pytraj not compatible with osx-arm64 arch

[xiki-tempula]

Also posted in the pytraj issue Amber-MD/pytraj#1654

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

If I tried to install pytraj through the ambertools from conda-forge I will get the error

In [1]: import pytraj
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[1], line 1
----> 1 import pytraj

File ~/miniconda3/envs/ambertools/lib/python3.12/site-packages/pytraj/__init__.py:24
     22 from .utils import c_commands
     23 from .utils import tools
---> 24 from .utils.misc import info
     25 from .utils.cyutils import _fast_iterptr as iterframe_from_array
     26 from .core.c_options import info as compiled_info

File ~/miniconda3/envs/ambertools/lib/python3.12/site-packages/pytraj/utils/misc.py:7
      5 import os
      6 from glob import glob
----> 7 from pytraj.core.c_options import set_world_silent
      9 from .context import capture_stdout
     11 try:

File ~/miniconda3/envs/ambertools/lib/python3.12/site-packages/pytraj/core/__init__.py:2
      1 """"""
----> 2 from .topology_objects import Atom, Residue, Molecule
      3 from .box import Box
      4 from .elements import mass_atomic_number_dict, mass_element_dict

ImportError: dlopen(/Users/zwu/miniconda3/envs/ambertools/lib/python3.12/site-packages/pytraj/core/topology_objects.cpython-312-darwin.so, 0x0002): tried: '/Users/zwu/miniconda3/envs/ambertools/lib/python3.12/site-packages/pytraj/core/topology_objects.cpython-312-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/zwu/miniconda3/envs/ambertools/lib/python3.12/site-packages/pytraj/core/topology_objects.cpython-312-darwin.so' (no such file), '/Users/zwu/miniconda3/envs/ambertools/lib/python3.12/site-packages/pytraj/core/topology_objects.cpython-312-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))

This is how I set up the env
conda create -n ambertools ambertools ipython

Installed packages

ambertools                23.6            nompi_py312hcf35e4f_102    conda-forge
amberutils                21.0                     pypi_0    pypi
arpack                    3.8.0           nompi_ha3438d0_101    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               h9c252e8_1    conda-forge
brotli                    1.1.0                hb547adb_1    conda-forge
brotli-bin                1.1.0                hb547adb_1    conda-forge
bzip2                     1.0.8                h93a5062_5    conda-forge
c-ares                    1.28.1               h93a5062_0    conda-forge
ca-certificates           2024.2.2             hf0a4a13_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1           py312h0fef576_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
edgembar                  0.2                      pypi_0    pypi
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fftw                      3.3.10          nompi_h3046061_108    conda-forge
fonttools                 4.52.4          py312h7e5086c_0    conda-forge
freetype                  2.12.1               hadb7bae_2    conda-forge
hdf4                      4.2.15               h2ee6834_7    conda-forge
hdf5                      1.14.3          nompi_h751145d_101    conda-forge
icu                       73.2                 hc8870d7_0    conda-forge
ipython                   8.24.0             pyh707e725_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.5           py312h389731b_1    conda-forge
krb5                      1.21.2               h92f50d5_0    conda-forge
lcms2                     2.16                 ha0e7c42_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libaec                    1.1.3                hebf3989_0    conda-forge
libblas                   3.9.0           22_osxarm64_openblas    conda-forge
libboost                  1.84.0               h17eb2be_3    conda-forge
libbrotlicommon           1.1.0                hb547adb_1    conda-forge
libbrotlidec              1.1.0                hb547adb_1    conda-forge
libbrotlienc              1.1.0                hb547adb_1    conda-forge
libcblas                  3.9.0           22_osxarm64_openblas    conda-forge
libcurl                   8.8.0                h7b6f9a7_0    conda-forge
libcxx                    17.0.6               h5f092b4_0    conda-forge
libdeflate                1.20                 h93a5062_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h93a5062_2    conda-forge
libexpat                  2.6.2                hebf3989_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
libiconv                  1.17                 h0d3ecfb_2    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
liblapack                 3.9.0           22_osxarm64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_h291a7c2_113    conda-forge
libnghttp2                1.58.0               ha4dd798_1    conda-forge
libopenblas               0.3.27          openmp_h6c19121_0    conda-forge
libpng                    1.6.43               h091b4b1_0    conda-forge
libsqlite                 3.45.3               h091b4b1_0    conda-forge
libssh2                   1.11.0               h7a5bd25_0    conda-forge
libtiff                   4.6.0                h07db509_3    conda-forge
libwebp-base              1.4.0                h93a5062_0    conda-forge
libxcb                    1.15                 hf346824_0    conda-forge
libxml2                   2.12.7               ha661575_0    conda-forge
libzip                    1.10.1               ha0bc3c6_3    conda-forge
libzlib                   1.2.13               hfb2fe0b_6    conda-forge
llvm-openmp               18.1.6               hde57baf_0    conda-forge
lz4-c                     1.9.4                hb7217d7_0    conda-forge
matplotlib-base           3.8.4           py312h4479663_2    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.5                  hb89a1cb_0    conda-forge
netcdf-fortran            4.6.1           nompi_he6a98ad_103    conda-forge
numpy                     1.26.4          py312h8442bc7_0    conda-forge
openjpeg                  2.5.2                h9f1df11_0    conda-forge
openssl                   3.3.0                hfb2fe0b_3    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
packmol-memgen            2024.2.9                 pypi_0    pypi
pandas                    2.2.2           py312h8ae5369_1    conda-forge
parmed                    4.2.2           py312h20a0b95_1    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          7_h4614cfb_perl5    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.3.0          py312h8a801b1_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_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
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
python                    3.12.3          h4a7b5fc_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.12                    4_cp312    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.13.1          py312h14ffa8f_0    conda-forge
setuptools                70.0.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.2.0                hd04f947_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
typing_extensions         4.11.0             pyha770c72_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xorg-kbproto              1.0.7             h27ca646_1002    conda-forge
xorg-libice               1.1.1                hb547adb_0    conda-forge
xorg-libsm                1.2.4                hb547adb_0    conda-forge
xorg-libx11               1.8.9                h570a39f_0    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xorg-libxext              1.3.4                h1a8c8d9_2    conda-forge
xorg-libxt                1.3.0                hb547adb_1    conda-forge
xorg-xextproto            7.3.0             h1a8c8d9_1003    conda-forge
xorg-xproto               7.0.31            h27ca646_1007    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
zlib                      1.2.13               hfb2fe0b_6    conda-forge
zstd                      1.5.6                hb46c0d2_0    conda-forge

Environment info

active environment : ambertools
    active env location : /Users/zwu/miniconda3/envs/ambertools
            shell level : 2
       user config file : /Users/zwu/.condarc
 populated config files : 
          conda version : 24.5.0
    conda-build version : 24.5.0
         python version : 3.12.2.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=m1
                          __conda=24.5.0=0
                          __osx=14.4.1=0
                          __unix=0=0
       base environment : /Users/zwu/miniconda3  (writable)
      conda av data dir : /Users/zwu/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/zwu/miniconda3/pkgs
                          /Users/zwu/.conda/pkgs
       envs directories : /Users/zwu/miniconda3/envs
                          /Users/zwu/.conda/envs
               platform : osx-arm64
             user-agent : conda/24.5.0 requests/2.31.0 CPython/3.12.2 Darwin/23.4.0 OSX/14.4.1 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8 aau/0.4.4 c/. s/. e/.
                UID:GID : 502:20
             netrc file : None
           offline mode : False

[xiki-tempula]

There seems to be some warning in the build process. https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=926796&view=logs&jobId=266f534b-1ce7-58d0-3a65-1de47ed517a3&j=266f534b-1ce7-58d0-3a65-1de47ed517a3&t=f6d6a041-258d-5cb2-03c5-b120fb5fdeff

clang++ -bundle -undefined dynamic_lookup -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-rpath,@loader_path/../../../.. -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -fPIE -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ambertools-23.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -mmacosx-version-min=11.0 $SRC_DIR/build_host_tools/build/AmberTools/src/pytraj/CMakeFiles/python-build/temp.macosx-11.0-arm64-cpython-310/pytraj/core/topology_objects.o -L$SRC_DIR/build_host_tools/build/AmberTools/src/cpptraj/src -lcpptraj -o $SRC_DIR/build_host_tools/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.macosx-11.0-arm64-cpython-310/pytraj/core/topology_objects.cpython-310-darwin.so -O0 -ggdb
2024-05-03T14:34:58.8935650Z ld: warning: -pie being ignored. It is only used when linking a main executable
2024-05-03T14:34:58.8937780Z ld: warning: ignoring file /Users/runner/miniforge3/conda-bld/ambertools_1714742026204/work/build_host_tools/build/AmberTools/src/pytraj/CMakeFiles/python-build/temp.macosx-11.0-arm64-cpython-310/pytraj/core/topology_objects.o, building for macOS-x86_64 but attempting to link with file built for unknown-arm64
2024-05-03T14:34:58.8940380Z ld: warning: ignoring file /Users/runner/miniforge3/conda-bld/ambertools_1714742026204/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/libc++.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
2024-05-03T14:34:58.8942390Z ld: warning: ignoring file /Users/runner/miniforge3/conda-bld/ambertools_1714742026204/work/build_host_tools/build/AmberTools/src/cpptraj/src/libcpptraj.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64

This problem could be fixed by running https://github.com/conda-forge/ambertools-feedstock/blob/main/build-locally.py to build it nativly on a M1 mac then copy the build pytraj across. Like

cp -r /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1717574254335/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.10/site-packages/pytraj /Users/zwu/miniconda3/envs/ambertools/lib/python3.10/site-packages/