>>> sc.tl.umap(adata_T) Segmentation fault

[Jane8166]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

Hello everyone,

Lately, I encountered an issue while executing the function sc.tl.umap(adata_T) within my Scanpy environment on an Ubuntu system. The process terminated unexpectedly with a “Segmentation fault” error, followed by the closure of the Python terminal. I’m seeking assistance from the community. Any help would be greatly appreciated.

Thank you very much!

Minimal code sample

Python 3.12.0 | packaged by conda-forge | (main, Oct  3 2023, 08:43:22) [GCC 1     2.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scanpy as sc

>>> import pandas as pd
>>> import anndata as ad
>>> import numpy as np
>>> #import matplotlib as plt
>>> import matplotlib.pyplot as plt
>>> import os
>>> sc.settings.logging = 4 # this does not work regardless of whether it exists or not
>>> adata=ad.read_h5ad("tumor.h5ad")
>>> adata_T=adata[(adata.obs["cell_type_lvl2"]=="T"),:]
>>> sc.pp.highly_variable_genes(adata_T, n_top_genes=2000)
>>> # dimensionality reduction
>>> sc.tl.pca(adata_T)
>>> # compute the neighborhood graph of cells
>>> sc.pp.neighbors(adata_T)
>>> sc.tl.umap(adata_T)

Error output

>>> sc.tl.umap(adata_T)
Segmentation fault
(scanpy2) user@server 12:17:13 ~

Versions

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
anndata                   0.11.1             pyhd8ed1ab_1    conda-forge
arpack                    3.9.1           nompi_hf03ea27_102    conda-forge
array-api-compat          1.10.0             pyhd8ed1ab_0    conda-forge
brotli                    1.1.0                hb9d3cd8_2    conda-forge
brotli-bin                1.1.0                hb9d3cd8_2    conda-forge
bzip2                     1.0.8                h4bc722e_7    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
c-ares                    1.34.4               hb9d3cd8_0    conda-forge
ca-certificates           2024.12.14           hbcca054_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
click                     8.1.8                    pypi_0    pypi
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
contourpy                 1.3.1           py312h68727a3_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_1    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
fonttools                 4.55.3          py312h178313f_1    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.3.0                hac33072_2    conda-forge
h5py                      3.12.1          nompi_py312hd203070_103    conda-forge
hdf5                      1.14.4          nompi_h2d575fe_105    conda-forge
igraph                    0.10.15              he44f51b_1    conda-forge
imageio                   2.36.1                   pypi_0    pypi
joblib                    1.4.2              pyhd8ed1ab_1    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.7           py312h68727a3_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
lazy-loader               0.4                      pypi_0    pypi
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
legacy-api-wrap           1.4.1              pyhd8ed1ab_0    conda-forge
leidenalg                 0.10.2          py312h30efb56_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libblas                   3.9.0           26_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hb9d3cd8_2    conda-forge
libbrotlidec              1.1.0                hb9d3cd8_2    conda-forge
libbrotlienc              1.1.0                hb9d3cd8_2    conda-forge
libcblas                  3.9.0           26_linux64_openblas    conda-forge
libcurl                   8.11.1               h332b0f4_0    conda-forge
libdeflate                1.23                 h4ddbbb0_0    conda-forge
libedit                   3.1.20240808    pl5321h7949ede_0    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.4                h5888daf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libffi                    3.4.2                h7f98852_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc                    14.2.0               h77fa898_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng                 14.2.0               h69a702a_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran               14.2.0               h69a702a_1    conda-forge
libgfortran5              14.2.0               hd5240d6_1    conda-forge
libgomp                   14.2.0               h77fa898_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libhwloc                  2.11.2          default_h0d58e46_1001    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           26_linux64_openblas    conda-forge
libleidenalg              0.11.1               h00ab1b0_0    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
liblzma                   5.6.3                hb9d3cd8_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
liblzma-devel             5.6.3                hb9d3cd8_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnghttp2                1.64.0               h161d5f1_0    conda-forge
libnsl                    2.0.1                hd590300_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libopenblas               0.3.28          pthreads_h94d23a6_1    conda-forge
libpng                    1.6.44               hadc24fc_0    conda-forge
libsqlite                 3.47.2               hee588c1_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libssh2                   1.11.1               hf672d98_0    conda-forge
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libtiff                   4.7.0                hd9ff511_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libwebp-base              1.5.0                h851e524_0    conda-forge
libxcb                    1.17.0               h8a09558_0    conda-forge
libxml2                   2.13.5               h0d44e9d_1    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
llvmlite                  0.43.0          py312h374181b_1    conda-forge
loompy                    3.0.7                    pypi_0    pypi
matplotlib-base           3.10.0          py312hd3ec401_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
natsort                   8.4.0              pyh29332c3_1    conda-forge
ncurses                   6.5                  he02047a_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
networkx                  3.4.2              pyh267e887_2    conda-forge
numba                     0.60.0          py312h83e6fd3_0    conda-forge
numpy                     2.0.2           py312h58c1407_1    conda-forge
numpy-groupies            0.11.2                   pypi_0    pypi
openjpeg                  2.5.3                h5fbd93e_0    conda-forge
openssl                   3.4.0                h7b32b05_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
packaging                 24.2               pyhd8ed1ab_2    conda-forge
pandas                    2.2.3           py312hf9745cd_1    conda-forge
patsy                     1.0.1              pyhd8ed1ab_1    conda-forge
pillow                    11.1.0          py312h80c1187_0    conda-forge
pip                       24.3.1             pyh8b19718_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
pynndescent               0.5.13             pyhd8ed1ab_1    conda-forge
pyparsing                 3.2.1              pyhd8ed1ab_0    conda-forge
python                    3.12.0          hab00c5b_0_cpython    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-dateutil           2.9.0.post0        pyhff2d567_1    conda-forge
python-igraph             0.11.8          py312h3262465_0    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_1    conda-forge
python_abi                3.12                    5_cp312    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
qhull                     2020.2               h434a139_5    conda-forge
readline                  8.2                  h8228510_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
scanpy                    1.10.4             pyhd8ed1ab_0    conda-forge
scikit-image              0.25.0                   pypi_0    pypi
scikit-learn              1.6.0           py312h7a48858_0    conda-forge
scipy                     1.15.0          py312h180e4f1_0    conda-forge
seaborn                   0.13.2               hd8ed1ab_3    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_3    conda-forge
session-info              1.0.0              pyhd8ed1ab_0    conda-forge
setuptools                75.6.0             pyhff2d567_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
six                       1.17.0             pyhd8ed1ab_0    conda-forge
statsmodels               0.14.4          py312hc0a28a1_0    conda-forge
stdlib-list               0.11.0             pyhd8ed1ab_1    conda-forge
tbb                       2022.0.0             hceb3a55_0    conda-forge
texttable                 1.7.0              pyhd8ed1ab_1    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tifffile                  2024.12.12               pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tqdm                      4.67.1             pyhd8ed1ab_1    conda-forge
typing                    3.10.0.0           pyhd8ed1ab_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tzdata                    2024b                hc8b5060_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
umap-learn                0.5.7           py312h7900ff3_0    conda-forge
unicodedata2              15.1.0          py312h66e93f0_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxau               1.0.12               hb9d3cd8_0    conda-forge
xorg-libxdmcp             1.1.5                hb9d3cd8_0    conda-forge
xz                        5.6.3                hbcc6ac9_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz-gpl-tools              5.6.3                hbcc6ac9_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz-tools                  5.6.3                hb9d3cd8_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

[flying-sheep]

Hi, this is very very likely a bug in some library that we can’t fix here.

But to figure that out, we’d need more info. Please use the faulthandler module to do so:

1. Add import faulthandler; faulthandler.enable() to the start of your reproducer
2. run it again
3. comment with the output

I can then tell you which upstream library you should update or file an issue for.

I’m closing this since as said, I’m quite sure this is not a scanpy issue.

[Jane8166]

Hi，this is new output:

sc.tl.umap(adata_T)
Fatal Python error: Segmentation fault

Thread 0x00007fdb354f9740 (most recent call first):
File "/raid5/user/00.software/miniconda3/envs/scanpy2/lib/python3.12/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py", line 542 in iterate
File "/raid5/user/00.software/miniconda3/envs/scanpy2/lib/python3.12/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py", line 1696 in eigsh
File Segmentation fault

Thank you!

[Jane8166]

Hi @flying-sheep , I tried to update the scipy from 1.50 to 1.51，and then reran the code. Here’s the output :

Python 3.12.0 | packaged by conda-forge | (main, Oct 3 2023, 08:43:22) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import faulthandler;faulthandler.enable()
import scanpy as sc
import pandas as pd
import anndata as ad
import numpy as np
import matplotlib.pyplot as plt
import os
adata=ad.read_h5ad("tumor.h5ad")
adata_T=adata[(adata.obs["cell_type_lvl2"]=="T"),:]
sc.pp.highly_variable_genes(adata_T, n_top_genes=2000)
/raid5/user/00.software/miniconda3/envs/scanpy2/lib/python3.12/site-packages/scanpy/p reprocessing/_highly_variable_genes.py:696: ImplicitModificationWarning: Trying to modify attr ibute ._uns of view, initializing view as actual.
adata.uns["hvg"] = {"flavor": flavor}
sc.tl.pca(adata_T)
sc.pp.neighbors(adata_T)
sc.tl.umap(adata_T)
Fatal Python error: Fatal Python error: Fatal Python error: Fatal Python error: Segmentation f aultSegmentation fault

Segmentation faultSegmentation fault

Thread 0x

00007f47e275f740 (most recent call first):
File "/raid5/user/00.software/miniconda3/envs/scanpy2/lib/python3.12/site-packages/ scipy/sparse/linalg/_eigen/arpack/arpack.py"Segmentation fault

[flying-sheep]

Hmm, looks indeed like a scipy issue, maybe related to scipy/scipy#11805 or so.

Please report it there! They probably want an actually working reproducer, so you need to upload tumor.h5ad and have a link to include before you file that issue.