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Fails to build with Python 3.13 #1677

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vedranmiletic opened this issue Dec 23, 2024 · 4 comments
Open

Fails to build with Python 3.13 #1677

vedranmiletic opened this issue Dec 23, 2024 · 4 comments

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@vedranmiletic
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Noticed this when building AmberTools 24:

[ 75%] Building pytraj native library
sys.argv ['setup.py', 'build', '-b', '/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build']
Original compiler envs
CXX = /usr/bin/g++-13
CC = /usr/bin/gcc-13
COMPILER =
use_pip = False, cpptraj_home =
compile_c_extension = True
2.0.6
use_prebuilt_cythonized_files =  False
pytraj is inside AMBERHOME
using environment: CC=/usr/bin/gcc-13, CXX=/usr/bin/g++-13
using CC=/usr/bin/gcc-13, CXX=/usr/bin/g++-13
Final compiler envs
CXX = /usr/bin/g++-13
CC = /usr/bin/gcc-13
COMPILER =
install = True
set rpath to /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/cpptraj/src
/usr/lib/python3.13/site-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!

        ********************************************************************************
        Usage of dash-separated 'description-file' will not be supported in future
        versions. Please use the underscore name 'description_file' instead.

        By 2025-Mar-03, you need to update your project and remove deprecated calls
        or your builds will no longer be supported.

        See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
        ********************************************************************************

!!
  opt = self.warn_dash_deprecation(opt, section)
/usr/lib/python3.13/site-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
running build
running build_py
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/all_actions.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/io.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
copying pytraj/version.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/context.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/convert.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/misc.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/get_common_objects.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/Timer.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/decorators.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/tools.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/c_commands.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/progress.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
copying pytraj/utils/check_and_assert.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/utils
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/builder
copying pytraj/builder/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/builder
copying pytraj/builder/build.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/builder
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/water.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/topology_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/dssp_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/base_holder.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/nmr.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/dihedral_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/rmsd.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/matrix.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/energy_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/hbond_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/nucleic_acid_analysis.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
copying pytraj/analysis/vector.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_action
copying pytraj/analysis/c_action/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_action
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_analysis
copying pytraj/analysis/c_analysis/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_analysis
copying pytraj/analysis/c_analysis/analysis_dict.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/analysis/c_analysis
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
copying pytraj/datasets/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
copying pytraj/datasets/array.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
copying pytraj/datasets/datasetlist.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datasets
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
copying pytraj/externals/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
copying pytraj/externals/magic.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
copying pytraj/externals/wurlitzer.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/externals
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/stripped_trajectory.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/shared_trajectory.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/frameiter.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/trajectory.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/shared_methods.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
copying pytraj/trajectory/trajectory_iterator.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory/c_traj
copying pytraj/trajectory/c_traj/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/trajectory/c_traj
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/topology
copying pytraj/topology/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/topology
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles
copying pytraj/datafiles/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles
copying pytraj/datafiles/load_samples.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/ala3
copying pytraj/datafiles/ala3/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/ala3
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/tz2
copying pytraj/datafiles/tz2/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/tz2
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/dpdp
copying pytraj/datafiles/dpdp/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/dpdp
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/trpcage
copying pytraj/datafiles/trpcage/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/trpcage
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/remd_ala2
copying pytraj/datafiles/remd_ala2/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/datafiles/remd_ala2
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/math
copying pytraj/math/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/math
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
copying pytraj/core/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
copying pytraj/core/elements.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/core
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/multiprocess.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/mpi.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/dataset.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
copying pytraj/parallel/base.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/parallel
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/cluster
copying pytraj/cluster/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/cluster
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/visualization
copying pytraj/visualization/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/visualization
copying pytraj/visualization/view.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/visualization
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/serialize
copying pytraj/serialize/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/serialize
copying pytraj/serialize/serialize.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/serialize
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/lazy.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
copying pytraj/sandbox/transform.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-313/pytraj/sandbox
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running build_ext
building 'pytraj.datasets.cast_dataset' extension
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/temp.linux-x86_64-cpython-313/pytraj/datasets
/usr/bin/g++-13 -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -I/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/../cpptraj/src -I/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/pytraj -I/usr/include/python3.13 -c pytraj/datasets/cast_dataset.cpp -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/temp.linux-x86_64-cpython-313/pytraj/datasets/cast_dataset.o -O0 -ggdb -fopenmp -Wl,-rpath=/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/build/AmberTools/src/cpptraj/src
In Datei, eingebunden von /usr/include/assert.h:35,
                 von /usr/include/python3.13/Python.h:19,
                 von pytraj/datasets/cast_dataset.cpp:20:
/usr/include/features.h:422:4: Warnung: #warning _FORTIFY_SOURCE requires compiling with optimization (-O) [-Wcpp]
  422 | #  warning _FORTIFY_SOURCE requires compiling with optimization (-O)
      |    ^~~~~~~
In Datei, eingebunden von /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/../cpptraj/src/Grid.h:3,
                 von pytraj/datasets/cast_dataset.cpp:799:
/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber24_src/AmberTools/src/pytraj/../cpptraj/src/ArrayIterator.h:6:35: Warnung: »template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator« ist veraltet [-Wdeprecated-declarations]
    6 | class ArrayIterator : public std::iterator<std::forward_iterator_tag, T> {
      |                                   ^~~~~~~~
In Datei, eingebunden von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/bits/stl_algobase.h:65,
                 von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/bits/specfun.h:43,
                 von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/cmath:3699,
                 von /usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/math.h:36,
                 von /usr/include/python3.13/Python.h:22:
/usr/lib/gcc/x86_64-pc-linux-gnu/13.3.1/include/c++/bits/stl_iterator_base_types.h:127:34: Anmerkung: hier deklariert
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
pytraj/datasets/cast_dataset.cpp:1015:72: Warnung: »Py_UNICODE« ist veraltet [-Wdeprecated-declarations]
 1015 | static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) {
      |                                                                        ^
In Datei, eingebunden von /usr/include/python3.13/unicodeobject.h:1014,
                 von /usr/include/python3.13/Python.h:79:
/usr/include/python3.13/cpython/unicodeobject.h:10:37: Anmerkung: hier deklariert
   10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE;
      |                                     ^~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE*)«:
pytraj/datasets/cast_dataset.cpp:1016:23: Warnung: »Py_UNICODE« ist veraltet [-Wdeprecated-declarations]
 1016 |     const Py_UNICODE *u_end = u;
      |                       ^~~~~
/usr/include/python3.13/cpython/unicodeobject.h:10:37: Anmerkung: hier deklariert
   10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE;
      |                                     ^~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »int __Pyx_PyList_Extend(PyObject*, PyObject*)«:
pytraj/datasets/cast_dataset.cpp:4164:22: Fehler: »_PyList_Extend« wurde in diesem Gültigkeitsbereich nicht deklariert; meinten Sie »PyList_Extend«?
 4164 |     PyObject* none = _PyList_Extend((PyListObject*)L, v);
      |                      ^~~~~~~~~~~~~~
      |                      PyList_Extend
pytraj/datasets/cast_dataset.cpp: In Funktion »void __Pyx_init_assertions_enabled()«:
pytraj/datasets/cast_dataset.cpp:4202:39: Fehler: »_PyInterpreterState_GetConfig« wurde in diesem Gültigkeitsbereich nicht deklariert; meinten Sie »PyInterpreterState_GetID«?
 4202 |     __pyx_assertions_enabled_flag = ! _PyInterpreterState_GetConfig(__Pyx_PyThreadState_Current->interp)->optimization_level;
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                       PyInterpreterState_GetID
pytraj/datasets/cast_dataset.cpp: In Funktion »int __Pyx_PyInt_As_int(PyObject*)«:
pytraj/datasets/cast_dataset.cpp:24717:46: Fehler: zu wenige Argumente für Funktion »int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)«
24717 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
      |                           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
24718 |                                               bytes, sizeof(val),
      |                                               ~~~~~~~~~~~~~~~~~~~
24719 |                                               is_little, !is_unsigned);
      |                                               ~~~~~~~~~~~~~~~~~~~~~~~~
In Datei, eingebunden von /usr/include/python3.13/longobject.h:107,
                 von /usr/include/python3.13/Python.h:81:
/usr/include/python3.13/cpython/longobject.h:111:17: Anmerkung: hier deklariert
  111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
      |                 ^~~~~~~~~~~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »long int __Pyx_PyInt_As_long(PyObject*)«:
pytraj/datasets/cast_dataset.cpp:24913:46: Fehler: zu wenige Argumente für Funktion »int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)«
24913 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
      |                           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
24914 |                                               bytes, sizeof(val),
      |                                               ~~~~~~~~~~~~~~~~~~~
24915 |                                               is_little, !is_unsigned);
      |                                               ~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: Anmerkung: hier deklariert
  111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
      |                 ^~~~~~~~~~~~~~~~~~~
pytraj/datasets/cast_dataset.cpp: In Funktion »char __Pyx_PyInt_As_char(PyObject*)«:
pytraj/datasets/cast_dataset.cpp:25185:46: Fehler: zu wenige Argumente für Funktion »int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)«
25185 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
      |                           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
25186 |                                               bytes, sizeof(val),
      |                                               ~~~~~~~~~~~~~~~~~~~
25187 |                                               is_little, !is_unsigned);
      |                                               ~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: Anmerkung: hier deklariert
  111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
      |                 ^~~~~~~~~~~~~~~~~~~
error: command '/usr/bin/g++-13' failed with exit code 1
make[2]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/build.make:535: AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Fehler 1
make[1]: *** [CMakeFiles/Makefile2:7341: AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Fehler 2
make[1]: *** Es wird auf noch nicht beendete Prozesse gewartet …
@hainm
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hainm commented Dec 23, 2024

Thanks @vedranmiletic for the report. For now, please try lower version since 3.13 is too new. Thanks.
I will have a look.

@vedranmiletic
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@hainm Thanks for the quick response.

By the way, I would, but it is not my choice to make. I am packaging AmberTools in Arch User Repository and Arch Linux recently moved to Python 3.13 as the default version.

@dacase
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dacase commented Dec 23, 2024

I am not familiar with the Arch User Repository, but is there some way to "pin" python to a given version? As an additional example, parts of AmberTools (I'm not sure about pytraj), still require version 1.26 of numpy, rather than the current version 2. And we know you will find problems if/when Arch upgrades to gcc14.

Of course, this dependency issue is a big part of what makes package managers like conda so complex.

But in any event, thanks for your work in this area. If you find code changes that would make AmberTools more compatible with current upstream software, let us know -- that would help everyone, not just the Arch Linux folks.

@vedranmiletic
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I am not familiar with the Arch User Repository, but is there some way to "pin" python to a given version?

In theory, yes. In practice this means that each user has to compile Python 3.12 before compiling AmberTools, and for me this is no go. I am considering depending on Miniforge (which includes 3.12) instead of that, but I would prefer patching software.

As an additional example, parts of AmberTools (I'm not sure about pytraj), still require version 1.26 of numpy, rather than the current version 2.

If that is the asarray()/asanyarray() change in ParmEd, I already have that patched locally and will publish it in the next go.

And we know you will find problems if/when Arch upgrades to gcc14.

Arch Linux has already upgraded to GCC 14, but GCC 13 is provided as a binary since CUDA needs it so we can easily depend on that.

Of course, this dependency issue is a big part of what makes package managers like conda so complex.

True, it is what it is. Furthermore, Arch is rolling-release with all advantages and disadvantages of that.

But in any event, thanks for your work in this area. If you find code changes that would make AmberTools more compatible with current upstream software, let us know -- that would help everyone, not just the Arch Linux folks.

Great! I would be glad to upstream the patches so I don't have to carry them locally.

For a start I patched a CUDA CMake config file to allow using CUDA 12.6 (the only version provided by Arch), but that file is not part of AmberClassic. Where should I submit a patch?

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