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From Igor Berman <igor.ber...@gmail.com>
Subject Re: Shuffle memory woes
Date Mon, 08 Feb 2016 08:02:53 GMT
It's interesting to see what spark dev people will say.
Corey do you have presentation available online?

On 8 February 2016 at 05:16, Corey Nolet <cjnolet@gmail.com> wrote:

> Charles,
>
> Thank you for chiming in and I'm glad someone else is experiencing this
> too and not just me. I know very well how the Spark shuffles work and I've
> done deep dive presentations @ Spark meetups in the past. This problem is
> somethng that goes beyond that and, I believe, it exposes a fundamental
> paradigm flaw in the design of Spark, unfortunately. Good thing is, I think
> it can be fixed.
>
> Also- in regards to how much data actually gets shuffled- believe it or
> not this problem can take a 30-40 minute job and make it run for 4 or more
> hours. If  let the job run for 4+ hours the amount of data being shuffled
> for this particular dataset will be 100 or more TB. Usually, however, I end
> up killing the job long before that point because I realize it should not
> be taking this long. The particular dataset we're doing is not for
> real-time exploration. These are very large joins we're doing for jobs that
> we run a few times a day.
>
> On Sun, Feb 7, 2016 at 9:56 PM, Charles Chao <xpnc54bypass@gmail.com>
> wrote:
>
>>  "The dataset is 100gb at most, the spills can up to 10T-100T"
>>
>> -- I have had the same experiences, although not to this extreme (the
>> spills were < 10T while the input was ~ 100s gb) and haven't found any
>> solution yet. I don't believe this is related to input data format. in my
>> case, I got my input data by loading from Hive tables.
>>
>> On Sun, Feb 7, 2016 at 6:28 AM, Sea <261810726@qq.com> wrote:
>>
>>> Hi,Corey:
>>>    "The dataset is 100gb at most, the spills can up to 10T-100T", Are
>>> your input files lzo format, and you use sc.text() ? If memory is not
>>> enough, spark will spill 3-4x of input data to disk.
>>>
>>>
>>> ------------------ 原始邮件 ------------------
>>> *发件人:* "Corey Nolet";<cjnolet@gmail.com>;
>>> *发送时间:* 2016年2月7日(星期天) 晚上8:56
>>> *收件人:* "Igor Berman"<igor.berman@gmail.com>;
>>> *抄送:* "user"<user@spark.apache.org>;
>>> *主题:* Re: Shuffle memory woes
>>>
>>> As for the second part of your questions- we have a fairly complex join
>>> process which requires a ton of stage orchestration from our driver. I've
>>> written some code to be able to walk down our DAG tree and execute siblings
>>> in the tree concurrently where possible (forcing cache to disk on children
>>> that that have multiple chiildren themselves so that they can be run
>>> concurrently). Ultimatey, we have seen significant speedup in our jobs by
>>> keeping tasks as busy as possible processing concurrent stages. Funny
>>> enough though, the stage that is causing problems with shuffling for us has
>>> a lot of children and doesn't even run concurrently with any other stages
>>> so I ruled out the concurrency of the stages as a culprit for the
>>> shuffliing problem we're seeing.
>>>
>>> On Sun, Feb 7, 2016 at 7:49 AM, Corey Nolet <cjnolet@gmail.com> wrote:
>>>
>>>> Igor,
>>>>
>>>> I don't think the question is "why can't it fit stuff in memory". I
>>>> know why it can't fit stuff in memory- because it's a large dataset that
>>>> needs to have a reduceByKey() run on it. My understanding is that when it
>>>> doesn't fit into memory it needs to spill in order to consolidate
>>>> intermediary files into a single file. The more data you need to run
>>>> through this, the more it will need to spill. My findings is that once it
>>>> gets stuck in this spill chain with our dataset it's all over @ that point
>>>> because it will spill and spill and spill and spill and spill. If I give
>>>> the shuffle enough memory it won't- irrespective of the number of
>>>> partitions we have (i've done everything from repartition(500) to
>>>> repartition(2500)). It's not a matter of running out of memory on a single
>>>> node because the data is skewed. It's more a matter of the shuffle buffer
>>>> filling up and needing to spill. I think what may be happening is that it
>>>> gets to a point where it's spending more time reading/writing from disk
>>>> while doing the spills then it is actually processing any data. I can tell
>>>> this because I can see that the spills sometimes get up into the 10's to
>>>> 100's of TB where the input data was maybe acquireExecutionMemory at
>>>> most. Unfortunately my code is on a private internal network and I'm
>>>> not able to share it.
>>>>
>>>> On Sun, Feb 7, 2016 at 3:38 AM, Igor Berman <igor.berman@gmail.com>
>>>> wrote:
>>>>
>>>>> so can you provide code snippets: especially it's interesting to see
>>>>> what are your transformation chain, how many partitions are there on
each
>>>>> side of shuffle operation
>>>>>
>>>>> the question is why it can't fit stuff in memory when you are
>>>>> shuffling - maybe your partitioner on "reduce" side is not configured
>>>>> properly? I mean if map side is ok, and you just reducing by key or
>>>>> something it should be ok, so some detail is missing...skewed data?
>>>>> aggregate by key?
>>>>>
>>>>> On 6 February 2016 at 20:13, Corey Nolet <cjnolet@gmail.com> wrote:
>>>>>
>>>>>> Igor,
>>>>>>
>>>>>> Thank you for the response but unfortunately, the problem I'm
>>>>>> referring to goes beyond this. I have set the shuffle memory fraction
to be
>>>>>> 90% and set the cache memory to be 0. Repartitioning the RDD helped
a tad
>>>>>> on the map side but didn't do much for the spilling when there was
no
>>>>>> longer any memory left for the shuffle. Also the new auto-memory
management
>>>>>> doesn't seem like it'll have too much of an effect after i've already
given
>>>>>> most the memory i've allocated to the shuffle. The problem I'm having
is
>>>>>> most specifically related to the shuffle performing declining by
several
>>>>>> orders of magnitude when it needs to spill multiple times (it ends
up
>>>>>> spilling several hundred for me when it can't fit stuff into memory).
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Sat, Feb 6, 2016 at 6:40 AM, Igor Berman <igor.berman@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>> usually you can solve this by 2 steps
>>>>>>> make rdd to have more partitions
>>>>>>> play with shuffle memory fraction
>>>>>>>
>>>>>>> in spark 1.6 cache vs shuffle memory fractions are adjusted
>>>>>>> automatically
>>>>>>>
>>>>>>> On 5 February 2016 at 23:07, Corey Nolet <cjnolet@gmail.com>
wrote:
>>>>>>>
>>>>>>>> I just recently had a discovery that my jobs were taking
several
>>>>>>>> hours to completely because of excess shuffle spills. What
I found was that
>>>>>>>> when I hit the high point where I didn't have enough memory
for the
>>>>>>>> shuffles to store all of their file consolidations at once,
it could spill
>>>>>>>> so many times that it causes my job's runtime to increase
by orders of
>>>>>>>> magnitude (and sometimes fail altogether).
>>>>>>>>
>>>>>>>> I've played with all the tuning parameters I can find. To
speed the
>>>>>>>> shuffles up, I tuned the akka threads to different values.
I also tuned the
>>>>>>>> shuffle buffering a tad (both up and down).
>>>>>>>>
>>>>>>>> I feel like I see a weak point here. The mappers are sharing
memory
>>>>>>>> space with reducers and the shuffles need enough memory to
consolidate and
>>>>>>>> pull otherwise they will need to spill and spill and spill.
What i've
>>>>>>>> noticed about my jobs is that this is a difference between
them taking 30
>>>>>>>> minutes and 4 hours or more. Same job- just different memory
tuning.
>>>>>>>>
>>>>>>>> I've found that, as a result of the spilling, I'm better
off not
>>>>>>>> caching any data in memory and lowering my storage fraction
to 0 and still
>>>>>>>> hoping I was able to give my shuffles enough memory that
my data doesn't
>>>>>>>> continuously spill. Is this the way it's supposed to be?
It makes it hard
>>>>>>>> because it seems like it forces the memory limits on my job-
otherwise it
>>>>>>>> could take orders of magnitude longer to execute.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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