Note that the usage of `breezeSquaredDistance` in
`org.apache.spark.mllib.util.MLUtils.fastSquaredDistance`
is in the critical path, and `breezeSquaredDistance` is slow.
We should replace it with our own implementation.
Here is the benchmark against mnist8m dataset.
Before
DenseVector: 70.04secs
SparseVector: 59.05secs
With this PR
DenseVector: 30.58secs
SparseVector: 21.14secs
Author: DB Tsai <dbtsai@alpinenow.com>
Closes#3565 from dbtsai/kmean and squashes the following commits:
08bc068 [DB Tsai] restyle
de24662 [DB Tsai] address feedback
b185a77 [DB Tsai] cleanup
4554ddd [DB Tsai] first commit
Renamed StreamingKMeans to StreamingKMeansExample to avoid warning about name conflict with StreamingKMeans class.
Added import to DecisionTreeRunner to eliminate warning.
CC: mengxr
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#3568 from jkbradley/ml-compilation-warnings and squashes the following commits:
64d6bc4 [Joseph K. Bradley] Updated DecisionTreeRunner.scala and StreamingKMeans.scala to eliminate compilation warnings, including renaming StreamingKMeans to StreamingKMeansExample.
As #3262 wasn't merged to branch 1.2, the `since` value of `deprecated` should be '1.3.0'.
Author: zsxwing <zsxwing@gmail.com>
Closes#3573 from zsxwing/SPARK-4397-version and squashes the following commits:
1daa03c [zsxwing] Change the 'since' value to '1.3.0'
The related JIRA is https://issues.apache.org/jira/browse/SPARK-4672
The f closure of `PartitionsRDD(ZippedPartitionsRDD2)` contains a `$outer` that references EdgeRDD/VertexRDD, which causes task's serialization chain become very long in iterative GraphX applications. As a result, StackOverflow error will occur. If we set "f = null" in `clearDependencies()`, checkpoint() can cut off the long serialization chain. More details and explanation can be found in the JIRA.
Author: JerryLead <JerryLead@163.com>
Author: Lijie Xu <csxulijie@gmail.com>
Closes#3545 from JerryLead/my_core and squashes the following commits:
f7faea5 [JerryLead] checkpoint() should clear the f to avoid StackOverflow error
c0169da [JerryLead] Merge branch 'master' of https://github.com/apache/spark
52799e3 [Lijie Xu] Merge pull request #1 from apache/master
The related JIRA is https://issues.apache.org/jira/browse/SPARK-4672
In a nutshell, if `val partitionsRDD` in EdgeRDDImpl and VertexRDDImpl are non-transient, the serialization chain can become very long in iterative algorithms and finally lead to the StackOverflow error. More details and explanation can be found in the JIRA.
Author: JerryLead <JerryLead@163.com>
Author: Lijie Xu <csxulijie@gmail.com>
Closes#3544 from JerryLead/my_graphX and squashes the following commits:
628f33c [JerryLead] set PartitionsRDD to be transient in EdgeRDDImpl and VertexRDDImpl
c0169da [JerryLead] Merge branch 'master' of https://github.com/apache/spark
52799e3 [Lijie Xu] Merge pull request #1 from apache/master
The related JIRA is https://issues.apache.org/jira/browse/SPARK-4672
Iterative GraphX applications always have long lineage, while checkpoint() on EdgeRDD and VertexRDD themselves cannot shorten the lineage. In contrast, if we perform checkpoint() on their ParitionsRDD, the long lineage can be cut off. Moreover, the existing operations such as cache() in this code is performed on the PartitionsRDD, so checkpoint() should do the same way. More details and explanation can be found in the JIRA.
Author: JerryLead <JerryLead@163.com>
Author: Lijie Xu <csxulijie@gmail.com>
Closes#3549 from JerryLead/my_graphX_checkpoint and squashes the following commits:
d1aa8d8 [JerryLead] Perform checkpoint() on PartitionsRDD not VertexRDD and EdgeRDD themselves
ff08ed4 [JerryLead] Merge branch 'master' of https://github.com/apache/spark
c0169da [JerryLead] Merge branch 'master' of https://github.com/apache/spark
52799e3 [Lijie Xu] Merge pull request #1 from apache/master
Using ```executeCollect``` to collect the result, because executeCollect is a custom implementation of collect in spark sql which better than rdd's collect
Author: wangfei <wangfei1@huawei.com>
Closes#3547 from scwf/executeCollect and squashes the following commits:
a5ab68e [wangfei] Revert "adding debug info"
a60d680 [wangfei] fix test failure
0db7ce8 [wangfei] adding debug info
184c594 [wangfei] using executeCollect instead collect
We should use `~` instead of `-` for bitwise NOT.
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#3528 from adrian-wang/symbol and squashes the following commits:
affd4ad [Daoyuan Wang] fix code gen test case
56efb79 [Daoyuan Wang] ensure bitwise NOT over byte and short persist data type
f55fbae [Daoyuan Wang] wrong symbol for bitwise not
SELECT max(1/0) FROM src
would return a very large number, which is obviously not right.
For hive-0.12, hive would return `Infinity` for 1/0, while for hive-0.13.1, it is `NULL` for 1/0.
I think it is better to keep our behavior with newer Hive version.
This PR ensures that when the divider is 0, the result of expression should be NULL, same with hive-0.13.1
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#3443 from adrian-wang/div and squashes the following commits:
2e98677 [Daoyuan Wang] fix code gen for divide 0
85c28ba [Daoyuan Wang] temp
36236a5 [Daoyuan Wang] add test cases
6f5716f [Daoyuan Wang] fix comments
cee92bd [Daoyuan Wang] avoid evaluation 2 times
22ecd9a [Daoyuan Wang] fix style
cf28c58 [Daoyuan Wang] divide fix
2dfe50f [Daoyuan Wang] return null when divider is 0 of Double type
val jsc = new org.apache.spark.api.java.JavaSparkContext(sc)
val jhc = new org.apache.spark.sql.hive.api.java.JavaHiveContext(jsc)
val nrdd = jhc.hql("select null from spark_test.for_test")
println(nrdd.schema)
Then the error is thrown as follows:
scala.MatchError: NullType (of class org.apache.spark.sql.catalyst.types.NullType$)
at org.apache.spark.sql.types.util.DataTypeConversions$.asJavaDataType(DataTypeConversions.scala:43)
Author: YanTangZhai <hakeemzhai@tencent.com>
Author: yantangzhai <tyz0303@163.com>
Author: Michael Armbrust <michael@databricks.com>
Closes#3538 from YanTangZhai/MatchNullType and squashes the following commits:
e052dff [yantangzhai] [SPARK-4676] [SQL] JavaSchemaRDD.schema may throw NullType MatchError if sql has null
4b4bb34 [yantangzhai] [SPARK-4676] [SQL] JavaSchemaRDD.schema may throw NullType MatchError if sql has null
896c7b7 [yantangzhai] fix NullType MatchError in JavaSchemaRDD when sql has null
6e643f8 [YanTangZhai] Merge pull request #11 from apache/master
e249846 [YanTangZhai] Merge pull request #10 from apache/master
d26d982 [YanTangZhai] Merge pull request #9 from apache/master
76d4027 [YanTangZhai] Merge pull request #8 from apache/master
03b62b0 [YanTangZhai] Merge pull request #7 from apache/master
8a00106 [YanTangZhai] Merge pull request #6 from apache/master
cbcba66 [YanTangZhai] Merge pull request #3 from apache/master
cdef539 [YanTangZhai] Merge pull request #1 from apache/master
Author: baishuo <vc_java@hotmail.com>
Closes#3526 from baishuo/master-trycatch and squashes the following commits:
d446e14 [baishuo] correct the code style
b36bf96 [baishuo] correct the code style
ae0e447 [baishuo] add finally to avoid resource leak
Spark SQL has embeded sqrt and abs but DSL doesn't support those functions.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#3401 from sarutak/dsl-missing-operator and squashes the following commits:
07700cf [Kousuke Saruta] Modified Literal(null, NullType) to Literal(null) in DslQuerySuite
8f366f8 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into dsl-missing-operator
1b88e2e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into dsl-missing-operator
0396f89 [Kousuke Saruta] Added sqrt and abs to Spark SQL DSL
A very small nit update.
Author: Reynold Xin <rxin@databricks.com>
Closes#3552 from rxin/license-header and squashes the following commits:
df8d1a4 [Reynold Xin] Indent license header properly for interfaces.scala.
The link points to the old scala programming guide; it should point to the submitting applications page.
This should be backported to 1.1.2 (it's been broken as of 1.0).
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#3542 from kayousterhout/SPARK-4686 and squashes the following commits:
a8fc43b [Kay Ousterhout] [SPARK-4686] Link to allowed master URLs is broken
This PR cleans up `import SparkContext._` in core for SPARK-4397(#3262) to prove it really works well.
Author: zsxwing <zsxwing@gmail.com>
Closes#3530 from zsxwing/SPARK-4397-cleanup and squashes the following commits:
04e2273 [zsxwing] Cleanup 'import SparkContext._' in core
The vector norm in breeze is implemented by `activeIterator` which is known to be very slow.
In this PR, an efficient vector norm is implemented, and with this API, `Normalizer` and
`k-means` have big performance improvement.
Here is the benchmark against mnist8m dataset.
a) `Normalizer`
Before
DenseVector: 68.25secs
SparseVector: 17.01secs
With this PR
DenseVector: 12.71secs
SparseVector: 2.73secs
b) `k-means`
Before
DenseVector: 83.46secs
SparseVector: 61.60secs
With this PR
DenseVector: 70.04secs
SparseVector: 59.05secs
Author: DB Tsai <dbtsai@alpinenow.com>
Closes#3462 from dbtsai/norm and squashes the following commits:
63c7165 [DB Tsai] typo
0c3637f [DB Tsai] add import org.apache.spark.SparkContext._ back
6fa616c [DB Tsai] address feedback
9b7cb56 [DB Tsai] move norm to static method
0b632e6 [DB Tsai] kmeans
dbed124 [DB Tsai] style
c1a877c [DB Tsai] first commit
This commit exists to close the following pull requests on Github:
Closes#1612 (close requested by 'marmbrus')
Closes#2723 (close requested by 'marmbrus')
Closes#1737 (close requested by 'marmbrus')
Closes#2252 (close requested by 'marmbrus')
Closes#2029 (close requested by 'marmbrus')
Closes#2386 (close requested by 'marmbrus')
Closes#2997 (close requested by 'marmbrus')
In addition, using `s.isEmpty` to eliminate the string comparison.
Author: zsxwing <zsxwing@gmail.com>
Closes#3132 from zsxwing/SPARK-4268 and squashes the following commits:
358e235 [zsxwing] Improvement of allCaseVersions
Support view definition like
CREATE VIEW view3(valoo)
TBLPROPERTIES ("fear" = "factor")
AS SELECT upper(value) FROM src WHERE key=86;
[valoo as the alias of upper(value)]. This is missing part of SPARK-4239, for a fully view support.
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#3396 from adrian-wang/viewcolumn and squashes the following commits:
4d001d0 [Daoyuan Wang] support view with column alias
Author: Daoyuan Wang <daoyuan.wang@intel.com>
Closes#3535 from adrian-wang/datedoc and squashes the following commits:
18ff1ed [Daoyuan Wang] [DOC] Date type
Author: ravipesala <ravindra.pesala@huawei.com>
Closes#3516 from ravipesala/ddl_doc and squashes the following commits:
d101fdf [ravipesala] Style issues fixed
d2238cd [ravipesala] Corrected documentation
Supporting multi column support in countDistinct function like count(distinct c1,c2..) in Spark SQL
Author: ravipesala <ravindra.pesala@huawei.com>
Author: Michael Armbrust <michael@databricks.com>
Closes#3511 from ravipesala/countdistinct and squashes the following commits:
cc4dbb1 [ravipesala] style
070e12a [ravipesala] Supporting multi column support in count(distinct c1,c2..) in Spark SQL
Remove hardcoding max and min values for types. Let BigDecimal do checking type compatibility.
Author: Liang-Chi Hsieh <viirya@gmail.com>
Closes#3208 from viirya/more_numericLit and squashes the following commits:
e9834b4 [Liang-Chi Hsieh] Remove byte and short types for number literal.
1bd1825 [Liang-Chi Hsieh] Fix Indentation and make the modification clearer.
cf1a997 [Liang-Chi Hsieh] Modified for comment to add a rule of analysis that adds a cast.
91fe489 [Liang-Chi Hsieh] add Byte and Short.
1bdc69d [Liang-Chi Hsieh] Let BigDecimal do checking type compatibility.
group tab is missing for scaladoc
Author: Jacky Li <jacky.likun@gmail.com>
Closes#3458 from jackylk/patch-7 and squashes the following commits:
0121a70 [Jacky Li] add @group tab in limit() and count()
Documents `spark.sql.parquet.filterPushdown`, explains why it's turned off by default and when it's safe to be turned on.
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Author: Cheng Lian <lian@databricks.com>
Closes#3440 from liancheng/parquet-filter-pushdown-doc and squashes the following commits:
2104311 [Cheng Lian] Documents spark.sql.parquet.filterPushdown
Author: zsxwing <zsxwing@gmail.com>
Closes#3521 from zsxwing/SPARK-4661 and squashes the following commits:
03cbe3f [zsxwing] Minor code and docs cleanup
If `spark.akka.frameSize` > 2047, it will overflow and become negative. Should have some assertion in `maxFrameSizeBytes` to warn people.
Author: zsxwing <zsxwing@gmail.com>
Closes#3527 from zsxwing/SPARK-4664 and squashes the following commits:
0089c7a [zsxwing] Throw an exception when spark.akka.frameSize > 2047
Simply, add data/ to distributions. This adds about 291KB (compressed) to the tarball, FYI.
Author: Sean Owen <sowen@cloudera.com>
Closes#3480 from srowen/SPARK-2192 and squashes the following commits:
47688f1 [Sean Owen] Add data/ to distributions
In .gitignore, there is an entry for spark-*-bin.tar.gz but considering make-distribution.sh, the name pattern should be spark-*-bin-*.tgz.
This change is really small so I don't open issue in JIRA. If it's needed, please let me know.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#3529 from sarutak/fix-wrong-tgz-pattern and squashes the following commits:
de3c70a [Kousuke Saruta] Fixed wrong file name pattern in .gitignore
This commit exists to close the following pull requests on Github:
Closes#2915 (close requested by 'JoshRosen')
Closes#3140 (close requested by 'JoshRosen')
Closes#3366 (close requested by 'JoshRosen')
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Author: Cheng Lian <lian@databricks.com>
Closes#3498 from liancheng/fix-sql-doc-typo and squashes the following commits:
865ecd7 [Cheng Lian] Fixes formatting typo in SQL programming guide
Grammatical error in Programming Guide document
Author: lewuathe <lewuathe@me.com>
Closes#3412 from Lewuathe/typo-programming-guide and squashes the following commits:
a3e2f00 [lewuathe] Typo in Programming Guide markdown
If using spark-sql in yarn-cluster mode, print an error infomation just as the spark shell in yarn-cluster mode.
Author: carlmartin <carlmartinmax@gmail.com>
Author: huangzhaowei <carlmartinmax@gmail.com>
Closes#3479 from SaintBacchus/sparkSqlShell and squashes the following commits:
35829a9 [carlmartin] improve the description of comment
e6c1eb7 [carlmartin] add a comment in bin/spark-sql to remind user who wants to change the class
f1c5c8d [carlmartin] Merge branch 'master' into sparkSqlShell
8e112c5 [huangzhaowei] singular form
ec957bc [carlmartin] Add the some error infomation if using spark-sql in yarn-cluster mode
7bcecc2 [carlmartin] Merge branch 'master' of https://github.com/apache/spark into codereview
4fad75a [carlmartin] Add the Error infomation using spark-sql in yarn-cluster mode
To build with Scala 2.11, we have to execute `change-version-to-2.11.sh` before Maven execute, otherwise inter-module dependencies are broken.
Author: Takuya UESHIN <ueshin@happy-camper.st>
Closes#3361 from ueshin/docs/building-spark_2.11 and squashes the following commits:
1d29126 [Takuya UESHIN] Add instruction to use change-version-to-2.11.sh in 'Building for Scala 2.11'.
This will fix SPARK-4507.
For pull requests that reference multiple JIRAs in their titles, it would be helpful if the PR merge script offered to close all of them.
Author: Takayuki Hasegawa <takayuki.hasegawa0311@gmail.com>
Closes#3428 from hase1031/SPARK-4507 and squashes the following commits:
bf6d64b [Takayuki Hasegawa] SPARK-4507: try to resolve issue when no JIRAs in title
401224c [Takayuki Hasegawa] SPARK-4507: moved codes as before
ce89021 [Takayuki Hasegawa] SPARK-4507: PR merge script should support closing multiple JIRA tickets
Added a ClassTag parameter to CompactBuffer. So CompactBuffer[T] can create primitive arrays for primitive types. It will reduce the memory usage for primitive types significantly and only pay minor performance lost.
Here is my test code:
```Scala
// Call org.apache.spark.util.SizeEstimator.estimate
def estimateSize(obj: AnyRef): Long = {
val c = Class.forName("org.apache.spark.util.SizeEstimator$")
val f = c.getField("MODULE$")
val o = f.get(c)
val m = c.getMethod("estimate", classOf[Object])
m.setAccessible(true)
m.invoke(o, obj).asInstanceOf[Long]
}
sc.parallelize(1 to 10000).groupBy(_ => 1).foreach {
case (k, v) =>
println(v.getClass() + " size: " + estimateSize(v))
}
```
Using the previous CompactBuffer outputed
```
class org.apache.spark.util.collection.CompactBuffer size: 313358
```
Using the new CompactBuffer outputed
```
class org.apache.spark.util.collection.CompactBuffer size: 65712
```
In this case, the new `CompactBuffer` only used 20% memory of the previous one. It's really helpful for `groupByKey` when using a primitive value.
Author: zsxwing <zsxwing@gmail.com>
Closes#3378 from zsxwing/SPARK-4505 and squashes the following commits:
4abdbba [zsxwing] Add a ClassTag parameter to reduce the memory usage of CompactBuffer[T] when T is a primitive type
In -launch-lib.bash, -Xdebug option is used for debugging. We should use -agentlib option for Java 6+.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#2904 from sarutak/SPARK-4057 and squashes the following commits:
39b5320 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-4057
26b4af8 [Kousuke Saruta] Improved java option for debugging
Admittedly a really small tweak.
Author: Stephen Haberman <stephen@exigencecorp.com>
Closes#3514 from stephenh/include-key-name-in-npe and squashes the following commits:
937740a [Stephen Haberman] Include the key name when failing on an invalid value.
This PR re-introduces [0e648bc](0e648bc2be) from PR #2339, which somehow never made it into the codebase.
Additionally, it removes a now-unnecessary linear backoff on the SSH checks since we are blocking on EC2 status checks before testing SSH.
Author: Nicholas Chammas <nicholas.chammas@gmail.com>
Closes#3195 from nchammas/remove-ec2-ssh-backoff and squashes the following commits:
efb29e1 [Nicholas Chammas] Revert "Remove linear backoff."
ef3ca99 [Nicholas Chammas] reuse conn
adb4eaa [Nicholas Chammas] Remove linear backoff.
55caa24 [Nicholas Chammas] Check EC2 status checks before SSH.
This commit exists to close the following pull requests on Github:
Closes#3451 (close requested by 'pwendell')
Closes#1310 (close requested by 'pwendell')
Closes#3207 (close requested by 'JoshRosen')
`File.exists()` and `File.mkdirs()` only throw `SecurityException` instead of `IOException`. Then, when an exception is thrown, `dir` should be reset too.
Author: Liang-Chi Hsieh <viirya@gmail.com>
Closes#3449 from viirya/fix_createtempdir and squashes the following commits:
36cacbd [Liang-Chi Hsieh] Use proper exception and reset variable.
This looks like a one-liner, so I took a shot at it. There can be no fixed default availability zone since the names are different per region. But the default behavior can be documented:
```
if opts.zone == "":
opts.zone = random.choice(conn.get_all_zones()).name
```
Author: Sean Owen <sowen@cloudera.com>
Closes#3454 from srowen/SPARK-1450 and squashes the following commits:
9193cf3 [Sean Owen] Document that --zone defaults to a single random zone
The security manager adds a lot of overhead to the runtime of the
app, and causes a severe performance regression. Even stubbing out
all unneeded methods (all except checkExit()) does not help.
So, instead, penalize users who do an explicit System.exit() by leaving
them in "undefined behavior" territory: if they do that, the Yarn
backend won't be able to report the final app status to the RM.
The result is that the final status of the application might not match
the user's expectations.
One side-effect of the change is that users who do an explicit
System.exit() will lose the AM retry functionality. Since there is
no way to know if the exit was because of success or failure, the
AM right now errs on the side of it being a successful exit.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#3484 from vanzin/SPARK-4584 and squashes the following commits:
21f2502 [Marcelo Vanzin] Do not retry apps that use System.exit().
4198b3b [Marcelo Vanzin] [SPARK-4584] [yarn] Remove security manager from Yarn AM.
