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Posted to reviews@spark.apache.org by sitalkedia <gi...@git.apache.org> on 2016/08/18 01:43:13 UTC
[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
GitHub user sitalkedia opened a pull request:
https://github.com/apache/spark/pull/14693
[SPARK-17113][Shuffle] Job failure due to Executor OOM in offheap mode
## What changes were proposed in this pull request?
Fix executor OOM in offheap mode due to bug in Cooperative Memory Management for UnsafeExternSorter.
Following is the stack trace this issue addresses -
java.lang.OutOfMemoryError: Unable to acquire 1220 bytes of memory, got 0
at org.apache.spark.memory.MemoryConsumer.allocatePage(MemoryConsumer.java:120)
at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter.acquireNewPageIfNecessary(UnsafeExternalSorter.java:341)
at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter.insertRecord(UnsafeExternalSorter.java:362)
at org.apache.spark.sql.execution.UnsafeExternalRowSorter.insertRow(UnsafeExternalRowSorter.java:93)
at org.apache.spark.sql.execution.UnsafeExternalRowSorter.sort(UnsafeExternalRowSorter.java:170)
## How was this patch tested?
Tested by running the failing job.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/sitalkedia/spark fix_offheap_oom
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/14693.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 #14693
----
commit 9e4e3eac7ac87a5be142344d5f7ee3d507fca97f
Author: Sital Kedia <sk...@fb.com>
Date: 2016-08-18T01:03:43Z
[SPARK-17113][Shuffle] Job failure due to Executor OOM in offheap mode
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14693
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14693
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #63991 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/63991/consoleFull)** for PR 14693 at commit [`03f7316`](https://github.com/apache/spark/commit/03f73162adecc8a61c6ff3c82dc09fba3d09c51c).
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by davies <gi...@git.apache.org>.
Github user davies commented on the issue:
https://github.com/apache/spark/pull/14693
@sitalkedia Your last commit is not correct, which fail this test. `upstream` is the one used for reading, `inMemIterator` is the one used for spilling, see #10142
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14693
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[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
Posted by srowen <gi...@git.apache.org>.
Github user srowen commented on a diff in the pull request:
https://github.com/apache/spark/pull/14693#discussion_r75576694
--- Diff: core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java ---
@@ -522,7 +522,7 @@ public long spill() throws IOException {
// is accessing the current record. We free this page in that caller's next loadNext()
// call.
for (MemoryBlock page : allocatedPages) {
- if (!loaded || page.getBaseObject() != upstream.getBaseObject()) {
+ if (!loaded || page.pageNumber != ((UnsafeInMemorySorter.SortedIterator)upstream).getCurrentPageNumber()) {
--- End diff --
Oh yes you're right. It's a clone and they will have a different page number.
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[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on a diff in the pull request:
https://github.com/apache/spark/pull/14693#discussion_r75242498
--- Diff: core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java ---
@@ -522,7 +522,7 @@ public long spill() throws IOException {
// is accessing the current record. We free this page in that caller's next loadNext()
--- End diff --
@rxin - We already have comment describing the spilling strategy here. Do you think we need more details?
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #64010 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64010/consoleFull)** for PR 14693 at commit [`03f7316`](https://github.com/apache/spark/commit/03f73162adecc8a61c6ff3c82dc09fba3d09c51c).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
Posted by srowen <gi...@git.apache.org>.
Github user srowen commented on a diff in the pull request:
https://github.com/apache/spark/pull/14693#discussion_r75259542
--- Diff: core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java ---
@@ -522,7 +522,7 @@ public long spill() throws IOException {
// is accessing the current record. We free this page in that caller's next loadNext()
// call.
for (MemoryBlock page : allocatedPages) {
- if (!loaded || page.getBaseObject() != upstream.getBaseObject()) {
+ if (!loaded || page.pageNumber != ((UnsafeInMemorySorter.SortedIterator)upstream).getCurrentPageNumber()) {
--- End diff --
Can you not just reference `inMemIterator` here? no cast needed/
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14693
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #63964 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/63964/consoleFull)** for PR 14693 at commit [`8581659`](https://github.com/apache/spark/commit/85816590f141d1785b2786610d29523ce249c59f).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/14693
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #64000 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64000/consoleFull)** for PR 14693 at commit [`03f7316`](https://github.com/apache/spark/commit/03f73162adecc8a61c6ff3c82dc09fba3d09c51c).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
@rxin - thanks updated the PR.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
cc - @davies
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14693
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
@rxin - I am not sure if there is an easy way to unit test this.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #63991 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/63991/consoleFull)** for PR 14693 at commit [`03f7316`](https://github.com/apache/spark/commit/03f73162adecc8a61c6ff3c82dc09fba3d09c51c).
* This patch **fails Spark unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
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Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14693
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[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on a diff in the pull request:
https://github.com/apache/spark/pull/14693#discussion_r75333091
--- Diff: core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java ---
@@ -522,7 +522,7 @@ public long spill() throws IOException {
// is accessing the current record. We free this page in that caller's next loadNext()
// call.
for (MemoryBlock page : allocatedPages) {
- if (!loaded || page.getBaseObject() != upstream.getBaseObject()) {
+ if (!loaded || page.pageNumber != ((UnsafeInMemorySorter.SortedIterator)upstream).getCurrentPageNumber()) {
--- End diff --
Good point, changed accordingly.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by davies <gi...@git.apache.org>.
Github user davies commented on the issue:
https://github.com/apache/spark/pull/14693
LGTM
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by rxin <gi...@git.apache.org>.
Github user rxin commented on the issue:
https://github.com/apache/spark/pull/14693
Is there a way to add a unit test for this?
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/14693
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #63964 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/63964/consoleFull)** for PR 14693 at commit [`8581659`](https://github.com/apache/spark/commit/85816590f141d1785b2786610d29523ce249c59f).
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
Weird, there are no test failure, still the job failed. May be Jenkins is unstable?
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #64027 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64027/consoleFull)** for PR 14693 at commit [`4101eb9`](https://github.com/apache/spark/commit/4101eb9a8efbed2c58d780a2e704d73b2b71d3c4).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #64027 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64027/consoleFull)** for PR 14693 at commit [`4101eb9`](https://github.com/apache/spark/commit/4101eb9a8efbed2c58d780a2e704d73b2b71d3c4).
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
Jenkins test this please.
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[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
Posted by davies <gi...@git.apache.org>.
Github user davies commented on a diff in the pull request:
https://github.com/apache/spark/pull/14693#discussion_r75529799
--- Diff: core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java ---
@@ -522,7 +522,7 @@ public long spill() throws IOException {
// is accessing the current record. We free this page in that caller's next loadNext()
// call.
for (MemoryBlock page : allocatedPages) {
- if (!loaded || page.getBaseObject() != upstream.getBaseObject()) {
+ if (!loaded || page.pageNumber != ((UnsafeInMemorySorter.SortedIterator)upstream).getCurrentPageNumber()) {
--- End diff --
We can't use `inMemIterator` here, it's different.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by rxin <gi...@git.apache.org>.
Github user rxin commented on the issue:
https://github.com/apache/spark/pull/14693
Can you update the pr description to say what the problem is? Also add some inline comment in the code. Thanks.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by davies <gi...@git.apache.org>.
Github user davies commented on the issue:
https://github.com/apache/spark/pull/14693
I'm sorry that did not pay enough attension on this part, thanks to the unit test!
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #64000 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64000/consoleFull)** for PR 14693 at commit [`03f7316`](https://github.com/apache/spark/commit/03f73162adecc8a61c6ff3c82dc09fba3d09c51c).
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
I see, that makes sense. Updated the PR.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
Not sure why the test UnsafeExternalSorterSuite.forcedSpillingWithReadIterator has become flaky. I am not able to reproduce the issue on my laptop. @davies - any idea?
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #63960 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/63960/consoleFull)** for PR 14693 at commit [`9e4e3ea`](https://github.com/apache/spark/commit/9e4e3eac7ac87a5be142344d5f7ee3d507fca97f).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by sitalkedia <gi...@git.apache.org>.
Github user sitalkedia commented on the issue:
https://github.com/apache/spark/pull/14693
Jenkins test this please.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by davies <gi...@git.apache.org>.
Github user davies commented on the issue:
https://github.com/apache/spark/pull/14693
Merging this into master and 2.0 and 1.6 (hopefully), thanks
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[GitHub] spark pull request #14693: [SPARK-17113][Shuffle] Job failure due to Executo...
Posted by rxin <gi...@git.apache.org>.
Github user rxin commented on a diff in the pull request:
https://github.com/apache/spark/pull/14693#discussion_r75244351
--- Diff: core/src/main/java/org/apache/spark/util/collection/unsafe/sort/UnsafeExternalSorter.java ---
@@ -522,7 +522,7 @@ public long spill() throws IOException {
// is accessing the current record. We free this page in that caller's next loadNext()
--- End diff --
Thanks - this is good.
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #64010 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/64010/consoleFull)** for PR 14693 at commit [`03f7316`](https://github.com/apache/spark/commit/03f73162adecc8a61c6ff3c82dc09fba3d09c51c).
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[GitHub] spark issue #14693: [SPARK-17113][Shuffle] Job failure due to Executor OOM i...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/14693
**[Test build #63960 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/63960/consoleFull)** for PR 14693 at commit [`9e4e3ea`](https://github.com/apache/spark/commit/9e4e3eac7ac87a5be142344d5f7ee3d507fca97f).
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