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Posted to issues@spark.apache.org by "Josh Rosen (JIRA)" <ji...@apache.org> on 2014/10/14 20:14:34 UTC
[jira] [Comment Edited] (SPARK-3948) Potential file append bugs in
ExternalSorter which leads to sort-based shuffle unexpected exception
[ https://issues.apache.org/jira/browse/SPARK-3948?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14171295#comment-14171295 ]
Josh Rosen edited comment on SPARK-3948 at 10/14/14 6:13 PM:
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Hi [~jerryshao],
Could you share the changes that you made to copyStream (maybe by attaching a {{git diff}} to this ticket)? I want to play around with your fix to see whether I can spot the problem.
was (Author: joshrosen):
Hi [~jerryshao]],
Could you share the changes that you made to copyStream (maybe by attaching a {{git diff}} to this ticket)? I want to play around with your fix to see whether I can spot the problem.
> Potential file append bugs in ExternalSorter which leads to sort-based shuffle unexpected exception
> ---------------------------------------------------------------------------------------------------
>
> Key: SPARK-3948
> URL: https://issues.apache.org/jira/browse/SPARK-3948
> Project: Spark
> Issue Type: Bug
> Components: Shuffle
> Affects Versions: 1.2.0
> Reporter: Saisai Shao
>
> Several exceptions occurred when running TPC-DS queries against latest master branch with sort-based shuffle enable, like PARSING_ERROR(2) in snappy, deserializing error in Kryo and offset out-range in FileManagedBuffer, all these exceptions are gone when we changed to hash-based shuffle.
> With deep investigation, we found that some shuffle output file is unexpectedly smaller than the others, as the log shows:
> {noformat}
> 14/10/14 18:25:06 INFO shuffle.IndexShuffleBlockManager: Block id: shuffle_6_9_11, offset: 3055635, length: 236708, file length: 47274167
> 14/10/14 18:25:06 INFO shuffle.IndexShuffleBlockManager: Block id: shuffle_6_10_11, offset: 2986484, length: 222755, file length: 47174539
> 14/10/14 18:25:06 INFO shuffle.IndexShuffleBlockManager: Block id: shuffle_6_11_11, offset: 2995341, length: 259871, file length: 383405
> 14/10/14 18:25:06 INFO shuffle.IndexShuffleBlockManager: Block id: shuffle_6_12_11, offset: 2991030, length: 268191, file length: 47478892
> 14/10/14 18:25:06 INFO shuffle.IndexShuffleBlockManager: Block id: shuffle_6_13_11, offset: 3016292, length: 230694, file length: 47420826
> 14/10/14 18:25:06 INFO shuffle.IndexShuffleBlockManager: Block id: shuffle_6_14_11, offset: 3061400, length: 241136, file length: 47395509
> {noformat}
> As you can see the total file length of shuffle_6_10_11 is much smaller than other same stage map output results.
> And we also dump the map outputs in map side to see if this small size output is correct or not, below is the log:
> {noformat}
> In bypass merge sort, file name: /mnt/DP_disk1/animal/spark/spark-local-
> 20141014182142-8345/22/shuffle_6_11_0.data, file length: 383405length:
> 274722 262597 291290 272902 264941 270358 291005 295285 252482
> 287142 232617 259871 233734 241439 228897 234282 253834 235619
> 233803 255532 270739 253825 262087 266404 234273 250120 262983
> 257024 255947 254971 258908 247862 221613 258566 245399 251684
> 274843 226150 264278 245279 225656 235084 239466 212851 242245
> 218781 222191 215500 211548 234256 208601 204113 191923 217895
> 227020 215331 212313 223725 250876 256875 239276 266777 235520
> 237462 234063 242270 246825 255888 235937 236956 233099 264508
> 260303 233294 239061 254856 257475 230105 246553 260412 210355
> 211201 219572 206636 226866 209937 226618 218208 206255 248069
> 221717 222112 215734 248088 239207 246125 239056 241133 253091
> 246738 233128 242794 231606 255737 221123 252115 247286 229688
> 251087 250047 237579 263079 256251 238214 208641 201120 204009
> 200825 211965 200600 194492 226471 194887 226975 215072 206008
> 233288 222132 208860 219064 218162 237126 220465 201343 225711
> 232178 233786 212767 211462 213671 215853 227822 233782 214727
> 247001 228968 247413 222674 214241 184122 215643 207665 219079
> 215185 207718 212723 201613 216600 212591 208174 204195 208099
> 229079 230274 223373 214999 256626 228895 231821 383405 229646
> 220212 245495 245960 227556 213266 237203 203805 240509 239306
> 242365 218416 238487 219397 240026 251011 258369 255365 259811
> 283313 248450 264286 264562 257485 279459 249187 257609 274964
> 292369 273826
> {noformat}
> Here I dump the file name, length and each partition's length, obviously the sum of all partition lengths is not equal to file length. So I think there may be a situation paritionWriter in ExternalSorter not always append to the end of previous written file, the file's content is overwritten in some parts, and this lead to the exceptions I mentioned before.
> Also I changed the code of copyStream by disable transferTo, use the previous one, all the issues are gone. So I think there maybe some flushing problems in transferTo when processed data is large.
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