rapids-single-cell-examples

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Because the cusparse API uses 32-bit integers to specify the size of the underlying workspaces in GPU memory, and because the Scipy/Cupy sparse APIs use them to specify the size...

cjnolet

OverflowError: value too large to convert to int

2

Could I ask if you might have any tips on how to overcome this error? I'm running your 1M cell code, but I tried it on my own set of...

slowkow

CUDA MemoryError for loading adata variable names to cudf.Series method

3

Hi Team, I'm getting CUDA memory error when I call cudf.Series method from the [hlca_lung_gpu_analysis-visualization notebook](https://github.com/clara-parabricks/rapids-single-cell-examples/blob/master/notebooks/hlca_lung_gpu_analysis-visualization.ipynb). **Error Log:** ```bash --------------------------------------------------------------------------- ArrowTypeError Traceback (most recent call last) ~/anaconda3/envs/rapidgenomics/lib/python3.7/site-packages/cudf/utils/utils.py in pyarrow_buffer_to_cudf_buffer(arrow_buf, mask_size)...

nullbyte91

Is there anyone to compare the consistency of results generated by scanpy pipeline and RAPIDS implementation? Such as the consistency of HVG genes?

111kakaluote

MultiGPU notebooks calculated differentially expressed PCAs

1

Hey Nvidia Genomics Team, In the Multi GPU Notebook the AnnData object post PCA is created with the PCA in `.X`. Therefore when you later later perform the differential gene...

Intron7

RuntimeError: exception occured! when analysis using multigpu

2

when I analysis 1 million cells collected by myself using multigpu, step of dask_sparse_arr.compute_chunk_sizes() is error. Error information is below: cuml/linear_model/linear_regression.pyx in cuml.linear_model.linear_regression.LinearRegression.fit() `RuntimeError: exception occured! file=_deps/raft-src/cpp/include/raft/linalg/eig.cuh line=144: eig.cuh: eigensolver...

111kakaluote

Residual GPU Memory usage

3

hi! i am trying to use the scanpy rapids functions to run multiple parallel operations on a server. the problem i am running into is that after running any scanpy...

r614

error in rapids_scanpy_funcs.highly_variable_genes

5

Hi, when I followd the jupyter notebook and tried use rapids_scanpy_funcs.highly_variable_genes, I came across the error: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) File :1, in File ~/autodl-tmp/rapids_scanpy_funcs.py:753, in highly_variable_genes(sparse_gpu_array,...

Wulin-Tan

weird UMAP results and very inconsistent with CPU results

1

Sometimes I find the results from rapids KNN and UMAP very weird. The majoy data points are in center and super small (see below). At the beginning I thought it...

yubin-ai

hardware: 24G memory GPU 10M dataset: 30min for KNN, 30min for UMAP, 3min for Leiden 70M dataset: not sure if it is feasible due to memory limit - 15h for...

yubin-ai