Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix garbage collection #1119

Merged
merged 40 commits into from
Jul 22, 2024

fix 3.9

e138fc9
Select commit
Loading
Failed to load commit list.
Merged

Fix garbage collection #1119

fix 3.9
e138fc9
Select commit
Loading
Failed to load commit list.
scverse-benchmark / benchmark succeeded Jul 22, 2024 in 14m 38s

Benchmark

Benchmark run successful

Details

All benchmarks:

Change Before [b2bdd7f] After [e138fc9] Ratio Benchmark (Parameter)
- 13135945.0 1709018.0 0.13 anndata.GarbargeCollectionSuite.track_peakmem_garbage_collection
136M 145M 1.07 readwrite.H5ADBackedWriteSuite.peakmem_write_compressed('pbmc3k')
137M 133M 0.97 readwrite.H5ADBackedWriteSuite.peakmem_write_full('pbmc3k')
689±0.8ms 683±8ms 0.99 readwrite.H5ADBackedWriteSuite.time_write_compressed('pbmc3k')
195±7ms 192±6ms 0.98 readwrite.H5ADBackedWriteSuite.time_write_full('pbmc3k')
14.8671875 14.8359375 1.00 readwrite.H5ADBackedWriteSuite.track_peakmem_write_compressed('pbmc3k')
14.53125 14.41796875 0.99 readwrite.H5ADBackedWriteSuite.track_peakmem_write_full('pbmc3k')
91235728 91242959 1.00 readwrite.H5ADInMemorySizeSuite.track_actual_in_memory_size('pbmc3k')
23564294 23564294 1.00 readwrite.H5ADInMemorySizeSuite.track_in_memory_size('pbmc3k')
5.26M 5.26M 1.00 readwrite.H5ADReadSuite.mem_read_backed_object('pbmc3k')
23.6M 23.6M 1.00 readwrite.H5ADReadSuite.mem_readfull_object('pbmc3k')
125M 127M 1.02 readwrite.H5ADReadSuite.peakmem_read_backed('pbmc3k')
152M 142M 0.93 readwrite.H5ADReadSuite.peakmem_read_full('pbmc3k')
145±0.3ms 139±2ms 0.96 readwrite.H5ADReadSuite.time_read_full('pbmc3k')
+ 1.208629755644912 1.5165922763438773 1.25 readwrite.H5ADReadSuite.track_read_full_memratio('pbmc3k')
152M 144M 0.95 readwrite.H5ADWriteSuite.peakmem_write_compressed('pbmc3k')
149M 149M 1.00 readwrite.H5ADWriteSuite.peakmem_write_full('pbmc3k')
574±1ms 566±4ms 0.99 readwrite.H5ADWriteSuite.time_write_compressed('pbmc3k')
89.6±0.9ms 84.6±5ms 0.94 readwrite.H5ADWriteSuite.time_write_full('pbmc3k')
6.89453125 7.01171875 1.02 readwrite.H5ADWriteSuite.track_peakmem_write_compressed('pbmc3k')
6.64453125 6.6796875 1.01 readwrite.H5ADWriteSuite.track_peakmem_write_full('pbmc3k')
159M 154M 0.97 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), '0:1000')
156M 158M 1.01 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), '0:9000')
156M 164M 1.05 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), ':9000:-1')
152M 156M 1.03 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), '::-2')
156M 161M 1.03 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), 'alternating')
159M 157M 0.99 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), 'arange')
157M 156M 1.00 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), 'array')
157M 166M 1.06 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem((10000, 10000), 'first')
152M 154M 1.01 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), '0:1000')
156M 163M 1.04 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), '0:9000')
160M 152M 0.95 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), ':9000:-1')
159M 160M 1.01 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), '::-2')
160M 156M 0.98 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), 'alternating')
161M 154M 0.96 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), 'arange')
156M 159M 1.02 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), 'array')
175M 164M 0.94 sparse_dataset.SparseCSRContiguousSlice.peakmem_getitem_adata((10000, 10000), 'first')
1.52±0.01ms 1.35±0.1ms ~0.89 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), '0:1000')
7.37±0.6ms 6.27±0.8ms ~0.85 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), '0:9000')
513±5ms 514±4ms 1.00 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), ':9000:-1')
2.55±0.03s 2.52±0.03s 0.99 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), '::-2')
527±2ms 523±2ms 0.99 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), 'alternating')
510±3ms 518±5ms 1.02 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), 'arange')
2.15±0.1ms 2.46±0.1ms ~1.14 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), 'array')
1.18±0.09ms 1.23±0.09ms 1.04 sparse_dataset.SparseCSRContiguousSlice.time_getitem((10000, 10000), 'first')
77.0±0.4μs 73.0±0.2μs 0.95 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), '0:1000')
77.7±0.07μs 73.6±0.4μs 0.95 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), '0:9000')
78.0±0.1μs 73.7±0.4μs 0.95 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), ':9000:-1')
78.1±0.08μs 73.0±0.2μs 0.93 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), '::-2')
276±20μs 265±2μs 0.96 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), 'alternating')
127±1μs 125±0.6μs 0.98 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), 'arange')
116±0.6μs 111±0.3μs 0.96 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), 'array')
79.0±0.5μs 77.2±2μs 0.98 sparse_dataset.SparseCSRContiguousSlice.time_getitem_adata((10000, 10000), 'first')
View more details on scverse-benchmark