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removes some atomics from qc #113

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merged 5 commits into from
Jan 3, 2024
Merged

removes some atomics from qc #113

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fb47916
removes some atomics from qc
Intron7 Jan 3, 2024
5044a7c
minimize global memory access
Intron7 Jan 3, 2024
ea6a323
remove empty lines
Intron7 Jan 3, 2024
d76d31b
Merge branch 'main' into remove-atomics-from-qc
Intron7 Jan 3, 2024
db1777a
added release note
Intron7 Jan 3, 2024
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3 changes: 2 additions & 1 deletion docs/release-notes/0.9.4.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
### 0.9.4 {small}`the future`
### 0.9.4

```{rubric} Features
```
* {func}`~rapids_singlecell.tl.leiden` now provides `random_state` parameter for initializing the optimization {pr}`102` {smaller}`J Pintar & S Dicks`
* {func}`~rapids_singlecell.tl.louvain` now provides `threshold` parameter for setting the minimum modularity gain between levels {pr}`103` {smaller}`J Pintar & S Dicks`
* added a kernel for sparse sum along the major axis {pr}`112` {smaller}`S Dicks`
* {func}`~rapids_singlecell.pp.calculate_qc_metrics` now uses less atomics and global memory during kernels {pr}`113` {smaller}`S Dicks`
24 changes: 15 additions & 9 deletions src/rapids_singlecell/preprocessing/_kernels/_qc_kernels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,17 @@
int start_idx = indptr[gene];
int stop_idx = indptr[gene+1];

{0} sums_genes_i = 0;
int gene_ex_i = 0;
for(int cell = start_idx; cell < stop_idx; cell++){
{0} value = data[cell];
int cell_number = index[cell];
atomicAdd(&sums_genes[gene], value);
sums_genes_i += value;
atomicAdd(&sums_cells[cell_number], value);
atomicAdd(&gene_ex[gene], 1);
gene_ex_i += 1;
atomicAdd(&cell_ex[cell_number], 1);

sums_genes[gene] = sums_genes_i;
gene_ex[gene] = gene_ex_i;
}
}
"""
Expand All @@ -36,14 +39,17 @@
int start_idx = indptr[cell];
int stop_idx = indptr[cell+1];

{0} sums_cells_i = 0;
int cell_ex_i = 0;
for(int gene = start_idx; gene < stop_idx; gene++){
{0} value = data[gene];
int gene_number = index[gene];
atomicAdd(&sums_genes[gene_number], value);
atomicAdd(&sums_cells[cell], value);
sums_cells_i += value;
atomicAdd(&gene_ex[gene_number], 1);
atomicAdd(&cell_ex[cell], 1);

cell_ex_i += 1;
sums_cells[cell] = sums_cells_i;
cell_ex[cell] = cell_ex_i;
}
}
"""
Expand All @@ -58,8 +64,6 @@
if(cell >= n_cells || gene >=n_genes){
return;
}


long long int index = static_cast<long long int>(cell) * n_genes + gene;
{0} value = data[index];
if (value>0.0){
Expand Down Expand Up @@ -103,12 +107,14 @@
int start_idx = indptr[cell];
int stop_idx = indptr[cell+1];

{0} sums_cells_i = 0;
for(int gene = start_idx; gene < stop_idx; gene++){
int gene_number = index[gene];
if (mask[gene_number]==true){
atomicAdd(&sums_cells[cell], data[gene]);
sums_cells_i += data[gene];

}
sums_cells[cell] = sums_cells_i;
}
}
"""
Expand Down