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Crashing during training on mac OS 14 (Sonoma) #1602

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hl8536 opened this issue Nov 16, 2023 · 3 comments
Closed

Crashing during training on mac OS 14 (Sonoma) #1602

hl8536 opened this issue Nov 16, 2023 · 3 comments
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bug Something isn't working

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@hl8536
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hl8536 commented Nov 16, 2023

Bug description

SLEAP crashing during training with the following error output.

Your personal set up

  • OS: macOS Sonoma 14.0
  • Version(s): SLEAP 1.3.3, Python 3.9.15
  • SLEAP installation method (listed here): Conda from package (M1)
Environment packages 
# Name                    Version                   Build  Channel
abseil-cpp                20211102.0           he4e09e4_3    conda-forge
absl-py                   1.4.0                    pypi_0    pypi
aiohttp                   3.8.6            py39h17cfd9d_1    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
aom                       3.5.0                h7ea286d_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
blinker                   1.7.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               hc338f07_0    conda-forge
brotli                    1.0.9                h1a8c8d9_9    conda-forge
brotli-bin                1.0.9                h1a8c8d9_9    conda-forge
brotli-python             1.0.9            py39h23fbdae_9    conda-forge
brunsli                   0.1                  h9f76cd9_0    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.21.0               h93a5062_0    conda-forge
c-blosc2                  2.10.5               h8eb3132_0    conda-forge
ca-certificates           2023.7.22            hf0a4a13_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.1                    pypi_0    pypi
cairo                     1.16.0            h73a0509_1014    conda-forge
cattrs                    1.1.1              pyhd8ed1ab_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.16.0           py39he153c15_0    conda-forge
cfitsio                   4.2.0                h2f961c4_0    conda-forge
charls                    2.3.4                hbdafb3b_0    conda-forge
charset-normalizer        3.2.0                    pypi_0    pypi
click                     8.1.7           unix_pyh707e725_0    conda-forge
contourpy                 1.1.1            py39hbd775c9_1    conda-forge
cryptography              39.0.0           py39haa0b8cc_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                hb547adb_0    conda-forge
efficientnet              1.0.0                    pypi_0    pypi
expat                     2.5.0                hb7217d7_1    conda-forge
ffmpeg                    4.4.2           gpl_hf318d42_112    conda-forge
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                 hab24e00_0    conda-forge
fontconfig                2.14.2               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.43.1           py39h17cfd9d_0    conda-forge
freetype                  2.12.1               hadb7bae_2    conda-forge
frozenlist                1.4.0            py39h0f82c59_1    conda-forge
gast                      0.4.0              pyh9f0ad1d_0    conda-forge
geos                      3.12.0               h13dd4ca_0    conda-forge
gettext                   0.21.1               h0186832_0    conda-forge
giflib                    5.2.1                h1a8c8d9_3    conda-forge
glib                      2.78.0               ha614eb4_0    conda-forge
glib-tools                2.78.0               ha614eb4_0    conda-forge
gmp                       6.2.1                h9f76cd9_0    conda-forge
gnutls                    3.7.8                h9f1a10d_0    conda-forge
google-auth               2.23.0                   pypi_0    pypi
google-auth-oauthlib      0.4.6              pyhd8ed1ab_0    conda-forge
google-pasta              0.2.0              pyh8c360ce_0    conda-forge
graphite2                 1.3.13            h9f76cd9_1001    conda-forge
grpc-cpp                  1.46.4               hcaf9be7_3    conda-forge
grpcio                    1.58.0                   pypi_0    pypi
gst-plugins-base          1.22.6               h27255cc_2    conda-forge
gstreamer                 1.22.6               h8c52bba_2    conda-forge
h5py                      3.8.0           nompi_py39hc9149d8_100    conda-forge
harfbuzz                  5.3.0                hddbc195_0    conda-forge
hdf5                      1.12.2          nompi_h55deafc_101    conda-forge
hdmf                      3.9.0                    pypi_0    pypi
icu                       70.1                 h6b3803e_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
image-classifiers         1.0.0                    pypi_0    pypi
imagecodecs               2022.9.26        py39hd7f743f_4    conda-forge
imageio                   2.31.5             pyh8c1a49c_0    conda-forge
imgaug                    0.4.0              pyhd8ed1ab_1    conda-forge
imgstore                  0.2.9                    pypi_0    pypi
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib-resources       6.1.0              pyhd8ed1ab_0    conda-forge
importlib_resources       6.1.0              pyhd8ed1ab_0    conda-forge
jasper                    2.0.33               hc3cd1e9_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h1a8c8d9_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                  h27ca646_2    conda-forge
keras                     2.9.0              pyhd8ed1ab_0    conda-forge
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.5            py39hbd775c9_1    conda-forge
krb5                      1.20.1               h127bd45_0    conda-forge
lame                      3.100             h1a8c8d9_1003    conda-forge
lazy_loader               0.3                pyhd8ed1ab_0    conda-forge
lcms2                     2.14                 h8193b64_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libabseil                 20211102.0      cxx17_h28b99d4_3    conda-forge
libaec                    1.1.2                h13dd4ca_1    conda-forge
libavif                   0.11.1               h9f83d30_2    conda-forge
libblas                   3.9.0           19_osxarm64_openblas    conda-forge
libbrotlicommon           1.0.9                h1a8c8d9_9    conda-forge
libbrotlidec              1.0.9                h1a8c8d9_9    conda-forge
libbrotlienc              1.0.9                h1a8c8d9_9    conda-forge
libcblas                  3.9.0           19_osxarm64_openblas    conda-forge
libclang                  16.0.6                   pypi_0    pypi
libclang13                14.0.6          default_hc7183e1_1    conda-forge
libcurl                   7.87.0               hbe9bab4_0    conda-forge
libcxx                    16.0.6               h4653b0c_0    conda-forge
libdeflate                1.14                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libexpat                  2.5.0                hb7217d7_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_1    conda-forge
libgfortran5              13.2.0               hf226fd6_1    conda-forge
libglib                   2.78.0               h24e9cb9_0    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
libidn2                   2.3.4                h1a8c8d9_0    conda-forge
liblapack                 3.9.0           19_osxarm64_openblas    conda-forge
liblapacke                3.9.0           19_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hd1a9a77_4    conda-forge
libnghttp2                1.51.0               hd184df1_0    conda-forge
libogg                    1.3.4                h27ca646_1    conda-forge
libopenblas               0.3.24          openmp_hd76b1f2_0    conda-forge
libopencv                 4.6.0            py39he1c1adf_3    conda-forge
libopus                   1.3.1                h27ca646_1    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libpq                     15.1                 hbce9e56_3    conda-forge
libprotobuf               3.20.3               hb5ab8b9_0    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.44.0               h091b4b1_0    conda-forge
libssh2                   1.10.0               hb80f160_3    conda-forge
libtasn1                  4.19.0               h1a8c8d9_0    conda-forge
libtiff                   4.4.0                heb92581_5    conda-forge
libunistring              0.9.10               h3422bc3_0    conda-forge
libvorbis                 1.3.7                h9f76cd9_0    conda-forge
libvpx                    1.11.0               hc470f4d_3    conda-forge
libwebp-base              1.3.2                hb547adb_0    conda-forge
libxcb                    1.13              h9b22ae9_1004    conda-forge
libxml2                   2.10.3               h67585b2_4    conda-forge
libxslt                   1.1.37               h1bd8bc4_0    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
libzopfli                 1.0.3                h9f76cd9_0    conda-forge
llvm-openmp               17.0.4               hcd81f8e_0    conda-forge
lz4-c                     1.9.4                hb7217d7_0    conda-forge
markdown                  3.4.4                    pypi_0    pypi
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.3            py39h0f82c59_1    conda-forge
matplotlib-base           3.8.1            py39h1a09f3e_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
multidict                 6.0.4            py39h02fc5c5_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.32               hab468bb_0    conda-forge
mysql-libs                8.0.32               hea58576_0    conda-forge
ncurses                   6.4                  h463b476_2    conda-forge
ndx-pose                  0.1.1                    pypi_0    pypi
nettle                    3.8.1                h63371fa_1    conda-forge
networkx                  3.2.1              pyhd8ed1ab_0    conda-forge
nixio                     1.5.3                    pypi_0    pypi
nspr                      4.35                 hb7217d7_0    conda-forge
nss                       3.94                 hc6b9969_0    conda-forge
numpy                     1.22.4           py39h7df2422_0    conda-forge
oauthlib                  3.2.2              pyhd8ed1ab_0    conda-forge
opencv                    4.6.0            py39hdf13c20_3    conda-forge
openh264                  2.3.1                hb7217d7_2    conda-forge
openjpeg                  2.5.0                h5d4e404_1    conda-forge
openssl                   1.1.1w               h53f4e23_0    conda-forge
opt_einsum                3.3.0              pyhc1e730c_2    conda-forge
p11-kit                   0.24.1               h29577a5_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.1.2            py39hf8cecc8_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hb34f9b4_0    conda-forge
pillow                    9.2.0            py39h139752e_3    conda-forge
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.42.2               h13dd4ca_0    conda-forge
protobuf                  3.19.6                   pypi_0    pypi
psutil                    5.9.5            py39h0f82c59_1    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
py-opencv                 4.6.0            py39hfa6204d_3    conda-forge
pyasn1                    0.5.0              pyhd8ed1ab_0    conda-forge
pyasn1-modules            0.3.0              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pyjwt                     2.8.0              pyhd8ed1ab_0    conda-forge
pykalman                  0.9.5                      py_1    conda-forge
pynwb                     2.5.0                    pypi_0    pypi
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyside2                   5.15.8           py39h0adaba8_2    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.15          h2d96c93_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-flatbuffers        1.12               pyhd8ed1ab_1    conda-forge
python-rapidjson          1.13             py39h4ce5507_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pywavelets                1.4.1            py39hf4a74a7_1    conda-forge
pyyaml                    6.0.1            py39h0f82c59_1    conda-forge
pyzmq                     25.1.1           py39he0a3c8b_2    conda-forge
qimage2ndarray            1.10.0                   pypi_0    pypi
qt-main                   5.15.8               hfe8d25c_6    conda-forge
qtpy                      2.4.1              pyhd8ed1ab_0    conda-forge
re2                       2022.06.01           h9a09cb3_1    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
referencing               0.30.2                   pypi_0    pypi
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
rich                      13.6.0             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              0.22.0           py39hf8cecc8_2    conda-forge
scikit-learn              1.0              py39h12ba089_1    conda-forge
scikit-video              1.1.11             pyh24bf2e0_0    conda-forge
scipy                     1.9.0            py39h14896cb_0    conda-forge
seaborn                   0.13.0               hd8ed1ab_0    conda-forge
seaborn-base              0.13.0             pyhd8ed1ab_0    conda-forge
segmentation-models       1.0.1                    pypi_0    pypi
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
shapely                   2.0.2            py39h4b213b6_0    conda-forge
six                       1.15.0                   pypi_0    pypi
sleap                     1.3.3                    pypi_0    pypi
snappy                    1.1.10               h17c5cce_0    conda-forge
sqlite                    3.44.0               hf2abe2d_0    conda-forge
statsmodels               0.14.0           py39h373d45f_2    conda-forge
svt-av1                   1.4.1                h7ea286d_0    conda-forge
tensorboard               2.9.1                    pypi_0    pypi
tensorboard-data-server   0.6.1            py39haa0b8cc_4    conda-forge
tensorboard-plugin-wit    1.8.1              pyhd8ed1ab_0    conda-forge
tensorflow                2.9.1           cpu_py39h2839aeb_0    conda-forge
tensorflow-base           2.9.1           cpu_py39ha1ad4ae_0    conda-forge
tensorflow-estimator      2.9.1           cpu_py39h7b621ec_0    conda-forge
tensorflow-hub            0.12.0             pyhca92ed8_0    conda-forge
tensorflow-macos          2.9.2                    pypi_0    pypi
tensorflow-metal          0.5.0                    pypi_0    pypi
termcolor                 2.3.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.2.0              pyha21a80b_0    conda-forge
tifffile                  2022.10.10         pyhd8ed1ab_0    conda-forge
tk                        8.6.13               hb31c410_0    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
tzlocal                   5.0.1                    pypi_0    pypi
unicodedata2              15.1.0           py39h0f82c59_0    conda-forge
urllib3                   1.26.16                  pypi_0    pypi
werkzeug                  2.3.7                    pypi_0    pypi
wheel                     0.41.3             pyhd8ed1ab_0    conda-forge
wrapt                     1.15.0           py39h0f82c59_1    conda-forge
x264                      1!164.3095           h57fd34a_2    conda-forge
x265                      3.5                  hbc6ce65_3    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
yarl                      1.9.2            py39h17cfd9d_1    conda-forge
zeromq                    4.3.5                h965bd2d_0    conda-forge
zfp                       1.0.0                h82938aa_4    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h53f4e23_5    conda-forge
zlib-ng                   2.0.7                h1a8c8d9_0    conda-forge
zstd                      1.5.5                h4f39d0f_0    conda-forge
Logs 
# paste relevant logs here, if any

Screenshots

Screenshot 2023-11-16 at 3 50 02 PM

How to reproduce

Run training from GUI via Predict -> Run Training... -> Run using single animal pipeline
@hl8536 hl8536 added the bug Something isn't working label Nov 16, 2023
@talmo
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talmo commented Dec 1, 2023

Hi @hl8536,

Apologies for the delay! It looks like this is a bug related to Mac OS Sonoma unfortunately breaking the TensorFlow 2.9 support.

We'll investigate, but unfortunately this might take a little while since it'll require a rework of our dependencies.

In the meantime, you could try using Google Colab or downgrading to Mac OS Ventura if possible.

If you want to try fixing it yourself, the thing to try would be to install from source and tweak the versions in requirements.txt:

sleap/requirements.txt

Lines 9 to 10 in 2d24296

tensorflow-macos==2.9.2; sys_platform == 'darwin' and platform_machine == 'arm64'
tensorflow-metal==0.5.0; sys_platform == 'darwin' and platform_machine == 'arm64'

And possibly related dependencies in environment_mac.yml.

Sorry about that! Let us know if you have any questions!

Talmo

@talmo talmo changed the title Crashing during training Crashing during training on mac OS 14 (Sonoma) Jan 5, 2024
@mjamagon
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mjamagon commented Jan 6, 2024

@talmo setting tensorflow-macos==2.8.0 worked for me when installing from source (apple silicon + Sonoma)

@talmo
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talmo commented Apr 8, 2024

We are now using macOS Sonoma + tensorflow-macos==2.9.2 in testing as of #1734.

So far, so good, but it's not clear if this specific bug would be caught there. This bug might still come up in regular use, but we should have added some fixes to how it's installed which will change the environment relative to the reported one here (namely, not pulling in conda-forge tensorflow). These fixes will be available in SLEAP v1.4.0.

I'm closing for now, but if needed, it sounds like tensorflow-macos=2.8.0 might be a workaround.

Related issue: #1547

@talmo talmo closed this as completed Apr 8, 2024
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@talmo @mjamagon @hl8536