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sleap-train in the command line: python(90851,0x7ff855b867c0) malloc: *** error for object 0x6000069b04e4: pointer being freed was not allocated #2020

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ValeriePineauNoel opened this issue Nov 8, 2024 · 1 comment
Open
1 of 4 tasks

sleap-train in the command line: python(90851,0x7ff855b867c0) malloc: *** error for object 0x6000069b04e4: pointer being freed was not allocated #2020

ValeriePineauNoel opened this issue Nov 8, 2024 · 1 comment
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@ValeriePineauNoel
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Bug description

Following issue #2016 I tried to not use the GUI and use command lines to train SLEAP (bottom-up) and I have the same error.

[...]
2024-11-08 09:03:13.525725: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'Placeholder/_50' with dtype resource
	 [[{{node Placeholder/_50}}]]
2024-11-08 09:03:13.679564: I tensorflow/core/grappler/optimizers/custom_graph_optimizer_registry.cc:114] Plugin optimizer for device_type GPU is enabled.
python(90851,0x7ff855b867c0) malloc: *** error for object 0x6000069b04e4: pointer being freed was not allocated
python(90851,0x7ff855b867c0) malloc: *** set a breakpoint in malloc_error_break to debug
zsh: abort   sleap-train

Expected behaviour

Training works.

Actual behaviour

I installed sleap with

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

In the venv, I uninstalled tensorflow and installed it back for macos.

pip uninstall tensorflow
pip install tensorflow-macos
pip install tensorflow-metal

Running the command python -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))" returns a list with my GPU.

Your personal set up

  • OS: MacOS Pro 2019
  • Processor : 3.2 GHz 16-Core Intel Xeon W
  • Memory : 768 GB 2933 MHz DDR4
  • GPU : AMD Radeon Pro Vega II, 32 GB of VRAM
  • Version(s): SLEAP 1.3.3, python 3.9.15, tensorflow 2.12.0 (I actually installed tensorflow-metal to use my GPU), numpy 1.23.00 (I changed that to make all dependencies work)
Environment packages 
absl-py @ file:///home/conda/feedstock_root/build_artifacts/absl-py_1705494584803/work
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 @ file:///home/conda/feedstock_root/build_artifacts/cachetools_1724028158384/work
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
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==24.3.25
fonttools @ file:///Users/runner/miniforge3/conda-bld/fonttools_1729530356476/work
frozenlist @ file:///Users/runner/miniforge3/conda-bld/frozenlist_1729699486805/work
gast @ file:///home/conda/feedstock_root/build_artifacts/gast_1596839682936/work
google-auth @ file:///home/conda/feedstock_root/build_artifacts/google-auth_1730952254284/work
google-auth-oauthlib==1.0.0
google-pasta @ file:///home/conda/feedstock_root/build_artifacts/google-pasta_1722873999312/work
grpcio==1.67.1
h2 @ file:///home/conda/feedstock_root/build_artifacts/h2_1634280454336/work
h5py @ file:///Users/runner/miniforge3/conda-bld/h5py_1674499365073/work
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
jax==0.4.30
jaxlib==0.4.30
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==2.12.0
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
libclang==18.1.1
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
ml_dtypes==0.5.0
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==1.23.5
oauthlib @ file:///home/conda/feedstock_root/build_artifacts/oauthlib_1666056362788/work
opencv-python==4.6.0
opt_einsum @ file:///home/conda/feedstock_root/build_artifacts/opt_einsum_1727392354687/work
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_1729847081697/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_1730763764885/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_1730592237829/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 @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
sleap==1.3.3
statsmodels @ file:///Users/runner/miniforge3/conda-bld/statsmodels_1727986739068/work
tensorboard==2.12.3
tensorboard-data-server==0.7.2
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-estimator==2.12.0
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==0.37.1
tensorflow-macos==2.12.0
tensorflow-metal==1.0.0
termcolor @ file:///home/conda/feedstock_root/build_artifacts/termcolor_1728288976871/work
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1714400101435/work
tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1665588749940/work
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1717802530399/work
tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1727140567071/work
tzlocal==5.0.1
unicodedata2 @ file:///Users/runner/miniforge3/conda-bld/unicodedata2_1729704644728/work
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1726496430923/work
Werkzeug @ file:///home/conda/feedstock_root/build_artifacts/werkzeug_1730762638373/work
wrapt==1.14.1
yarl @ file:///Users/runner/miniforge3/conda-bld/yarl_1729798487102/work
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1726248574750/work
zstandard==0.23.0
Logs 
2024-11-08 10:04:23.349623: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.

==========SYSTEM==========

utc:			2024-11-08 15:04:26.037275
python:			3.9.15
system:			Darwin, x86_64, 23.3.0, Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64
path:			/Users/dcclab/miniforge3/envs/sleaptest/bin:/Users/dcclab/miniforge3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.10/bin:/usr/local/mysql/bin:/opt/anaconda3/bin:/opt/local/bin:/opt/local/sbin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/Apple/usr/bin

==========IMPORTS==========

sleap import:			True
sleap path:			/Users/dcclab/miniforge3/envs/sleaptest/lib/python3.9/site-packages/sleap/__init__.py
sleap version:			1.3.3
pyside2 import:			True
pyside path:			/Users/dcclab/miniforge3/envs/sleaptest/lib/python3.9/site-packages/PySide2/__init__.py
successfully created PySide2.QtWidgets.QApplication instance

pyside6 import:			False
cv2 import:			True

==========GIT==========

f511b8ca6db020b389933b8280c31193262a9b82

Valerie-Train-SLEAP-with-multanimal-bottom-up-(better-comparison-with-DeepLabCut)


==========TENSORFLOW==========

tensorflow import:			True
tensorflow version:			2.12.0
tensorflow path:			/Users/dcclab/miniforge3/envs/sleaptest/lib/python3.9/site-packages/tensorflow/__init__.py
gpus:			[PhysicalDevice(name='/physical_device:GPU:0', device_type='GPU')]

==========CONDA==========

# packages in environment at /Users/dcclab/miniforge3/envs/sleaptest:
#
# Name                    Version                   Build  Channel
abseil-cpp                20211102.0           hddbf539_3    conda-forge
absl-py                   2.1.0              pyhd8ed1ab_0    conda-forge
aiohappyeyeballs          2.4.3              pyhd8ed1ab_0    conda-forge
aiohttp                   3.10.10          py39h33701b3_0    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
aom                       3.5.0                hf0c8a7f_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_2    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0                   pypi_0    pypi
blinker                   1.8.2              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               heccf04b_0    conda-forge
brotli                    1.0.9                hb7f2c08_9    conda-forge
brotli-bin                1.0.9                hb7f2c08_9    conda-forge
brotli-python             1.0.9            py39h7a8716b_9    conda-forge
brunsli                   0.1                  h046ec9c_0    conda-forge
bzip2                     1.0.8                hfdf4475_7    conda-forge
c-ares                    1.34.2               h32b1619_0    conda-forge
c-blosc2                  2.12.0               h0ae8482_0    conda-forge
ca-certificates           2024.8.30            h8857fd0_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.5.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h56d7d38_1012    conda-forge
cattrs                    1.1.1              pyhd8ed1ab_0    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1           py39h8ddeee6_0    conda-forge
cfitsio                   4.2.0                hd56cc12_0    conda-forge
charls                    2.3.4                he49afe7_0    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
contourpy                 1.2.1            py39h0ca7971_0    conda-forge
cryptography              39.0.0           py39h7eb6a14_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                h0dc2134_0    conda-forge
efficientnet              1.0.0                    pypi_0    pypi
ffmpeg                    4.4.2           gpl_h8b4fe81_112    conda-forge
flatbuffers               24.3.25                  pypi_0    pypi
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.15.0               h37eeddb_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.54.1           py39h20cc651_1    conda-forge
freetype                  2.12.1               h60636b9_2    conda-forge
frozenlist                1.5.0            py39h296a897_0    conda-forge
gast                      0.4.0              pyh9f0ad1d_0    conda-forge
geos                      3.13.0               hac325c4_0    conda-forge
gettext                   0.22.5               hdfe23c8_3    conda-forge
gettext-tools             0.22.5               hdfe23c8_3    conda-forge
giflib                    5.2.2                h10d778d_0    conda-forge
glib                      2.82.2               hbe7352d_0    conda-forge
glib-tools                2.82.2               h8a9f880_0    conda-forge
gmp                       6.3.0                hf036a51_2    conda-forge
gnutls                    3.7.9                h1951705_0    conda-forge
google-auth               2.36.0             pyhff2d567_0    conda-forge
google-auth-oauthlib      1.0.0                    pypi_0    pypi
google-pasta              0.2.0              pyhd8ed1ab_1    conda-forge
graphite2                 1.3.13            h73e2aa4_1003    conda-forge
grpc-cpp                  1.46.3               hf40b151_3    conda-forge
grpcio                    1.67.1                   pypi_0    pypi
gst-plugins-base          1.22.9               h3fb38fc_1    conda-forge
gstreamer                 1.22.9               hf63bbb8_1    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
h5py                      3.8.0           nompi_py39h7d40783_100    conda-forge
harfbuzz                  5.3.0                h08f8713_0    conda-forge
hdf5                      1.12.2          nompi_h70e9adf_101    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.10               pyhd8ed1ab_0    conda-forge
image-classifiers         1.0.0                    pypi_0    pypi
imagecodecs               2022.9.26        py39h8036967_4    conda-forge
imageio                   2.36.0             pyh12aca89_1    conda-forge
imgaug                    0.4.0              pyhd8ed1ab_1    conda-forge
imgstore                  0.2.9                    pypi_0    pypi
importlib-metadata        8.5.0              pyha770c72_0    conda-forge
importlib-resources       6.4.5              pyhd8ed1ab_0    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_0    conda-forge
jasper                    2.0.33               h7c6fec8_1    conda-forge
jax                       0.4.30                   pypi_0    pypi
jaxlib                    0.4.30                   pypi_0    pypi
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hb7f2c08_3    conda-forge
jsmin                     3.0.1              pyhd8ed1ab_0    conda-forge
jsonpickle                1.2                        py_0    conda-forge
jsonschema                4.19.0                   pypi_0    pypi
jsonschema-specifications 2023.7.1                 pypi_0    pypi
jxrlib                    1.1                  h10d778d_3    conda-forge
keras                     2.12.0                   pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.7            py39h0d8d0ca_0    conda-forge
krb5                      1.20.1               h0165f36_0    conda-forge
lame                      3.100             hb7f2c08_1003    conda-forge
lazy-loader               0.4                pyhd8ed1ab_1    conda-forge
lazy_loader               0.4                pyhd8ed1ab_1    conda-forge
lcms2                     2.14                 h90f4b2a_0    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libabseil                 20211102.0      cxx17_h844d122_3    conda-forge
libaec                    1.1.3                h73e2aa4_0    conda-forge
libasprintf               0.22.5               hdfe23c8_3    conda-forge
libasprintf-devel         0.22.5               hdfe23c8_3    conda-forge
libavif                   0.11.1               h22361c6_2    conda-forge
libblas                   3.9.0           20_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_9    conda-forge
libbrotlidec              1.0.9                hb7f2c08_9    conda-forge
libbrotlienc              1.0.9                hb7f2c08_9    conda-forge
libcblas                  3.9.0           20_osx64_openblas    conda-forge
libclang                  18.1.1                   pypi_0    pypi
libclang13                16.0.1          default_h395b6a0_0    conda-forge
libcurl                   7.87.0               haf73cf8_0    conda-forge
libcxx                    19.1.3               hf95d169_0    conda-forge
libdeflate                1.14                 hb7f2c08_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 h10d778d_2    conda-forge
libexpat                  2.6.4                h240833e_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgettextpo              0.22.5               hdfe23c8_3    conda-forge
libgettextpo-devel        0.22.5               hdfe23c8_3    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
libgfortran5              13.2.0               h2873a65_3    conda-forge
libglib                   2.82.2               hb6ef654_0    conda-forge
libiconv                  1.17                 hd75f5a5_2    conda-forge
libidn2                   2.3.7                h10d778d_0    conda-forge
libintl                   0.22.5               hdfe23c8_3    conda-forge
libintl-devel             0.22.5               hdfe23c8_3    conda-forge
liblapack                 3.9.0           20_osx64_openblas    conda-forge
liblapacke                3.9.0           20_osx64_openblas    conda-forge
libllvm13                 13.0.1               h64f94b2_2    conda-forge
libllvm16                 16.0.1               h7001e86_0    conda-forge
libnghttp2                1.51.0               h0dd9d14_0    conda-forge
libogg                    1.3.5                hfdf4475_0    conda-forge
libopenblas               0.3.25          openmp_hfef2a42_0    conda-forge
libopencv                 4.6.0            py39h93c2317_3    conda-forge
libopus                   1.3.1                hc929b4f_1    conda-forge
libpng                    1.6.44               h4b8f8c9_0    conda-forge
libpq                     15.1                 hdbdeef1_3    conda-forge
libprotobuf               3.20.3               hbc0c0cd_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.47.0               h2f8c449_1    conda-forge
libssh2                   1.10.0               h7535e13_3    conda-forge
libtasn1                  4.19.0               hb7f2c08_0    conda-forge
libtiff                   4.4.0                h6268bbc_5    conda-forge
libunistring              0.9.10               h0d85af4_0    conda-forge
libvorbis                 1.3.7                h046ec9c_0    conda-forge
libvpx                    1.11.0               he49afe7_3    conda-forge
libwebp-base              1.4.0                h10d778d_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.10.3               h201ad9d_4    conda-forge
libxslt                   1.1.37               h5d22bc9_0    conda-forge
libzlib                   1.3.1                hd23fc13_2    conda-forge
libzopfli                 1.0.3                h046ec9c_0    conda-forge
llvm-openmp               19.1.3               hf78d878_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markdown                  3.6                pyhd8ed1ab_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                3.0.2            py39h20cc651_0    conda-forge
matplotlib-base           3.8.4            py39hfca4cae_2    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
ml-dtypes                 0.5.0                    pypi_0    pypi
multidict                 6.1.0            py39h781ac47_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.32               h7ebae80_0    conda-forge
mysql-libs                8.0.32               hc37e033_0    conda-forge
ncurses                   6.5                  hf036a51_1    conda-forge
ndx-pose                  0.1.1                    pypi_0    pypi
nettle                    3.9.1                h8e11ae5_0    conda-forge
networkx                  3.2.1              pyhd8ed1ab_0    conda-forge
nixio                     1.5.3                    pypi_0    pypi
nspr                      4.36                 h97d8b74_0    conda-forge
nss                       3.106                hbde9d96_0    conda-forge
numpy                     1.23.5                   pypi_0    pypi
oauthlib                  3.2.2              pyhd8ed1ab_0    conda-forge
opencv                    4.6.0            py39h6e9494a_3    conda-forge
openh264                  2.3.1                hf0c8a7f_2    conda-forge
openjpeg                  2.5.0                h5d0d7b0_1    conda-forge
openssl                   1.1.1w               h8a1eda9_0    conda-forge
opt_einsum                3.4.0              pyhd8ed1ab_0    conda-forge
p11-kit                   0.24.1               h65f8906_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.3            py39h88a5ddd_1    conda-forge
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pcre2                     10.44                h7634a1b_2    conda-forge
pillow                    9.2.0            py39h35d4919_3    conda-forge
pip                       24.3.1             pyh8b19718_0    conda-forge
pixman                    0.43.4               h73e2aa4_0    conda-forge
propcache                 0.2.0            py39h06d86d0_2    conda-forge
protobuf                  3.20.3           py39h7a8716b_1    conda-forge
psutil                    6.1.0            py39h296a897_0    conda-forge
pthread-stubs             0.4               h00291cd_1002    conda-forge
py-opencv                 4.6.0            py39h71a6800_3    conda-forge
pyasn1                    0.6.1              pyhd8ed1ab_1    conda-forge
pyasn1-modules            0.4.1              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.9.0              pyhd8ed1ab_1    conda-forge
pykalman                  0.9.7              pyhd8ed1ab_0    conda-forge
pynwb                     2.5.0                    pypi_0    pypi
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.2.0              pyhd8ed1ab_1    conda-forge
pyside2                   5.15.8           py39heedc0ee_2    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.15          h531fd05_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-rapidjson          1.20             py39h09c4c31_0    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      5_cp39    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pywavelets                1.6.0            py39hb943cd9_0    conda-forge
pyyaml                    6.0.2            py39h06d86d0_1    conda-forge
pyzmq                     26.2.0           py39ha6bd863_0    conda-forge
qimage2ndarray            1.10.0                   pypi_0    pypi
qt-main                   5.15.8               h1d3b3f8_6    conda-forge
qtpy                      2.4.2              pyhdecd6ff_0    conda-forge
re2                       2022.06.01           hb486fe8_1    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
referencing               0.30.2                   pypi_0    pypi
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
requests-oauthlib         2.0.0              pyhd8ed1ab_0    conda-forge
rich                      13.9.4             pyhd8ed1ab_0    conda-forge
rpds-py                   0.10.3                   pypi_0    pypi
rsa                       4.9                pyhd8ed1ab_0    conda-forge
ruamel-yaml               0.17.32                  pypi_0    pypi
ruamel-yaml-clib          0.2.7                    pypi_0    pypi
scikit-image              0.24.0           py39hbb604f3_1    conda-forge
scikit-learn              1.0              py39hd2caeff_1    conda-forge
scikit-video              1.1.11             pyh24bf2e0_0    conda-forge
scipy                     1.9.0            py39h29d19b3_0    conda-forge
seaborn                   0.13.2               hd8ed1ab_2    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_2    conda-forge
segmentation-models       1.0.1                    pypi_0    pypi
setuptools                75.3.0             pyhd8ed1ab_0    conda-forge
shapely                   2.0.6            py39hfde7aa9_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleap                     1.3.3                    pypi_0    pypi
snappy                    1.1.10               h6dc393e_1    conda-forge
sqlite                    3.47.0               h6285a30_1    conda-forge
statsmodels               0.14.4           py39hff9a475_0    conda-forge
svt-av1                   1.4.1                hf0c8a7f_0    conda-forge
tensorboard               2.12.3                   pypi_0    pypi
tensorboard-data-server   0.7.2                    pypi_0    pypi
tensorboard-plugin-wit    1.8.1              pyhd8ed1ab_0    conda-forge
tensorflow                2.9.1           cpu_py39hb0a6171_0    conda-forge
tensorflow-estimator      2.12.0                   pypi_0    pypi
tensorflow-hub            0.12.0             pyhca92ed8_0    conda-forge
tensorflow-io-gcs-filesystem 0.37.1                   pypi_0    pypi
tensorflow-macos          2.12.0                   pypi_0    pypi
tensorflow-metal          1.0.0                    pypi_0    pypi
termcolor                 2.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tifffile                  2022.10.10         pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
tzlocal                   5.0.1                    pypi_0    pypi
unicodedata2              15.1.0           py39h296a897_1    conda-forge
urllib3                   2.2.3              pyhd8ed1ab_0    conda-forge
werkzeug                  3.1.2              pyhd8ed1ab_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.14.1                   pypi_0    pypi
x264                      1!164.3095           h775f41a_2    conda-forge
x265                      3.5                  hbb4e6a2_3    conda-forge
xorg-libxau               1.0.11               h00291cd_1    conda-forge
xorg-libxdmcp             1.1.5                h00291cd_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
yarl                      1.16.0           py39h296a897_0    conda-forge
zeromq                    4.3.5                h93d8f39_0    conda-forge
zfp                       1.0.1                h469392a_2    conda-forge
zipp                      3.20.2             pyhd8ed1ab_0    conda-forge
zlib-ng                   2.0.7                hb7f2c08_0    conda-forge
zstandard                 0.23.0           py39hc23f734_1    conda-forge
zstd                      1.5.6                h915ae27_0    conda-forge


==========PIP==========

absl-py @ file:///home/conda/feedstock_root/build_artifacts/absl-py_1705494584803/work
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 @ file:///home/conda/feedstock_root/build_artifacts/cachetools_1724028158384/work
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
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==24.3.25
fonttools @ file:///Users/runner/miniforge3/conda-bld/fonttools_1729530356476/work
frozenlist @ file:///Users/runner/miniforge3/conda-bld/frozenlist_1729699486805/work
gast @ file:///home/conda/feedstock_root/build_artifacts/gast_1596839682936/work
google-auth @ file:///home/conda/feedstock_root/build_artifacts/google-auth_1730952254284/work
google-auth-oauthlib==1.0.0
google-pasta @ file:///home/conda/feedstock_root/build_artifacts/google-pasta_1722873999312/work
grpcio==1.67.1
h2 @ file:///home/conda/feedstock_root/build_artifacts/h2_1634280454336/work
h5py @ file:///Users/runner/miniforge3/conda-bld/h5py_1674499365073/work
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
jax==0.4.30
jaxlib==0.4.30
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==2.12.0
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
libclang==18.1.1
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
ml_dtypes==0.5.0
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==1.23.5
oauthlib @ file:///home/conda/feedstock_root/build_artifacts/oauthlib_1666056362788/work
opencv-python==4.6.0
opt_einsum @ file:///home/conda/feedstock_root/build_artifacts/opt_einsum_1727392354687/work
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_1729847081697/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_1730763764885/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_1730592237829/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 @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
sleap==1.3.3
statsmodels @ file:///Users/runner/miniforge3/conda-bld/statsmodels_1727986739068/work
tensorboard==2.12.3
tensorboard-data-server==0.7.2
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-estimator==2.12.0
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==0.37.1
tensorflow-macos==2.12.0
tensorflow-metal==1.0.0
termcolor @ file:///home/conda/feedstock_root/build_artifacts/termcolor_1728288976871/work
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1714400101435/work
tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1665588749940/work
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1717802530399/work
tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1727140567071/work
tzlocal==5.0.1
unicodedata2 @ file:///Users/runner/miniforge3/conda-bld/unicodedata2_1729704644728/work
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1726496430923/work
Werkzeug @ file:///home/conda/feedstock_root/build_artifacts/werkzeug_1730762638373/work
wrapt==1.14.1
yarl @ file:///Users/runner/miniforge3/conda-bld/yarl_1729798487102/work
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1726248574750/work
zstandard==0.23.0


==========NVIDIA==========

unable to locate nvidia-smi

Screenshots

How to reproduce

  1. Install a sleap environment with mamba
  2. In the sleap venv, uninstall tensorflow with pip
  3. Install tensorflow-macos with pip
  4. Install tensorflow-metal with pip
  5. Make sure that tensorflow can identify the GPU
  6. Run in the command line sleap-train multi_instance.jsonlabeled_data.slp
@ValeriePineauNoel ValeriePineauNoel added the bug Something isn't working label Nov 8, 2024
@eberrigan
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Hi @ValeriePineauNoel,

The GUI communicates with the command line, so we do expect this error. Please see the response in #2016.

We do not support training on your GPU. Please let us know if you need more help with your training setup.

Best,

Elizabeth

@eberrigan eberrigan added documentation This issue exists because the documentation is outdated. and removed bug Something isn't working labels Nov 8, 2024
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