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* SPARK-2047: Introduce an in-mem Sorter, and use it to reduce mem usageAaron Davidson2014-07-221-0/+915
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ### Why and what? Currently, the AppendOnlyMap performs an "in-place" sort by converting its array of [key, value, key, value] pairs into a an array of [(key, value), (key, value)] pairs. However, this causes us to allocate many Tuple2 objects, which come at a nontrivial overhead. This patch adds a Sorter API, intended for in memory sorts, which simply ports the Android Timsort implementation (available under Apache v2) and abstracts the interface in a way which introduces no more than 1 virtual function invocation of overhead at each abstraction point. Please compare our port of the Android Timsort sort with the original implementation: http://www.diffchecker.com/wiwrykcl ### Memory implications An AppendOnlyMap contains N kv pairs, which results in roughly 2N elements within its underlying array. Each of these elements is 4 bytes wide in a [compressed OOPS](https://wikis.oracle.com/display/HotSpotInternals/CompressedOops) system, which is the default. Today's approach immediately allocates N Tuple2 objects, which take up 24N bytes in total (exposed via YourKit), and undergoes a Java sort. The Java 6 version immediately copies the entire array (4N bytes here), while the Java 7 version has a worst-case allocation of half the array (2N bytes). This results in a worst-case sorting overhead of 24N + 2N = 26N bytes (for Java 7). The Sorter does not require allocating any tuples, but since it uses Timsort, it may copy up to half the entire array in the worst case. This results in a worst-case sorting overhead of 4N bytes. Thus, we have reduced the worst-case overhead of the sort by roughly 22 bytes times the number of elements. ### Performance implications As the destructiveSortedIterator is used for spilling in an ExternalAppendOnlyMap, the purpose of this patch is to provide stability by reducing memory usage rather than improve performance. However, because it implements Timsort, it also brings a substantial performance boost over our prior implementation. Here are the results of a microbenchmark that sorted 25 million, randomly distributed (Float, Int) pairs. The Java Arrays.sort() tests were run **only on the keys**, and thus moved less data. Our current implementation is called "Tuple-sort using Arrays.sort()" while the new implementation is "KV-array using Sorter". <table> <tr><th>Test</th><th>First run (JDK6)</th><th>Average of 10 (JDK6)</th><th>First run (JDK7)</th><th>Average of 10 (JDK7)</th></tr> <tr><td>primitive Arrays.sort()</td><td>3216 ms</td><td>1190 ms</td><td>2724 ms</td><td>131 ms (!!)</td></tr> <tr><td>Arrays.sort()</td><td>18564 ms</td><td>2006 ms</td><td>13201 ms</td><td>878 ms</td></tr> <tr><td>Tuple-sort using Arrays.sort()</td><td>31813 ms</td><td>3550 ms</td><td>20990 ms</td><td>1919 ms</td></tr> <tr><td><b>KV-array using Sorter</b></td><td></td><td></td><td><b>15020 ms</b></td><td><b>834 ms</b></td></tr> </table> The results show that this Sorter performs exactly as expected (after the first run) -- it is as fast as the Java 7 Arrays.sort() (which shares the same algorithm), but is significantly faster than the Tuple-sort on Java 6 or 7. In short, this patch should significantly improve performance for users running either Java 6 or 7. Author: Aaron Davidson <aaron@databricks.com> Closes #1502 from aarondav/sort and squashes the following commits: 652d936 [Aaron Davidson] Update license, move Sorter to java src a7b5b1c [Aaron Davidson] fix licenses 5c0efaf [Aaron Davidson] Update tmpLength ec395c8 [Aaron Davidson] Ignore benchmark (again) and fix docs 034bf10 [Aaron Davidson] Change to Apache v2 Timsort b97296c [Aaron Davidson] Don't try to run benchmark on Jenkins + private[spark] 6307338 [Aaron Davidson] SPARK-2047: Introduce an in-mem Sorter, and use it to reduce mem usage
* Package docsPrashant Sharma2014-05-142-0/+48
| | | | | | | | | | | | | | This is a few changes based on the original patch by @scrapcodes. Author: Prashant Sharma <prashant.s@imaginea.com> Author: Patrick Wendell <pwendell@gmail.com> Closes #785 from pwendell/package-docs and squashes the following commits: c32b731 [Patrick Wendell] Changes based on Prashant's patch c0463d3 [Prashant Sharma] added eof new line ce8bf73 [Prashant Sharma] Added eof new line to all files. 4c35f2e [Prashant Sharma] SPARK-1563 Add package-info.java and package.scala files for all packages that appear in docs
* [SPARK-1439, SPARK-1440] Generate unified Scaladoc across projects and JavadocsMatei Zaharia2014-04-211-0/+23
| | | | | | | | | | | | | | | | | | | | | | I used the sbt-unidoc plugin (https://github.com/sbt/sbt-unidoc) to create a unified Scaladoc of our public packages, and generate Javadocs as well. One limitation is that I haven't found an easy way to exclude packages in the Javadoc; there is a SBT task that identifies Java sources to run javadoc on, but it's been very difficult to modify it from outside to change what is set in the unidoc package. Some SBT-savvy people should help with this. The Javadoc site also lacks package-level descriptions and things like that, so we may want to look into that. We may decide not to post these right now if it's too limited compared to the Scala one. Example of the built doc site: http://people.csail.mit.edu/matei/spark-unified-docs/ Author: Matei Zaharia <matei@databricks.com> This patch had conflicts when merged, resolved by Committer: Patrick Wendell <pwendell@gmail.com> Closes #457 from mateiz/better-docs and squashes the following commits: a63d4a3 [Matei Zaharia] Skip Java/Scala API docs for Python package 5ea1f43 [Matei Zaharia] Fix links to Java classes in Java guide, fix some JS for scrolling to anchors on page load f05abc0 [Matei Zaharia] Don't include java.lang package names 995e992 [Matei Zaharia] Skip internal packages and class names with $ in JavaDoc a14a93c [Matei Zaharia] typo 76ce64d [Matei Zaharia] Add groups to Javadoc index page, and a first package-info.java ed6f994 [Matei Zaharia] Generate JavaDoc as well, add titles, update doc site to use unified docs acb993d [Matei Zaharia] Add Unidoc plugin for the projects we want Unidoced
* Remove Unnecessary Whitespace'sSandeep2014-04-102-2/+2
| | | | | | | | | | stack these together in a commit else they show up chunk by chunk in different commits. Author: Sandeep <sandeep@techaddict.me> Closes #380 from techaddict/white_space and squashes the following commits: b58f294 [Sandeep] Remove Unnecessary Whitespace's
* SPARK-1305: Support persisting RDD's directly to TachyonHaoyuan Li2014-04-041-13/+33
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Move the PR#468 of apache-incubator-spark to the apache-spark "Adding an option to persist Spark RDD blocks into Tachyon." Author: Haoyuan Li <haoyuan@cs.berkeley.edu> Author: RongGu <gurongwalker@gmail.com> Closes #158 from RongGu/master and squashes the following commits: 72b7768 [Haoyuan Li] merge master 9f7fa1b [Haoyuan Li] fix code style ae7834b [Haoyuan Li] minor cleanup a8b3ec6 [Haoyuan Li] merge master branch e0f4891 [Haoyuan Li] better check offheap. 55b5918 [RongGu] address matei's comment on the replication of offHeap storagelevel 7cd4600 [RongGu] remove some logic code for tachyonstore's replication 51149e7 [RongGu] address aaron's comment on returning value of the remove() function in tachyonstore 8adfcfa [RongGu] address arron's comment on inTachyonSize 120e48a [RongGu] changed the root-level dir name in Tachyon 5cc041c [Haoyuan Li] address aaron's comments 9b97935 [Haoyuan Li] address aaron's comments d9a6438 [Haoyuan Li] fix for pspark 77d2703 [Haoyuan Li] change python api.git status 3dcace4 [Haoyuan Li] address matei's comments 91fa09d [Haoyuan Li] address patrick's comments 589eafe [Haoyuan Li] use TRY_CACHE instead of MUST_CACHE 64348b2 [Haoyuan Li] update conf docs. ed73e19 [Haoyuan Li] Merge branch 'master' of github.com:RongGu/spark-1 619a9a8 [RongGu] set number of directories in TachyonStore back to 64; added a TODO tag for duplicated code from the DiskStore be79d77 [RongGu] find a way to clean up some unnecessay metods and classed to make the code simpler 49cc724 [Haoyuan Li] update docs with off_headp option 4572f9f [RongGu] reserving the old apply function API of StorageLevel 04301d3 [RongGu] rename StorageLevel.TACHYON to Storage.OFF_HEAP c9aeabf [RongGu] rename the StorgeLevel.TACHYON as StorageLevel.OFF_HEAP 76805aa [RongGu] unifies the config properties name prefix; add the configs into docs/configuration.md e700d9c [RongGu] add the SparkTachyonHdfsLR example and some comments fd84156 [RongGu] use randomUUID to generate sparkapp directory name on tachyon;minor code style fix 939e467 [Haoyuan Li] 0.4.1-thrift from maven central 86a2eab [Haoyuan Li] tachyon 0.4.1-thrift is in the staging repo. but jenkins failed to download it. temporarily revert it back to 0.4.1 16c5798 [RongGu] make the dependency on tachyon as tachyon-0.4.1-thrift eacb2e8 [RongGu] Merge branch 'master' of https://github.com/RongGu/spark-1 bbeb4de [RongGu] fix the JsonProtocolSuite test failure problem 6adb58f [RongGu] Merge branch 'master' of https://github.com/RongGu/spark-1 d827250 [RongGu] fix JsonProtocolSuie test failure 716e93b [Haoyuan Li] revert the version ca14469 [Haoyuan Li] bump tachyon version to 0.4.1-thrift 2825a13 [RongGu] up-merging to the current master branch of the apache spark 6a22c1a [Haoyuan Li] fix scalastyle 8968b67 [Haoyuan Li] exclude more libraries from tachyon dependency to be the same as referencing tachyon-client. 77be7e8 [RongGu] address mateiz's comment about the temp folder name problem. The implementation followed mateiz's advice. 1dcadf9 [Haoyuan Li] typo bf278fa [Haoyuan Li] fix python tests e82909c [Haoyuan Li] minor cleanup 776a56c [Haoyuan Li] address patrick's and ali's comments from the previous PR 8859371 [Haoyuan Li] various minor fixes and clean up e3ddbba [Haoyuan Li] add doc to use Tachyon cache mode. fcaeab2 [Haoyuan Li] address Aaron's comment e554b1e [Haoyuan Li] add python code 47304b3 [Haoyuan Li] make tachyonStore in BlockMananger lazy val; add more comments StorageLevels. dc8ef24 [Haoyuan Li] add old storelevel constructor e01a271 [Haoyuan Li] update tachyon 0.4.1 8011a96 [RongGu] fix a brought-in mistake in StorageLevel 70ca182 [RongGu] a bit change in comment 556978b [RongGu] fix the scalastyle errors 791189b [RongGu] "Adding an option to persist Spark RDD blocks into Tachyon." move the PR#468 of apache-incubator-spark to the apache-spark
* [java8API] SPARK-964 Investigate the potential for using JDK 8 lambda ↵Prashant Sharma2014-03-0310-0/+277
| | | | | | | | | | | | | | | | | | | expressions for the Java/Scala APIs Author: Prashant Sharma <prashant.s@imaginea.com> Author: Patrick Wendell <pwendell@gmail.com> Closes #17 from ScrapCodes/java8-lambdas and squashes the following commits: 95850e6 [Patrick Wendell] Some doc improvements and build changes to the Java 8 patch. 85a954e [Prashant Sharma] Nit. import orderings. 673f7ac [Prashant Sharma] Added support for -java-home as well 80a13e8 [Prashant Sharma] Used fake class tag syntax 26eb3f6 [Prashant Sharma] Patrick's comments on PR. 35d8d79 [Prashant Sharma] Specified java 8 building in the docs 31d4cd6 [Prashant Sharma] Maven build to support -Pjava8-tests flag. 4ab87d3 [Prashant Sharma] Review feedback on the pr c33dc2c [Prashant Sharma] SPARK-964, Java 8 API Support.
* Migrate Java code to Scala or move it to src/main/javaPunya Biswal2014-02-222-0/+111
| | | | | | | | | | | | | | | These classes can't be migrated: StorageLevels: impossible to create static fields in Scala JavaSparkContextVarargsWorkaround: incompatible varargs JavaAPISuite: should test Java APIs in pure Java (for sanity) Author: Punya Biswal <pbiswal@palantir.com> Closes #605 from punya/move-java-sources and squashes the following commits: 25b00b2 [Punya Biswal] Remove redundant type param; reformat 853da46 [Punya Biswal] Use factory method rather than constructor e5d53d9 [Punya Biswal] Migrate Java code to Scala or move it to src/main/java
* Optimized importsNirmalReddy2014-02-182-4/+4
| | | | | | | | | | | | | | Optimized imports and arranged according to scala style guide @ https://cwiki.apache.org/confluence/display/SPARK/Spark+Code+Style+Guide#SparkCodeStyleGuide-Imports Author: NirmalReddy <nirmal.reddy@imaginea.com> Author: NirmalReddy <nirmal_reddy2000@yahoo.com> Closes #613 from NirmalReddy/opt-imports and squashes the following commits: 578b4f5 [NirmalReddy] imported java.lang.Double as JDouble a2cbcc5 [NirmalReddy] addressed the comments 776d664 [NirmalReddy] Optimized imports in core
* Suggested small changes to Java code for slightly more standard style, ↵Sean Owen2014-01-026-38/+39
| | | | encapsulation and in some cases performance
* Fix failed unit testsBinh Nguyen2013-12-273-13/+24
| | | | Also clean up a bit.
* Fix imports orderBinh Nguyen2013-12-243-5/+2
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* Remove import * and fix some formattingBinh Nguyen2013-12-242-7/+4
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* upgrade Netty from 4.0.0.Beta2 to 4.0.13.FinalBinh Nguyen2013-12-245-29/+40
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* Merge branch 'master' into scala-2.10Raymond Liu2013-11-133-21/+16
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| * Address Josh and Reynold's commentsAaron Davidson2013-10-201-1/+1
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| * Basic shuffle file consolidationAaron Davidson2013-10-201-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The Spark shuffle phase can produce a large number of files, as one file is created per mapper per reducer. For large or repeated jobs, this often produces millions of shuffle files, which sees extremely degredaded performance from the OS file system. This patch seeks to reduce that burden by combining multipe shuffle files into one. This PR draws upon the work of Jason Dai in https://github.com/mesos/spark/pull/669. However, it simplifies the design in order to get the majority of the gain with less overall intellectual and code burden. The vast majority of code in this pull request is a refactor to allow the insertion of a clean layer of indirection between logical block ids and physical files. This, I feel, provides some design clarity in addition to enabling shuffle file consolidation. The main goal is to produce one shuffle file per reducer per active mapper thread. This allows us to isolate the mappers (simplifying the failure modes), while still allowing us to reduce the number of mappers tremendously for large tasks. In order to accomplish this, we simply create a new set of shuffle files for every parallel task, and return the files to a pool which will be given out to the next run task.
| * Refactor of DiskStore for shuffle file consolidationAaron Davidson2013-10-202-18/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The main goal of this refactor was to allow the interposition of a new layer which maps logical BlockIds to physical locations other than a file with the same name as the BlockId. In particular, BlockIds will need to be mappable to chunks of files, as multiple will be stored in the same file. In order to accomplish this, the following changes have been made: - Creation of DiskBlockManager, which manages the association of logical BlockIds to physical disk locations (called FileSegments). By default, Blocks are simply mapped to physical files of the same name, as before. - The DiskStore now indirects all requests for a given BlockId through the DiskBlockManager in order to resolve the actual File location. - DiskBlockObjectWriter has been merged into BlockObjectWriter. - The Netty PathResolver has been changed to map BlockIds into FileSegments, as this codepath is the only one that uses Netty, and that is likely to remain the case. Overall, I think this refactor produces a clearer division between the logical Block paradigm and their physical on-disk location. There is now an explicit (and documented) mapping from one to the other.
| * Address Matei's commentsAaron Davidson2013-10-141-1/+1
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| * Change BlockId filename to name + rest of Patrick's commentsAaron Davidson2013-10-131-1/+1
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| * Add unit test and address rest of Reynold's commentsAaron Davidson2013-10-121-1/+1
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| * Refactor BlockId into an actual typeAaron Davidson2013-10-122-3/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is an unfortunately invasive change which converts all of our BlockId strings into actual BlockId types. Here are some advantages of doing this now: + Type safety + Code clarity - it's now obvious what the key of a shuffle or rdd block is, for instance. Additionally, appearing in tuple/map type signatures is a big readability bonus. A Seq[(String, BlockStatus)] is not very clear. Further, we can now use more Scala features, like matching on BlockId types. + Explicit usage - we can now formally tell where various BlockIds are being used (without doing string searches); this makes updating current BlockIds a much clearer process, and compiler-supported. (I'm looking at you, shuffle file consolidation.) + It will only get harder to make this change as time goes on. Since this touches a lot of files, it'd be best to either get this patch in quickly or throw it on the ground to avoid too many secondary merge conflicts.
* | fixed some warningsMartin Weindel2013-10-052-3/+0
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* Initial work to rename package to org.apache.sparkMatei Zaharia2013-09-017-7/+7
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* Add Apache license headers and LICENSE and NOTICE filesMatei Zaharia2013-07-167-0/+119
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* Fix some comments and styleShivaram Venkataraman2013-06-131-1/+1
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* Make connect timeout configurableShivaram Venkataraman2013-05-311-2/+4
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* Another round of Netty fixes.Shivaram Venkataraman2013-05-312-18/+14
| | | | | | 1. Avoid race condition between stop and copier completion 2. Handle socket exceptions by reporting them and filling in a failed FetchResult
* Couple of Netty fixesShivaram Venkataraman2013-05-281-21/+24
| | | | | | a. Fix the port number by reading it from the bound channel b. Fix the shutdown sequence to make sure we actually block on the channel c. Fix the unit test to use two JVMs.
* Automatically configure Netty port. This makes unit tests usingReynold Xin2013-05-241-18/+50
| | | | | | | local-cluster pass. Previously they were failing because Netty was trying to bind to the same port for all processes. Pair programmed with @shivaram.
* Cleaned up the Java files from Shane's PR.Reynold Xin2013-05-077-116/+83
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* fix a bug in netty Block Fetchershane-huang2013-04-161-1/+0
| | | | Signed-off-by: shane-huang <shengsheng.huang@intel.com>
* Shuffle Performance fix: Use netty embeded OIO file server instead of ↵shane-huang2013-04-077-0/+328
ConnectionManager Shuffle Performance Optimization: do not send 0-byte block requests to reduce network messages change reference from io.Source to scala.io.Source to avoid looking into io.netty package Signed-off-by: shane-huang <shengsheng.huang@intel.com>
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