Fix computation of root-sigma-inverse in multivariate Gaussian; add a test and fix related Python mixture model test.
Supersedes https://github.com/apache/spark/pull/9293
Author: Sean Owen <sowen@cloudera.com>
Closes#9309 from srowen/SPARK-11302.2.
In some cases, we can broadcast the smaller relation in cartesian join, which improve the performance significantly.
Author: Cheng Hao <hao.cheng@intel.com>
Closes#8652 from chenghao-intel/cartesian.
Commit af3bc59d1f introduced new
functionality so that if an executor dies for a reason that's not
caused by one of the tasks running on the executor (e.g., due to
pre-emption), Spark doesn't count the failure towards the maximum
number of failures for the task. That commit introduced some vague
naming that this commit attempts to fix; in particular:
(1) The variable "isNormalExit", which was used to refer to cases where
the executor died for a reason unrelated to the tasks running on the
machine, has been renamed (and reversed) to "exitCausedByApp". The problem
with the existing name is that it's not clear (at least to me!) what it
means for an exit to be "normal"; the new name is intended to make the
purpose of this variable more clear.
(2) The variable "shouldEventuallyFailJob" has been renamed to
"countTowardsTaskFailures". This variable is used to determine whether
a task's failure should be counted towards the maximum number of failures
allowed for a task before the associated Stage is aborted. The problem
with the existing name is that it can be confused with implying that
the task's failure should immediately cause the stage to fail because it
is somehow fatal (this is the case for a fetch failure, for example: if
a task fails because of a fetch failure, there's no point in retrying,
and the whole stage should be failed).
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#9164 from kayousterhout/SPARK-11178.
… ReceiverTracker and ReceiverSchedulingPolicy to use it
This PR includes the following changes:
1. Add a new preferred location format, `executor_<host>_<executorID>` (e.g., "executor_localhost_2"), to support specifying the executor locations for RDD.
2. Use the new preferred location format in `ReceiverTracker` to optimize the starting time of Receivers when there are multiple executors in a host.
The goal of this PR is to enable the streaming scheduler to place receivers (which run as tasks) in specific executors. Basically, I want to have more control on the placement of the receivers such that they are evenly distributed among the executors. We tried to do this without changing the core scheduling logic. But it does not allow specifying particular executor as preferred location, only at the host level. So if there are two executors in the same host, and I want two receivers to run on them (one on each executor), I cannot specify that. Current code only specifies the host as preference, which may end up launching both receivers on the same executor. We try to work around it but restarting a receiver when it does not launch in the desired executor and hope that next time it will be started in the right one. But that cause lots of restarts, and delays in correctly launching the receiver.
So this change, would allow the streaming scheduler to specify the exact executor as the preferred location. Also this is not exposed to the user, only the streaming scheduler uses this.
Author: zsxwing <zsxwing@gmail.com>
Closes#9181 from zsxwing/executor-location.
Currently the Write Ahead Log in Spark Streaming flushes data as writes need to be made. S3 does not support flushing of data, data is written once the stream is actually closed.
In case of failure, the data for the last minute (default rolling interval) will not be properly written. Therefore we need a flag to close the stream after the write, so that we achieve read after write consistency.
cc tdas zsxwing
Author: Burak Yavuz <brkyvz@gmail.com>
Closes#9285 from brkyvz/caw-wal.
implement {RandomForest, GBT, TreeEnsemble, TreeClassifier, TreeRegressor}Params for Python API
in pyspark/ml/{classification, regression}.py
Author: vectorijk <jiangkai@gmail.com>
Closes#9233 from vectorijk/spark-10024.
This PR adds a new operation `joinWith` to a `Dataset`, which returns a `Tuple` for each pair where a given `condition` evaluates to true.
```scala
case class ClassData(a: String, b: Int)
val ds1 = Seq(ClassData("a", 1), ClassData("b", 2)).toDS()
val ds2 = Seq(("a", 1), ("b", 2)).toDS()
> ds1.joinWith(ds2, $"_1" === $"a").collect()
res0: Array((ClassData("a", 1), ("a", 1)), (ClassData("b", 2), ("b", 2)))
```
This operation is similar to the relation `join` function with one important difference in the result schema. Since `joinWith` preserves objects present on either side of the join, the result schema is similarly nested into a tuple under the column names `_1` and `_2`.
This type of join can be useful both for preserving type-safety with the original object types as well as working with relational data where either side of the join has column names in common.
## Required Changes to Encoders
In the process of working on this patch, several deficiencies to the way that we were handling encoders were discovered. Specifically, it turned out to be very difficult to `rebind` the non-expression based encoders to extract the nested objects from the results of joins (and also typed selects that return tuples).
As a result the following changes were made.
- `ClassEncoder` has been renamed to `ExpressionEncoder` and has been improved to also handle primitive types. Additionally, it is now possible to take arbitrary expression encoders and rewrite them into a single encoder that returns a tuple.
- All internal operations on `Dataset`s now require an `ExpressionEncoder`. If the users tries to pass a non-`ExpressionEncoder` in, an error will be thrown. We can relax this requirement in the future by constructing a wrapper class that uses expressions to project the row to the expected schema, shielding the users code from the required remapping. This will give us a nice balance where we don't force user encoders to understand attribute references and binding, but still allow our native encoder to leverage runtime code generation to construct specific encoders for a given schema that avoid an extra remapping step.
- Additionally, the semantics for different types of objects are now better defined. As stated in the `ExpressionEncoder` scaladoc:
- Classes will have their sub fields extracted by name using `UnresolvedAttribute` expressions
and `UnresolvedExtractValue` expressions.
- Tuples will have their subfields extracted by position using `BoundReference` expressions.
- Primitives will have their values extracted from the first ordinal with a schema that defaults
to the name `value`.
- Finally, the binding lifecycle for `Encoders` has now been unified across the codebase. Encoders are now `resolved` to the appropriate schema in the constructor of `Dataset`. This process replaces an unresolved expressions with concrete `AttributeReference` expressions. Binding then happens on demand, when an encoder is going to be used to construct an object. This closely mirrors the lifecycle for standard expressions when executing normal SQL or `DataFrame` queries.
Author: Michael Armbrust <michael@databricks.com>
Closes#9300 from marmbrus/datasets-tuples.
This PR adds addition and multiplication to PySpark's `BlockMatrix` class via `add` and `multiply` functions.
Author: Mike Dusenberry <mwdusenb@us.ibm.com>
Closes#9139 from dusenberrymw/SPARK-6488_Add_Addition_and_Multiplication_to_PySpark_BlockMatrix.
This commit fixes a bug where, in Standalone mode, if a task fails and crashes the JVM, the
failure is considered a "normal failure" (meaning it's considered unrelated to the task), so
the failure isn't counted against the task's maximum number of failures:
af3bc59d1f (diff-a755f3d892ff2506a7aa7db52022d77cL138).
As a result, if a task fails in a way that results in it crashing the JVM, it will continuously be
re-launched, resulting in a hang. This commit fixes that problem.
This bug was introduced by #8007; andrewor14 mccheah vanzin can you take a look at this?
This error is hard to trigger because we handle executor losses through 2 code paths (the second is via Akka, where Akka notices that the executor endpoint is disconnected). In my setup, the Akka code path completes first, and doesn't have this bug, so things work fine (see my recent email to the dev list about this). If I manually disable the Akka code path, I can see the hang (and this commit fixes the issue).
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#9273 from kayousterhout/SPARK-11306.
When sampling and then filtering DataFrame, the SQL Optimizer will push down filter into sample and produce wrong result. This is due to the sampler is calculated based on the original scope rather than the scope after filtering.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#9294 from yanboliang/spark-11303.
I'm new to spark. I was trying out the sort_array function then hit this exception. I looked into the spark source code. I found the root cause is that sort_array does not check for an array of NULLs. It's not meaningful to sort an array of entirely NULLs anyway.
I'm adding a check on the input array type to SortArray. If the array consists of NULLs entirely, there is no need to sort such array. I have also added a test case for this.
Please help to review my fix. Thanks!
Author: Jia Li <jiali@us.ibm.com>
Closes#9247 from jliwork/SPARK-11277.
When use Kafka DirectStream API to create checkpoint and restore saved checkpoint when restart,
ClassNotFound exception would occur.
The reason for this error is that ObjectInputStreamWithLoader extends the ObjectInputStream class and override its resolveClass method. But Instead of Using Class.forName(desc,false,loader), Spark uses loader.loadClass(desc) to instance the class, which do not works with array class.
For example:
Class.forName("[Lorg.apache.spark.streaming.kafka.OffsetRange.",false,loader) works well while loader.loadClass("[Lorg.apache.spark.streaming.kafka.OffsetRange") would throw an class not found exception.
details of the difference between Class.forName and loader.loadClass can be found here.
http://bugs.java.com/view_bug.do?bug_id=6446627
Author: maxwell <maxwellzdm@gmail.com>
Author: DEMING ZHU <deming.zhu@linecorp.com>
Closes#8955 from maxwellzdm/master.
jerryshao tdas
I know this is kind of minor, and I know you all are busy, but this brings this class in line with the `OffsetRange` class, and makes tests a little more concise.
Instead of doing something like:
```
assert topic_and_partition_instance._topic == "foo"
assert topic_and_partition_instance._partition == 0
```
You can do something like:
```
assert topic_and_partition_instance == TopicAndPartition("foo", 0)
```
Before:
```
>>> from pyspark.streaming.kafka import TopicAndPartition
>>> TopicAndPartition("foo", 0) == TopicAndPartition("foo", 0)
False
```
After:
```
>>> from pyspark.streaming.kafka import TopicAndPartition
>>> TopicAndPartition("foo", 0) == TopicAndPartition("foo", 0)
True
```
I couldn't find any tests - am I missing something?
Author: Nick Evans <me@nicolasevans.org>
Closes#9236 from manygrams/topic_and_partition_equality.
The SizeEstimator keeps a cache of ClassInfos but this cache uses Class objects as keys.
Which results in strong references to the Class objects. If these classes are dynamically created
this prevents the corresponding ClassLoader from being GCed. Leading to PermGen exhaustion.
We use a Map with WeakKeys to prevent this issue.
Author: Sem Mulder <sem.mulder@site2mobile.com>
Closes#9244 from SemMulder/fix-sizeestimator-classunloading.
Add columnSimilarities to IndexedRowMatrix by delegating to functionality already in RowMatrix.
With a test.
Author: Reza Zadeh <reza@databricks.com>
Closes#8792 from rezazadeh/colsims.
Remove "Experimental" from .mllib code that has been around since 1.4.0 or earlier
Author: Sean Owen <sowen@cloudera.com>
Closes#9169 from srowen/SPARK-11184.
Duplicated the since decorator from pyspark.sql into pyspark (also tweaked to handle functions without docstrings).
Added since to methods + "versionadded::" to classes (derived from the git file history in pyspark).
Author: noelsmith <mail@noelsmith.com>
Closes#8627 from noel-smith/SPARK-10271-since-mllib-clustering.
mengxr https://issues.apache.org/jira/browse/SPARK-11289
I make some changes in ML feature extractors. I.e. TF-IDF, Word2Vec, and CountVectorizer. I add new example code in spark/examples, hope it is the right place to add those examples.
Author: Xusen Yin <yinxusen@gmail.com>
Closes#9266 from yinxusen/SPARK-11289.
Currently, when a schema is inferred from a JSON file using sqlContext.read.json, the primitive object types are inferred as string, long, boolean, etc.
However, if the inferred type is too specific (JSON obviously does not enforce types itself), this can cause issues with merging dataframe schemas.
This pull request adds the option "primitivesAsString" to the JSON DataFrameReader which when true (defaults to false if not set) will infer all primitives as strings.
Below is an example usage of this new functionality.
```
val jsonDf = sqlContext.read.option("primitivesAsString", "true").json(sampleJsonFile)
scala> jsonDf.printSchema()
root
|-- bigInteger: string (nullable = true)
|-- boolean: string (nullable = true)
|-- double: string (nullable = true)
|-- integer: string (nullable = true)
|-- long: string (nullable = true)
|-- null: string (nullable = true)
|-- string: string (nullable = true)
```
Author: Stephen De Gennaro <stepheng@realitymine.com>
Closes#9249 from stephend-realitymine/stephend-primitives.
AWS SDK 1.9.40 is the latest 1.9.x release. KCL 1.5.1 is the latest release that using AWS SDK 1.9.x. The main goal is to have Kinesis consumer be able to read messages generated from Kinesis Producer Library (KPL). The API should be compatible with old versions.
tdas brkyvz
Author: Xiangrui Meng <meng@databricks.com>
Closes#9153 from mengxr/SPARK-11127.
This patch refactors the MemoryManager class structure. After #9000, Spark had the following classes:
- MemoryManager
- StaticMemoryManager
- ExecutorMemoryManager
- TaskMemoryManager
- ShuffleMemoryManager
This is fairly confusing. To simplify things, this patch consolidates several of these classes:
- ShuffleMemoryManager and ExecutorMemoryManager were merged into MemoryManager.
- TaskMemoryManager is moved into Spark Core.
**Key changes and tasks**:
- [x] Merge ExecutorMemoryManager into MemoryManager.
- [x] Move pooling logic into Allocator.
- [x] Move TaskMemoryManager from `spark-unsafe` to `spark-core`.
- [x] Refactor the existing Tungsten TaskMemoryManager interactions so Tungsten code use only this and not both this and ShuffleMemoryManager.
- [x] Refactor non-Tungsten code to use the TaskMemoryManager instead of ShuffleMemoryManager.
- [x] Merge ShuffleMemoryManager into MemoryManager.
- [x] Move code
- [x] ~~Simplify 1/n calculation.~~ **Will defer to followup, since this needs more work.**
- [x] Port ShuffleMemoryManagerSuite tests.
- [x] Move classes from `unsafe` package to `memory` package.
- [ ] Figure out how to handle the hacky use of the memory managers in HashedRelation's broadcast variable construction.
- [x] Test porting and cleanup: several tests relied on mock functionality (such as `TestShuffleMemoryManager.markAsOutOfMemory`) which has been changed or broken during the memory manager consolidation
- [x] AbstractBytesToBytesMapSuite
- [x] UnsafeExternalSorterSuite
- [x] UnsafeFixedWidthAggregationMapSuite
- [x] UnsafeKVExternalSorterSuite
**Compatiblity notes**:
- This patch introduces breaking changes in `ExternalAppendOnlyMap`, which is marked as `DevloperAPI` (likely for legacy reasons): this class now cannot be used outside of a task.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#9127 from JoshRosen/SPARK-10984.
This PR allows users to map a Kinesis `Record` to a generic `T` when creating a Kinesis stream. This is particularly useful, if you would like to do extra work with Kinesis metadata such as sequence number, and partition key.
TODO:
- [x] add tests
Author: Burak Yavuz <brkyvz@gmail.com>
Closes#8954 from brkyvz/kinesis-handler.
Executing deploy.client.TestClient fails due to bad class name for TestExecutor in ApplicationDescription.
Author: Bryan Cutler <bjcutler@us.ibm.com>
Closes#9255 from BryanCutler/fix-TestClient-classname-SPARK-11287.
marmbrus rxin I believe these typecasts are not required in the presence of explicit return types.
Author: Alexander Slesarenko <avslesarenko@gmail.com>
Closes#9262 from aslesarenko/remove-typecasts.
The SQL programming guide's link to the DataFrame functions reference points to the wrong location; this patch fixes that.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#9269 from JoshRosen/SPARK-11299.
Two typos squashed.
BTW Let me know how to proceed with other typos if I ran across any. I don't feel well to leave them aside as much as sending pull requests with such tiny changes. Guide me.
Author: Jacek Laskowski <jacek.laskowski@deepsense.io>
Closes#9250 from jaceklaskowski/typos-hunting.
Temporarily remove GREP_OPTIONS if set in bin/spark-class.
Some GREP_OPTIONS will modify the output of the grep commands that are looking for the assembly jars.
For example, if the -n option is specified, the grep output will look like:
5:spark-assembly-1.5.1-hadoop2.4.0.jar
This will not match the regular expressions, and so the jar files will not be found. We could improve the regular expression to handle this case and trim off extra characters, but it is difficult to know which options may or may not be set. Unsetting GREP_OPTIONS within the script handles all the cases and gives the desired output.
Author: Jeffrey Naisbitt <jnaisbitt@familysearch.org>
Closes#9231 from naisbitt/unset-GREP_OPTIONS.
…ut building with -Phive-thriftserver and SPARK_PREPEND_CLASSES is set
This is the exception after this patch. Please help review.
```
java.lang.NoClassDefFoundError: org/apache/hadoop/hive/cli/CliDriver
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:412)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:270)
at org.apache.spark.util.Utils$.classForName(Utils.scala:173)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:647)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hive.cli.CliDriver
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 21 more
Failed to load hive class.
You need to build Spark with -Phive and -Phive-thriftserver.
```
Author: Jeff Zhang <zjffdu@apache.org>
Closes#9134 from zjffdu/SPARK-11125.
Add examples for read.df, write.df; fix grouping for read.df, loadDF; fix formatting and text truncation for write.df, saveAsTable.
Several text issues:
- text collapsed into a single paragraph
- text truncated at 2 places, eg. "overwrite: Existing data is expected to be overwritten by the contents of error:"
shivaram
Author: felixcheung <felixcheung_m@hotmail.com>
Closes#9261 from felixcheung/rdocreadwritedf.
This adds API for reading and writing text files, similar to SparkContext.textFile and RDD.saveAsTextFile.
```
SQLContext.read.text("/path/to/something.txt")
DataFrame.write.text("/path/to/write.txt")
```
Using the new Dataset API, this also supports
```
val ds: Dataset[String] = SQLContext.read.text("/path/to/something.txt").as[String]
```
Author: Reynold Xin <rxin@databricks.com>
Closes#9240 from rxin/SPARK-11274.
This is a PR for Parquet-based model import/export.
* Added save/load for ChiSqSelectorModel
* Updated the test suite ChiSqSelectorSuite
Author: Jayant Shekar <jayant@user-MBPMBA-3.local>
Closes#6785 from jayantshekhar/SPARK-6723.
A POC code for making example code in user guide testable.
mengxr We still need to talk about the labels in code.
Author: Xusen Yin <yinxusen@gmail.com>
Closes#9109 from yinxusen/SPARK-10382.
For nested StructType, the underline buffer could be used for others before, we should zero out the padding bytes for those primitive types that have less than 8 bytes.
cc cloud-fan
Author: Davies Liu <davies@databricks.com>
Closes#9217 from davies/zero_out.
