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Added test to try and repro #1282. #1292

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fnothaft commented Nov 26, 2016

@heuermh I couldn't reproduce the hang you were seeing in #1282. Any thoughts as to a test to reproduce the hang? Perhaps we diagnosed the hang wrong?

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AmplabJenkins Nov 26, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1639/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1639/
Test PASSed.

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heuermh Nov 28, 2016

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From the jenkins test failure linked in the original issue above

Build timed out (after 45 minutes). Marking the build as aborted.
Build was aborted
Recording test results
Publishing Scoverage XML and HTML report...
2016-11-16 16:28:18 ERROR Executor:95 - Exception in task 0.0 in stage 2.0 (TID 2)
java.lang.RuntimeException: Piped command List(tee, /dev/null) exited with error code 143.
	at org.bdgenomics.adam.rdd.GenomicRDD$$anonfun$12.apply(GenomicRDD.scala:297)
	at org.bdgenomics.adam.rdd.GenomicRDD$$anonfun$12.apply(GenomicRDD.scala:254)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
...
- don't lose any variants when piping as VCF *** FAILED ***
  org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0
failed 1 times, most recent failure: Lost task 0.0 in stage 2.0 (TID 2, localhost):
java.lang.RuntimeException: Piped command List(tee, /dev/null) exited with error code 143.

Is the error code 143 from tee being sent a kill/interrupt from the Jenkins test runner?

I was thinking the actual error causing the problem was an invalid VCF stream being read back in via VCFInFormatter, which threw an exception or something and then couldn't close the streams in the external process.

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heuermh commented Nov 28, 2016

From the jenkins test failure linked in the original issue above

Build timed out (after 45 minutes). Marking the build as aborted.
Build was aborted
Recording test results
Publishing Scoverage XML and HTML report...
2016-11-16 16:28:18 ERROR Executor:95 - Exception in task 0.0 in stage 2.0 (TID 2)
java.lang.RuntimeException: Piped command List(tee, /dev/null) exited with error code 143.
	at org.bdgenomics.adam.rdd.GenomicRDD$$anonfun$12.apply(GenomicRDD.scala:297)
	at org.bdgenomics.adam.rdd.GenomicRDD$$anonfun$12.apply(GenomicRDD.scala:254)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$20.apply(RDD.scala:710)
...
- don't lose any variants when piping as VCF *** FAILED ***
  org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0
failed 1 times, most recent failure: Lost task 0.0 in stage 2.0 (TID 2, localhost):
java.lang.RuntimeException: Piped command List(tee, /dev/null) exited with error code 143.

Is the error code 143 from tee being sent a kill/interrupt from the Jenkins test runner?

I was thinking the actual error causing the problem was an invalid VCF stream being read back in via VCFInFormatter, which threw an exception or something and then couldn't close the streams in the external process.

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fnothaft Mar 3, 2017

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Closing as out of date.

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fnothaft commented Mar 3, 2017

Closing as out of date.

@fnothaft fnothaft closed this Mar 3, 2017

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