- Nov 29, 2016
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hyukjinkwon authored
## What changes were proposed in this pull request? Currently, single line comment does not mark down backticks to `<code>..</code>` but prints as they are (`` `..` ``). For example, the line below: ```scala /** Return an RDD with the pairs from `this` whose keys are not in `other`. */ ``` So, we could work around this as below: ```scala /** * Return an RDD with the pairs from `this` whose keys are not in `other`. */ ``` - javadoc - **Before**  - **After**  - scaladoc (this one looks fine either way) - **Before**  - **After**  I suspect this is related with SPARK-16153 and genjavadoc issue in ` typesafehub/genjavadoc#85`. ## How was this patch tested? I found them via ``` grep -r "\/\*\*.*\`" . | grep .scala ```` and then checked if each is in the public API documentation with manually built docs (`jekyll build`) with Java 7. Author: hyukjinkwon <gurwls223@gmail.com> Closes #16050 from HyukjinKwon/javadoc-markdown. -
hyukjinkwon authored
[SPARK-3359][DOCS] Make javadoc8 working for unidoc/genjavadoc compatibility in Java API documentation ## What changes were proposed in this pull request? This PR make `sbt unidoc` complete with Java 8. This PR roughly includes several fixes as below: - Fix unrecognisable class and method links in javadoc by changing it from `[[..]]` to `` `...` `` ```diff - * A column that will be computed based on the data in a [[DataFrame]]. + * A column that will be computed based on the data in a `DataFrame`. ``` - Fix throws annotations so that they are recognisable in javadoc - Fix URL links to `<a href="http..."></a>`. ```diff - * [[http://en.wikipedia.org/wiki/Decision_tree_learning Decision tree]] model for regression. + * <a href="http://en.wikipedia.org/wiki/Decision_tree_learning"> + * Decision tree (Wikipedia)</a> model for regression. ``` ```diff - * see http://en.wikipedia.org/wiki/Receiver_operating_characteristic + * see <a href="http://en.wikipedia.org/wiki/Receiver_operating_characteristic"> + * Receiver operating characteristic (Wikipedia)</a> ``` - Fix < to > to - `greater than`/`greater than or equal to` or `less than`/`less than or equal to` where applicable. - Wrap it with `{{{...}}}` to print them in javadoc or use `{code ...}` or `{literal ..}`. Please refer https://github.com/apache/spark/pull/16013#discussion_r89665558 - Fix `</p>` complaint ## How was this patch tested? Manually tested by `jekyll build` with Java 7 and 8 ``` java version "1.7.0_80" Java(TM) SE Runtime Environment (build 1.7.0_80-b15) Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode) ``` ``` java version "1.8.0_45" Java(TM) SE Runtime Environment (build 1.8.0_45-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode) ``` Author: hyukjinkwon <gurwls223@gmail.com> Closes #16013 from HyukjinKwon/SPARK-3359-errors-more.
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Davies Liu authored
## What changes were proposed in this pull request? A TorrentBroadcast is serialized and compressed first, then splitted as fixed size blocks, if any block is corrupt when fetching from remote, the decompression/deserialization will fail without knowing which block is corrupt. Also, the corrupt block is kept in block manager and reported to driver, so other tasks (in same executor or from different executor) will also fail because of it. This PR add checksum for each block, and check it after fetching a block from remote executor, because it's very likely that the corruption happen in network. When the corruption happen, it will throw the block away and throw an exception to fail the task, which will be retried. Added a config for it: `spark.broadcast.checksum`, which is true by default. ## How was this patch tested? Existing tests. Author: Davies Liu <davies@databricks.com> Closes #15935 from davies/broadcast_checksum.
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- Nov 28, 2016
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Marcelo Vanzin authored
This change modifies the method used to propagate encryption keys used during shuffle. Instead of relying on YARN's UserGroupInformation credential propagation, this change explicitly distributes the key using the messages exchanged between driver and executor during registration. When RPC encryption is enabled, this means key propagation is also secure. This allows shuffle encryption to work in non-YARN mode, which means that it's easier to write unit tests for areas of the code that are affected by the feature. The key is stored in the SecurityManager; because there are many instances of that class used in the code, the key is only guaranteed to exist in the instance managed by the SparkEnv. This path was chosen to avoid storing the key in the SparkConf, which would risk having the key being written to disk as part of the configuration (as, for example, is done when starting YARN applications). Tested by new and existing unit tests (which were moved from the YARN module to core), and by running apps with shuffle encryption enabled. Author: Marcelo Vanzin <vanzin@cloudera.com> Closes #15981 from vanzin/SPARK-18547.
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Imran Rashid authored
## What changes were proposed in this pull request? This adds tests to verify the interaction between TaskSetBlacklist and TaskSchedulerImpl. TaskSetBlacklist was introduced by SPARK-17675 but it neglected to add these tests. This change does not fix any bugs -- it is just for increasing test coverage. ## How was this patch tested? Jenkins Author: Imran Rashid <irashid@cloudera.com> Closes #15644 from squito/taskset_blacklist_test_update.
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Mark Grover authored
## What changes were proposed in this pull request? This patch adds a new property called `spark.secret.redactionPattern` that allows users to specify a scala regex to decide which Spark configuration properties and environment variables in driver and executor environments contain sensitive information. When this regex matches the property or environment variable name, its value is redacted from the environment UI and various logs like YARN and event logs. This change uses this property to redact information from event logs and YARN logs. It also, updates the UI code to adhere to this property instead of hardcoding the logic to decipher which properties are sensitive. Here's an image of the UI post-redaction:  Here's the text in the YARN logs, post-redaction: ``HADOOP_CREDSTORE_PASSWORD -> *********(redacted)`` Here's the text in the event logs, post-redaction: ``...,"spark.executorEnv.HADOOP_CREDSTORE_PASSWORD":"*********(redacted)","spark.yarn.appMasterEnv.HADOOP_CREDSTORE_PASSWORD":"*********(redacted)",...`` ## How was this patch tested? 1. Unit tests are added to ensure that redaction works. 2. A YARN job reading data off of S3 with confidential information (hadoop credential provider password) being provided in the environment variables of driver and executor. And, afterwards, logs were grepped to make sure that no mention of secret password was present. It was also ensure that the job was able to read the data off of S3 correctly, thereby ensuring that the sensitive information was being trickled down to the right places to read the data. 3. The event logs were checked to make sure no mention of secret password was present. 4. UI environment tab was checked to make sure there was no secret information being displayed. Author: Mark Grover <mark@apache.org> Closes #15971 from markgrover/master_redaction.
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- Nov 25, 2016
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Takuya UESHIN authored
## What changes were proposed in this pull request? The nullability of `InputFileName` should be `false`. ## How was this patch tested? Existing tests. Author: Takuya UESHIN <ueshin@happy-camper.st> Closes #16007 from ueshin/issues/SPARK-18583.
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hyukjinkwon authored
[SPARK-3359][BUILD][DOCS] More changes to resolve javadoc 8 errors that will help unidoc/genjavadoc compatibility ## What changes were proposed in this pull request? This PR only tries to fix things that looks pretty straightforward and were fixed in other previous PRs before. This PR roughly fixes several things as below: - Fix unrecognisable class and method links in javadoc by changing it from `[[..]]` to `` `...` `` ``` [error] .../spark/sql/core/target/java/org/apache/spark/sql/streaming/DataStreamReader.java:226: error: reference not found [error] * Loads text files and returns a {link DataFrame} whose schema starts with a string column named ``` - Fix an exception annotation and remove code backticks in `throws` annotation Currently, sbt unidoc with Java 8 complains as below: ``` [error] .../java/org/apache/spark/sql/streaming/StreamingQuery.java:72: error: unexpected text [error] * throws StreamingQueryException, if <code>this</code> query has terminated with an exception. ``` `throws` should specify the correct class name from `StreamingQueryException,` to `StreamingQueryException` without backticks. (see [JDK-8007644](https://bugs.openjdk.java.net/browse/JDK-8007644)). - Fix `[[http..]]` to `<a href="http..."></a>`. ```diff - * [[https://blogs.oracle.com/java-platform-group/entry/diagnosing_tls_ssl_and_https Oracle - * blog page]]. + * <a href="https://blogs.oracle.com/java-platform-group/entry/diagnosing_tls_ssl_and_https"> + * Oracle blog page</a>. ``` `[[http...]]` link markdown in scaladoc is unrecognisable in javadoc. - It seems class can't have `return` annotation. So, two cases of this were removed. ``` [error] .../java/org/apache/spark/mllib/regression/IsotonicRegression.java:27: error: invalid use of return [error] * return New instance of IsotonicRegression. ``` - Fix < to `<` and > to `>` according to HTML rules. - Fix `</p>` complaint - Exclude unrecognisable in javadoc, `constructor`, `todo` and `groupname`. ## How was this patch tested? Manually tested by `jekyll build` with Java 7 and 8 ``` java version "1.7.0_80" Java(TM) SE Runtime Environment (build 1.7.0_80-b15) Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode) ``` ``` java version "1.8.0_45" Java(TM) SE Runtime Environment (build 1.8.0_45-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode) ``` Note: this does not yet make sbt unidoc suceed with Java 8 yet but it reduces the number of errors with Java 8. Author: hyukjinkwon <gurwls223@gmail.com> Closes #15999 from HyukjinKwon/SPARK-3359-errors. -
n.fraison authored
[SPARK-18119][SPARK-CORE] Namenode safemode check is only performed on one namenode which can stuck the startup of SparkHistory server ## What changes were proposed in this pull request? Instead of using the setSafeMode method that check the first namenode used the one which permitts to check only for active NNs ## How was this patch tested? manual tests Please review https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark before opening a pull request. This commit is contributed by Criteo SA under the Apache v2 licence. Author: n.fraison <n.fraison@criteo.com> Closes #15648 from ashangit/SPARK-18119.
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- Nov 23, 2016
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Reynold Xin authored
## What changes were proposed in this pull request? TaskMemoryManager has a memory leak detector that gets called at task completion callback and checks whether any memory has not been released. If they are not released by the time the callback is invoked, TaskMemoryManager releases them. The current error message says something like the following: ``` WARN [Executor task launch worker-0] org.apache.spark.memory.TaskMemoryManager - leak 16.3 MB memory from org.apache.spark.unsafe.map.BytesToBytesMap33fb6a15 In practice, there are multiple reasons why these can be triggered in the normal code path (e.g. limit, or task failures), and the fact that these messages are log means the "leak" is fixed by TaskMemoryManager. ``` To not confuse users, this patch downgrade the message from warning to debug level, and avoids using the word "leak" since it is not actually a leak. ## How was this patch tested? N/A - this is a simple logging improvement. Author: Reynold Xin <rxin@databricks.com> Closes #15989 from rxin/SPARK-18557.
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Eric Liang authored
## What changes were proposed in this pull request? This would help catch accidental O(n) calls to the hive client as in https://issues.apache.org/jira/browse/SPARK-18507 ## How was this patch tested? Checked that the test fails before https://issues.apache.org/jira/browse/SPARK-18507 was patched. cc cloud-fan Author: Eric Liang <ekl@databricks.com> Closes #15985 from ericl/spark-18545.
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- Nov 19, 2016
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Kazuaki Ishizaki authored
## What changes were proposed in this pull request? This PR avoids that a result of an expression is negative due to signed integer overflow (e.g. 0x10?????? * 8 < 0). This PR casts each operand to `long` before executing a calculation. Since the result is interpreted as long, the result of the expression is positive. ## How was this patch tested? Manually executed query82 of TPC-DS with 100TB Author: Kazuaki Ishizaki <ishizaki@jp.ibm.com> Closes #15907 from kiszk/SPARK-18458.
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Stavros Kontopoulos authored
Adds --conf option to set spark configuration properties in mesos dispacther. Properties provided with --conf take precedence over properties within the properties file. The reason for this PR is that for simple configuration or testing purposes we need to provide a property file (ideally a shared one for a cluster) even if we just provide a single property. Manually tested. Author: Stavros Kontopoulos <st.kontopoulos@gmail.com> Author: Stavros Kontopoulos <stavros.kontopoulos@lightbend.com> Closes #14650 from skonto/dipatcher_conf.
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Sean Owen authored
## What changes were proposed in this pull request? Avoid hard-coding spark.rpc.askTimeout to non-default in Client; fix doc about spark.rpc.askTimeout default ## How was this patch tested? Existing tests Author: Sean Owen <sowen@cloudera.com> Closes #15833 from srowen/SPARK-18353.
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hyukjinkwon authored
[SPARK-18445][BUILD][DOCS] Fix the markdown for `Note:`/`NOTE:`/`Note that`/`'''Note:'''` across Scala/Java API documentation ## What changes were proposed in this pull request? It seems in Scala/Java, - `Note:` - `NOTE:` - `Note that` - `'''Note:'''` - `note` This PR proposes to fix those to `note` to be consistent. **Before** - Scala  - Java  **After** - Scala  - Java  ## How was this patch tested? The notes were found via ```bash grep -r "NOTE: " . | \ # Note:|NOTE:|Note that|'''Note:''' grep -v "// NOTE: " | \ # starting with // does not appear in API documentation. grep -E '.scala|.java' | \ # java/scala files grep -v Suite | \ # exclude tests grep -v Test | \ # exclude tests grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation -e 'org.apache.spark.api.java.function' \ # note that this is a regular expression. So actual matches were mostly `org/apache/spark/api/java/functions ...` -e 'org.apache.spark.api.r' \ ... ``` ```bash grep -r "Note that " . | \ # Note:|NOTE:|Note that|'''Note:''' grep -v "// Note that " | \ # starting with // does not appear in API documentation. grep -E '.scala|.java' | \ # java/scala files grep -v Suite | \ # exclude tests grep -v Test | \ # exclude tests grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation -e 'org.apache.spark.api.java.function' \ -e 'org.apache.spark.api.r' \ ... ``` ```bash grep -r "Note: " . | \ # Note:|NOTE:|Note that|'''Note:''' grep -v "// Note: " | \ # starting with // does not appear in API documentation. grep -E '.scala|.java' | \ # java/scala files grep -v Suite | \ # exclude tests grep -v Test | \ # exclude tests grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation -e 'org.apache.spark.api.java.function' \ -e 'org.apache.spark.api.r' \ ... ``` ```bash grep -r "'''Note:'''" . | \ # Note:|NOTE:|Note that|'''Note:''' grep -v "// '''Note:''' " | \ # starting with // does not appear in API documentation. grep -E '.scala|.java' | \ # java/scala files grep -v Suite | \ # exclude tests grep -v Test | \ # exclude tests grep -e 'org.apache.spark.api.java' \ # packages appear in API documenation -e 'org.apache.spark.api.java.function' \ -e 'org.apache.spark.api.r' \ ... ``` And then fixed one by one comparing with API documentation/access modifiers. After that, manually tested via `jekyll build`. Author: hyukjinkwon <gurwls223@gmail.com> Closes #15889 from HyukjinKwon/SPARK-18437.
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- Nov 18, 2016
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hyukjinkwon authored
## What changes were proposed in this pull request? This PR fixes the test `wholeTextFiles` in `JavaAPISuite.java`. This is failed due to the different path format on Windows. For example, the path in `container` was ``` C:\projects\spark\target\tmp\1478967560189-0/part-00000 ``` whereas `new URI(res._1()).getPath()` was as below: ``` /C:/projects/spark/target/tmp/1478967560189-0/part-00000 ``` ## How was this patch tested? Tests in `JavaAPISuite.java`. Tested via AppVeyor. **Before** Build: https://ci.appveyor.com/project/spark-test/spark/build/63-JavaAPISuite-1 Diff: https://github.com/apache/spark/compare/master...spark-test:JavaAPISuite-1 ``` [info] Test org.apache.spark.JavaAPISuite.wholeTextFiles started [error] Test org.apache.spark.JavaAPISuite.wholeTextFiles failed: java.lang.AssertionError: expected:<spark is easy to use. [error] > but was:<null>, took 0.578 sec [error] at org.apache.spark.JavaAPISuite.wholeTextFiles(JavaAPISuite.java:1089) ... ``` **After** Build started: [CORE] `org.apache.spark.JavaAPISuite` [](https://ci.appveyor.com/project/spark-test/spark/branch/198DDA52-F201-4D2B-BE2F-244E0C1725B2) Diff: https://github.com/apache/spark/compare/master...spark-test:198DDA52-F201-4D2B-BE2F-244E0C1725B2 ``` [info] Test org.apache.spark.JavaAPISuite.wholeTextFiles started ... ``` Author: hyukjinkwon <gurwls223@gmail.com> Closes #15866 from HyukjinKwon/SPARK-18422.
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- Nov 17, 2016
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anabranch authored
## What changes were proposed in this pull request? I found the documentation for the sample method to be confusing, this adds more clarification across all languages. - [x] Scala - [x] Python - [x] R - [x] RDD Scala - [ ] RDD Python with SEED - [X] RDD Java - [x] RDD Java with SEED - [x] RDD Python ## How was this patch tested? NA Please review https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark before opening a pull request. Author: anabranch <wac.chambers@gmail.com> Author: Bill Chambers <bill@databricks.com> Closes #15815 from anabranch/SPARK-18365.
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- Nov 16, 2016
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Xianyang Liu authored
## What changes were proposed in this pull request? Small fix, fix the errors caused by lint check in Java - Clear unused objects and `UnusedImports`. - Add comments around the method `finalize` of `NioBufferedFileInputStream`to turn off checkstyle. - Cut the line which is longer than 100 characters into two lines. ## How was this patch tested? Travis CI. ``` $ build/mvn -T 4 -q -DskipTests -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install $ dev/lint-java ``` Before: ``` Checkstyle checks failed at following occurrences: [ERROR] src/main/java/org/apache/spark/network/util/TransportConf.java:[21,8] (imports) UnusedImports: Unused import - org.apache.commons.crypto.cipher.CryptoCipherFactory. [ERROR] src/test/java/org/apache/spark/network/sasl/SparkSaslSuite.java:[516,5] (modifier) RedundantModifier: Redundant 'public' modifier. [ERROR] src/main/java/org/apache/spark/io/NioBufferedFileInputStream.java:[133] (coding) NoFinalizer: Avoid using finalizer method. [ERROR] src/main/java/org/apache/spark/sql/catalyst/expressions/UnsafeMapData.java:[71] (sizes) LineLength: Line is longer than 100 characters (found 113). [ERROR] src/main/java/org/apache/spark/sql/catalyst/expressions/UnsafeArrayData.java:[112] (sizes) LineLength: Line is longer than 100 characters (found 110). [ERROR] src/test/java/org/apache/spark/sql/catalyst/expressions/HiveHasherSuite.java:[31,17] (modifier) ModifierOrder: 'static' modifier out of order with the JLS suggestions. [ERROR]src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionWithElasticNetExample.java:[64] (sizes) LineLength: Line is longer than 100 characters (found 103). [ERROR] src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java:[22,8] (imports) UnusedImports: Unused import - org.apache.spark.ml.linalg.Vectors. [ERROR] src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java:[51] (regexp) RegexpSingleline: No trailing whitespace allowed. ``` After: ``` $ build/mvn -T 4 -q -DskipTests -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install $ dev/lint-java Using `mvn` from path: /home/travis/build/ConeyLiu/spark/build/apache-maven-3.3.9/bin/mvn Checkstyle checks passed. ``` Author: Xianyang Liu <xyliu0530@icloud.com> Closes #15865 from ConeyLiu/master.
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- Nov 14, 2016
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WangTaoTheTonic authored
[SPARK-18396][HISTORYSERVER] Duration" column makes search result confused, maybe we should make it unsearchable ## What changes were proposed in this pull request? When we search data in History Server, it will check if any columns contains the search string. Duration is represented as long value in table, so if we search simple string like "003", "111", the duration containing "003", ‘111“ will be showed, which make not much sense to users. We cannot simply transfer the long value to meaning format like "1 h", "3.2 min" because they are also used for sorting. Better way to handle it is ban "Duration" columns from searching. ## How was this patch tested manually tests. Before("local-1478225166651" pass the filter because its duration in long value, which is "257244245" contains search string "244"):  After:  Author: WangTaoTheTonic <wangtao111@huawei.com> Closes #15838 from WangTaoTheTonic/duration. -
Sean Owen authored
## What changes were proposed in this pull request? Avoid reporting null/-1 file / line number in call sites if encountering StackTraceElement without this info ## How was this patch tested? Existing tests Author: Sean Owen <sowen@cloudera.com> Closes #15862 from srowen/SPARK-18382.
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- Nov 12, 2016
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Guoqiang Li authored
## What changes were proposed in this pull request? One of the important changes for 4.0.42.Final is "Support any FileRegion implementation when using epoll transport netty/netty#5825". In 4.0.42.Final, `MessageWithHeader` can work properly when `spark.[shuffle|rpc].io.mode` is set to epoll ## How was this patch tested? Existing tests Author: Guoqiang Li <witgo@qq.com> Closes #15830 from witgo/SPARK-18375_netty-4.0.42.
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- Nov 11, 2016
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Weiqing Yang authored
[SPARK-16759][CORE] Add a configuration property to pass caller contexts of upstream applications into Spark ## What changes were proposed in this pull request? Many applications take Spark as a computing engine and run on it. This PR adds a configuration property `spark.log.callerContext` that can be used by Spark's upstream applications (e.g. Oozie) to set up their caller contexts into Spark. In the end, Spark will combine its own caller context with the caller contexts of its upstream applications, and write them into Yarn RM log and HDFS audit log. The audit log has a config to truncate the caller contexts passed in (default 128). The caller contexts will be sent over rpc, so it should be concise. The call context written into HDFS log and Yarn log consists of two parts: the information `A` specified by Spark itself and the value `B` of `spark.log.callerContext` property. Currently `A` typically takes 64 to 74 characters, so `B` can have up to 50 characters (mentioned in the doc `running-on-yarn.md`) ## How was this patch tested? Manual tests. I have run some Spark applications with `spark.log.callerContext` configuration in Yarn client/cluster mode, and verified that the caller contexts were written into Yarn RM log and HDFS audit log correctly. The ways to configure `spark.log.callerContext` property: - In spark-defaults.conf: ``` spark.log.callerContext infoSpecifiedByUpstreamApp ``` - In app's source code: ``` val spark = SparkSession .builder .appName("SparkKMeans") .config("spark.log.callerContext", "infoSpecifiedByUpstreamApp") .getOrCreate() ``` When running on Spark Yarn cluster mode, the driver is unable to pass 'spark.log.callerContext' to Yarn client and AM since Yarn client and AM have already started before the driver performs `.config("spark.log.callerContext", "infoSpecifiedByUpstreamApp")`. The following example shows the command line used to submit a SparkKMeans application and the corresponding records in Yarn RM log and HDFS audit log. Command: ``` ./bin/spark-submit --verbose --executor-cores 3 --num-executors 1 --master yarn --deploy-mode client --class org.apache.spark.examples.SparkKMeans examples/target/original-spark-examples_2.11-2.1.0-SNAPSHOT.jar hdfs://localhost:9000/lr_big.txt 2 5 ``` Yarn RM log: <img width="1440" alt="screen shot 2016-10-19 at 9 12 03 pm" src="https://cloud.githubusercontent.com/assets/8546874/19547050/7d2f278c-9649-11e6-9df8-8d5ff12609f0.png"> HDFS audit log: <img width="1400" alt="screen shot 2016-10-19 at 10 18 14 pm" src="https://cloud.githubusercontent.com/assets/8546874/19547102/096060ae-964a-11e6-981a-cb28efd5a058.png"> Author: Weiqing Yang <yangweiqing001@gmail.com> Closes #15563 from weiqingy/SPARK-16759. -
Vinayak authored
## What changes were proposed in this pull request? History Server UI's application listing to display information on currently under process event logs so a user knows that pending this processing an application may not list on the UI. When there are no event logs under process, the application list page has a "Last Updated" date-time at the top indicating the date-time of the last _completed_ scan of the event logs. The value is displayed to the user in his/her local time zone. ## How was this patch tested? All unit tests pass. Particularly all the suites under org.apache.spark.deploy.history.\* were run to test changes. - Very first startup - Pending logs - no logs processed yet: <img width="1280" alt="screen shot 2016-10-24 at 3 07 04 pm" src="https://cloud.githubusercontent.com/assets/12079825/19640981/b8d2a96a-99fc-11e6-9b1f-2d736fe90e48.png"> - Very first startup - Pending logs - some logs processed: <img width="1280" alt="screen shot 2016-10-24 at 3 18 42 pm" src="https://cloud.githubusercontent.com/assets/12079825/19641087/3f8e3bae-99fd-11e6-9ef1-e0e70d71d8ef.png"> - Last updated - No currently pending logs: <img width="1280" alt="screen shot 2016-10-17 at 8 34 37 pm" src="https://cloud.githubusercontent.com/assets/12079825/19443100/4d13946c-94a9-11e6-8ee2-c442729bb206.png"> - Last updated - With some currently pending logs: <img width="1280" alt="screen shot 2016-10-24 at 3 09 31 pm" src="https://cloud.githubusercontent.com/assets/12079825/19640903/7323ba3a-99fc-11e6-8359-6a45753dbb28.png"> - No applications found and No currently pending logs: <img width="1280" alt="screen shot 2016-10-24 at 3 24 26 pm" src="https://cloud.githubusercontent.com/assets/12079825/19641364/03a2cb04-99fe-11e6-87d6-d09587fc6201.png"> Author: Vinayak <vijoshi5@in.ibm.com> Closes #15410 from vijoshi/SAAS-608_master.
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- Nov 10, 2016
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Eric Liang authored
## What changes were proposed in this pull request? As of current 2.1, INSERT OVERWRITE with dynamic partitions against a Datasource table will overwrite the entire table instead of only the partitions matching the static keys, as in Hive. It also doesn't respect custom partition locations. This PR adds support for all these operations to Datasource tables managed by the Hive metastore. It is implemented as follows - During planning time, the full set of partitions affected by an INSERT or OVERWRITE command is read from the Hive metastore. - The planner identifies any partitions with custom locations and includes this in the write task metadata. - FileFormatWriter tasks refer to this custom locations map when determining where to write for dynamic partition output. - When the write job finishes, the set of written partitions is compared against the initial set of matched partitions, and the Hive metastore is updated to reflect the newly added / removed partitions. It was necessary to introduce a method for staging files with absolute output paths to `FileCommitProtocol`. These files are not handled by the Hadoop output committer but are moved to their final locations when the job commits. The overwrite behavior of legacy Datasource tables is also changed: no longer will the entire table be overwritten if a partial partition spec is present. cc cloud-fan yhuai ## How was this patch tested? Unit tests, existing tests. Author: Eric Liang <ekl@databricks.com> Author: Wenchen Fan <wenchen@databricks.com> Closes #15814 from ericl/sc-5027.
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wm624@hotmail.com authored
## What changes were proposed in this pull request? This is a follow-up work of #15618. Close file source; For any newly created streaming context outside the withContext, explicitly close the context. ## How was this patch tested? Existing unit tests. Author: wm624@hotmail.com <wm624@hotmail.com> Closes #15818 from wangmiao1981/rtest.
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- Nov 09, 2016
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jiangxingbo authored
## What changes were proposed in this pull request? We should call `setConf` if `OutputFormat` is `Configurable`, this should be done before we create `OutputCommitter` and `RecordWriter`. This is follow up of #15769, see discussion [here](https://github.com/apache/spark/pull/15769/files#r87064229) ## How was this patch tested? Add test of this case in `PairRDDFunctionsSuite`. Author: jiangxingbo <jiangxb1987@gmail.com> Closes #15823 from jiangxb1987/config-format.
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Vinayak authored
## What changes were proposed in this pull request? Application links generated on the history server UI no longer (regression from 1.6) contain the configured spark.ui.proxyBase in the links. To address this, made the uiRoot available globally to all javascripts for Web UI. Updated the mustache template (historypage-template.html) to include the uiroot for rendering links to the applications. The existing test was not sufficient to verify the scenario where ajax call is used to populate the application listing template, so added a new selenium test case to cover this scenario. ## How was this patch tested? Existing tests and a new unit test. No visual changes to the UI. Author: Vinayak <vijoshi5@in.ibm.com> Closes #15742 from vijoshi/SPARK-16808_master.
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- Nov 08, 2016
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Shixiong Zhu authored
## What changes were proposed in this pull request? "StandaloneSchedulerBackend.dead" is called in a RPC thread, so it should not call "SparkContext.stop" in the same thread. "SparkContext.stop" will block until all RPC threads exit, if it's called inside a RPC thread, it will be dead-lock. This PR add a thread local flag inside RPC threads. `SparkContext.stop` uses it to decide if launching a new thread to stop the SparkContext. ## How was this patch tested? Jenkins Author: Shixiong Zhu <shixiong@databricks.com> Closes #15775 from zsxwing/SPARK-18280.
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jiangxingbo authored
## What changes were proposed in this pull request? This PR port RDD API to use commit protocol, the changes made here: 1. Add new internal helper class that saves an RDD using a Hadoop OutputFormat named `SparkNewHadoopWriter`, it's similar with `SparkHadoopWriter` but uses commit protocol. This class supports the newer `mapreduce` API, instead of the old `mapred` API which is supported by `SparkHadoopWriter`; 2. Rewrite `PairRDDFunctions.saveAsNewAPIHadoopDataset` function, so it uses commit protocol now. ## How was this patch tested? Exsiting test cases. Author: jiangxingbo <jiangxb1987@gmail.com> Closes #15769 from jiangxb1987/rdd-commit.
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- Nov 07, 2016
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fidato authored
## What changes were proposed in this pull request? This Pull request comprises of the critical bug SPARK-16575 changes. This change rectifies the issue with BinaryFileRDD partition calculations as upon creating an RDD with sc.binaryFiles, the resulting RDD always just consisted of two partitions only. ## How was this patch tested? The original issue ie. getNumPartitions on binary Files RDD (always having two partitions) was first replicated and then tested upon the changes. Also the unit tests have been checked and passed. This contribution is my original work and I licence the work to the project under the project's open source license srowen hvanhovell rxin vanzin skyluc kmader zsxwing datafarmer Please have a look . Author: fidato <fidato.july13@gmail.com> Closes #15327 from fidato13/SPARK-16575.
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Josh Rosen authored
## What changes were proposed in this pull request? When profiling heap dumps from the HistoryServer and live Spark web UIs, I found a large amount of memory being wasted on duplicated objects and strings. This patch's changes remove most of this duplication, resulting in over 40% memory savings for some benchmarks. - **Task metrics** (6441f0624dfcda9c7193a64bfb416a145b5aabdf): previously, every `TaskUIData` object would have its own instances of `InputMetricsUIData`, `OutputMetricsUIData`, `ShuffleReadMetrics`, and `ShuffleWriteMetrics`, but for many tasks these metrics are irrelevant because they're all zero. This patch changes how we construct these metrics in order to re-use a single immutable "empty" value for the cases where these metrics are empty. - **TaskInfo.accumulables** (ade86db901127bf13c0e0bdc3f09c933a093bb76): Previously, every `TaskInfo` object had its own empty `ListBuffer` for holding updates from named accumulators. Tasks which didn't use named accumulators still paid for the cost of allocating and storing this empty buffer. To avoid this overhead, I changed the `val` with a mutable buffer into a `var` which holds an immutable Scala list, allowing tasks which do not have named accumulator updates to share the same singleton `Nil` object. - **String.intern() in JSONProtocol** (7e05630e9a78c455db8c8c499f0590c864624e05): in the HistoryServer, executor hostnames and ids are deserialized from JSON, leading to massive duplication of these string objects. By calling `String.intern()` on the deserialized values we can remove all of this duplication. Since Spark now requires Java 7+ we don't have to worry about string interning exhausting the permgen (see http://java-performance.info/string-intern-in-java-6-7-8/). ## How was this patch tested? I ran ``` sc.parallelize(1 to 100000, 100000).count() ``` in `spark-shell` with event logging enabled, then loaded that event log in the HistoryServer, performed a full GC, and took a heap dump. According to YourKit, the changes in this patch reduced memory consumption by roughly 28 megabytes (or 770k Java objects):  Here's a table illustrating the drop in objects due to deduplication (the drop is <100k for some objects because some events were dropped from the listener bus; this is a separate, existing bug that I'll address separately after CPU-profiling):  Author: Josh Rosen <joshrosen@databricks.com> Closes #15743 from JoshRosen/spark-ui-memory-usage.
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Hyukjin Kwon authored
## What changes were proposed in this pull request? Close `FileStreams`, `ZipFiles` etc to release the resources after using. Not closing the resources will cause IO Exception to be raised while deleting temp files. ## How was this patch tested? Existing tests Author: U-FAREAST\tl <tl@microsoft.com> Author: hyukjinkwon <gurwls223@gmail.com> Author: Tao LI <tl@microsoft.com> Closes #15618 from HyukjinKwon/SPARK-14914-1.
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- Nov 05, 2016
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Susan X. Huynh authored
## What changes were proposed in this pull request? Enabled SparkR with Mesos client mode and cluster mode. Just a few changes were required to get this working on Mesos: (1) removed the SparkR on Mesos error checks and (2) do not require "--class" to be specified for R apps. The logic to check spark.mesos.executor.home was already in there. sun-rui ## How was this patch tested? 1. SparkSubmitSuite 2. On local mesos cluster (on laptop): ran SparkR shell, spark-submit client mode, and spark-submit cluster mode, with the "examples/src/main/R/dataframe.R" example application. 3. On multi-node mesos cluster: ran SparkR shell, spark-submit client mode, and spark-submit cluster mode, with the "examples/src/main/R/dataframe.R" example application. I tested with the following --conf values set: spark.mesos.executor.docker.image and spark.mesos.executor.home This contribution is my original work and I license the work to the project under the project's open source license. Author: Susan X. Huynh <xhuynh@mesosphere.com> Closes #15700 from susanxhuynh/susan-r-branch.
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Weiqing Yang authored
## What changes were proposed in this pull request? Add comments. ## How was this patch tested? Build passed. Author: Weiqing Yang <yangweiqing001@gmail.com> Closes #15776 from weiqingy/SPARK-17710.
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- Nov 04, 2016
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Josh Rosen authored
## What changes were proposed in this pull request? This patch significantly improves the performance of event log replay in the HistoryServer via two simple changes: - **Don't use `extractOpt`**: it turns out that `json4s`'s `extractOpt` method uses exceptions for control flow, causing huge performance bottlenecks due to the overhead of initializing exceptions. To avoid this overhead, we can simply use our own` Utils.jsonOption` method. This patch replaces all uses of `extractOpt` with `Utils.jsonOption` and adds a style checker rule to ban the use of the slow `extractOpt` method. - **Don't call `Utils.getFormattedClassName` for every event**: the old code called` Utils.getFormattedClassName` dozens of times per replayed event in order to match up class names in events with SparkListener event names. By simply storing the results of these calls in constants rather than recomputing them, we're able to eliminate a huge performance hotspot by removing thousands of expensive `Class.getSimpleName` calls. ## How was this patch tested? Tested by profiling the replay of a long event log using YourKit. For an event log containing 1000+ jobs, each of which had thousands of tasks, the changes in this patch cut the replay time in half:  Prior to this patch's changes, the two slowest methods in log replay were internal exceptions thrown by `Json4S` and calls to `Class.getSimpleName()`:  After this patch, these hotspots are completely eliminated. Author: Josh Rosen <joshrosen@databricks.com> Closes #15756 from JoshRosen/speed-up-jsonprotocol.
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Adam Roberts authored
## What changes were proposed in this pull request? This improvement works by using the fastest comparison test first and we observed a 1% throughput performance improvement on PageRank (HiBench large profile) with this change. We used tprof and before the change in AppendOnlyMap.changeValue (where the optimisation occurs) this method was being used for 8053 profiling ticks representing 0.72% of the overall application time. After this change we observed this method only occurring for 2786 ticks and for 0.25% of the overall time. ## How was this patch tested? Existing unit tests and for performance we used HiBench large, profiling with tprof and IBM Healthcenter. Author: Adam Roberts <aroberts@uk.ibm.com> Closes #15714 from a-roberts/patch-9.
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Dongjoon Hyun authored
## What changes were proposed in this pull request? This is a follow-up PR of #15741 in order to keep `nextPowerOf2` consistent. **Before** ``` nextPowerOf2(0) => 2 nextPowerOf2(1) => 1 nextPowerOf2(2) => 2 nextPowerOf2(3) => 4 nextPowerOf2(4) => 4 nextPowerOf2(5) => 8 ``` **After** ``` nextPowerOf2(0) => 1 nextPowerOf2(1) => 1 nextPowerOf2(2) => 2 nextPowerOf2(3) => 4 nextPowerOf2(4) => 4 nextPowerOf2(5) => 8 ``` ## How was this patch tested? N/A Author: Dongjoon Hyun <dongjoon@apache.org> Closes #15754 from dongjoon-hyun/SPARK-18200-2.
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- Nov 03, 2016
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Sean Owen authored
[SPARK-18138][DOCS] Document that Java 7, Python 2.6, Scala 2.10, Hadoop < 2.6 are deprecated in Spark 2.1.0 ## What changes were proposed in this pull request? Document that Java 7, Python 2.6, Scala 2.10, Hadoop < 2.6 are deprecated in Spark 2.1.0. This does not actually implement any of the change in SPARK-18138, just peppers the documentation with notices about it. ## How was this patch tested? Doc build Author: Sean Owen <sowen@cloudera.com> Closes #15733 from srowen/SPARK-18138.
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Reynold Xin authored
## What changes were proposed in this pull request? This patch moves the new commit protocol API from sql/core to core module, so we can use it in the future in the RDD API. As part of this patch, I also moved the speficiation of the random uuid for the write path out of the commit protocol, and instead pass in a job id. ## How was this patch tested? N/A Author: Reynold Xin <rxin@databricks.com> Closes #15731 from rxin/SPARK-18219.
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Dongjoon Hyun authored
## What changes were proposed in this pull request? [SPARK-18200](https://issues.apache.org/jira/browse/SPARK-18200) reports Apache Spark 2.x raises `java.lang.IllegalArgumentException: requirement failed: Invalid initial capacity` while running `triangleCount`. The root cause is that `VertexSet`, a type alias of `OpenHashSet`, does not allow zero as a initial size. This PR loosens the restriction to allow zero. ## How was this patch tested? Pass the Jenkins test with a new test case in `OpenHashSetSuite`. Author: Dongjoon Hyun <dongjoon@apache.org> Closes #15741 from dongjoon-hyun/SPARK-18200.
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