ml-mlip-speed

Benchmark MLIP inference speed and memory across NaCl supercell sizes.

144|21|Updated Jan 8, 2026
One-click install
npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill ml-mlip-speed
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: ml-mlip-speed
Source: https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/ml-mlip-speed
Command: npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill ml-mlip-speed

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and assets (resource) and references (resource) components.

What problem does it solve?

Selecting an MLIP for atomistic simulations is hard because inference latency and memory footprint vary widely by model and system size, which can make planned MD runs too slow or crash with OOM errors.

Core Features & Use Cases

  • Inference speed benchmarking: Measures per-atom inference time by running short NVE MD steps on NaCl supercells across increasing sizes.
  • Peak memory/VRAM estimation: Tracks peak memory usage during inference (GPU VRAM via PyTorch or host RAM via psutil).
  • Multi-environment model coverage: Supports benchmarking models that require separate Conda environments by incrementally updating a shared speed_benchmark.yaml.
  • Plot consolidation: Regenerates comparative speed and memory plots from accumulated YAML results using a single flag for final visualization.
  • Use Case: Compare MACE, MatGL, and FAIRCHEM checkpoints to pick a model tier (fast/low-cost vs heavier/accurate) for long MD on large cells.

Quick Start

Run the benchmark script with models and providers specified so it produces speed_benchmark.yaml and per-hardware plots in your chosen output directory.

Frequently Asked Questions about ml-mlip-speed

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I benchmark MLIP inference speed and VRAM for molecular dynamics?

You can benchmark MLIP inference speed and VRAM by executing short NVE molecular dynamics runs on NaCl supercells. This process measures per-atom inference latency and peak memory consumption, persisting the results into a YAML file for comparison.

How do I compare MACE, MatGL, and FAIRCHEM memory consumption for large supercells?

To compare MACE, MatGL, and FAIRCHEM memory consumption, you run short MD steps across increasing NaCl supercell sizes. The benchmark tracks peak GPU VRAM via PyTorch or host RAM via psutil to guide model selection.

Can I benchmark machine learning interatomic potentials that require separate Conda environments?

Yes, you can benchmark machine learning interatomic potentials across separate Conda environments. The script incrementally updates a shared speed_benchmark.yaml file, allowing you to aggregate results from different model providers without conflicts.

How do I regenerate comparative speed and memory plots without rerunning MD simulations?

You can regenerate comparative speed and memory plots without rerunning MD simulations by using a specific plot consolidation flag. This reads the accumulated results from your existing speed_benchmark.yaml file to produce final visualizations.

Why does my chosen MLIP crash with OOM errors during atomistic simulation throughput?

Your chosen MLIP crashes with OOM errors because inference latency and memory footprint vary widely by model and system size. Benchmarking peak memory consumption across different supercell sizes helps prevent these out-of-memory crashes during long MD runs.

What is the best way to select an MLIP model tier for long MD on large cells?

The best way to select an MLIP model tier for long MD on large cells is to benchmark per-atom latency and peak VRAM. Comparing results across providers like MACE, MatGL, and FAIRCHEM helps balance fast low-cost models against heavier accurate ones.