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adam-submit transform fails with Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing class #1306

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PrakashShanmugam opened this issue Dec 9, 2016 · 3 comments

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@PrakashShanmugam
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@PrakashShanmugam PrakashShanmugam commented Dec 9, 2016

The adam-submit command fails with the following exception

Exception in thread "main" java.lang.IncompatibleClassChangeError: Implementing class
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)

This was tested in macOS sierra machine with java 1.8.0_111 with spark 2.0.

The github instruction was followed and made clean package with the same machine. It fails at this step
adam-submit transform $ADAM_HOME/adam-core/src/test/resources/small.sam /tmp/small.adam

@heuermh
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@heuermh heuermh commented Dec 9, 2016

Hello @PrakashShanmugam!

To confirm, the steps you took were something like

$ git clone https://github.com/bigdatagenomics/adam.git
$ cd adam
$ mvn clean package
$ export $ADAM_HOME=`pwd`
$ export $PATH=$ADAM_HOME/bin:$PATH
$ adam-submit transform $ADAM_HOME/adam-core/src/test/resources/small.sam /tmp/small.adam

And then when you run adam-submit with Spark 2.0 installed you get the error above.

I believe this is because building from source builds against Spark 1.6.3 by default, and those artifacts won't work when run with Spark 2.0.x.

If you run the script to reconfigure the build against Spark 2.0.x and then clean package

$ ./scripts/move_to_spark_2.sh
$ mvn clean package

you should be able to run with Spark 2.0.x. We should update the README to mention this.

@PrakashShanmugam
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@PrakashShanmugam PrakashShanmugam commented Dec 9, 2016

@heuermh
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@heuermh heuermh commented Dec 9, 2016

Great, thank you! We'll get the README fixes in for #1307 soon.

@heuermh heuermh closed this Dec 9, 2016
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