Use throughput data for Conformer RMSD benchmark#187
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Replace the per-mol, hardcoded-SMILES benchmark with a batch-mode bench that: * Loads a slice of SMILES from a file (via bench_utils.load_smiles). * Embeds one base conformer per mol in parallel and jitters via the shared bench_utils.embed_and_jitter (with add_hs so ETKDG sees a chemically reasonable graph). * Times a single GetConformerRMSMatrixBatch call vs a serial RDKit loop. * Sweeps confs_per_mol with a single embed run plus _slice_to_confs reuse, so every row sees the same molecule selection. * Validates GPU output against RDKit (per-pair, with a tolerance) before timing and aborts on mismatch. * Honors --rdkit_max_seconds for the RDKit comparison and --no-rdkit / --no-nvmolkit for mode selection.
Cosmetic only; matches the formatting style used in adjacent benches.
evasnow1992
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Jun 1, 2026
evasnow1992
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Jun 2, 2026
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Changes look good to me. Thanks!
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Before, it had been based on single smiles. Modified to be more like our other benchmarks, and added RDKit early exit. The early exit is a bit annoying right now because we can't use
time_it, added a tracking bug