Jark Wu created FLINK-18118:
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             Summary: Some SQL Jobs with two input operators are loosing data 
with unaligned checkpoints
                 Key: FLINK-18118
                 URL: https://issues.apache.org/jira/browse/FLINK-18118
             Project: Flink
          Issue Type: Bug
          Components: Runtime / Checkpointing, Table SQL / Runtime
    Affects Versions: 1.11.0
            Reporter: Jark Wu
             Fix For: 1.11.0


After trying to enable unaligned checkpoints by default, a lot of Blink 
streaming SQL/Table API tests containing joins or set operations are throwing 
errors that are indicating we are loosing some data (full records, without 
deserialisation errors). Example errors:

{noformat}
[ERROR] Failures: 
[ERROR]   JoinITCase.testFullJoinWithEqualPk:775 expected:<List(1,1, 2,2, 3,3, 
null,4, null,5)> but was:<List(2,2, 3,3, null,1, null,4, null,5)>
[ERROR]   JoinITCase.testStreamJoinWithSameRecord:391 expected:<List(1,1,1,1, 
1,1,1,1, 2,2,2,2, 2,2,2,2, 3,3,3,3, 3,3,3,3, 4,4,4,4, 4,4,4,4, 5,5,5,5, 
5,5,5,5)> but was:<List()>
[ERROR]   SemiAntiJoinStreamITCase.testAntiJoin:352 expected:<0> but was:<1>
[ERROR]   SetOperatorsITCase.testIntersect:55 expected:<MutableList(1,1,Hi, 
2,2,Hello, 3,2,Hello world)> but was:<List()>
[ERROR]   JoinITCase.testJoinPushThroughJoin:1272 expected:<List(1,0,Hi, 
2,1,Hello, 2,1,Hello world)> but was:<List(2,1,Hello, 2,1,Hello world)>
{noformat}
 



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