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- nvidia-cuda-crt==13.3.73.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'crt') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'crt') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'crt') - - nvidia-cublas==13.6.0.2.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cublas') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cublas') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cublas') - - nvidia-cuda-nvrtc==13.3.33.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cublas') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cublas') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cublas') - - nvidia-cuda-runtime==13.3.29.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cudart') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cudart') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cudart') - - nvidia-cudla==13.3.29.* ; platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cudla' - - nvidia-cufft==12.3.0.29.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cufft') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cufft') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cufft') - - nvidia-nvjitlink>=13.3.33,<14 ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cufft') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cufft') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cufft') - - nvidia-cufile==1.18.1.6.* ; (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cufile') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cufile') - - nvidia-cuda-culibos==13.3.33.* ; (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'culibos') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'culibos') - 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nvidia-cublas==13.6.0.2.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cusolver') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cusolver') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cusolver') + - nvidia-cusolver==12.2.6.9.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cusolver') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cusolver') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cusolver') + - nvidia-cusparse==12.8.2.51.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cusolver') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cusolver') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cusolver') + - nvidia-nvjitlink>=13.3.33,<14 ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cusolver') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cusolver') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cusolver') + - nvidia-cusparse==12.8.2.51.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cusparse') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cusparse') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cusparse') + - nvidia-nvjitlink>=13.3.33,<14 ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cusparse') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cusparse') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cusparse') + - nvidia-cuda-cuxxfilt==13.3.29.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'cuxxfilt') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cuxxfilt') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cuxxfilt') + - nvidia-npp==13.1.2.81.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'npp') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'npp') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'npp') + - nvidia-cuda-crt==13.3.73.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'nvcc') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'nvcc') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'nvcc') + - nvidia-cuda-nvcc==13.3.73.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'nvcc') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'nvcc') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'nvcc') + - nvidia-cuda-runtime==13.3.29.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'nvcc') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'nvcc') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'nvcc') + - nvidia-nvvm==13.3.73.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'nvcc') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'nvcc') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'nvcc') + - 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-Steps measured: - 1. load_zarr lazy zarr -> AnnData (X = dask array of sparse blocks) - 2. h2d_transfer anndata_to_GPU (block structure preserved; one block/GPU) - 3. preprocessing calculate_qc_metrics + normalize_total + log1p - 4. hvg highly_variable_genes + subset + rechunk/persist - 5. scaling (optional float64 cast) + scale - 6. pca pca + materialize X_pca to host - 7. harmony harmony_integrate -> X_pca_harmony (only if --batch-key set) - 8. neighbors neighbors - 9. umap umap - 10. leiden leiden - 11. write_results (default on) persist the UMAP embedding (obsm/X_umap) + leiden - labels (obs/leiden), anndata-readable, no X rematerialization. Full - run: appended onto the master root. Subset run: a self-contained no-X - store under data_path/subsets/ (--subset-dir-name). Skip with - --no-write-results. - -Everything that was hardcoded is now a knob: GPUs, zarr read concurrency/threads, -dask-cuda threads/protocol/RMM, chunk size, data path, and the pipeline params. -Defaults live in the `Config` dataclass; every field has a matching `--flag`, so -you can script a sweep of near-identical runs without editing source: - - # 4-GPU baseline, capacity preset (tcp + managed memory) - pixi run python rapids_benchmark.py \ - --data-path /home/workspace/temp/2M_50M.zarr --gpus 0,1,2,3 \ - --label 2M_4gpu - - # same store, single GPU, smaller chunk, more zarr read threads per worker - pixi run python rapids_benchmark.py \ - --data-path /home/workspace/temp/2M_50M.zarr --gpus 0 \ - --chunk-rows 12000 --zarr-max-workers 8 --label 2M_1gpu - - # speed preset (ucx + rmm pool) with a hard protocol override - pixi run python rapids_benchmark.py --gpus 0,1,2,3 --preset speed \ - --protocol tcp --rmm-pool-size 0.7 - - # subset: run the whole pipeline on just one cell type (store sorted by that column, - # so the match is a contiguous X[start:end] slice). Results land in a no-X store under - # data_path/subsets/ (name defaults to a slug of the column/value; override below). - pixi run python rapids_benchmark.py --gpus 0 \ - --data-path /path/to/sorted.zarr \ - --subset-column cell_type --subset-value "T cell" --subset-dir-name tcell - -Key correctness notes (see CLAUDE.md): - * ZARR CONFIG REACHES THE WORKERS. `zarr.config` is a *runtime* (donfig) setting, - not an env var, so setting it in the client process does NOT propagate to the - dask-cuda worker processes — and the lazy chunk reads happen ON the workers. - We apply it on every worker via `client.run(_set_zarr_config, ...)` (and on the - client too). Env-var thread pins (OMP/BLAS below) DO inherit, because workers - are spawned as child processes. - * THREADS MULTIPLY. host decode budget ≈ n_gpus × threads_per_worker × - zarr.threading.max_workers. The out-of-core doc recommends threads_per_worker=1 - for GPU work (more threads spike VRAM); we log the effective product. - * GPU SELECTION IS SINGLE-SOURCED. `--gpus` is a list of PHYSICAL device ids. - NVML enumerates physical devices (ignores CUDA_VISIBLE_DEVICES), so it uses the - physical ids directly; the cluster and client-RMM use the same list. Keeping the - client unrestricted (it sees all GPUs) is what keeps the three consistent. - -Environment: GPU/CUDA-only (rapids-singlecell, dask-cuda, cupy, rmm). Not runnable -on a CPU box; run it in the GPU node's pixi env. `--help` works anywhere (heavy -deps are imported lazily inside functions). -""" +#GPU configuration, will not run on CPU box. + from __future__ import annotations import argparse diff --git a/tools/rapids-benchmark/sweep_single_gpu.sh b/tools/rapids-benchmark/sweep_single_gpu.sh index 94460e4..6a2a3e5 100644 --- a/tools/rapids-benchmark/sweep_single_gpu.sh +++ b/tools/rapids-benchmark/sweep_single_gpu.sh @@ -10,14 +10,13 @@ OUTDIR="${OUTDIR:-$HERE/results}" DATASETS=( #"/mnt/5M_sparse_sorted_9.zarr" "/mnt/subset3M_megazarr_v1.0.zarr", - "/mnt" ) RMM=(managed) #pool) -CHUNK_ROWS=(48000 24000) +CHUNK_ROWS=(24000 48000 6000) THREAD_SPLITS=(12:12) #12:12) -ZARR_CONCURRENCY=12 +ZARR_CONCURRENCY=(12) #------------RUN LOOP @@ -25,10 +24,11 @@ for data in "${DATASETS[@]}"; do dtag="$(basename "$data" .zarr)" for rmm in "${RMM[@]}"; do for ck in "${CHUNK_ROWS[@]}"; do + for zarr_c in "${ZARR_CONCURRENCY[@]}"; do for split in "${THREAD_SPLITS[@]}"; do tpw="${split%%:*}"; zmw="${split##*:}" # threads_per_worker : zarr_max_workers label="${dtag}_g0_${rmm}_ck${ck}" - label="${label}_t${tpw}x${zmw}" + label="${label}_t${tpw}x${zmw}c${zarr_c}" args=(--data-path "$data" --gpus 0 --protocol tcp --rmm-mode "$rmm" --chunk-rows "$ck" --neighbors-algorithm ivfflat --batch-key "" --threads-per-worker "$tpw" --zarr-max-workers "$zmw" @@ -38,6 +38,7 @@ for data in "${DATASETS[@]}"; do pixi run python "$BENCH" "${args[@]}" \ || echo "# -> FAILED ($label), continuing" done + done done done done From 9b5e288c897b88f3bb2f56bde017d0665ce8c58e Mon Sep 17 00:00:00 2001 From: Alex Holly Date: Wed, 26 Aug 2026 23:54:18 +0000 Subject: [PATCH 2/3] chunk size run results --- .../rapids-benchmark/results/Run_results.txt | 304 ++++++++++++++++++ 1 file changed, 304 insertions(+) create mode 100644 tools/rapids-benchmark/results/Run_results.txt diff --git a/tools/rapids-benchmark/results/Run_results.txt b/tools/rapids-benchmark/results/Run_results.txt new file mode 100644 index 0000000..f1b36b1 --- /dev/null +++ b/tools/rapids-benchmark/results/Run_results.txt @@ -0,0 +1,304 @@ +Rapids-Singlecell Benchmark — 2026-08-20T21:35:15 — label: - +store: /mnt/5M_sparse_sorted_9.zarr — GPUs: [0] +changed cfg: (defaults) +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 15.55s 5167 MB 1721 MB + h2d_transfer 0.40s 4154 MB 1723 MB + preprocessing 136.39s 15406 MB 5183 MB + hvg 162.06s 16328 MB 9715 MB + scaling 0.52s 9467 MB 4483 MB + pca 7.94s 10987 MB 6305 MB + neighbors 47.13s 11931 MB 15819 MB + umap 37.14s 14648 MB 9679 MB + leiden 104.53s 14279 MB 9953 MB + write_results 0.19s 12344 MB 5181 MB + ---------------- -------- ------------ ------------ + TOTAL 511.85s 16328 MB 15819 MB + +Rapids-Singlecell Benchmark — 2026-08-20T21:46:27 — label: - +store: /mnt/2M_sparse_sorted_9M.zarr — GPUs: [0] +changed cfg: (defaults) +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 1.94s 1910 MB 1721 MB + h2d_transfer 0.06s 1926 MB 1723 MB + preprocessing 37.53s 9820 MB 6893 MB + hvg 41.04s 10289 MB 8963 MB + scaling 0.12s 6324 MB 3261 MB + pca 1.52s 7005 MB 3893 MB + neighbors 9.35s 7496 MB 7475 MB + umap 10.72s 8259 MB 5061 MB + leiden 24.07s 8559 MB 5441 MB + write_results 0.15s 8026 MB 3661 MB + ---------------- -------- ------------ ------------ + TOTAL 126.49s 10289 MB 8963 MB + +Rapids-Singlecell Benchmark — 2026-08-20T23:26:40 — label: - +store: /mnt/13M_50M_pbmc_soundlife.zarr — GPUs: [0] +changed cfg: (defaults) +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 121.13s 34298 MB 1721 MB + h2d_transfer 0.06s 20980 MB 1723 MB + preprocessing 332.87s 28335 MB 5677 MB + hvg 378.88s 31932 MB 25029 MB + scaling 0.40s 27403 MB 9653 MB + pca 6.71s 30794 MB 14373 MB + neighbors 114.14s 33338 MB 37675 MB + umap 203.90s 39102 MB 22933 MB + leiden 265.34s 39228 MB 23223 MB + write_results 0.38s 33921 MB 11347 MB + ---------------- -------- ------------ ------------ + TOTAL 1423.81s 39228 MB 37675 MB + +Rapids-Singlecell Benchmark — 2026-08-25T19:54:40 — label: - +store: /mnt/13M_50M_pbmc_soundlife.zarr — GPUs: [0] +changed cfg: (defaults) +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 125.43s 34380 MB 1721 MB + h2d_transfer 0.10s 21271 MB 1723 MB + preprocessing 333.99s 28026 MB 4819 MB + hvg 379.95s 32220 MB 24915 MB + scaling 0.36s 27953 MB 9653 MB + pca 6.56s 31363 MB 14373 MB + neighbors 115.19s 33838 MB 37755 MB + umap 209.70s 39600 MB 22757 MB + leiden 285.91s 39772 MB 23145 MB + write_results 0.41s 34441 MB 11261 MB + ---------------- -------- ------------ ------------ + TOTAL 1457.60s 39772 MB 37755 MB + +Rapids-Singlecell Benchmark — 2026-08-25T23:53:47 — label: subset3M_megazarr_v1.0_g0_managed_ck24000_t12x12c12 +store: /mnt/subset3M_megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 8.99s 3808 MB 1721 MB + h2d_transfer 0.06s 3282 MB 1723 MB + preprocessing 47.07s 10307 MB 7585 MB + hvg 56.02s 10668 MB 8573 MB + scaling 0.15s 6894 MB 3423 MB + pca 1.79s 7754 MB 4479 MB + neighbors 15.04s 8374 MB 9597 MB + umap 22.57s 9762 MB 6275 MB + leiden 59.88s 9829 MB 6405 MB + write_results 0.18s 8891 MB 3827 MB + ---------------- -------- ------------ ------------ + TOTAL 211.75s 10668 MB 9597 MB + +Rapids-Singlecell Benchmark — 2026-08-25T23:57:32 — label: subset3M_megazarr_v1.0_g0_managed_ck48000_t12x12c12 +store: /mnt/subset3M_megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=48000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 8.96s 3810 MB 1721 MB + h2d_transfer 0.06s 3253 MB 1723 MB + preprocessing 45.61s 16866 MB 15087 MB + hvg 54.88s 19465 MB 15003 MB + scaling 0.15s 10810 MB 3433 MB + pca 1.78s 11662 MB 4445 MB + neighbors 14.92s 12289 MB 9605 MB + umap 22.52s 13677 MB 6155 MB + leiden 57.97s 13726 MB 6411 MB + write_results 0.18s 12801 MB 3835 MB + ---------------- -------- ------------ ------------ + TOTAL 207.04s 19465 MB 15087 MB + +Rapids-Singlecell Benchmark — 2026-08-26T00:01:12 — label: subset3M_megazarr_v1.0_g0_managed_ck6000_t12x12c12 +store: /mnt/subset3M_megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=6000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 8.81s 3813 MB 1721 MB + h2d_transfer 0.06s 3277 MB 1723 MB + preprocessing 59.92s 5520 MB 2757 MB + hvg 68.28s 6000 MB 7055 MB + scaling 0.14s 4986 MB 3587 MB + pca 1.81s 5846 MB 4599 MB + neighbors 14.91s 6465 MB 9759 MB + umap 22.19s 7853 MB 6437 MB + leiden 56.38s 7915 MB 6591 MB + write_results 0.18s 6977 MB 4009 MB + ---------------- -------- ------------ ------------ + TOTAL 232.67s 7915 MB 9759 MB + +Rapids-Singlecell Benchmark — 2026-08-26T00:05:17 — label: subset3M_megazarr_v1.0_g0_managed_ck12000_t12x12c12 +store: /mnt/subset3M_megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=12000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 9.06s 3830 MB 1721 MB + h2d_transfer 0.06s 3259 MB 1723 MB + preprocessing 50.38s 7360 MB 4515 MB + hvg 59.46s 8188 MB 6707 MB + scaling 0.14s 5779 MB 3433 MB + pca 1.77s 6642 MB 4441 MB + neighbors 14.95s 7258 MB 9573 MB + umap 22.13s 8646 MB 6367 MB + leiden 65.04s 8708 MB 6485 MB + write_results 0.18s 7770 MB 3897 MB + ---------------- -------- ------------ ------------ + TOTAL 223.18s 8708 MB 9573 MB + +Rapids-Singlecell Benchmark — 2026-08-26T02:18:42 — label: 13M_50M_pbmc_soundlife_g0_managed_ck24000_t12x12c12 +store: /mnt/13M_50M_pbmc_soundlife.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 120.66s 34274 MB 1721 MB + h2d_transfer 0.07s 21002 MB 1723 MB + preprocessing 331.82s 29512 MB 8707 MB + hvg 378.40s 32577 MB 24981 MB + scaling 0.38s 27780 MB 9647 MB + pca 6.82s 31204 MB 14367 MB + neighbors 112.98s 33664 MB 37683 MB + umap 206.21s 39427 MB 22945 MB + leiden 261.97s 39598 MB 23185 MB + write_results 0.39s 34272 MB 11303 MB + ---------------- -------- ------------ ------------ + TOTAL 1419.70s 39598 MB 37683 MB + +Rapids-Singlecell Benchmark — 2026-08-26T02:42:41 — label: 13M_50M_pbmc_soundlife_g0_managed_ck48000_t12x12c12 +store: /mnt/13M_50M_pbmc_soundlife.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=48000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 120.71s 34338 MB 1721 MB + h2d_transfer 0.07s 21038 MB 1723 MB + preprocessing 256.62s 34128 MB 7979 MB + hvg 310.32s 39555 MB 24961 MB + scaling 0.36s 30713 MB 9643 MB + pca 6.46s 34108 MB 14363 MB + neighbors 112.85s 36565 MB 37657 MB + umap 204.31s 42328 MB 22659 MB + leiden 272.45s 42506 MB 23183 MB + write_results 0.40s 37176 MB 11301 MB + ---------------- -------- ------------ ------------ + TOTAL 1284.53s 42506 MB 37657 MB + +Rapids-Singlecell Benchmark — 2026-08-26T03:04:25 — label: 13M_50M_pbmc_soundlife_g0_managed_ck6000_t12x12c12 +store: /mnt/13M_50M_pbmc_soundlife.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=6000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 120.31s 34319 MB 1721 MB + h2d_transfer 0.08s 21158 MB 1723 MB + preprocessing 817.00s 25359 MB 2541 MB + hvg 860.33s 29122 MB 27709 MB + scaling 0.35s 26418 MB 10217 MB + pca 6.56s 29761 MB 14977 MB + neighbors 113.12s 32226 MB 38303 MB + umap 204.76s 37989 MB 23183 MB + leiden 271.12s 38124 MB 23795 MB + write_results 0.40s 32832 MB 11913 MB + ---------------- -------- ------------ ------------ + TOTAL 2394.03s 38124 MB 38303 MB + +Rapids-Singlecell Benchmark — 2026-08-26T03:44:38 — label: 13M_50M_pbmc_soundlife_g0_managed_ck12000_t12x12c12 +store: /mnt/13M_50M_pbmc_soundlife.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=12000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 120.25s 34410 MB 1721 MB + h2d_transfer 0.07s 21249 MB 1723 MB + preprocessing 490.95s 26437 MB 3261 MB + hvg 534.79s 30346 MB 25069 MB + scaling 0.39s 26897 MB 9683 MB + pca 6.52s 30220 MB 14403 MB + neighbors 113.10s 32697 MB 37785 MB + umap 205.58s 38461 MB 22915 MB + leiden 269.45s 38589 MB 23199 MB + write_results 0.38s 33270 MB 11321 MB + ---------------- -------- ------------ ------------ + TOTAL 1741.49s 38589 MB 37785 MB + +Rapids-Singlecell Benchmark — 2026-08-26T04:13:59 — label: megazarr_v1.0_g0_managed_ck24000_t12x12c12 +store: /mnt/megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 97.51s 22231 MB 1721 MB + h2d_transfer 0.07s 14900 MB 1723 MB + preprocessing 457.59s 22862 MB 5545 MB + hvg 590.77s 26074 MB 47583 MB + scaling 0.77s 21641 MB 17427 MB + pca 38.83s 28700 MB 27651 MB + neighbors 434.43s 33974 MB 78791 MB + umap 366.68s 45819 MB 46151 MB + leiden 595.94s 46626 MB 46869 MB + write_results 0.55s 34684 MB 20823 MB + ---------------- -------- ------------ ------------ + TOTAL 2583.16s 46626 MB 78791 MB + +Rapids-Singlecell Benchmark — 2026-08-26T04:57:20 — label: megazarr_v1.0_g0_managed_ck48000_t12x12c12 +store: /mnt/megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=48000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 97.43s 23383 MB 1721 MB + h2d_transfer 0.13s 15065 MB 1723 MB + preprocessing 404.56s 28623 MB 12129 MB + hvg 546.86s 34956 MB 47555 MB + scaling 0.67s 26587 MB 17261 MB + pca 12.81s 33731 MB 27599 MB + neighbors 369.63s 38994 MB 78713 MB + umap 349.67s 50842 MB 46207 MB + leiden 626.41s 51651 MB 46783 MB + write_results 0.58s 39704 MB 20737 MB + ---------------- -------- ------------ ------------ + TOTAL 2408.76s 51651 MB 78713 MB + +Rapids-Singlecell Benchmark — 2026-08-26T05:37:48 — label: megazarr_v1.0_g0_managed_ck6000_t12x12c12 +store: /mnt/megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=6000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 97.58s 22169 MB 1721 MB + h2d_transfer 0.07s 15054 MB 1723 MB + preprocessing 710.22s 18766 MB 3081 MB + hvg 851.94s 21016 MB 49839 MB + scaling 0.69s 20052 MB 19201 MB + pca 12.85s 27064 MB 29557 MB + neighbors 372.24s 32373 MB 80549 MB + umap 350.39s 44220 MB 47787 MB + leiden 602.00s 44886 MB 48581 MB + write_results 0.57s 33091 MB 22533 MB + ---------------- -------- ------------ ------------ + TOTAL 2998.56s 44886 MB 80549 MB + +Rapids-Singlecell Benchmark — 2026-08-26T06:28:06 — label: megazarr_v1.0_g0_managed_ck12000_t12x12c12 +store: /mnt/megazarr_v1.0.zarr — GPUs: [0] +changed cfg: protocol=tcp, rmm_mode=managed, chunk_rows=12000 +================================================================================ + Step Wall Peak Host Peak GPU + ---- ---- --------- -------- + load_zarr 97.31s 22112 MB 1721 MB + h2d_transfer 0.07s 14609 MB 1723 MB + preprocessing 521.92s 19690 MB 4093 MB + hvg 666.45s 21952 MB 48575 MB + scaling 0.69s 20149 MB 17693 MB + pca 12.96s 27139 MB 28099 MB + neighbors 370.48s 32439 MB 79047 MB + umap 348.87s 44287 MB 46529 MB + leiden 575.77s 45102 MB 47187 MB + write_results 0.60s 33153 MB 21141 MB + ---------------- -------- ------------ ------------ + TOTAL 2595.13s 45102 MB 79047 MB + From c2a98488e7d21232482b5c1b4c194e331741fdb5 Mon Sep 17 00:00:00 2001 From: Alex Holly Date: Wed, 26 Aug 2026 17:11:03 -0700 Subject: [PATCH 3/3] adding dask-chunk-size results --- .../rapids_vs_scanpy/README.md | 24 +++++++++++++++++++ .../results/dask_chunk_results.txt | 0 2 files changed, 24 insertions(+) rename tools/rapids-benchmark/results/Run_results.txt => benchmarking_results/rapids_vs_scanpy/results/dask_chunk_results.txt (100%) diff --git a/benchmarking_results/rapids_vs_scanpy/README.md b/benchmarking_results/rapids_vs_scanpy/README.md index 8b0c39f..d0ae213 100644 --- a/benchmarking_results/rapids_vs_scanpy/README.md +++ b/benchmarking_results/rapids_vs_scanpy/README.md @@ -158,3 +158,27 @@ read-config sweep mostly moves preprocessing/HVG: `--zarr-max-workers 1` starves not fetch concurrency, are the lever. Cost of the extra GPUs is host RAM: ~50–60 GB peak (4 GPU, 16 workers) vs ~18–40 GB single-GPU, and ~48 GB VRAM spread over 4 devices vs ~15 GB on one. + +--- + +## Dask chunk size: `chunk_rows` sweep (single GPU) + +Raw runs in [`results/dask_chunk_results.txt`](results/dask_chunk_results.txt): three stores +(3M subset megazarr, 13M Soundlife, ~30M megazarr) each run at `chunk_rows` = 6k / 12k / +24k (default) / 48k — the rows per **dask block** streamed from the store. Store row chunks: +13M Soundlife every **50M nnz** (~28k rows); 3M subset and ~30M megazarr every **9M nnz**. + +Total wall by `chunk_rows`: + +| Dataset | 6k | 12k | 24k (default) | 48k | +|---|---:|---:|---:|---:| +| 3M subset megazarr | 233 s | 223 s | 212 s | 207 s | +| 13M Soundlife | 39.9 min | 29.0 min | 23.7 min | 21.4 min | +| ~30M megazarr | 50.0 min | 43.3 min | 43.1 min | 40.1 min | + +- **Chunk size only moves the streamed front half.** Preprocessing + HVG absorb the spread + (13M preprocessing: 817 s → 257 s); neighbors / UMAP / Leiden are flat at every size. +- **Bigger blocks trade memory for wall.** Peak host rises with chunk size (3M: 7.9 → + 19.5 GB), and at 3M the 48k blocks set the GPU peak (15.1 GB vs ~9.6 GB). +- **Small chunks are the real hazard.** 6k costs up to **1.9× total** (13M); the 24k default + is the sweet spot, 48k buys another ~7–10% for a few GB of host RAM. diff --git a/tools/rapids-benchmark/results/Run_results.txt b/benchmarking_results/rapids_vs_scanpy/results/dask_chunk_results.txt similarity index 100% rename from tools/rapids-benchmark/results/Run_results.txt rename to benchmarking_results/rapids_vs_scanpy/results/dask_chunk_results.txt