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STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
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data.tl.phenograph use error #240

Closed ffZhang2003 closed 4 months ago

ffZhang2003 commented 5 months ago

Hi,I used data.tl.phenograph data.tl.phenograph(phenograph_k=50,pca_res_key='pca',res_key='phenograph') on jupyterlab and the command line,it raised an error: jupyterlab：Kernel Restarting The kernel for space/Untitled.ipynb appears to havedied. lt will restart automatically. Command line: Segmentation fault Finding 50 nearest neighbors using minkowski metric and 'auto' algorithm OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.

The server configuration is: 1T memory, 256 threads

Zhenbin24 commented 5 months ago

Hello, this kind of situation is mostly caused by insufficient memory. You can monitor the remaining memory when running (free -h). It is recommended to try again when fewer people are using the service.