SPARK-3716 [GraphX] Update Analytics.scala for partitionStrategy assignment

Previously, when the val partitionStrategy was created it called a function in the Analytics object which was a copy of the PartitionStrategy.fromString() method. This function has been removed, and the assignment of partitionStrategy now uses the PartitionStrategy.fromString method instead. In this way, it better matches the declarations of edge/vertex StorageLevel variables.

Author: NamelessAnalyst <NamelessAnalyst@users.noreply.github.com>

Closes #2569 from NamelessAnalyst/branch-1.1 and squashes the following commits:

c24ff51 [NamelessAnalyst] Update Analytics.scala
Merge branch 'branch-1.1' of github.com:apache/spark into csd-1.1
[SPARK-3121] Wrong implementation of implicit bytesWritableConverter

val path = ... //path to seq file with BytesWritable as type of both key and value
val file = sc.sequenceFile[Array[Byte],Array[Byte]](path)
file.take(1)(0)._1

This prints incorrect content of byte array. Actual content starts with correct one and some "random" bytes and zeros are appended. BytesWritable has two methods:

getBytes() - return content of all internal array which is often longer then actual value stored. It usually contains the rest of previous longer values

copyBytes() - return just begining of internal array determined by internal length property

It looks like in implicit conversion between BytesWritable and Array[byte] getBytes is used instead of correct copyBytes.

dbtsai

Author: Jakub Dubovský <james64@inMail.sk>
Author: Dubovsky Jakub <dubovsky@avast.com>

Closes #2712 from james64/3121-bugfix and squashes the following commits:

f85d24c [Jakub Dubovský] Test name changed, comments added
1b20d51 [Jakub Dubovský] Import placed correctly
406e26c [Jakub Dubovský] Scala style fixed
f92ffa6 [Dubovsky Jakub] performance tuning
480f9cd [Dubovsky Jakub] Bug 3121 fixed

(cherry picked from commit fc616d51a510f82627b5be949a5941419834cf70)
Signed-off-by: Josh Rosen <joshrosen@apache.org>
[SPARK-3905][Web UI]The keys for sorting the columns of Executor page ,Stage page Storage page are incorrect

Author: GuoQiang Li <witgo@qq.com>

Closes #2763 from witgo/SPARK-3905 and squashes the following commits:

17d7990 [GuoQiang Li] The keys for sorting the columns of Executor page ,Stage page Storage page are incorrect

(cherry picked from commit b4a7fa7a663c462bf537ca9d63af0dba6b4a8033)
Signed-off-by: Josh Rosen <joshrosen@apache.org>
[SPARK-3899][Doc]fix wrong links in streaming doc

There are three  [Custom Receiver Guide] links in streaming doc, the first is wrong.

Author: w00228970 <wangfei1@huawei.com>
Author: wangfei <wangfei1@huawei.com>

Closes #2749 from scwf/streaming-doc and squashes the following commits:

0cd76b7 [wangfei] update link tojump to the Akka-specific section
45b0646 [w00228970] wrong link in streaming doc

(cherry picked from commit 92e017fb894be1e8e2b2b5274fec4c31a7a4412e)
Signed-off-by: Josh Rosen <joshrosen@apache.org>
SPARK-3807: SparkSql does not work for tables created using custom serde

SparkSql crashes on selecting tables using custom serde.

Example:
----------------

CREATE EXTERNAL TABLE table_name PARTITIONED BY ( a int) ROW FORMAT 'SERDE "org.apache.hadoop.hive.serde2.thrift.ThriftDeserializer" with serdeproperties("serialization.format"="org.apache.thrift.protocol.TBinaryProtocol","serialization.class"="ser_class") STORED AS SEQUENCEFILE;

The following exception is seen on running a query like 'select * from table_name limit 1':

ERROR CliDriver: org.apache.hadoop.hive.serde2.SerDeException: java.lang.NullPointerException
at org.apache.hadoop.hive.serde2.thrift.ThriftDeserializer.initialize(ThriftDeserializer.java:68)
at org.apache.hadoop.hive.ql.plan.TableDesc.getDeserializer(TableDesc.java:80)
at org.apache.spark.sql.hive.execution.HiveTableScan.addColumnMetadataToConf(HiveTableScan.scala:86)
at org.apache.spark.sql.hive.execution.HiveTableScan.<init>(HiveTableScan.scala:100)
at org.apache.spark.sql.hive.HiveStrategies$HiveTableScans$$anonfun$14.apply(HiveStrategies.scala:188)
at org.apache.spark.sql.hive.HiveStrategies$HiveTableScans$$anonfun$14.apply(HiveStrategies.scala:188)
at org.apache.spark.sql.SQLContext$SparkPlanner.pruneFilterProject(SQLContext.scala:364)
at org.apache.spark.sql.hive.HiveStrategies$HiveTableScans$.apply(HiveStrategies.scala:184)
at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58)
at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at org.apache.spark.sql.catalyst.planning.QueryPlanner.apply(QueryPlanner.scala:59)
at org.apache.spark.sql.catalyst.planning.QueryPlanner.planLater(QueryPlanner.scala:54)
at org.apache.spark.sql.execution.SparkStrategies$BasicOperators$.apply(SparkStrategies.scala:280)
at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58)
at org.apache.spark.sql.catalyst.planning.QueryPlanner$$anonfun$1.apply(QueryPlanner.scala:58)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at org.apache.spark.sql.catalyst.planning.QueryPlanner.apply(QueryPlanner.scala:59)
at org.apache.spark.sql.SQLContext$QueryExecution.sparkPlan$lzycompute(SQLContext.scala:402)
at org.apache.spark.sql.SQLContext$QueryExecution.sparkPlan(SQLContext.scala:400)
at org.apache.spark.sql.SQLContext$QueryExecution.executedPlan$lzycompute(SQLContext.scala:406)
at org.apache.spark.sql.SQLContext$QueryExecution.executedPlan(SQLContext.scala:406)
at org.apache.spark.sql.hive.HiveContext$QueryExecution.stringResult(HiveContext.scala:406)
at org.apache.spark.sql.hive.thriftserver.SparkSQLDriver.run(SparkSQLDriver.scala:59)
at org.apache.spark.sql.hive.thriftserver.SparkSQLCLIDriver.processCmd(SparkSQLCLIDriver.scala:291)
at org.apache.hadoop.hive.cli.CliDriver.processLine(CliDriver.java:413)
at org.apache.spark.sql.hive.thriftserver.SparkSQLCLIDriver$.main(SparkSQLCLIDriver.scala:226)
at org.apache.spark.sql.hive.thriftserver.SparkSQLCLIDriver.main(SparkSQLCLIDriver.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:328)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.NullPointerException

Author: chirag <chirag.aggarwal@guavus.com>

Closes #2674 from chiragaggarwal/branch-1.1 and squashes the following commits:

370c31b [chirag] SPARK-3807: Add a test case to validate the fix.
1f26805 [chirag] SPARK-3807: SparkSql does not work for tables created using custom serde (Incorporated Review Comments)
ba4bc0c [chirag] SPARK-3807: SparkSql does not work for tables created using custom serde
5c73b72 [chirag] SPARK-3807: SparkSql does not work for tables created using custom serde
bumped guava
Merge branch 'branch-1.1' of github.com:apache/spark into csd-1.1
[SQL]typo in HiveFromSpark

Author: Kun Li <jacky.likun@gmail.com>

Closes #2809 from jackylk/patch-1 and squashes the following commits:

46c926b [Kun Li] typo in HiveFromSpark

(cherry picked from commit be2ec4a91d14f48e6323989fb0e0226a9d65bf7e)
Signed-off-by: Andrew Or <andrewor14@gmail.com>
[SPARK-3890][Docs]remove redundant spark.executor.memory in doc

Introduced in https://github.com/pwendell/spark/commit/f7e79bc42c1635686c3af01eef147dae92de2529, I'm not sure why we need two spark.executor.memory here.

Author: WangTaoTheTonic <barneystinson@aliyun.com>
Author: WangTao <barneystinson@aliyun.com>

Closes #2745 from WangTaoTheTonic/redundantconfig and squashes the following commits:

e7564dc [WangTao] too long line
fdbdb1f [WangTaoTheTonic] trivial workaround
d06b6e5 [WangTaoTheTonic] remove redundant spark.executor.memory in doc

(cherry picked from commit e7f4ea8a52f0d3d56684b4f9caadce978eac4816)
Signed-off-by: Andrew Or <andrewor14@gmail.com>
[SPARK-3067] JobProgressPage could not show Fair Scheduler Pools section sometimes

JobProgressPage could not show Fair Scheduler Pools section sometimes.
SparkContext starts webui and then postEnvironmentUpdate. Sometimes JobProgressPage is accessed between webui starting and postEnvironmentUpdate, then the lazy val isFairScheduler will be false. The Fair Scheduler Pools section will not display any more.

Author: yantangzhai <tyz0303@163.com>
Author: YanTangZhai <hakeemzhai@tencent.com>

Closes #1966 from YanTangZhai/SPARK-3067 and squashes the following commits:

d4323f8 [yantangzhai] update [SPARK-3067] JobProgressPage could not show Fair Scheduler Pools section sometimes
8a00106 [YanTangZhai] Merge pull request #6 from apache/master
b6391cc [yantangzhai] revert [SPARK-3067] JobProgressPage could not show Fair Scheduler Pools section sometimes
d2226cd [yantangzhai] [SPARK-3067] JobProgressPage could not show Fair Scheduler Pools section sometimes
cbcba66 [YanTangZhai] Merge pull request #3 from apache/master
aac7f7b [yantangzhai] [SPARK-3067] JobProgressPage could not show Fair Scheduler Pools section sometimes
cdef539 [YanTangZhai] Merge pull request #1 from apache/master

(cherry picked from commit dedace83f35cba0f833d962acbd75572318948c4)
Signed-off-by: Andrew Or <andrewor14@gmail.com>
Merge branch 'branch-1.1' of github.com:apache/spark into csd-1.1
[SPARK-3606] [yarn] Correctly configure AmIpFilter for Yarn HA (1.1 vers...

...ion).

This is a backport of SPARK-3606 to branch-1.1. Some of the code had to be
duplicated since branch-1.1 doesn't have the cleanup work that was done to
the Yarn codebase.

I don't know whether the version issue in yarn/alpha/pom.xml was intentional,
but I couldn't compile the code without fixing it.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #2497 from vanzin/SPARK-3606-1.1 and squashes the following commits:

4fd3c27 [Marcelo Vanzin] Remove unused imports.
75cde8c [Marcelo Vanzin] Scala is weird.
b27ebda [Marcelo Vanzin] Review feedback.
72ceafb [Marcelo Vanzin] Undelete needed import.
61162a6 [Marcelo Vanzin] Use separate config for each param instead of json.
3b7205f [Marcelo Vanzin] Review feedback.
b3b3e50 [Marcelo Vanzin] [SPARK-3606] [yarn] Correctly configure AmIpFilter for Yarn HA (1.1 version).
SPARK-3926 [CORE] Result of JavaRDD.collectAsMap() is not Serializable

Make JavaPairRDD.collectAsMap result Serializable since Java Maps generally are

Author: Sean Owen <sowen@cloudera.com>

Closes #2805 from srowen/SPARK-3926 and squashes the following commits:

ecb78ee [Sean Owen] Fix conflict between java.io.Serializable and use of Scala's Serializable
f4717f9 [Sean Owen] Oops, fix compile problem
ae1b36f [Sean Owen] Expand to cover Maps returned from other Java API methods as well
51c26c2 [Sean Owen] Make JavaPairRDD.collectAsMap result Serializable since Java Maps generally are
[SPARK-2546] Clone JobConf for each task (branch-1.0 / 1.1 backport)

This patch attempts to fix SPARK-2546 in `branch-1.0` and `branch-1.1`.  The underlying problem is that thread-safety issues in Hadoop Configuration objects may cause Spark tasks to get stuck in infinite loops.  The approach taken here is to clone a new copy of the JobConf for each task rather than sharing a single copy between tasks.  Note that there are still Configuration thread-safety issues that may affect the driver, but these seem much less likely to occur in practice and will be more complex to fix (see discussion on the SPARK-2546 ticket).

This cloning is guarded by a new configuration option (`spark.hadoop.cloneConf`) and is disabled by default in order to avoid unexpected performance regressions for workloads that are unaffected by the Configuration thread-safety issues.

Author: Josh Rosen <joshrosen@apache.org>

Closes #2684 from JoshRosen/jobconf-fix-backport and squashes the following commits:

f14f259 [Josh Rosen] Add configuration option to control cloning of Hadoop JobConf.
b562451 [Josh Rosen] Remove unused jobConfCacheKey field.
dd25697 [Josh Rosen] [SPARK-2546] [1.0 / 1.1 backport] Clone JobConf for each task.
Merge branch 'branch-1.1' of github.com:apache/spark into csd-1.1
[SPARK-3948][Shuffle]Fix stream corruption bug in sort-based shuffle

Kernel 2.6.32 bug will lead to unexpected behavior of transferTo in copyStream, and this will corrupt the shuffle output file in sort-based shuffle, which will somehow introduce PARSING_ERROR(2), deserialization error or offset out of range. Here fix this by adding append flag, also add some position checking code. Details can be seen in [SPARK-3948](https://issues.apache.org/jira/browse/SPARK-3948).

Author: jerryshao <saisai.shao@intel.com>

Closes #2824 from jerryshao/SPARK-3948 and squashes the following commits:

be0533a [jerryshao] Address the comments
a82b184 [jerryshao] add configuration to control the NIO way of copying stream
e17ada2 [jerryshao] Fix kernel 2.6.32 bug led unexpected behavior of transferTo

(cherry picked from commit c7aeecd08fd329085760fa89025ec0d9c04f5e3f)
Signed-off-by: Josh Rosen <joshrosen@databricks.com>

Conflicts:
	core/src/main/scala/org/apache/spark/util/Utils.scala
[SPARK-4010][Web UI]Spark UI returns 500 in yarn-client mode

The problem caused by #1966
CC YanTangZhai andrewor14

Author: GuoQiang Li <witgo@qq.com>

Closes #2858 from witgo/SPARK-4010 and squashes the following commits:

9866fbf [GuoQiang Li] Spark UI returns 500 in yarn-client mode

(cherry picked from commit 51afde9d8b8a67958c4632a13af143d7c7fd1f04)
Signed-off-by: Andrew Or <andrewor14@gmail.com>
Merge branch 'branch-1.1' of github.com:apache/spark into csd-1.1
[SPARK-3877][YARN] Throw an exception when application is not successful so that the exit code wil be set to 1 (for branch-1.1)

This is a patch to fix SPARK-3877 in branch-1.1. See also #2732

Author: zsxwing <zsxwing@gmail.com>

Closes #2748 from zsxwing/SPARK-3877-branch-1.1 and squashes the following commits:

3701984 [zsxwing] Remove System.exit from Client.scala
8681881 [zsxwing] [SPARK-3877] Throw an exception when application is not successful so that the exit code wil be set to 1