Building GATK 3.7 and a stackoverflow building Queue Extensions

hemphemp Raleigh, NCMember
edited February 2017 in Ask the GATK team

Occasionally when my CI docker image build runs mvn verify, it gets a stack-overflow error when building GATK Queue Extensions Distribution. This is not 100% of the time and hard to reproduce...sorry for the lack of information. I've tried to capture as much as I could and wondered if anyone else has encountered this in their CI? Increasing the stack size -Xss via MAVEN_OPTS does not help.

Docker information (FROM openjdk:8):

[email protected]:/opt/gatk# git describe --tags
3.7
[email protected]:/opt/gatk# cat /etc/debian_version
8.7
[email protected]:/opt/gatk# java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
[email protected]:/opt/gatk#

I've attached the full log file. But here is a snippet from it:

...
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.silent(Typers.scala:728)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.normalTypedApply$1(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedApply$1(Typers.scala:4621)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed1(Typers.scala:5526)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5689)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5697)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.adaptMember(Erasure.scala:786)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.silent(Typers.scala:728)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.normalTypedApply$1(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedApply$1(Typers.scala:4621)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed1(Typers.scala:5526)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5689)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5697)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.adaptMember(Erasure.scala:786)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.silent(Typers.scala:728)
...
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