Lineage for partitionAndJoin in ShuffleRegionJoin causes StackOverflow Errors #1308

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akmorrow13 opened this Issue Dec 10, 2016 · 11 comments

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akmorrow13 commented Dec 10, 2016

I am having issues with partitionAndJoin for LeftOuterShuffleRegionJoin. There is a stack overflow issue. I can oddly avoid this issue by putting counts in partitionAndJoin() after operations, if the inputs are cached.

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Can you post a stack trace?

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fnothaft commented Dec 10, 2016

Can you post a stack trace?

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Also, is the version of ADAM you're using before or after #1253 merged?

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fnothaft commented Dec 10, 2016

Also, is the version of ADAM you're using before or after #1253 merged?

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The stack fills up with only Iter.hasNext() until it overflows. It is the most recent version of ADAM, with #1253 merged in.

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devin-petersohn commented Dec 10, 2016

The stack fills up with only Iter.hasNext() until it overflows. It is the most recent version of ADAM, with #1253 merged in.

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I can haz stack plz?

Subjective descriptions of the stack trace are just not quite as good as the stack trace itself. ;)

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fnothaft commented Dec 10, 2016

I can haz stack plz?

Subjective descriptions of the stack trace are just not quite as good as the stack trace itself. ;)

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16/12/09 08:35:20 WARN scheduler.TaskSetManager: Lost task 529.3 in stage 72.0 (TID 31810, amp-bdg-37.amplab.net): java.lang.StackOverflowError
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
Member

devin-petersohn commented Dec 10, 2016

16/12/09 08:35:20 WARN scheduler.TaskSetManager: Lost task 529.3 in stage 72.0 (TID 31810, amp-bdg-37.amplab.net): java.lang.StackOverflowError
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
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Sigh. In this case, it may be true that the stack trace and the subjective description of the stack trace are indeed equally useful... @akmorrow13 or @devin-petersohn do either of you have an example join I could look at with data? Is this just left outer? Is this only after #1253?

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fnothaft commented Dec 10, 2016

Sigh. In this case, it may be true that the stack trace and the subjective description of the stack trace are indeed equally useful... @akmorrow13 or @devin-petersohn do either of you have an example join I could look at with data? Is this just left outer? Is this only after #1253?

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I didn't have this problem before. I am performing a ShuffleRegionJoin.

I can send you the example I am working with for benchmarking through Slack.

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devin-petersohn commented Dec 11, 2016

I didn't have this problem before. I am performing a ShuffleRegionJoin.

I can send you the example I am working with for benchmarking through Slack.

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https://github.com/akmorrow13/endive/blob/master/src/main/scala/net/akmorrow13/endive/pipelines/KernelPipeline.scala calls this (eventually). Specifically https://github.com/akmorrow13/endive/blob/master/src/main/scala/net/akmorrow13/endive/pipelines/VectorizedDnase.scala#L181 calls this. My working version of adam join is here: https://github.com/akmorrow13/adam/blob/endive_changes/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoin.scala#L90 (this only works if the input RDDs are cached). Does adam allow users to specify checkpoint locations? That may be helpful for these long lineage tasks.

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akmorrow13 commented Dec 11, 2016

https://github.com/akmorrow13/endive/blob/master/src/main/scala/net/akmorrow13/endive/pipelines/KernelPipeline.scala calls this (eventually). Specifically https://github.com/akmorrow13/endive/blob/master/src/main/scala/net/akmorrow13/endive/pipelines/VectorizedDnase.scala#L181 calls this. My working version of adam join is here: https://github.com/akmorrow13/adam/blob/endive_changes/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoin.scala#L90 (this only works if the input RDDs are cached). Does adam allow users to specify checkpoint locations? That may be helpful for these long lineage tasks.

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Good to see everyone taking the weekend off! If either of you can ping me scripts to run on the cluster, that'd be a huge help!

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fnothaft commented Dec 11, 2016

Good to see everyone taking the weekend off! If either of you can ping me scripts to run on the cluster, that'd be a huge help!

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Sure! From my directory on the cluster, you can 'cd ADAM/endive' and run './bin/run-single-tf-datasetcreation-pipeline.sh confs/datasetcreation.conf '. This should take a bit but will reach the problem at https://github.com/akmorrow13/endive/blob/master/src/main/scala/net/akmorrow13/endive/pipelines/VectorizedDnase.scala#L181 . LMK if you have permission errors or such.

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akmorrow13 commented Dec 12, 2016

Sure! From my directory on the cluster, you can 'cd ADAM/endive' and run './bin/run-single-tf-datasetcreation-pipeline.sh confs/datasetcreation.conf '. This should take a bit but will reach the problem at https://github.com/akmorrow13/endive/blob/master/src/main/scala/net/akmorrow13/endive/pipelines/VectorizedDnase.scala#L181 . LMK if you have permission errors or such.

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