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macos jaxlib cpu_py313hd85e7f4_0 can't load with latest libabseil cxx17_h07bc746_2 #296

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traversaro opened this issue Jan 2, 2025 · 5 comments
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macos jaxlib cpu_py313hd85e7f4_0 can't load with latest libabseil cxx17_h07bc746_2 #296

traversaro opened this issue Jan 2, 2025 · 5 comments
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bug Something isn't working

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@traversaro
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Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

Installing a fresh environment with jax and tryng to load jax on macos, results in the following error:

 ___________ ERROR collecting tests/parametric/test_jax_parametric.py ___________
ImportError while importing test module '/Users/runner/work/adam/adam/tests/parametric/test_jax_parametric.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../micromamba/envs/adamdev/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/parametric/test_jax_parametric.py:3: in <module>
    from adam.parametric.jax import KinDynComputationsParametric
../../../micromamba/envs/adamdev/lib/python3.13/site-packages/adam/parametric/jax/__init__.py:5: in <module>
    from .computations_parametric import KinDynComputationsParametric
../../../micromamba/envs/adamdev/lib/python3.13/site-packages/adam/parametric/jax/computations_parametric.py:7: in <module>
    import jax.numpy as jnp
../../../micromamba/envs/adamdev/lib/python3.13/site-packages/jax/__init__.py:25: in <module>
    from jax._src.cloud_tpu_init import cloud_tpu_init as _cloud_tpu_init
../../../micromamba/envs/adamdev/lib/python3.13/site-packages/jax/_src/cloud_tpu_init.py:17: in <module>
    from jax._src import config
../../../micromamba/envs/adamdev/lib/python3.13/site-packages/jax/_src/config.py:27: in <module>
    from jax._src import lib
../../../micromamba/envs/adamdev/lib/python3.13/site-packages/jax/_src/lib/__init__.py:87: in <module>
    import jaxlib.xla_client as xla_client
../../../micromamba/envs/adamdev/lib/python3.13/site-packages/jaxlib/xla_client.py:33: in <module>
    from . import xla_extension as _xla
E   ImportError: dlopen(/Users/runner/micromamba/envs/adamdev/lib/python3.13/site-packages/jaxlib/xla_extension.so, 0x0002): Symbol not found: __ZN4absl12lts_2024072212log_internal10LogMessagelsIPKvLi0EEERS2_RKT_
E     Referenced from: <05E679BA-8DDA-37BF-BA62-E2CC01CA7001> /Users/runner/micromamba/envs/adamdev/lib/python3.13/site-packages/jaxlib/xla_extension.so
E     Expected in:     <D623F952-8116-35EC-859D-F7F8D5DD7699> /Users/runner/micromamba/envs/adamdev/lib/libabsl_log_internal_message.2407.0.0.dylib

The problem is described in conda-forge/abseil-cpp-feedstock#87 (comment) , but I opened an issue also here for visibility.

Installed packages

~~~
  ampl-asl            1.0.0       h286801f_2                    conda-forge
  assimp              5.4.3       ha9c0b8d_0                    conda-forge
  brotli-python       1.1.0       py313h3579c5c_2               conda-forge
  bzip2               1.0.8       h99b78c6_7                    conda-forge
  c-ares              1.34.4      h5505292_0                    conda-forge
  ca-certificates     2024.12.14  hf0a4a13_0                    conda-forge
  casadi              3.6.7       py313h2d9e3a2_1               conda-forge
  certifi             2024.12.14  pyhd8ed1ab_0                  conda-forge
  cffi                1.17.1      py313hc845a76_0               conda-forge
  charset-normalizer  3.4.0       pyhd8ed1ab_1                  conda-forge
  colorama            0.4.6       pyhd8ed1ab_1                  conda-forge
  cpython             3.13.1      py313hd8ed1ab_102             conda-forge
  eigen               3.4.0       h1995070_0                    conda-forge
  exceptiongroup      1.2.2       pyhd8ed1ab_1                  conda-forge
  filelock            3.16.1      pyhd8ed1ab_1                  conda-forge
  fsspec              2024.12.0   pyhd8ed1ab_0                  conda-forge
  glfw                3.4         h93a5062_0                    conda-forge
  gmp                 6.3.0       h7bae524_2                    conda-forge
  gmpy2               2.1.5       py313h2cdc120_3               conda-forge
  h2                  4.1.0       pyhd8ed1ab_1                  conda-forge
  hpack               4.0.0       pyhd8ed1ab_1                  conda-forge
  hyperframe          6.0.1       pyhd8ed1ab_1                  conda-forge
  icu                 75.1        hfee45f7_0                    conda-forge
  icub-models         3.0.0       py313h928ef07_0               conda-forge
  idna                3.10        pyhd8ed1ab_1                  conda-forge
  idyntree            13.2.0      py313h6a9655c_1               conda-forge
  importlib-metadata  8.5.0       pyha770c72_1                  conda-forge
  iniconfig           2.0.0       pyhd8ed1ab_1                  conda-forge
  ipopt               3.14.17     h3e4dc2c_0                    conda-forge
  irrlicht            1.8.5       hdfd4c6d_5                    conda-forge
  jax                 0.4.35      pyhd8ed1ab_1                  conda-forge
  jax2torch           0.0.7       pyhd8ed1ab_0                  conda-forge
  jaxlib              0.4.35      cpu_py313hd85e7f4_0           conda-forge
  jinja2              3.1.5       pyhd8ed1ab_0                  conda-forge
  libabseil           20240722.0  cxx17_h07bc746_2              conda-forge
  libblas             3.9.0       26_osxarm64_openblas          conda-forge
  libboost            1.86.0      hc9fb7c5_3                    conda-forge
  libcblas            3.9.0       26_osxarm64_openblas          conda-forge
  libcxx              19.1.6      ha82da77_1                    conda-forge
  libexpat            2.6.4       h286801f_0                    conda-forge
  libffi              3.4.2       h3422bc3_5                    conda-forge
  libgfortran         5.0.0       13_2_0_hd922786_3             conda-forge
  libgfortran5        13.2.0      hf226fd6_3                    conda-forge
  libgrpc             1.67.1      hc70892a_0                    conda-forge
  libiconv            1.17        h0d3ecfb_2                    conda-forge
  libjpeg-turbo       3.0.0       hb547adb_1                    conda-forge
  liblapack           3.9.0       26_osxarm64_openblas          conda-forge
  liblzma             5.6.3       h39f12f2_1                    conda-forge
  libmpdec            4.0.0       h99b78c6_0                    conda-forge
  libopenblas         0.3.28      openmp_hf332438_1             conda-forge
  libosqp             0.6.3       h5833ebf_1                    conda-forge
  libpng              1.6.44      hc14010f_0                    conda-forge
  libprotobuf         5.28.2      h8f0b736_0                    conda-forge
  libqdldl            0.1.7       hb7217d7_0                    conda-forge
  libre2-11           2024.07.02  h07bc746_2                    conda-forge
  libscotch           7.0.5       hc2b2845_4                    conda-forge
  libsqlite           3.47.2      h3f77e49_0                    conda-forge
  libtorch            2.5.1       cpu_generic_h4c131e9_7        conda-forge
  libuv               1.49.2      h7ab814d_0                    conda-forge
  libxcb              1.17.0      hdb1d25a_0                    conda-forge
  libxml2             2.13.5      h178c5d8_1                    conda-forge
  libxslt             1.1.39      h223e5b9_0                    conda-forge
  libzlib             1.3.1       h8359307_2                    conda-forge
  llvm-openmp         19.1.6      hdb05f8b_0                    conda-forge
  lxml                5.3.0       py313h6b44993_2               conda-forge
  markupsafe          3.0.2       py313ha9b7d5b_1               conda-forge
  metis               5.1.0       h15f6cfe_1007                 conda-forge
  ml_dtypes           0.5.0       py313h47b39a6_0               conda-forge
  mpc                 1.3.1       h8f1351a_1                    conda-forge
  mpfr                4.2.1       hb693164_3                    conda-forge
  mpmath              1.3.0       pyhd8ed1ab_1                  conda-forge
  mumps-include       5.7.3       hce30654_5                    conda-forge
  mumps-seq           5.7.3       he17653c_5                    conda-forge
  ncurses             6.5         h7bae524_1                    conda-forge
  networkx            3.4.2       pyh267e887_2                  conda-forge
  nomkl               1.0         h5ca1d4c_0                    conda-forge
  numpy               2.2.1       py313ha4a2180_0               conda-forge
  openssl             3.4.0       h39f12f2_0                    conda-forge
  opt-einsum          3.4.0       hd8ed1ab_1                    conda-forge
  opt_einsum          3.4.0       pyhd8ed1ab_1                  conda-forge
  osqp-eigen          0.8.1       h136a8c3_1                    conda-forge
  packaging           24.2        pyhd8ed1ab_2                  conda-forge
  pip                 24.3.1      pyh145f28c_2                  conda-forge
  pluggy              1.5.0       pyhd8ed1ab_1                  conda-forge
  prettytable         3.12.0      pyhd8ed1ab_1                  conda-forge
  proxsuite           0.6.7       py313h27638e2_2               conda-forge
  pthread-stubs       0.4         hd74edd7_1002                 conda-forge
  pycparser           2.22        pyh29332c3_1                  conda-forge
  pysocks             1.7.1       pyha55dd90_7                  conda-forge
  pytest              8.3.4       pyhd8ed1ab_1                  conda-forge
  pytest-repeat       0.9.3       pyhff2d567_0                  conda-forge
  python              3.13.1      h4f43103_102_cp313            conda-forge
  python_abi          3.13        5_cp313                       conda-forge
  pytorch             2.5.1       cpu_generic_py313_h44dfc17_7  conda-forge
  pyyaml              6.0.2       py313h20a7fcf_1               conda-forge
  re2                 2024.07.02  h6589ca4_2                    conda-forge
  readline            8.2         h92ec313_1                    conda-forge
  requests            2.32.3      pyhd8ed1ab_1                  conda-forge
  scipy               1.14.1      py313hc010ede_2               conda-forge
  sdl                 1.2.68      hfc12253_0                    conda-forge
  sdl2                2.30.10     h994913f_0                    conda-forge
  setuptools          75.6.0      pyhff2d567_1                  conda-forge
  setuptools-scm      8.1.0       pyhd8ed1ab_1                  conda-forge
  setuptools_scm      8.1.0       hd8ed1ab_1                    conda-forge
  simde               0.8.2       h7b3277c_0                    conda-forge
  sleef               3.7         h8391f65_2                    conda-forge
  sympy               1.13.3      pyh2585a3b_104                conda-forge
  tinyxml2            10.0.0      hebf3989_0                    conda-forge
  tk                  8.6.13      h5083fa2_1                    conda-forge
  tomli               2.2.1       pyhd8ed1ab_1                  conda-forge
  typing-extensions   4.12.2      hd8ed1ab_1                    conda-forge
  typing_extensions   4.12.2      pyha770c72_1                  conda-forge
  tzdata              2024b       hc8b5060_0                    conda-forge
  urdfdom-py          1.2.1       py313h8f79df9_5               conda-forge
  urllib3             2.3.0       pyhd8ed1ab_0                  conda-forge
  wcwidth             0.2.13      pyhd8ed1ab_1                  conda-forge
  wheel               0.45.1      pyhd8ed1ab_1                  conda-forge
  xorg-libx11         1.8.10      h6a5fb8c_1                    conda-forge
  xorg-libxau         1.0.12      h5505292_0                    conda-forge
  xorg-libxdmcp       1.1.5       hd74edd7_0                    conda-forge
  xorg-libxext        1.3.6       hd74edd7_0                    conda-forge
  yaml                0.2.5       h3422bc3_2                    conda-forge
  zipp                3.21.0      pyhd8ed1ab_1                  conda-forge
  zlib                1.3.1       h8359307_2                    conda-forge
  zstandard           0.23.0      py313hf2da073_1               conda-forge
  zstd                1.5.6       hb46c0d2_0                    conda-forge
~~~

Environment info

Not available (CI machine).
@traversaro traversaro added the bug Something isn't working label Jan 2, 2025
@traversaro traversaro mentioned this issue Jan 2, 2025
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@scottstanie scottstanie mentioned this issue Jan 2, 2025
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This was referenced Jan 3, 2025
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@fxcoudert
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This should be fixed now, thanks to conda-forge/abseil-cpp-feedstock#88

@fxcoudert
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Wait no, there is more breakage: conda-forge/abseil-cpp-feedstock#89

@matthewfeickert
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I think this is fixed now with conda-forge/abseil-cpp-feedstock#90 and libabseil 20240722.0 build_number 4.

@fxcoudert
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Yes, I think it is fixed indeed.

@traversaro
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Thanks to everyone that worked on this!

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