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talmolab / sleap

A deep learning framework for multi-animal pose tracking.
https://sleap.ai
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Failure to Start GUI #1476

Closed Nike-Nay closed 1 year ago

Nike-Nay commented 1 year ago

Bug description

I have installed sleap using mambaforge and installed it via the 'conda package' instructions at https://sleap.ai/installation.html I believe everything is installed correctly as I can activate sleap in the terminal. However, when I attempt to load up the GUI using 'sleap-label' it returns the following: FileNotFoundError: [Errno 2] No such file or directory: 'c:\users\asus\mambaforge\envs\sleap\lib\site-packages\tensorflow_estimator-2.6.0.dist-info\METADATA'

I am not sure why there is no METADATA file. Is this an issue with the downloaded package or an issue on my system?

Expected behaviour

Actual behaviour

Your personal set up

Environment packages ``` # paste output of `pip freeze` or `conda list` here (sleap) C:\Users\asus>sleap-label Traceback (most recent call last): File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 573, in _build_master ws.require(__requires__) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 891, in require needed = self.resolve(parse_requirements(requirements)) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 782, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (importlib-metadata 4.13.0 (c:\users\asus\mambaforge\envs\sleap\lib\site-packages), Requirement.parse('importlib-metadata<4.3; python_version < "3.8"'), {'hdmf'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3031, in _dep_map return self.__dep_map File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 2828, in __getattr__ raise AttributeError(attr) AttributeError: _DistInfoDistribution__dep_map During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3022, in _parsed_pkg_info return self._pkg_info File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 2828, in __getattr__ raise AttributeError(attr) AttributeError: _pkg_info During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-label-script.py", line 33, in sys.exit(load_entry_point('sleap==1.3.1', 'console_scripts', 'sleap-label')()) File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-label-script.py", line 25, in importlib_load_entry_point return next(matches).load() File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\importlib_metadata\__init__.py", line 207, in load module = import_module(match.group('module')) File "C:\Users\asus\mambaforge\envs\sleap\lib\importlib\__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 953, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 953, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 677, in _load_unlocked File "", line 728, in exec_module File "", line 219, in _call_with_frames_removed File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\__init__.py", line 10, in from sleap.io.dataset import Labels, load_file File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\dataset.py", line 71, in from sleap.instance import ( File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\instance.py", line 32, in from sleap.io.video import Video File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\video.py", line 17, in from sleap.util import json_loads, json_dumps File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\util.py", line 22, in from pkg_resources import Requirement, resource_filename File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3266, in @_call_aside File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3241, in _call_aside f(*args, **kwargs) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3279, in _initialize_master_working_set working_set = WorkingSet._build_master() File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 575, in _build_master return cls._build_from_requirements(__requires__) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 588, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 785, in resolve new_requirements = dist.requires(req.extras)[::-1] File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 2749, in requires dm = self._dep_map File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3033, in _dep_map self.__dep_map = self._compute_dependencies() File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3042, in _compute_dependencies for req in self._parsed_pkg_info.get_all('Requires-Dist') or []: File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3024, in _parsed_pkg_info metadata = self.get_metadata(self.PKG_INFO) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 1412, in get_metadata value = self._get(path) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 1616, in _get with open(path, 'rb') as stream: FileNotFoundError: [Errno 2] No such file or directory: 'c:\\users\\asus\\mambaforge\\envs\\sleap\\lib\\site-packages\\tensorflow_estimator-2.6.0.dist-info\\METADATA' ```
Logs ``` (sleap) C:\Users\asus>sleap-diagnostic Traceback (most recent call last): File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 573, in _build_master ws.require(__requires__) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 891, in require needed = self.resolve(parse_requirements(requirements)) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 782, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (importlib-metadata 4.13.0 (c:\users\asus\mambaforge\envs\sleap\lib\site-packages), Requirement.parse('importlib-metadata<4.3; python_version < "3.8"'), {'hdmf'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-diagnostic-script.py", line 33, in sys.exit(load_entry_point('sleap==1.3.1', 'console_scripts', 'sleap-diagnostic')()) File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-diagnostic-script.py", line 25, in importlib_load_entry_point return next(matches).load() File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\importlib_metadata\__init__.py", line 207, in load module = import_module(match.group('module')) File "C:\Users\asus\mambaforge\envs\sleap\lib\importlib\__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 953, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 967, in _find_and_load_unlocked File "", line 677, in _load_unlocked File "", line 728, in exec_module File "", line 219, in _call_with_frames_removed File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\__init__.py", line 10, in from sleap.io.dataset import Labels, load_file File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\dataset.py", line 71, in from sleap.instance import ( File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\instance.py", line 32, in from sleap.io.video import Video File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\video.py", line 17, in from sleap.util import json_loads, json_dumps File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\util.py", line 22, in from pkg_resources import Requirement, resource_filename File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3266, in @_call_aside File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3241, in _call_aside f(*args, **kwargs) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3279, in _initialize_master_working_set working_set = WorkingSet._build_master() File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 575, in _build_master return cls._build_from_requirements(__requires__) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 588, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 782, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (numpy 1.21.6 (c:\users\asus\mambaforge\envs\sleap\lib\site-packages), Requirement.parse('numpy~=1.19.2'), {'six'}) ```

Screenshots

How to reproduce

  1. conda activate sleap
  2. sleap-label
roomrys commented 1 year ago

Hi @Nike-Nay,

From reading through some of the linked issues below, it seems this is an error with a failed pip install during the SLEAP installation process. Thanks for sending the output of sleap-label and sleap-diagnostic. Are you able to also send the packages that were installed (pip freeze and mamba list while in your SLEAP environment).

I'm linking some related issues here:

Thanks, Liezl

Nike-Nay commented 1 year ago

Hi Liezl, thanks for the quick response. I have added the output for both pip freeze and mamba list here:

pip freeze

(sleap) C:\Users\asus>pip freeze
WARNING: No metadata found in c:\users\asus\mambaforge\envs\sleap\lib\site-packages
absl-py==0.15.0
astunparse==1.6.3
attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1640799537051/work
backports.zoneinfo==0.2.1
cached-property==1.5.2
cachetools==4.2.4
cattrs @ file:///home/conda/feedstock_root/build_artifacts/cattrs_1604136207372/work
certifi==2023.7.22
charset-normalizer==2.0.9
clang==5.0
cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1674202310934/work
cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work
cytoolz @ file:///D:/bld/cytoolz_1657553564801/work
dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1644602974678/work
efficientnet==1.0.0
flatbuffers==1.12
fonttools @ file:///D:/bld/fonttools_1666390069478/work
fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1674184942191/work
gast==0.4.0
google-auth==1.35.0
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
grpcio==1.43.0
h5py==3.1.0
hdmf==3.6.1
idna==3.3
image-classifiers==1.0.0
imagecodecs @ file:///D:/bld/imagecodecs_1644819718476/work
imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1686552404404/work
imgaug @ file:///home/conda/feedstock_root/build_artifacts/imgaug_1640909786103/work
imgstore==0.2.9
importlib-metadata==4.13.0
importlib-resources==5.12.0
joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1691577114857/work
jsmin @ file:///home/conda/feedstock_root/build_artifacts/jsmin_1642532731678/work
jsonpickle==1.2
jsonschema==4.17.3
keras==2.6.0
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.2
kiwisolver @ file:///D:/bld/kiwisolver_1657953189205/work
libclang==12.0.0
locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work
Markdown==3.3.6
markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1677100944732/work
matplotlib @ file:///D:/bld/matplotlib-suite_1661439973878/work
mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1639515908913/work
munkres==1.1.4
ndx-pose==0.1.1
networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1635253012265/work
nixio==1.5.3
numpy==1.19.2
oauthlib==3.1.1
opencv-python-headless==4.2.0.34
opt-einsum==3.3.0
packaging==21.3
pandas @ file:///D:/bld/pandas_1639398349358/work
partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1681246756246/work
patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1665356157073/work
Pillow @ file:///D:/bld/pillow_1660386017560/work
pkgutil_resolve_name==1.3.10
protobuf==3.19.1
psutil @ file:///D:/bld/psutil_1666155596250/work
pyasn1==0.4.8
pyasn1-modules==0.2.8
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1691408637400/work
pykalman==0.9.5
pynwb==2.3.3
pyparsing==3.0.6
pyrsistent==0.19.3
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work
python-rapidjson @ file:///D:/bld/python-rapidjson_1666000124084/work
pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1680088766131/work
PyWavelets @ file:///D:/bld/pywavelets_1649616556601/work
PyYAML @ file:///D:/bld/pyyaml_1648757357341/work
pyzmq @ file:///D:/bld/pyzmq_1663830622471/work
qimage2ndarray==1.10.0
QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1693347765905/work
requests==2.26.0
requests-oauthlib==1.3.0
rich @ file:///home/conda/feedstock_root/build_artifacts/rich-split_1690807641695/work/dist
rsa==4.8
ruamel.yaml==0.17.32
ruamel.yaml.clib==0.2.7
scikit-image @ file:///D:/bld/scikit-image_1660146603458/work
scikit-learn @ file:///D:/bld/scikit-learn_1632611530541/work
scikit-video==1.1.11
scipy @ file:///C:/bld/scipy_1637806996411/work
seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1672497695270/work
segmentation-models==1.0.1
setuptools-scm==6.3.2
Shapely==1.8.5
six==1.15.0
sleap==1.3.1
statsmodels @ file:///D:/bld/statsmodels_1654787262041/work
tensorboard==2.6.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
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
tensorflow-io-gcs-filesystem==0.23.1
termcolor==1.1.0
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1643647933166/work
tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1635944860688/work
tomli==2.0.0
toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work
typing-extensions==3.10.0.2
tzdata==2023.3
tzlocal==5.0.1
unicodedata2 @ file:///D:/bld/unicodedata2_1649112131705/work
urllib3==1.26.7
Werkzeug==2.0.2
wrapt==1.12.1
zipp==3.15.0

mamba list

(sleap) C:\Users\asus>mamba list
# packages in environment at C:\Users\asus\mambaforge\envs\sleap:
#
# Name                    Version                   Build  Channel
absl-py                   0.15.0                   pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
backports-zoneinfo        0.2.1                    pypi_0    pypi
blosc                     1.21.5               hdccc3a2_0    conda-forge
brotli                    1.0.9                hcfcfb64_9    conda-forge
brotli-bin                1.0.9                hcfcfb64_9    conda-forge
bzip2                     1.0.8                h8ffe710_4    conda-forge
c-blosc2                  2.10.2               h183a6f4_0    conda-forge
ca-certificates           2023.7.22            h56e8100_0    conda-forge
cached-property           1.5.2                    pypi_0    pypi
cachetools                4.2.4                    pypi_0    pypi
cattrs                    1.1.1              pyhd8ed1ab_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cfitsio                   4.0.0                hd67004f_0    conda-forge
charls                    2.3.4                h39d44d4_0    conda-forge
charset-normalizer        2.0.9                    pypi_0    pypi
clang                     5.0                      pypi_0    pypi
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
cuda-nvcc                 11.3.58              hb8d16a4_0    nvidia
cudatoolkit               11.3.1              hf2f0253_12    conda-forge
cudnn                     8.2.1.32             h754d62a_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py37hcc03f2d_0    conda-forge
dask-core                 2022.2.0           pyhd8ed1ab_0    conda-forge
efficientnet              1.0.0                    pypi_0    pypi
flatbuffers               1.12                     pypi_0    pypi
fonttools                 4.38.0           py37h51bd9d9_0    conda-forge
freeglut                  3.2.2                h63175ca_2    conda-forge
freetype                  2.12.1               h546665d_1    conda-forge
fsspec                    2023.1.0           pyhd8ed1ab_0    conda-forge
gast                      0.4.0                    pypi_0    pypi
geos                      3.11.0               h39d44d4_0    conda-forge
giflib                    5.2.1                h64bf75a_3    conda-forge
google-auth               1.35.0                   pypi_0    pypi
google-auth-oauthlib      0.4.6                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
grpcio                    1.43.0                   pypi_0    pypi
h5py                      3.1.0                    pypi_0    pypi
hdmf                      3.6.1                    pypi_0    pypi
icu                       69.1                 h0e60522_0    conda-forge
idna                      3.3                      pypi_0    pypi
image-classifiers         1.0.0                    pypi_0    pypi
imagecodecs               2021.11.20       py37hfea8715_2    conda-forge
imageio                   2.31.1             pyh24c5eb1_0    conda-forge
imgaug                    0.4.0              pyhd8ed1ab_1    conda-forge
imgstore                  0.2.9                    pypi_0    pypi
importlib-metadata        4.13.0                   pypi_0    pypi
importlib-resources       5.12.0                   pypi_0    pypi
intel-openmp              2023.2.0         h57928b3_49496    conda-forge
jasper                    2.0.33               hc2e4405_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hcfcfb64_3    conda-forge
jsmin                     3.0.1              pyhd8ed1ab_0    conda-forge
jsonpickle                1.2                        py_0    conda-forge
jsonschema                4.17.3                   pypi_0    pypi
jxrlib                    1.1                  h8ffe710_2    conda-forge
keras                     2.6.0                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.4.4            py37h8c56517_0    conda-forge
krb5                      1.20.1               h6609f42_0    conda-forge
lcms2                     2.14                 h90d422f_0    conda-forge
lerc                      3.0                  h0e60522_0    conda-forge
libaec                    1.0.6                h63175ca_1    conda-forge
libblas                   3.9.0              17_win64_mkl    conda-forge
libbrotlicommon           1.0.9                hcfcfb64_9    conda-forge
libbrotlidec              1.0.9                hcfcfb64_9    conda-forge
libbrotlienc              1.0.9                hcfcfb64_9    conda-forge
libcblas                  3.9.0              17_win64_mkl    conda-forge
libclang                  12.0.0                   pypi_0    pypi
libcurl                   8.1.2                h68f0423_0    conda-forge
libdeflate                1.10                 h8ffe710_0    conda-forge
libhwloc                  2.9.1                h51c2c0f_0    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
liblapack                 3.9.0              17_win64_mkl    conda-forge
liblapacke                3.9.0              17_win64_mkl    conda-forge
libopencv                 4.5.1            py37ha0199f4_0    conda-forge
libpng                    1.6.39               h19919ed_0    conda-forge
libprotobuf               3.21.8               h12be248_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.43.0               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h680486a_3    conda-forge
libtiff                   4.4.0                hc4061b1_0    conda-forge
libwebp-base              1.3.1                hcfcfb64_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.10.4               hc3477c8_0    conda-forge
libxslt                   1.1.37               h0192164_0    conda-forge
libzlib                   1.2.13               hcfcfb64_5    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lz4-c                     1.9.3                h8ffe710_1    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
markdown                  3.3.6                    pypi_0    pypi
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
matplotlib-base           3.5.3            py37hbaab90a_2    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ndx-pose                  0.1.1                    pypi_0    pypi
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
nixio                     1.5.3                    pypi_0    pypi
numpy                     1.19.2                   pypi_0    pypi
oauthlib                  3.1.1                    pypi_0    pypi
opencv                    4.5.1            py37h03978a9_0    conda-forge
opencv-python-headless    4.2.0.34                 pypi_0    pypi
openjpeg                  2.5.0                hc9384bd_1    conda-forge
openssl                   1.1.1v               hcfcfb64_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 21.3                     pypi_0    pypi
pandas                    1.3.5            py37h9386db6_0    conda-forge
partd                     1.4.0              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pillow                    9.2.0            py37h42a8222_2    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10                   pypi_0    pypi
protobuf                  3.19.1                   pypi_0    pypi
psutil                    5.9.3            py37h51bd9d9_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
py-opencv                 4.5.1            py37heaed05f_0    conda-forge
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.8                    pypi_0    pypi
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pykalman                  0.9.5                      py_1    conda-forge
pynwb                     2.3.3                    pypi_0    pypi
pyparsing                 3.0.6                    pypi_0    pypi
pyrsistent                0.19.3                   pypi_0    pypi
pyside2                   5.13.2           py37h760f651_8    conda-forge
python                    3.7.12          h7840368_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-rapidjson          1.9              py37h7f67f24_0    conda-forge
python_abi                3.7                     3_cp37m    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pywavelets                1.3.0            py37h3a130e4_1    conda-forge
pyyaml                    6.0              py37hcc03f2d_4    conda-forge
pyzmq                     24.0.1           py37h7347f05_0    conda-forge
qimage2ndarray            1.10.0                   pypi_0    pypi
qt                        5.12.9               h556501e_6    conda-forge
qtpy                      2.4.0              pyhd8ed1ab_0    conda-forge
requests                  2.26.0                   pypi_0    pypi
requests-oauthlib         1.3.0                    pypi_0    pypi
rich                      13.5.1             pyhd8ed1ab_0    conda-forge
ruamel-yaml               0.17.32                  pypi_0    pypi
ruamel-yaml-clib          0.2.7                    pypi_0    pypi
scikit-image              0.19.3           py37h3182a2c_1    conda-forge
scikit-learn              1.0              py37ha78be43_1    conda-forge
scikit-video              1.1.11             pyh24bf2e0_0    conda-forge
scipy                     1.7.3            py37hb6553fb_0    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
segmentation-models       1.0.1                    pypi_0    pypi
setuptools                59.8.0           py37h03978a9_1    conda-forge
setuptools-scm            6.3.2                    pypi_0    pypi
shapely                   1.8.5            py37h475e9a0_0    conda-forge
six                       1.15.0                   pypi_0    pypi
sleap                     1.3.1                    pypi_0    pypi
snappy                    1.1.10               hfb803bf_0    conda-forge
sqlite                    3.43.0               hcfcfb64_0    conda-forge
statsmodels               0.13.2           py37h3a130e4_0    conda-forge
tbb                       2021.9.0             h91493d7_0    conda-forge
tensorboard               2.6.0                    pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-wit    1.8.0                    pypi_0    pypi
tensorflow                2.6.3                    pypi_0    pypi
tensorflow-hub            0.12.0             pyhca92ed8_0    conda-forge
tensorflow-io-gcs-filesystem 0.23.1                   pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2021.11.2          pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h8ffe710_0    conda-forge
tomli                     2.0.0                    pypi_0    pypi
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
typing-extensions         3.10.0.2                 pypi_0    pypi
typing_extensions         4.7.1              pyha770c72_0    conda-forge
tzdata                    2023.3                   pypi_0    pypi
tzlocal                   5.0.1                    pypi_0    pypi
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
unicodedata2              14.0.0           py37hcc03f2d_1    conda-forge
urllib3                   1.26.7                   pypi_0    pypi
vc                        14.3                h64f974e_17    conda-forge
vc14_runtime              14.36.32532         hfdfe4a8_17    conda-forge
vs2015_runtime            14.36.32532         h05e6639_17    conda-forge
werkzeug                  2.0.2                    pypi_0    pypi
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
wrapt                     1.12.1                   pypi_0    pypi
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zfp                       0.5.5                h0e60522_8    conda-forge
zipp                      3.15.0                   pypi_0    pypi
zlib                      1.2.13               hcfcfb64_5    conda-forge
zlib-ng                   2.0.7                hcfcfb64_0    conda-forge
zstd                      1.5.5                h12be248_0    conda-forge
rgough5 commented 1 year ago

I see you have tensorflow version 2.6.3. After the conda install, did you downgrade tensorflow via pip? I believe the issue is due to issues with dependency management between conda and pip. My solution was to install SLEAP via pip and then downgrade tf. This resulted in both the GPU being detected by tf and the gui loading.

roomrys commented 1 year ago

Hi @rgough5,

Did you have a similar problem with the conda package? On Windows as well?

@Nike-Nay we released a new package and I am wondering if this would bypass your problem?

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2

If it does end up in a failure, would you mind posting the output of the installation command and the sleap-label command.

Thanks, Liezl

rgough5 commented 1 year ago

@roomrys I had a similar issue on SLEAP v1.3.2 although on Fedora Linux. I tried installing with conda from both the package and source, but in both cases tensorflow could not detect our GPU (NVIDIA GeForce RTX 4090). Downgrading tensorflow via pip did allow for the GPU to be detected, but the GUI would not open with sleap-label. I tried downgrading with conda to tensorflow 2.6.2, but it was unable resolve the environment.

talmo commented 1 year ago

Hi @rgough5,

Could you try:

  1. Start fresh: mamba env remove -n sleap
  2. Create a SLEAP conda environment: mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2
  3. Reinstall tensorflow via pip: pip install --upgrade --no-deps tensorflow==2.6.2

You could also try the same method but with tensorflow==2.7.0 in the last step.

Let us know what you get!

Cheers,

Talmo

rgough5 commented 1 year ago

@talmo

Unforunately, it did not work. I did get a different error

File "/home/redacted/Miniconda3/envs/sleap/lib/python3.7/site-packages/tensorflow/python/eager/monitoring.py", line 135, in __init__
    self._metric = self._metric_methods[self._label_length].create(*args)
tensorflow.python.framework.errors_impl.AlreadyExistsError: Another metric with the same name already exists.

as opposed to the previous error when I just used pip install tensorflow==2.6.3

  File "/home/redacted/Miniconda3/envs/sleap1/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1616, in _get
    with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: '/home/redacted/Miniconda3/envs/sleap1/lib/python3.7/site-packages/six-1.16.0.dist-info/METADATA'

If it helps, when I downgrade using the second method I get the warning

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
rich 13.5.1 requires typing-extensions<5.0,>=4.0.0; python_version < "3.9", but you have typing-extensions 3.10.0.2 which is incompatible.
tensorflow-hub 0.13.0 requires protobuf>=3.19.6, but you have protobuf 3.16.0 which is incompatible.

Which is why I switched to installing everything via pip. Installing with pip came with it's own set of issues, but it didn't take too much effort to get it working from there.

roomrys commented 1 year ago

Linux-5.15.0-78-generic-x86_64-with-debian-bookworm-sid

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2

sleap-label GUI launches, but does not auto-detect anaconda

(sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ sleap-label
2023-09-12 10:09:46.962824: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2023-09-12 10:09:46.962865: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml
Restoring GUI state...
2023-09-12 10:09:50.526712: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2023-09-12 10:09:50.527690: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527752: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcublas.so.11'; dlerror: libcublas.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527793: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcublasLt.so.11'; dlerror: libcublasLt.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527830: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcufft.so.10'; dlerror: libcufft.so.10: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527867: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcurand.so.10'; dlerror: libcurand.so.10: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527904: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcusolver.so.11'; dlerror: libcusolver.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527941: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcusparse.so.11'; dlerror: libcusparse.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527978: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527984: W tensorflow/core/common_runtime/gpu/gpu_device.cc:1850] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.
Skipping registering GPU devices...

Software versions:
SLEAP: 1.3.2
TensorFlow: 2.7.0
Numpy: 1.19.5
Python: 3.7.12
OS: Linux-5.15.0-78-generic-x86_64-with-debian-bookworm-sid

Happy SLEAPing! :)
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml

Setting LD_LIBRARY_PATH and then running sleap-label detects GPU

We can run the following commands to set the LD_LIBRARY_PATH environment variable upon activating our environment. These commands will be run each time we activate our environment, so no need to always run them - just once is fine! Make sure you are in the environment you want GPUs to be found (i.e. sleap for our use case)! We can build an activate script into our recipe for #1484 so users don't need to do this manually. This is related to #1390.

mkdir -p $CONDA_PREFIX/etc/conda/activate.d
echo '#!/bin/sh' >> $CONDA_PREFIX/etc/conda/activate.d/libcudart_activate.sh
echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH' >> $CONDA_PREFIX/etc/conda/activate.d/libcudart_activate.sh
source $CONDA_PREFIX/etc/conda/activate.d/libcudart_activate.sh
(sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ sleap-label
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml
Restoring GUI state...
2023-09-12 10:19:31.051975: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2023-09-12 10:19:31.081791: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2023-09-12 10:19:31.082752: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero

Software versions:
SLEAP: 1.3.2
TensorFlow: 2.7.0
Numpy: 1.19.5
Python: 3.7.12
OS: Linux-5.15.0-78-generic-x86_64-with-debian-bookworm-sid

Happy SLEAPing! :)
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml
conda dependencies ```bash (sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ mm list List of packages in environment: "/home/talmolab/micromamba/envs/sleap" Name Version Build Channel ──────────────────────────────────────────────────────────────────────── _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alsa-lib 1.2.3.2 h166bdaf_0 conda-forge attrs 21.4.0 pyhd8ed1ab_0 conda-forge blosc 1.21.5 h0f2a231_0 conda-forge brotli 1.0.9 h166bdaf_9 conda-forge brotli-bin 1.0.9 h166bdaf_9 conda-forge brunsli 0.1 h9c3ff4c_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_0 conda-forge c-blosc2 2.10.2 hb4ffafa_0 conda-forge ca-certificates 2023.7.22 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 h6cf1ce9_1008 conda-forge cattrs 1.1.1 pyhd8ed1ab_0 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cfitsio 4.0.0 h9a35b8e_0 conda-forge charls 2.3.4 h9c3ff4c_0 conda-forge cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge cuda-nvcc 11.3.58 h2467b9f_0 nvidia cudatoolkit 11.3.1 hb98b00a_12 conda-forge cudnn 8.2.1.32 h86fa8c9_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cytoolz 0.12.0 py37h540881e_0 conda-forge dask-core 2022.2.0 pyhd8ed1ab_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge expat 2.5.0 hcb278e6_1 conda-forge ffmpeg 4.3.2 h37c90e5_3 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonttools 4.38.0 py37h540881e_0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fsspec 2023.1.0 pyhd8ed1ab_0 conda-forge geos 3.11.0 h27087fc_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gnutls 3.6.13 h85f3911_1 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge gst-plugins-base 1.18.5 hf529b03_3 conda-forge gstreamer 1.18.5 h9f60fe5_3 conda-forge h5py 3.1.0 nompi_py37h1e651dc_100 conda-forge harfbuzz 2.9.1 h83ec7ef_1 conda-forge hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge icu 68.2 h9c3ff4c_0 conda-forge imagecodecs 2021.11.20 py37h119f88a_2 conda-forge imageio 2.31.1 pyh24c5eb1_0 conda-forge imgaug 0.4.0 pyhd8ed1ab_1 conda-forge jasper 1.900.1 h07fcdf6_1006 conda-forge joblib 1.3.2 pyhd8ed1ab_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge jsmin 3.0.1 pyhd8ed1ab_0 conda-forge jsonpickle 1.2 py_0 conda-forge jxrlib 1.1 h7f98852_2 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py37h7cecad7_0 conda-forge krb5 1.19.3 h3790be6_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lcms2 2.14 h6ed2654_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 3.0 h9c3ff4c_0 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libblas 3.9.0 18_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_9 conda-forge libbrotlidec 1.0.9 h166bdaf_9 conda-forge libbrotlienc 1.0.9 h166bdaf_9 conda-forge libcblas 3.9.0 18_linux64_openblas conda-forge libclang 11.1.0 default_ha53f305_1 conda-forge libcurl 7.86.0 h7bff187_1 conda-forge libdeflate 1.10 h7f98852_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 h9b69904_4 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_0 conda-forge libgfortran-ng 13.2.0 h69a702a_0 conda-forge libgfortran5 13.2.0 ha4646dd_0 conda-forge libglib 2.78.0 hebfc3b9_0 conda-forge libgomp 13.2.0 h807b86a_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 18_linux64_openblas conda-forge liblapacke 3.9.0 18_linux64_openblas conda-forge libllvm11 11.1.0 he0ac6c6_5 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge libopencv 4.5.3 py37h25009ff_1 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 13.8 hd77ab85_0 conda-forge libprotobuf 3.16.0 h780b84a_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.43.0 h2797004_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 13.2.0 h7e041cc_0 conda-forge libtiff 4.4.0 h0fcbabc_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.3.1 hd590300_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.12 h72842e0_0 conda-forge libxslt 1.1.33 h15afd5d_2 conda-forge libzlib 1.2.13 hd590300_5 conda-forge libzopfli 1.0.3 h9c3ff4c_0 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge matplotlib-base 3.5.3 py37hf395dca_2 conda-forge mdurl 0.1.0 pyhd8ed1ab_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-common 8.0.32 h14678bc_0 conda-forge mysql-libs 8.0.32 h54cf53e_0 conda-forge ncurses 6.4 hcb278e6_0 conda-forge nettle 3.6 he412f7d_0 conda-forge networkx 2.7 pyhd8ed1ab_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.92 h1d7d5a4_0 conda-forge numpy 1.21.6 py37h976b520_0 conda-forge opencv 4.5.3 py37h89c1867_1 conda-forge openh264 2.1.1 h780b84a_0 conda-forge openjpeg 2.5.0 h7d73246_1 conda-forge openssl 1.1.1w hd590300_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 1.3.5 py37he8f5f7f_0 conda-forge partd 1.4.0 pyhd8ed1ab_0 conda-forge patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge pillow 9.2.0 py37h850a105_2 conda-forge pip 23.2.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge protobuf 3.16.0 py37hcd2ae1e_0 conda-forge psutil 5.9.3 py37h540881e_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge py-opencv 4.5.3 py37h6531663_1 conda-forge pygments 2.16.1 pyhd8ed1ab_0 conda-forge pykalman 0.9.5 py_1 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pyside2 5.13.2 py37hfa98aef_7 conda-forge python 3.7.12 hb7a2778_100_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-rapidjson 1.9 py37hd23a5d3_0 conda-forge python_abi 3.7 3_cp37m conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pywavelets 1.3.0 py37hda87dfa_1 conda-forge pyyaml 6.0 py37h540881e_4 conda-forge pyzmq 24.0.1 py37h0c0c2a8_0 conda-forge qt 5.12.9 hda022c4_4 conda-forge qtpy 2.4.0 pyhd8ed1ab_0 conda-forge readline 8.2 h8228510_1 conda-forge rich 13.5.1 pyhd8ed1ab_0 conda-forge scikit-image 0.19.2 py37he8f5f7f_0 conda-forge scikit-learn 1.0 py37hf0f1638_1 conda-forge scikit-video 1.1.11 pyh24bf2e0_0 conda-forge scipy 1.7.3 py37hf2a6cf1_0 conda-forge seaborn 0.12.2 hd8ed1ab_0 conda-forge seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge setuptools 59.8.0 py37h89c1867_1 conda-forge shapely 1.8.5 py37ha4e3bd1_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sleap 1.3.2 py37_1 sleap snappy 1.1.10 h9fff704_0 conda-forge sqlite 3.43.0 h2c6b66d_0 conda-forge statsmodels 0.13.2 py37hda87dfa_0 conda-forge tensorflow 2.7.0 py37hb93dfd8_3 sleap tensorflow-hub 0.13.0 pyh56297ac_0 conda-forge threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tifffile 2021.11.2 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.7.1 hd8ed1ab_0 conda-forge typing_extensions 4.7.1 pyha770c72_0 conda-forge unicodedata2 14.0.0 py37h540881e_1 conda-forge wheel 0.41.2 pyhd8ed1ab_0 conda-forge x264 1!161.3030 h7f98852_1 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zfp 0.5.5 h9c3ff4c_8 conda-forge zlib 1.2.13 hd590300_5 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge ```
pypi dependencies ```bash (sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ pip freeze absl-py==1.0.0 astunparse==1.6.3 attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1640799537051/work backports.zoneinfo==0.2.1 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==2023.7.22 charset-normalizer==2.0.9 cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1674202310934/work cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work cytoolz @ file:///home/conda/feedstock_root/build_artifacts/cytoolz_1657553457169/work dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1644602974678/work efficientnet==1.0.0 flatbuffers==2.0 fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1666389892786/work fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1674184942191/work gast==0.4.0 google-auth==2.3.3 google-auth-oauthlib==0.4.6 google-pasta==0.2.0 grpcio==1.43.0 h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1604753641401/work hdmf==3.6.1 idna==3.3 image-classifiers==1.0.0 imagecodecs @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs_1644819473370/work imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1686552404404/work imgaug @ file:///home/conda/feedstock_root/build_artifacts/imgaug_1640909786103/work imgstore==0.2.9 importlib-metadata==4.10.0 importlib-resources==5.12.0 joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1691577114857/work jsmin @ file:///home/conda/feedstock_root/build_artifacts/jsmin_1642532731678/work jsonpickle==1.2 jsonschema==4.17.3 keras==2.7.0 Keras-Applications==1.0.8 Keras-Preprocessing==1.1.2 kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1657953088445/work libclang==12.0.0 locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work Markdown==3.3.6 markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1677100944732/work matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1661439848456/work mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1639515908913/work munkres==1.1.4 ndx-pose==0.1.1 networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1646092782768/work nixio==1.5.3 numpy==1.19.5 oauthlib==3.1.1 opencv-python-headless==4.2.0.34 opt-einsum==3.3.0 packaging==21.3 pandas==1.3.5 partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1681246756246/work patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1665356157073/work Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1660385854171/work pkgutil_resolve_name==1.3.10 protobuf==3.16.0 psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1666155398032/work pyasn1==0.4.8 pyasn1-modules==0.2.8 Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1691408637400/work pykalman==0.9.5 pynwb==2.3.3 pyparsing==3.0.6 pyrsistent==0.19.3 PySide2==5.13.2 python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work python-rapidjson @ file:///home/conda/feedstock_root/build_artifacts/python-rapidjson_1665999896718/work pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1693930252784/work PyWavelets @ file:///home/conda/feedstock_root/build_artifacts/pywavelets_1649616401885/work PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1648757092905/work pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1663830492333/work qimage2ndarray==1.10.0 QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1693347765905/work requests==2.26.0 requests-oauthlib==1.3.0 rich @ file:///home/conda/feedstock_root/build_artifacts/rich-split_1690807641695/work/dist rsa==4.8 ruamel.yaml==0.17.32 ruamel.yaml.clib==0.2.7 scikit-image @ file:///home/conda/feedstock_root/build_artifacts/scikit-image_1645196656256/work scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1632611341839/work scikit-video==1.1.11 scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1637806658031/work seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1672497695270/work segmentation-models==1.0.1 setuptools-scm==6.3.2 Shapely @ file:///home/conda/feedstock_root/build_artifacts/shapely_1665624546039/work shiboken2==5.13.2 six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work sleap==1.3.2 statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1654787101575/work tensorboard==2.7.0 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.0 tensorflow==2.7.0 tensorflow-estimator==2.7.0 tensorflow-hub @ file:///home/conda/feedstock_root/build_artifacts/tensorflow-hub_1678880940235/work/wheel_dir/tensorflow_hub-0.13.0-py2.py3-none-any.whl tensorflow-io-gcs-filesystem==0.23.1 termcolor==1.1.0 threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1643647933166/work tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1635944860688/work tomli==2.0.0 toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work typing_extensions==4.0.1 tzlocal==5.0.1 unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1649111917568/work urllib3==1.26.7 Werkzeug==2.0.2 wrapt==1.13.3 zipp==3.15.0 ```
roomrys commented 1 year ago

Hi @Nike-Nay, @rgough5,

We released a new version at the end of last week which aimed to address the problems @rgough5 brought up and put restrictions on protobuf which seems to be used everywhere, so that could have also affected @Nike-Nay's problem as well. I am going to pre-emptively close this issue, but would feel more confident with some feedback on whether

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

is working for both of you?

The pip package has also been updated @rgough5.

Thanks! Liezl

rgough5 commented 1 year ago

@roomrys No issues here: one line install and SLEAP work with our GPUs! Thank you so much.