rapids-single-cell-examples

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gpu memory issue - 8M cell 24G GPU out of memory during umap

1

Code I used: `sc.tl.umap(ad,min_dist=0.1,method='rapids',neighbors_key='neighbors')` AWS G5 4xlarge 1 GPU 24G GPU memory. During the process the GPU usage is 4G/24G but at the end, it crashed saying out of memory....

yubin-ai

the recent upgrade cuml has moved cuml.common.memory_utils to cuml.internals.memory_utils

yubin-ai

ImportError: /usr/lib/x86_64-linux-gnu/libcuda.so.1: file too short

1

Hello RAPIDS, Thanks for developing this amazing package. I met 'ImportError: /usr/lib/x86_64-linux-gnu/libcuda.so.1: file too short' when importing packages. ```python import scanpy as sc import anndata import time import os, wget...

hyjforesight

In [`/notebooks/hlca_lung_gpu_analysis.ipynb`](https://github.com/NVIDIA-Genomics-Research/rapids-single-cell-examples/blob/master/notebooks/hlca_lung_gpu_analysis.ipynb), when run cell 19 ``` %%time hvg = rapids_scanpy_funcs.highly_variable_genes(sparse_gpu_array, genes, n_top_genes=5000) ``` it raises error: ``` --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) in /workspace/notebooks/rapids_scanpy_funcs.py in highly_variable_genes(sparse_gpu_array, genes,...

hw-ju

Hi! I'm trying to run this notebook https://github.com/NVIDIA-Genomics-Research/rapids-single-cell-examples/blob/master/notebooks/5k_pbmc_coverage_gpu.ipynb within the container https://hub.docker.com/r/claraparabricks/single-cell-examples_rapids_cuda11.0 on A100 GPU. Everything works until executing this line ``` atacworks_results = coverage.atacworks_denoise(noisy_coverage, model, gpu, interval_size) ``` which...

hw-ju

Hi! The jupyter notebooks in the repo here https://github.com/NVIDIA-Genomics-Research/rapids-single-cell-examples/tree/master/notebooks are not exactly the same as the ones within the container https://hub.docker.com/r/claraparabricks/single-cell-examples_rapids_cuda11.0 (which has more comments). Which version is better? Thanks!

hw-ju

I am running the Example 4: Droplet Single-cell ATAC-seq of 60K Bone Marrow Cells demo data in a GPU cluster in Google Cloud. All the codes ran perfectly well around...

archieandrews10

Cannot open UCX library: (null) in PCA analysis of 1M_brain_gpu_analysis_multigpu

3

Dear authors, Thank you for share the valuable pipelines to use GPU in single cell genomics data analysis. When I go through the 1M_brain_gpu_analysis_multigpu pipeline you have provided, I meet...

ChenPeizhan

when I filter cell with funcion read_with_filter function wieh dataset krasnow_hlca_10x.sparse.h5ad, no cell filtered with different parameters. But it worked normally when used function scanpy.pp.filter_cells

111kakaluote

Hello @rilango @cjnolet @mlgill @raydouglass @pentschev, I am trying to run leiden clustering on ~40 M cells. During the run I see the GPU is idle in terms of power...

siddharthamantrala