In StagePage, the SchedulerDelay is calculated as totalExecutionTime - executorRunTime - executorOverhead - gettingResultTime.
But the totalExecutionTime is calculated in the way that doesn't include the gettingResultTime.
Author: Carson Wang <carson.wang@intel.com>
Closes#7319 from carsonwang/SchedulerDelayTime and squashes the following commits:
f66fb6e [Carson Wang] Update the code style
7d971ae [Carson Wang] Correct the calculation of SchedulerDelay
This PR enables SparkR to dynamically ship the SparkR binary package to the AM node in YARN cluster mode, thus it is no longer required that the SparkR package be installed on each worker node.
This PR uses the JDK jar tool to package the SparkR package, because jar is thought to be available on both Linux/Windows platforms where JDK has been installed.
This PR does not address the R worker involved in RDD API. Will address it in a separate JIRA issue.
This PR does not address SBT build. SparkR installation and packaging by SBT will be addressed in a separate JIRA issue.
R/install-dev.bat is not tested. shivaram , Could you help to test it?
Author: Sun Rui <rui.sun@intel.com>
Closes#6743 from sun-rui/SPARK-6797 and squashes the following commits:
ca63c86 [Sun Rui] Adjust MimaExcludes after rebase.
7313374 [Sun Rui] Fix unit test errors.
72695fb [Sun Rui] Fix unit test failures.
193882f [Sun Rui] Fix Mima test error.
fe25a33 [Sun Rui] Fix Mima test error.
35ecfa3 [Sun Rui] Fix comments.
c38a005 [Sun Rui] Unzipped SparkR binary package is still required for standalone and Mesos modes.
b05340c [Sun Rui] Fix scala style.
2ca5048 [Sun Rui] Fix comments.
1acefd1 [Sun Rui] Fix scala style.
0aa1e97 [Sun Rui] Fix scala style.
41d4f17 [Sun Rui] Add support for locating SparkR package for R workers required by RDD APIs.
49ff948 [Sun Rui] Invoke jar.exe with full path in install-dev.bat.
7b916c5 [Sun Rui] Use 'rem' consistently.
3bed438 [Sun Rui] Add a comment.
681afb0 [Sun Rui] Fix a bug that RRunner does not handle client deployment modes.
cedfbe2 [Sun Rui] [SPARK-6797][SPARKR] Add support for YARN cluster mode.
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#7275 from kayousterhout/SPARK-8880 and squashes the following commits:
3e9ce7c [Kay Ousterhout] Added missing return type
e150278 [Kay Ousterhout] [SPARK-8880] Fix confusing Stage.attemptId member variable
This patch adds a cache-friendly external sorter which operates on serialized bytes and uses this sorter to implement a new sort operator for Spark SQL and DataFrames.
### Overview of the new sorter
The new sorter design is inspired by [Alphasort](http://research.microsoft.com/pubs/68249/alphasort.doc) and implements a key-prefix optimization in order to improve the cache friendliness of the sort. In naive sort implementations, the sorting algorithm operates on an array of record pointers. To compare two records for ordering, the sorter must dereference these pointers, which likely involves random memory access, then compare the objects themselves.
In a key-prefix sort, the sort operates on an array which stores the record pointer alongside a prefix of the record's key. When comparing two records for ordering, the sorter first compares the the stored key prefixes. If the ordering can be determined from the key prefixes (i.e. the prefixes are unequal), then the sort can avoid directly comparing the records, avoiding random memory accesses and full record comparisons. For example, if we're sorting a list of strings then we can store the first 8 bytes of the UTF-8 encoded string as the key-prefix and can perform unsigned byte-at-a-time comparisons to determine the ordering of strings based on their prefixes, only resorting to full comparisons for strings that share a common prefix. In cases where the sort key can fit entirely in the space allotted for the key prefix (e.g. the sorting key is an integer), we completely avoid direct record comparison.
In this patch's implementation of key-prefix sorting, our sorter's internal array stores a 64-bit long and 64-bit pointer for each record being sorted. The key prefixes are generated by the user when inserting records into the sorter, which uses a user-defined comparison function for comparing them. The `PrefixComparators` object implements a set of comparators for many common types, including primitive numeric types and UTF-8 strings.
The actual sorting is implemented by `UnsafeInMemorySorter`. Most consumers will not use this directly, but instead will use `UnsafeExternalSorter`, a class which implements a sort that can spill to disk in response to memory pressure. Internally, `UnsafeExternalSorter` creates `UnsafeInMemorySorters` to perform sorting and uses `UnsafeSortSpillReader/Writer` to spill and read back runs of sorted records and `UnsafeSortSpillMerger` to merge multiple sorted spills into a single sorted iterator. This external sorter integrates with Spark's existing ShuffleMemoryManager for controlling spilling.
Many parts of this sorter's design are based on / copied from the more specialized external sort implementation that I designed for the new UnsafeShuffleManager write path; see #5868 for more details on that patch.
### Sorting rows in Spark SQL
For now, `UnsafeExternalSorter` is only used by Spark SQL, which uses it to implement a new sort operator, `UnsafeExternalSort`. This sort operator uses a SQL-specific class called `UnsafeExternalRowSorter` that configures an `UnsafeExternalSorter` to use prefix generators and comparators that operate on rows encoded in the UnsafeRow format that was designed for Project Tungsten.
I used some interesting unit-testing techniques to test this patch's SQL-specific components. `UnsafeExternalSortSuite` uses the SQL random data generators introduced in #7176 to test the UnsafeSort operator with all atomic types both with and without nullability and in both ascending and descending sort orders. `PrefixComparatorsSuite` contains a cool use of ScalaCheck + ScalaTest's `GeneratorDrivenPropertyChecks` in order to test UTF8String prefix comparison.
### Misc. additional improvements made in this patch
This patch made several miscellaneous improvements to related code in Spark SQL:
- The logic for selecting physical sort operator implementations, which was partially duplicated in both `Exchange` and `SparkStrategies, has now been consolidated into a `getSortOperator()` helper function in `SparkStrategies`.
- The `SparkPlanTest` unit testing helper trait has been extended with new methods for comparing the output produced by two different physical plans. This makes it easy to write tests which assert that two physical operator implementations should produce the same output. I also added a method for disabling the implicit sorting of outputs prior to comparing them, a change which is necessary in order to be able to write proper SparkPlan tests for sort operators.
### Tasks deferred to followup patches
While most of this patch's features are reasonably well-tested and complete, there are a number of tasks that are intentionally being deferred to followup patches:
- Add tests which mock the ShuffleMemoryManager to check that memory pressure properly triggers spilling (there are examples of this type of test in #5868).
- Add tests to ensure that spill files are properly cleaned up after errors. I'd like to do this in the context of a patch which introduces more general metrics for ensuring proper cleanup of tasks' temporary files; see https://issues.apache.org/jira/browse/SPARK-8966 for more details.
- Metrics integration: there are some open questions regarding how to track / report spill metrics for non-shuffle operations, so I've deferred most of the IO / shuffle metrics integration for now.
- Performance profiling.
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Author: Josh Rosen <joshrosen@databricks.com>
Closes#6444 from JoshRosen/sql-external-sort and squashes the following commits:
6beb467 [Josh Rosen] Remove a bunch of overloaded methods to avoid default args. issue
2bbac9c [Josh Rosen] Merge remote-tracking branch 'origin/master' into sql-external-sort
35dad9f [Josh Rosen] Make sortAnswers = false the default in SparkPlanTest
5135200 [Josh Rosen] Fix spill reading for large rows; add test
2f48777 [Josh Rosen] Add test and fix bug for sorting empty arrays
d1e28bc [Josh Rosen] Merge remote-tracking branch 'origin/master' into sql-external-sort
cd05866 [Josh Rosen] Fix scalastyle
3947fc1 [Josh Rosen] Merge remote-tracking branch 'origin/master' into sql-external-sort
d13ac55 [Josh Rosen] Hacky approach to copying of UnsafeRows for sort followed by limit.
845bea3 [Josh Rosen] Remove unnecessary zeroing of row conversion buffer
c56ec18 [Josh Rosen] Clean up final row copying code.
d31f180 [Josh Rosen] Re-enable NullType sorting test now that SPARK-8868 is fixed
844f4ca [Josh Rosen] Merge remote-tracking branch 'origin/master' into sql-external-sort
293f109 [Josh Rosen] Add missing license header.
f99a612 [Josh Rosen] Fix bugs in string prefix comparison.
9d00afc [Josh Rosen] Clean up prefix comparators for integral types
88aff18 [Josh Rosen] NULL_PREFIX has to be negative infinity for floating point types
613e16f [Josh Rosen] Test with larger data.
1d7ffaa [Josh Rosen] Somewhat hacky fix for descending sorts
08701e7 [Josh Rosen] Fix prefix comparison of null primitives.
b86e684 [Josh Rosen] Set global = true in UnsafeExternalSortSuite.
1c7bad8 [Josh Rosen] Make sorting of answers explicit in SparkPlanTest.checkAnswer().
b81a920 [Josh Rosen] Temporarily enable only the passing sort tests
5d6109d [Josh Rosen] Fix inconsistent handling / encoding of record lengths.
87b6ed9 [Josh Rosen] Fix critical issues in test which led to false negatives.
8d7fbe7 [Josh Rosen] Fixes to multiple spilling-related bugs.
82e21c1 [Josh Rosen] Force spilling in UnsafeExternalSortSuite.
88b72db [Josh Rosen] Test ascending and descending sort orders.
f27be09 [Josh Rosen] Fix tests by binding attributes.
0a79d39 [Josh Rosen] Revert "Undo part of a SparkPlanTest change in #7162 that broke my test."
7c3c864 [Josh Rosen] Undo part of a SparkPlanTest change in #7162 that broke my test.
9969c14 [Josh Rosen] Merge remote-tracking branch 'origin/master' into sql-external-sort
5822e6f [Josh Rosen] Fix test compilation issue
939f824 [Josh Rosen] Remove code gen experiment.
0dfe919 [Josh Rosen] Implement prefix sort for strings (albeit inefficiently).
66a813e [Josh Rosen] Prefix comparators for float and double
b310c88 [Josh Rosen] Integrate prefix comparators for Int and Long (others coming soon)
95058d9 [Josh Rosen] Add missing SortPrefixUtils file
4c37ba6 [Josh Rosen] Add tests for sorting on all primitive types.
6890863 [Josh Rosen] Fix memory leak on empty inputs.
d246e29 [Josh Rosen] Fix consideration of column types when choosing sort implementation.
6b156fb [Josh Rosen] Some WIP work on prefix comparison.
7f875f9 [Josh Rosen] Commit failing test demonstrating bug in handling objects in spills
41b8881 [Josh Rosen] Get UnsafeInMemorySorterSuite to pass (WIP)
90c2b6a [Josh Rosen] Update test name
6d6a1e6 [Josh Rosen] Centralize logic for picking sort operator implementations
9869ec2 [Josh Rosen] Clean up Exchange code a bit
82bb0ec [Josh Rosen] Fix IntelliJ complaint due to negated if condition
1db845a [Josh Rosen] Many more changes to harmonize with shuffle sorter
ebf9eea [Josh Rosen] Harmonization with shuffle's unsafe sorter
206bfa2 [Josh Rosen] Add some missing newlines at the ends of files
26c8931 [Josh Rosen] Back out some Hive changes that aren't needed anymore
62f0bb8 [Josh Rosen] Update to reflect SparkPlanTest changes
21d7d93 [Josh Rosen] Back out of BlockObjectWriter change
7eafecf [Josh Rosen] Port test to SparkPlanTest
d468a88 [Josh Rosen] Update for InternalRow refactoring
269cf86 [Josh Rosen] Back out SMJ operator change; isolate changes to selection of sort op.
1b841ca [Josh Rosen] WIP towards copying
b420a71 [Josh Rosen] Move most of the existing SMJ code into Java.
dfdb93f [Josh Rosen] SparkFunSuite change
73cc761 [Josh Rosen] Fix whitespace
9cc98f5 [Josh Rosen] Move more code to Java; fix bugs in UnsafeRowConverter length type.
c8792de [Josh Rosen] Remove some debug logging
dda6752 [Josh Rosen] Commit some missing code from an old git stash.
58f36d0 [Josh Rosen] Merge in a sketch of a unit test for the new sorter (now failing).
2bd8c9a [Josh Rosen] Import my original tests and get them to pass.
d5d3106 [Josh Rosen] WIP towards external sorter for Spark SQL.
AFAIK, some spark application always use LocalBackend to do some local initiatives, spark sql is an example. Starting a LocalPoint won't add user classpath into executor.
```java
override def start() {
localEndpoint = SparkEnv.get.rpcEnv.setupEndpoint(
"LocalBackendEndpoint", new LocalEndpoint(SparkEnv.get.rpcEnv, scheduler, this, totalCores))
}
```
Thus will cause local executor fail with these scenarios, loading hadoop built-in native libraries, loading other user defined native libraries, loading user jars, reading s3 config from a site.xml file, etc
Author: Min Zhou <coderplay@gmail.com>
Closes#7091 from coderplay/master and squashes the following commits:
365838f [Min Zhou] Fixed java.net.MalformedURLException, add default scheme, support relative path
d215b7f [Min Zhou] Follows spark standard scala style, make the auto testing happy
84ad2cd [Min Zhou] Use system specific path separator instead of ','
01f5d1a [Min Zhou] Merge branch 'master' of https://github.com/apache/spark
e528be7 [Min Zhou] Merge branch 'master' of https://github.com/apache/spark
45bf62c [Min Zhou] SPARK-8675 Executors created by LocalBackend won't get the same classpath as other executor backends
Too many logs even when set the log level to warning.
Author: Cheng Hao <hao.cheng@intel.com>
Closes#7340 from chenghao-intel/log and squashes the following commits:
59658cf [Cheng Hao] change the log level to info
pwendell and I discussed this a little more offline and concluded that it would be good to keep it more conservative. Losing cached blocks may be very expensive and we should only allow it if the user knows what he/she is doing.
FYI harishreedharan sryza.
Author: Andrew Or <andrew@databricks.com>
Closes#7329 from andrewor14/da-cached-timeout and squashes the following commits:
cef0b4e [Andrew Or] Change timeout to infinity
Author: Jonathan Alter <jonalter@users.noreply.github.com>
Closes#7093 from jonalter/SPARK-7977 and squashes the following commits:
ccd44cc [Jonathan Alter] Changed println to log in ThreadingSuite
7fcac3e [Jonathan Alter] Reverting to println in ThreadingSuite
10724b6 [Jonathan Alter] Changing some printlns to logs in tests
eeec1e7 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
0b1dcb4 [Jonathan Alter] More println cleanup
aedaf80 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
925fd98 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
0c16fa3 [Jonathan Alter] Replacing some printlns with logs
45c7e05 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
5c8e283 [Jonathan Alter] Allowing println in audit-release examples
5b50da1 [Jonathan Alter] Allowing printlns in example files
ca4b477 [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
83ab635 [Jonathan Alter] Fixing new printlns
54b131f [Jonathan Alter] Merge branch 'master' of github.com:apache/spark into SPARK-7977
1cd8a81 [Jonathan Alter] Removing some unnecessary comments and printlns
b837c3a [Jonathan Alter] Disallowing println
This is largely based on extracting the dynamic allocation parts from tnachen's #3861.
Author: Iulian Dragos <jaguarul@gmail.com>
Closes#4984 from dragos/issue/mesos-coarse-dynamicAllocation and squashes the following commits:
39df8cd [Iulian Dragos] Update tests to latest changes in core.
9d2c9fa [Iulian Dragos] Remove adjustment of executorLimitOption in doKillExecutors.
8b00f52 [Iulian Dragos] Latest round of reviews.
0cd00e0 [Iulian Dragos] Add persistent shuffle directory
15c45c1 [Iulian Dragos] Add dynamic allocation to the Spark coarse-grained scheduler.
(This reopens a patch that was closed in the past: #6248)
When you view the stage page while running the following:
```
sc.parallelize(1 to X, 10000).count()
```
The page never loads, the job is stalled, and you end up running into an OOM:
```
HTTP ERROR 500
Problem accessing /stages/stage/. Reason:
Server Error
Caused by:
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:2367)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
```
This patch compresses Jetty responses in gzip. The correct long-term fix is to add pagination.
Author: Andrew Or <andrew@databricks.com>
Closes#7296 from andrewor14/gzip-jetty and squashes the following commits:
a051c64 [Andrew Or] Use GZIP to compress Jetty responses
The configuration ```SPARK_EXECUTOR_CORES``` won't put into ```SparkConf```, so it has no effect to the dynamic executor allocation.
Author: xutingjun <xutingjun@huawei.com>
Closes#7322 from XuTingjun/SPARK_EXECUTOR_CORES and squashes the following commits:
2cafa89 [xutingjun] make SPARK_EXECUTOR_CORES has effect to dynamicAllocation
Currently, the mesos scheduler only looks at the 'cpu' and 'mem' resources when trying to determine the usablility of a resource offer from a mesos slave node. It may be preferable for the user to be able to ensure that the spark jobs are only started on a certain set of nodes (based on attributes).
For example, If the user sets a property, let's say `spark.mesos.constraints` is set to `tachyon=true;us-east-1=false`, then the resource offers will be checked to see if they meet both these constraints and only then will be accepted to start new executors.
Author: Ankur Chauhan <achauhan@brightcove.com>
Closes#5563 from ankurcha/mesos_attribs and squashes the following commits:
902535b [Ankur Chauhan] Fix line length
d83801c [Ankur Chauhan] Update code as per code review comments
8b73f2d [Ankur Chauhan] Fix imports
c3523e7 [Ankur Chauhan] Added docs
1a24d0b [Ankur Chauhan] Expand scope of attributes matching to include all data types
482fd71 [Ankur Chauhan] Update access modifier to private[this] for offer constraints
5ccc32d [Ankur Chauhan] Fix nit pick whitespace
1bce782 [Ankur Chauhan] Fix nit pick whitespace
c0cbc75 [Ankur Chauhan] Use offer id value for debug message
7fee0ea [Ankur Chauhan] Add debug statements
fc7eb5b [Ankur Chauhan] Fix import codestyle
00be252 [Ankur Chauhan] Style changes as per code review comments
662535f [Ankur Chauhan] Incorporate code review comments + use SparkFunSuite
fdc0937 [Ankur Chauhan] Decline offers that did not meet criteria
67b58a0 [Ankur Chauhan] Add documentation for spark.mesos.constraints
63f53f4 [Ankur Chauhan] Update codestyle - uniform style for config values
02031e4 [Ankur Chauhan] Fix scalastyle warnings in tests
c09ed84 [Ankur Chauhan] Fixed the access modifier on offerConstraints val to private[mesos]
0c64df6 [Ankur Chauhan] Rename overhead fractions to memory_*, fix spacing
8cc1e8f [Ankur Chauhan] Make exception message more explicit about the source of the error
addedba [Ankur Chauhan] Added test case for malformed constraint string
ec9d9a6 [Ankur Chauhan] Add tests for parse constraint string
72fe88a [Ankur Chauhan] Fix up tests + remove redundant method override, combine utility class into new mesos scheduler util trait
92b47fd [Ankur Chauhan] Add attributes based constraints support to MesosScheduler
Spark standalone master web UI show "Alive Workers" total core, total used cores and "Alive workers" total memory, memory used.
But the JSON API page "http://MASTERURL:8088/json" shows "ALL workers" core, memory number.
This webUI data is not sync with the JSON API.
The proper way is to sync the number with webUI and JSON API.
Author: Wisely Chen <wiselychen@appier.com>
Closes#7038 from thegiive/SPARK-8656 and squashes the following commits:
9e54bf0 [Wisely Chen] Change variable name to camel case
2c8ea89 [Wisely Chen] Change some styling and add local variable
431d2b0 [Wisely Chen] Worker List should contain DEAD node also
8b3b8e8 [Wisely Chen] [SPARK-8656] Fix the webUI and JSON API number is not synced
Latest changes after refactoring to the RPC layer. I rebased against trunk to make sure to get any recent changes since it had been a while. I wasn't crazy about the name `ConfigureTimeout` and `RpcTimeout` seemed to fit better, but I'm open to suggestions!
I ran most of the tests and they pass, but others would get stuck with "WARN TaskSchedulerImpl: Initial job has not accepted any resources". I think its just my machine, so I'd though I would push what I have anyway.
Still left to do:
* I only added a couple unit tests so far, there are probably some more cases to test
* Make sure all uses require a `RpcTimeout`
* Right now, both the `ask` and `Await.result` use the same timeout, should we differentiate between these in the TimeoutException message?
* I wrapped `Await.result` in `RpcTimeout`, should we also wrap `Await.ready`?
* Proper scoping of classes and methods
hardmettle, feel free to help out with any of these!
Author: Bryan Cutler <bjcutler@us.ibm.com>
Author: Harsh Gupta <harsh@Harshs-MacBook-Pro.local>
Author: BryanCutler <cutlerb@gmail.com>
Closes#6205 from BryanCutler/configTimeout-6980 and squashes the following commits:
46c8d48 [Bryan Cutler] [SPARK-6980] Changed RpcEnvSuite test to never reply instead of just sleeping, to avoid possible sync issues
06afa53 [Bryan Cutler] [SPARK-6980] RpcTimeout class extends Serializable, was causing error in MasterSuite
7bb70f1 [Bryan Cutler] Merge branch 'master' into configTimeout-6980
dbd5f73 [Bryan Cutler] [SPARK-6980] Changed RpcUtils askRpcTimeout and lookupRpcTimeout scope to private[spark] and improved deprecation warning msg
4e89c75 [Bryan Cutler] [SPARK-6980] Missed one usage of deprecated RpcUtils.askTimeout in YarnSchedulerBackend although it is not being used, and fixed SparkConfSuite UT to not use deprecated RpcUtils functions
6a1c50d [Bryan Cutler] [SPARK-6980] Minor cleanup of test case
7f4d78e [Bryan Cutler] [SPARK-6980] Fixed scala style checks
287059a [Bryan Cutler] [SPARK-6980] Removed extra import in AkkaRpcEnvSuite
3d8b1ff [Bryan Cutler] [SPARK-6980] Cleaned up imports in AkkaRpcEnvSuite
3a168c7 [Bryan Cutler] [SPARK-6980] Rewrote Akka RpcTimeout UTs in RpcEnvSuite
7636189 [Bryan Cutler] [SPARK-6980] Fixed call to askWithReply in DAGScheduler to use RpcTimeout - this was being compiled by auto-tupling and changing the message type of BlockManagerHeartbeat
be11c4e [Bryan Cutler] Merge branch 'master' into configTimeout-6980
039afed [Bryan Cutler] [SPARK-6980] Corrected import organization
218aa50 [Bryan Cutler] [SPARK-6980] Corrected issues from feedback
fadaf6f [Bryan Cutler] [SPARK-6980] Put back in deprecated RpcUtils askTimeout and lookupTimout to fix MiMa errors
fa6ed82 [Bryan Cutler] [SPARK-6980] Had to increase timeout on positive test case because a processor slowdown could trigger an Future TimeoutException
b05d449 [Bryan Cutler] [SPARK-6980] Changed constructor to use val duration instead of getter function, changed name of string property from conf to timeoutProp for consistency
c6cfd33 [Bryan Cutler] [SPARK-6980] Changed UT ask message timeout to explicitly intercept a SparkException
1394de6 [Bryan Cutler] [SPARK-6980] Moved MessagePrefix to createRpcTimeoutException directly
1517721 [Bryan Cutler] [SPARK-6980] RpcTimeout object scope should be private[spark]
2206b4d [Bryan Cutler] [SPARK-6980] Added unit test for ask then immediat awaitReply
1b9beab [Bryan Cutler] [SPARK-6980] Cleaned up import ordering
08f5afc [Bryan Cutler] [SPARK-6980] Added UT for constructing RpcTimeout with default value
d3754d1 [Bryan Cutler] [SPARK-6980] Added akkaConf to prevent dead letter logging
995d196 [Bryan Cutler] [SPARK-6980] Cleaned up import ordering, comments, spacing from PR feedback
7774d56 [Bryan Cutler] [SPARK-6980] Cleaned up UT imports
4351c48 [Bryan Cutler] [SPARK-6980] Added UT for addMessageIfTimeout, cleaned up UTs
1607a5f [Bryan Cutler] [SPARK-6980] Changed addMessageIfTimeout to PartialFunction, cleanup from PR comments
2f94095 [Bryan Cutler] [SPARK-6980] Added addMessageIfTimeout for when a Future is completed with TimeoutException
235919b [Bryan Cutler] [SPARK-6980] Resolved conflicts after master merge
c07d05c [Bryan Cutler] Merge branch 'master' into configTimeout-6980-tmp
b7fb99f [BryanCutler] Merge pull request #2 from hardmettle/configTimeoutUpdates_6980
4be3a8d [Harsh Gupta] Modifying loop condition to find property match
0ee5642 [Harsh Gupta] Changing the loop condition to halt at the first match in the property list for RpcEnv exception catch
f74064d [Harsh Gupta] Retrieving properties from property list using iterator and while loop instead of chained functions
a294569 [Bryan Cutler] [SPARK-6980] Added creation of RpcTimeout with Seq of property keys
23d2f26 [Bryan Cutler] [SPARK-6980] Fixed await result not being handled by RpcTimeout
49f9f04 [Bryan Cutler] [SPARK-6980] Minor cleanup and scala style fix
5b59a44 [Bryan Cutler] [SPARK-6980] Added some RpcTimeout unit tests
78a2c0a [Bryan Cutler] [SPARK-6980] Using RpcTimeout.awaitResult for future in AppClient now
97523e0 [Bryan Cutler] [SPARK-6980] Akka ask timeout description refactored to RPC layer
The existing test suite has a lot of duplicate code and doesn't even cover the most fundamental feature of the HeartbeatReceiver, which is expiring hosts that have not responded in a while.
This introduces manual clocks in `HeartbeatReceiver` and makes it respond to heartbeats only for registered executors. A few internal messages are moved to `receiveAndReply` to increase determinism of the tests so we don't have to rely on flaky constructs like `eventually`.
Author: Andrew Or <andrew@databricks.com>
Closes#7173 from andrewor14/heartbeat-receiver-tests and squashes the following commits:
4a903d6 [Andrew Or] Increase HeartReceiverSuite coverage and clean up
This patch rewrites the old checkpointing code in a way that is easier to understand. It also adds a guard against an invalid specification of checkpoint directory to provide a clearer error message. Most of the changes here are relatively minor.
Author: Andrew Or <andrew@databricks.com>
Closes#6968 from andrewor14/checkpoint-cleanup and squashes the following commits:
4ef8263 [Andrew Or] Use global synchronized instead
6f6fd84 [Andrew Or] Merge branch 'master' of github.com:apache/spark into checkpoint-cleanup
b1437ad [Andrew Or] Warn instead of throw
5484293 [Andrew Or] Merge branch 'master' of github.com:apache/spark into checkpoint-cleanup
7fb4af5 [Andrew Or] Guard against bad settings of checkpoint directory
691da98 [Andrew Or] Simplify checkpoint code / code style / comments
I've updated default values in comments, documentation, and in the command line builder to be 1g based on comments in the JIRA. I've also updated most usages to point at a single variable defined in the Utils.scala and JavaUtils.java files. This wasn't possible in all cases (R, shell scripts etc.) but usage in most code is now pointing at the same place.
Please let me know if I've missed anything.
Will the spark-shell use the value within the command line builder during instantiation?
Author: Ilya Ganelin <ilya.ganelin@capitalone.com>
Closes#7132 from ilganeli/SPARK-3071 and squashes the following commits:
4074164 [Ilya Ganelin] String fix
271610b [Ilya Ganelin] Merge branch 'SPARK-3071' of github.com:ilganeli/spark into SPARK-3071
273b6e9 [Ilya Ganelin] Test fix
fd67721 [Ilya Ganelin] Update JavaUtils.java
26cc177 [Ilya Ganelin] test fix
e5db35d [Ilya Ganelin] Fixed test failure
39732a1 [Ilya Ganelin] merge fix
a6f7deb [Ilya Ganelin] Created default value for DRIVER MEM in Utils that's now used in almost all locations instead of setting manually in each
09ad698 [Ilya Ganelin] Update SubmitRestProtocolSuite.scala
19b6f25 [Ilya Ganelin] Missed one doc update
2698a3d [Ilya Ganelin] Updated default value for driver memory
Author: Holden Karau <holden@pigscanfly.ca>
Closes#7171 from holdenk/SPARK-8769-toLocalIterator-documentation-improvement and squashes the following commits:
97ddd99 [Holden Karau] Add note
Author: Holden Karau <holden@pigscanfly.ca>
Closes#7172 from holdenk/SPARK-8771-actor-system-deprecation-tag-uses-deprecated-deprecation-tag and squashes the following commits:
7f1455b [Holden Karau] Add .0s to the versions for the derpecated anotations in SparkEnv.scala
ca13c9d [Holden Karau] Add a version to the deprecated annotation for the actorSystem in SparkEnv
If `fs.hdfs.impl.disable.cache` was `false`(default), `FileSystem` will use the cached `DFSClient` which use old token.
[AMDelegationTokenRenewer](https://github.com/apache/spark/blob/master/yarn/src/main/scala/org/apache/spark/deploy/yarn/AMDelegationTokenRenewer.scala#L196)
```scala
val credentials = UserGroupInformation.getCurrentUser.getCredentials
credentials.writeTokenStorageFile(tempTokenPath, discachedConfiguration)
```
Although the `credentials` had the new Token, but it still use the cached client and old token.
So It's better to set the `fs.hdfs.impl.disable.cache` as `true` to avoid token expired.
[Jira](https://issues.apache.org/jira/browse/SPARK-8688)
Author: huangzhaowei <carlmartinmax@gmail.com>
Closes#7069 from SaintBacchus/SPARK-8688 and squashes the following commits:
f94cd0b [huangzhaowei] modify function parameter
8fb9eb9 [huangzhaowei] explicit the comment
0cd55c9 [huangzhaowei] Rename function name to be an accurate one
cf776a1 [huangzhaowei] [SPARK-8688][YARN]Bug fix: disable the cache fs to gain the HDFS connection.
Otherwise other tests don't log anything useful...
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#7140 from vanzin/SPARK-3444 and squashes the following commits:
de14836 [Marcelo Vanzin] Better fix.
6cff13a [Marcelo Vanzin] [SPARK-3444] [core] Restore INFO level after log4j test.
This PR updates the rest Actors in core to RpcEndpoint.
Because there is no `ActorSelection` in RpcEnv, I changes the logic of `registerWithMaster` in Worker and AppClient to avoid blocking the message loop. These changes need to be reviewed carefully.
Author: zsxwing <zsxwing@gmail.com>
Closes#5392 from zsxwing/rpc-rewrite-part3 and squashes the following commits:
2de7bed [zsxwing] Merge branch 'master' into rpc-rewrite-part3
f12d943 [zsxwing] Address comments
9137b82 [zsxwing] Fix the code style
e734c71 [zsxwing] Merge branch 'master' into rpc-rewrite-part3
2d24fb5 [zsxwing] Fix the code style
5a82374 [zsxwing] Merge branch 'master' into rpc-rewrite-part3
fa47110 [zsxwing] Merge branch 'master' into rpc-rewrite-part3
72304f0 [zsxwing] Update the error strategy for AkkaRpcEnv
e56cb16 [zsxwing] Always send failure back to the sender
a7b86e6 [zsxwing] Use JFuture for java.util.concurrent.Future
aa34b9b [zsxwing] Fix the code style
bd541e7 [zsxwing] Merge branch 'master' into rpc-rewrite-part3
25a84d8 [zsxwing] Use ThreadUtils
060ff31 [zsxwing] Merge branch 'master' into rpc-rewrite-part3
dbfc916 [zsxwing] Improve the docs and comments
837927e [zsxwing] Merge branch 'master' into rpc-rewrite-part3
5c27f97 [zsxwing] Merge branch 'master' into rpc-rewrite-part3
fadbb9e [zsxwing] Fix the code style
6637e3c [zsxwing] Merge remote-tracking branch 'origin/master' into rpc-rewrite-part3
7fdee0e [zsxwing] Fix the return type to ExecutorService and ScheduledExecutorService
e8ad0a5 [zsxwing] Fix the code style
6b2a104 [zsxwing] Log error and use SparkExitCode.UNCAUGHT_EXCEPTION exit code
fbf3194 [zsxwing] Add Utils.newDaemonSingleThreadExecutor and newDaemonSingleThreadScheduledExecutor
b776817 [zsxwing] Update Master, Worker, Client, AppClient and related classes to use RpcEndpoint
This issue was reported by saurfang. Thanks!
There is a following code in StagePage.scala.
```
|width="$serializationTimeProportion%"></rect>
|<rect class="getting-result-time-proportion"
|x="$gettingResultTimeProportionPos%" y="0px" height="26px"
|width="$gettingResultTimeProportion%"></rect></svg>',
|'start': new Date($launchTime),
|'end': new Date($finishTime)
|}
|""".stripMargin.replaceAll("\n", " ")
```
The last `replaceAll("\n", "")` doesn't work when we checkout and build source code on Windows and deploy on Linux.
It's because when we checkout the source code on Windows, new-line-code is replaced with `"\r\n"` and `replaceAll("\n", "")` replaces only `"\n"`.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#7133 from sarutak/SPARK-8739 and squashes the following commits:
17fb044 [Kousuke Saruta] Fixed a new-line-code issue
Because `System.currentTimeMillis()` is not accurate for tasks that only need several milliseconds, sometimes `totalExecutionTime` in `makeTimeline` will be 0. If `totalExecutionTime` is 0, there will the following error in the console.
This PR fixes it by using an empty svg tag when `totalExecutionTime` is 0. This is a screenshot for a task that its totalExecutionTime is 0 after fixing it.
Author: zsxwing <zsxwing@gmail.com>
Closes#7088 from zsxwing/SPARK-8705 and squashes the following commits:
9ee4ef5 [zsxwing] Address comments
ef2ecfa [zsxwing] Don't display rects when totalExecutionTime is 0
Showing these applications may lead to weird behavior in the History Server. For old logs, if
the app ID is recorded later, you may end up with a duplicate entry. For new logs, the app might
be listed with a ".inprogress" suffix.
So ignore those, but still allow old applications that don't record app IDs at all (1.0 and 1.1) to be shown.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Author: Carson Wang <carson.wang@intel.com>
Closes#7097 from vanzin/SPARK-8372 and squashes the following commits:
a24eab2 [Marcelo Vanzin] Feedback.
112ae8f [Marcelo Vanzin] Merge branch 'master' into SPARK-8372
7b91b74 [Marcelo Vanzin] Handle logs generated by 1.0 and 1.1.
1eca3fe [Carson Wang] [SPARK-8372] History server shows incorrect information for application not started
when the ```taskEnd.reason``` is ```Resubmitted```, it shouldn't do statistics. Because this tasks has a ```SUCCESS``` taskEnd before.
Author: xutingjun <xutingjun@huawei.com>
Closes#6950 from XuTingjun/pageError and squashes the following commits:
af35dc3 [xutingjun] When taskEnd is Resubmitted, don't do statistics
Note that 'dir/*' can be more efficient in some Hadoop FS implementations that 'dir/' (now fixed scaladoc by using HTML entity for *)
Author: Sean Owen <sowen@cloudera.com>
Closes#7126 from srowen/SPARK-8437.2 and squashes the following commits:
7bb45da [Sean Owen] Note that 'dir/*' can be more efficient in some Hadoop FS implementations that 'dir/' (now fixed scaladoc by using HTML entity for *)
Look detail of this issue at [SPARK-8592](https://issues.apache.org/jira/browse/SPARK-8592)
**CoarseGrainedExecutorBackend** should exit when **RegisterExecutor** failed
Author: xuchenCN <chenxu198511@gmail.com>
Closes#7110 from xuchenCN/SPARK-8592 and squashes the following commits:
71e0077 [xuchenCN] [SPARK-8592] [CORE] CoarseGrainedExecutorBackend: Cannot register with driver => NPE
Subset the enabled algorithms in an SSLOptions to the elements that are supported by the protocol provider.
Update the list of ciphers in the sample config to include modern algorithms, and specify both Oracle and IBM names. In practice the user would either specify their own chosen cipher suites, or specify none, and delegate the decision to the provider.
Author: Tim Ellison <t.p.ellison@gmail.com>
Closes#7043 from tellison/SSLEnhancements and squashes the following commits:
034efa5 [Tim Ellison] Ensure Java imports are grouped and ordered by package.
3797f8b [Tim Ellison] Remove unnecessary use of Option to improve clarity, and fix import style ordering.
4b5c89f [Tim Ellison] More robust SSL options processing.
This is a simple change to add a new environment variable
"spark.sparkr.r.command" that specifies the command that SparkR will
use when creating an R engine process. If this is not specified,
"Rscript" will be used by default.
I did not add any documentation, since I couldn't find any place where
environment variables (such as "spark.sparkr.use.daemon") are
documented.
I also did not add a unit test. The only test that would work
generally would be one starting SparkR with
sparkR.init(sparkEnvir=list(spark.sparkr.r.command="Rscript")), just
using the default value. I think that this is a low-risk change.
Likely committers: shivaram
Author: Michael Sannella x268 <msannell@tibco.com>
Closes#6557 from msannell/altR and squashes the following commits:
7eac142 [Michael Sannella x268] add spark.sparkr.r.command config parameter
This PR also includes re-ordering the order that repositories are used when resolving packages. User provided repositories will be prioritized.
cc andrewor14
Author: Burak Yavuz <brkyvz@gmail.com>
Closes#7089 from brkyvz/delete-prev-ivy-resolution and squashes the following commits:
a21f95a [Burak Yavuz] remove previous ivy resolution when using spark-submit
Note that 'dir/*' can be more efficient in some Hadoop FS implementations that 'dir/'
Author: Sean Owen <sowen@cloudera.com>
Closes#7036 from srowen/SPARK-8437 and squashes the following commits:
0e813ae [Sean Owen] Note that 'dir/*' can be more efficient in some Hadoop FS implementations that 'dir/'
Hopefully, this suite will not be flaky anymore.
Author: Yin Huai <yhuai@databricks.com>
Closes#7027 from yhuai/SPARK-8567 and squashes the following commits:
c0167e2 [Yin Huai] Add sc.stop().
This patch excludes `hadoop-client`'s dependency on `mockito-all`. As of #7061, Spark depends on `mockito-core` instead of `mockito-all`, so the dependency from Hadoop was leading to test compilation failures for some of the Hadoop 2 SBT builds.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7090 from JoshRosen/SPARK-8709 and squashes the following commits:
e190122 [Josh Rosen] [SPARK-8709] Exclude hadoop-client's mockito-all dependency.
This is a follow up of #6404, the ScriptTransformation prints the error msg into stderr directly, probably be a disaster for application log.
Author: Cheng Hao <hao.cheng@intel.com>
Closes#6882 from chenghao-intel/verbose and squashes the following commits:
bfedd77 [Cheng Hao] revert the write
76ff46b [Cheng Hao] update the CircularBuffer
692b19e [Cheng Hao] check the process exitValue for ScriptTransform
47e0970 [Cheng Hao] Use the RedirectThread instead
1de771d [Cheng Hao] naming the threads in ScriptTransformation
8536e81 [Cheng Hao] disable the error message redirection for stderr
Use case - we want to log applicationId (YARN in hour case) to request help with troubleshooting from the DevOps
Author: Vladimir Vladimirov <vladimir.vladimirov@magnetic.com>
Closes#6936 from smartkiwi/master and squashes the following commits:
870338b [Vladimir Vladimirov] this would make doctest to run in python3
0eae619 [Vladimir Vladimirov] Scala doesn't use u'...' for unicode literals
14d77a8 [Vladimir Vladimirov] stop using ELLIPSIS
b4ebfc5 [Vladimir Vladimirov] addressed PR feedback - updated docstring
223a32f [Vladimir Vladimirov] fixed test - applicationId is property that returns the string
3221f5a [Vladimir Vladimirov] [SPARK-8528] added documentation for Scala
2cff090 [Vladimir Vladimirov] [SPARK-8528] add applicationId property for SparkContext object in pyspark
When there are massive tasks, such as `sc.parallelize(1 to 100000, 10000).count()`, the generated JS codes have a lot of string concatenations in the stage page, nearly 40 string concatenations for one task.
We can generate the whole string for a task instead of execution string concatenations in the browser.
Before this patch, the load time of the page is about 21 seconds.
After this patch, it reduces to about 17 seconds.
One disadvantage is that the generated JS codes become hard to read.
Author: zsxwing <zsxwing@gmail.com>
Closes#7082 from zsxwing/js-string and squashes the following commits:
b29231d [zsxwing] Avoid massive concating strings in Javascript
Spark's tests currently depend on `mockito-all`, which bundles Hamcrest and Objenesis classes. Instead, it should depend on `mockito-core`, which declares those libraries as Maven dependencies. This is necessary in order to fix a dependency conflict that leads to a NoSuchMethodError when using certain Hamcrest matchers.
See https://github.com/mockito/mockito/wiki/Declaring-mockito-dependency for more details.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7061 from JoshRosen/mockito-core-instead-of-all and squashes the following commits:
70eccbe [Josh Rosen] Depend on mockito-core instead of mockito-all.
If `RDD.getPreferredLocations()` throws an exception it may crash the DAGScheduler and SparkContext. This patch addresses this by adding a try-catch block.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7023 from JoshRosen/SPARK-8606 and squashes the following commits:
770b169 [Josh Rosen] Fix getPreferredLocations() DAGScheduler crash with try block.
44a9b55 [Josh Rosen] Add test of a buggy getPartitions() method
19aa9f7 [Josh Rosen] Add (failing) regression test for getPreferredLocations() DAGScheduler crash
Author: Sandy Ryza <sandy@cloudera.com>
Closes#7050 from sryza/sandy-spark-8623 and squashes the following commits:
58a8079 [Sandy Ryza] SPARK-8623. Hadoop RDDs fail to properly serialize configuration
Add `getStaticClass` method in SparkR's `RBackendHandler`
This is a fix for the problem referenced in [SPARK-5185](https://issues.apache.org/jira/browse/SPARK-5185).
cc shivaram
Author: cafreeman <cfreeman@alteryx.com>
Closes#7001 from cafreeman/branch-1.4 and squashes the following commits:
8f81194 [cafreeman] Add missing license
31aedcf [cafreeman] Refactor test to call an external R script
2c22073 [cafreeman] Merge branch 'branch-1.4' of github.com:apache/spark into branch-1.4
0bea809 [cafreeman] Fixed relative path issue and added smaller JAR
ee25e60 [cafreeman] Merge branch 'branch-1.4' of github.com:apache/spark into branch-1.4
9a5c362 [cafreeman] test for including JAR when launching sparkContext
9101223 [cafreeman] Merge branch 'branch-1.4' of github.com:apache/spark into branch-1.4
5a80844 [cafreeman] Fix style nits
7c6bd0c [cafreeman] [SPARK-8607] SparkR
(cherry picked from commit 2579948bf5)
Signed-off-by: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
This commit adds a new metric, `messageProcessingTime`, to the DAGScheduler metrics source. This metrics tracks the time taken to process messages in the scheduler's event processing loop, which is a helpful debugging aid for diagnosing performance issues in the scheduler (such as SPARK-4961).
In order to do this, I moved the creation of the DAGSchedulerSource metrics source into DAGScheduler itself, similar to how MasterSource is created and registered in Master.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7002 from JoshRosen/SPARK-8344 and squashes the following commits:
57f914b [Josh Rosen] Fix import ordering
7d6bb83 [Josh Rosen] Add message processing time metrics to DAGScheduler
Fix for incorrect memory in Spark UI as per SPARK-5768
Author: Joshi <rekhajoshm@gmail.com>
Author: Rekha Joshi <rekhajoshm@gmail.com>
Closes#6972 from rekhajoshm/SPARK-5768 and squashes the following commits:
b678a91 [Joshi] Fix for incorrect memory in Spark UI
2fe53d9 [Joshi] Fix for incorrect memory in Spark UI
eb823b8 [Joshi] SPARK-5768: Fix for incorrect memory in Spark UI
0be142d [Rekha Joshi] Merge pull request #3 from apache/master
106fd8e [Rekha Joshi] Merge pull request #2 from apache/master
e3677c9 [Rekha Joshi] Merge pull request #1 from apache/master
This commit updates the shuffle read path to enable ShuffleReader implementations more control over the deserialization process.
The BlockStoreShuffleFetcher.fetch() method has been renamed to BlockStoreShuffleFetcher.fetchBlockStreams(). Previously, this method returned a record iterator; now, it returns an iterator of (BlockId, InputStream). Deserialization of records is now handled in the ShuffleReader.read() method.
This change creates a cleaner separation of concerns and allows implementations of ShuffleReader more flexibility in how records are retrieved.
Author: Matt Massie <massie@cs.berkeley.edu>
Author: Kay Ousterhout <kayousterhout@gmail.com>
Closes#6423 from massie/shuffle-api-cleanup and squashes the following commits:
8b0632c [Matt Massie] Minor Scala style fixes
d0a1b39 [Matt Massie] Merge pull request #1 from kayousterhout/massie_shuffle-api-cleanup
290f1eb [Kay Ousterhout] Added test for HashShuffleReader.read()
5186da0 [Kay Ousterhout] Revert "Add test to ensure HashShuffleReader is freeing resources"
f98a1b9 [Matt Massie] Add test to ensure HashShuffleReader is freeing resources
a011bfa [Matt Massie] Use PrivateMethodTester on check that delegate stream is closed
4ea1712 [Matt Massie] Small code cleanup for readability
7429a98 [Matt Massie] Update tests to check that BufferReleasingStream is closing delegate InputStream
f458489 [Matt Massie] Remove unnecessary map() on return Iterator
4abb855 [Matt Massie] Consolidate metric code. Make it clear why InterrubtibleIterator is needed.
5c30405 [Matt Massie] Return visibility of BlockStoreShuffleFetcher to private[hash]
7eedd1d [Matt Massie] Small Scala import cleanup
28f8085 [Matt Massie] Small import nit
f93841e [Matt Massie] Update shuffle read metrics in ShuffleReader instead of BlockStoreShuffleFetcher.
7e8e0fe [Matt Massie] Minor Scala style fixes
01e8721 [Matt Massie] Explicitly cast iterator in branches for type clarity
7c8f73e [Matt Massie] Close Block InputStream immediately after all records are read
208b7a5 [Matt Massie] Small code style changes
b70c945 [Matt Massie] Make BlockStoreShuffleFetcher visible to shuffle package
19135f2 [Matt Massie] [SPARK-7884] Allow Spark shuffle APIs to be more customizable
Author: Holden Karau <holden@pigscanfly.ca>
Closes#6918 from holdenk/SPARK-8498-fix-npe-in-errorhandling-path-in-unsafeshuffle-writer and squashes the following commits:
f807832 [Holden Karau] Log error if we can't throw it
855f9aa [Holden Karau] Spelling - not my strongest suite. Fix Propegates to Propagates.
039d620 [Holden Karau] Add missing closeandwriteoutput
30e558d [Holden Karau] go back to try/finally
e503b8c [Holden Karau] Improve the test to ensure we aren't masking the underlying exception
ae0b7a7 [Holden Karau] Fix the test
2e6abf7 [Holden Karau] Be more cautious when cleaning up during failed write and re-throw user exceptions
This patch also reenables the tests. Now that we have access to the log4j logs it should be easier to debug the flakiness.
yhuai brkyvz
Author: Andrew Or <andrew@databricks.com>
Closes#6886 from andrewor14/spark-submit-suite-fix and squashes the following commits:
3f99ff1 [Andrew Or] Move destroy to finally block
9a62188 [Andrew Or] Re-enable ignored tests
2382672 [Andrew Or] Check for exit code
