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From Sven Krasser <kras...@gmail.com>
Subject Re: Problems saving a large RDD (1 TB) to S3 as a sequence file
Date Fri, 23 Jan 2015 22:12:56 GMT
Hey Darin,

Are you running this over EMR or as a standalone cluster? I've had
occasional success in similar cases by digging through all executor logs
and trying to find exceptions that are not caused by the application
shutdown (but the logs remain my main pain point with Spark).

That aside, another explanation could be S3 throttling you due to volume
(and hence causing write requests to fail). You can try to split your file
into multiple pieces and store those as S3 objects with different prefixes
to make sure they end up in different partitions in S3. See here for
details:
http://docs.aws.amazon.com/AmazonS3/latest/dev/request-rate-perf-considerations.html.
If that works, that'll narrow the cause down.

Best,
-Sven


On Fri, Jan 23, 2015 at 12:04 PM, Darin McBeath <ddmcbeath@yahoo.com.invalid
> wrote:

> I've tried various ideas, but I'm really just shooting in the dark.
>
> I have an 8 node cluster of r3.8xlarge machines. The RDD (with 1024
> partitions) I'm trying to save off to S3 is approximately 1TB in size (with
> the partitions pretty evenly distributed in size).
>
> I just tried a test to dial back the number of executors on my cluster
> from using the entire cluster (256 cores) down to 128.  Things seemed to
> get a bit farther (maybe) before the wheels started spinning off again.
> But, the job always fails when all I'm trying to do is save the 1TB file to
> S3.
>
> I see the following in my master log file.
>
> 15/01/23 19:01:54 WARN master.Master: Removing worker-20150123172316
> because we got no heartbeat in 60 seconds
> 15/01/23 19:01:54 INFO master.Master: Removing worker
> worker-20150123172316 on
> 15/01/23 19:01:54 INFO master.Master: Telling app of lost executor: 3
>
> For the stage that eventually fails, I see the following summary
> information.
>
> Summary Metrics for 729 Completed Tasks
> Duration 2.5 min 4.8 min 5.5 min 6.3 min 9.2 min
> GC Time   0 ms 0.3 s 0.4 s 0.5 s 5 s
>
> Shuffle Read (Remote) 309.3 MB 321.7 MB 325.4 MB 329.6 MB 350.6 MB
>
> So, the max GC was only 5s for 729 completed tasks.  This sounds
> reasonable.  As people tend to indicate GC is the reason one loses
> executors, this does not appear to be my case.
>
> Here is a typical snapshot for some completed tasks.  So, you can see that
> they tend to complete in approximately 6 minutes.  So, it takes about 6
> minutes to write one partition to S3 (a partition being roughly 1 GB)
>
> 65      23619   0       SUCCESS         ANY     5 /  2015/01/23 18:30:32
>       5.8 min         0.9 s   344.6 MB
> 59      23613   0       SUCCESS         ANY     7 /  2015/01/23 18:30:32
>       6.0 min         0.4 s   324.1 MB
> 68      23622   0       SUCCESS         ANY     1 /  2015/01/23 18:30:32
>       5.7 min         0.5 s   329.9 MB
> 62      23616   0       SUCCESS         ANY     6 /  2015/01/23 18:30:32
>       5.8 min         0.7 s   326.4 MB
> 61      23615   0       SUCCESS         ANY     3 /  2015/01/23 18:30:32
>       5.5 min         1 s     335.7 MB
> 64      23618   0       SUCCESS         ANY     2 /  2015/01/23 18:30:32
>       5.6 min         2 s     328.1 MB
>
> Then towards the end, when things start heading south, I see the
> following.  These tasks never complete but you can see that they have taken
> more than 47 minutes (so far) before the job finally fails.  Not really
> sure why.
>
> 671     24225   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 672     24226   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 673     24227   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 674     24228   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 675     24229   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 676     24230   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 677     24231   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 678     24232   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 679     24233   0       RUNNING         ANY     1 /  2015/01/23 18:59:14
>       47 min
> 680     24234   0       RUNNING         ANY     1 /  2015/01/23 18:59:17
>       47 min
> 681     24235   0       RUNNING         ANY     1 /  2015/01/23 18:59:18
>       47 min
> 682     24236   0       RUNNING         ANY     1 /  2015/01/23 18:59:18
>       47 min
> 683     24237   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 684     24238   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 685     24239   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 686     24240   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 687     24241   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 688     24242   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 689     24243   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 690     24244   0       RUNNING         ANY     5 /  2015/01/23 18:59:20
>       47 min
> 691     24245   0       RUNNING         ANY     5 /  2015/01/23 18:59:21
>       47 min
>
> What's odd is that even on the same machine (see below) some tasks are
> still completing (in less than 5 minutes) while other tasks on the same
> machine seem to be hung after 46 minutes.  Keep in mind all I'm doing is
> saving the file to S3 so one would think the amount of work per
> task/partition would be fairly equal.
>
> 694     24248   0       SUCCESS         ANY     0 /  2015/01/23 18:59:32
>       4.5 min         0.3 s   326.5 MB
> 695     24249   0       SUCCESS         ANY     0 /  2015/01/23 18:59:32
>       4.5 min         0.3 s   330.8 MB
> 696     24250   0       RUNNING         ANY     0 /  2015/01/23 18:59:32
>       46 min
> 697     24251   0       RUNNING         ANY     0 /  2015/01/23 18:59:32
>       46 min
> 698     24252   0       SUCCESS         ANY     0 /  2015/01/23 18:59:32
>       4.5 min         0.3 s   325.8 MB
> 699     24253   0       SUCCESS         ANY     0 /  2015/01/23 18:59:32
>       4.5 min         0.3 s   325.2 MB
> 700     24254   0       SUCCESS         ANY     0 /  2015/01/23 18:59:32
>       4.5 min         0.3 s   323.4 MB
>
> If anyone has some suggestions please let me know.  I've tried playing
> around with various configuration options but I've found nothing yet that
> will fix the underlying issue.
>
> Thanks.
>
> Darin.
>
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