scale function(_get_mean_var) updated for dense array, speedup upto ~4.65x #3099
scverse-benchmark / benchmark
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Jun 18, 2024 in 11m 52s
Benchmark
Benchmark run successful
Details
All benchmarks:
| Change | Before [ad657ed] | After [e7a4662] | Ratio | Benchmark (Parameter) |
|---|---|---|---|---|
| 325M | 332M | 1.02 | preprocessing_counts.peakmem_calculate_qc_metrics('pbmc3k') | |
| 252M | 263M | 1.04 | preprocessing_counts.peakmem_calculate_qc_metrics('pbmc68k_reduced') | |
| 339M | 338M | 0.99 | preprocessing_counts.peakmem_filter_cells('pbmc3k') | |
| 261M | 255M | 0.98 | preprocessing_counts.peakmem_filter_cells('pbmc68k_reduced') | |
| 338M | 337M | 1.00 | preprocessing_counts.peakmem_filter_genes('pbmc3k') | |
| 248M | 258M | 1.04 | preprocessing_counts.peakmem_filter_genes('pbmc68k_reduced') | |
| 338M | 330M | 0.98 | preprocessing_counts.peakmem_log1p('pbmc3k') | |
| 250M | 252M | 1.01 | preprocessing_counts.peakmem_log1p('pbmc68k_reduced') | |
| 355M | 351M | 0.99 | preprocessing_counts.peakmem_normalize_total('pbmc3k') | |
| 246M | 248M | 1.01 | preprocessing_counts.peakmem_normalize_total('pbmc68k_reduced') | |
| 1G | 996M | 0.99 | preprocessing_counts.peakmem_scrublet('pbmc3k') | |
| 360M | 361M | 1.00 | preprocessing_counts.peakmem_scrublet('pbmc68k_reduced') | |
| 70.6±5ms | 74.1±0.2ms | 1.05 | preprocessing_counts.time_calculate_qc_metrics('pbmc3k') | |
| 7.97±0.02ms | 7.52±0.4ms | 0.94 | preprocessing_counts.time_calculate_qc_metrics('pbmc68k_reduced') | |
| 17.5±0.7ms | 23.6±2ms | ~1.35 | preprocessing_counts.time_filter_cells('pbmc3k') | |
| 7.85±0.5ms | 7.74±0.5ms | 0.99 | preprocessing_counts.time_filter_cells('pbmc68k_reduced') | |
| 36.3±2ms | 37.0±3ms | 1.02 | preprocessing_counts.time_filter_genes('pbmc3k') | |
| 7.96±0.5ms | 8.68±0.6ms | 1.09 | preprocessing_counts.time_filter_genes('pbmc68k_reduced') | |
| 6.92±0.1ms | 6.87±0.06ms | 0.99 | preprocessing_counts.time_log1p('pbmc3k') | |
| 325±20μs | 303±5μs | 0.93 | preprocessing_counts.time_log1p('pbmc68k_reduced') | |
| 14.4±0.6ms | 15.6±3ms | 1.08 | preprocessing_counts.time_normalize_total('pbmc3k') | |
| 353±3μs | 363±4μs | 1.03 | preprocessing_counts.time_normalize_total('pbmc68k_reduced') | |
| 3.33±0.8s | 3.22±0.08s | 0.97 | preprocessing_counts.time_scrublet('pbmc3k') | |
| 390±100ms | 396±100ms | 1.02 | preprocessing_counts.time_scrublet('pbmc68k_reduced') | |
| 728M | 725M | 1.00 | preprocessing_log.FastSuite.peakmem_mean_var('bmmc') | |
| 2.16G | 2.16G | 1.00 | preprocessing_log.FastSuite.peakmem_mean_var('lung93k') | |
| 386M | 397M | 1.03 | preprocessing_log.FastSuite.peakmem_mean_var('pbmc3k') | |
| + | 259M | 310M | 1.20 | preprocessing_log.FastSuite.peakmem_mean_var('pbmc68k_reduced') |
| 9.96±2ms | 10.0±0.8ms | 1.01 | preprocessing_log.FastSuite.time_mean_var('bmmc') | |
| 33.5±0.3ms | 33.1±0.4ms | 0.99 | preprocessing_log.FastSuite.time_mean_var('lung93k') | |
| 8.25±0.3ms | 9.76±0.7ms | ~1.18 | preprocessing_log.FastSuite.time_mean_var('pbmc3k') | |
| + | 1.16±0.04ms | 1.97±0.5ms | 1.69 | preprocessing_log.FastSuite.time_mean_var('pbmc68k_reduced') |
| 426M | 423M | 0.99 | preprocessing_log.peakmem_highly_variable_genes('pbmc3k') | |
| + | 255M | 315M | 1.23 | preprocessing_log.peakmem_highly_variable_genes('pbmc68k_reduced') |
| 544M | 529M | 0.97 | preprocessing_log.peakmem_pca('pbmc3k') | |
| - | 373M | 322M | 0.86 | preprocessing_log.peakmem_pca('pbmc68k_reduced') |
| n/a | n/a | n/a | preprocessing_log.peakmem_regress_out('pbmc3k') | |
| 307M | 309M | 1.01 | preprocessing_log.peakmem_regress_out('pbmc68k_reduced') | |
| - | 1.03G | 779M | 0.76 | preprocessing_log.peakmem_scale('pbmc3k') |
| 291M | 320M | 1.10 | preprocessing_log.peakmem_scale('pbmc68k_reduced') | |
| 33.4±0.5ms | 32.7±0.2ms | 0.98 | preprocessing_log.time_highly_variable_genes('pbmc3k') | |
| 10.6±1ms | 10.5±0.4ms | 0.99 | preprocessing_log.time_highly_variable_genes('pbmc68k_reduced') | |
| 2.69±0.01s | 2.66±0.01s | 0.99 | preprocessing_log.time_pca('pbmc3k') | |
| 34.7±0.9ms | 37.1±4ms | 1.07 | 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 | 1.00 | preprocessing_log.time_regress_out('pbmc68k_reduced') | |
| - | 729±5ms | 517±5ms | 0.71 | preprocessing_log.time_scale('pbmc3k') |
| 5.18±0.04ms | 5.50±0.4ms | 1.06 | preprocessing_log.time_scale('pbmc68k_reduced') | |
| 256M | 252M | 0.98 | tools.peakmem_diffmap | |
| 262M | 257M | 0.98 | tools.peakmem_leiden | |
| 339M | 329M | 0.97 | tools.peakmem_umap | |
| 17.2±0.5ms | 17.3±0.4ms | 1.01 | tools.time_diffmap | |
| 15.4±0.1ms | 15.4±0.1ms | 1.00 | tools.time_leiden | |
| 1.60±0s | 1.60±0s | 1.00 | tools.time_umap |
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