Hvg seurat v3 numba kernel #3017
+36
−8
Merged
scverse-benchmark / benchmark
succeeded
May 23, 2024 in 18m 1s
Benchmark
Benchmark run successful
Details
All benchmarks:
| Change | Before [3ba3f46] | After [277c1bf] | Ratio | Benchmark (Parameter) |
|---|---|---|---|---|
| 334M | 336M | 1.01 | preprocessing_counts.peakmem_calculate_qc_metrics('pbmc3k') | |
| 250M | 250M | 1.00 | preprocessing_counts.peakmem_calculate_qc_metrics('pbmc68k_reduced') | |
| 333M | 341M | 1.02 | preprocessing_counts.peakmem_filter_cells('pbmc3k') | |
| 256M | 259M | 1.01 | preprocessing_counts.peakmem_filter_cells('pbmc68k_reduced') | |
| 346M | 342M | 0.99 | preprocessing_counts.peakmem_filter_genes('pbmc3k') | |
| 260M | 246M | 0.95 | preprocessing_counts.peakmem_filter_genes('pbmc68k_reduced') | |
| 328M | 330M | 1.01 | preprocessing_counts.peakmem_log1p('pbmc3k') | |
| 246M | 250M | 1.02 | preprocessing_counts.peakmem_log1p('pbmc68k_reduced') | |
| 353M | 359M | 1.02 | preprocessing_counts.peakmem_normalize_total('pbmc3k') | |
| 254M | 250M | 0.98 | preprocessing_counts.peakmem_normalize_total('pbmc68k_reduced') | |
| 1.08G | 1.09G | 1.01 | preprocessing_counts.peakmem_scrublet('pbmc3k') | |
| 371M | 380M | 1.02 | preprocessing_counts.peakmem_scrublet('pbmc68k_reduced') | |
| 69.3±5ms | 69.4±4ms | 1.00 | preprocessing_counts.time_calculate_qc_metrics('pbmc3k') | |
| 7.53±0.5ms | 7.56±0.4ms | 1.00 | preprocessing_counts.time_calculate_qc_metrics('pbmc68k_reduced') | |
| 19.7±2ms | 17.1±1ms | ~0.87 | preprocessing_counts.time_filter_cells('pbmc3k') | |
| 7.80±0.6ms | 7.84±0.6ms | 1.01 | preprocessing_counts.time_filter_cells('pbmc68k_reduced') | |
| 37.2±2ms | 32.4±1ms | ~0.87 | preprocessing_counts.time_filter_genes('pbmc3k') | |
| 8.48±0.5ms | 7.88±0.5ms | 0.93 | preprocessing_counts.time_filter_genes('pbmc68k_reduced') | |
| - | 9.09±1ms | 6.90±0.06ms | 0.76 | preprocessing_counts.time_log1p('pbmc3k') |
| 304±2μs | 321±20μs | 1.05 | preprocessing_counts.time_log1p('pbmc68k_reduced') | |
| 12.1±0.2ms | 12.0±0.3ms | 0.99 | preprocessing_counts.time_normalize_total('pbmc3k') | |
| 361±6μs | 356±2μs | 0.99 | preprocessing_counts.time_normalize_total('pbmc68k_reduced') | |
| 3.21±0.07s | 3.17±0.1s | 0.99 | preprocessing_counts.time_scrublet('pbmc3k') | |
| 387±100ms | 385±100ms | 0.99 | preprocessing_counts.time_scrublet('pbmc68k_reduced') | |
| 732M | 729M | 1.00 | preprocessing_log.FastSuite.peakmem_mean_var('bmmc') | |
| 2.17G | 2.15G | 0.99 | preprocessing_log.FastSuite.peakmem_mean_var('lung93k') | |
| 400M | 393M | 0.98 | preprocessing_log.FastSuite.peakmem_mean_var('pbmc3k') | |
| 256M | 250M | 0.98 | preprocessing_log.FastSuite.peakmem_mean_var('pbmc68k_reduced') | |
| 8.65±2ms | 8.16±0.6ms | 0.94 | preprocessing_log.FastSuite.time_mean_var('bmmc') | |
| 32.9±0.4ms | 32.3±1ms | 0.98 | preprocessing_log.FastSuite.time_mean_var('lung93k') | |
| 8.71±0.8ms | 10.1±0.4ms | ~1.16 | preprocessing_log.FastSuite.time_mean_var('pbmc3k') | |
| 1.16±0.04ms | 1.07±0.03ms | 0.92 | preprocessing_log.FastSuite.time_mean_var('pbmc68k_reduced') | |
| 417M | 423M | 1.01 | preprocessing_log.peakmem_highly_variable_genes('pbmc3k') | |
| 259M | 252M | 0.97 | preprocessing_log.peakmem_highly_variable_genes('pbmc68k_reduced') | |
| 532M | 521M | 0.98 | preprocessing_log.peakmem_pca('pbmc3k') | |
| 316M | 316M | 1.00 | preprocessing_log.peakmem_pca('pbmc68k_reduced') | |
| n/a | n/a | n/a | preprocessing_log.peakmem_regress_out('pbmc3k') | |
| 311M | 305M | 0.98 | preprocessing_log.peakmem_regress_out('pbmc68k_reduced') | |
| 1.03G | 1.03G | 1.00 | preprocessing_log.peakmem_scale('pbmc3k') | |
| 255M | 252M | 0.99 | preprocessing_log.peakmem_scale('pbmc68k_reduced') | |
| 32.5±0.4ms | 32.3±0.5ms | 0.99 | preprocessing_log.time_highly_variable_genes('pbmc3k') | |
| 10.3±1ms | 10.2±0.1ms | 0.99 | preprocessing_log.time_highly_variable_genes('pbmc68k_reduced') | |
| 2.68±0.02s | 2.68±0.02s | 1.00 | preprocessing_log.time_pca('pbmc3k') | |
| 34.3±1ms | 34.0±1ms | 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 | 1.00 | preprocessing_log.time_regress_out('pbmc68k_reduced') | |
| 830±20ms | 837±10ms | 1.01 | preprocessing_log.time_scale('pbmc3k') | |
| 4.21±0.3ms | 3.83±0.1ms | ~0.91 | preprocessing_log.time_scale('pbmc68k_reduced') | |
| 260M | 252M | 0.97 | tools.peakmem_diffmap | |
| 251M | 262M | 1.04 | tools.peakmem_leiden | |
| 337M | 335M | 0.99 | tools.peakmem_umap | |
| 16.2±0.4ms | 16.5±0.5ms | 1.02 | tools.time_diffmap | |
| 15.5±0.2ms | 15.4±0.1ms | 0.99 | tools.time_leiden | |
| 1.60±0.02s | 1.60±0s | 1.00 | tools.time_umap |
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