[jira] [Commented] (SPARK-24801) Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can waste a lot of memory
[
https://issues.apache.org/jira/browse/SPARK-24801?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16549745#comment-16549745
]
Imran Rashid commented on SPARK-24801:
--
[~felixcheung] [~mshen]
> Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can
> waste a lot of memory
> ---
>
> Key: SPARK-24801
> URL: https://issues.apache.org/jira/browse/SPARK-24801
> Project: Spark
> Issue Type: Improvement
> Components: YARN
>Affects Versions: 2.3.0
>Reporter: Misha Dmitriev
>Priority: Major
>
> I recently analyzed another Yarn NM heap dump with jxray
> ([www.jxray.com),|http://www.jxray.com),/] and found that 81% of memory is
> wasted by empty (all zeroes) byte[] arrays. Most of these arrays are
> referenced by
> {{org.apache.spark.network.util.ByteArrayWritableChannel.data}}, and these in
> turn come from
> {{spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel}}. Here is
> the full reference chain that leads to the problematic arrays:
> {code:java}
> 2,597,946K (64.1%): byte[]: 40583 / 100% of empty 2,597,946K (64.1%)
> ↖org.apache.spark.network.util.ByteArrayWritableChannel.data
> ↖org.apache.spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.msg
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.{next}
> ↖io.netty.channel.ChannelOutboundBuffer.flushedEntry
> ↖io.netty.channel.socket.nio.NioSocketChannel$NioSocketChannelUnsafe.outboundBuffer
> ↖io.netty.channel.socket.nio.NioSocketChannel.unsafe
> ↖org.apache.spark.network.server.OneForOneStreamManager$StreamState.associatedChannel
> ↖{java.util.concurrent.ConcurrentHashMap}.values
> ↖org.apache.spark.network.server.OneForOneStreamManager.streams
> ↖org.apache.spark.network.shuffle.ExternalShuffleBlockHandler.streamManager
> ↖org.apache.spark.network.yarn.YarnShuffleService.blockHandler
> ↖Java Static org.apache.spark.network.yarn.YarnShuffleService.instance{code}
>
> Checking the code of {{SaslEncryption$EncryptedMessage}}, I see that
> byteChannel is always initialized eagerly in the constructor:
> {code:java}
> this.byteChannel = new ByteArrayWritableChannel(maxOutboundBlockSize);{code}
> So I think to address the problem of empty byte[] arrays flooding the memory,
> we should initialize {{byteChannel}} lazily, upon the first use. As far as I
> can see, it's used only in one method, {{private void nextChunk()}}.
>
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[jira] [Commented] (SPARK-24801) Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can waste a lot of memory
[
https://issues.apache.org/jira/browse/SPARK-24801?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16548578#comment-16548578
]
Apache Spark commented on SPARK-24801:
--
User 'countmdm' has created a pull request for this issue:
https://github.com/apache/spark/pull/21811
> Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can
> waste a lot of memory
> ---
>
> Key: SPARK-24801
> URL: https://issues.apache.org/jira/browse/SPARK-24801
> Project: Spark
> Issue Type: Improvement
> Components: YARN
>Affects Versions: 2.3.0
>Reporter: Misha Dmitriev
>Priority: Major
>
> I recently analyzed another Yarn NM heap dump with jxray
> ([www.jxray.com),|http://www.jxray.com),/] and found that 81% of memory is
> wasted by empty (all zeroes) byte[] arrays. Most of these arrays are
> referenced by
> {{org.apache.spark.network.util.ByteArrayWritableChannel.data}}, and these in
> turn come from
> {{spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel}}. Here is
> the full reference chain that leads to the problematic arrays:
> {code:java}
> 2,597,946K (64.1%): byte[]: 40583 / 100% of empty 2,597,946K (64.1%)
> ↖org.apache.spark.network.util.ByteArrayWritableChannel.data
> ↖org.apache.spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.msg
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.{next}
> ↖io.netty.channel.ChannelOutboundBuffer.flushedEntry
> ↖io.netty.channel.socket.nio.NioSocketChannel$NioSocketChannelUnsafe.outboundBuffer
> ↖io.netty.channel.socket.nio.NioSocketChannel.unsafe
> ↖org.apache.spark.network.server.OneForOneStreamManager$StreamState.associatedChannel
> ↖{java.util.concurrent.ConcurrentHashMap}.values
> ↖org.apache.spark.network.server.OneForOneStreamManager.streams
> ↖org.apache.spark.network.shuffle.ExternalShuffleBlockHandler.streamManager
> ↖org.apache.spark.network.yarn.YarnShuffleService.blockHandler
> ↖Java Static org.apache.spark.network.yarn.YarnShuffleService.instance{code}
>
> Checking the code of {{SaslEncryption$EncryptedMessage}}, I see that
> byteChannel is always initialized eagerly in the constructor:
> {code:java}
> this.byteChannel = new ByteArrayWritableChannel(maxOutboundBlockSize);{code}
> So I think to address the problem of empty byte[] arrays flooding the memory,
> we should initialize {{byteChannel}} lazily, upon the first use. As far as I
> can see, it's used only in one method, {{private void nextChunk()}}.
>
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[jira] [Commented] (SPARK-24801) Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can waste a lot of memory
[
https://issues.apache.org/jira/browse/SPARK-24801?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16546981#comment-16546981
]
Misha Dmitriev commented on SPARK-24801:
[~irashid] yes, I'll submit a change to lazily initialize
{{SaslEncryption$EncryptedMessage}}.{{byteChannel}}, that won't hurt anyway.
> Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can
> waste a lot of memory
> ---
>
> Key: SPARK-24801
> URL: https://issues.apache.org/jira/browse/SPARK-24801
> Project: Spark
> Issue Type: Improvement
> Components: YARN
>Affects Versions: 2.3.0
>Reporter: Misha Dmitriev
>Priority: Major
>
> I recently analyzed another Yarn NM heap dump with jxray
> ([www.jxray.com),|http://www.jxray.com),/] and found that 81% of memory is
> wasted by empty (all zeroes) byte[] arrays. Most of these arrays are
> referenced by
> {{org.apache.spark.network.util.ByteArrayWritableChannel.data}}, and these in
> turn come from
> {{spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel}}. Here is
> the full reference chain that leads to the problematic arrays:
> {code:java}
> 2,597,946K (64.1%): byte[]: 40583 / 100% of empty 2,597,946K (64.1%)
> ↖org.apache.spark.network.util.ByteArrayWritableChannel.data
> ↖org.apache.spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.msg
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.{next}
> ↖io.netty.channel.ChannelOutboundBuffer.flushedEntry
> ↖io.netty.channel.socket.nio.NioSocketChannel$NioSocketChannelUnsafe.outboundBuffer
> ↖io.netty.channel.socket.nio.NioSocketChannel.unsafe
> ↖org.apache.spark.network.server.OneForOneStreamManager$StreamState.associatedChannel
> ↖{java.util.concurrent.ConcurrentHashMap}.values
> ↖org.apache.spark.network.server.OneForOneStreamManager.streams
> ↖org.apache.spark.network.shuffle.ExternalShuffleBlockHandler.streamManager
> ↖org.apache.spark.network.yarn.YarnShuffleService.blockHandler
> ↖Java Static org.apache.spark.network.yarn.YarnShuffleService.instance{code}
>
> Checking the code of {{SaslEncryption$EncryptedMessage}}, I see that
> byteChannel is always initialized eagerly in the constructor:
> {code:java}
> this.byteChannel = new ByteArrayWritableChannel(maxOutboundBlockSize);{code}
> So I think to address the problem of empty byte[] arrays flooding the memory,
> we should initialize {{byteChannel}} lazily, upon the first use. As far as I
> can see, it's used only in one method, {{private void nextChunk()}}.
>
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[jira] [Commented] (SPARK-24801) Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can waste a lot of memory
[
https://issues.apache.org/jira/browse/SPARK-24801?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16546916#comment-16546916
]
Imran Rashid commented on SPARK-24801:
--
I don't think the messages themselves are actually empty, its just that the
bytebuffer is empty until the {{transferTo}} call, as you mentioned earlier.
Netty can buffer these messages up after spark calls
{{ChannelHandlerContext.write(msg)}}, but I can't believe there are so many of
them. I dunno if you can see anything unusual about the {{buf}} or {{region}}
field of those encrypted messages and if they are all empty.
But in any case, I guess what you're proposing is a simple fix in the meantime
before we figure that out. Would you like to submit a pr?
> Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can
> waste a lot of memory
> ---
>
> Key: SPARK-24801
> URL: https://issues.apache.org/jira/browse/SPARK-24801
> Project: Spark
> Issue Type: Improvement
> Components: YARN
>Affects Versions: 2.3.0
>Reporter: Misha Dmitriev
>Priority: Major
>
> I recently analyzed another Yarn NM heap dump with jxray
> ([www.jxray.com),|http://www.jxray.com),/] and found that 81% of memory is
> wasted by empty (all zeroes) byte[] arrays. Most of these arrays are
> referenced by
> {{org.apache.spark.network.util.ByteArrayWritableChannel.data}}, and these in
> turn come from
> {{spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel}}. Here is
> the full reference chain that leads to the problematic arrays:
> {code:java}
> 2,597,946K (64.1%): byte[]: 40583 / 100% of empty 2,597,946K (64.1%)
> ↖org.apache.spark.network.util.ByteArrayWritableChannel.data
> ↖org.apache.spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.msg
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.{next}
> ↖io.netty.channel.ChannelOutboundBuffer.flushedEntry
> ↖io.netty.channel.socket.nio.NioSocketChannel$NioSocketChannelUnsafe.outboundBuffer
> ↖io.netty.channel.socket.nio.NioSocketChannel.unsafe
> ↖org.apache.spark.network.server.OneForOneStreamManager$StreamState.associatedChannel
> ↖{java.util.concurrent.ConcurrentHashMap}.values
> ↖org.apache.spark.network.server.OneForOneStreamManager.streams
> ↖org.apache.spark.network.shuffle.ExternalShuffleBlockHandler.streamManager
> ↖org.apache.spark.network.yarn.YarnShuffleService.blockHandler
> ↖Java Static org.apache.spark.network.yarn.YarnShuffleService.instance{code}
>
> Checking the code of {{SaslEncryption$EncryptedMessage}}, I see that
> byteChannel is always initialized eagerly in the constructor:
> {code:java}
> this.byteChannel = new ByteArrayWritableChannel(maxOutboundBlockSize);{code}
> So I think to address the problem of empty byte[] arrays flooding the memory,
> we should initialize {{byteChannel}} lazily, upon the first use. As far as I
> can see, it's used only in one method, {{private void nextChunk()}}.
>
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[jira] [Commented] (SPARK-24801) Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can waste a lot of memory
[
https://issues.apache.org/jira/browse/SPARK-24801?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16545820#comment-16545820
]
Misha Dmitriev commented on SPARK-24801:
Correct, there are indeed 40583 instances of {{EncryptedMessage}} in memory.
From the other section of jxray report, which shows reference chains starting
from GC roots, and shows the number of objects at each level, I see the
following:
{code:java}
2,929,966K (72.3%) Object tree for GC root(s) Java Static
org.apache.spark.network.yarn.YarnShuffleService.instance
org.apache.spark.network.yarn.YarnShuffleService.blockHandler ↘ 2,753,031K
(67.9%), 1 reference(s)
org.apache.spark.network.shuffle.ExternalShuffleBlockHandler.streamManager ↘
2,753,019K (67.9%), 1 reference(s)
org.apache.spark.network.server.OneForOneStreamManager.streams ↘ 2,753,019K
(67.9%), 1 reference(s)
{java.util.concurrent.ConcurrentHashMap}.values ↘ 2,753,008K (67.9%), 169
reference(s)
org.apache.spark.network.server.OneForOneStreamManager$StreamState.associatedChannel
↘ 2,640,203K (65.1%), 32 reference(s)
io.netty.channel.socket.nio.NioSocketChannel.unsafe ↘ 2,640,039K (65.1%), 32
reference(s)
io.netty.channel.socket.nio.NioSocketChannel$NioSocketChannelUnsafe.outboundBuffer
↘ 2,640,037K (65.1%), 30 reference(s)
io.netty.channel.ChannelOutboundBuffer.flushedEntry ↘ 2,639,382K (65.1%), 15
reference(s)
io.netty.channel.ChannelOutboundBuffer$Entry.{next} ↘ 2,637,973K (65.1%),
40,583 reference(s)
io.netty.channel.ChannelOutboundBuffer$Entry.msg ↘ 2,622,966K (64.7%), 40,583
reference(s)
org.apache.spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel ↘
2,598,897K (64.1%), 40,583 reference(s)
org.apache.spark.network.util.ByteArrayWritableChannel.data ↘ 2,597,946K
(64.1%), 40,583 reference(s)
org.apache.spark.network.util.ByteArrayWritableChannel self 951K (< 0.1%),
40,583 object(s){code}
So basically we have 15 netty {{ChannelOutboundBuffer}} objects, and then
collectively , via linked lists starting from their {{flushedEntry}} data
fields, they end up referencing 40,583 {{ChannelOutboundBuffer$Entry}} objects,
which ultimately reference all these {{EncryptedMessage}} objects.
So looks like here netty for some reason accumulated (didn't send) a very large
number of messages, and thus netty is likely the main culprit. But then I
wonder why all these messages are empty
> Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can
> waste a lot of memory
> ---
>
> Key: SPARK-24801
> URL: https://issues.apache.org/jira/browse/SPARK-24801
> Project: Spark
> Issue Type: Improvement
> Components: YARN
>Affects Versions: 2.3.0
>Reporter: Misha Dmitriev
>Priority: Major
>
> I recently analyzed another Yarn NM heap dump with jxray
> ([www.jxray.com),|http://www.jxray.com),/] and found that 81% of memory is
> wasted by empty (all zeroes) byte[] arrays. Most of these arrays are
> referenced by
> {{org.apache.spark.network.util.ByteArrayWritableChannel.data}}, and these in
> turn come from
> {{spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel}}. Here is
> the full reference chain that leads to the problematic arrays:
> {code:java}
> 2,597,946K (64.1%): byte[]: 40583 / 100% of empty 2,597,946K (64.1%)
> ↖org.apache.spark.network.util.ByteArrayWritableChannel.data
> ↖org.apache.spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.msg
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.{next}
> ↖io.netty.channel.ChannelOutboundBuffer.flushedEntry
> ↖io.netty.channel.socket.nio.NioSocketChannel$NioSocketChannelUnsafe.outboundBuffer
> ↖io.netty.channel.socket.nio.NioSocketChannel.unsafe
> ↖org.apache.spark.network.server.OneForOneStreamManager$StreamState.associatedChannel
> ↖{java.util.concurrent.ConcurrentHashMap}.values
> ↖org.apache.spark.network.server.OneForOneStreamManager.streams
> ↖org.apache.spark.network.shuffle.ExternalShuffleBlockHandler.streamManager
> ↖org.apache.spark.network.yarn.YarnShuffleService.blockHandler
> ↖Java Static org.apache.spark.network.yarn.YarnShuffleService.instance{code}
>
> Checking the code of {{SaslEncryption$EncryptedMessage}}, I see that
> byteChannel is always initialized eagerly in the constructor:
> {code:java}
> this.byteChannel = new ByteArrayWritableChannel(maxOutboundBlockSize);{code}
> So I think to address the problem of empty byte[] arrays flooding the memory,
> we should initialize {{byteChannel}} lazily, upon the first use. As far as I
> can see, it's used only in one method, {{private void nextChunk()}}.
>
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[jira] [Commented] (SPARK-24801) Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can waste a lot of memory
[
https://issues.apache.org/jira/browse/SPARK-24801?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16545676#comment-16545676
]
Imran Rashid commented on SPARK-24801:
--
I'm surprised there are so many {{EncryptedMessage}} objects sitting around.
Are there 40583 of them? that sounds like an extremely overloaded shuffle
service -- or a leak. You're proposal would probably help some in that case,
but really there is probably something else we should be doing differently.
> Empty byte[] arrays in spark.network.sasl.SaslEncryption$EncryptedMessage can
> waste a lot of memory
> ---
>
> Key: SPARK-24801
> URL: https://issues.apache.org/jira/browse/SPARK-24801
> Project: Spark
> Issue Type: Improvement
> Components: YARN
>Affects Versions: 2.3.0
>Reporter: Misha Dmitriev
>Priority: Major
>
> I recently analyzed another Yarn NM heap dump with jxray
> ([www.jxray.com),|http://www.jxray.com),/] and found that 81% of memory is
> wasted by empty (all zeroes) byte[] arrays. Most of these arrays are
> referenced by
> {{org.apache.spark.network.util.ByteArrayWritableChannel.data}}, and these in
> turn come from
> {{spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel}}. Here is
> the full reference chain that leads to the problematic arrays:
> {code:java}
> 2,597,946K (64.1%): byte[]: 40583 / 100% of empty 2,597,946K (64.1%)
> ↖org.apache.spark.network.util.ByteArrayWritableChannel.data
> ↖org.apache.spark.network.sasl.SaslEncryption$EncryptedMessage.byteChannel
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.msg
> ↖io.netty.channel.ChannelOutboundBuffer$Entry.{next}
> ↖io.netty.channel.ChannelOutboundBuffer.flushedEntry
> ↖io.netty.channel.socket.nio.NioSocketChannel$NioSocketChannelUnsafe.outboundBuffer
> ↖io.netty.channel.socket.nio.NioSocketChannel.unsafe
> ↖org.apache.spark.network.server.OneForOneStreamManager$StreamState.associatedChannel
> ↖{java.util.concurrent.ConcurrentHashMap}.values
> ↖org.apache.spark.network.server.OneForOneStreamManager.streams
> ↖org.apache.spark.network.shuffle.ExternalShuffleBlockHandler.streamManager
> ↖org.apache.spark.network.yarn.YarnShuffleService.blockHandler
> ↖Java Static org.apache.spark.network.yarn.YarnShuffleService.instance{code}
>
> Checking the code of {{SaslEncryption$EncryptedMessage}}, I see that
> byteChannel is always initialized eagerly in the constructor:
> {code:java}
> this.byteChannel = new ByteArrayWritableChannel(maxOutboundBlockSize);{code}
> So I think to address the problem of empty byte[] arrays flooding the memory,
> we should initialize {{byteChannel}} lazily, upon the first use. As far as I
> can see, it's used only in one method, {{private void nextChunk()}}.
>
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