In principle, after talking with support and reading the documentation, I see that 2 options are available for this:
1 - pass log4j.properties through the configuration passed when creating EMR. Jonathan mentioned this in his answer.
2 - Turn on the switch --files / path / to / log4j.properties in the spark-submit command. This will distribute the log4j.properties file into the working directory of each Spark Executor, and then change your -Dlog4j configuration to only point to the file name: "spark.driver.extraJavaOptions = -Dlog4j.configuration = log4j.properties"
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