Segmentation fault when importing amici on Mac

[anamariemartinez]

Hi,

I tried to install AMICI in a conda environment on my Mac. I followed the installation instructions, and I installed all of the dependencies. When I tried to import amici in a Jupyter notebook it instantly killed the kernel, and when I tried to import it from the terminal, it gives me a segmentation fault. My advisor tried to install and import AMICI on his Mac (same OS), and he also got the segmentation fault.

To Reproduce

1. I installed AMICI in a conda environment following the instructions.
2. python
3. import amici
4. it returns zsh: segmentation fault python
5. I tried to resolve this by installing Xcode 15..4 and running pip install amici --force-reinstall

AMICI version and system environment

• OS and version: Mac OS: Sanoma 14.5
• AMICI interface: Python 3.10.13 (also encountered with Python 3.12.4)

Thanks!

[dweindl]

Hi @anamariemartinez, sorry to hear amici isn't working on your system.

Could you please post the complete output of python3 -m pip install -v amici --force-reinstall?

[anamariemartinez]

Hi, thank you so much for getting back to me. Here is the output. I tried to downgrade numpy to version 1.26, but the issue was still occurring.

Details

`(bayes) anamariemartinez@Anamaries-MacBook-Pro ~ % python3 -m pip install -v amici --force-reinstall Using pip 24.0 from /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pip (python 3.10) Collecting amici Using cached amici-0.26.1-cp310-cp310-macosx_14_0_arm64.whl Collecting cmake-build-extension==0.6.0 (from amici) Obtaining dependency information for cmake-build-extension==0.6.0 from https://files.pythonhosted.org/packages/ac/c5/75d8fa41225c62a91615fbd3583d5bd9d1c81ab966c3232829c0ea70314e/cmake_build_extension-0.6.0-py3-none-any.whl.metadata Using cached cmake_build_extension-0.6.0-py3-none-any.whl.metadata (11 kB) Collecting sympy>=1.12.1 (from amici) Obtaining dependency information for sympy>=1.12.1 from https://files.pythonhosted.org/packages/b2/fe/81695a1aa331a842b582453b605175f419fe8540355886031328089d840a/sympy-1.13.1-py3-none-any.whl.metadata Using cached sympy-1.13.1-py3-none-any.whl.metadata (12 kB) Collecting python-libsbml (from amici) Obtaining dependency information for python-libsbml from https://files.pythonhosted.org/packages/3d/45/98defd138e1901f301b49dd88290617a1d9d9d0e8e595ab515380429773a/python_libsbml-5.20.2-cp310-cp310-macosx_11_0_arm64.whl.metadata Using cached python_libsbml-5.20.2-cp310-cp310-macosx_11_0_arm64.whl.metadata (532 bytes) Collecting pandas>=2.0.2 (from amici) Obtaining dependency information for pandas>=2.0.2 from https://files.pythonhosted.org/packages/fd/4b/0cd38e68ab690b9df8ef90cba625bf3f93b82d1c719703b8e1b333b2c72d/pandas-2.2.2-cp310-cp310-macosx_11_0_arm64.whl.metadata Using cached pandas-2.2.2-cp310-cp310-macosx_11_0_arm64.whl.metadata (19 kB) Collecting pyarrow (from amici) Obtaining dependency information for pyarrow from https://files.pythonhosted.org/packages/3b/73/8ed168db7642e91180330e4ea9f3ff8bab404678f00d32d7df0871a4933b/pyarrow-17.0.0-cp310-cp310-macosx_11_0_arm64.whl.metadata Using cached pyarrow-17.0.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (3.3 kB) Collecting toposort (from amici) Obtaining dependency information for toposort from https://files.pythonhosted.org/packages/f6/17/57b444fd314d5e1593350b9a31d000e7411ba8e17ce12dc7ad54ca76b810/toposort-1.10-py3-none-any.whl.metadata Using cached toposort-1.10-py3-none-any.whl.metadata (4.1 kB) Collecting setuptools>=48 (from amici) Obtaining dependency information for setuptools>=48 from https://files.pythonhosted.org/packages/e1/58/e0ef3b9974a04ce9cde2a7a33881ddcb2d68450803745804545cdd8d258f/setuptools-72.1.0-py3-none-any.whl.metadata Downloading setuptools-72.1.0-py3-none-any.whl.metadata (6.6 kB) Collecting mpmath (from amici) Obtaining dependency information for mpmath from https://files.pythonhosted.org/packages/43/e3/7d92a15f894aa0c9c4b49b8ee9ac9850d6e63b03c9c32c0367a13ae62209/mpmath-1.3.0-py3-none-any.whl.metadata Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB) Collecting numpy>=1.21.4 (from amici) Obtaining dependency information for numpy>=1.21.4 from https://files.pythonhosted.org/packages/5f/f7/d9db3db9ff23af6ed1d948441a4805cfcb24119a3edbe1d5d8bcc89b2496/numpy-2.0.1-cp310-cp310-macosx_14_0_arm64.whl.metadata Using cached numpy-2.0.1-cp310-cp310-macosx_14_0_arm64.whl.metadata (60 kB) Collecting cmake (from cmake-build-extension==0.6.0->amici) Obtaining dependency information for cmake from https://files.pythonhosted.org/packages/57/24/bd87254c67ce63457dcd8a1f1538f797c6a6d2e19c1b2985a2323e263e88/cmake-3.30.1-py3-none-macosx_10_10_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl.metadata Using cached cmake-3.30.1-py3-none-macosx_10_10_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl.metadata (6.1 kB) Collecting ninja (from cmake-build-extension==0.6.0->amici) Obtaining dependency information for ninja from https://files.pythonhosted.org/packages/3d/6e/04ed11bb244039908f6f212cb5f3e97933e238655248e4ce307c1687ba1f/ninja-1.11.1.1-py2.py3-none-macosx_10_9_universal2.macosx_10_9_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl.metadata Using cached ninja-1.11.1.1-py2.py3-none-macosx_10_9_universal2.macosx_10_9_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl.metadata (5.3 kB) Collecting GitPython (from cmake-build-extension==0.6.0->amici) Obtaining dependency information for GitPython from https://files.pythonhosted.org/packages/e9/bd/cc3a402a6439c15c3d4294333e13042b915bbeab54edc457c723931fed3f/GitPython-3.1.43-py3-none-any.whl.metadata Using cached GitPython-3.1.43-py3-none-any.whl.metadata (13 kB) Collecting setuptools-scm (from cmake-build-extension==0.6.0->amici) Obtaining dependency information for setuptools-scm from https://files.pythonhosted.org/packages/a0/b9/1906bfeb30f2fc13bb39bf7ddb8749784c05faadbd18a21cf141ba37bff2/setuptools_scm-8.1.0-py3-none-any.whl.metadata Using cached setuptools_scm-8.1.0-py3-none-any.whl.metadata (6.6 kB) Collecting python-dateutil>=2.8.2 (from pandas>=2.0.2->amici) Obtaining dependency information for python-dateutil>=2.8.2 from https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting pytz>=2020.1 (from pandas>=2.0.2->amici) Obtaining dependency information for pytz>=2020.1 from https://files.pythonhosted.org/packages/9c/3d/a121f284241f08268b21359bd425f7d4825cffc5ac5cd0e1b3d82ffd2b10/pytz-2024.1-py2.py3-none-any.whl.metadata Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.7 (from pandas>=2.0.2->amici) Obtaining dependency information for tzdata>=2022.7 from https://files.pythonhosted.org/packages/65/58/f9c9e6be752e9fcb8b6a0ee9fb87e6e7a1f6bcab2cdc73f02bb7ba91ada0/tzdata-2024.1-py2.py3-none-any.whl.metadata Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB) Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas>=2.0.2->amici) Obtaining dependency information for six>=1.5 from https://files.pythonhosted.org/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl.metadata Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting gitdb<5,>=4.0.1 (from GitPython->cmake-build-extension==0.6.0->amici) Obtaining dependency information for gitdb<5,>=4.0.1 from https://files.pythonhosted.org/packages/fd/5b/8f0c4a5bb9fd491c277c21eff7ccae71b47d43c4446c9d0c6cff2fe8c2c4/gitdb-4.0.11-py3-none-any.whl.metadata Using cached gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB) Collecting packaging>=20 (from setuptools-scm->cmake-build-extension==0.6.0->amici) Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/08/aa/cc0199a5f0ad350994d660967a8efb233fe0416e4639146c089643407ce6/packaging-24.1-py3-none-any.whl.metadata Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB) Collecting tomli>=1 (from setuptools-scm->cmake-build-extension==0.6.0->amici) Obtaining dependency information for tomli>=1 from https://files.pythonhosted.org/packages/97/75/10a9ebee3fd790d20926a90a2547f0bf78f371b2f13aa822c759680ca7b9/tomli-2.0.1-py3-none-any.whl.metadata Using cached tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB) Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->GitPython->cmake-build-extension==0.6.0->amici) Obtaining dependency information for smmap<6,>=3.0.1 from https://files.pythonhosted.org/packages/a7/a5/10f97f73544edcdef54409f1d839f6049a0d79df68adbc1ceb24d1aaca42/smmap-5.0.1-py3-none-any.whl.metadata Using cached smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB) Using cached cmake_build_extension-0.6.0-py3-none-any.whl (13 kB) Using cached numpy-2.0.1-cp310-cp310-macosx_14_0_arm64.whl (5.3 MB) Using cached pandas-2.2.2-cp310-cp310-macosx_11_0_arm64.whl (11.3 MB) Downloading setuptools-72.1.0-py3-none-any.whl (2.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 18.6 MB/s eta 0:00:00 Using cached sympy-1.13.1-py3-none-any.whl (6.2 MB) Using cached mpmath-1.3.0-py3-none-any.whl (536 kB) Using cached pyarrow-17.0.0-cp310-cp310-macosx_11_0_arm64.whl (27.2 MB) Using cached python_libsbml-5.20.2-cp310-cp310-macosx_11_0_arm64.whl (5.7 MB) Using cached toposort-1.10-py3-none-any.whl (8.5 kB) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB) Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB) Using cached cmake-3.30.1-py3-none-macosx_10_10_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl (47.9 MB) Using cached GitPython-3.1.43-py3-none-any.whl (207 kB) Using cached ninja-1.11.1.1-py2.py3-none-macosx_10_9_universal2.macosx_10_9_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl (270 kB) Using cached setuptools_scm-8.1.0-py3-none-any.whl (43 kB) Using cached gitdb-4.0.11-py3-none-any.whl (62 kB) Using cached packaging-24.1-py3-none-any.whl (53 kB) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Using cached tomli-2.0.1-py3-none-any.whl (12 kB) Using cached smmap-5.0.1-py3-none-any.whl (24 kB) Installing collected packages: toposort, pytz, python-libsbml, ninja, mpmath, tzdata, tomli, sympy, smmap, six, setuptools, packaging, numpy, cmake, setuptools-scm, python-dateutil, pyarrow, gitdb, pandas, GitPython, cmake-build-extension, amici Attempting uninstall: toposort Found existing installation: toposort 1.10 Uninstalling toposort-1.10: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/__pycache__/toposort.cpython-310.pyc Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/toposort-1.10.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/toposort.py Successfully uninstalled toposort-1.10 Attempting uninstall: pytz Found existing installation: pytz 2024.1 Uninstalling pytz-2024.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pytz-2024.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pytz/ Successfully uninstalled pytz-2024.1 Attempting uninstall: python-libsbml Found existing installation: python-libsbml 5.20.2 Uninstalling python-libsbml-5.20.2: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/libsbml/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/python_libsbml-5.20.2.dist-info/ Successfully uninstalled python-libsbml-5.20.2 Attempting uninstall: ninja Found existing installation: ninja 1.11.1.1 Uninstalling ninja-1.11.1.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/ninja Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/ninja-1.11.1.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/ninja/ Successfully uninstalled ninja-1.11.1.1 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/ninja to 755 Attempting uninstall: mpmath Found existing installation: mpmath 1.3.0 Uninstalling mpmath-1.3.0: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/mpmath-1.3.0.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/mpmath/ Successfully uninstalled mpmath-1.3.0 Attempting uninstall: tzdata Found existing installation: tzdata 2024.1 Uninstalling tzdata-2024.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/tzdata-2024.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/tzdata/ Successfully uninstalled tzdata-2024.1 Attempting uninstall: tomli Found existing installation: tomli 2.0.1 Uninstalling tomli-2.0.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/tomli-2.0.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/tomli/ Successfully uninstalled tomli-2.0.1 Attempting uninstall: sympy Found existing installation: sympy 1.13.1 Uninstalling sympy-1.13.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/isympy Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/__pycache__/isympy.cpython-310.pyc Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/isympy.py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/sympy-1.13.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/sympy/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/share/man/man1/isympy.1 Successfully uninstalled sympy-1.13.1 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/isympy to 755 Attempting uninstall: smmap Found existing installation: smmap 5.0.1 Uninstalling smmap-5.0.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/smmap-5.0.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/smmap/ Successfully uninstalled smmap-5.0.1 Attempting uninstall: six Found existing installation: six 1.16.0 Uninstalling six-1.16.0: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/__pycache__/six.cpython-310.pyc Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/six-1.16.0.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/six.py Successfully uninstalled six-1.16.0 Attempting uninstall: setuptools Found existing installation: setuptools 69.5.1 Uninstalling setuptools-69.5.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/_distutils_hack Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pkg_resources Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/setuptools Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/setuptools-69.5.1-py3.10.egg-info Successfully uninstalled setuptools-69.5.1 Attempting uninstall: packaging Found existing installation: packaging 24.1 Uninstalling packaging-24.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/packaging-24.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/packaging/ Successfully uninstalled packaging-24.1 Attempting uninstall: numpy Found existing installation: numpy 1.26.4 Uninstalling numpy-1.26.4: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/f2py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy-1.26.4.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__config__.py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__init__.pxd Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__init__.py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__init__.pyi Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__pycache__/__config__.cpython-310.pyc Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__pycache__/__init__.cpython-310.pyc Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/__pycache__/_distributor_init.cpython-310.pyc Removing file or directory 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/Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/typing/tests/test_isfile.py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/typing/tests/test_runtime.py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/typing/tests/test_typing.py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/numpy/version.py Successfully uninstalled numpy-1.26.4 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/f2py to 755 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/numpy-config to 755 Attempting uninstall: cmake Found existing installation: cmake 3.30.1 Uninstalling cmake-3.30.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/cmake Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/cpack Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/ctest Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/cmake-3.30.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/cmake/ Successfully uninstalled cmake-3.30.1 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/cmake to 755 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/cpack to 755 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/ctest to 755 Attempting uninstall: setuptools-scm Found existing installation: setuptools-scm 8.1.0 Uninstalling setuptools-scm-8.1.0: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/setuptools_scm-8.1.0.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/setuptools_scm/ Successfully uninstalled setuptools-scm-8.1.0 Attempting uninstall: python-dateutil Found existing installation: python-dateutil 2.9.0.post0 Uninstalling python-dateutil-2.9.0.post0: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/dateutil/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/python_dateutil-2.9.0.post0.dist-info/ Successfully uninstalled python-dateutil-2.9.0.post0 Attempting uninstall: pyarrow Found existing installation: pyarrow 17.0.0 Uninstalling pyarrow-17.0.0: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/benchmarks/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/cmake_modules/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/examples/dataset/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/examples/flight/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/examples/minimal_build/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/examples/parquet_encryption/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pyarrow-17.0.0.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pyarrow/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/scripts/ Successfully uninstalled pyarrow-17.0.0 Attempting uninstall: gitdb Found existing installation: gitdb 4.0.11 Uninstalling gitdb-4.0.11: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/gitdb-4.0.11.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/gitdb/ Successfully uninstalled gitdb-4.0.11 Attempting uninstall: pandas Found existing installation: pandas 2.2.2 Uninstalling pandas-2.2.2: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pandas-2.2.2.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/pandas/ Successfully uninstalled pandas-2.2.2 Attempting uninstall: GitPython Found existing installation: GitPython 3.1.43 Uninstalling GitPython-3.1.43: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/GitPython-3.1.43.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/git/ Successfully uninstalled GitPython-3.1.43 Attempting uninstall: cmake-build-extension Found existing installation: cmake-build-extension 0.6.0 Uninstalling cmake-build-extension-0.6.0: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/cmake_build_extension-0.6.0.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/cmake_build_extension/ Successfully uninstalled cmake-build-extension-0.6.0 Attempting uninstall: amici Found existing installation: amici 0.26.1 Uninstalling amici-0.26.1: Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/amici_import_petab Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/bin/amici_import_petab.py Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/amici-0.26.1.dist-info/ Removing file or directory /Users/anamariemartinez/anaconda3/envs/bayes/lib/python3.10/site-packages/amici/ Successfully uninstalled amici-0.26.1 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/amici_import_petab to 755 changing mode of /Users/anamariemartinez/anaconda3/envs/bayes/bin/amici_import_petab.py to 755 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. libroadrunner 2.7.0 requires numpy~=1.26, but you have numpy 2.0.1 which is incompatible. Successfully installed GitPython-3.1.43 amici-0.26.1 cmake-3.30.1 cmake-build-extension-0.6.0 gitdb-4.0.11 mpmath-1.3.0 ninja-1.11.1.1 numpy-2.0.1 packaging-24.1 pandas-2.2.2 pyarrow-17.0.0 python-dateutil-2.9.0.post0 python-libsbml-5.20.2 pytz-2024.1 setuptools-71.1.0 setuptools-scm-8.1.0 six-1.16.0 smmap-5.0.1 sympy-1.13.1 tomli-2.0.1 toposort-1.10 tzdata-2024.1`

Thanks again!

[dweindl]

Thanks. Unfortunately, this did not rebuild amici (Using cached amici-0.26.1-cp310-cp310-macosx_14_0_arm64.whl). Can you please run python3 -m pip install -v amici --force-reinstall --no-cache-dir and post the complete output of that? And after that, run python -m amici or python -c "import amici" to confirm that it is still crashing.

[anamariemartinez]

Here is a file with the output of running, python3 -m pip install -v amici --force-reinstall --no-cache-dir output_file.txt

When I run, python -m amici it still crashes:

zsh: segmentation fault python -m amici

[dweindl]

Thanks, unfortunately this still doesn't include the relevant output. When redirecting the output to file, please make sure that stderr is also included. E.g. via python3 -m pip install -v amici --force-reinstall --no-cache-dir > amici.log 2>&1

[anamariemartinez]

Hi, sorry for the delayed reply. Here is that file

amici.log

[dweindl]

Thanks, this is what I needed. I didn't see anything suspicious in there. Could you show the output of ls -1 /Users/anamariemartinez/anaconda3/envs/bayes/include /Users/anamariemartinez/anaconda3/envs/bayes/bin to see if there is anything potentially interfering with some system libraries?

On other Mac/ARM computers amici was working fine so far. Without any debugger output, this will be hard to pinpoint, I'm afraid. Unfortunately, I am not familiar with available debuggers on Mac.

[dweindl]

While I don't really think this is the issue, you could retry it with a more recent version of swig (https://anaconda.org/conda-forge/swig instead of https://anaconda.org/anaconda/swig) and see if that changes anything.

[dweindl]

Additionally, to exclude any issues related to the hdf5 dependency you can try AMICI_TRY_ENABLE_HDF5=OFF python3 -m pip install -v amici --force-reinstall --no-cache-dir and see if that changes anything.