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From Koert Kuipers <ko...@tresata.com>
Subject Re: OS killing Executor due to high (possibly off heap) memory usage
Date Sat, 26 Nov 2016 15:31:39 GMT
i agree that offheap memory usage is unpredictable.

when we used rdds the memory was mostly on heap and total usage
predictable, and we almost never had yarn killing executors.

now with dataframes the memory usage is both on and off heap, and we have
no way of limiting the off heap memory usage by spark, yet yarn requires a
maximum total memory usage and if you go over it yarn kills the executor.

On Fri, Nov 25, 2016 at 12:14 PM, Aniket Bhatnagar <
aniket.bhatnagar@gmail.com> wrote:

> Thanks Rohit, Roddick and Shreya. I tried changing spark.yarn.executor.memoryOverhead
> to be 10GB and lowering executor memory to 30 GB and both of these didn't
> work. I finally had to reduce the number of cores per executor to be 18
> (from 36) in addition to setting higher spark.yarn.executor.memoryOverhead
> and lower executor memory size. I had to trade off performance for
> reliability.
>
> Unfortunately, spark does a poor job reporting off heap memory usage. From
> the profiler, it seems that the job's heap usage is pretty static but the
> off heap memory fluctuates quiet a lot. It looks like bulk of off heap is
> used by io.netty.buffer.UnpooledUnsafeDirectByteBuf while the shuffle
> client is trying to read block from shuffle service. It looks
> like org.apache.spark.network.util.TransportFrameDecoder retains them
> in buffers field while decoding responses from the shuffle service. So far,
> it's not clear why it needs to hold multiple GBs in the buffers. Perhaps
> increasing the number of partitions may help with this.
>
> Thanks,
> Aniket
>
> On Fri, Nov 25, 2016 at 1:09 AM Shreya Agarwal <shreyagr@microsoft.com>
> wrote:
>
> I don’t think it’s just memory overhead. It might be better to use an
> execute with lesser heap space(30GB?). 46 GB would mean more data load into
> memory and more GC, which can cause issues.
>
>
>
> Also, have you tried to persist data in any way? If so, then that might be
> causing an issue.
>
>
>
> Lastly, I am not sure if your data has a skew and if that is forcing a lot
> of data to be on one executor node.
>
>
>
> Sent from my Windows 10 phone
>
>
>
> *From: *Rodrick Brown <rodrick@orchardplatform.com>
> *Sent: *Friday, November 25, 2016 12:25 AM
> *To: *Aniket Bhatnagar <aniket.bhatnagar@gmail.com>
> *Cc: *user <user@spark.apache.org>
> *Subject: *Re: OS killing Executor due to high (possibly off heap) memory
> usage
>
>
> Try setting spark.yarn.executor.memoryOverhead 10000
>
> On Thu, Nov 24, 2016 at 11:16 AM, Aniket Bhatnagar <
> aniket.bhatnagar@gmail.com> wrote:
>
> Hi Spark users
>
> I am running a job that does join of a huge dataset (7 TB+) and the
> executors keep crashing randomly, eventually causing the job to crash.
> There are no out of memory exceptions in the log and looking at the dmesg
> output, it seems like the OS killed the JVM because of high memory usage.
> My suspicion is towards off heap usage of executor is causing this as I am
> limiting the on heap usage of executor to be 46 GB and each host running
> the executor has 60 GB of RAM. After the executor crashes, I can see that
> the external shuffle manager (org.apache.spark.network.server.TransportRequestHandler)
> logs a lot of channel closed exceptions in yarn node manager logs. This
> leads me to believe that something triggers out of memory during shuffle
> read. Is there a configuration to completely disable usage of off heap
> memory? I have tried setting spark.shuffle.io.preferDirectBufs=false but
> the executor is still getting killed by the same error.
>
> Cluster details:
> 10 AWS c4.8xlarge hosts
> RAM on each host - 60 GB
> Number of cores on each host - 36
> Additional hard disk on each host - 8 TB
>
> Spark configuration:
> dynamic allocation enabled
> external shuffle service enabled
> spark.driver.memory 1024M
> spark.executor.memory 47127M
> Spark master yarn-cluster
>
> Sample error in yarn node manager:
> 2016-11-24 10:34:06,507 ERROR org.apache.spark.network.server.TransportRequestHandler
> (shuffle-server-50): Error sending result ChunkFetchSuccess{
> streamChunkId=StreamChunkId{streamId=919299554123, chunkIndex=0}, buffer=
> FileSegmentManagedBuffer{file=/mnt3/yarn/usercache/hadoop/
> appcache/application_1479898345621_0006/blockmgr-ad5301a9-e1e9-4723-a8c4-
> 9276971b2259/2c/shuffle_3_963_0.data, offset=0, length=669014456}} to /
> 10.192.108.170:52782; closing connection
> java.nio.channels.ClosedChannelException
>
> Error in dmesg:
> [799873.309897] Out of memory: Kill process 50001 (java) score 927 or
> sacrifice child
> [799873.314439] Killed process 50001 (java) total-vm:65652448kB,
> anon-rss:57246528kB, file-rss:0kB
>
> Thanks,
> Aniket
>
>
>
>
> --
>
> [image: Orchard Platform] <http://www.orchardplatform.com/>
>
> *Rodrick Brown */ *DevOPs*
>
> 9174456839 / rodrick@orchardplatform.com
>
> Orchard Platform
> 101 5th Avenue, 4th Floor, New York, NY
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