spark-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Bharath Ravi Kumar <reachb...@gmail.com>
Subject Re: OOM with groupBy + saveAsTextFile
Date Sun, 02 Nov 2014 15:48:10 GMT
Thanks for responding. This is what I initially suspected, and hence asked
why the library needed to construct the entire value buffer on a single
host before writing it out. The stacktrace appeared to suggest that user
code is not constructing the large buffer. I'm simply calling groupBy and
saveAsText on the resulting grouped rdd. The value after grouping is an
Iterable<Tuple4<String, Double, String, String>>. None of the strings are
large. I also do not need a single large string created out of the Iterable
for writing to disk. Instead, I expect the iterable to get written out in
chunks in response to saveAsText. This shouldn't be the default behaviour
of saveAsText perhaps? Hence my original question of the behavior of
saveAsText. The tuning / partitioning attempts were aimed at reducing
memory pressure so that multiple such buffers aren't constructed at the
same time on a host. I'll take a second look at the data and code before
updating this thread. Thanks.
None of your tuning will help here because the problem is actually the way
you are saving the output. If you take a look at the stacktrace, it is
trying to build a single string that is too large for the VM to allocate
memory. The VM is actually not running out of memory, but rather, JVM
cannot support a single String so large.

I suspect this is due to the fact that the value in your key, value pair
after group by is too long (maybe it concatenates every single record). Do
you really want to save the key, value output this way using a text file?
Maybe you can write them out as multiple strings rather than a single super
giant string.




On Sat, Nov 1, 2014 at 9:52 PM, Arthur.hk.chan@gmail.com <
arthur.hk.chan@gmail.com> wrote:

>
> Hi,
>
> FYI as follows.  Could you post your heap size settings as well your Spark
> app code?
>
> Regards
> Arthur
>
> 3.1.3 Detail Message: Requested array size exceeds VM limitThe detail
> message Requested array size exceeds VM limit indicates that the
> application (or APIs used by that application) attempted to allocate an
> array that is larger than the heap size. For example, if an application
> attempts to allocate an array of 512MB but the maximum heap size is 256MB
> then OutOfMemoryError will be thrown with the reason Requested array size
> exceeds VM limit. In most cases the problem is either a configuration
> issue (heap size too small), or a bug that results in an application
> attempting to create a huge array, for example, when the number of elements
> in the array are computed using an algorithm that computes an incorrect
> size.”
>
>
>
>
> On 2 Nov, 2014, at 12:25 pm, Bharath Ravi Kumar <reachbach@gmail.com>
> wrote:
>
> Resurfacing the thread. Oom shouldn't be the norm for a common groupby /
> sort use case in a framework that is leading in sorting bench marks? Or is
> there something fundamentally wrong in the usage?
> On 02-Nov-2014 1:06 am, "Bharath Ravi Kumar" <reachbach@gmail.com> wrote:
>
>> Hi,
>>
>> I'm trying to run groupBy(function) followed by saveAsTextFile on an RDD
>> of count ~ 100 million. The data size is 20GB and groupBy results in an RDD
>> of 1061 keys with values being Iterable<Tuple4<String, Integer, Double,
>> String>>. The job runs on 3 hosts in a standalone setup with each host's
>> executor having 100G RAM and 24 cores dedicated to it. While the groupBy
>> stage completes successfully with ~24GB of shuffle write, the
>> saveAsTextFile fails after repeated retries with each attempt failing due
>> to an out of memory error *[1]*. I understand that a few partitions may
>> be overloaded as a result of the groupBy and I've tried the following
>> config combinations unsuccessfully:
>>
>> 1) Repartition the initial rdd (44 input partitions but 1061 keys) across
>> 1061 paritions and have max cores = 3 so that each key is a "logical"
>> partition (though many partitions will end up on very few hosts), and each
>> host likely runs saveAsTextFile on a single key at a time due to max cores
>> = 3 with 3 hosts in the cluster. The level of parallelism is unspecified.
>>
>> 2) Leave max cores unspecified, set the level of parallelism to 72, and
>> leave number of partitions unspecified (in which case the # input
>> partitions was used, which is 44)
>> Since I do not intend to cache RDD's, I have set
>> spark.storage.memoryFraction=0.2 in both cases.
>>
>> My understanding is that if each host is processing a single logical
>> partition to saveAsTextFile and is reading from other hosts to write out
>> the RDD, it is unlikely that it would run out of memory. My interpretation
>> of the spark tuning guide is that the degree of parallelism has little
>> impact in case (1) above since max cores = number of hosts. Can someone
>> explain why there are still OOM's with 100G being available? On a related
>> note, intuitively (though I haven't read the source), it appears that an
>> entire key-value pair needn't fit into memory of a single host for
>> saveAsTextFile since a single shuffle read from a remote can be written to
>> HDFS before the next remote read is carried out. This way, not all data
>> needs to be collected at the same time.
>>
>> Lastly, if an OOM is (but shouldn't be) a common occurrence (as per the
>> tuning guide and even as per Datastax's spark introduction), there may need
>> to be more documentation around the internals of spark to help users take
>> better informed tuning decisions with parallelism, max cores, number
>> partitions and other tunables. Is there any ongoing effort on that front?
>>
>> Thanks,
>> Bharath
>>
>>
>> *[1]* OOM stack trace and logs
>> 14/11/01 12:26:37 WARN TaskSetManager: Lost task 61.0 in stage 36.0 (TID
>> 1264, proc1.foo.bar.com): java.lang.OutOfMemoryError: Requested array
>> size exceeds VM limit
>>         java.util.Arrays.copyOf(Arrays.java:3326)
>>
>> java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137)
>>
>> java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:121)
>>
>> java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:421)
>>         java.lang.StringBuilder.append(StringBuilder.java:136)
>>
>> scala.collection.mutable.StringBuilder.append(StringBuilder.scala:197)
>>         scala.Tuple2.toString(Tuple2.scala:22)
>>
>> org.apache.spark.rdd.RDD$$anonfun$saveAsTextFile$1.apply(RDD.scala:1158)
>>
>> org.apache.spark.rdd.RDD$$anonfun$saveAsTextFile$1.apply(RDD.scala:1158)
>>         scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
>>
>> org.apache.spark.rdd.PairRDDFunctions$$anonfun$13.apply(PairRDDFunctions.scala:984)
>>
>> org.apache.spark.rdd.PairRDDFunctions$$anonfun$13.apply(PairRDDFunctions.scala:974)
>>         org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:62)
>>         org.apache.spark.scheduler.Task.run(Task.scala:54)
>>
>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:177)
>>
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>>
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>>         java.lang.Thread.run(Thread.java:745)
>> 14/11/01 12:26:40 WARN TaskSetManager: Lost task 92.0 in stage 36.0 (TID
>> 1295, proc1.foo.bar.com): FetchFailed(BlockManagerId(1, proc1.foo.bar.com,
>> 43704, 0), shuffleId=0, mapId=13, reduceId=92)
>> 14/11/01 12:26:40 INFO DAGScheduler: Marking Stage 36 (saveAsTextFile at
>> ModelTrainer.java:141) as failed due to a fetch failure from Stage 37
>> (groupBy at ModelTrainer.java:133)
>> 14/11/01 12:26:40 INFO DAGScheduler: Stage 36 (saveAsTextFile at
>> ModelTrainer.java:141) failed in 55.259 s
>> 14/11/01 12:26:40 INFO DAGScheduler: Resubmitting Stage 37 (groupBy at
>> ModelTrainer.java:133) and Stage 36 (saveAsTextFile at
>> ModelTrainer.java:141) due to fetch failure
>>
>>
>>
>>
>>
>

Mime
View raw message