mango
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bigdatagenomics
does not run
I managed to successfuly build mango (using move to 2.11 and move to spark2 scripts) but when I run bin/mango-submit.sh and other shell scripts, nothing happens (no output) even though I have SPARK_HOME in the Path. My OS is Linux Mint 18.2 (Ubuntu based)
Hi @antonkulaga ! What version is your SPARK_HOME pointing to? Are you just trying to run this locally?
Spark 2.20. I run move to 2.11 and move to spark.2 scripts before running Mango. I run spark locally. I wish I got at least some output from scripts (even with errors), by now I have zero
OOC, does this work with Spark 2.1.x? Spark 2.2.0 moves the Parquet dependency version, which causes classpath conflicts. We're working on a fix to this, see https://github.com/bigdatagenomics/adam/pull/1518.
Have not checked for Spark 2.1.x but latest master of ADAM works pretty well with Spark 2.2.0 for me (I use latest ADAM's master a lot right now). Anyway, even if it does not work, it should at least emit errors/warnings
Oh, interesting! It hadn't worked for me, but that was on one of the RCs. I'll retest today.
@antonkulaga locally you should be able to run the following: ./scripts/move_to_scala_2.11.sh ./scripts/move_to_spark_2.sh mvn clean package -DskipTests ./example-files/run-example.sh
And see the results at localhost:8080
This should be able to run with Spark 2.11 and 2.2.0 locally. If you are not getting any printout in the start script, can you change line 22 of the bin/mango-submit script from set -e to set -ex , then rerun and post the output here?