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* [SPARK-2777][MLLIB] change ALS factors storage level to MEMORY_AND_DISKXiangrui Meng2014-07-311-2/+2
| | | | | | | | | | | | Now the factors are persisted in memory only. If they get kicked off by later jobs, we might have to start the computation from very beginning. A better solution is changing the storage level to `MEMORY_AND_DISK`. srowen Author: Xiangrui Meng <meng@databricks.com> Closes #1700 from mengxr/als-level and squashes the following commits: c103d76 [Xiangrui Meng] change ALS factors storage level to MEMORY_AND_DISK
* SPARK-2766: ScalaReflectionSuite throw an llegalArgumentException in JDK 6GuoQiang Li2014-07-311-1/+1
| | | | | | | | Author: GuoQiang Li <witgo@qq.com> Closes #1683 from witgo/SPARK-2766 and squashes the following commits: d0db00c [GuoQiang Li] ScalaReflectionSuite throw an llegalArgumentException in JDK 6
* [SPARK-2779] [SQL] asInstanceOf[Map[...]] should use scala.collection.Map ↵Yin Huai2014-07-314-0/+24
| | | | | | | | | | | | | | instead of scala.collection.immutable.Map Since we let users create Rows. It makes sense to accept mutable Maps as values of MapType columns. JIRA: https://issues.apache.org/jira/browse/SPARK-2779 Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1705 from yhuai/SPARK-2779 and squashes the following commits: 00d72fd [Yin Huai] Use scala.collection.Map.
* [SPARK-2756] [mllib] Decision tree bug fixesJoseph K. Bradley2014-07-3110-193/+538
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (1) Inconsistent aggregate (agg) indexing for unordered features. (2) Fixed gain calculations for edge cases. (3) One-off error in choosing thresholds for continuous features for small datasets. (4) (not a bug) Changed meaning of tree depth by 1 to fit scikit-learn and rpart. (Depth 1 used to mean 1 leaf node; depth 0 now means 1 leaf node.) Other updates, to help with tests: * Updated DecisionTreeRunner to print more info. * Added utility functions to DecisionTreeModel: toString, depth, numNodes * Improved internal DecisionTree documentation Bug fix details: (1) Indexing was inconsistent for aggregate calculations for unordered features (in multiclass classification with categorical features, where the features had few enough values such that they could be considered unordered, i.e., isSpaceSufficientForAllCategoricalSplits=true). * updateBinForUnorderedFeature indexed agg as (node, feature, featureValue, binIndex), where ** featureValue was from arr (so it was a feature value) ** binIndex was in [0,…, 2^(maxFeatureValue-1)-1) * The rest of the code indexed agg as (node, feature, binIndex, label). * Corrected this bug by changing updateBinForUnorderedFeature to use the second indexing pattern. Unit tests in DecisionTreeSuite * Updated a few tests to train a model and test its training accuracy, which catches the indexing bug from updateBinForUnorderedFeature() discussed above. * Added new test (“stump with categorical variables for multiclass classification, with just enough bins”) to test bin extremes. (2) Bug fix: calculateGainForSplit (for classification): * It used to return dummy prediction values when either the right or left children had 0 weight. These were incorrect for multiclass classification. It has been corrected. Updated impurities to allow for count = 0. This was related to the above bug fix for calculateGainForSplit (for classification). Small updates to documentation and coding style. (3) Bug fix: Off-by-1 when finding thresholds for splits for continuous features. * Exhibited bug in new test in DecisionTreeSuite: “stump with 1 continuous variable for binary classification, to check off-by-1 error” * Description: When finding thresholds for possible splits for continuous features in DecisionTree.findSplitsBins, the thresholds were set according to individual training examples’ feature values. * Fix: The threshold is set to be the average of 2 consecutive (sorted) examples’ feature values. E.g.: If the old code set the threshold using example i, the new code sets the threshold using exam * Note: In 4 DecisionTreeSuite tests with all labels identical, removed check of threshold since it is somewhat arbitrary. CC: mengxr manishamde Please let me know if I missed something! Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #1673 from jkbradley/decisiontree-bugfix and squashes the following commits: 2b20c61 [Joseph K. Bradley] Small doc and style updates dab0b67 [Joseph K. Bradley] Added documentation for DecisionTree internals 8bb8aa0 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix 978cfcf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix 6eed482 [Joseph K. Bradley] In DecisionTree: Changed from using procedural syntax for functions returning Unit to explicitly writing Unit return type. 376dca2 [Joseph K. Bradley] Updated meaning of maxDepth by 1 to fit scikit-learn and rpart. * In code, replaced usages of maxDepth <-- maxDepth + 1 * In params, replace settings of maxDepth <-- maxDepth - 1 59750f8 [Joseph K. Bradley] * Updated Strategy to check numClassesForClassification only if algo=Classification. * Updates based on comments: ** DecisionTreeRunner *** Made dataFormat arg default to libsvm ** Small cleanups ** tree.Node: Made recursive helper methods private, and renamed them. 52e17c5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix da50db7 [Joseph K. Bradley] Added one more test to DecisionTreeSuite: stump with 2 continuous variables for binary classification. Caused problems in past, but fixed now. 8ea8750 [Joseph K. Bradley] Bug fix: Off-by-1 when finding thresholds for splits for continuous features. 2283df8 [Joseph K. Bradley] 2 bug fixes. 73fbea2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix 5f920a1 [Joseph K. Bradley] Demonstration of bug before submitting fix: Updated DecisionTreeSuite so that 3 tests fail. Will describe bug in next commit.
* [SPARK-2724] Python version of RandomRDDGeneratorsDoris Xin2014-07-316-36/+348
| | | | | | | | | | | | | | | | | | | | | | RandomRDDGenerators but without support for randomRDD and randomVectorRDD, which take in arbitrary DistributionGenerator. `randomRDD.py` is named to avoid collision with the built-in Python `random` package. Author: Doris Xin <doris.s.xin@gmail.com> Closes #1628 from dorx/pythonRDD and squashes the following commits: 55c6de8 [Doris Xin] review comments. all python units passed. f831d9b [Doris Xin] moved default args logic into PythonMLLibAPI 2d73917 [Doris Xin] fix for linalg.py 8663e6a [Doris Xin] reverting back to a single python file for random f47c481 [Doris Xin] docs update 687aac0 [Doris Xin] add RandomRDDGenerators.py to run-tests 4338f40 [Doris Xin] renamed randomRDD to rand and import as random 29d205e [Doris Xin] created mllib.random package bd2df13 [Doris Xin] typos 07ddff2 [Doris Xin] units passed. 23b2ecd [Doris Xin] WIP
* [SPARK-2531 & SPARK-2436] [SQL] Optimize the BuildSide when planning ↵Zongheng Yang2014-07-312-28/+55
| | | | | | | | | | | | | | | | | | BroadcastNestedLoopJoin. This PR resolves the following two tickets: - [SPARK-2531](https://issues.apache.org/jira/browse/SPARK-2531): BNLJ currently assumes the build side is the right relation. This patch refactors some of its logic to take into account a BuildSide properly. - [SPARK-2436](https://issues.apache.org/jira/browse/SPARK-2436): building on top of the above, we simply use the physical size statistics (if available) of both relations, and make the smaller relation the build side in the planner. Author: Zongheng Yang <zongheng.y@gmail.com> Closes #1448 from concretevitamin/bnlj-buildSide and squashes the following commits: 1780351 [Zongheng Yang] Use size estimation to decide optimal build side of BNLJ. 68e6c5b [Zongheng Yang] Consolidate two adjacent pattern matchings. 96d312a [Zongheng Yang] Use a while loop instead of collection methods chaining. 4bc525e [Zongheng Yang] Make BroadcastNestedLoopJoin take a BuildSide.
* SPARK-2282: Reuse Socket for sending accumulator updates to PysparkAaron Davidson2014-07-312-12/+42
| | | | | | | | | | | | | | | | Prior to this change, every PySpark task completion opened a new socket to the accumulator server, passed its updates through, and then quit. I'm not entirely sure why PySpark always sends accumulator updates, but regardless this causes a very rapid buildup of ephemeral TCP connections that remain in the TCP_WAIT state for around a minute before being cleaned up. Rather than trying to allow these sockets to be cleaned up faster, this patch simply reuses the connection between tasks completions (since they're fed updates in a single-threaded manner by the DAGScheduler anyway). The only tricky part here was making sure that the AccumulatorServer was able to shutdown in a timely manner (i.e., stop polling for new data), and this was accomplished via minor feats of magic. I have confirmed that this patch eliminates the buildup of ephemeral sockets due to the accumulator updates. However, I did note that there were still significant sockets being created against the PySpark daemon port, but my machine was not able to create enough sockets fast enough to fail. This may not be the last time we've seen this issue, though. Author: Aaron Davidson <aaron@databricks.com> Closes #1503 from aarondav/accum and squashes the following commits: b3e12f7 [Aaron Davidson] SPARK-2282: Reuse Socket for sending accumulator updates to Pyspark
* SPARK-2740: allow user to specify ascending and numPartitions for sortBy...Rui Li2014-07-311-0/+11
| | | | | | | | | | It should be more convenient if user can specify ascending and numPartitions when calling sortByKey. Author: Rui Li <rui.li@intel.com> Closes #1645 from lirui-intel/spark-2740 and squashes the following commits: fb5d52e [Rui Li] SPARK-2740: allow user to specify ascending and numPartitions for sortByKey
* Docs: monitoring, streaming programming guidekballou2014-07-312-4/+4
| | | | | | | | | | | | | | | Fix several awkward wordings and grammatical issues in the following documents: * docs/monitoring.md * docs/streaming-programming-guide.md Author: kballou <kballou@devnulllabs.io> Closes #1662 from kennyballou/grammar_fixes and squashes the following commits: e1b8ad6 [kballou] Docs: monitoring, streaming programming guide
* Improvements to merge_spark_pr.pyJosh Rosen2014-07-311-19/+34
| | | | | | | | | | | | | | | | This commit fixes a couple of issues in the merge_spark_pr.py developer script: - Allow recovery from failed cherry-picks. - Fix detection of pull requests that have already been merged. Both of these fixes are useful when backporting changes. Author: Josh Rosen <joshrosen@apache.org> Closes #1668 from JoshRosen/pr-script-improvements and squashes the following commits: ff4f33a [Josh Rosen] Default SPARK_HOME to cwd(); detect missing JIRA credentials. ed5bc57 [Josh Rosen] Improvements for backporting using merge_spark_pr:
* [SPARK-2523] [SQL] Hadoop table scan bug fixing (fix failing Jenkins maven test)Yin Huai2014-07-316-26/+19
| | | | | | | | | | This PR tries to resolve the broken Jenkins maven test issue introduced by #1439. Now, we create a single query test to run both the setup work and the test query. Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1669 from yhuai/SPARK-2523-fixTest and squashes the following commits: 358af1a [Yin Huai] Make partition_based_table_scan_with_different_serde run atomically.
* [SPARK-2511][MLLIB] add HashingTF and IDFXiangrui Meng2014-07-315-0/+454
| | | | | | | | | | | | | | | | This is roughly the TF-IDF implementation used in the Databricks Cloud Demo: http://databricks.com/cloud/ . Both `HashingTF` and `IDF` are implemented as transformers, similar to scikit-learn. Author: Xiangrui Meng <meng@databricks.com> Closes #1671 from mengxr/tfidf and squashes the following commits: 7d65888 [Xiangrui Meng] use JavaConverters._ 5fe9ec4 [Xiangrui Meng] fix unit test 6e214ec [Xiangrui Meng] add apache header cfd9aed [Xiangrui Meng] add Java-friendly methods move classes to mllib.feature 3814440 [Xiangrui Meng] add HashingTF and IDF
* SPARK-2646. log4j initialization not quite compatible with log4j 2.xSean Owen2014-07-311-11/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The logging code that handles log4j initialization leads to an stack overflow error when used with log4j 2.x, which has just been released. This occurs even a downstream project has correctly adjusted SLF4J bindings, and that is the right thing to do for log4j 2.x, since it is effectively a separate project from 1.x. Here is the relevant bit of Logging.scala: ``` private def initializeLogging() { // If Log4j is being used, but is not initialized, load a default properties file val binder = StaticLoggerBinder.getSingleton val usingLog4j = binder.getLoggerFactoryClassStr.endsWith("Log4jLoggerFactory") val log4jInitialized = LogManager.getRootLogger.getAllAppenders.hasMoreElements if (!log4jInitialized && usingLog4j) { val defaultLogProps = "org/apache/spark/log4j-defaults.properties" Option(Utils.getSparkClassLoader.getResource(defaultLogProps)) match { case Some(url) => PropertyConfigurator.configure(url) log.info(s"Using Spark's default log4j profile: $defaultLogProps") case None => System.err.println(s"Spark was unable to load $defaultLogProps") } } Logging.initialized = true // Force a call into slf4j to initialize it. Avoids this happening from mutliple threads // and triggering this: http://mailman.qos.ch/pipermail/slf4j-dev/2010-April/002956.html log } ``` The first minor issue is that there is a call to a logger inside this method, which is initializing logging. In this situation, it ends up causing the initialization to be called recursively until the stack overflow. It would be slightly tidier to log this only after Logging.initialized = true. Or not at all. But it's not the root problem, or else, it would not work at all now. The calls to log4j classes here always reference log4j 1.2 no matter what. For example, there is not getAllAppenders in log4j 2.x. That's fine. Really, "usingLog4j" means "using log4j 1.2" and "log4jInitialized" means "log4j 1.2 is initialized". usingLog4j should be false for log4j 2.x, because the initialization only matters for log4j 1.2. But, it's true, and that's the real issue. And log4jInitialized is always false, since calls to the log4j 1.2 API are stubs and no-ops in this setup, where the caller has swapped in log4j 2.x. Hence the loop. This is fixed, I believe, if "usingLog4j" can be false for log4j 2.x. The SLF4J static binding class has the same name for both versions, unfortunately, which causes the issue. However they're in different packages. For example, if the test included "... and begins with org.slf4j", it should work, as the SLF4J binding for log4j 2.x is provided by log4j 2.x at the moment, and is in package org.apache.logging.slf4j. Of course, I assume that SLF4J will eventually offer its own binding. I hope to goodness they at least name the binding class differently, or else this will again not work. But then some other check can probably be made. Author: Sean Owen <srowen@gmail.com> Closes #1547 from srowen/SPARK-2646 and squashes the following commits: 92a9898 [Sean Owen] System.out -> System.err 94be4c7 [Sean Owen] Add back log message as System.out, with informational comment a7f8876 [Sean Owen] Updates from review 6f3c1d3 [Sean Owen] Remove log statement in logging initialization, and distinguish log4j 1.2 from 2.0, to avoid stack overflow in initialization
* SPARK-2749 [BUILD] Part 2. Fix a follow-on scalastyle errorSean Owen2014-07-311-3/+4
| | | | | | | | | | | | The test compile error is fixed, but the build still fails because of one scalastyle error. https://amplab.cs.berkeley.edu/jenkins/view/Spark/job/Spark-Master-Maven-pre-YARN/lastFailedBuild/hadoop.version=1.0.4,label=centos/console Author: Sean Owen <srowen@gmail.com> Closes #1690 from srowen/SPARK-2749 and squashes the following commits: 1c9e7a6 [Sean Owen] Also: fix scalastyle error by wrapping a long line
* SPARK-2664. Deal with `--conf` options in spark-submit that relate to fl...Sandy Ryza2014-07-313-15/+38
| | | | | | | | | | ...ags Author: Sandy Ryza <sandy@cloudera.com> Closes #1665 from sryza/sandy-spark-2664 and squashes the following commits: 0518c63 [Sandy Ryza] SPARK-2664. Deal with `--conf` options in spark-submit that relate to flags
* SPARK-2028: Expose mapPartitionsWithInputSplit in HadoopRDDAaron Davidson2014-07-317-11/+222
| | | | | | | | | | | | | | This allows users to gain access to the InputSplit which backs each partition. An alternative solution would have been to have a .withInputSplit() method which returns a new RDD[(InputSplit, (K, V))], but this is confusing because you could not cache this RDD or shuffle it, as InputSplit is not inherently serializable. Author: Aaron Davidson <aaron@databricks.com> Closes #973 from aarondav/hadoop and squashes the following commits: 9c9112b [Aaron Davidson] Add JavaAPISuite test 9942cd7 [Aaron Davidson] Add Java API 1284a3a [Aaron Davidson] SPARK-2028: Expose mapPartitionsWithInputSplit in HadoopRDD
* [SPARK-2397][SQL] Deprecate LocalHiveContextMichael Armbrust2014-07-316-12/+30
| | | | | | | | | | | | | LocalHiveContext is redundant with HiveContext. The only difference is it creates `./metastore` instead of `./metastore_db`. Author: Michael Armbrust <michael@databricks.com> Closes #1641 from marmbrus/localHiveContext and squashes the following commits: e5ec497 [Michael Armbrust] Add deprecation version 626e056 [Michael Armbrust] Don't remove from imports yet 905cc5f [Michael Armbrust] Merge remote-tracking branch 'apache/master' into localHiveContext 1c2727e [Michael Armbrust] Deprecate LocalHiveContext
* [SPARK-2743][SQL] Resolve original attributes in ParquetTableScanMichael Armbrust2014-07-313-17/+28
| | | | | | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #1647 from marmbrus/parquetCase and squashes the following commits: a1799b7 [Michael Armbrust] move comment 2a2a68b [Michael Armbrust] Merge remote-tracking branch 'apache/master' into parquetCase bb35d5b [Michael Armbrust] Fix test case that produced an invalid plan. e6870bf [Michael Armbrust] Better error message. 539a2e1 [Michael Armbrust] Resolve original attributes in ParquetTableScan
* [SPARK-2762] SparkILoop leaks memory in multi-repl configurationsTimothy Hunter2014-07-311-19/+20
| | | | | | | | | | This pull request is a small refactor so that a partial function (hence a closure) is not created. Instead, a regular function is used. The behavior of the code is not changed. Author: Timothy Hunter <timhunter@databricks.com> Closes #1674 from thunterdb/closure_issue and squashes the following commits: e1e664d [Timothy Hunter] simplify closure
* automatically set master according to `spark.master` in `spark-defaults....CrazyJvm2014-07-301-3/+0
| | | | | | | | | | automatically set master according to `spark.master` in `spark-defaults.conf` Author: CrazyJvm <crazyjvm@gmail.com> Closes #1644 from CrazyJvm/standalone-guide and squashes the following commits: bb12b95 [CrazyJvm] automatically set master according to `spark.master` in `spark-defaults.conf`
* [SPARK-2497] Included checks for module symbols too.Prashant Sharma2014-07-301-11/+9
| | | | | | | | | Author: Prashant Sharma <prashant.s@imaginea.com> Closes #1463 from ScrapCodes/SPARK-2497/mima-exclude-all and squashes the following commits: 72077b1 [Prashant Sharma] Check separately for module symbols. cd96192 [Prashant Sharma] SPARK-2497 Produce "member excludes" irrespective of the fact that class itself is excluded or not.
* [SPARK-2737] Add retag() method for changing RDDs' ClassTags.Josh Rosen2014-07-303-0/+42
| | | | | | | | | | | | | | | | | The Java API's use of fake ClassTags doesn't seem to cause any problems for Java users, but it can lead to issues when passing JavaRDDs' underlying RDDs to Scala code (e.g. in the MLlib Java API wrapper code). If we call collect() on a Scala RDD with an incorrect ClassTag, this causes ClassCastExceptions when we try to allocate an array of the wrong type (for example, see SPARK-2197). There are a few possible fixes here. An API-breaking fix would be to completely remove the fake ClassTags and require Java API users to pass java.lang.Class instances to all parallelize() calls and add returnClass fields to all Function implementations. This would be extremely verbose. Instead, this patch adds internal APIs to "repair" a Scala RDD with an incorrect ClassTag by wrapping it and overriding its ClassTag. This should be okay for cases where the Scala code that calls collect() knows what type of array should be allocated, which is the case in the MLlib wrappers. Author: Josh Rosen <joshrosen@apache.org> Closes #1639 from JoshRosen/SPARK-2737 and squashes the following commits: 572b4c8 [Josh Rosen] Replace newRDD[T] with mapPartitions(). 469d941 [Josh Rosen] Preserve partitioner in retag(). af78816 [Josh Rosen] Allow retag() to get classTag implicitly. d1d54e6 [Josh Rosen] [SPARK-2737] Add retag() method for changing RDDs' ClassTags.
* [SPARK-2340] Resolve event logging and History Server paths properlyAndrew Or2014-07-307-29/+28
| | | | | | | | | | | | | | | | We resolve relative paths to the local `file:/` system for `--jars` and `--files` in spark submit (#853). We should do the same for the history server. Author: Andrew Or <andrewor14@gmail.com> Closes #1280 from andrewor14/hist-serv-fix and squashes the following commits: 13ff406 [Andrew Or] Merge branch 'master' of github.com:apache/spark into hist-serv-fix b393e17 [Andrew Or] Strip trailing "/" from logging directory 622a471 [Andrew Or] Fix test in EventLoggingListenerSuite 0e20f71 [Andrew Or] Shift responsibility of resolving paths up one level b037c0c [Andrew Or] Use resolved paths for everything in history server c7e36ee [Andrew Or] Resolve paths for event logging too 40e3933 [Andrew Or] Resolve history server file paths
* Required AM memory is "amMem", not "args.amMemory"derek ma2014-07-301-1/+1
| | | | | | | | | | "ERROR yarn.Client: Required AM memory (1024) is above the max threshold (1048) of this cluster" appears if this code is not changed. obviously, 1024 is less than 1048, so change this Author: derek ma <maji3@asiainfo-linkage.com> Closes #1494 from maji2014/master and squashes the following commits: b0f6640 [derek ma] Required AM memory is "amMem", not "args.amMemory"
* [SPARK-2758] UnionRDD's UnionPartition should not reference parent RDDsReynold Xin2014-07-302-11/+42
| | | | | | | | | Author: Reynold Xin <rxin@apache.org> Closes #1675 from rxin/unionrdd and squashes the following commits: 941d316 [Reynold Xin] Clear RDDs for checkpointing. c9f05f2 [Reynold Xin] [SPARK-2758] UnionRDD's UnionPartition should not reference parent RDDs
* SPARK-2045 Sort-based shuffleMatei Zaharia2014-07-3035-159/+1969
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This adds a new ShuffleManager based on sorting, as described in https://issues.apache.org/jira/browse/SPARK-2045. The bulk of the code is in an ExternalSorter class that is similar to ExternalAppendOnlyMap, but sorts key-value pairs by partition ID and can be used to create a single sorted file with a map task's output. (Longer-term I think this can take on the remaining functionality in ExternalAppendOnlyMap and replace it so we don't have code duplication.) The main TODOs still left are: - [x] enabling ExternalSorter to merge across spilled files - [x] with an Ordering - [x] without an Ordering, using the keys' hash codes - [x] adding more tests (e.g. a version of our shuffle suite that runs on this) - [x] rebasing on top of the size-tracking refactoring in #1165 when that is merged - [x] disabling spilling if spark.shuffle.spill is set to false Despite this though, this seems to work pretty well (running successfully in cases where the hash shuffle would OOM, such as 1000 reduce tasks on executors with only 1G memory), and it seems to be comparable in speed or faster than hash-based shuffle (it will create much fewer files for the OS to keep track of). So I'm posting it to get some early feedback. After these TODOs are done, I'd also like to enable ExternalSorter to sort data within each partition by a key as well, which will allow us to use it to implement external spilling in reduce tasks in `sortByKey`. Author: Matei Zaharia <matei@databricks.com> Closes #1499 from mateiz/sort-based-shuffle and squashes the following commits: bd841f9 [Matei Zaharia] Various review comments d1c137fd [Matei Zaharia] Various review comments a611159 [Matei Zaharia] Compile fixes due to rebase 62c56c8 [Matei Zaharia] Fix ShuffledRDD sometimes not returning Tuple2s. f617432 [Matei Zaharia] Fix a failing test (seems to be due to change in SizeTracker logic) 9464d5f [Matei Zaharia] Simplify code and fix conflicts after latest rebase 0174149 [Matei Zaharia] Add cleanup behavior and cleanup tests for sort-based shuffle eb4ee0d [Matei Zaharia] Remove customizable element type in ShuffledRDD fa2e8db [Matei Zaharia] Allow nextBatchStream to be called after we're done looking at all streams a34b352 [Matei Zaharia] Fix tracking of indices within a partition in SpillReader, and add test 03e1006 [Matei Zaharia] Add a SortShuffleSuite that runs ShuffleSuite with sort-based shuffle 3c7ff1f [Matei Zaharia] Obey the spark.shuffle.spill setting in ExternalSorter ad65fbd [Matei Zaharia] Rebase on top of Aaron's Sorter change, and use Sorter in our buffer 44d2a93 [Matei Zaharia] Use estimateSize instead of atGrowThreshold to test collection sizes 5686f71 [Matei Zaharia] Optimize merging phase for in-memory only data: 5461cbb [Matei Zaharia] Review comments and more tests (e.g. tests with 1 element per partition) e9ad356 [Matei Zaharia] Update ContextCleanerSuite to make sure shuffle cleanup tests use hash shuffle (since they were written for it) c72362a [Matei Zaharia] Added bug fix and test for when iterators are empty de1fb40 [Matei Zaharia] Make trait SizeTrackingCollection private[spark] 4988d16 [Matei Zaharia] tweak c1b7572 [Matei Zaharia] Small optimization ba7db7f [Matei Zaharia] Handle null keys in hash-based comparator, and add tests for collisions ef4e397 [Matei Zaharia] Support for partial aggregation even without an Ordering 4b7a5ce [Matei Zaharia] More tests, and ability to sort data if a total ordering is given e1f84be [Matei Zaharia] Fix disk block manager test 5a40a1c [Matei Zaharia] More tests 614f1b4 [Matei Zaharia] Add spill metrics to map tasks cc52caf [Matei Zaharia] Add more error handling and tests for error cases bbf359d [Matei Zaharia] More work 3a56341 [Matei Zaharia] More partial work towards sort-based shuffle 7a0895d [Matei Zaharia] Some more partial work towards sort-based shuffle b615476 [Matei Zaharia] Scaffolding for sort-based shuffle
* Update DecisionTreeRunner.scalastrat0sphere2014-07-301-1/+1
| | | | | | | | Author: strat0sphere <stratos.dimopoulos@gmail.com> Closes #1676 from strat0sphere/patch-1 and squashes the following commits: 044d2fa [strat0sphere] Update DecisionTreeRunner.scala
* SPARK-2341 [MLLIB] loadLibSVMFile doesn't handle regression datasetsSean Owen2014-07-308-154/+46
| | | | | | | | | | | | 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-2734][SQL] Remove tables from cache when DROP TABLE is run.Michael Armbrust2014-07-304-1/+74
| | | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #1650 from marmbrus/dropCached and squashes the following commits: e6ab80b [Michael Armbrust] Support if exists. 83426c6 [Michael Armbrust] Remove tables from cache when DROP TABLE is run.
* SPARK-2741 - Publish version of spark assembly which does not contain HiveBrock Noland2014-07-301-0/+2
| | | | | | | | | | Provide a version of the Spark tarball which does not package Hive. This is meant for HIve + Spark users. Author: Brock Noland <brock@apache.org> Closes #1667 from brockn/master and squashes the following commits: 5beafb2 [Brock Noland] SPARK-2741 - Publish version of spark assembly which does not contain Hive
* SPARK-2749 [BUILD]. Spark SQL Java tests aren't compiling in Jenkins' Maven ↵Sean Owen2014-07-3010-0/+50
| | | | | | | | | | | | | | | | | | | | | | | | | | | builds; missing junit:junit dep The Maven-based builds in the build matrix have been failing for a few days: https://amplab.cs.berkeley.edu/jenkins/view/Spark/ On inspection, it looks like the Spark SQL Java tests don't compile: https://amplab.cs.berkeley.edu/jenkins/view/Spark/job/Spark-Master-Maven-pre-YARN/hadoop.version=1.0.4,label=centos/244/consoleFull I confirmed it by repeating the command vs master: `mvn -Dhadoop.version=1.0.4 -Dlabel=centos -DskipTests clean package` The problem is that this module doesn't depend on JUnit. In fact, none of the modules do, but `com.novocode:junit-interface` (the SBT-JUnit bridge) pulls it in, in most places. However this module doesn't depend on `com.novocode:junit-interface` Adding the `junit:junit` dependency fixes the compile problem. In fact, the other modules with Java tests should probably depend on it explicitly instead of happening to get it via `com.novocode:junit-interface`, since that is a bit SBT/Scala-specific (and I am not even sure it's needed). Author: Sean Owen <srowen@gmail.com> Closes #1660 from srowen/SPARK-2749 and squashes the following commits: 858ff7c [Sean Owen] Add explicit junit dep to other modules with Java tests for robustness 9636794 [Sean Owen] Add junit dep so that Spark SQL Java tests compile
* Properly pass SBT_MAVEN_PROFILES into sbt.Reynold Xin2014-07-301-14/+13
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* Set AMPLAB_JENKINS_BUILD_PROFILE.Reynold Xin2014-07-301-0/+12
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* Wrap JAR_DL in dev/check-license.Reynold Xin2014-07-301-2/+2
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* [SPARK-2024] Add saveAsSequenceFile to PySparkKan Zhang2014-07-3014-186/+1085
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | JIRA issue: https://issues.apache.org/jira/browse/SPARK-2024 This PR is a followup to #455 and adds capabilities for saving PySpark RDDs using SequenceFile or any Hadoop OutputFormats. * Added RDD methods ```saveAsSequenceFile```, ```saveAsHadoopFile``` and ```saveAsHadoopDataset```, for both old and new MapReduce APIs. * Default converter for converting common data types to Writables. Users may specify custom converters to convert to desired data types. * No out-of-box support for reading/writing arrays, since ArrayWritable itself doesn't have a no-arg constructor for creating an empty instance upon reading. Users need to provide ArrayWritable subtypes. Custom converters for converting arrays to suitable ArrayWritable subtypes are also needed when writing. When reading, the default converter will convert any custom ArrayWritable subtypes to ```Object[]``` and they get pickled to Python tuples. * Added HBase and Cassandra output examples to show how custom output formats and converters can be used. cc MLnick mateiz ahirreddy pwendell Author: Kan Zhang <kzhang@apache.org> Closes #1338 from kanzhang/SPARK-2024 and squashes the following commits: c01e3ef [Kan Zhang] [SPARK-2024] code formatting 6591e37 [Kan Zhang] [SPARK-2024] renaming pickled -> pickledRDD d998ad6 [Kan Zhang] [SPARK-2024] refectoring to get method params below 10 57a7a5e [Kan Zhang] [SPARK-2024] correcting typo 75ca5bd [Kan Zhang] [SPARK-2024] Better type checking for batch serialized RDD 0bdec55 [Kan Zhang] [SPARK-2024] Refactoring newly added tests 9f39ff4 [Kan Zhang] [SPARK-2024] Adding 2 saveAsHadoopDataset tests 0c134f3 [Kan Zhang] [SPARK-2024] Test refactoring and adding couple unbatched cases 7a176df [Kan Zhang] [SPARK-2024] Add saveAsSequenceFile to PySpark
* dev/check-license wrap folders in quotes.Reynold Xin2014-07-301-5/+5
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* [SQL] Fix compiling of catalyst docs.Michael Armbrust2014-07-301-1/+4
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #1653 from marmbrus/fixDocs and squashes the following commits: 0aa1feb [Michael Armbrust] Fix compiling of catalyst docs.
* More wrapping FWDIR in quotes.Reynold Xin2014-07-303-3/+3
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* Wrap FWDIR in quotes in dev/check-license.Reynold Xin2014-07-301-1/+1
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* Wrap FWDIR in quotes.Reynold Xin2014-07-301-1/+1
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* [SPARK-2746] Set SBT_MAVEN_PROFILES only when it is not set explicitly by ↵Reynold Xin2014-07-301-1/+4
| | | | | | | | | | the user. Author: Reynold Xin <rxin@apache.org> Closes #1655 from rxin/SBT_MAVEN_PROFILES and squashes the following commits: b268c4b [Reynold Xin] [SPARK-2746] Set SBT_MAVEN_PROFILES only when it is not set explicitly by the user.
* [SPARK-2544][MLLIB] Improve ALS algorithm resource usageGuoQiang Li2014-07-301-0/+6
| | | | | | | | | | | Author: GuoQiang Li <witgo@qq.com> Author: witgo <witgo@qq.com> Closes #929 from witgo/improve_als and squashes the following commits: ea25033 [GuoQiang Li] checkpoint products 3,6,9 ... 154dccf [GuoQiang Li] checkpoint products only c5779ff [witgo] Improve ALS algorithm resource usage
* Avoid numerical instabilityNaftali Harris2014-07-301-1/+2
| | | | | | | | | | | | | | | | | | | | This avoids basically doing 1 - 1, for example: ```python >>> from math import exp >>> margin = -40 >>> 1 - 1 / (1 + exp(margin)) 0.0 >>> exp(margin) / (1 + exp(margin)) 4.248354255291589e-18 >>> ``` Author: Naftali Harris <naftaliharris@gmail.com> Closes #1652 from naftaliharris/patch-2 and squashes the following commits: 0d55a9f [Naftali Harris] Avoid numerical instability
* [SPARK-2747] git diff --dirstat can miss sql changes and not run Hive testsReynold Xin2014-07-301-1/+1
| | | | | | | | | | | | dev/run-tests use "git diff --dirstat master" to check whether sql is changed. However, --dirstat won't show sql if sql's change is negligible (e.g. 1k loc change in core, and only 1 loc change in hive). We should use "git diff --name-only master" instead. Author: Reynold Xin <rxin@apache.org> Closes #1656 from rxin/hiveTest and squashes the following commits: f5eab9f [Reynold Xin] [SPARK-2747] git diff --dirstat can miss sql changes and not run Hive tests.
* [SPARK-2521] Broadcast RDD object (instead of sending it along with every task)Reynold Xin2014-07-3012-302/+198
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is a resubmission of #1452. It was reverted because it broke the build. Currently (as of Spark 1.0.1), Spark sends RDD object (which contains closures) using Akka along with the task itself to the executors. This is inefficient because all tasks in the same stage use the same RDD object, but we have to send RDD object multiple times to the executors. This is especially bad when a closure references some variable that is very large. The current design led to users having to explicitly broadcast large variables. The patch uses broadcast to send RDD objects and the closures to executors, and use Akka to only send a reference to the broadcast RDD/closure along with the partition specific information for the task. For those of you who know more about the internals, Spark already relies on broadcast to send the Hadoop JobConf every time it uses the Hadoop input, because the JobConf is large. The user-facing impact of the change include: 1. Users won't need to decide what to broadcast anymore, unless they would want to use a large object multiple times in different operations 2. Task size will get smaller, resulting in faster scheduling and higher task dispatch throughput. In addition, the change will simplify some internals of Spark, eliminating the need to maintain task caches and the complex logic to broadcast JobConf (which also led to a deadlock recently). A simple way to test this: ```scala val a = new Array[Byte](1000*1000); scala.util.Random.nextBytes(a); sc.parallelize(1 to 1000, 1000).map { x => a; x }.groupBy { x => a; x }.count ``` Numbers on 3 r3.8xlarge instances on EC2 ``` master branch: 5.648436068 s, 4.715361895 s, 5.360161877 s with this change: 3.416348793 s, 1.477846558 s, 1.553432156 s ``` Author: Reynold Xin <rxin@apache.org> Closes #1498 from rxin/broadcast-task and squashes the following commits: f7364db [Reynold Xin] Code review feedback. f8535dc [Reynold Xin] Fixed the style violation. 252238d [Reynold Xin] Serialize the final task closure as well as ShuffleDependency in taskBinary. 111007d [Reynold Xin] Fix broadcast tests. 797c247 [Reynold Xin] Properly send SparkListenerStageSubmitted and SparkListenerStageCompleted. bab1d8b [Reynold Xin] Check for NotSerializableException in submitMissingTasks. cf38450 [Reynold Xin] Use TorrentBroadcastFactory. 991c002 [Reynold Xin] Use HttpBroadcast. de779f8 [Reynold Xin] Fix TaskContextSuite. cc152fc [Reynold Xin] Don't cache the RDD broadcast variable. d256b45 [Reynold Xin] Fixed unit test failures. One more to go. cae0af3 [Reynold Xin] [SPARK-2521] Broadcast RDD object (instead of sending it along with every task).
* SPARK-2748 [MLLIB] [GRAPHX] Loss of precision for small arguments to ↵Sean Owen2014-07-302-6/+8
| | | | | | | | | | | | | | | | | | Math.exp, Math.log In a few places in MLlib, an expression of the form `log(1.0 + p)` is evaluated. When p is so small that `1.0 + p == 1.0`, the result is 0.0. However the correct answer is very near `p`. This is why `Math.log1p` exists. Similarly for one instance of `exp(m) - 1` in GraphX; there's a special `Math.expm1` method. While the errors occur only for very small arguments, given their use in machine learning algorithms, this is entirely possible. Also note the related PR for Python: https://github.com/apache/spark/pull/1652 Author: Sean Owen <srowen@gmail.com> Closes #1659 from srowen/SPARK-2748 and squashes the following commits: c5926d4 [Sean Owen] Use log1p, expm1 for better precision for tiny arguments
* SPARK-2543: Allow user to set maximum Kryo buffer sizeKoert Kuipers2014-07-303-5/+44
| | | | | | | | | | | | Author: Koert Kuipers <koert@tresata.com> Closes #735 from koertkuipers/feat-kryo-max-buffersize and squashes the following commits: 15f6d81 [Koert Kuipers] change default for spark.kryoserializer.buffer.max.mb to 64mb and add some documentation 1bcc22c [Koert Kuipers] Merge branch 'master' into feat-kryo-max-buffersize 0c9f8eb [Koert Kuipers] make default for kryo max buffer size 16MB 143ec4d [Koert Kuipers] test resizable buffer in kryo Output 0732445 [Koert Kuipers] support setting maxCapacity to something different than capacity in kryo Output
* [SPARK-2179][SQL] Public API for DataTypes and SchemaYin Huai2014-07-3061-386/+3442
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The current PR contains the following changes: * Expose `DataType`s in the sql package (internal details are private to sql). * Users can create Rows. * Introduce `applySchema` to create a `SchemaRDD` by applying a `schema: StructType` to an `RDD[Row]`. * Add a function `simpleString` to every `DataType`. Also, the schema represented by a `StructType` can be visualized by `printSchema`. * `ScalaReflection.typeOfObject` provides a way to infer the Catalyst data type based on an object. Also, we can compose `typeOfObject` with some custom logics to form a new function to infer the data type (for different use cases). * `JsonRDD` has been refactored to use changes introduced by this PR. * Add a field `containsNull` to `ArrayType`. So, we can explicitly mark if an `ArrayType` can contain null values. The default value of `containsNull` is `false`. New APIs are introduced in the sql package object and SQLContext. You can find the scaladoc at [sql package object](http://yhuai.github.io/site/api/scala/index.html#org.apache.spark.sql.package) and [SQLContext](http://yhuai.github.io/site/api/scala/index.html#org.apache.spark.sql.SQLContext). An example of using `applySchema` is shown below. ```scala import org.apache.spark.sql._ val sqlContext = new org.apache.spark.sql.SQLContext(sc) val schema = StructType( StructField("name", StringType, false) :: StructField("age", IntegerType, true) :: Nil) val people = sc.textFile("examples/src/main/resources/people.txt").map(_.split(",")).map(p => Row(p(0), p(1).trim.toInt)) val peopleSchemaRDD = sqlContext. applySchema(people, schema) peopleSchemaRDD.printSchema // root // |-- name: string (nullable = false) // |-- age: integer (nullable = true) peopleSchemaRDD.registerAsTable("people") sqlContext.sql("select name from people").collect.foreach(println) ``` I will add new contents to the SQL programming guide later. JIRA: https://issues.apache.org/jira/browse/SPARK-2179 Author: Yin Huai <huai@cse.ohio-state.edu> Closes #1346 from yhuai/dataTypeAndSchema and squashes the following commits: 1d45977 [Yin Huai] Clean up. a6e08b4 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema c712fbf [Yin Huai] Converts types of values based on defined schema. 4ceeb66 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema e5f8df5 [Yin Huai] Scaladoc. 122d1e7 [Yin Huai] Address comments. 03bfd95 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema 2476ed0 [Yin Huai] Minor updates. ab71f21 [Yin Huai] Format. fc2bed1 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema bd40a33 [Yin Huai] Address comments. 991f860 [Yin Huai] Move "asJavaDataType" and "asScalaDataType" to DataTypeConversions.scala. 1cb35fe [Yin Huai] Add "valueContainsNull" to MapType. 3edb3ae [Yin Huai] Python doc. 692c0b9 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema 1d93395 [Yin Huai] Python APIs. 246da96 [Yin Huai] Add java data type APIs to javadoc index. 1db9531 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema d48fc7b [Yin Huai] Minor updates. 33c4fec [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema b9f3071 [Yin Huai] Java API for applySchema. 1c9f33c [Yin Huai] Java APIs for DataTypes and Row. 624765c [Yin Huai] Tests for applySchema. aa92e84 [Yin Huai] Update data type tests. 8da1a17 [Yin Huai] Add Row.fromSeq. 9c99bc0 [Yin Huai] Several minor updates. 1d9c13a [Yin Huai] Update applySchema API. 85e9b51 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema e495e4e [Yin Huai] More comments. 42d47a3 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema c3f4a02 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema 2e58dbd [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema b8b7db4 [Yin Huai] 1. Move sql package object and package-info to sql-core. 2. Minor updates on APIs. 3. Update scala doc. 68525a2 [Yin Huai] Update JSON unit test. 3209108 [Yin Huai] Add unit tests. dcaf22f [Yin Huai] Add a field containsNull to ArrayType to indicate if an array can contain null values or not. If an ArrayType is constructed by "ArrayType(elementType)" (the existing constructor), the value of containsNull is false. 9168b83 [Yin Huai] Update comments. fc649d7 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema eca7d04 [Yin Huai] Add two apply methods which will be used to extract StructField(s) from a StructType. 949d6bb [Yin Huai] When creating a SchemaRDD for a JSON dataset, users can apply an existing schema. 7a6a7e5 [Yin Huai] Fix bug introduced by the change made on SQLContext.inferSchema. 43a45e1 [Yin Huai] Remove sql.util.package introduced in a previous commit. 0266761 [Yin Huai] Format 03eec4c [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema 90460ac [Yin Huai] Infer the Catalyst data type from an object and cast a data value to the expected type. 3fa0df5 [Yin Huai] Provide easier ways to construct a StructType. 16be3e5 [Yin Huai] This commit contains three changes: * Expose `DataType`s in the sql package (internal details are private to sql). * Introduce `createSchemaRDD` to create a `SchemaRDD` from an `RDD` with a provided schema (represented by a `StructType`) and a provided function to construct `Row`, * Add a function `simpleString` to every `DataType`. Also, the schema represented by a `StructType` can be visualized by `printSchema`.
* [SPARK-2260] Fix standalone-cluster mode, which was brokenAndrew Or2014-07-2916-51/+93
| | | | | | | | | | | | | | | | | | | | | | | | | | | | The main thing was that spark configs were not propagated to the driver, and so applications that do not specify `master` or `appName` automatically failed. This PR fixes that and a couple of miscellaneous things that are related. One thing that may or may not be an issue is that the jars must be available on the driver node. In `standalone-cluster` mode, this effectively means these jars must be available on all the worker machines, since the driver is launched on one of them. The semantics here are not the same as `yarn-cluster` mode, where all the relevant jars are uploaded to a distributed cache automatically and shipped to the containers. This is probably not a concern, but still worth a mention. Author: Andrew Or <andrewor14@gmail.com> Closes #1538 from andrewor14/standalone-cluster and squashes the following commits: 8c11a0d [Andrew Or] Clean up imports / comments (minor) 2678d13 [Andrew Or] Handle extraJavaOpts properly 7660547 [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-cluster 6f64a9b [Andrew Or] Revert changes in YARN 2f2908b [Andrew Or] Fix tests ed01491 [Andrew Or] Don't go overboard with escaping 8e105e1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-cluster b890949 [Andrew Or] Abstract usages of converting spark opts to java opts 79f63a3 [Andrew Or] Move sparkProps into javaOpts 78752f8 [Andrew Or] Fix tests 5a9c6c7 [Andrew Or] Fix line too long c141a00 [Andrew Or] Don't display "unknown app" on driver log pages d7e2728 [Andrew Or] Avoid deprecation warning in standalone Client 6ceb14f [Andrew Or] Allow relevant configs to propagate to standalone Driver 7f854bc [Andrew Or] Fix test 855256e [Andrew Or] Fix standalone-cluster mode fd9da51 [Andrew Or] Formatting changes (minor)
* [SQL] Handle null values in debug()Michael Armbrust2014-07-291-1/+3
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #1646 from marmbrus/nullDebug and squashes the following commits: 49050a8 [Michael Armbrust] Handle null values in debug()
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-24 07:26:38 +0000