hpc-context

Guidance for running Mycelia on HPC systems with SLURM.

Benchmark Commands

Local small/medium/large benchmarks:

julia --project=. benchmarking/benchmark_runner.jl small
julia --project=. benchmarking/benchmark_runner.jl medium
julia --project=. benchmarking/benchmark_runner.jl large

SLURM submission (resource-intensive):

sbatch benchmarking/run_all_benchmarks.sh

Key Directories

• benchmarking/ - Heavy benchmark scripts
• results/ - Generated artifacts
• ci/hpc/ - HPC-specific CI configuration

Resource Considerations

• Use memory estimation utilities from utility-functions.jl for large-scale analyses
• Keep external tool calls isolated in helpers under src/
• Avoid committing generated outputs or large files
• Note external tool or dataset requirements explicitly

Portability

• Use joinpath for all file paths
• Test on multiple environments when possible
• Document any HPC-specific requirements
• Consider job scheduler compatibility (SLURM, PBS, etc.)

Tutorial/Benchmark Guidelines

• Do NOT add generally useful functions in tutorials/, test/, or benchmarking/
• If a helper is broadly useful, add it under src/ and call from tutorial
• Tutorials demonstrate core Mycelia functionality
• Avoid defining new helper functions except true one-offs
• Prefer Rhizomorph graph/assembly functionality over legacy base-graph APIs