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7205 commits

Author SHA1 Message Date
Ryan Blue 31b59bd805 [SPARK-28843][PYTHON] Set OMP_NUM_THREADS to executor cores for python if not set
### What changes were proposed in this pull request?

When starting python processes, set `OMP_NUM_THREADS` to the number of cores allocated to an executor or driver if `OMP_NUM_THREADS` is not already set. Each python process will use the same `OMP_NUM_THREADS` setting, even if workers are not shared.

This avoids creating an OpenMP thread pool for parallel processing with a number of threads equal to the number of cores on the executor and [significantly reduces memory consumption](https://github.com/numpy/numpy/issues/10455). Instead, this threadpool should use the number of cores allocated to the executor, if available. If a setting for number of cores is not available, this doesn't change any behavior. OpenMP is used by numpy and pandas.

### Why are the changes needed?

To reduce memory consumption for PySpark jobs.

### Does this PR introduce any user-facing change?

No.

### How was this patch tested?

Validated this reduces python worker memory consumption by more than 1GB on our cluster.

Closes #25545 from rdblue/SPARK-28843-set-omp-num-cores.

Authored-by: Ryan Blue <blue@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
2019-08-30 10:29:46 +09:00
wuyi 70f4bbccc5 [SPARK-28414][WEBUI] UI updates to show resource info in Standalone
## What changes were proposed in this pull request?

Since SPARK-27371 has supported GPU-aware resource scheduling in Standalone, this PR adds resources info in Standalone UI.

## How was this patch tested?

Updated `JsonProtocolSuite` and tested manually.

Master page:

![masterpage](https://user-images.githubusercontent.com/16397174/62835958-b933c100-bc90-11e9-814f-22bae048303d.png)

Worker page

![workerpage](https://user-images.githubusercontent.com/16397174/63417947-d2790200-c434-11e9-8979-36b8f558afd3.png)

Application page

![applicationpage](https://user-images.githubusercontent.com/16397174/62835964-cbadfa80-bc90-11e9-99a2-26e05421619a.png)

Closes #25409 from Ngone51/SPARK-28414.

Authored-by: wuyi <ngone_5451@163.com>
Signed-off-by: Thomas Graves <tgraves@apache.org>
2019-08-27 08:59:29 -05:00
mcheah 2efa6f5dd3 [SPARK-28607][CORE][SHUFFLE] Don't store partition lengths twice
## What changes were proposed in this pull request?

The shuffle writer API introduced in SPARK-28209 has a flaw that leads to a memory usage regression - we ended up tracking the partition lengths in two places. Here, we modify the API slightly to avoid redundant tracking. The implementation of the shuffle writer plugin is now responsible for tracking the lengths of partitions, and propagating this back up to the higher shuffle writer as part of the commitAllPartitions API.

## How was this patch tested?

Existing unit tests.

Closes #25341 from mccheah/dont-redundantly-store-part-lengths.

Authored-by: mcheah <mcheah@palantir.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-08-26 10:39:29 -07:00
Nikita Gorbachevsky 9f8c7a2804 [SPARK-28709][DSTREAMS] Fix StreamingContext leak through Streaming
## What changes were proposed in this pull request?

In my application spark streaming is restarted programmatically by stopping StreamingContext without stopping of SparkContext and creating/starting a new one. I use it for automatic detection of Kafka topic/partition changes and automatic failover in case of non fatal exceptions.

However i notice that after multiple restarts driver fails with OOM. During investigation of heap dump i figured out that StreamingContext object isn't cleared by GC after stopping.

<img width="1901" alt="Screen Shot 2019-08-14 at 12 23 33" src="https://user-images.githubusercontent.com/13151161/63010149-83f4c200-be8e-11e9-9f48-12b6e97839f4.png">

There are several places which holds reference to it :

1. StreamingTab registers StreamingJobProgressListener which holds reference to Streaming Context directly to LiveListenerBus shared queue via ssc.sc.addSparkListener(listener) method invocation. However this listener isn't unregistered at stop method.
2. json handlers (/streaming/json and /streaming/batch/json) aren't unregistered in SparkUI, while they hold reference to StreamingJobProgressListener. Basically the same issue affects all the pages, i assume that renderJsonHandler should be added to pageToHandlers cache on attachPage method invocation in order to unregistered it as well on detachPage.
3. SparkUi holds reference to StreamingJobProgressListener in the corresponding local variable which isn't cleared after stopping of StreamingContext.

## How was this patch tested?

Added tests to existing test suites.
After i applied these changes via reflection in my app OOM on driver side gone.

Closes #25439 from choojoyq/SPARK-28709-fix-streaming-context-leak-on-stop.

Authored-by: Nikita Gorbachevsky <nikitag@playtika.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
2019-08-26 09:30:36 -05:00
Anton Kirillov f17f1d01e2 [SPARK-28778][MESOS] Fixed executors advertised address when running in virtual network
### What changes were proposed in this pull request?
Resolves [SPARK-28778: Shuffle jobs fail due to incorrect advertised address when running in a virtual network on Mesos](https://issues.apache.org/jira/browse/SPARK-28778).

This patch fixes a bug which occurs when shuffle jobs are launched by Mesos in a virtual network. Mesos scheduler sets executor `--hostname` parameter to `0.0.0.0` in the case when `spark.mesos.network.name` is provided. This makes executors use `0.0.0.0` as their advertised address and, in the presence of shuffle, executors fail to fetch shuffle blocks from each other using `0.0.0.0` as the origin. When a virtual network is used the hostname or IP address is not known upfront and assigned to a container at its start time so the executor process needs to advertise the correct dynamically assigned address to be reachable by other executors.

Changes:
- added a fallback to `Utils.localHostName()` in Spark Executors when `--hostname` is not provided
- removed setting executor address to `0.0.0.0` from Mesos scheduler
- refactored the code related to building executor command in Mesos scheduler
- added network configuration support to Docker containerizer
- added unit tests

### Why are the changes needed?
The bug described above prevents Mesos users from running any jobs which involve shuffle due to the inability of executors to fetch shuffle blocks because of incorrect advertised address when virtual network is used.

### Does this PR introduce any user-facing change?
No

### How was this patch tested?
- added unit test to `MesosCoarseGrainedSchedulerBackendSuite` which verifies the absence of `--hostname` parameter  when `spark.mesos.network.name` is provided and its presence otherwise
- added unit test to `MesosSchedulerBackendUtilSuite` which verifies that `MesosSchedulerBackendUtil.buildContainerInfo` sets network-related properties for Docker containerizer
- unit tests from this repo launched with profiles: `./build/mvn test -Pmesos -Pnetlib-lgpl -Psparkr -Phive -Phive-thriftserver`, build log attached: [mvn.test.log](https://github.com/apache/spark/files/3516891/mvn.test.log)
- integration tests from [DCOS Spark repo](https://github.com/mesosphere/spark-build), more specifically - [test_spark_cni.py](https://github.com/mesosphere/spark-build/blob/master/tests/test_spark_cni.py) which runs a specific [shuffle job](https://github.com/mesosphere/spark-build/blob/master/tests/jobs/scala/src/main/scala/ShuffleApp.scala) and verifies its successful completion, Mesos task network configuration, and IP addresses for both Mesos and Docker containerizers

Closes #25500 from akirillov/DCOS-45840-fix-advertised-ip-in-virtual-networks.

Authored-by: Anton Kirillov <akirillov@mesosophere.io>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-08-23 18:30:05 -07:00
HyukjinKwon d25cbd44ee [SPARK-28839][CORE] Avoids NPE in context cleaner when dynamic allocation and shuffle service are on
### What changes were proposed in this pull request?

This PR proposes to avoid to thrown NPE at context cleaner when shuffle service is on - it is kind of a small followup of https://github.com/apache/spark/pull/24817

Seems like it sets `null` for `shuffleIds` to track when the service is on. Later, `removeShuffle` tries to remove an element at `shuffleIds` which leads to NPE. It fixes it by explicitly not sending the event (`ShuffleCleanedEvent`) in this case.

See the code path below:

cbad616d4c/core/src/main/scala/org/apache/spark/SparkContext.scala (L584)

cbad616d4c/core/src/main/scala/org/apache/spark/ContextCleaner.scala (L125)

cbad616d4c/core/src/main/scala/org/apache/spark/ContextCleaner.scala (L190)

cbad616d4c/core/src/main/scala/org/apache/spark/ContextCleaner.scala (L220-L230)

cbad616d4c/core/src/main/scala/org/apache/spark/scheduler/dynalloc/ExecutorMonitor.scala (L353-L357)

cbad616d4c/core/src/main/scala/org/apache/spark/scheduler/dynalloc/ExecutorMonitor.scala (L347)

cbad616d4c/core/src/main/scala/org/apache/spark/scheduler/dynalloc/ExecutorMonitor.scala (L400-L406)

cbad616d4c/core/src/main/scala/org/apache/spark/scheduler/dynalloc/ExecutorMonitor.scala (L475)

cbad616d4c/core/src/main/scala/org/apache/spark/scheduler/dynalloc/ExecutorMonitor.scala (L427)

### Why are the changes needed?

This is a bug fix.

### Does this PR introduce any user-facing change?

It prevents the exception:

```
19/08/21 06:44:01 ERROR AsyncEventQueue: Listener ExecutorMonitor threw an exception
java.lang.NullPointerException
	at org.apache.spark.scheduler.dynalloc.ExecutorMonitor$Tracker.removeShuffle(ExecutorMonitor.scala:479)
	at org.apache.spark.scheduler.dynalloc.ExecutorMonitor.$anonfun$cleanupShuffle$2(ExecutorMonitor.scala:408)
	at org.apache.spark.scheduler.dynalloc.ExecutorMonitor.$anonfun$cleanupShuffle$2$adapted(ExecutorMonitor.scala:407)
	at scala.collection.Iterator.foreach(Iterator.scala:941)
	at scala.collection.Iterator.foreach$(Iterator.scala:941)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
	at org.apache.spark.scheduler.dynalloc.ExecutorMonitor.cleanupShuffle(ExecutorMonitor.scala:407)
	at org.apache.spark.scheduler.dynalloc.ExecutorMonitor.onOtherEvent(ExecutorMonitor.sc
```

### How was this patch test?

Unittest was added.

Closes #25551 from HyukjinKwon/SPARK-28839.

Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-08-23 12:44:56 -07:00
Kousuke Saruta 33e45ec7b8 [SPARK-28769][CORE] Improve warning message of BarrierExecutionMode when required slots > maximum slots
### What changes were proposed in this pull request?
Improved warning message in Barrier Execution Mode when required slots > maximum slots.
The new message contains information about required slots, maximum slots and how many times retry failed.

### Why are the changes needed?
Providing to users with the number of required slots, maximum slots and how many times retry failed might help users to decide what they should do.
For example, continuing to wait for retry succeeded or killing jobs.

### Does this PR introduce any user-facing change?
Yes.
If `spark.scheduler.barrier.maxConcurrentTaskCheck.maxFailures=3`, we get following warning message.

Before applying this change:

```
19/08/18 15:18:09 WARN DAGScheduler: The job 2 requires to run a barrier stage that requires more slots than the total number of slots in the cluster currently.
19/08/18 15:18:24 WARN DAGScheduler: The job 2 requires to run a barrier stage that requires more slots than the total number of slots in the cluster currently.
19/08/18 15:18:39 WARN DAGScheduler: The job 2 requires to run a barrier stage that requires more slots than the total number of slots in the cluster currently.
19/08/18 15:18:54 WARN DAGScheduler: The job 2 requires to run a barrier stage that requires more slots than the total number of slots in the cluster currently.
org.apache.spark.scheduler.BarrierJobSlotsNumberCheckFailed: [SPARK-24819]: Barrier execution mode does not allow run a barrier stage that requires more slots than the total number of slots in the cluster currently. Please init a new cluster with more CPU cores or repartition the input RDD(s) to reduce the number of slots required to run this barrier stage.
  at org.apache.spark.scheduler.DAGScheduler.checkBarrierStageWithNumSlots(DAGScheduler.scala:439)
  at org.apache.spark.scheduler.DAGScheduler.createResultStage(DAGScheduler.scala:453)
  at org.apache.spark.scheduler.DAGScheduler.handleJobSubmitted(DAGScheduler.scala:983)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2140)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2132)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2121)
  at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
  at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:749)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2080)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2120)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2145)
  at org.apache.spark.rdd.RDD.$anonfun$collect$1(RDD.scala:961)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
  at org.apache.spark.rdd.RDD.withScope(RDD.scala:366)
  at org.apache.spark.rdd.RDD.collect(RDD.scala:960)
  ... 47 elided
```
After applying this change:

```
19/08/18 16:52:23 WARN DAGScheduler: The job 0 requires to run a barrier stage that requires 3 slots than the total number of slots(2) in the cluster currently.
19/08/18 16:52:38 WARN DAGScheduler: The job 0 requires to run a barrier stage that requires 3 slots than the total number of slots(2) in the cluster currently (Retry 1/3 failed).
19/08/18 16:52:53 WARN DAGScheduler: The job 0 requires to run a barrier stage that requires 3 slots than the total number of slots(2) in the cluster currently (Retry 2/3 failed).
19/08/18 16:53:08 WARN DAGScheduler: The job 0 requires to run a barrier stage that requires 3 slots than the total number of slots(2) in the cluster currently (Retry 3/3 failed).
org.apache.spark.scheduler.BarrierJobSlotsNumberCheckFailed: [SPARK-24819]: Barrier execution mode does not allow run a barrier stage that requires more slots than the total number of slots in the cluster currently. Please init a new cluster with more CPU cores or repartition the input RDD(s) to reduce the number of slots required to run this barrier stage.
  at org.apache.spark.scheduler.DAGScheduler.checkBarrierStageWithNumSlots(DAGScheduler.scala:439)
  at org.apache.spark.scheduler.DAGScheduler.createResultStage(DAGScheduler.scala:453)
  at org.apache.spark.scheduler.DAGScheduler.handleJobSubmitted(DAGScheduler.scala:983)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2140)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2132)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2121)
  at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
  at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:749)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2080)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2120)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2145)
  at org.apache.spark.rdd.RDD.$anonfun$collect$1(RDD.scala:961)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
  at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
  at org.apache.spark.rdd.RDD.withScope(RDD.scala:366)
  at org.apache.spark.rdd.RDD.collect(RDD.scala:960)
  ... 47 elided
```

### How was this patch tested?
I tested manually using Spark Shell with following configuration and script. And then, checked log message.

```
$ bin/spark-shell --master local[2] --conf spark.scheduler.barrier.maxConcurrentTasksCheck.maxFailures=3
scala> sc.parallelize(1 to 100, sc.defaultParallelism+1).barrier.mapPartitions(identity(_)).collect
```

Closes #25487 from sarutak/barrier-exec-mode-warning-message.

Authored-by: Kousuke Saruta <sarutak@oss.nttdata.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
2019-08-22 14:06:58 -05:00
Sean Owen 9ea37b09cf [SPARK-17875][CORE][BUILD] Remove dependency on Netty 3
### What changes were proposed in this pull request?

Spark uses Netty 4 directly, but also includes Netty 3 only because transitive dependencies do. The dependencies (Hadoop HDFS, Zookeeper, Avro) don't seem to need this dependency as used in Spark. I think we can forcibly remove it to slim down the dependencies.

Previous attempts were blocked by its usage in Flume, but that dependency has gone away.
https://github.com/apache/spark/pull/15436

### Why are the changes needed?

Mostly to reduce the transitive dependency size and complexity a little bit and avoid triggering spurious security alerts on Netty 3.x usage.

### Does this PR introduce any user-facing change?

No

### How was this patch tested?

Existing tests

Closes #25544 from srowen/SPARK-17875.

Authored-by: Sean Owen <sean.owen@databricks.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-08-21 21:27:56 -07:00
WeichenXu 9779a82ea0 [SPARK-28483][CORE][FOLLOW-UP] Dealing with interrupted exception in BarrierTaskContext.barrier()
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### What changes were proposed in this pull request?
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Dealing with interrupted exception in BarrierTaskContext.barrier()

### Why are the changes needed?
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Interrupted exception will happen in the case sparkContext local property "spark.job.interruptOnCancel" set true.

### Does this PR introduce any user-facing change?
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No.

### How was this patch tested?
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UT.

Closes #25519 from WeichenXu123/barrier_fl.

Authored-by: WeichenXu <weichen.xu@databricks.com>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-08-21 19:51:45 +08:00
Dhruve Ashar a50959a7f6 [SPARK-27937][CORE] Revert partial logic for auto namespace discovery
## What changes were proposed in this pull request?
This change reverts the logic which was introduced as a part of SPARK-24149 and a subsequent followup PR.

With existing logic:
- Spark fails to launch with HDFS federation enabled while trying to get a path to a logical nameservice.
- It gets tokens for unrelated namespaces if they are used in HDFS Federation
- Automatic namespace discovery is supported only if these are on the same cluster.

Rationale for change:
- For accessing data from related namespaces, viewfs should handle getting tokens for spark
- For accessing data from unrelated namespaces(user explicitly specifies them using existing configs) as these could be on the same or different cluster.

(Please fill in changes proposed in this fix)
Revert the changes.

## How was this patch tested?
Ran few manual tests and unit test.

Closes #24785 from dhruve/bug/SPARK-27937.

Authored-by: Dhruve Ashar <dhruveashar@gmail.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-08-20 12:42:35 -07:00
WeichenXu bc75ed675b [SPARK-28483][CORE] Fix canceling a spark job using barrier mode but barrier tasks blocking on BarrierTaskContext.barrier()
## What changes were proposed in this pull request?

Fix canceling a spark job using barrier mode but barrier tasks do not exit.
Currently, when spark tasks are killed, `BarrierTaskContext.barrier()` cannot be killed (it will blocking on RPC request), cause the task blocking and cannot exit.

In my PR I implement an interface for RPC which support `abort` in class `RpcEndpointRef`
```
  def askAbortable[T: ClassTag](
      message: Any,
      timeout: RpcTimeout): AbortableRpcFuture[T]
```

The returned `AbortableRpcFuture` instance include an `abort` method so that we can abort the RPC before it timeout.

## How was this patch tested?

Unit test added.

Manually test:

### Test code
launch spark-shell via `spark-shell --master local[4]`
and run following code:
```
sc.setLogLevel("INFO")
import org.apache.spark.BarrierTaskContext
val n = 4
def taskf(iter: Iterator[Int]): Iterator[Int] = {
  val context = BarrierTaskContext.get()
  val x = iter.next()
  if (x % 2 == 0) {
    // sleep 6000000 seconds with task killed checking
    for (i <- 0 until 6000000) {
      Thread.sleep(1000)
      if (context.isInterrupted()) {
        throw new org.apache.spark.TaskKilledException()
      }
    }
  }
  context.barrier()
  return Iterator.empty
}

// launch spark job, including 4 tasks, tasks 1/3 will enter `barrier()`, and tasks 0/2 will enter `sleep`
sc.parallelize((0 to n), n).barrier().mapPartitions(taskf).collect()
```
And then press Ctrl+C to exit the running job.

### Before
press Ctrl+C to exit the running job, then open spark UI we can see 2 tasks (task 1/3) are not killed. They are blocking.

### After
press Ctrl+C to exit the running job,  we can see in spark UI all tasks killed successfully.

Please review https://spark.apache.org/contributing.html before opening a pull request.

Closes #25235 from WeichenXu123/sc_14848.

Authored-by: WeichenXu <weichen.xu@databricks.com>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-08-20 14:21:47 +08:00
Yuanjian Li 0d3a783cc5 [SPARK-28699][CORE] Fix a corner case for aborting indeterminate stage
### What changes were proposed in this pull request?
Change the logic of collecting the indeterminate stage, we should look at stages from mapStage, not failedStage during handle FetchFailed.

### Why are the changes needed?
In the fetch failed error handle logic, the original logic of collecting indeterminate stage from the fetch failed stage. And in the scenario of the fetch failed happened in the first task of this stage, this logic will cause the indeterminate stage to resubmit partially. Eventually, we are capable of getting correctness bug.

### Does this PR introduce any user-facing change?
It makes the corner case of indeterminate stage abort as expected.

### How was this patch tested?
New UT in DAGSchedulerSuite.
Run below integrated test with `local-cluster[5, 2, 5120]`, and set `spark.sql.execution.sortBeforeRepartition`=false, it will abort the indeterminate stage as expected:
```
import scala.sys.process._
import org.apache.spark.TaskContext

val res = spark.range(0, 10000 * 10000, 1).map{ x => (x % 1000, x)}
// kill an executor in the stage that performs repartition(239)
val df = res.repartition(113).map{ x => (x._1 + 1, x._2)}.repartition(239).map { x =>
  if (TaskContext.get.attemptNumber == 0 && TaskContext.get.partitionId < 1 && TaskContext.get.stageAttemptNumber == 0) {
    throw new Exception("pkill -f -n java".!!)
  }
  x
}
val r2 = df.distinct.count()
```

Closes #25498 from xuanyuanking/SPARK-28699-followup.

Authored-by: Yuanjian Li <xyliyuanjian@gmail.com>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-08-20 13:47:59 +08:00
Sean Owen c9b49f3978 [SPARK-28737][CORE] Update Jersey to 2.29
## What changes were proposed in this pull request?

Update Jersey to 2.27+, ideally 2.29, for possible JDK 11 fixes.

## How was this patch tested?

Existing tests.

Closes #25455 from srowen/SPARK-28737.

Authored-by: Sean Owen <sean.owen@databricks.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-08-16 15:08:04 -07:00
angerszhu 036fd3903f [SPARK-27637][SHUFFLE][FOLLOW-UP] For nettyBlockTransferService, if IOException occurred while create client, check whether relative executor is alive before retry #24533
### What changes were proposed in this pull request?

In pr #[24533](https://github.com/apache/spark/pull/24533/files) , it prevent retry to a removed Executor.
In my test, I can't catch exceptions from
` new OneForOneBlockFetcher(client, appId, execId, blockIds, listener,
              transportConf, tempFileManager).start()`
And I check the code carefully, method **start()** will handle exception of IOException in it's retry logical, won't throw it out. until it meet maxRetry times or meet exception that is not  IOException.

And if we meet the situation that when we fetch block , the executor is dead, when we rerun
`RetryingBlockFetcher.BlockFetchStarter.createAndStart()`
we may failed when we create a transport client to dead executor. it will throw a IOException.
We should catch this IOException.

### Why are the changes needed?
Old solution not comprehensive. Didn't cover more case.

### Does this PR introduce any user-facing change?
No

### How was this patch tested?
Existed Unit Test

Closes #25469 from AngersZhuuuu/SPARK-27637-FLLOW-UP.

Authored-by: angerszhu <angers.zhu@gmail.com>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-08-16 23:24:32 +08:00
Steve Loughran 2ac6163a5d [SPARK-23977][SQL] Support High Performance S3A committers [test-hadoop3.2]
This patch adds the binding classes to enable spark to switch dataframe output to using the S3A zero-rename committers shipping in Hadoop 3.1+. It adds a source tree into the hadoop-cloud-storage module which only compiles with the hadoop-3.2 profile, and contains a binding for normal output and a specific bridge class for Parquet (as the parquet output format requires a subclass of `ParquetOutputCommitter`.

Commit algorithms are a critical topic. There's no formal proof of correctness, but the algorithms are documented an analysed in [A Zero Rename Committer](https://github.com/steveloughran/zero-rename-committer/releases). This also reviews the classic v1 and v2 algorithms, IBM's swift committer and the one from EMRFS which they admit was based on the concepts implemented here.

Test-wise

* There's a public set of scala test suites [on github](https://github.com/hortonworks-spark/cloud-integration)
* We have run integration tests against Spark on Yarn clusters.
* This code has been shipping for ~12 months in HDP-3.x.

Closes #24970 from steveloughran/cloud/SPARK-23977-s3a-committer.

Authored-by: Steve Loughran <stevel@cloudera.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-08-15 09:39:26 -07:00
Xianjin YE 3ec24fd128 [SPARK-28203][CORE][PYTHON] PythonRDD should respect SparkContext's hadoop configuration
## What changes were proposed in this pull request?
1. PythonHadoopUtil.mapToConf generates a Configuration with loadDefaults disabled
2. merging hadoop conf in several places of PythonRDD is consistent.

## How was this patch tested?
Added a new test and existed tests

Closes #25002 from advancedxy/SPARK-28203.

Authored-by: Xianjin YE <advancedxy@gmail.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
2019-08-15 10:39:33 +09:00
Marcelo Vanzin 0343854f54 [SPARK-28487][K8S] More responsive dynamic allocation with K8S
This change implements a few changes to the k8s pod allocator so
that it behaves a little better when dynamic allocation is on.

(i) Allow the application to ramp up immediately when there's a
change in the target number of executors. Without this change,
scaling would only trigger when a change happened in the state of
the cluster, e.g. an executor going down, or when the periodical
snapshot was taken (default every 30s).

(ii) Get rid of pending pod requests, both acknowledged (i.e. Spark
knows that a pod is pending resource allocation) and unacknowledged
(i.e. Spark has requested the pod but the API server hasn't created it
yet), when they're not needed anymore. This avoids starting those
executors to just remove them after the idle timeout, wasting resources
in the meantime.

(iii) Re-work some of the code to avoid unnecessary logging. While not
bad without dynamic allocation, the existing logging was very chatty
when dynamic allocation was on. With the changes, all the useful
information is still there, but only when interesting changes happen.

(iv) Gracefully shut down executors when they become idle. Just deleting
the pod causes a lot of ugly logs to show up, so it's better to ask pods
to exit nicely. That also allows Spark to respect the "don't delete
pods" option when dynamic allocation is on.

Tested on a small k8s cluster running different TPC-DS workloads.

Closes #25236 from vanzin/SPARK-28487.

Authored-by: Marcelo Vanzin <vanzin@cloudera.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-08-13 17:29:54 -07:00
Kousuke Saruta 247bebcf94 [SPARK-28561][WEBUI] DAG viz for barrier-execution mode
## What changes were proposed in this pull request?

In the current UI, we cannot identify which RDDs are barrier. Visualizing it will make easy to debug.
Following images are shown after this change.

![Screenshot from 2019-07-30 16-30-35](https://user-images.githubusercontent.com/4736016/62110508-83cec100-b2e9-11e9-83b9-bc2e485a4cbe.png)
![Screenshot from 2019-07-30 16-31-09](https://user-images.githubusercontent.com/4736016/62110509-83cec100-b2e9-11e9-9e2e-47c4dae23a52.png)

The boxes in pale green mean barrier (We might need to discuss which color is proper).

## How was this patch tested?

Tested manually.
The images above are shown by following operations.

```
val rdd1 = sc.parallelize(1 to 10)
val rdd2 = sc.parallelize(1 to 10)
val rdd3 = rdd1.zip(rdd2).barrier.mapPartitions(identity(_))
val rdd4 = rdd3.map(identity(_))
val rdd5 = rdd4.reduceByKey(_+_)
rdd5.collect
```

Closes #25296 from sarutak/barrierexec-dagviz.

Authored-by: Kousuke Saruta <sarutak@oss.nttdata.com>
Signed-off-by: Xingbo Jiang <xingbo.jiang@databricks.com>
2019-08-12 22:38:10 -07:00
Kousuke Saruta 25857c6559 [SPARK-28647][WEBUI] Recover additional metric feature and remove additional-metrics.js
## What changes were proposed in this pull request?

By SPARK-17019, `On Heap Memory` and `Off Heap Memory` are introduced as optional metrics.
But they are not displayed because they are made `display: none` in css and there are no way to appear them.

I know #22595 also try to resolve this issue but that will use `additional-metrics.js`.
Initially, `additional-metrics.js` is created for `StagePage` but `StagePage` currently uses `stagepage.js` for its additional metrics to be toggle because `DataTable (one of jQuery plugins)` was introduced and we needed another mechanism to add/remove columns for additional metrics.

Now that `ExecutorsPage` also uses `DataTable` so it might be better to introduce same mechanism as `StagePage` for additional metrics.

![Screenshot from 2019-08-10 05-37-25](https://user-images.githubusercontent.com/4736016/62807960-c4240f80-bb31-11e9-8e1a-1a44e2f91597.png)

And then, we can remove `additional-metrics.js` which is no longer used from anywhere.

## How was this patch tested?

After this change is applied, I confirmed `ExecutorsPage` and `StagePage` are properly rendered and all checkboxes for additional metrics work.

Closes #25374 from sarutak/remove-additional-metrics.js.

Authored-by: Kousuke Saruta <sarutak@oss.nttdata.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-08-12 17:02:28 -07:00
Gengliang Wang 48d04f74ca [SPARK-28638][WEBUI] Task summary should only contain successful tasks' metrics
## What changes were proposed in this pull request?

Currently, on requesting summary metrics, cached data are returned if the current number of "SUCCESS" tasks is the same as the value in cached data.
However, the number of "SUCCESS" tasks is wrong when there are running tasks. In `AppStatusStore`, the KVStore is `ElementTrackingStore`, instead of `InMemoryStore`. The value count is always the number of "SUCCESS" tasks + "RUNNING" tasks.
Thus, even when the running tasks are finished, the out-of-update cached data is returned.

This PR is to fix the code in getting the number of "SUCCESS" tasks.

## How was this patch tested?

Test manually, run
```
sc.parallelize(1 to 160, 40).map(i => Thread.sleep(i*100)).collect()
```
and keep refreshing the stage page , we can see the task summary metrics is wrong.

### Before fix:
![image](https://user-images.githubusercontent.com/1097932/62560343-6a141780-b8af-11e9-8942-d88540659a93.png)

### After fix:
![image](https://user-images.githubusercontent.com/1097932/62560355-7009f880-b8af-11e9-8ba8-10c083a48d7b.png)

Closes #25369 from gengliangwang/fixStagePage.

Authored-by: Gengliang Wang <gengliang.wang@databricks.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-08-12 11:47:29 -07:00
WeichenXu 0f2efe6825 [SPARK-28366][CORE][FOLLOW-UP] Refine logging in driver when loading single large unsplittable file
## What changes were proposed in this pull request?

* Add log in `NewHadoopRDD`
* Remove some words in logs which related to specific user API.

## How was this patch tested?

Manual.

Please review https://spark.apache.org/contributing.html before opening a pull request.

Closes #25391 from WeichenXu123/log_sf.

Authored-by: WeichenXu <weichen.xu@databricks.com>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-08-12 19:15:00 +08:00
Kousuke Saruta 31ef268bae [SPARK-28639][CORE][DOC] Configuration doc for Barrier Execution Mode
## What changes were proposed in this pull request?

SPARK-24817 and SPARK-24819 introduced new 3 non-internal properties for barrier-execution mode but they are not documented.
So I've added a section into configuration.md for barrier-mode execution.

## How was this patch tested?
Built using jekyll and confirm the layout by browser.

Closes #25370 from sarutak/barrier-exec-mode-conf-doc.

Authored-by: Kousuke Saruta <sarutak@oss.nttdata.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
2019-08-11 08:13:19 -05:00
Kousuke Saruta dd5599efaf [SPARK-28677][WEBUI] "Select All" checkbox in StagePage doesn't work properly
## What changes were proposed in this pull request?

In StagePage, only the first optional column (Scheduler Delay, in this case) appears even though "Select All" checkbox is checked.

![Screenshot from 2019-08-09 18-46-05](https://user-images.githubusercontent.com/4736016/62771600-8f379e80-bad8-11e9-9faa-6da8d57739d2.png)

The cause is that wrong method is used to manipulate multiple columns. columns should have been used but column was used.
I've fixed this issue by replacing the `column` with `columns`.

## How was this patch tested?

Confirmed behavior of the check-box.

![Screenshot from 2019-08-09 18-54-33](https://user-images.githubusercontent.com/4736016/62771614-98c10680-bad8-11e9-9cc0-5879ac47d1e1.png)

Closes #25397 from sarutak/fix-stagepage.js.

Authored-by: Kousuke Saruta <sarutak@oss.nttdata.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
2019-08-10 16:51:12 -05:00
younggyu chun 8535df7261 [MINOR] Fix typos in comments and replace an explicit type with <>
## What changes were proposed in this pull request?
This PR fixed typos in comments and replace the explicit type with '<>' for Java 8+.

## How was this patch tested?
Manually tested.

Closes #25338 from younggyuchun/younggyu.

Authored-by: younggyu chun <younggyuchun@gmail.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
2019-08-10 16:47:11 -05:00
Ajith ef80c32266 [SPARK-28676][CORE] Avoid Excessive logging from ContextCleaner
## What changes were proposed in this pull request?

In high workload environments, ContextCleaner seems to have excessive logging at INFO level which do not give much information. In one Particular case we see that ``INFO ContextCleaner: Cleaned accumulator`` message is 25-30% of the generated logs. We can log this information for cleanup in DEBUG level instead.

## How was this patch tested?

This do not modify any functionality. This is just changing cleanup log levels to DEBUG for  ContextCleaner

Closes #25396 from ajithme/logss.

Authored-by: Ajith <ajith2489@gmail.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-08-09 15:49:20 -07:00
wuyi cbad616d4c [SPARK-27371][CORE] Support GPU-aware resources scheduling in Standalone
## What changes were proposed in this pull request?

In this PR, we implements a complete process of GPU-aware resources scheduling
in Standalone. The whole process looks like: Worker sets up isolated resources
when it starts up and registers to master along with its resources. And, Master
picks up usable workers according to driver/executor's resource requirements to
launch driver/executor on them. Then, Worker launches the driver/executor after
preparing resources file, which is created under driver/executor's working directory,
with specified resource addresses(told by master). When driver/executor finished,
their resources could be recycled to worker. Finally, if a worker stops, it
should always release its resources firstly.

For the case of Workers and Drivers in **client** mode run on the same host, we introduce
a config option named `spark.resources.coordinate.enable`(default true) to indicate
whether Spark should coordinate resources for user. If `spark.resources.coordinate.enable=false`, user should be responsible for configuring different resources for Workers and Drivers when use resourcesFile or discovery script. If true, Spark would help user to assign different  resources for Workers and Drivers.

The solution for Spark to coordinate resources among Workers and Drivers is:

Generally, use a shared file named *____allocated_resources____.json* to sync allocated
resources info among Workers and Drivers on the same host.

After a Worker or Driver found all resources using the configured resourcesFile and/or
discovery script during launching, it should filter out available resources by excluding resources already allocated in *____allocated_resources____.json* and acquire resources from available resources according to its own requirement. After that, it should write its allocated resources along with its process id (pid) into *____allocated_resources____.json*.  Pid (proposed by tgravescs) here used to check whether the allocated resources are still valid in case of Worker or Driver crashes and doesn't release resources properly. And when a Worker or Driver finished, normally, it would always clean up its own allocated resources in *____allocated_resources____.json*.

Note that we'll always get a file lock before any access to file *____allocated_resources____.json*
and release the lock finally.

Futhermore, we appended resources info in `WorkerSchedulerStateResponse` to work
around master change behaviour in HA mode.

## How was this patch tested?

Added unit tests in WorkerSuite, MasterSuite, SparkContextSuite.

Manually tested with client/cluster mode (e.g. multiple workers) in a single node Standalone.

Closes #25047 from Ngone51/SPARK-27371.

Authored-by: wuyi <ngone_5451@163.com>
Signed-off-by: Thomas Graves <tgraves@apache.org>
2019-08-09 07:49:03 -05:00
Jungtaek Lim (HeartSaVioR) 128ea37bda [SPARK-28601][CORE][SQL] Use StandardCharsets.UTF_8 instead of "UTF-8" string representation, and get rid of UnsupportedEncodingException
## What changes were proposed in this pull request?

This patch tries to keep consistency whenever UTF-8 charset is needed, as using `StandardCharsets.UTF_8` instead of using "UTF-8". If the String type is needed, `StandardCharsets.UTF_8.name()` is used.

This change also brings the benefit of getting rid of `UnsupportedEncodingException`, as we're providing `Charset` instead of `String` whenever possible.

This also changes some private Catalyst helper methods to operate on encodings as `Charset` objects rather than strings.

## How was this patch tested?

Existing unit tests.

Closes #25335 from HeartSaVioR/SPARK-28601.

Authored-by: Jungtaek Lim (HeartSaVioR) <kabhwan@gmail.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-08-05 20:45:54 -07:00
wuyi 94499af6f0 [SPARK-28486][CORE][PYTHON] Map PythonBroadcast's data file to a BroadcastBlock to avoid delete by GC
## What changes were proposed in this pull request?

Currently, PythonBroadcast may delete its data file while a python worker still needs it. This happens because PythonBroadcast overrides the `finalize()` method to delete its data file. So, when GC happens and no  references on broadcast variable, it may trigger `finalize()` to delete
data file. That's also means, data under python Broadcast variable couldn't be deleted when `unpersist()`/`destroy()` called but relys on GC.

In this PR, we removed the `finalize()` method, and map the PythonBroadcast data file to a BroadcastBlock(which has the same broadcast id with the broadcast variable who wrapped this PythonBroadcast) when PythonBroadcast is deserializing. As a result, the data file could be deleted just like other pieces of the Broadcast variable when `unpersist()`/`destroy()` called and do not rely on GC any more.

## How was this patch tested?

Added a Python test, and tested manually(verified create/delete the broadcast block).

Closes #25262 from Ngone51/SPARK-28486.

Authored-by: wuyi <ngone_5451@163.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
2019-08-05 20:18:53 +09:00
Yuanjian Li db39f45baf [SPARK-28593][CORE] Rename ShuffleClient to BlockStoreClient which more close to its usage
## What changes were proposed in this pull request?

After SPARK-27677, the shuffle client not only handles the shuffle block but also responsible for local persist RDD blocks. For better code scalability and precise semantics(as the [discussion](https://github.com/apache/spark/pull/24892#discussion_r300173331)), here we did several changes:

- Rename ShuffleClient to BlockStoreClient.
- Correspondingly rename the ExternalShuffleClient to ExternalBlockStoreClient, also change the server-side class from ExternalShuffleBlockHandler to ExternalBlockHandler.
- Move MesosExternalBlockStoreClient to Mesos package.

Note, we still keep the name of BlockTransferService, because the `Service` contains both client and server, also the name of BlockTransferService is not referencing shuffle client only.

## How was this patch tested?

Existing UT.

Closes #25327 from xuanyuanking/SPARK-28593.

Lead-authored-by: Yuanjian Li <xyliyuanjian@gmail.com>
Co-authored-by: Yuanjian Li <yuanjian.li@databricks.com>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-08-05 14:54:45 +08:00
yunzoud c212c9d9ed
[SPARK-28574][CORE] Allow to config different sizes for event queues
## What changes were proposed in this pull request?
Add configuration spark.scheduler.listenerbus.eventqueue.${name}.capacity to allow configuration of different event queue size.

## How was this patch tested?
Unit test in core/src/test/scala/org/apache/spark/scheduler/SparkListenerSuite.scala

Closes #25307 from yunzoud/SPARK-28574.

Authored-by: yunzoud <yun.zou@databricks.com>
Signed-off-by: Shixiong Zhu <zsxwing@gmail.com>
2019-08-02 15:27:33 -07:00
Nick Karpov 6d32deeecc [SPARK-28475][CORE] Add regex MetricFilter to GraphiteSink
## What changes were proposed in this pull request?

Today all registered metric sources are reported to GraphiteSink with no filtering mechanism, although the codahale project does support it.

GraphiteReporter (ScheduledReporter) from the codahale project requires you implement and supply the MetricFilter interface (there is only a single implementation by default in the codahale project, MetricFilter.ALL).

Propose to add an additional regex config to match and filter metrics to the GraphiteSink

## How was this patch tested?

Included a GraphiteSinkSuite that tests:

1. Absence of regex filter (existing default behavior maintained)
2. Presence of `regex=<regexexpr>` correctly filters metric keys

Closes #25232 from nkarpov/graphite_regex.

Authored-by: Nick Karpov <nick@nickkarpov.com>
Signed-off-by: jerryshao <jerryshao@tencent.com>
2019-08-02 17:50:15 +08:00
Marcelo Vanzin 607fb87906 [SPARK-28584][CORE] Fix thread safety issue in blacklist timer, tests
There's a small, probably very hard to hit thread-safety issue in the blacklist
abort timers in the task scheduler, where they access a non-thread-safe map without
locks.

In the tests, the code was also calling methods on the TaskSetManager without
holding the proper locks, which could cause threads to call non-thread-safe
TSM methods concurrently.

Closes #25317 from vanzin/SPARK-28584.

Authored-by: Marcelo Vanzin <vanzin@cloudera.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-08-01 10:37:47 -07:00
Wing Yew Poon 80ab19b9fd [SPARK-26329][CORE] Faster polling of executor memory metrics.
## What changes were proposed in this pull request?

Prior to this change, in an executor, on each heartbeat, memory metrics are polled and sent in the heartbeat. The heartbeat interval is 10s by default. With this change, in an executor, memory metrics can optionally be polled in a separate poller at a shorter interval.

For each executor, we use a map of (stageId, stageAttemptId) to (count of running tasks, executor metric peaks) to track what stages are active as well as the per-stage memory metric peaks. When polling the executor memory metrics, we attribute the memory to the active stage(s), and update the peaks. In a heartbeat, we send the per-stage peaks (for stages active at that time), and then reset the peaks. The semantics would be that the per-stage peaks sent in each heartbeat are the peaks since the last heartbeat.

We also keep a map of taskId to memory metric peaks. This tracks the metric peaks during the lifetime of the task. The polling thread updates this as well. At end of a task, we send the peak metric values in the task result. In case of task failure, we send the peak metric values in the `TaskFailedReason`.

We continue to do the stage-level aggregation in the EventLoggingListener.

For the driver, we still only poll on heartbeats. What the driver sends will be the current values of the metrics in the driver at the time of the heartbeat. This is semantically the same as before.

## How was this patch tested?

Unit tests. Manually tested applications on an actual system and checked the event logs; the metrics appear in the SparkListenerTaskEnd and SparkListenerStageExecutorMetrics events.

Closes #23767 from wypoon/wypoon_SPARK-26329.

Authored-by: Wing Yew Poon <wypoon@cloudera.com>
Signed-off-by: Imran Rashid <irashid@cloudera.com>
2019-08-01 09:09:46 -05:00
WeichenXu 26d03b62e2 [SPARK-28366][CORE] Logging in driver when loading single large unsplittable file
## What changes were proposed in this pull request?

Logging in driver when loading single large unsplittable file via `sc.textFile` or csv/json datasouce.
Current condition triggering logging is
* only generate one partition
* file is unsplittable, possible reason is:
   - compressed by unsplittable compression algo such as gzip.
   - multiLine mode in csv/json datasource
   - wholeText mode in text datasource
* file size exceed the config threshold `spark.io.warning.largeFileThreshold` (default value is 1GB)

## How was this patch tested?

Manually test.
Generate one gzip file exceeding 1GB,
```
base64 -b 50 /dev/urandom | head -c 2000000000 > file1.txt
cat file1.txt | gzip > file1.gz
```
then launch spark-shell,

run
```
sc.textFile("file:///path/to/file1.gz").count()
```
Will print log like:
```
WARN HadoopRDD: Loading one large unsplittable file file:/.../f1.gz with only one partition, because the file is compressed by unsplittable compression codec
```

run
```
sc.textFile("file:///path/to/file1.txt").count()
```
Will print log like:
```
WARN HadoopRDD: Loading one large file file:/.../f1.gz with only one partition, we can increase partition numbers by the `minPartitions` argument in method `sc.textFile
```

run
```
spark.read.csv("file:///path/to/file1.gz").count
```
Will print log like:
```
WARN CSVScan: Loading one large unsplittable file file:/.../f1.gz with only one partition, the reason is: the file is compressed by unsplittable compression codec
```

run
```
spark.read.option("multiLine", true).csv("file:///path/to/file1.gz").count
```
Will print log like:
```
WARN CSVScan: Loading one large unsplittable file file:/.../f1.gz with only one partition, the reason is: the csv datasource is set multiLine mode
```

JSON and Text datasource also tested with similar cases.

Please review https://spark.apache.org/contributing.html before opening a pull request.

Closes #25134 from WeichenXu123/log_gz.

Authored-by: WeichenXu <weichen.xu@databricks.com>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-08-01 20:29:18 +08:00
Marcelo Vanzin b3ffd8be14 [SPARK-24352][CORE][TESTS] De-flake StandaloneDynamicAllocationSuite blacklist test
The issue is that the test tried to stop an existing scheduler and replace it with
a new one set up for the test. That can cause issues because both were sharing the
same RpcEnv underneath, and unregistering RpcEndpoints is actually asynchronous
(see comment in Dispatcher.unregisterRpcEndpoint). So that could lead to races where
the new scheduler tried to register before the old one was fully unregistered.

The updated test avoids the issue by using a separate RpcEnv / scheduler instance
altogether, and also avoids a misleading NPE in the test logs.

Closes #25318 from vanzin/SPARK-24352.

Authored-by: Marcelo Vanzin <vanzin@cloudera.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-07-31 17:44:20 -07:00
sychen 70ef9064a8 [SPARK-28564][CORE] Access history application defaults to the last attempt id
## What changes were proposed in this pull request?
When we set ```spark.history.ui.maxApplications``` to a small value, we can't get some apps from the page search.
If the url is spliced (http://localhost:18080/history/local-xxx), it can be accessed if the app has no attempt.
But in the case of multiple attempted apps, such a url cannot be accessed, and the page displays Not Found.

## How was this patch tested?
Add UT

Closes #25301 from cxzl25/hs_app_last_attempt_id.

Authored-by: sychen <sychen@ctrip.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-07-31 13:24:36 -07:00
HyukjinKwon b8e13b0aea [SPARK-28153][PYTHON] Use AtomicReference at InputFileBlockHolder (to support input_file_name with Python UDF)
## What changes were proposed in this pull request?

This PR proposes to use `AtomicReference` so that parent and child threads can access to the same file block holder.

Python UDF expressions are turned to a plan and then it launches a separate thread to consume the input iterator. In the separate child thread, the iterator sets `InputFileBlockHolder.set` before the parent does which the parent thread is unable to read later.

1. In this separate child thread, if it happens to call `InputFileBlockHolder.set` first without initialization of the parent's thread local (which is done when the `ThreadLocal.get()` is first called), the child thread seems calling its own `initialValue` to initialize.

2. After that, the parent calls its own `initialValue` to initializes at the first call of `ThreadLocal.get()`.

3. Both now have two different references. Updating at child isn't reflected to parent.

This PR fixes it via initializing parent's thread local with `AtomicReference` for file status so that they can be used in each task, and children thread's update is reflected.

I also tried to explain this a bit more at https://github.com/apache/spark/pull/24958#discussion_r297203041.

## How was this patch tested?

Manually tested and unittest was added.

Closes #24958 from HyukjinKwon/SPARK-28153.

Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: Wenchen Fan <wenchen@databricks.com>
2019-07-31 22:40:01 +08:00
mcheah abef84a868 [SPARK-28209][CORE][SHUFFLE] Proposed new shuffle writer API
## What changes were proposed in this pull request?

As part of the shuffle storage API proposed in SPARK-25299, this introduces an API for persisting shuffle data in arbitrary storage systems.

This patch introduces several concepts:
* `ShuffleDataIO`, which is the root of the entire plugin tree that will be proposed over the course of the shuffle API project.
* `ShuffleExecutorComponents` - the subset of plugins for managing shuffle-related components for each executor. This will in turn instantiate shuffle readers and writers.
* `ShuffleMapOutputWriter` interface - instantiated once per map task. This provides child `ShufflePartitionWriter` instances for persisting the bytes for each partition in the map task.

The default implementation of these plugins exactly mirror what was done by the existing shuffle writing code - namely, writing the data to local disk and writing an index file. We leverage the APIs in the `BypassMergeSortShuffleWriter` only. Follow-up PRs will use the APIs in `SortShuffleWriter` and `UnsafeShuffleWriter`, but are left as future work to minimize the review surface area.

## How was this patch tested?

New unit tests were added. Micro-benchmarks indicate there's no slowdown in the affected code paths.

Closes #25007 from mccheah/spark-shuffle-writer-refactor.

Lead-authored-by: mcheah <mcheah@palantir.com>
Co-authored-by: mccheah <mcheah@palantir.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-07-30 14:17:30 -07:00
pgandhi 70910e6ad0 [SPARK-26755][SCHEDULER] : Optimize Spark Scheduler to dequeue speculative tasks…
… more efficiently

This PR improves the performance of scheduling speculative tasks to be O(1) instead of O(numSpeculativeTasks), using the same approach used for scheduling regular tasks. The performance of this method is particularly important because a lock is held on the TaskSchedulerImpl which is a bottleneck for all scheduling operations. We ran a Join query on a large dataset with speculation enabled and out of 100000 tasks for the ShuffleMapStage, the maximum number of speculatable tasks that was noted was close to 7900-8000 at a point. That is when we start seeing the bottleneck on the scheduler lock.

In particular, this works by storing a separate stack of tasks by executor, node, and rack locality preferences. Then when trying to schedule a speculative task, rather than scanning all speculative tasks to find ones which match the given executor (or node, or rack) preference, we can jump to a quick check of tasks matching the resource offer. This technique was already used for regular tasks -- this change refactors the code to allow sharing with regular and speculative task execution.

## What changes were proposed in this pull request?

Have split the main queue "speculatableTasks" into 5 separate queues based on locality preference similar to how normal tasks are enqueued. Thus, the "dequeueSpeculativeTask" method will avoid performing locality checks for each task at runtime and simply return the preferable task to be executed.

## How was this patch tested?
We ran a spark job that performed a join on a 10 TB dataset to test the code change.
Original Code:
<img width="1433" alt="screen shot 2019-01-28 at 5 07 22 pm" src="https://user-images.githubusercontent.com/22228190/51873321-572df280-2322-11e9-9149-0aae08d5edc6.png">

Optimized Code:
<img width="1435" alt="screen shot 2019-01-28 at 5 08 19 pm" src="https://user-images.githubusercontent.com/22228190/51873343-6745d200-2322-11e9-947b-2cfd0f06bcab.png">

As you can see, the run time of the ShuffleMapStage came down from 40 min to 6 min approximately, thus, reducing the overall running time of the spark job by a significant amount.

Another example for the same job:

Original Code:
<img width="1440" alt="screen shot 2019-01-28 at 5 11 30 pm" src="https://user-images.githubusercontent.com/22228190/51873355-70cf3a00-2322-11e9-9c3a-af035449a306.png">

Optimized Code:
<img width="1440" alt="screen shot 2019-01-28 at 5 12 16 pm" src="https://user-images.githubusercontent.com/22228190/51873367-7dec2900-2322-11e9-8d07-1b1b49285f71.png">

Closes #23677 from pgandhi999/SPARK-26755.

Lead-authored-by: pgandhi <pgandhi@verizonmedia.com>
Co-authored-by: pgandhi <pgandhi@oath.com>
Signed-off-by: Imran Rashid <irashid@cloudera.com>
2019-07-30 09:54:51 -05:00
Lee Dongjin d98aa2a184 [MINOR] Trivial cleanups
These are what I found during working on #22282.

- Remove unused value: `UnsafeArraySuite#defaultTz`
- Remove redundant new modifier to the case class, `KafkaSourceRDDPartition`
- Remove unused variables from `RDD.scala`
- Remove trailing space from `structured-streaming-kafka-integration.md`
- Remove redundant parameter from `ArrowConvertersSuite`: `nullable` is `true` by default.
- Remove leading empty line: `UnsafeRow`
- Remove trailing empty line: `KafkaTestUtils`
- Remove unthrown exception type: `UnsafeMapData`
- Replace unused declarations: `expressions`
- Remove duplicated default parameter: `AnalysisErrorSuite`
- `ObjectExpressionsSuite`: remove duplicated parameters, conversions and unused variable

Closes #25251 from dongjinleekr/cleanup/201907.

Authored-by: Lee Dongjin <dongjin@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
2019-07-29 23:38:02 +09:00
Dongjoon Hyun a428f40669 [SPARK-28549][BUILD][CORE][SQL] Use text.StringEscapeUtils instead lang3.StringEscapeUtils
## What changes were proposed in this pull request?

`org.apache.commons.lang3.StringEscapeUtils` was deprecated over two years ago at [LANG-1316](https://issues.apache.org/jira/browse/LANG-1316). There is no bug fixes after that.
```java
/**
 * <p>Escapes and unescapes {code String}s for
 * Java, Java Script, HTML and XML.</p>
 *
 * <p>#ThreadSafe#</p>
 * since 2.0
 * deprecated as of 3.6, use commons-text
 * <a href="https://commons.apache.org/proper/commons-text/javadocs/api-release/org/apache/commons/text/StringEscapeUtils.html">
 * StringEscapeUtils</a> instead
 */
Deprecated
public class StringEscapeUtils {
```

This PR aims to use the latest one from `commons-text` module which has more bug fixes like
[TEXT-100](https://issues.apache.org/jira/browse/TEXT-100), [TEXT-118](https://issues.apache.org/jira/browse/TEXT-118) and [TEXT-120](https://issues.apache.org/jira/browse/TEXT-120) by the following replacement.
```scala
-import org.apache.commons.lang3.StringEscapeUtils
+import org.apache.commons.text.StringEscapeUtils
```

This will add a new dependency to `hadoop-2.7` profile distribution. In `hadoop-3.2` profile, we already have it.
```
+commons-text-1.6.jar
```

## How was this patch tested?

Pass the Jenkins with the existing tests.
- [Hadoop 2.7](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/108281)
- [Hadoop 3.2](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/108282)

Closes #25281 from dongjoon-hyun/SPARK-28549.

Authored-by: Dongjoon Hyun <dhyun@apple.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
2019-07-29 11:45:29 +09:00
Marcelo Vanzin 7f84104b39 [SPARK-28535][CORE][TEST] Slow down tasks to de-flake JobCancellationSuite
This test tries to detect correct behavior in racy code, where the event
thread is racing with the executor thread that's trying to kill the running
task.

If the event that signals the stage end arrives first, any delay in the
delivery of the message to kill the task causes the code to rapidly process
elements, and may cause the test to assert. Adding a 10ms delay in
LocalSchedulerBackend before the task kill makes the test run through
~1000 elements. A longer delay can easily cause the 10000 elements to
be processed.

Instead, by adding a small delay (10ms) in the test code that processes
elements, there's a much lower probability that the kill event will not
arrive before the end; that leaves a window of 100s for the event
to be delivered to the executor. And because each element only sleeps for
10ms, the test is not really slowed down at all.

Closes #25270 from vanzin/SPARK-28535.

Authored-by: Marcelo Vanzin <vanzin@cloudera.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-07-27 11:06:35 -07:00
Luca Canali f2a2d980ed [SPARK-25285][CORE] Add startedTasks and finishedTasks to the metrics system in the executor instance
## What changes were proposed in this pull request?

The motivation for these additional metrics is to help in troubleshooting and monitoring task execution workload when running on a cluster. Currently available metrics include executor threadpool metrics for task completed and for active tasks. The addition of threadpool taskStarted metric will allow for example to collect info on the (approximate) number of failed tasks by computing the difference thread started – (active threads + completed tasks and/or successfully finished tasks).
The proposed metric finishedTasks is also intended for this type of troubleshooting. The difference between finshedTasks and threadpool.completeTasks, is that the latter is a (dropwizard library) gauge taken from the threadpool, while the former is a (dropwizard) counter computed in the [[Executor]] class, when a task successfully finishes, together with several other task metrics counters.
Note, there are similarities with some of the metrics introduced in SPARK-24398, however there are key differences, coming from the fact that this PR concerns the executor source, therefore providing metric values per executor + metric values do not require to pass through the listerner bus in this case.

## How was this patch tested?

Manually tested on a YARN cluster

Closes #22290 from LucaCanali/AddMetricExecutorStartedTasks.

Lead-authored-by: Luca Canali <luca.canali@cern.ch>
Co-authored-by: LucaCanali <luca.canali@cern.ch>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-07-26 14:03:57 -07:00
Marcelo Vanzin a3e013391e [SPARK-28455][CORE] Avoid overflow when calculating executor timeout time
This would cause the timeout time to be negative, so executors would be
timed out immediately (instead of never).

I also tweaked a couple of log messages that could get pretty long when
lots of executors were active.

Added unit test (which failed without the fix).

Closes #25208 from vanzin/SPARK-28455.

Authored-by: Marcelo Vanzin <vanzin@cloudera.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-07-22 14:31:58 -07:00
Josh Rosen 3776fbdfde [SPARK-28430][UI] Fix stage table rendering when some tasks' metrics are missing
## What changes were proposed in this pull request?

The Spark UI's stages table misrenders the input/output metrics columns when some tasks are missing input metrics. See the screenshot below for an example of the problem:

![image](https://user-images.githubusercontent.com/50748/61420042-a3abc100-a8b5-11e9-8a92-7986563ee712.png)

This is because those columns' are defined as

```scala
 {if (hasInput(stage)) {
  metricInfo(task) { m =>
    ...
   <td>....</td>
  }
}
```

where `metricInfo` renders the node returned by the closure in case metrics are defined or returns `Nil` in case metrics are not defined. If metrics are undefined then we'll fail to render the empty `<td></td>` tag, causing columns to become misaligned as shown in the screenshot.

To fix this, this patch changes this to

```scala
 {if (hasInput(stage)) {
  <td>{
    metricInfo(task) { m =>
      ...
     Unparsed(...)
    }
  }</td>
}
```

which is an idiom that's already in use for the shuffle read / write columns.

## How was this patch tested?

It isn't. I'm arguing for correctness because the modifications are consistent with rendering methods that work correctly for other columns.

Closes #25183 from JoshRosen/joshrosen/fix-task-table-with-partial-io-metrics.

Authored-by: Josh Rosen <rosenville@gmail.com>
Signed-off-by: Dongjoon Hyun <dhyun@apple.com>
2019-07-18 13:15:39 -07:00
Marcelo Vanzin 2ddeff97d7 [SPARK-27963][CORE] Allow dynamic allocation without a shuffle service.
This change adds a new option that enables dynamic allocation without
the need for a shuffle service. This mode works by tracking which stages
generate shuffle files, and keeping executors that generate data for those
shuffles alive while the jobs that use them are active.

A separate timeout is also added for shuffle data; so that executors that
hold shuffle data can use a separate timeout before being removed because
of being idle. This allows the shuffle data to be kept around in case it
is needed by some new job, or allow users to be more aggressive in timing
out executors that don't have shuffle data in active use.

The code also hooks up to the context cleaner so that shuffles that are
garbage collected are detected, and the respective executors not held
unnecessarily.

Testing done with added unit tests, and also with TPC-DS workloads on
YARN without a shuffle service.

Closes #24817 from vanzin/SPARK-27963.

Authored-by: Marcelo Vanzin <vanzin@cloudera.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-07-16 16:37:38 -07:00
Angers be4a55220a [SPARK-28106][SQL] When Spark SQL use "add jar" , before add to SparkContext, check jar path exist first.
## What changes were proposed in this pull request?
ISSUE :  https://issues.apache.org/jira/browse/SPARK-28106
When we use add jar in SQL, it will have three step:

- add jar to HiveClient's classloader
- HiveClientImpl.runHiveSQL("ADD JAR" + PATH)
- SessionStateBuilder.addJar

The second step seems has no impact to the whole process. Since event it failed, we still can execute.
The first step will add jar path to HiveClient's ClassLoader, then we can use the jar in HiveClientImpl
The Third Step will add this jar path to SparkContext. But expect local file path, it will call RpcServer's FileServer to add this to Env, the is you pass wrong path. it will cause error, but if you pass HDFS path or VIEWFS path, it won't check it and just add it to jar Path Map.

Then when next TaskSetManager send out Task, this path will be brought by TaskDescription. Then Executor will call updateDependencies, this method will check all jar path and file path in TaskDescription. Then error happends like below:

![image](https://user-images.githubusercontent.com/46485123/59817635-4a527f80-9353-11e9-9e08-9407b2b54023.png)

## How was this patch tested?
Exist Unit Test
Environment Test

Closes #24909 from AngersZhuuuu/SPARK-28106.

Lead-authored-by: Angers <angers.zhu@gamil.com>
Co-authored-by: 朱夷 <zhuyi01@corp.netease.com>
Signed-off-by: jerryshao <jerryshao@tencent.com>
2019-07-16 15:29:05 +08:00
Marcelo Vanzin 8d1e87ac90 [SPARK-28150][CORE][FOLLOW-UP] Don't try to log in when impersonating.
When fetching delegation tokens for a proxy user, don't try to log in,
since it will fail.

Closes #25141 from vanzin/SPARK-28150.2.

Authored-by: Marcelo Vanzin <vanzin@cloudera.com>
Signed-off-by: Marcelo Vanzin <vanzin@cloudera.com>
2019-07-15 10:32:34 -07:00
Liang-Chi Hsieh 591de42351 [SPARK-28381][PYSPARK] Upgraded version of Pyrolite to 4.30
## What changes were proposed in this pull request?

This upgraded to a newer version of Pyrolite. Most updates [1] in the newer version are for dotnot. For java, it includes a bug fix to Unpickler regarding cleaning up Unpickler memo, and support of protocol 5.

After upgrading, we can remove the fix at SPARK-27629 for the bug in Unpickler.

[1] https://github.com/irmen/Pyrolite/compare/pyrolite-4.23...master

## How was this patch tested?

Manually tested on Python 3.6 in local on existing tests.

Closes #25143 from viirya/upgrade-pyrolite.

Authored-by: Liang-Chi Hsieh <viirya@gmail.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
2019-07-15 12:29:58 +09:00
Jesse Cai 79e2047703 [SPARK-28355][CORE][PYTHON] Use Spark conf for threshold at which command is compressed by broadcast
## What changes were proposed in this pull request?

The `_prepare_for_python_RDD` method currently broadcasts a pickled command if its length is greater than the hardcoded value `1 << 20` (1M). This change sets this value as a Spark conf instead.

## How was this patch tested?

Unit tests, manual tests.

Closes #25123 from jessecai/SPARK-28355.

Authored-by: Jesse Cai <jesse.cai@databricks.com>
Signed-off-by: gatorsmile <gatorsmile@gmail.com>
2019-07-13 08:44:16 -07:00