[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-08-01 Thread mateiz
Github user mateiz commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50930691
  
@aarondav can you update the name of this PR to reference this sub-task 
JIRA instead: https://issues.apache.org/jira/browse/SPARK-2791?


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-08-01 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50927468
  
QA results for PR 1678:- This patch PASSES unit tests.- This patch 
merges cleanly- This patch adds no public classesFor more 
information see test 
ouptut:https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17689/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-08-01 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50921522
  
QA tests have started for PR 1678. This patch merges cleanly. View 
progress: 
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17689/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-08-01 Thread mateiz
Github user mateiz commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50921018
  
Jenkins, test this please


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-08-01 Thread mridulm
Github user mridulm commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15701250
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
 if (initialized) {
   // NOTE: Because Kryo doesn't flush the underlying stream we 
explicitly flush both the
   //   serializer stream and the lower level stream.
   objOut.flush()
   bs.flush()
-  val prevPos = lastValidPosition
-  lastValidPosition = channel.position()
-  lastValidPosition - prevPos
-} else {
-  // lastValidPosition is zero if stream is uninitialized
-  lastValidPosition
+  close()
 }
+finalPosition = file.length()
   }
 
-  override def revertPartialWrites() {
-if (initialized) {
-  // Discard current writes. We do this by flushing the outstanding 
writes and
-  // truncate the file to the last valid position.
-  objOut.flush()
-  bs.flush()
-  channel.truncate(lastValidPosition)
+  // Discard current writes. We do this by flushing the outstanding writes 
and then
+  // truncating the file to its initial position.
+  override def revertPartialWritesAndClose() {
+try {
+  if (initialized) {
+objOut.flush()
+bs.flush()
+close()
+  }
+
+  val truncateStream = new FileOutputStream(file, true)
+  try {
+truncateStream.getChannel.truncate(initialPosition)
+  } finally {
+truncateStream.close()
+  }
+} catch {
+  case e: Exception =>
+logError("Uncaught exception while reverting partial writes to 
file " + file, e)
--- End diff --

Ah, did not notice that the "if (initialized)" did not include the truncate 
call !


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread aarondav
Github user aarondav commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15684100
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
--- End diff --

Removing close() actually now requires a very minor refactor of 
ExternalSorter for the `objectsWritten == 0` case -- I'd actually rather not 
risk it in this PR.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread aarondav
Github user aarondav commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15683958
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
 if (initialized) {
   // NOTE: Because Kryo doesn't flush the underlying stream we 
explicitly flush both the
   //   serializer stream and the lower level stream.
   objOut.flush()
   bs.flush()
-  val prevPos = lastValidPosition
-  lastValidPosition = channel.position()
-  lastValidPosition - prevPos
-} else {
-  // lastValidPosition is zero if stream is uninitialized
-  lastValidPosition
+  close()
 }
+finalPosition = file.length()
   }
 
-  override def revertPartialWrites() {
-if (initialized) {
-  // Discard current writes. We do this by flushing the outstanding 
writes and
-  // truncate the file to the last valid position.
-  objOut.flush()
-  bs.flush()
-  channel.truncate(lastValidPosition)
+  // Discard current writes. We do this by flushing the outstanding writes 
and then
+  // truncating the file to its initial position.
+  override def revertPartialWritesAndClose() {
+try {
+  if (initialized) {
+objOut.flush()
+bs.flush()
+close()
+  }
+
+  val truncateStream = new FileOutputStream(file, true)
+  try {
+truncateStream.getChannel.truncate(initialPosition)
+  } finally {
+truncateStream.close()
+  }
+} catch {
+  case e: Exception =>
+logError("Uncaught exception while reverting partial writes to 
file " + file, e)
--- End diff --

I'm not certain I understand. The situation I am imagining is that we 
commit to the first Writer, then the second one fails. In HashShuffleWriter, we 
will then call revertPartialWritesAndClose() on all Writers, causing us to 
revert all the changes back to "initialPosition", which should revert even the 
committed data.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread mridulm
Github user mridulm commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15683224
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
--- End diff --

When I merged the sort patch, and modified EAOM, it was simply replace 
close with commitAndClose.
commitAndClose should be semantically equivalent to close actually.
It is not equivalent to commit() - but we want to remove that :-)


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread mridulm
Github user mridulm commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15683205
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
 if (initialized) {
   // NOTE: Because Kryo doesn't flush the underlying stream we 
explicitly flush both the
   //   serializer stream and the lower level stream.
   objOut.flush()
   bs.flush()
-  val prevPos = lastValidPosition
-  lastValidPosition = channel.position()
-  lastValidPosition - prevPos
-} else {
-  // lastValidPosition is zero if stream is uninitialized
-  lastValidPosition
+  close()
 }
+finalPosition = file.length()
   }
 
-  override def revertPartialWrites() {
-if (initialized) {
-  // Discard current writes. We do this by flushing the outstanding 
writes and
-  // truncate the file to the last valid position.
-  objOut.flush()
-  bs.flush()
-  channel.truncate(lastValidPosition)
+  // Discard current writes. We do this by flushing the outstanding writes 
and then
+  // truncating the file to its initial position.
+  override def revertPartialWritesAndClose() {
+try {
+  if (initialized) {
+objOut.flush()
+bs.flush()
+close()
+  }
+
+  val truncateStream = new FileOutputStream(file, true)
+  try {
+truncateStream.getChannel.truncate(initialPosition)
+  } finally {
+truncateStream.close()
+  }
+} catch {
+  case e: Exception =>
+logError("Uncaught exception while reverting partial writes to 
file " + file, e)
--- End diff --

I meant the former case : close on a writer fails with an exception; while 
earlier streams succeeded.
So now we have some writers which have committed data (which is not removed 
by subsequent revert) while others are reverted.

On the face of it, I agree, it should not cause issues : but then since the 
expectation from this class is never enforced; and so can silently fail. 


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread aarondav
Github user aarondav commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15682607
  
--- Diff: 
core/src/main/scala/org/apache/spark/shuffle/hash/HashShuffleWriter.scala ---
@@ -120,8 +121,7 @@ private[spark] class HashShuffleWriter[K, V](
   private def revertWrites(): Unit = {
 if (shuffle != null && shuffle.writers != null) {
   for (writer <- shuffle.writers) {
-writer.revertPartialWrites()
-writer.close()
+writer.revertPartialWritesAndClose()
--- End diff --

Revert actually doesn't throw, per its (updated) comment.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread aarondav
Github user aarondav commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15682605
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
--- End diff --

Absolutely -- I did not do that in this patch because ExternalAppendOnlyMap 
did a close without a commit, which is a fix outside of the scope of this PR, 
but definitely one that should be made.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread aarondav
Github user aarondav commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15682590
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
 if (initialized) {
   // NOTE: Because Kryo doesn't flush the underlying stream we 
explicitly flush both the
   //   serializer stream and the lower level stream.
   objOut.flush()
   bs.flush()
-  val prevPos = lastValidPosition
-  lastValidPosition = channel.position()
-  lastValidPosition - prevPos
-} else {
-  // lastValidPosition is zero if stream is uninitialized
-  lastValidPosition
+  close()
 }
+finalPosition = file.length()
   }
 
-  override def revertPartialWrites() {
-if (initialized) {
-  // Discard current writes. We do this by flushing the outstanding 
writes and
-  // truncate the file to the last valid position.
-  objOut.flush()
-  bs.flush()
-  channel.truncate(lastValidPosition)
+  // Discard current writes. We do this by flushing the outstanding writes 
and then
+  // truncating the file to its initial position.
+  override def revertPartialWritesAndClose() {
+try {
+  if (initialized) {
+objOut.flush()
+bs.flush()
+close()
+  }
+
+  val truncateStream = new FileOutputStream(file, true)
+  try {
+truncateStream.getChannel.truncate(initialPosition)
+  } finally {
+truncateStream.close()
+  }
+} catch {
+  case e: Exception =>
+logError("Uncaught exception while reverting partial writes to 
file " + file, e)
--- End diff --

Closed streams should not inherently throw (since we check `initialized` 
before flushing and closing). However, we may be left with leftover data, as 
you said. I don't see a way to prevent the possibility of that occurring, but 
it should be possible to recover if users only rely on the returned 
fileSegment().


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread mridulm
Github user mridulm commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15682457
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
--- End diff --

We should remove close from the interface, and make it private to this 
class btw.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread mridulm
Github user mridulm commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15682412
  
--- Diff: 
core/src/main/scala/org/apache/spark/storage/BlockObjectWriter.scala ---
@@ -147,28 +147,36 @@ private[spark] class DiskBlockObjectWriter(
 
   override def isOpen: Boolean = objOut != null
 
-  override def commit(): Long = {
+  override def commitAndClose(): Unit = {
 if (initialized) {
   // NOTE: Because Kryo doesn't flush the underlying stream we 
explicitly flush both the
   //   serializer stream and the lower level stream.
   objOut.flush()
   bs.flush()
-  val prevPos = lastValidPosition
-  lastValidPosition = channel.position()
-  lastValidPosition - prevPos
-} else {
-  // lastValidPosition is zero if stream is uninitialized
-  lastValidPosition
+  close()
 }
+finalPosition = file.length()
   }
 
-  override def revertPartialWrites() {
-if (initialized) {
-  // Discard current writes. We do this by flushing the outstanding 
writes and
-  // truncate the file to the last valid position.
-  objOut.flush()
-  bs.flush()
-  channel.truncate(lastValidPosition)
+  // Discard current writes. We do this by flushing the outstanding writes 
and then
+  // truncating the file to its initial position.
+  override def revertPartialWritesAndClose() {
+try {
+  if (initialized) {
+objOut.flush()
+bs.flush()
+close()
+  }
+
+  val truncateStream = new FileOutputStream(file, true)
+  try {
+truncateStream.getChannel.truncate(initialPosition)
+  } finally {
+truncateStream.close()
+  }
+} catch {
+  case e: Exception =>
+logError("Uncaught exception while reverting partial writes to 
file " + file, e)
--- End diff --

In the use of writers in HashShuffleWriter, it is possible for a closed 
stream to be reverted (if some other stream's close failed for example).
In the above, that will leave this file with leftover data - I am not sure 
what the impact of this would be.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread mridulm
Github user mridulm commented on a diff in the pull request:

https://github.com/apache/spark/pull/1678#discussion_r15682389
  
--- Diff: 
core/src/main/scala/org/apache/spark/shuffle/hash/HashShuffleWriter.scala ---
@@ -120,8 +121,7 @@ private[spark] class HashShuffleWriter[K, V](
   private def revertWrites(): Unit = {
 if (shuffle != null && shuffle.writers != null) {
   for (writer <- shuffle.writers) {
-writer.revertPartialWrites()
-writer.close()
+writer.revertPartialWritesAndClose()
--- End diff --

revert can throw exception : which will cause other writers to not revert.
We need to wrap it in try/catch, log and continue


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50793796
  
QA results for PR 1678:- This patch PASSES unit tests.- This patch 
merges cleanly- This patch adds no public classesFor more 
information see test 
ouptut:https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17585/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50786593
  
QA tests have started for PR 1678. This patch merges cleanly. View 
progress: 
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17585/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread aarondav
Github user aarondav commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50785949
  
Both prior failures are due to being unable to bind to ports, which sounds 
like leftover state from other jenkins runs (especially since they were two 
entirely disjoint sets of failed tests related to port binding).


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread aarondav
Github user aarondav commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50785966
  
Jenkins, retest this please.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-31 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50724029
  
QA results for PR 1678:- This patch FAILED unit tests.- This patch 
merges cleanly- This patch adds no public classesFor more 
information see test 
ouptut:https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17565/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50718818
  
QA tests have started for PR 1678. This patch merges cleanly. View 
progress: 
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17565/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread aarondav
Github user aarondav commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50718425
  
Jenkins, retest this please.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50718100
  
QA results for PR 1678:- This patch FAILED unit tests.- This patch 
merges cleanly- This patch adds no public classesFor more 
information see test 
ouptut:https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17553/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50714957
  
QA tests have started for PR 1678. This patch merges cleanly. View 
progress: 
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17553/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50710747
  
QA results for PR 1678:- This patch FAILED unit tests.- This patch 
merges cleanly- This patch adds no public classesFor more 
information see test 
ouptut:https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17537/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread mateiz
Github user mateiz commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50706164
  
That's true, this is small enough to add back into branch-1.0 too. We 
should see if we can do the same for the rest of #1609 too (ideally I would 
like to merge that whole PR into branch-1.0, but I'm not sure how easy that is).


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread witgo
Github user witgo commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50706018
  
We can also merge it to 1.0 branch.


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread aarondav
Github user aarondav commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50705532
  
@mridulm Please take a look if possible.

@mateiz This now interacts with the ExternalSorter stuff, and it's possible 
it partially helps fix a serialization bug (since some serializers apparently 
write things during a close() after a flush()).


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50705494
  
QA tests have started for PR 1678. This patch merges cleanly. View 
progress: 
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17537/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50704906
  
QA results for PR 1678:- This patch FAILED unit tests.- This patch 
merges cleanly- This patch adds no public classesFor more 
information see test 
ouptut:https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17535/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread SparkQA
Github user SparkQA commented on the pull request:

https://github.com/apache/spark/pull/1678#issuecomment-50704721
  
QA tests have started for PR 1678. This patch merges cleanly. View 
progress: 
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/17535/consoleFull


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[GitHub] spark pull request: SPARK-2532: Minimal shuffle consolidation fixe...

2014-07-30 Thread aarondav
GitHub user aarondav opened a pull request:

https://github.com/apache/spark/pull/1678

SPARK-2532: Minimal shuffle consolidation fixes

All changes from this PR are by @mridulm and are drawn from his work in 
#1609. This patch is intended to fix all major issues related to shuffle file 
consolidation that @mridulm found, while minimizing changes to the code, with 
the hope that it may be more easily merged into 1.1.

This patch is **not** intended as a replacement for #1609, which provides 
many additional benefits, including fixes to ExternalAppendOnlyMap, 
improvements to DiskBlockObjectWriter's API, and several new unit tests.

If it is feasible to merge #1609 for the 1.1 deadline, that is a preferable 
option.

You can merge this pull request into a Git repository by running:

$ git pull https://github.com/aarondav/spark consol

Alternatively you can review and apply these changes as the patch at:

https://github.com/apache/spark/pull/1678.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 #1678


commit f298ac92f7df30f53636fca874c8bc6ed764af19
Author: Aaron Davidson 
Date:   2014-07-28T19:02:24Z

SPARK-2532: Minimal shuffle consolidation fixes

All changes from this PR are by @mridulm and are drawn from his work in 
#1609.
This patch is intended to fix all major issues related to shuffle file 
consolidation
that @mridulm found, while minimizing changes to the code, with the hope 
that it may
be more easily merged into 1.1.

This patch is **not** intended as a replacement for #1609, which provides 
many
additional benefits, including fixes to ExternalAppendOnlyMap, improvements 
to
DiskBlockObjectWriter's API, and several new unit tests.

If it is feasible to merge #1609 for the 1.1 deadline, that is a preferable 
option.




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