Backport PR #3031 on branch 1.10.x (Extend benchmarks from basic tutorial) #3056
scverse-benchmark / benchmark
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May 14, 2024 in 28m 38s
Benchmark
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Details
All benchmarks:
| Change | Before [19a0bb8] | After [0e14441] | Ratio | Benchmark (Parameter) |
|---|---|---|---|---|
| 330M | 329M | 1.00 | preprocessing_counts.peakmem_calculate_qc_metrics('pbmc3k') | |
| 260M | 252M | 0.97 | preprocessing_counts.peakmem_calculate_qc_metrics('pbmc68k_reduced') | |
| 347M | 339M | 0.98 | preprocessing_counts.peakmem_filter_cells('pbmc3k') | |
| 257M | 252M | 0.98 | preprocessing_counts.peakmem_filter_cells('pbmc68k_reduced') | |
| 353M | 338M | 0.96 | preprocessing_counts.peakmem_filter_genes('pbmc3k') | |
| 259M | 260M | 1.00 | preprocessing_counts.peakmem_filter_genes('pbmc68k_reduced') | |
| 328M | 328M | 1.00 | preprocessing_counts.peakmem_log1p('pbmc3k') | |
| 255M | 252M | 0.99 | preprocessing_counts.peakmem_log1p('pbmc68k_reduced') | |
| 360M | 351M | 0.98 | preprocessing_counts.peakmem_normalize_total('pbmc3k') | |
| 246M | 246M | 1.00 | preprocessing_counts.peakmem_normalize_total('pbmc68k_reduced') | |
| - | 1.32G | 1.13G | 0.85 | preprocessing_counts.peakmem_scrublet('pbmc3k') |
| - | 473M | 406M | 0.86 | preprocessing_counts.peakmem_scrublet('pbmc68k_reduced') |
| 70.1±4ms | 62.5±0.4ms | ~0.89 | preprocessing_counts.time_calculate_qc_metrics('pbmc3k') | |
| 7.52±0.4ms | 7.05±0.02ms | 0.94 | preprocessing_counts.time_calculate_qc_metrics('pbmc68k_reduced') | |
| 20.0±3ms | 20.1±4ms | 1.01 | preprocessing_counts.time_filter_cells('pbmc3k') | |
| 8.51±0.7ms | 8.59±0.6ms | 1.01 | preprocessing_counts.time_filter_cells('pbmc68k_reduced') | |
| 33.1±1ms | 38.4±3ms | ~1.16 | preprocessing_counts.time_filter_genes('pbmc3k') | |
| 8.86±0.7ms | 8.07±0.6ms | 0.91 | preprocessing_counts.time_filter_genes('pbmc68k_reduced') | |
| 8.12±0.2ms | 7.19±0.5ms | ~0.89 | preprocessing_counts.time_log1p('pbmc3k') | |
| 317±3μs | 343±6μs | 1.08 | preprocessing_counts.time_log1p('pbmc68k_reduced') | |
| 12.3±0.2ms | 12.1±0.1ms | 0.98 | preprocessing_counts.time_normalize_total('pbmc3k') | |
| 355±6μs | 373±20μs | 1.05 | preprocessing_counts.time_normalize_total('pbmc68k_reduced') | |
| - | 11.7±0.07s | 3.28±0.2s | 0.28 | preprocessing_counts.time_scrublet('pbmc3k') |
| - | 2.48±0s | 407±100ms | 0.16 | preprocessing_counts.time_scrublet('pbmc68k_reduced') |
| 732M | 733M | 1.00 | preprocessing_log.FastSuite.peakmem_mean_var('bmmc') | |
| 2.18G | 2.17G | 1.00 | preprocessing_log.FastSuite.peakmem_mean_var('lung93k') | |
| 401M | 400M | 1.00 | preprocessing_log.FastSuite.peakmem_mean_var('pbmc3k') | |
| 260M | 261M | 1.00 | preprocessing_log.FastSuite.peakmem_mean_var('pbmc68k_reduced') | |
| 9.85±1ms | 10.6±1ms | 1.07 | preprocessing_log.FastSuite.time_mean_var('bmmc') | |
| 34.7±0.7ms | 33.1±1ms | 0.95 | preprocessing_log.FastSuite.time_mean_var('lung93k') | |
| 10.4±0.4ms | 9.28±1ms | ~0.89 | preprocessing_log.FastSuite.time_mean_var('pbmc3k') | |
| 1.23±0.03ms | 1.35±0.02ms | 1.10 | preprocessing_log.FastSuite.time_mean_var('pbmc68k_reduced') | |
| 424M | 417M | 0.98 | preprocessing_log.peakmem_highly_variable_genes('pbmc3k') | |
| 250M | 259M | 1.03 | preprocessing_log.peakmem_highly_variable_genes('pbmc68k_reduced') | |
| - | 639M | 527M | 0.83 | preprocessing_log.peakmem_pca('pbmc3k') |
| 310M | 324M | 1.05 | preprocessing_log.peakmem_pca('pbmc68k_reduced') | |
| n/a | n/a | n/a | preprocessing_log.peakmem_regress_out('pbmc3k') | |
| 303M | 303M | 1.00 | preprocessing_log.peakmem_regress_out('pbmc68k_reduced') | |
| 1.02G | 1.04G | 1.01 | preprocessing_log.peakmem_scale('pbmc3k') | |
| 252M | 246M | 0.98 | preprocessing_log.peakmem_scale('pbmc68k_reduced') | |
| 38.5±5ms | 33.0±0.8ms | ~0.86 | preprocessing_log.time_highly_variable_genes('pbmc3k') | |
| 10.5±0.9ms | 10.1±0.08ms | 0.96 | preprocessing_log.time_highly_variable_genes('pbmc68k_reduced') | |
| 2.68±0.01s | 2.67±0.01s | 1.00 | preprocessing_log.time_pca('pbmc3k') | |
| 38.8±3ms | 38.4±3ms | 0.99 | preprocessing_log.time_pca('pbmc68k_reduced') | |
| n/a | n/a | n/a | preprocessing_log.time_regress_out('pbmc3k') | |
| 1.60±0.01s | 1.61±0.01s | 1.01 | preprocessing_log.time_regress_out('pbmc68k_reduced') | |
| 844±10ms | 835±30ms | 0.99 | preprocessing_log.time_scale('pbmc3k') | |
| 3.93±0.1ms | 3.94±0.09ms | 1.00 | preprocessing_log.time_scale('pbmc68k_reduced') | |
| 253M | 256M | 1.01 | tools.peakmem_diffmap | |
| 261M | 253M | 0.97 | tools.peakmem_leiden | |
| 345M | 330M | 0.96 | tools.peakmem_umap | |
| 16.2±0.4ms | 16.9±0.6ms | 1.04 | tools.time_diffmap | |
| 15.5±0.09ms | 15.4±0.08ms | 0.99 | tools.time_leiden | |
| 1.60±0s | 1.60±0s | 1.00 | tools.time_umap |
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