Benchmarking documentation

[ccbaumler]

Examples of benchmarking from lab

An example of using snakemake for benchmarking

The benchmark output files from the above repo

The use of mprof which profile memory usage on sourmash gather

Jessica's benchmarking process

sourmash compare memory needs profiling!!

Tools for benchmarking software

Flamegraph

• Repo
• Flamegraph
• Memory profile flamegraph
• differential flamegraph
• Rust edition (Read the bottom)

py-spy

• documentation
• repo

timeit

• documentation

snakemake

• Benchmarking a workflow
• Explanation of benchmarking variables
• Git repo organization for snakemake workflow
• Catalog of workflow
• example of properly organized workflow