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From Jonathan Ellis <jbel...@gmail.com>
Subject Re: Native heap leaks?
Date Sun, 15 May 2011 14:09:23 GMT
Great debugging work!

That workaround sounds like the best alternative to me too.

On Sat, May 14, 2011 at 9:46 PM, Hannes Schmidt <hannes@eyealike.com> wrote:
> Ok, so I think I found one major cause contributing to the increasing
> resident size of the Cassandra process. Looking at the OpenJDK sources
> was of great help in understanding the problem but my findings also
> apply to the Sun/Oracle JDK because the affected code is shared by
> both.
>
> Each IncomingTcpConnection (ITC) thread handles a socket to another
> node. That socket is a server socket returned from
> ServerSocket.accept() and as such it is implemented on top of an NIO
> socket channel (sun.nio.ch.SocketAdaptor) which in turn makes use of
> direct byte buffers. It obtains these buffers from sun.nio.ch.Util
> which caches the 3 most recently used buffers per thread. If a cached
> buffer isn't large enough for a message, a new one that is will
> replace it. The size of the buffer is determined by the amount of data
> that the application requests to be read. ITC uses the readFully()
> method of DataInputStream (DIS) to read data into a byte array
> allocated to hold the entire message:
>
> int size = socketStream.readInt();
> byte[] buffer = new byte[size];
> socketStream.readFully(buffer);
>
> Whatever the value of 'size' will end up being the size of the direct
> buffer allocated by the socket channel code.
>
> Our application uses range queries whose result sets are around 40
> megabytes in size. If a range isn't hosted on the node the application
> client is connected to, the range result set will be fetched from
> another node. When that other node has prepared the result it will
> send it back (asynchonously, this took me a while to grasp) and it
> will end up in the direct byte buffer that is cached by
> sun.nio.ch.Util for the ITC thread on the original node.
>
> The thing is that the buffer holds the entire message, all 40 megs of
> it. ITC is rather long-lived and so the buffers will simply stick
> around. Our range queries cover the entire ring (we do a lot of "map
> reduce") and so each node ends up with as many 40M buffers as we have
> nodes in the ring, 10 in our case. That's 400M of native heap space
> wasted on each node.
>
> Each ITC thread holds onto the historically largest direct buffer,
> possibly for a long time. This could be alleviated by periodically
> closing the connection and thereby releasing a potentially large
> buffer and replacing it with a new thread that starts with a clean
> slate. If all queries have large result sets, this solution won't
> help. Another alternative is to read the message incrementally rather
> than buffering it in its entirety in a byte array as ITC currently
> does. A third and possibly the simplest solution would be to read the
> messages into the buffer in chunks of say 1M. DIS has offers
> readFully( data, offset, length ) for that. I have tried this solution
> and it fixes this problem for us. I'll open an issue and submit my
> patch. We have observed the issue with 0.6.12 but from looking at ITC
> in trunk it seems to be affected too.
>
> It gets worse though: even after the ITC thread dies, the cached
> buffers stick around as they are being held via SoftReferences. SR's
> are released only as a last resort to prevent an OutOfMemoryException.
> Using SR's for caching direct buffers is silly because direct buffers
> have negligible impact on the Java heap but may have dramatic impact
> on the native heap. I am not the only one who thinks so [1]. In other
> words, sun.nio.ch.Util's buffer caching is severely broken. I tried to
> find a way to explicitly release soft references but haven't found
> anything other than the allocation of an oversized array to force an
> OutOfMemoryException. The only thing we can do is to keep the buffer
> sizes small in order to reduce the impact of the leak. My patch takes
> care of that.
>
> I will post a link to the JIRA issue with the patch shortly.
>
> [1] http://bugs.sun.com/view_bug.do?bug_id=6210541
>
> On Wed, May 4, 2011 at 11:50 AM, Hannes Schmidt <hannes@eyealike.com> wrote:
>> Hi,
>>
>> We are using Cassandra 0.6.12 in a cluster of 9 nodes. Each node is
>> 64-bit, has 4 cores and 4G of RAM and runs on Ubuntu Lucid with the
>> stock 2.6.32-31-generic kernel. We use the Sun/Oracle JDK.
>>
>> Here's the problem: The Cassandra process starts up with 1.1G resident
>> memory (according to top) but slowly grows to 2.1G at a rate that
>> seems proportional to the write load. No writes, no growth. The node
>> is running other memory-sensitive applications (a second JVM for our
>> in-house webapp and a short-lived C++ program) so we need to ensure
>> that each process stays within certain bounds as far as memory
>> requirements go. The nodes OOM and crash when the Cassandra process is
>> at 2.1G so I can't say if the growth is bounded or not.
>>
>> Looking at theĀ /proc/$pid/smapsĀ for the Cassandra process it seems to
>> me that it is the native heap of the Cassandra JVM that is leaking. I
>> attached a readable version of the smaps file generated by [1].
>>
>> Some more data: Cassandra runs with default command line arguments,
>> which means it gets 1G heap. The JNA jar is present and Cassandra logs
>> that the memory locking was successful. In storage-conf.xml,
>> DiskAccessMode is mmap_index_only. Other than that and some increased
>> timeouts we left the defaults. Swap is completely disabled. I don't
>> think this is related but I am mentioning it anyways: overcommit [2]
>> is always-on (vm.overcommit_memory=1). Without that we get OOMs when
>> our application JVM is fork()'ing and exec()'ing our C++program even
>> though there is enough free RAM to satisfy the demands of the C++
>> program. We think this is caused by a flawed kernel heuristic that
>> assumes that the forked process (our C++ app) is as big as the forking
>> one (the 2nd JVM). Anyways, the Cassandra process leaks with both,
>> vm.overcommit_memory=0 (the default) and 1.
>>
>> Whether it is the native heap that leaks or something else, I think
>> that 1.1G of additional RAM for 1G of Java heap can't be normal. I'd
>> be grateful for any insights or pointers at what to try next.
>>
>> [1] http://bmaurer.blogspot.com/2006/03/memory-usage-with-smaps.html
>> [2] http://www.win.tue.nl/~aeb/linux/lk/lk-9.html#ss9.6
>>
>



-- 
Jonathan Ellis
Project Chair, Apache Cassandra
co-founder of DataStax, the source for professional Cassandra support
http://www.datastax.com

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