-0.9 and squashes the following commits: 7fc16b6 [Xiangrui Meng] don't know why but exclude a private method for mima dcc502e [Xiangrui Meng] update breeze to 0.9
* Revert "[SPARK-1470][SPARK-1842] Use the scala-logging wrapper instead of ↵Patrick Wendell2014-08-011-89/+2
| | | | | | the directly sfl4j api" This reverts commit adc8303294e26efb4ed15e5f5ba1062f7988625d.
* [SPARK-1470][SPARK-1842] Use the scala-logging wrapper instead of the ↵GuoQiang Li2014-08-011-2/+89
| | | | | | | | | | | directly sfl4j api Author: GuoQiang Li <witgo@qq.com> Closes #1369 from witgo/SPARK-1470_new and squashes the following commits: 66a1641 [GuoQiang Li] IncompatibleResultTypeProblem 73a89ba [GuoQiang Li] Use the scala-logging wrapper instead of the directly sfl4j api.
* [SPARK-2103][Streaming] Change to ClassTag for KafkaInputDStream and fix ↵jerryshao2014-08-011-1/+6
| | | | | | | | | | | | | | | | | | | reflection issue This PR updates previous Manifest for KafkaInputDStream's Decoder to ClassTag, also fix the problem addressed in [SPARK-2103](https://issues.apache.org/jira/browse/SPARK-2103). Previous Java interface cannot actually get the type of Decoder, so when using this Manifest to reconstruct the decode object will meet reflection exception. Also for other two Java interfaces, ClassTag[String] is useless because calling Scala API will get the right implicit ClassTag. Current Kafka unit test cannot actually verify the interface. I've tested these interfaces in my local and distribute settings. Author: jerryshao <saisai.shao@intel.com> Closes #1508 from jerryshao/SPARK-2103 and squashes the following commits: e90c37b [jerryshao] Add Mima excludes 7529810 [jerryshao] Change Manifest to ClassTag for KafkaInputDStream's Decoder and fix Decoder construct issue when using Java API
* SPARK-2341 [MLLIB] loadLibSVMFile doesn't handle regression datasetsSean Owen2014-07-301-0/+8
| | | | | | | | | | | | Per discussion at https://issues.apache.org/jira/browse/SPARK-2341 , this is a look at deprecating the multiclass parameter. Thoughts welcome of course. Author: Sean Owen <srowen@gmail.com> Closes #1663 from srowen/SPARK-2341 and squashes the following commits: 8a3abd7 [Sean Owen] Suppress MIMA error for removed package private classes 18a8c8e [Sean Owen] Updates from review 83d0092 [Sean Owen] Deprecated methods with multiclass, and instead always parse target as a double (ie. multiclass = true)
* [SPARK-1777] Prevent OOMs from single partitionsAndrew Or2014-07-271-1/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | **Problem.** When caching, we currently unroll the entire RDD partition before making sure we have enough free memory. This is a common cause for OOMs especially when (1) the BlockManager has little free space left in memory, and (2) the partition is large. **Solution.** We maintain a global memory pool of `M` bytes shared across all threads, similar to the way we currently manage memory for shuffle aggregation. Then, while we unroll each partition, periodically check if there is enough space to continue. If not, drop enough RDD blocks to ensure we have at least `M` bytes to work with, then try again. If we still don't have enough space to unroll the partition, give up and drop the block to disk directly if applicable. **New configurations.** - `spark.storage.bufferFraction` - the value of `M` as a fraction of the storage memory. (default: 0.2) - `spark.storage.safetyFraction` - a margin of safety in case size estimation is slightly off. This is the equivalent of the existing `spark.shuffle.safetyFraction`. (default 0.9) For more detail, see the [design document](https://issues.apache.org/jira/secure/attachment/12651793/spark-1777-design-doc.pdf). Tests pending for performance and memory usage patterns. Author: Andrew Or <andrewor14@gmail.com> Closes #1165 from andrewor14/them-rdd-memories and squashes the following commits: e77f451 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories c7c8832 [Andrew Or] Simplify logic + update a few comments 269d07b [Andrew Or] Very minor changes to tests 6645a8a [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories b7e165c [Andrew Or] Add new tests for unrolling blocks f12916d [Andrew Or] Slightly clean up tests 71672a7 [Andrew Or] Update unrollSafely tests 369ad07 [Andrew Or] Correct ensureFreeSpace and requestMemory behavior f4d035c [Andrew Or] Allow one thread to unroll multiple blocks a66fbd2 [Andrew Or] Rename a few things + update comments 68730b3 [Andrew Or] Fix weird scalatest behavior e40c60d [Andrew Or] Fix MIMA excludes ff77aa1 [Andrew Or] Fix tests 1a43c06 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories b9a6eee [Andrew Or] Simplify locking behavior on unrollMemoryMap ed6cda4 [Andrew Or] Formatting fix (super minor) f9ff82e [Andrew Or] putValues -> putIterator + putArray beb368f [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 8448c9b [Andrew Or] Fix tests a49ba4d [Andrew Or] Do not expose unroll memory check period 69bc0a5 [Andrew Or] Always synchronize on putLock before unrollMemoryMap 3f5a083 [Andrew Or] Simplify signature of ensureFreeSpace dce55c8 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 8288228 [Andrew Or] Synchronize put and unroll properly 4f18a3d [Andrew Or] bufferFraction -> unrollFraction 28edfa3 [Andrew Or] Update a few comments / log messages 728323b [Andrew Or] Do not synchronize every 1000 elements 5ab2329 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 129c441 [Andrew Or] Fix bug: Use toArray rather than array 9a65245 [Andrew Or] Update a few comments + minor control flow changes 57f8d85 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories abeae4f [Andrew Or] Add comment clarifying the MEMORY_AND_DISK case 3dd96aa [Andrew Or] AppendOnlyBuffer -> Vector (+ a few small changes) f920531 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 0871835 [Andrew Or] Add an effective storage level interface to BlockManager 64e7d4c [Andrew Or] Add/modify a few comments (minor) 8af2f35 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 4f4834e [Andrew Or] Use original storage level for blocks dropped to disk ecc8c2d [Andrew Or] Fix binary incompatibility 24185ea [Andrew Or] Avoid dropping a block back to disk if reading from disk 2b7ee66 [Andrew Or] Fix bug in SizeTracking* 9b9a273 [Andrew Or] Fix tests 20eb3e5 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 649bdb3 [Andrew Or] Document spark.storage.bufferFraction a10b0e7 [Andrew Or] Add initial memory request threshold + rename a few things e9c3cb0 [Andrew Or] cacheMemoryMap -> unrollMemoryMap 198e374 [Andrew Or] Unfold -> unroll 0d50155 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories d9d02a8 [Andrew Or] Remove unused param in unfoldSafely ec728d8 [Andrew Or] Add tests for safe unfolding of blocks 22b2209 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 078eb83 [Andrew Or] Add check for hasNext in PrimitiveVector.iterator 0871535 [Andrew Or] Fix tests in BlockManagerSuite d68f31e [Andrew Or] Safely unfold blocks for all memory puts 5961f50 [Andrew Or] Fix tests 195abd7 [Andrew Or] Refactor: move unfold logic to MemoryStore 1e82d00 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 3ce413e [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories d5dd3b4 [Andrew Or] Free buffer memory in finally ea02eec [Andrew Or] Fix tests b8e1d9c [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories a8704c1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories e1b8b25 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories 87aa75c [Andrew Or] Fix mima excludes again (typo) 11eb921 [Andrew Or] Clarify comment (minor) 50cae44 [Andrew Or] Remove now duplicate mima exclude 7de5ef9 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories df47265 [Andrew Or] Fix binary incompatibility 6d05a81 [Andrew Or] Merge branch 'master' of github.com:apache/spark into them-rdd-memories f94f5af [Andrew Or] Update a few comments (minor) 776aec9 [Andrew Or] Prevent OOM if a single RDD partition is too large bbd3eea [Andrew Or] Fix CacheManagerSuite to use Array 97ea499 [Andrew Or] Change BlockManager interface to use Arrays c12f093 [Andrew Or] Add SizeTrackingAppendOnlyBuffer and tests
* [SPARK-2549] Functions defined inside of other functions trigger failuresPrashant Sharma2014-07-231-104/+79
| | | | | | | | | Author: Prashant Sharma <prashant.s@imaginea.com> Closes #1510 from ScrapCodes/SPARK-2549/fun-in-fun and squashes the following commits: 9458bc5 [Prashant Sharma] Tested by removing an inner function from excludes. bc03b1c [Prashant Sharma] SPARK-2549 Functions defined inside of other functions trigger failures
* [MLLIB] make Mima ignore updateFeatures (private) in ALSXiangrui Meng2014-07-221-1/+3
| | | | | | | | | | Fix Mima issues in #1521. Author: Xiangrui Meng <meng@databricks.com> Closes #1533 from mengxr/mima-als and squashes the following commits: 78386e1 [Xiangrui Meng] make Mima ignore updateFeatures (private) in ALS
* [SPARK-2086] Improve output of toDebugString to make shuffle boundaries more ↵Gregory Owen2014-07-211-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | clear Changes RDD.toDebugString() to show hierarchy and shuffle transformations more clearly New output: ``` (3) FlatMappedValuesRDD[325] at apply at Transformer.scala:22 | MappedValuesRDD[324] at apply at Transformer.scala:22 | CoGroupedRDD[323] at apply at Transformer.scala:22 +-(5) MappedRDD[320] at apply at Transformer.scala:22 | | MappedRDD[319] at apply at Transformer.scala:22 | | MappedValuesRDD[318] at apply at Transformer.scala:22 | | MapPartitionsRDD[317] at apply at Transformer.scala:22 | | ShuffledRDD[316] at apply at Transformer.scala:22 | +-(10) MappedRDD[315] at apply at Transformer.scala:22 | | ParallelCollectionRDD[314] at apply at Transformer.scala:22 +-(100) MappedRDD[322] at apply at Transformer.scala:22 | ParallelCollectionRDD[321] at apply at Transformer.scala:22 ``` Author: Gregory Owen <greowen@gmail.com> Closes #1364 from GregOwen/to-debug-string and squashes the following commits: 08f5c78 [Gregory Owen] toDebugString: prettier debug printing to show shuffles and joins more clearly 1603f7b [Gregory Owen] toDebugString: prettier debug printing to show shuffles and joins more clearly
* [MLlib] SPARK-1536: multiclass classification support for decision treeManish Amde2014-07-181-1/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The ability to perform multiclass classification is a big advantage for using decision trees and was a highly requested feature for mllib. This pull request adds multiclass classification support to the MLlib decision tree. It also adds sample weights support using WeightedLabeledPoint class for handling unbalanced datasets during classification. It will also support algorithms such as AdaBoost which requires instances to be weighted. It handles the special case where the categorical variables cannot be ordered for multiclass classification and thus the optimizations used for speeding up binary classification cannot be directly used for multiclass classification with categorical variables. More specifically, for m categories in a categorical feature, it analyses all the ```2^(m-1) - 1``` categorical splits provided that #splits are less than the maxBins provided in the input. This condition will not be met for features with large number of categories -- using decision trees is not recommended for such datasets in general since the categorical features are favored over continuous features. Moreover, the user can use a combination of tricks (increasing bin size of the tree algorithms, use binary encoding for categorical features or use one-vs-all classification strategy) to avoid these constraints. The new code is accompanied by unit tests and has also been tested on the iris and covtype datasets. cc: mengxr, etrain, hirakendu, atalwalkar, srowen Author: Manish Amde <manish9ue@gmail.com> Author: manishamde <manish9ue@gmail.com> Author: Evan Sparks <sparks@cs.berkeley.edu> Closes #886 from manishamde/multiclass and squashes the following commits: 26f8acc [Manish Amde] another attempt at fixing mima c5b2d04 [Manish Amde] more MIMA fixes 1ce7212 [Manish Amde] change problem filter for mima 10fdd82 [Manish Amde] fixing MIMA excludes e1c970d [Manish Amde] merged master abf2901 [Manish Amde] adding classes to MimaExcludes.scala 45e767a [Manish Amde] adding developer api annotation for overriden methods c8428c4 [Manish Amde] fixing weird multiline bug afced16 [Manish Amde] removed label weights support 2d85a48 [Manish Amde] minor: fixed scalastyle issues reprise 4e85f2c [Manish Amde] minor: fixed scalastyle issues b2ae41f [Manish Amde] minor: scalastyle e4c1321 [Manish Amde] using while loop for regression histograms d75ac32 [Manish Amde] removed WeightedLabeledPoint from this PR 0fecd38 [Manish Amde] minor: add newline to EOF 2061cf5 [Manish Amde] merged from master 06b1690 [Manish Amde] fixed off-by-one error in bin to split conversion 9cc3e31 [Manish Amde] added implicit conversion import 5c1b2ca [Manish Amde] doc for PointConverter class 485eaae [Manish Amde] implicit conversion from LabeledPoint to WeightedLabeledPoint 3d7f911 [Manish Amde] updated doc 8e44ab8 [Manish Amde] updated doc adc7315 [Manish Amde] support ordered categorical splits for multiclass classification e3e8843 [Manish Amde] minor code formatting 23d4268 [Manish Amde] minor: another minor code style 34ee7b9 [Manish Amde] minor: code style 237762d [Manish Amde] renaming functions 12e6d0a [Manish Amde] minor: removing line in doc 9a90c93 [Manish Amde] Merge branch 'master' into multiclass 1892a2c [Manish Amde] tests and use multiclass binaggregate length when atleast one categorical feature is present f5f6b83 [Manish Amde] multiclass for continous variables 8cfd3b6 [Manish Amde] working for categorical multiclass classification 828ff16 [Manish Amde] added categorical variable test bce835f [Manish Amde] code cleanup 7e5f08c [Manish Amde] minor doc 1dd2735 [Manish Amde] bin search logic for multiclass f16a9bb [Manish Amde] fixing while loop d811425 [Manish Amde] multiclass bin aggregate logic ab5cb21 [Manish Amde] multiclass logic d8e4a11 [Manish Amde] sample weights ed5a2df [Manish Amde] fixed classification requirements d012be7 [Manish Amde] fixed while loop 18d2835 [Manish Amde] changing default values for num classes 6b912dc [Manish Amde] added numclasses to tree runner, predict logic for multiclass, add multiclass option to train 75f2bfc [Manish Amde] minor code style fix e547151 [Manish Amde] minor modifications 34549d0 [Manish Amde] fixing error during merge 098e8c5 [Manish Amde] merged master e006f9d [Manish Amde] changing variable names 5c78e1a [Manish Amde] added multiclass support 6c7af22 [Manish Amde] prepared for multiclass without breaking binary classification 46e06ee [Manish Amde] minor mods 3f85a17 [Manish Amde] tests for multiclass classification 4d5f70c [Manish Amde] added multiclass support for find splits bins 46f909c [Manish Amde] todo for multiclass support 455bea9 [Manish Amde] fixed tests 14aea48 [Manish Amde] changing instance format to weighted labeled point a1a6e09 [Manish Amde] added weighted point class 968ca9d [Manish Amde] merged master 7fc9545 [Manish Amde] added docs ce004a1 [Manish Amde] minor formatting b27ad2c [Manish Amde] formatting 426bb28 [Manish Amde] programming guide blurb 8053fed [Manish Amde] more formatting 5eca9e4 [Manish Amde] grammar 4731cda [Manish Amde] formatting 5e82202 [Manish Amde] added documentation, fixed off by 1 error in max level calculation cbd9f14 [Manish Amde] modified scala.math to math dad9652 [Manish Amde] removed unused imports e0426ee [Manish Amde] renamed parameter 718506b [Manish Amde] added unit test 1517155 [Manish Amde] updated documentation 9dbdabe [Manish Amde] merge from master 719d009 [Manish Amde] updating user documentation fecf89a [manishamde] Merge pull request #6 from etrain/deep_tree 0287772 [Evan Sparks] Fixing scalastyle issue. 2f1e093 [Manish Amde] minor: added doc for maxMemory parameter 2f6072c [manishamde] Merge pull request #5 from etrain/deep_tree abc5a23 [Evan Sparks] Parameterizing max memory. 50b143a [Manish Amde] adding support for very deep trees
* [SPARK-2534] Avoid pulling in the entire RDD in various operatorsReynold Xin2014-07-171-72/+87
| | | | | | | | | | | | | | | This should go into both master and branch-1.0. Author: Reynold Xin <rxin@apache.org> Closes #1450 from rxin/agg-closure and squashes the following commits: e40f363 [Reynold Xin] Mima check excludes. 9186364 [Reynold Xin] Define the return type more explicitly. 38e348b [Reynold Xin] Fixed the cases in RDD.scala. ea6b34d [Reynold Xin] Blah 89b9c43 [Reynold Xin] Fix other instances of accidentally pulling in extra stuff in closures. 73b2783 [Reynold Xin] [SPARK-2534] Avoid pulling in the entire RDD in groupByKey.
* [SPARK-1969][MLlib] Online summarizer APIs for mean, variance, min, and maxDB Tsai2014-07-111-0/+1
| | | | | | | | | | | | | | | | It basically moved the private ColumnStatisticsAggregator class from RowMatrix to public available DeveloperApi with documentation and unitests. Changes: 1) Moved the private implementation from org.apache.spark.mllib.linalg.ColumnStatisticsAggregator to org.apache.spark.mllib.stat.MultivariateOnlineSummarizer 2) When creating OnlineSummarizer object, the number of columns is not needed in the constructor. It's determined when users add the first sample. 3) Added the APIs documentation for MultivariateOnlineSummarizer. 4) Added the unittests for MultivariateOnlineSummarizer. Author: DB Tsai <dbtsai@dbtsai.com> Closes #955 from dbtsai/dbtsai-summarizer and squashes the following commits: b13ac90 [DB Tsai] dbtsai-summarizer
* [SPARK-1478].3: Upgrade FlumeInputDStream's FlumeReceiver to support FLUME-1915tmalaska2014-07-101-0/+3
| | | | | | | | | | | | | | This is a modified version of this PR https://github.com/apache/spark/pull/1168 done by @tmalaska Adds MIMA binary check exclusions. Author: tmalaska <ted.malaska@cloudera.com> Author: Tathagata Das <tathagata.das1565@gmail.com> Closes #1347 from tdas/FLUME-1915 and squashes the following commits: 96065df [Tathagata Das] Added Mima exclusion for FlumeReceiver. 41d5338 [tmalaska] Address line 57 that was too long 12617e5 [tmalaska] SPARK-1478: Upgrade FlumeInputDStream's Flume...
* [SPARK-1776] Have Spark's SBT build read dependencies from Maven.Prashant Sharma2014-07-101-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Patch introduces the new way of working also retaining the existing ways of doing things. For example build instruction for yarn in maven is `mvn -Pyarn -PHadoop2.2 clean package -DskipTests` in sbt it can become `MAVEN_PROFILES="yarn, hadoop-2.2" sbt/sbt clean assembly` Also supports `sbt/sbt -Pyarn -Phadoop-2.2 -Dhadoop.version=2.2.0 clean assembly` Author: Prashant Sharma <prashant.s@imaginea.com> Author: Patrick Wendell <pwendell@gmail.com> Closes #772 from ScrapCodes/sbt-maven and squashes the following commits: a8ac951 [Prashant Sharma] Updated sbt version. 62b09bb [Prashant Sharma] Improvements. fa6221d [Prashant Sharma] Excluding sql from mima 4b8875e [Prashant Sharma] Sbt assembly no longer builds tools by default. 72651ca [Prashant Sharma] Addresses code reivew comments. acab73d [Prashant Sharma] Revert "Small fix to run-examples script." ac4312c [Prashant Sharma] Revert "minor fix" 6af91ac [Prashant Sharma] Ported oldDeps back. + fixes issues with prev commit. 65cf06c [Prashant Sharma] Servelet API jars mess up with the other servlet jars on the class path. 446768e [Prashant Sharma] minor fix 89b9777 [Prashant Sharma] Merge conflicts d0a02f2 [Prashant Sharma] Bumped up pom versions, Since the build now depends on pom it is better updated there. + general cleanups. dccc8ac [Prashant Sharma] updated mima to check against 1.0 a49c61b [Prashant Sharma] Fix for tools jar a2f5ae1 [Prashant Sharma] Fixes a bug in dependencies. cf88758 [Prashant Sharma] cleanup 9439ea3 [Prashant Sharma] Small fix to run-examples script. 96cea1f [Prashant Sharma] SPARK-1776 Have Spark's SBT build read dependencies from Maven. 36efa62 [Patrick Wendell] Set project name in pom files and added eclipse/intellij plugins. 4973dbd [Patrick Wendell] Example build using pom reader.
* [SPARK-1768] History server enhancements.Marcelo Vanzin2014-06-231-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Two improvements to the history server: - Separate the HTTP handling from history fetching, so that it's easy to add new backends later (thinking about SPARK-1537 in the long run) - Avoid loading all UIs in memory. Do lazy loading instead, keeping a few in memory for faster access. This allows the app limit to go away, since holding just the listing in memory shouldn't be too expensive unless the user has millions of completed apps in the history (at which point I'd expect other issues to arise aside from history server memory usage, such as FileSystem.listStatus() starting to become ridiculously expensive). I also fixed a few minor things along the way which aren't really worth mentioning. I also removed the app's log path from the UI since that information may not even exist depending on which backend is used (even though there is only one now). Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #718 from vanzin/hist-server and squashes the following commits: 53620c9 [Marcelo Vanzin] Add mima exclude, fix scaladoc wording. c21f8d8 [Marcelo Vanzin] Feedback: formatting, docs. dd8cc4b [Marcelo Vanzin] Standardize on using spark.history.* configuration. 4da3a52 [Marcelo Vanzin] Remove UI from ApplicationHistoryInfo. 2a7f68d [Marcelo Vanzin] Address review feedback. 4e72c77 [Marcelo Vanzin] Remove comment about ordering. 249bcea [Marcelo Vanzin] Remove offset / count from provider interface. ca5d320 [Marcelo Vanzin] Remove code that deals with unfinished apps. 6e2432f [Marcelo Vanzin] Second round of feedback. b2c570a [Marcelo Vanzin] Make class package-private. 4406f61 [Marcelo Vanzin] Cosmetic change to listing header. e852149 [Marcelo Vanzin] Initialize new app array to expected size. e8026f4 [Marcelo Vanzin] Review feedback. 49d2fd3 [Marcelo Vanzin] Fix a comment. 91e96ca [Marcelo Vanzin] Fix scalastyle issues. 6fbe0d8 [Marcelo Vanzin] Better handle failures when loading app info. eee2f5a [Marcelo Vanzin] Ensure server.stop() is called when shutting down. bda2fa1 [Marcelo Vanzin] Rudimentary paging support for the history UI. b284478 [Marcelo Vanzin] Separate history server from history backend.
* HOTFIX: Fix missing MIMA ignorePatrick Wendell2014-06-211-0/+2
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* [Minor] Fix style, formatting and naming in BlockManager etc.Andrew Or2014-06-121-1/+6
| | | | | | | | | | | | | | | | | | | | | | | This is a precursor to a bigger change. I wanted to separate out the relatively insignificant changes so the ultimate PR is not inflated. (Warning: this PR is full of unimportant nitpicks) Author: Andrew Or <andrewor14@gmail.com> Closes #1058 from andrewor14/bm-minor and squashes the following commits: 8e12eaf [Andrew Or] SparkException -> BlockException c36fd53 [Andrew Or] Make parts of BlockManager more readable 0a5f378 [Andrew Or] Entry -> MemoryEntry e9762a5 [Andrew Or] Tone down string interpolation (minor reverts) c4de9ac [Andrew Or] Merge branch 'master' of github.com:apache/spark into bm-minor b3470f1 [Andrew Or] More string interpolation (minor) 7f9dcab [Andrew Or] Use string interpolation (minor) 94a425b [Andrew Or] Refactor against duplicate code + minor changes 8a6a7dc [Andrew Or] Exception -> SparkException 97c410f [Andrew Or] Deal with MIMA excludes 2480f1d [Andrew Or] Fixes in StorgeLevel.scala abb0163 [Andrew Or] Style, formatting and naming fixes
* SPARK-554. Add aggregateByKey.Sandy Ryza2014-06-121-1/+4
| | | | | | | | | | | | | | Author: Sandy Ryza <sandy@cloudera.com> Closes #705 from sryza/sandy-spark-554 and squashes the following commits: 2302b8f [Sandy Ryza] Add MIMA exclude f52e0ad [Sandy Ryza] Fix Python tests for real 2f3afa3 [Sandy Ryza] Fix Python test 0b735e9 [Sandy Ryza] Fix line lengths ae56746 [Sandy Ryza] Fix doc (replace T with V) c2be415 [Sandy Ryza] Java and Python aggregateByKey 23bf400 [Sandy Ryza] SPARK-554. Add aggregateByKey.
* [SPARK-1672][MLLIB] Separate user and product partitioning in ALSTor Myklebust2014-06-111-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Some clean up work following #593. 1. Allow to set different number user blocks and number product blocks in `ALS`. 2. Update `MovieLensALS` to reflect the change. Author: Tor Myklebust <tmyklebu@gmail.com> Author: Xiangrui Meng <meng@databricks.com> Closes #1014 from mengxr/SPARK-1672 and squashes the following commits: 0e910dd [Xiangrui Meng] change private[this] to private[recommendation] 36420c7 [Xiangrui Meng] set exclusion rules for ALS 9128b77 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-1672 294efe9 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-1672 9bab77b [Xiangrui Meng] clean up add numUserBlocks and numProductBlocks to MovieLensALS 84c8e8c [Xiangrui Meng] Merge branch 'master' into SPARK-1672 d17a8bf [Xiangrui Meng] merge master a4925fd [Tor Myklebust] Style. bd8a75c [Tor Myklebust] Merge branch 'master' of github.com:apache/spark into alsseppar 021f54b [Tor Myklebust] Separate user and product blocks. dcf583a [Tor Myklebust] Remove the partitioner member variable; instead, thread that needle everywhere it needs to go. 23d6f91 [Tor Myklebust] Stop making the partitioner configurable. 495784f [Tor Myklebust] Merge branch 'master' of https://github.com/apache/spark 674933a [Tor Myklebust] Fix style. 40edc23 [Tor Myklebust] Fix missing space. f841345 [Tor Myklebust] Fix daft bug creating 'pairs', also for -> foreach. 5ec9e6c [Tor Myklebust] Clean a couple of things up using 'map'. 36a0f43 [Tor Myklebust] Make the partitioner private. d872b09 [Tor Myklebust] Add negative id ALS test. df27697 [Tor Myklebust] Support custom partitioners. Currently we use the same partitioner for users and products. c90b6d8 [Tor Myklebust] Scramble user and product ids before bucketing. c774d7d [Tor Myklebust] Make the partitioner a member variable and use it instead of modding directly.
* [SPARK-1817] RDD.zip() should verify partition sizes for each partitionKan Zhang2014-06-031-0/+2
| | | | | | | | | | | RDD.zip() will throw an exception if it finds partition sizes are not the same. Author: Kan Zhang <kzhang@apache.org> Closes #944 from kanzhang/SPARK-1817 and squashes the following commits: c073848 [Kan Zhang] [SPARK-1817] Cosmetic updates 524c670 [Kan Zhang] [SPARK-1817] RDD.zip() should verify partition sizes for each partition
* SPARK-1941: Update streamlib to 2.7.0 and use HyperLogLogPlus instead of ↵Reynold Xin2014-06-031-2/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | HyperLogLog. I also corrected some errors made in the previous HLL count approximate API, including relativeSD wasn't really a measure for error (and we used it to test error bounds in test results). Author: Reynold Xin <rxin@apache.org> Closes #897 from rxin/hll and squashes the following commits: 4d83f41 [Reynold Xin] New error bound and non-randomness. f154ea0 [Reynold Xin] Added a comment on the value bound for testing. e367527 [Reynold Xin] One more round of code review. 41e649a [Reynold Xin] Update final mima list. 9e320c8 [Reynold Xin] Incorporate code review feedback. e110d70 [Reynold Xin] Merge branch 'master' into hll 354deb8 [Reynold Xin] Added comment on the Mima exclude rules. acaa524 [Reynold Xin] Added the right exclude rules in MimaExcludes. 6555bfe [Reynold Xin] Added a default method and re-arranged MimaExcludes. 1db1522 [Reynold Xin] Excluded util.SerializableHyperLogLog from MIMA check. 9221b27 [Reynold Xin] Merge branch 'master' into hll 88cfe77 [Reynold Xin] Updated documentation and restored the old incorrect API to maintain API compatibility. 1294be6 [Reynold Xin] Updated HLL+. e7786cb [Reynold Xin] Merge branch 'master' into hll c0ef0c2 [Reynold Xin] SPARK-1941: Update streamlib to 2.7.0 and use HyperLogLogPlus instead of HyperLogLog.
* Synthetic GraphX BenchmarkJoseph E. Gonzalez2014-06-031-2/+2
| | | | | | | | | | | | | | | | | | | | This PR accomplishes two things: 1. It introduces a Synthetic Benchmark application that generates an arbitrarily large log-normal graph and executes either PageRank or connected components on the graph. This can be used to profile GraphX system on arbitrary clusters without access to large graph datasets 2. This PR improves the implementation of the log-normal graph generator. Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com> Author: Ankur Dave <ankurdave@gmail.com> Closes #720 from jegonzal/graphx_synth_benchmark and squashes the following commits: e40812a [Ankur Dave] Exclude all of GraphX from compatibility checks vs. 1.0.0 bccccad [Ankur Dave] Fix long lines 374678a [Ankur Dave] Bugfix and style changes 1bdf39a [Joseph E. Gonzalez] updating options d943972 [Joseph E. Gonzalez] moving the benchmark application into the examples folder. f4f839a [Joseph E. Gonzalez] Creating a synthetic benchmark script.
* Better explanation for how to use MIMA excludes.Patrick Wendell2014-06-011-0/+61
This patch does a few things: 1. We have a file MimaExcludes.scala exclusively for excludes. 2. The test runner tells users about that file if a test fails. 3. I've added back the excludes used from 0.9->1.0. We should keep these in the project as an official audit trail of times where we decided to make exceptions. Author: Patrick Wendell <pwendell@gmail.com> Closes #937 from pwendell/mima and squashes the following commits: 7ee0db2 [Patrick Wendell] Better explanation for how to use MIMA excludes.
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