Author: Sun Rui <rui.sun@intel.com>
Closes#5613 from sun-rui/SPARK-6852 and squashes the following commits:
abaf02e [Sun Rui] Change the type of default numPartitions from integer to numeric in generics.R.
29d67c1 [Sun Rui] [SPARK-6852][SPARKR] Accept numeric as numPartitions in SparkR.
Author: Sun Rui <rui.sun@intel.com>
Closes#5628 from sun-rui/SPARK-7033 and squashes the following commits:
046bc9e [Sun Rui] Clean split usage in tests.
d531c86 [Sun Rui] [SPARK-7033][SPARKR] Clean usage of split. Use partition instead where applicable.
See [SPARK-6528](https://issues.apache.org/jira/browse/SPARK-6528). Add IDF transformer in ML package.
Author: Xusen Yin <yinxusen@gmail.com>
Closes#5266 from yinxusen/SPARK-6528 and squashes the following commits:
741db31 [Xusen Yin] get param from new paramMap
d169967 [Xusen Yin] add final to param and IDF class
c9c3759 [Xusen Yin] simplify test suite
5867c09 [Xusen Yin] refine IDF transformer with new interfaces
7727cae [Xusen Yin] Merge branch 'master' into SPARK-6528
4338a37 [Xusen Yin] Merge branch 'master' into SPARK-6528
aef2cdf [Xusen Yin] add doc and group for param
5760b49 [Xusen Yin] fix code style
2add691 [Xusen Yin] fix code style and test
03fbecb [Xusen Yin] remove duplicated code
2aa4be0 [Xusen Yin] clean test suite
4802c67 [Xusen Yin] add IDF transformer and test suite
yinxusen
Author: Xiangrui Meng <meng@databricks.com>
Closes#5681 from mengxr/SPARK-7115 and squashes the following commits:
9ac27cd [Xiangrui Meng] skip the very first 1 in poly expansion
Also took the chance to improve documentation for various types.
Author: Reynold Xin <rxin@databricks.com>
Closes#5675 from rxin/data-type-matching-expr and squashes the following commits:
0f31856 [Reynold Xin] One more function documentation.
27c1973 [Reynold Xin] Added more documentation.
336a36d [Reynold Xin] [SQL] Fixed expression data type matching.
fix typo
Author: Ken Geis <geis.ken@gmail.com>
Closes#5674 from kgeis/patch-1 and squashes the following commits:
5ae67de [Ken Geis] Update sql-programming-guide.md
This pr tries to provide a way to let python users workaround https://issues.apache.org/jira/browse/SPARK-6231.
Author: Yin Huai <yhuai@databricks.com>
Closes#5634 from yhuai/pythonDFAlias and squashes the following commits:
8465acd [Yin Huai] Add an alias to a Python DF.
When specifying non-spark properties (i.e. names don't start with spark.) in the command line and config file, spark-submit and spark-shell behave differently, causing confusion to users.
Here is the summary-
* spark-submit
* --conf k=v => silently ignored
* spark-defaults.conf => applied
* spark-shell
* --conf k=v => show a warning message and ignored
* spark-defaults.conf => show a warning message and ignored
I assume that ignoring non-spark properties is intentional. If so, it should always be ignored with a warning message in all cases.
Author: Cheolsoo Park <cheolsoop@netflix.com>
Closes#5617 from piaozhexiu/SPARK-7037 and squashes the following commits:
8957950 [Cheolsoo Park] Add IgnoreNonSparkProperties method
fedd01c [Cheolsoo Park] Ignore non-spark properties with a warning message in all cases
Author: Sun Rui <rui.sun@intel.com>
Closes#5655 from sun-rui/SPARK-6818 and squashes the following commits:
7c66570 [Sun Rui] [SPARK-6818][SPARKR] Support column deletion in SparkR DataFrame API.
It was over 1000 lines of code, making it harder to find all the types. Only moved code around, and didn't change any.
Author: Reynold Xin <rxin@databricks.com>
Closes#5670 from rxin/break-types and squashes the following commits:
8c59023 [Reynold Xin] Check in missing files.
dcd5193 [Reynold Xin] [SQL] Break dataTypes.scala into multiple files.
jkbradley
Author: Xiangrui Meng <meng@databricks.com>
Closes#5649 from mengxr/SPARK-7070 and squashes the following commits:
c66023c [Xiangrui Meng] setBeta should call setTopicConcentration
Author: Tijo Thomas <tijoparacka@gmail.com>
Closes#5656 from tijoparacka/FIX_PATHISSUE_CHANGE_VERSION_SCRIPT and squashes the following commits:
ab4f4b1 [Tijo Thomas] removed whitespace
24478c9 [Tijo Thomas] modified to provide the spark base dir while searching for pom and also while changing the vesrion no
7b8e10b [Tijo Thomas] Modified for providing the base directories while finding the list of pom files and also while changing the version no
https://issues.apache.org/jira/browse/SPARK-6879
Use `applications` to replace `FileStatus`, and check if the app is completed before clean it up.
If an exception was throwed, add it to `applications` to wait for the next loop.
Author: WangTaoTheTonic <wangtao111@huawei.com>
Closes#5491 from WangTaoTheTonic/SPARK-6879 and squashes the following commits:
4a533eb [WangTaoTheTonic] treat ACE specially
cb45105 [WangTaoTheTonic] rebase
d4d5251 [WangTaoTheTonic] per Marcelo's comments
d7455d8 [WangTaoTheTonic] slightly change when delete file
b0abca5 [WangTaoTheTonic] use global var to store apps to clean
94adfe1 [WangTaoTheTonic] leave expired apps alone to be deleted
9872a9d [WangTaoTheTonic] use the right path
fdef4d6 [WangTaoTheTonic] check if app is completed before clean it up
Author: wizz <wizz@wizz-dev01.kawasaki.flab.fujitsu.com>
Closes#5658 from kuromatsu-nobuyuki/SPARK-7085 and squashes the following commits:
6ec2d21 [wizz] Fix miniBatchFraction parameter in train method called with 4 arguments
The web UI's "task deserialization time" metric is slightly misleading because it does not capture the time taken to deserialize the broadcasted RDD.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#5635 from JoshRosen/SPARK-7058 and squashes the following commits:
ed90f75 [Josh Rosen] Update UI tooltip
a3743b4 [Josh Rosen] Update comments.
4f52910 [Josh Rosen] Roll back whitespace change
e9cf9f4 [Josh Rosen] Remove unused variable
9f32e55 [Josh Rosen] Expose executorDeserializeTime on Task instead of pushing runtime calculation into Task.
21f5b47 [Josh Rosen] Don't double-count the broadcast deserialization time in task runtime
1752f0e [Josh Rosen] [SPARK-7058] Incorporate RDD deserialization time in task deserialization time metric
Author: Vinod K C <vinod.kc@huawei.com>
Closes#5633 from vinodkc/use_correct_classloader_driverload and squashes the following commits:
73c5380 [Vinod K C] Use correct ClassLoader for JDBC Driver
Currently if you want to create a StreamingContext from checkpoint information, the system will create a new SparkContext. This prevent StreamingContext to be recreated from checkpoints in managed environments where SparkContext is precreated.
The solution in this PR: Introduce the following methods on StreamingContext
1. `new StreamingContext(checkpointDirectory, sparkContext)`
Recreate StreamingContext from checkpoint using the provided SparkContext
2. `StreamingContext.getOrCreate(checkpointDirectory, sparkContext, createFunction: SparkContext => StreamingContext)`
If checkpoint file exists, then recreate StreamingContext using the provided SparkContext (that is, call 1.), else create StreamingContext using the provided createFunction
TODO: the corresponding Java and Python API has to be added as well.
Author: Tathagata Das <tathagata.das1565@gmail.com>
Closes#5428 from tdas/SPARK-6752 and squashes the following commits:
94db63c [Tathagata Das] Fix long line.
524f519 [Tathagata Das] Many changes based on PR comments.
eabd092 [Tathagata Das] Added Function0, Java API and unit tests for StreamingContext.getOrCreate
36a7823 [Tathagata Das] Minor changes.
204814e [Tathagata Das] Added StreamingContext.getOrCreate with existing SparkContext
Author: Cheng Hao <hao.cheng@intel.com>
Closes#5625 from chenghao-intel/transform and squashes the following commits:
5ec1dd2 [Cheng Hao] fix the deadlock issue in ScriptTransform
Author: Prabeesh K <prabeesh.k@namshi.com>
Closes#5653 from prabeesh/fix and squashes the following commits:
9d7a9f5 [Prabeesh K] fixed scala string interpolation error
Author: Prashant Sharma <prashant.s@imaginea.com>
Closes#5652 from ScrapCodes/hf/compilation-fix-scala-2.11 and squashes the following commits:
819ff06 [Prashant Sharma] [HOTFIX] Fix compilation for scala 2.11.
Also renamed JvmType to InternalType.
Author: Reynold Xin <rxin@databricks.com>
Closes#5651 from rxin/native-to-atomic-type and squashes the following commits:
cbd4028 [Reynold Xin] [SPARK-7069][SQL] Rename NativeType -> AtomicType.
Author: Reynold Xin <rxin@databricks.com>
Closes#5646 from rxin/remove-primitive-type and squashes the following commits:
01b673d [Reynold Xin] [SPARK-7068][SQL] Remove PrimitiveType
Author: Reynold Xin <rxin@databricks.com>
Closes#5648 from rxin/vectorAssembler-boolean and squashes the following commits:
1bf3d40 [Reynold Xin] [MLlib] Add support for BooleanType to VectorAssembler.
Added in #5475. Pointed as broken in #5639.
/cc marmbrus
Author: Liang-Chi Hsieh <viirya@gmail.com>
Closes#5640 from viirya/fix_cached_test and squashes the following commits:
c0cf69a [Liang-Chi Hsieh] Fix broken cached test.
This is a code cleanup.
The BlockResult class originally contained an InputMetrics object so that InputMetrics could
directly be used as the InputMetrics for the whole task. Now we copy the fields out of here, and
the presence of this object is confusing because it's only a partial input metrics (it doesn't
include the records read). Because this object is no longer useful (and is confusing), it should
be removed.
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#5627 from kayousterhout/SPARK-7046 and squashes the following commits:
bf64bbe [Kay Ousterhout] Import fix
a08ca19 [Kay Ousterhout] [SPARK-7046] Remove InputMetrics from BlockResult
Author: Reynold Xin <rxin@databricks.com>
Closes#5642 from rxin/mllib-native-type and squashes the following commits:
e23af5b [Reynold Xin] Remove StringType
7cbb205 [Reynold Xin] [SPARK-7066][MLlib] VectorAssembler should use NumericType and StringType, not NativeType.
Author: Reynold Xin <rxin@databricks.com>
Closes#5644 from rxin/mllib-nullable and squashes the following commits:
a727e5b [Reynold Xin] [MLlib] UnaryTransformer nullability should not depend on primitive types.
This pr convert java.sql.Date type into Int for JDBCRDD.
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#5590 from adrian-wang/datebug and squashes the following commits:
f897b81 [Daoyuan Wang] add a test case
3c9184c [Daoyuan Wang] fix date type convertion in jdbcrdd
Make PySpark ```FPGrowthModel.freqItemsets``` consistent with Java/Scala API like ```MatrixFactorizationModel.userFeatures```
It return a RDD with each tuple is composed of an array and a long value.
I think it's difficult to implement namedtuples to wrap the output because items of freqItemsets can be any type with arbitrary length which is tedious to impelement corresponding SerDe function.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#5614 from yanboliang/spark-6827 and squashes the following commits:
da8c404 [Yanbo Liang] use namedtuple
5532e78 [Yanbo Liang] Wrap FPGrowthModel.freqItemsets and make it consistent with Java API
Author: Reynold Xin <rxin@databricks.com>
Closes#5638 from rxin/joinUsing and squashes the following commits:
13e9cc9 [Reynold Xin] Code review + Python.
b1bd914 [Reynold Xin] [SPARK-7059][SQL] Create a DataFrame join API to facilitate equijoin and self join.
I was looking at the code gen code and got confused by a few of use cases of apply, in particular apply on objects. So I went ahead and changed a few of them. Hopefully slightly more clear with a proper verb.
Author: Reynold Xin <rxin@databricks.com>
Closes#5624 from rxin/apply-rename and squashes the following commits:
ee45034 [Reynold Xin] [SQL] Rename some apply functions.
As per rxin 's suggestion in https://github.com/apache/spark/pull/5392/files#r28757176
What's more, there is a race condition in the global shared `daemonThreadFactoryBuilder`. `daemonThreadFactoryBuilder` may be modified by multiple threads. This PR removed the global `daemonThreadFactoryBuilder` and created a new `ThreadFactoryBuilder` every time.
Author: zsxwing <zsxwing@gmail.com>
Closes#5631 from zsxwing/thread-utils and squashes the following commits:
9fe5b0e [zsxwing] Add ThreadUtils and move thread methods from Utils to ThreadUtils
This does a few clean-ups. With this PR, all spark.ml tree components have ```private[ml]``` constructors.
CC: mengxr
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#5567 from jkbradley/dt-api-dt2 and squashes the following commits:
2263b5b [Joseph K. Bradley] Added note about tree example issue.
bb9f610 [Joseph K. Bradley] Small cleanups after original tree API PR
1. Clearly specifies the contract/interactions for users of this class.
2. Minor fix in one doc to avoid ambiguity.
Author: Patrick Wendell <patrick@databricks.com>
Closes#5620 from pwendell/cleanup and squashes the following commits:
8d8f44f [Patrick Wendell] [Minor] Comment improvements in ExternalSorter.
Added docs for rpc configurations and also fixed two places that should have been fixed in #5595.
Author: zsxwing <zsxwing@gmail.com>
Closes#5607 from zsxwing/SPARK-6490-docs and squashes the following commits:
25a6736 [zsxwing] Increase the default timeout to 120s
6e37c30 [zsxwing] Update docs
5577540 [zsxwing] Use spark.network.timeout as the default timeout if it presents
4f07174 [zsxwing] Fix unit tests
1c2cf26 [zsxwing] Add docs for rpc configurations
Cleans up the pull request title in the merge script to follow conventions outlined in the wiki under Contributing Code.
https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark#ContributingtoSpark-ContributingCode
[MODULE] SPARK-XXXX: Description
Author: texasmichelle <texasmichelle@gmail.com>
Closes#5149 from texasmichelle/master and squashes the following commits:
9b6b0a7 [texasmichelle] resolved variable scope issue
7d5fa20 [texasmichelle] only prompt if title has been modified
8c195bb [texasmichelle] removed erroneous line
4f1ed46 [texasmichelle] Deque removal, logic simplifications, & prompt user to pick a title (orig or modified)
df73f6a [texasmichelle] reworked regex's to enforce brackets around JIRA ref
43b5aed [texasmichelle] Merge remote-tracking branch 'apache/master'
25229c6 [texasmichelle] Merge remote-tracking branch 'apache/master'
aa20a6e [texasmichelle] Move code into main() and add doctest for new text parsing method
48520ba [texasmichelle] SPARK-1684: Corrected import statement
042099d [texasmichelle] SPARK-1684 Merge script should standardize SPARK-XXX prefix
8f4a7d1 [texasmichelle] SPARK-1684 Merge script should standardize SPARK-XXX prefix
This PR try to speed up some python tests:
```
tests.py 144s -> 103s -41s
mllib/classification.py 24s -> 17s -7s
mllib/regression.py 27s -> 15s -12s
mllib/tree.py 27s -> 13s -14s
mllib/tests.py 64s -> 31s -33s
streaming/tests.py 185s -> 84s -101s
```
Considering python3, the total saving will be 558s (almost 10 minutes) (core, and streaming run three times, mllib runs twice).
During testing, it will show used time for each test file:
```
Run core tests ...
Running test: pyspark/rdd.py ... ok (22s)
Running test: pyspark/context.py ... ok (16s)
Running test: pyspark/conf.py ... ok (4s)
Running test: pyspark/broadcast.py ... ok (4s)
Running test: pyspark/accumulators.py ... ok (4s)
Running test: pyspark/serializers.py ... ok (6s)
Running test: pyspark/profiler.py ... ok (5s)
Running test: pyspark/shuffle.py ... ok (1s)
Running test: pyspark/tests.py ... ok (103s) 144s
```
Author: Reynold Xin <rxin@databricks.com>
Author: Xiangrui Meng <meng@databricks.com>
Closes#5605 from rxin/python-tests-speed and squashes the following commits:
d08542d [Reynold Xin] Merge pull request #14 from mengxr/SPARK-6953
89321ee [Xiangrui Meng] fix seed in tests
3ad2387 [Reynold Xin] Merge pull request #5427 from davies/python_tests
This change adds some new utility code to handle shutdown hooks in
Spark. The main goal is to take advantage of Hadoop 2.x's API for
shutdown hooks, which allows Spark to register a hook that will
run before the one that cleans up HDFS clients, and thus avoids
some races that would cause exceptions to show up and other issues
such as failure to properly close event logs.
Unfortunately, Hadoop 1.x does not have such APIs, so in that case
correctness is still left to chance.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#5560 from vanzin/SPARK-6014 and squashes the following commits:
edfafb1 [Marcelo Vanzin] Better scaladoc.
fcaeedd [Marcelo Vanzin] Merge branch 'master' into SPARK-6014
e7039dc [Marcelo Vanzin] [SPARK-6014] [core] Revamp Spark shutdown hooks, fix shutdown races.
Starting with version 0.21.0, Apache Mesos is very noisy if the filter parameter refuse_seconds is set to an invalid value like `-1`.
I have seen systems with millions of log lines like
```
W0420 18:00:48.773059 32352 hierarchical_allocator_process.hpp:589] Using the default value of 'refuse_seconds' to create the refused resources filter because the input value is negative
```
in the Mesos master INFO and WARNING log files.
Therefore the CoarseMesosSchedulerBackend should set the default value for refuse seconds (i.e. 5 seconds) directly.
This is no problem for the fine-grained MesosSchedulerBackend, as it uses the value 1 second for this parameter.
Author: mweindel <m.weindel@usu-software.de>
Closes#5597 from MartinWeindel/master and squashes the following commits:
2f99ffd [mweindel] Avoid warning message about invalid refuse_seconds value in Mesos >=0.21.
add missing comma and space
Author: Alain <aihe@usc.edu>
Closes#5621 from AiHe/tree-node-issue and squashes the following commits:
159a7bb [Alain] [Minor][MLLIB] Fix a minor formatting bug in toString methods in Node.scala
(cherry picked from commit 4508f01890a723f80d631424ff8eda166a13a727)
Signed-off-by: Xiangrui Meng <meng@databricks.com>
SchemaRDD works with ALS.train in 1.2, so we should continue support DataFrames for compatibility. coderxiang
Author: Xiangrui Meng <meng@databricks.com>
Closes#5619 from mengxr/SPARK-7036 and squashes the following commits:
dfcaf5a [Xiangrui Meng] ALS.train should support DataFrames in PySpark
1. Use blas calls to find the dot product between two vectors.
2. Prevent re-computing the L2 norm of the given vector for each word in model.
Author: MechCoder <manojkumarsivaraj334@gmail.com>
Closes#5467 from MechCoder/spark-6065 and squashes the following commits:
dd0b0b2 [MechCoder] Preallocate wordVectors
ffc9240 [MechCoder] Minor
6b74c81 [MechCoder] Switch back to native blas calls
da1642d [MechCoder] Explicit types and indexing
64575b0 [MechCoder] Save indexedmap and a wordvecmat instead of matrix
fbe0108 [MechCoder] Made the following changes 1. Calculate norms during initialization. 2. Use Blas calls from linalg.blas
1350cf3 [MechCoder] [SPARK-6065] Optimize word2vec.findSynonynms using blas calls
The default java options make the call to GenerateMIMAIgnore take
forever to run since it's gc'ing all the time. Improve things by
setting the perm gen size / max heap size to larger values.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#5615 from vanzin/gen-mima-fix and squashes the following commits:
f44e921 [Marcelo Vanzin] [minor] [build] Set java options when generating mima ignores.
This patch modifies several shuffle-related code paths to share and re-use SerializerInstances instead of creating new ones. Some serializers, such as KryoSerializer or SqlSerializer, can be fairly expensive to create or may consume moderate amounts of memory, so it's probably best to avoid unnecessary serializer creation in hot code paths.
The key change in this patch is modifying `getDiskWriter()` / `DiskBlockObjectWriter` to accept `SerializerInstance`s instead of `Serializer`s (which are factories for instances). This allows the disk writer's creator to decide whether the serializer instance can be shared or re-used.
The rest of the patch modifies several write and read paths to use shared serializers. One big win is in `ShuffleBlockFetcherIterator`, where we used to create a new serializer per received block. Similarly, the shuffle write path used to create a new serializer per file even though in many cases only a single thread would be writing to a file at a time.
I made a small serializer reuse optimization in CoarseGrainedExecutorBackend as well, since it seemed like a small and obvious improvement.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#5606 from JoshRosen/SPARK-3386 and squashes the following commits:
f661ce7 [Josh Rosen] Remove thread local; add comment instead
64f8398 [Josh Rosen] Use ThreadLocal for serializer instance in CoarseGrainedExecutorBackend
aeb680e [Josh Rosen] [SPARK-3386] Reuse SerializerInstance in shuffle code paths
