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

[mwalker174]

Hi @jingydz, the original repo https://github.com/talkowski-lab/svtk.git is no longer being maintained. You should use install the svtk module from gatk-sv instead and install:

git clone https://github.com/broadinstitute/gatk-sv.git
cd src/svtk/
pipe install -e .