Same-Workload DHFR Stretch Status

Date: 2026-05-23

Engine pair: mlx_atomistic vs openmm-reference. Pair ids: dhfr-implicit, dhfr-explicit-pme.

These are the real-system DHFR stretch rows for the same-workload comparison plan. dhfr-implicit now runs as a one-step MLX/OpenMM Reference smoke comparison. dhfr-explicit-pme remains blocked on the MLX side, so it still has no ratio.

Row Status

Pair id	Intended system	Physics target	Metric	Status	Raw output
`dhfr-implicit`	DHFR implicit solvent, ~2.5k atoms	implicit GBSA/OBC target	`ns/day`	`comparable` one-step smoke row; ratio in summary	MLX: `results/same-workload-openmm-comparison/mlx-dhfr-implicit.json`; OpenMM Reference: `results/same-workload-openmm-comparison/openmm-dhfr-implicit.json`; summary: `results/same-workload-openmm-comparison/summary.json`
`dhfr-explicit-pme`	DHFR explicit PME, 23.6k atoms	explicit solvent PME target	`ns/day`	`blocked`; no ratio	MLX: `results/same-workload-openmm-comparison/mlx-dhfr-explicit-pme.json`; OpenMM Reference: `results/same-workload-openmm-comparison/openmm-dhfr-explicit-pme.json`

OpenMM Reference

The reference side is already measured in openmm-opencl-dhfr.md:

OpenMM system	Size	Result
DHFR Implicit GBSA	~2.5k atoms	1762.1 ns/day
DHFR Explicit PME	23.6k atoms	752.5 ns/day

The committed OpenMM OpenCL numbers are reference context, not the same thing as the one-step OpenMM Reference shape-check rows used by the same-workload comparison helper.

MLX Status

mlx_atomistic can resolve the local DHFR inputs. The two rows now differ:

dhfr-implicit: runnable. The prep path derives a DHFR GBSA/OBC artifact from OpenMM amber99sb.xml and amber99_obc.xml, including gbsa_radius, gbsa_scale, bonded terms, torsions, constraints, and nonbonded exceptions. The MLX runtime currently reports a one-step 0.004 ps smoke row.
dhfr-explicit-pme: blocked before PME runtime because the local Amber20/JAC artifact has net_charge=-11 and the current MLX PME artifact policy requires neutral systems.

The comparison helper computes a ratio only for dhfr-implicit. It keeps dhfr-explicit-pme blocked and does not compute a ratio for that row.

Reproducer Boundary

MLX row reproducers:

UV_CACHE_DIR=/tmp/mlx-atomistic-uv-cache uv run python -m mlx_atomistic.benchmarks.dhfr --case dhfr-implicit --steps 1 --json > results/same-workload-openmm-comparison/mlx-dhfr-implicit.json
UV_CACHE_DIR=/tmp/mlx-atomistic-uv-cache uv run python -m mlx_atomistic.benchmarks.dhfr --case dhfr-explicit-pme --steps 1 --json > results/same-workload-openmm-comparison/mlx-dhfr-explicit-pme.json

OpenMM same-workload shape-check reproducers:

UV_CACHE_DIR=/tmp/mlx-atomistic-uv-cache uv run python scripts/benchmark_openmm_dhfr.py --case dhfr-implicit --platform Reference --steps 1 --json > results/same-workload-openmm-comparison/openmm-dhfr-implicit.json
UV_CACHE_DIR=/tmp/mlx-atomistic-uv-cache uv run python scripts/benchmark_openmm_dhfr.py --case dhfr-explicit-pme --platform Reference --steps 1 --json > results/same-workload-openmm-comparison/openmm-dhfr-explicit-pme.json

OpenMM OpenCL context reproducer:

cd vendors/openmm/examples/benchmarks
UV_CACHE_DIR=/tmp/mlx-atomistic-uv-cache uv run --project ../../../.. \
  python benchmark.py \
    --platform OpenCL \
    --test pme \
    --seconds 30 \
    --precision single \
    --outfile ../../../../results/openmm-opencl-dhfr-m5max.json

The OpenMM Reference commands above are one-step same-workload shape checks. They are not the OpenCL performance numbers in the context table.