ImportError: dlopen: cannot load any more object with static TLS

[jingydz]

Instructions

Hi, I had successfully installed svtk and used it correctly, but I'm not sure why it stopped working properly after some time. I wonder if I updated some Python modules. Can you help me with this?

When I tried to use it again, I encountered the following error message. File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/genomeslink.py", line 18, in from scipy.sparse import csgraph ImportError: cannot import name 'csgraph' from 'scipy.sparse' (unknown location)

Subsequently, I upgraded the scipy module, and it resulted in the following error. Traceback (most recent call last): File "/xxx/software/miniconda3/bin/svtk", line 45, in import svtk.cli as cli File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/cli/init.py", line 12, in from .adjudicate import main as adjudicate File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/cli/adjudicate.py", line 14, in from svtk.adjudicate import adjudicate_SV File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/adjudicate/init.py", line 1, in from .random_forest import RandomForest, rf_classify File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/adjudicate/random_forest.py", line 14, in from sklearn.ensemble import RandomForestClassifier File "/xxx/software/miniconda3/lib/python3.9/site-packages/sklearn/init.py", line 84, in from .utils._show_versions import show_versions File "/xxx/software/miniconda3/lib/python3.9/site-packages/sklearn/utils/_show_versions.py", line 13, in from ._openmp_helpers import _openmp_parallelism_enabled ImportError: dlopen: cannot load any more object with static TLS

I attempted to reinstall svtk again, and here's what I did, but I encountered a similar error. Could you help me resolve it? git clone https://github.com/talkowski-lab/svtk.git cd svtk/ python setup.py Compiling svtk/utils/helpers.pyx because it changed. [1/1] Cythonizing svtk/utils/helpers.pyx usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help error: no commands supplied find -name svtk ./scripts/svtk ./svtk ./scripts/svtk --help Traceback (most recent call last): File "/xxx/software/svtk/./scripts/svtk", line 42, in import svtk.cli as cli File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/cli/init.py", line 12, in from .adjudicate import main as adjudicate File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/cli/adjudicate.py", line 14, in from svtk.adjudicate import adjudicate_SV File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/adjudicate/init.py", line 1, in from .random_forest import RandomForest, rf_classify File "/xxx/software/miniconda3/lib/python3.9/site-packages/svtk/adjudicate/random_forest.py", line 14, in from sklearn.ensemble import RandomForestClassifier File "/xxx/software/miniconda3/lib/python3.9/site-packages/sklearn/init.py", line 84, in from .utils._show_versions import show_versions File "/xxx/software/miniconda3/lib/python3.9/site-packages/sklearn/utils/_show_versions.py", line 13, in from ._openmp_helpers import _openmp_parallelism_enabled ImportError: dlopen: cannot load any more object with static TLS

I tried to replace the Python 3.9 under Miniconda with another Python 3.6 under Anaconda, but I was still unable to use svtk, and it gave me the following error. I think it might be because I didn't install the svtk.cli module. Can you help me with this? Traceback (most recent call last): File "/xxx/software/miniconda3/bin/svtk", line 45, in import svtk.cli as cli ModuleNotFoundError: No module named 'svtk.cli'

pip install svtk.cli Collecting svtk.cli Could not find a version that satisfies the requirement svtk.cli (from versions: ) No matching distribution found for svtk.cli You are using pip version 10.0.1, however version 21.3.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

Bug Report

File "/xxx/software/miniconda3/lib/python3.9/site-packages/sklearn/utils/_show_versions.py", line 13, in from ._openmp_helpers import _openmp_parallelism_enabled ImportError: dlopen: cannot load any more object with static TLS

Traceback (most recent call last): File "/xxx/software/miniconda3/bin/svtk", line 45, in import svtk.cli as cli ModuleNotFoundError: No module named 'svtk.cli'

Affected version(s)

$ python --version Python 3.9.7