Cannot detect GPUs - ImportError: C extension: None not built

[ValeriePineauNoel]

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:

MacOS 14.4

• Version(s):

• SLEAP installation method (listed here):
  • Conda from package
  • Conda from source
  • pip package
  • 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

How to reproduce

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3. Scroll down to '....'
4. See error

[eberrigan]

Hi @ValeriePineauNoel,

Do you have an M1 Apple Silicon Mac?

Thanks,

Elizabeth

[ValeriePineauNoel]

Hi Elizabeth,

Yes I do!

[eberrigan]

Ok I think you might have mixed up a few steps. You have an Apple Silicon M1 so you just want to follow Apple Silicon installation instructions (not Linux or pre-M1 instructions).

I am not sure if your miniforge3 was installed correctly. You can follow these instructions for MacOS arm64 / Apple Silicon to uninstall and reinstall miniforge3. https://github.com/conda-forge/miniforge#mambaforge

Then you will want to remove the environment you made previously:

mamba env remove --name sleap

clean your cache:

mamba clean --all

and reinstall sleap for Apple Silicon:

mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.3

[ValeriePineauNoel]

Oh I see! I followed your steps and now I can open the GUI and I can detect a GPU. Thank you so much for you help! :)