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README inference example fail on M1 macbook after fresh install #218

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bgriffen opened this issue Feb 9, 2023 · 2 comments
Open

README inference example fail on M1 macbook after fresh install #218

bgriffen opened this issue Feb 9, 2023 · 2 comments
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bug Something isn't working

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@bgriffen
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bgriffen commented Feb 9, 2023 •
edited

Describe the bug
Crashing on M1 Mac, upon following README and sample image provided as per example.

To reproduce
Create conda environment, pip install stardist then run the first few lines of the README

Expected behavior
Inference to be performed

Data and screenshots

In [6]: labels, _ = model.predict_instances(normalize(im))
2023-02-09 22:10:39.930079: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
2023-02-09 22:10:39.933592: W tensorflow/core/platform/profile_utils/cpu_utils.cc:126] Failed to get CPU frequency: 0 Hz
2023-02-09 22:10:39.943672: F tensorflow/core/grappler/costs/op_level_cost_estimator.cc:710] Check failed: 0 < gflops (0 vs. 0)type: "CPU"
model: "0"
num_cores: 8
environment {
  key: "cpu_instruction_set"
  value: "ARM NEON"
}
environment {
  key: "eigen"
  value: "3.3.90"
}
l1_cache_size: 16384
l2_cache_size: 524288
l3_cache_size: 524288
memory_size: 268435456

Abort trap: 6

**Environment (please complete the following information):**
packages in environment at /Users/username/miniforge3/envs/caltrans:
Name                    Version                   Build  Channel
abseil-cpp                20200923.3           h9f76cd9_0    conda-forge
absl-py                   1.4.0              pyhd8ed1ab_0    conda-forge
aiohttp                   3.8.3            py38hb991d35_1    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
aom                       3.5.0                h7ea286d_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38hb991d35_3    conda-forge
astor                     0.8.1              pyh9f0ad1d_0    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bcrypt                    4.0.1                    pypi_0    pypi
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blinker                   1.5                pyhd8ed1ab_0    conda-forge
blosc                     1.21.3               h1d6ff8b_0    conda-forge
brotli                    1.0.9                h1a8c8d9_8    conda-forge
brotli-bin                1.0.9                h1a8c8d9_8    conda-forge
brotlipy                  0.7.0           py38hb991d35_1005    conda-forge
brunsli                   0.1                  h9f76cd9_0    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.18.1               h3422bc3_0    conda-forge
c-blosc2                  2.6.1                h303ed30_0    conda-forge
ca-certificates           2022.12.7            h4653dfc_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                4.2.4              pyhd8ed1ab_0    conda-forge
cellpose                  2.2                      pypi_0    pypi
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py38ha45ccd6_3    conda-forge
cfitsio                   4.2.0                h2f961c4_0    conda-forge
charls                    2.4.1                hb7217d7_0    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
clang                     14.0                     pypi_0    pypi
clang-15                  15.0.7          default_h9e54d93_0    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7            py38h9dc3d6a_0    conda-forge
cryptography              39.0.0           py38h5eb7249_0    conda-forge
csbdeep                   0.7.2            py38h10201cd_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py38hb991d35_1    conda-forge
dask-core                 2023.1.1           pyhd8ed1ab_0    conda-forge
dav1d                     1.0.0                he4db4b2_1    conda-forge
debugpy                   1.6.6            py38h2b1e499_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fonttools                 4.38.0           py38hb991d35_1    conda-forge
freetype                  2.12.1               hd633e50_1    conda-forge
frozenlist                1.3.3            py38hb991d35_0    conda-forge
fsspec                    2023.1.0           pyhd8ed1ab_0    conda-forge
gast                      0.3.3                      py_0    conda-forge
giflib                    5.2.1                h27ca646_2    conda-forge
google-auth               1.35.0             pyh6c4a22f_0    conda-forge
google-auth-oauthlib      0.4.6              pyhd8ed1ab_0    conda-forge
google-pasta              0.2.0              pyh8c360ce_0    conda-forge
grpc-cpp                  1.36.4               hfad0885_1    conda-forge
grpcio                    1.36.1           py38h446835f_0    conda-forge
h5py                      3.8.0                    pypi_0    pypi
hdf5                      1.10.6          nompi_h0fc092c_1114    conda-forge
icu                       70.1                 h6b3803e_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagecodecs               2023.1.23        py38h57345ed_0    conda-forge
imageio                   2.25.0             pyh24c5eb1_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib_resources       5.10.2             pyhd8ed1ab_0    conda-forge
ipykernel                 6.20.2             pyh736e0ef_0    conda-forge
ipython                   8.9.0              pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.4              pyhd8ed1ab_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0                    pypi_0    pypi
jpeg                      9e                   he4db4b2_2    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py38h10201cd_8    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.4              pyhd8ed1ab_0    conda-forge
jupyter_core              5.1.5            py38h10201cd_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.1.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.5              pyhd8ed1ab_0    conda-forge
jxrlib                    1.1                  h27ca646_2    conda-forge
keras-preprocessing       1.1.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.4            py38h9dc3d6a_1    conda-forge
krb5                      1.20.1               h127bd45_0    conda-forge
lcms2                     2.14                 h481adae_1    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libaec                    1.0.6                hb7217d7_1    conda-forge
libavif                   0.11.1               h3d80962_0    conda-forge
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libbrotlicommon           1.0.9                h1a8c8d9_8    conda-forge
libbrotlidec              1.0.9                h1a8c8d9_8    conda-forge
libbrotlienc              1.0.9                h1a8c8d9_8    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libclang-cpp15            15.0.7          default_h9e54d93_0    conda-forge
libcurl                   7.87.0               hbe9bab4_0    conda-forge
libcxx                    14.0.6               h2692d47_0    conda-forge
libdeflate                1.17                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           11_3_0_hd922786_27    conda-forge
libgfortran5              11.3.0              hdaf2cc0_27    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
libjpeg-turbo             2.1.4                h1a8c8d9_0    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
libllvm11                 11.1.0               hfa12f05_5    conda-forge
libllvm15                 15.0.7               h62b9111_0    conda-forge
libnghttp2                1.51.0               hd184df1_0    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libprotobuf               3.15.8               hccf11d3_1    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.40.0               h76d750c_0    conda-forge
libssh2                   1.10.0               hb80f160_3    conda-forge
libtiff                   4.5.0                h5dffbdd_2    conda-forge
libwebp-base              1.2.4                h57fd34a_0    conda-forge
libxcb                    1.13              h9b22ae9_1004    conda-forge
libxml2                   2.10.3               h87b0503_0    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
libzopfli                 1.0.3                h9f76cd9_0    conda-forge
llvm-openmp               15.0.7               h7cfbb63_0    conda-forge
llvmlite                  0.39.1                   pypi_0    pypi
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lz4-c                     1.9.4                hb7217d7_0    conda-forge
markdown                  3.4.1              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.2            py38hb991d35_0    conda-forge
matplotlib                3.7.0rc1                 pypi_0    pypi
matplotlib-base           3.6.3            py38hbbe890c_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
multidict                 6.0.4            py38hb991d35_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
natsort                   8.2.0                    pypi_0    pypi
nbclassic                 0.4.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numba                     0.56.4                   pypi_0    pypi
numpy                     1.23.5           py38h09ac2d9_0    conda-forge
oauthlib                  3.2.2              pyhd8ed1ab_0    conda-forge
opencv-python             4.7.0.68                 pypi_0    pypi
opencv-python-headless    4.7.0.68                 pypi_0    pypi
openjpeg                  2.5.0                hbc2ba62_2    conda-forge
openssl                   1.1.1s               h03a7124_1    conda-forge
opt_einsum                3.3.0              pyhd8ed1ab_1    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3            py38h61dac83_0    conda-forge
pandoc                    2.19.2               hce30654_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
paramiko                  3.0.0                    pypi_0    pypi
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.3.0              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0            py38h01505ee_0    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              2.6.2              pyhd8ed1ab_0    conda-forge
polyroi                   0.0.4                    pypi_0    pypi
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
prompt_toolkit            3.0.36               hd8ed1ab_0    conda-forge
protobuf                  3.15.8           py38h6f2b01f_0    conda-forge
psutil                    5.9.4            py38hb991d35_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.6.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqtgraph                 0.13.1                   pypi_0    pypi
pyrsistent                0.19.3           py38hb991d35_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.8.15          hf452327_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-flatbuffers        1.12               pyhd8ed1ab_1    conda-forge
python-json-logger        2.0.4              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      3_cp38    conda-forge
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pywavelets                1.4.1            py38hb39dbe9_0    conda-forge
pyyaml                    6.0              py38hb991d35_5    conda-forge
pyzmq                     25.0.0           py38hb72be9f_0    conda-forge
rastermap                 0.1.3                    pypi_0    pypi
re2                       2021.04.01           hbdafb3b_0    conda-forge
readline                  8.1.2                h46ed386_0    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rsa                       4.9                pyhd8ed1ab_0    conda-forge
sbxreader                 0.2.2                    pypi_0    pypi
scanimage-tiff-reader     1.4.1                    pypi_0    pypi
scikit-image              0.19.3           py38h61dac83_2    conda-forge
scikit-learn              1.2.1                    pypi_0    pypi
scipy                     1.10.0                   pypi_0    pypi
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                66.1.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.9                h17c5cce_2    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
stardist                  0.8.3            py38ha3abf1e_0    conda-forge
suite2p                   0.12.1.dev14+g2579413          pypi_0    pypi
tensorboard               2.4.1              pyhd8ed1ab_1    conda-forge
tensorboard-plugin-wit    1.8.1              pyhd8ed1ab_0    conda-forge
tensorflow                2.4.0            py38h150bfb4_0    conda-forge
tensorflow-base           2.4.0            py38h267a8af_0    conda-forge
tensorflow-estimator      2.4.0              pyh9656e83_0    conda-forge
termcolor                 2.2.0              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
threadpoolctl             3.1.0                    pypi_0    pypi
tifffile                  2023.1.23.1        pyhd8ed1ab_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
torch                     1.11.0                   pypi_0    pypi
tornado                   6.2              py38hb991d35_1    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.8.1              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
unicodedata2              15.0.0           py38hb991d35_0    conda-forge
urllib3                   1.26.14            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.0              pyhd8ed1ab_0    conda-forge
werkzeug                  2.2.2              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.5              pyhd8ed1ab_0    conda-forge
wrapt                     1.14.1           py38hb991d35_1    conda-forge
xorg-libxau               1.0.9                h27ca646_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                      1.8.2            py38hb991d35_0    conda-forge
zeromq                    4.3.4                hbdafb3b_1    conda-forge
zfp                       1.0.0                hb6e4faa_3    conda-forge
zipp                      3.11.0                   pypi_0    pypi
zlib                      1.2.13               h03a7124_4    conda-forge
zlib-ng                   2.0.6                he4db4b2_0    conda-forge
zstd                      1.5.2                hf913c23_6    conda-forge

Versions:

os: macOS-12.5.1-arm64-arm-64bit
stardist: 0.8.3
csbdeep: 0.7.2
tensorflow: 2.4.0
WARNING:tensorflow:From <ipython-input-1-de739a17937a>:12: is_gpu_available (from tensorflow.python.framework.test_util) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.config.list_physical_devices('GPU')` instead.
tensorflow GPU: False
@bgriffen bgriffen added the bug Something isn't working label Feb 9, 2023
@bgriffen
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bgriffen commented Feb 9, 2023

Update: uninstalling tensorflow and running pip install tensorflow-macos, pip install tensorflow-metal then re-running pip install stardist seems to have connected tensorflow to the gpu and now it's working. 👍 I think this should be added to the README for M1 Mac users.

@psobolewskiPhD
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Can you clarify which part of the instructions didn't work or wasn't clear?
https://github.com/stardist/stardist#apple-silicon

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@bgriffen @psobolewskiPhD