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Posted to reviews@spark.apache.org by vundela <gi...@git.apache.org> on 2017/04/20 01:46:11 UTC
[GitHub] spark pull request #17694: [SPARK-12717][PYSPARK] Resolving race condition w...
GitHub user vundela opened a pull request:
https://github.com/apache/spark/pull/17694
[SPARK-12717][PYSPARK] Resolving race condition with pyspark broadcas\u2026
\u2026ts when using multiple threads
## What changes were proposed in this pull request?
In pyspark when multiple threads are used, broadcast variables are picked with wrong PythonRDD wrap functions which leads to the following exception(Because of the race condition between the threads on java side with py4j).
16/01/08 17:10:20 ERROR Executor: Exception in task 0.0 in stage 9.0 (TID 9)
org.apache.spark.api.python.PythonException: Traceback (most recent call last):
File "/Network/Servers/mother.adverplex.com/Volumes/homeland/Users/walker/.spark/spark-1.6.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/worker.py", line 98, in main
command = pickleSer._read_with_length(infile)
File "/Network/Servers/mother.adverplex.com/Volumes/homeland/Users/walker/.spark/spark-1.6.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/serializers.py", line 164, in _read_with_length
return self.loads(obj)
File "/Network/Servers/mother.adverplex.com/Volumes/homeland/Users/walker/.spark/spark-1.6.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/serializers.py", line 422, in loads
return pickle.loads(obj)
File "/Network/Servers/mother.adverplex.com/Volumes/homeland/Users/walker/.spark/spark-1.6.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/broadcast.py", line 39, in _from_id
raise Exception("Broadcast variable '%s' not loaded!" % bid)
Exception: (Exception("Broadcast variable '6' not loaded!",), <function _from_id at 0xce7a28>, (6L,))
at org.apache.spark.api.python.PythonRunner$$anon$1.read(PythonRDD.scala:166)
at org.apache.spark.api.python.PythonRunner$$anon$1.<init>(PythonRDD.scala:207)
at org.apache.spark.api.python.PythonRunner.compute(PythonRDD.scala:125)
at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:70)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
This change will fix the race condition by making sure that broadcast variables are picked with same pythonRDD function.
## How was this patch tested?
1) Reproduced the issue mentioned in SPARK-12717, following the instructions specified in jira
2) Make sure that issue is fixed with the changes.
Please review http://spark.apache.org/contributing.html before opening a pull request.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/vundela/spark SPARK-12717
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/17694.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #17694
----
commit 4670678ba4fa7f2a7f66bc9309716fcefb05c54d
Author: Srinivasa Reddy Vundela <vs...@cloudera.com>
Date: 2017-04-20T01:37:12Z
[SPARK-12717][PYSPARK] Resolving race condition with pyspark broadcasts when using multiple threads
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vundela <gi...@git.apache.org>.
Github user vundela commented on the issue:
https://github.com/apache/spark/pull/17694
Filed a PR for fixing the issue in spark1.6 branch.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by maver1ck <gi...@git.apache.org>.
Github user maver1ck commented on the issue:
https://github.com/apache/spark/pull/17694
OK. I did additional tests.
Fix is working only with Spark 2.1.
I tried to apply it on 2.0.2 and that was the reason of my problem.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17694
Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/77800/
Test FAILed.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17694
Can one of the admins verify this patch?
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by holdenk <gi...@git.apache.org>.
Github user holdenk commented on the issue:
https://github.com/apache/spark/pull/17694
Interesting, I don't think I have all of the required context to review, but I'll try and take a look this weekend (I've got some other things happening this week already).
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vundela <gi...@git.apache.org>.
Github user vundela commented on the issue:
https://github.com/apache/spark/pull/17694
Thanks for testing @maver1ck. I will look into 1.6 and 2.0.2.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by jsoltren <gi...@git.apache.org>.
Github user jsoltren commented on the issue:
https://github.com/apache/spark/pull/17694
This seems reasonable to me.
There are some typos in the PR description. I think you meant "pickled" instead of "picked" in a few places.
Using threading.Lock seems okay here from my admittedly limited understanding of the deep details of Python, and my reading of https://docs.python.org/2/library/threading.html#lock-objects.
@vundela and I chatted off thread about this some. The precise race is this: the call to _wrap_function will define a number of broadcast variables. In the time between when the _wrap_function call finishes and self.ctx._jvm.PythonRDD executes, the RDD itself can be modified, perhaps changing broadcast variables and introducing the "Broadcast variable '%s' not loaded!" exception.
My understanding is that, due to the Global Interpreter Lock, this lock will cause all other execution to cease while this block of code runs, implicitly preventing any races. This is a very coarse grained lock for this action but it is as good as we can get. (Someone please correct me if I\u2019m wrong here.)
It would be good if the PR description captured some of the above discussion.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by maver1ck <gi...@git.apache.org>.
Github user maver1ck commented on the issue:
https://github.com/apache/spark/pull/17694
The funny thing is this code works for me on 4 threads and throws exception on 10 threads
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vundela <gi...@git.apache.org>.
Github user vundela commented on the issue:
https://github.com/apache/spark/pull/17694
Hi @maver1ck, Thanks for your time in testing the patch.
I did run the patch with 1000 threads and it works fine.
Can you please check /grid/3/hadoop/yarn/log/usercache/bi/appcache/application_1492634694033_0092/container_e538_1492634694033_0092_01_000003/pyspark.zip/pyspark/rdd.py whether the changes are available.
My guess is you might be missing changes in psypark.zip.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/17694
Merged build finished. Test FAILed.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vundela <gi...@git.apache.org>.
Github user vundela commented on the issue:
https://github.com/apache/spark/pull/17694
Thanks for your time @holdenk.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by maver1ck <gi...@git.apache.org>.
Github user maver1ck commented on the issue:
https://github.com/apache/spark/pull/17694
@vundela
Great.
But I'm planning to migrate to 2.1 as soon as 2.1.1 will be released.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17694
**[Test build #77800 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77800/testReport)** for PR 17694 at commit [`4670678`](https://github.com/apache/spark/commit/4670678ba4fa7f2a7f66bc9309716fcefb05c54d).
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/17694
**[Test build #77800 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77800/testReport)** for PR 17694 at commit [`4670678`](https://github.com/apache/spark/commit/4670678ba4fa7f2a7f66bc9309716fcefb05c54d).
* This patch **fails Python style tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by BryanCutler <gi...@git.apache.org>.
Github user BryanCutler commented on the issue:
https://github.com/apache/spark/pull/17694
Hi @vundela , thanks for your PR. I was able to reproduce your issue, but I think your fix here uses too broad of lock, since the shared resource is the SparkContext pickle registry and needs to be locked only while the python command is being pickled. Please see #18695 and if you wouldn't mind checking if that solves your issue as well. Thanks!
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vanzin <gi...@git.apache.org>.
Github user vanzin commented on the issue:
https://github.com/apache/spark/pull/17694
ok to test
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by maver1ck <gi...@git.apache.org>.
Github user maver1ck commented on the issue:
https://github.com/apache/spark/pull/17694
I tested your patch in our environment.
Problem still exists.
```
Job aborted due to stage failure: Task 0 in stage 22.0 failed 8 times, most recent failure: Lost task 0.7 in stage 22.0 (TID 138, dwh-hn30.adpilot.co): org.apache.spark.api.python.PythonException: Traceback (most recent call last):
File "/grid/3/hadoop/yarn/log/usercache/bi/appcache/application_1492634694033_0092/container_e538_1492634694033_0092_01_000003/pyspark.zip/pyspark/worker.py", line 161, in main
func, profiler, deserializer, serializer = read_command(pickleSer, infile)
File "/grid/3/hadoop/yarn/log/usercache/bi/appcache/application_1492634694033_0092/container_e538_1492634694033_0092_01_000003/pyspark.zip/pyspark/worker.py", line 54, in read_command
command = serializer._read_with_length(file)
File "/grid/3/hadoop/yarn/log/usercache/bi/appcache/application_1492634694033_0092/container_e538_1492634694033_0092_01_000003/pyspark.zip/pyspark/serializers.py", line 164, in _read_with_length
return self.loads(obj)
File "/grid/3/hadoop/yarn/log/usercache/bi/appcache/application_1492634694033_0092/container_e538_1492634694033_0092_01_000003/pyspark.zip/pyspark/serializers.py", line 419, in loads
return pickle.loads(obj, encoding=encoding)
File "/grid/3/hadoop/yarn/log/usercache/bi/appcache/application_1492634694033_0092/container_e538_1492634694033_0092_01_000003/pyspark.zip/pyspark/broadcast.py", line 39, in _from_id
raise Exception("Broadcast variable '%s' not loaded!" % bid)
Exception: Broadcast variable '22' not loaded!
at org.apache.spark.api.python.PythonRunner$$anon$1.read(PythonRDD.scala:193)
at org.apache.spark.api.python.PythonRunner$$anon$1.<init>(PythonRDD.scala:234)
at org.apache.spark.api.python.PythonRunner.compute(PythonRDD.scala:152)
at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:63)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
at org.apache.spark.scheduler.Task.run(Task.scala:86)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
```
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by maver1ck <gi...@git.apache.org>.
Github user maver1ck commented on the issue:
https://github.com/apache/spark/pull/17694
I checked pyspark.zip of running container and everything is on its place.
So I assume that there is more that one race condition in this code.
I'll try to prepare example of the problem.
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vundela <gi...@git.apache.org>.
Github user vundela commented on the issue:
https://github.com/apache/spark/pull/17694
ping @holdenk, checking if you have some time to review this.
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[GitHub] spark pull request #17694: [SPARK-12717][PYSPARK] Resolving race condition w...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/17694
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vundela <gi...@git.apache.org>.
Github user vundela commented on the issue:
https://github.com/apache/spark/pull/17694
cc @holdenk
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[GitHub] spark issue #17694: [SPARK-12717][PYSPARK] Resolving race condition with pys...
Posted by vanzin <gi...@git.apache.org>.
Github user vanzin commented on the issue:
https://github.com/apache/spark/pull/17694
Please remove the boilerplate message at the end of your PR description.
ok to test
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