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

Closed
PrakashShanmugam opened this Issue Dec 9, 2016 · 3 comments

Comments

Projects
None yet
2 participants
@PrakashShanmugam

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

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Dec 9, 2016

Member

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.

Member

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

This comment has been minimized.

Show comment
Hide comment
@PrakashShanmugam

PrakashShanmugam Dec 9, 2016

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Dec 9, 2016

Member

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

Member

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment