Hi,
Here’s my data situation:
AnnData object with n_obs × n_vars = 16000 × 3000
obs: 'sample', 'group1', 'group2', 'batch', 'decontX_contamination', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_20_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'total_counts_hb', 'log1p_total_counts_hb', 'pct_counts_hb', 'passing_mt', 'passing_nUMIs', 'passing_ngenes', 'passing_decontX', 'predicted_labels', 'over_clustering', 'majority_voting', 'conf_score', 'leiden', 'annotation_level1', 'annotation_level2', 'annotation_level3', 'main_celltype', '_scvi_batch', '_scvi_labels'
var: 'gene_ids', 'feature_types', 'symbol', 'mt', 'ribo', 'hb', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches', 'highly_variable_intersection'
uns: '_scvi_manager_uuid', '_scvi_uuid', 'annotation_level1_colors', 'annotation_level2_colors', 'annotation_level3_colors', 'dendrogram_leiden', 'group1_colors', 'hvg', 'layers_counts', 'leiden', 'leiden_wilcoxon', 'log1p', 'main_celltype_colors', 'neighbors', 'over_clustering', 'pca', 'sample_colors', 'umap'
obsm: 'X_pca', 'X_pca_harmony', 'X_scanorama'
varm: 'PCs'
layers: 'counts'
obsp: 'connectivities', 'distances'
nvidia-smi
information before starting training is:
Wed Dec 4 13:56:51 2024
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 550.120 Driver Version: 566.14 CUDA Version: 12.7 |
|-----------------------------------------+------------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA GeForce RTX 4060 Ti On | 00000000:01:00.0 On | N/A |
| 0% 34C P5 15W / 180W | 620MiB / 16380MiB | 1% Default |
| | | N/A |
+-----------------------------------------+------------------------+----------------------+
+-----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| No running processes found |
+-----------------------------------------------------------------------------------------+
and while do vae.train()
Wed Dec 4 13:58:22 2024
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 550.120 Driver Version: 566.14 CUDA Version: 12.7 |
|-----------------------------------------+------------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA GeForce RTX 4060 Ti On | 00000000:01:00.0 On | N/A |
| 0% 36C P3 22W / 180W | 839MiB / 16380MiB | 31% Default |
| | | N/A |
+-----------------------------------------+------------------------+----------------------+
+-----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| 0 N/A N/A 1778 C /python3.10 N/A |
+-----------------------------------------------------------------------------------------+