polars-bio-bench

Benchmarks of various genomic ranges operations

Pre-requisites

• pyenv

➜  polars-bio-bench git:(init) ✗ pyenv --version
pyenv 2.5.0

• poetry

➜  polars-bio-bench git:(init) ✗ poetry --version
Poetry (version 2.0.0)

Setup

pyenv install 3.12.8
pyenv local 3.12.8
poetry env use 3.12
poetry update

Hardware requirements

Please note that you need at least 64GB of RAM to run the full benchmarks. For the default 16-32GB should be enough.

Run

All the benchmarking scenarios are defined in the conf/benchmark_*.yaml files. By default, the conf/benchmark_small.yaml file is used. If you would like to run the benchmarks with a different configuration file, you can specify it using the --bench-config option.

export BENCH_DATA_ROOT=/tmp/polars-bio-bench/

poetry run python src/run-benchmarks.py --help
INFO:polars_bio:Creating BioSessionContext
Usage: run-benchmarks.py [OPTIONS]

Options:
  --bench-config TEXT  Benchmark config file (default:
                       conf/benchmark_small.yaml)
  --help               Show this message and exit.

Sample benchmark scenarios

• conf/benchmark_small.yaml - small dataset, small number of operations for nearest and overlap, native DataFusion input
• conf/benchmark_dataframes.yaml - as above but with DataFrames (Polars/Pandas) as input
• conf/benchmark_large.yaml - large dataset, large number of operations for nearest and overlap, native DataFusion input