navid-mahmoudian
commented
4 years ago Hello, I upgraded my gcc to gcc 9.1.0, and I am getting another error:
ImportError: dlopen: cannot load any more object with static TLS
Contents of /nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/sklearn/check_build: _check_build.cpython-36m-x86_64-linux-gnu.sosetup.py init.py pycache__
It seems that scikit-learn has not been built correctly.
If you have installed scikit-learn from source, please do not forget to build the package before using it: run
python setup.py installormakein the source directory.If you have used an installer, please check that it is suited for your Python version, your operating system and your platform.
I have installed scikit-learn using pip and I verified its correct installation according to this link. When I do:
python -c "import sklearn; sklearn.show_versions()"
I get:
System: python: 3.6.5 (default, Dec 19 2019, 19:22:19) [GCC 9.1.0] executable: /nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/bin/python machine: Linux-3.16.0-6-amd64-x86_64-with-debian-8.10
Python dependencies: pip: 20.0.2 setuptools: 46.1.3 sklearn: 0.22.2.post1 numpy: 1.17.0 scipy: 1.4.1 Cython: None pandas: 1.0.3 matplotlib: 3.2.1 joblib: 0.14.1
Built with OpenMP: True
The full traceback of error is as follows:
Traceback (most recent call last): File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/sklearn/__check_build/init.py", line 44, in
from ._check_build import check_build # noqa ImportError: dlopen: cannot load any more object with static TLS During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/nfs/nas4/sirocco-intercom/sirocco-intercom/Codes/train.py", line 3, in
import model_sphere_autoencoder File "/nfs/nas4/sirocco-intercom/sirocco-intercom/Codes/model_sphere_autoencoder.py", line 3, in import torch_geometric.nn as nn_torch_geometric File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/init.py", line 2, in import torch_geometric.nn File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/nn/init.py", line 10, in from .models import * # noqa File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/nn/models/init.py", line 2, in from .node2vec import Node2Vec File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/nn/models/node2vec.py", line 2, in from sklearn.linear_model import LogisticRegression File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/sklearn/init.py", line 81, in from . import check_build # noqa: F401 File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/sklearn/check_build/init.py", line 46, in raise_build_error(e) File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/sklearn/__check_build/init.py", line 41, in raise_build_error %s""" % (e, local_dir, ''.join(dir_content).strip(), msg)) ImportError: dlopen: cannot load any more object with static TLS
Contents of /nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/sklearn/check_build: _check_build.cpython-36m-x86_64-linux-gnu.sosetup.py init.py pycache__
It seems that scikit-learn has not been built correctly.
If you have installed scikit-learn from source, please do not forget to build the package before using it: run
python setup.py installormakein the source directory.If you have used an installer, please check that it is suited for your Python version, your operating system and your platform.
🐛 Bug
Hello, I followed exactly the instruction given in this link, but I keep getting the following error OSError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_sparse/_convert.so)
I tried to use the suggestion given in this link by doing
pip install libgcc,but I get the following error:Environment
Additional context
Here is the complete trace of the error I get: File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_sparse/init.py", line 15, in
library, [osp.dirname(file)]).origin)
File "/soft/igrida/pytorch/1.4-py3.6/lib/python3.6/site-packages/torch/_ops.py", line 106, in load_library
ctypes.CDLL(path)
File "/soft/igrida/spack/opt/spack/linux-debian8-x86_64/gcc-9.1.0/python-3.6.5-xu2dmz5rdvjfmiizbt65hyy2hsqsn3ri/lib/python3.6/ctypes/init.py", line 348, in init
self._handle = _dlopen(self._name, mode)
OSError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_sparse/_convert.so)
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/nfs/nas4/sirocco-intercom/sirocco-intercom/Codes/train.py", line 3, in
import model_sphere_autoencoder
File "/nfs/nas4/sirocco-intercom/sirocco-intercom/Codes/model_sphere_autoencoder.py", line 3, in
import torch_geometric.nn as nn_torch_geometric
File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/init.py", line 2, in
import torch_geometric.nn
File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/nn/init.py", line 2, in
from .data_parallel import DataParallel
File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/nn/data_parallel.py", line 5, in
from torch_geometric.data import Batch
File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/data/init.py", line 1, in
from .data import Data
File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_geometric/data/data.py", line 7, in
from torch_sparse import coalesce
File "/nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_sparse/init.py", line 23, in
raise OSError(e)
OSError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /nfs/nas4/sirocco-intercom/sirocco-intercom/python3-virtual-env/pytorch1.4_healpy/lib/python3.6/site-packages/torch_sparse/_convert.so)