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talmolab
Cannot detect GPUs - ImportError: C extension: None not built
Bug description
Cannot detect GPU in the SLEAP environment with the command python -c "import sleap; sleap.system_summary()". I have an error instead.
Expected behaviour
I would expect the command python -c "import sleap; sleap.system_summary()" to return the number of available GPUs and so on.
Actual behaviour
I installed SLEAP correctly (I think). I am able to find the environment in the conda environment list:
# conda environments:
#
base * /Users/valeriepineaunoel/mambaforge
sleap /Users/valeriepineaunoel/mambaforge/envs/sleap
/Users/valeriepineaunoel/miniforge3
/Users/valeriepineaunoel/miniforge3/envs/sleap
/Users/valeriepineaunoel/miniforge3/envs/social-interactions
/Users/valeriepineaunoel/miniforge3/envs/tutorial_env
/Users/valeriepineaunoel/opt/anaconda3
/Users/valeriepineaunoel/opt/anaconda3/envs/ads_venv
/Users/valeriepineaunoel/opt/anaconda3/envs/cellpose-env
conda activate sleap works. Now when I want to make sure that SLEAP detects the GPU on my system with python -c "import sleap; sleap.system_summary()", I get an error
Traceback (most recent call last):
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/pandas/__init__.py", line 26, in <module>
from pandas.compat import (
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/pandas/compat/__init__.py", line 26, in <module>
from pandas.compat.numpy import is_numpy_dev
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py", line 21, in <module>
raise ImportError(
ImportError: this version of pandas is incompatible with numpy < 1.22.4
your numpy version is 1.19.5.
Please upgrade numpy to >= 1.22.4 to use this pandas version
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/sleap/__init__.py", line 10, in <module>
from sleap.io.dataset import Labels, load_file
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/sleap/io/dataset.py", line 72, in <module>
from sleap.instance import (
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/sleap/instance.py", line 32, in <module>
from sleap.io.video import Video
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/sleap/io/video.py", line 8, in <module>
import imgstore
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/imgstore/__init__.py", line 1, in <module>
from .stores import new_for_filename, new_for_format, extract_only_frame, get_supported_formats,\
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/imgstore/stores.py", line 19, in <module>
import pandas as pd
File "/Users/valeriepineaunoel/mambaforge/envs/sleap/lib/python3.9/site-packages/pandas/__init__.py", line 31, in <module>
raise ImportError(
ImportError: C extension: None not built. If you want to import pandas from the source directory, you may need to run 'python setup.py build_ext' to build the C extensions first.
Running python setup.py build_ext gives me
python: can't open file '/Users/valeriepineaunoel/Documents/PhD/AutomaticBehaviourAnalysis/setup.py': [Errno 2] No such file or directory
Running sleap-label gives me the same error.
I followed the instructions under If you are on Linux, have a NVIDIA GPU, but cannot detect your GPU: in the documentation for SLEAP installation, but I get the same errors.
Your personal set up
I followed the pre-installation for M1 steps, next the installing mambaforge section and finally the conda package section. For some reason, I am not able to activate the SLEAP environment with mamba activate sleap (I have the error Run 'mamba init' to be able to run mamba activate/deactivate and start a new shell session. Or use conda to activate/deactivate., and these instructions do not work), but it is working with conda activate sleap.
- OS:
- Version(s):
- SLEAP installation method (listed here):
- [X] Conda from package
- [ ] Conda from source
- [ ] pip package
- [X] Apple Silicon Macs
Environment packages
# paste output of `pip freeze` or `conda list` here
absl-py==0.15.0 aiohappyeyeballs @ file:///home/conda/feedstock_root/build_artifacts/aiohappyeyeballs_1727779797566/work aiohttp @ file:///Users/runner/miniforge3/conda-bld/aiohttp_1728629000337/work aiosignal @ file:///home/conda/feedstock_root/build_artifacts/aiosignal_1667935791922/work astunparse @ file:///home/conda/feedstock_root/build_artifacts/astunparse_1728923142236/work async-timeout @ file:///home/conda/feedstock_root/build_artifacts/async-timeout_1691763562544/work attrs==23.1.0 blinker @ file:///home/conda/feedstock_root/build_artifacts/blinker_1715091184126/work Brotli @ file:///Users/runner/miniforge3/conda-bld/brotli-split_1687884187023/work cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work cachetools==4.2.4 cattrs @ file:///home/conda/feedstock_root/build_artifacts/cattrs_1604136207372/work certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1725278078093/work/certifi cffi @ file:///Users/runner/miniforge3/conda-bld/cffi_1725560567968/work charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1728479282467/work clang==5.0 click @ file:///home/conda/feedstock_root/build_artifacts/click_1692311806742/work contourpy @ file:///Users/runner/miniforge3/conda-bld/contourpy_1712429956050/work cryptography @ file:///Users/runner/miniforge3/conda-bld/cryptography-split_1672672491497/work cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work efficientnet==1.0.0 flatbuffers @ file:///home/conda/feedstock_root/build_artifacts/python-flatbuffers_1617723079010/work fonttools @ file:///Users/runner/miniforge3/conda-bld/fonttools_1729530356476/work frozenlist @ file:///Users/runner/miniforge3/conda-bld/frozenlist_1725395664823/work gast @ file:///home/conda/feedstock_root/build_artifacts/gast_1596839682936/work google-auth==1.35.0 google-auth-oauthlib @ file:///home/conda/feedstock_root/build_artifacts/google-auth-oauthlib_1630497468950/work google-pasta @ file:///home/conda/feedstock_root/build_artifacts/google-pasta_1722873999312/work grpcio @ file:///Users/runner/miniforge3/conda-bld/grpc-split_1660349735869/work h2 @ file:///home/conda/feedstock_root/build_artifacts/h2_1634280454336/work h5py==3.1.0 hdmf==3.9.0 hpack==4.0.0 hyperframe @ file:///home/conda/feedstock_root/build_artifacts/hyperframe_1619110129307/work idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1726459485162/work image-classifiers==1.0.0 imagecodecs @ file:///Users/runner/miniforge3/conda-bld/imagecodecs_1668867656682/work imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1729190692267/work imgaug @ file:///home/conda/feedstock_root/build_artifacts/imgaug_1640909786103/work imgstore==0.2.9 importlib_metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1726082825846/work importlib_resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1725921340658/work joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1714665484399/work jsmin @ file:///home/conda/feedstock_root/build_artifacts/jsmin_1642532731678/work jsonpickle==1.2 jsonschema==4.19.0 jsonschema-specifications==2023.7.1 keras==2.6.0 Keras-Applications==1.0.8 Keras-Preprocessing @ file:///home/conda/feedstock_root/build_artifacts/keras-preprocessing_1610713559828/work kiwisolver @ file:///Users/runner/miniforge3/conda-bld/kiwisolver_1725459195356/work lazy_loader @ file:///home/conda/feedstock_root/build_artifacts/lazy-loader_1723774329602/work Markdown @ file:///home/conda/feedstock_root/build_artifacts/markdown_1710435156458/work markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1686175045316/work MarkupSafe @ file:///Users/runner/miniforge3/conda-bld/markupsafe_1729351318299/work matplotlib @ file:///Users/runner/miniforge3/conda-bld/matplotlib-suite_1715976186715/work mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1704317613764/work multidict @ file:///Users/runner/miniforge3/conda-bld/multidict_1729065493631/work munkres==1.1.4 ndx-pose==0.1.1 networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1698504735452/work nixio==1.5.3 numpy==1.19.5 oauthlib @ file:///home/conda/feedstock_root/build_artifacts/oauthlib_1666056362788/work opencv-python==4.6.0 opt-einsum==3.3.0 packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1718189413536/work pandas @ file:///Users/runner/miniforge3/conda-bld/pandas_1726878426767/work patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1704469236901/work Pillow @ file:///Users/runner/miniforge3/conda-bld/pillow_1666920647802/work propcache @ file:///Users/runner/miniforge3/conda-bld/propcache_1728545746686/work protobuf==3.20.3 psutil @ file:///Users/runner/miniforge3/conda-bld/psutil_1728965164785/work pyasn1 @ file:///home/conda/feedstock_root/build_artifacts/pyasn1_1726839225972/work pyasn1_modules @ file:///home/conda/feedstock_root/build_artifacts/pyasn1-modules_1726029546107/work pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1711811537435/work Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1714846767233/work PyJWT @ file:///home/conda/feedstock_root/build_artifacts/pyjwt_1722701264352/work pykalman @ file:///home/conda/feedstock_root/build_artifacts/pykalman_1711547707628/work pynwb==2.5.0 pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1685514481738/work pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1728880423364/work PySide2==5.15.8 PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1709299778482/work python-rapidjson @ file:///Users/runner/miniforge3/conda-bld/python-rapidjson_1722901885195/work pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1706886791323/work pyu2f @ file:///home/conda/feedstock_root/build_artifacts/pyu2f_1604248910016/work PyWavelets==1.6.0 PyYAML @ file:///Users/runner/miniforge3/conda-bld/pyyaml_1725456176118/work pyzmq @ file:///Users/runner/miniforge3/conda-bld/pyzmq_1724399128390/work qimage2ndarray==1.10.0 QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1698112029416/work referencing==0.30.2 requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1717057054362/work requests-oauthlib @ file:///home/conda/feedstock_root/build_artifacts/requests-oauthlib_1711290127547/work rich @ file:///home/conda/feedstock_root/build_artifacts/rich_1728057819683/work/dist rpds-py==0.10.3 rsa @ file:///home/conda/feedstock_root/build_artifacts/rsa_1658328885051/work ruamel.yaml==0.17.32 ruamel.yaml.clib==0.2.7 scikit-image @ file:///Users/runner/miniforge3/conda-bld/scikit-image_1719499435765/work/dist/scikit_image-0.24.0-cp39-cp39-macosx_10_13_x86_64.whl#sha256=dc1cb9c710a4541be80ed6d8503634ad2ba466ccd9a3abe9d2e6617fe07dc874 scikit-learn @ file:///Users/runner/miniforge3/conda-bld/scikit-learn_1632611470401/work scikit-video==1.1.11 scipy==1.9.0 seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1714494649443/work segmentation-models==1.0.1 shapely @ file:///Users/runner/miniforge3/conda-bld/shapely_1727273432006/work shiboken2==5.15.8 six==1.15.0 sleap==1.3.3 statsmodels @ file:///Users/runner/miniforge3/conda-bld/statsmodels_1727986739068/work tensorboard==2.6.0 tensorboard-data-server @ file:///Users/runner/miniforge3/conda-bld/tensorboard-data-server_1670043848285/work/tensorboard_data_server-0.6.1-py3-none-macosx_10_9_x86_64.whl tensorboard-plugin-wit @ file:///home/conda/feedstock_root/build_artifacts/tensorboard-plugin-wit_1641458951060/work/tensorboard_plugin_wit-1.8.1-py3-none-any.whl tensorflow==2.6.3 tensorflow-estimator==2.6.0 tensorflow-hub @ file:///home/conda/feedstock_root/build_artifacts/tensorflow-hub_1618768305670/work/wheel_dir/tensorflow_hub-0.12.0-py2.py3-none-any.whl termcolor==1.1.0 threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1714400101435/work tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1665588749940/work typing-extensions==3.10.0.2 tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1727140567071/work tzlocal==5.0.1 unicodedata2 @ file:///Users/runner/miniforge3/conda-bld/unicodedata2_1695848049988/work urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1726496430923/work Werkzeug @ file:///home/conda/feedstock_root/build_artifacts/werkzeug_1724330738730/work wrapt==1.12.1 yarl @ file:///Users/runner/miniforge3/conda-bld/yarl_1729423571118/work zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1726248574750/work zstandard==0.23.0
Logs
# paste relevant logs here, if any
Screenshots
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