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Transform should run with spark.kryo.requireRegistration=true #1136

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fnothaft opened this issue Aug 27, 2016 · 2 comments · Fixed by #1138
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Transform should run with spark.kryo.requireRegistration=true #1136

fnothaft opened this issue Aug 27, 2016 · 2 comments · Fixed by #1138
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fnothaft commented Aug 27, 2016 •
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Ran into this when trying to hunt down a stack overflow during serialization with Kryo's FieldSerializer inside the indel realigner, where all serialization should use custom serializers. Anyways, I'm running into a variety of bugs:

  • scala.reflect.ManifestFactory$ClassTypeManifest.class during MarkDups
@fnothaft fnothaft added the bug label Aug 27, 2016
@fnothaft fnothaft self-assigned this Aug 27, 2016
fnothaft added a commit to fnothaft/adam that referenced this issue Aug 28, 2016
@fnothaft
[ADAM-1136] Transform runs successfully with kryo registration required
95f3528 
Resolves bigdatagenomics#1136. Rewrote IndelRealignmentTarget/ZippedTargetSet serializers to
resolve potential StackOverflowException.
@fnothaft fnothaft mentioned this issue Aug 28, 2016
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heuermh commented Aug 29, 2016

What's the best way to test this change?

adam-submit --conf spark.kryo.requireRegistration=true -- transform -realign_indels ...

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@heuermh that's correct.

heuermh pushed a commit to heuermh/adam that referenced this issue Sep 27, 2016
@fnothaft @heuermh
[ADAM-1136] Transform runs successfully with kryo registration required
5ff31be 
Resolves bigdatagenomics#1136. Rewrote IndelRealignmentTarget/ZippedTargetSet serializers to
resolve potential StackOverflowException.
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[ADAM-1136] Transform runs successfully with kryo registration required fnothaft/adam
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