Replies: 2 comments 4 replies
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Hey @janosh! I am technical marketing engineer with ALCHEMI. These numbers for NL in Toolkit-Ops are not what we expected, and I would like to have a closer look if possible. Can you, please, share the structures you are testing on and potentially benchmark suite or script? Thanks a lot |
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i can't share the structures i'm running but here's a script that downloads the WBM structures via
nl_benchmark.py# /// script
# requires-python = ">=3.11"
# dependencies = [
# "ase",
# "ferrox",
# "matbench-discovery",
# "mp-api",
# "nequip",
# "numpy",
# "openequivariance",
# "pymatgen",
# "torch",
# "torch-sim",
# ]
# ///
Neighbor-list benchmark using random MP or WBM structures.
Example:
uv run python scripts/geo_opt_pipeline/nl_benchmark_public.py \
--source wbm --n-structures 100 --nl-backend matscipy --device cuda
"""
from __future__ import annotations
import argparse
import json
import os
import random
import subprocess
import sys
import time
from pathlib import Path
from typing import Any
import numpy as np
NEQUIP_MODEL_ID = "mir-group/NequIP-OAM-L:0.1"
VALID_NL_BACKENDS = ("matscipy", "vesin", "ase", "alchemi")
def parse_args() -> argparse.Namespace:
"""Parse CLI args."""
parser = argparse.ArgumentParser(
description=(
"Benchmark torch-sim neighbor-list backends on random public structures."
)
)
parser.add_argument(
"--source",
choices=("mp", "wbm"),
required=True,
help="Public structure source: mp (Materials Project) or wbm (Matbench Discovery).",
)
parser.add_argument(
"--n-structures",
type=int,
default=100,
help="How many random structures to benchmark.",
)
parser.add_argument(
"--seed",
type=int,
default=0,
help="Random seed for reproducible sampling.",
)
parser.add_argument(
"--nl-backend",
choices=VALID_NL_BACKENDS,
default="matscipy",
help="Neighbor-list backend passed to NequIPFrameworkModel.",
)
parser.add_argument(
"--max-steps",
type=int,
default=1000,
help="Maximum LBFGS optimization steps.",
)
parser.add_argument(
"--f-max",
"--fmax",
dest="f_max",
type=float,
default=5e-3,
help="Force convergence threshold.",
)
parser.add_argument(
"--device",
default="cuda",
help='Torch device, e.g. "cuda" or "cpu".',
)
parser.add_argument(
"--dtype",
choices=("float32", "float64"),
default="float64",
help="Torch dtype for simulation tensors.",
)
parser.add_argument(
"--max-memory-scaler",
type=int,
default=None,
help="Optional InFlightAutoBatcher max_memory_scaler.",
)
parsed_args = parser.parse_args()
if parsed_args.n_structures <= 0:
parser.error("--n-structures must be > 0")
if parsed_args.max_steps <= 0:
parser.error("--max-steps must be > 0")
if parsed_args.f_max <= 0:
parser.error("--f-max must be > 0")
return parsed_args
def compile_nequip_model(
model_id: str = NEQUIP_MODEL_ID,
device: str = "cuda",
) -> Path:
"""Compile (and cache) the NequIP model used by torch-sim."""
compiled_dir = Path.home() / ".nequip" / "compiled"
model_slug = model_id.split("/")[-1].replace(":", "-")
device_slug = device.replace(":", "-")
compiled_path = compiled_dir / f"{model_slug}.{device_slug}.oeq.nequip.pth"
if compiled_path.exists():
return compiled_path
compiled_dir.mkdir(parents=True, exist_ok=True)
compile_cmd = [
sys.executable,
"-m",
"nequip.scripts.compile",
f"nequip.net:{model_id}",
str(compiled_path),
"--mode",
"torchscript",
"--device",
device,
"--target",
"batch",
"--modifiers",
"enable_OpenEquivariance",
]
env = os.environ.copy()
venv_bin = str(Path(sys.executable).parent)
env["PATH"] = f"{venv_bin}:{env.get('PATH', '')}"
result = subprocess.run(
compile_cmd,
capture_output=True,
text=True,
env=env,
check=False,
)
if result.returncode != 0:
raise RuntimeError(
f"NequIP compile failed (exit={result.returncode}).\n"
f"stdout:\n{result.stdout}\n\nstderr:\n{result.stderr}"
)
return compiled_path
def _sample_mp_structures(n_structures: int, seed: int) -> list[dict[str, Any]]:
"""Fetch random MP structures as pymatgen dicts."""
from mp_api.client import MPRester
if not os.environ.get("MP_API_KEY"):
raise RuntimeError("MP_API_KEY is required for --source mp")
with MPRester() as mpr:
# Reservoir sampling gives an unbiased sample over the full result stream
# without loading all IDs into memory.
sampled_material_ids: list[str] = []
py_rng = random.Random(seed)
id_docs = mpr.summary.search(
fields=["material_id"],
all_fields=False,
chunk_size=2_000,
)
for stream_idx, doc in enumerate(id_docs):
material_id = str(doc.material_id)
if stream_idx < n_structures:
sampled_material_ids.append(material_id)
continue
replacement_idx = py_rng.randint(0, stream_idx)
if replacement_idx < n_structures:
sampled_material_ids[replacement_idx] = material_id
if len(sampled_material_ids) < n_structures:
raise RuntimeError(
f"Requested {n_structures} structures but only found "
f"{len(sampled_material_ids)} in MP."
)
structure_docs = mpr.summary.search(
material_ids=sampled_material_ids,
fields=["material_id", "structure"],
all_fields=False,
)
structure_by_id: dict[str, dict[str, Any]] = {}
for doc in structure_docs:
structure_by_id[str(doc.material_id)] = doc.structure.as_dict()
missing_ids = [
material_id
for material_id in sampled_material_ids
if material_id not in structure_by_id
]
if missing_ids:
raise RuntimeError(
f"Failed to fetch structures for {len(missing_ids)} sampled MP IDs."
)
return [structure_by_id[material_id] for material_id in sampled_material_ids]
def _sample_wbm_structures(n_structures: int, seed: int) -> list[dict[str, Any]]:
"""Fetch random WBM structures as pymatgen dicts.
Uses ``matbench_discovery.data.ase_atoms_from_zip`` to match upstream WBM loading.
"""
from matbench_discovery.data import DataFiles, ase_atoms_from_zip
from pymatgen.io.ase import AseAtomsAdaptor
wbm_zip_path = DataFiles.wbm_initial_atoms.path
all_atoms = ase_atoms_from_zip(wbm_zip_path)
if n_structures > len(all_atoms):
raise RuntimeError(
f"Requested {n_structures} structures, but WBM has {len(all_atoms)}"
)
np_rng = np.random.default_rng(seed=seed)
sampled_indices = np_rng.choice(len(all_atoms), size=n_structures, replace=False)
sampled_atoms = [all_atoms[int(idx)] for idx in sampled_indices.tolist()]
adaptor = AseAtomsAdaptor()
return [adaptor.get_structure(atoms).as_dict() for atoms in sampled_atoms]
def load_public_structures(
source: str,
n_structures: int,
seed: int,
) -> list[dict[str, Any]]:
"""Load random structures from the requested public source."""
if source == "mp":
return _sample_mp_structures(n_structures=n_structures, seed=seed)
if source == "wbm":
return _sample_wbm_structures(n_structures=n_structures, seed=seed)
raise ValueError(f"Unsupported source: {source}")
def _configure_torch_serialization_compat() -> None:
"""Configure safe globals for older e3nn constants on newer torch.
PyTorch 2.6 switched ``torch.load(..., weights_only=True)`` by default. Some
e3nn releases still load ``constants.pt`` with Python ``slice`` objects. This
allowlist preserves secure loading while restoring compatibility.
"""
import torch
add_safe_globals = getattr(torch.serialization, "add_safe_globals", None)
if callable(add_safe_globals):
add_safe_globals([slice])
def run_benchmark(args: argparse.Namespace) -> dict[str, Any]:
"""Run one benchmark and return compact metrics."""
import ferrox
import torch
import torch_sim as ts
from torch_sim.autobatching import InFlightAutoBatcher
_configure_torch_serialization_compat()
try:
from torch_sim.models.nequip_framework import NequIPFrameworkModel
except Exception as exc:
raise RuntimeError(
"Failed to import NequIP/torch-sim dependencies. "
"This usually means a local torch/torchvision/torchmetrics/nequip "
"version mismatch in the active environment."
) from exc
wall_start = time.perf_counter()
structures = load_public_structures(
source=args.source,
n_structures=args.n_structures,
seed=args.seed,
)
json_structures = [json.dumps(structure) for structure in structures]
batch = ferrox.io.structures_to_torch_sim_state(json_structures)
torch_dtype = torch.float64 if args.dtype == "float64" else torch.float32
sim_state = ts.SimState(
positions=torch.tensor(
batch["positions"], dtype=torch_dtype, device=args.device
),
masses=torch.tensor(batch["masses"], dtype=torch_dtype, device=args.device),
cell=torch.tensor(batch["cell"], dtype=torch_dtype, device=args.device),
pbc=True,
atomic_numbers=torch.tensor(
batch["atomic_numbers"], dtype=torch.int, device=args.device
),
system_idx=torch.tensor(
batch["system_idx"], dtype=torch.long, device=args.device
),
)
model_load_start = time.perf_counter()
compiled_path = compile_nequip_model(model_id=NEQUIP_MODEL_ID, device=args.device)
model = NequIPFrameworkModel.from_compiled_model(
compile_path=str(compiled_path),
device=args.device,
chemical_species_to_atom_type_map=True,
neighbor_list_backend=args.nl_backend,
)
model_load_s = time.perf_counter() - model_load_start
opt_start = time.perf_counter()
convergence_fn = ts.runners.generate_force_convergence_fn(force_tol=args.f_max)
autobatcher = InFlightAutoBatcher(
model=model,
memory_scales_with="n_atoms_x_density",
max_memory_scaler=args.max_memory_scaler,
)
final_state = ts.optimize(
system=sim_state,
model=model,
optimizer=ts.Optimizer.lbfgs,
max_steps=args.max_steps,
convergence_fn=convergence_fn,
steps_between_swaps=5,
autobatcher=autobatcher,
init_kwargs={"cell_filter": ts.CellFilter.frechet},
)
opt_s = time.perf_counter() - opt_start
final_states = (
final_state.split() if isinstance(final_state, ts.SimState) else final_state
)
converged_count = 0
for single_state in final_states:
forces = model(single_state)["forces"]
f_max_value = float(torch.linalg.norm(forces, dim=1).max().item())
if f_max_value <= args.f_max:
converged_count += 1
measured_count = len(final_states)
total_s = time.perf_counter() - wall_start
throughput_struct_per_min = (
(measured_count / total_s) * 60.0 if total_s > 0 else 0.0
)
return {
"source": args.source,
"nl_backend": args.nl_backend,
"n_structures": measured_count,
"seed": args.seed,
"device": args.device,
"dtype": args.dtype,
"f_max": args.f_max,
"max_steps": args.max_steps,
"model_load_s": round(model_load_s, 3),
"opt_s": round(opt_s, 3),
"total_s": round(total_s, 3),
"converged": converged_count,
"throughput_struct_per_min": round(throughput_struct_per_min, 2),
}
if __name__ == "__main__":
print(json.dumps(run_benchmark(parse_args()), indent=2)) |
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Hi @janosh — I've been investigating this and have some findings to share, but first a quick question: what version of NequIP were you running for this benchmark? With Want to make sure we're looking at the same code before posting our full analysis. |
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@Jussmith01 thanks for taking a look! here's some more info about my local env:
i added debug instrumentation into i also reran the script i posted above since it relaxes different structures than the table i posted initially. every NL now a bit faster because the structures are smaller:
should i be adding debug logs at a different level? not seeing any |
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Thanks @janosh for the detailed follow-up. Based on the information you've shared, we believe the ALCHEMI numbers in your benchmark may not be using ALCHEMI's batched GPU neighbor list correctly — though we can't be 100% certain without seeing your exact patch. Here's our reasoning. What we think happenedYou mentioned manually adding an 1. Per-system loop. # nequip/data/_nl.py, compute_neighborlist_()
for idx in range(AtomicDataDict.num_frames(data)):
data_per_frame = AtomicDataDict.frame_from_batched(data, idx)
...
edge_index, edge_cell_shift = _nl_fn(
pos=data_per_frame[AtomicDataDict.POSITIONS_KEY],
...
)If ALCHEMI is called inside 2. CPU conversion before dispatch. Your debug logs are consistent with per-system dispatch: 370 calls for 10 structures = ~37 NL calls per structure, which is what you'd expect from the per-frame loop running once per optimization step. That said, if your patch was structured differently (e.g., short-circuiting before the numpy conversion, or patching at the Temporary fix to use ALCHEMI correctly with NequIPThe fix is to replace import torch
from nequip.data import AtomicDataDict
from nequip.data.transforms.neighborlist import (
NeighborListTransform,
SortedNeighborListTransform,
)
from torch_sim.neighbors import alchemiops_nl_cell_list
class AlchemiNLTransform(torch.nn.Module):
"""Drop-in replacement for NeighborListTransform that calls
ALCHEMI's batched GPU kernel on the full batch in one shot."""
def __init__(self, r_max: float):
super().__init__()
self.r_max = r_max
def forward(self, data: AtomicDataDict.Type) -> AtomicDataDict.Type:
positions = data[AtomicDataDict.POSITIONS_KEY]
cell = data[AtomicDataDict.CELL_KEY]
pbc = data[AtomicDataDict.PBC_KEY]
system_idx = data[AtomicDataDict.BATCH_KEY]
cutoff = torch.tensor(
self.r_max, dtype=positions.dtype, device=positions.device
)
mapping, _sys_map, shifts_idx = alchemiops_nl_cell_list(
positions=positions,
cell=cell,
pbc=pbc,
cutoff=cutoff,
system_idx=system_idx,
)
data[AtomicDataDict.EDGE_INDEX_KEY] = mapping
data[AtomicDataDict.EDGE_CELL_SHIFT_KEY] = shifts_idx
return data
def patch_nequip_with_alchemi(model):
"""Swap NeighborListTransform for AlchemiNLTransform in-place."""
for i, transform in enumerate(model.transforms):
if isinstance(transform, (NeighborListTransform, SortedNeighborListTransform)):
model.transforms[i] = AlchemiNLTransform(
r_max=transform.r_max
).to(model._device)
return
raise RuntimeError("NeighborListTransform not found in model.transforms")Usage: model = NequIPFrameworkModel.from_compiled_model(
"path/to/model.nequip",
device="cuda",
neighbor_list_backend="matscipy", # initial backend doesn't matter
)
patch_nequip_with_alchemi(model)
# NL now runs as a single batched GPU kernel on the full batchWhat we see with correct batchingIn our testing with NequIP-OAM-L on an RTX 6000 Ada (full inference calls: NL build + energy + autograd forces), we see up to ~1.7x e2e speedup on the full inference call when using ALCHEMI's batched GPU NL versus CPU alternatives on large batches of small structures where the GPU is fully saturated. If our diagnosis is correct, the reason your benchmark didn't see this is that the |
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thanks so much, excellent troubleshooting! i tried the
at @Jussmith01 how preliminary is your proposed |
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posting this here for later reference and as a prompt in case others have related/contradictory results worth sharing: NL benchmark comparing
matscipy,vesin,ase,alchemion 1, 10, 100, 1000 structure relaxations using Nequip-OAM-L + LBFGS running on single H200 withInflightAutoBatcher,f_max=5e-3,max_steps=1000main surprise was that
nvalchemi-toolkit-ops==0.2.0didn't provide a speedup even though it's the (only?) GPU-compatible batched neighbor list implementation.vesinbeats it at every structure count andmatscipynot far behind. maybe i didn't usenvalchemi-toolkit-ops==0.2.0correctly but i thought there's no setup.aseis the main outlier, lot slower than the other 3Beta Was this translation helpful? Give feedback.
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