Heap out of memory

[tpoterba]

This indicates that you’re running on one machine with 32 cores, and have less than 400 MB (!) allocated for the entire process. This should solve things:

How do I increase the memory or RAM available to the JVM when I start Hail through Python?

You can set the memory using an environment variable: PYSPARK_SUBMIT_ARGS="--driver-memory 8g --executor-memory 8g pyspark-shell" ipython This will start an ipython notebook with 8 GB of memory. If you want ipython to always start with 8 GB of memory, you can add this to your .bashrc (or the equivalent file for your shell): export PYSPARK_SUBMIT_ARGS="--driver-memory 8g --executor-memory 8g pyspark-shell"