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docker image fails to build with lima (docker alternative) on apple M2: scipy missing BLAS #192

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kidmose opened this issue Apr 21, 2023 · 2 comments · May be fixed by #193
Open

docker image fails to build with lima (docker alternative) on apple M2: scipy missing BLAS #192

kidmose opened this issue Apr 21, 2023 · 2 comments · May be fixed by #193

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@kidmose
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kidmose commented Apr 21, 2023

I'm trying to build the docker image on a MBP with an M2 Pro processor, using lima and nerdctl as docker replacements. This means I'm using nerdctl instead of docker, inside a VM running an 64bit arm ubuntu 22.10 on my mac.

Installation of pandas=1.2.3 as pinned in requirements/requirements.txt fails when installing numpy==1.17.3 (dependency), apparently because a lot of libraries are missing (BLAS among others). I suspect this could be due to the version of numpy (Released Oct. 17 2019) doesn't play well with 64 bit arm.

The error log is as follows:

egk@egk:~/git-reps/tram$ lima nerdctl build .
[+] Building 8.2s (6/6) FINISHED                                                                                                         
 => [internal] load .dockerignore                                                                                                   0.0s
 => => transferring context: 117B                                                                                                   0.0s
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 400B                                                                                                0.0s
 => [internal] load metadata for docker.io/library/ubuntu:20.04                                                                     0.8s
 => [1/3] FROM docker.io/library/ubuntu:20.04@sha256:db8bf6f4fb351aa7a26e27ba2686cf35a6a409f65603e59d4c203e58387dc6b3               0.0s
 => => resolve docker.io/library/ubuntu:20.04@sha256:db8bf6f4fb351aa7a26e27ba2686cf35a6a409f65603e59d4c203e58387dc6b3               0.0s
 => CACHED [2/3] RUN apt-get update &&     apt-get -y upgrade &&     apt-get -y install --no-install-recommends     ca-certificate  0.0s
 => ERROR [3/3] RUN python3 -m pip install pandas==1.2.3                                                                            7.4s
------                                                                                                                                   
 > [3/3] RUN python3 -m pip install pandas==1.2.3:                                                                                       
#0 0.791 Collecting pandas==1.2.3                                                                                                        
#0 0.925   Downloading pandas-1.2.3.tar.gz (5.5 MB)                                                                                      
#0 2.754   Installing build dependencies: started                                                                                        
#0 7.308   Installing build dependencies: finished with status 'error'                                                                   
#0 7.308   ERROR: Command errored out with exit status 1:
#0 7.308    command: /usr/bin/python3 /usr/lib/python3/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-9i_hfnvd/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.29.21,<3' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy; python_version>='"'"'3.9'"'"''
#0 7.308        cwd: None
#0 7.308   Complete output (581 lines):
#0 7.308   Ignoring numpy: markers 'python_version == "3.7" and platform_system != "AIX"' don't match your environment
#0 7.308   Ignoring numpy: markers 'python_version == "3.7" and platform_system == "AIX"' don't match your environment
#0 7.308   Ignoring numpy: markers 'python_version == "3.8" and platform_system == "AIX"' don't match your environment
#0 7.308   Ignoring numpy: markers 'python_version >= "3.9"' don't match your environment
#0 7.308   Collecting setuptools
#0 7.308     Downloading setuptools-67.7.1-py3-none-any.whl (1.1 MB)
#0 7.308   Collecting wheel
#0 7.308     Downloading wheel-0.40.0-py3-none-any.whl (64 kB)
#0 7.308   Collecting Cython<3,>=0.29.21
#0 7.308     Downloading Cython-0.29.34-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl (1.8 MB)
#0 7.308   Collecting numpy==1.17.3
#0 7.308     Downloading numpy-1.17.3.zip (6.4 MB)
#0 7.308   Building wheels for collected packages: numpy
#0 7.308     Building wheel for numpy (setup.py): started
#0 7.308     Building wheel for numpy (setup.py): finished with status 'error'
#0 7.308     ERROR: Command errored out with exit status 1:
#0 7.308      command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ldbsuhua
#0 7.308          cwd: /tmp/pip-install-46pmyfff/numpy/
#0 7.308     Complete output (262 lines):
#0 7.308     Running from numpy source directory.
#0 7.308     blas_opt_info:
#0 7.308     blas_mkl_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     blis_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries blis not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     openblas_info:
#0 7.308     customize UnixCCompiler
#0 7.308     customize UnixCCompiler
#0 7.308       libraries openblas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_3_10_blas_threads_info:
#0 7.308     Setting PTATLAS=ATLAS
#0 7.308     customize UnixCCompiler
#0 7.308       libraries tatlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_3_10_blas_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries satlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_blas_threads_info:
#0 7.308     Setting PTATLAS=ATLAS
#0 7.308     customize UnixCCompiler
#0 7.308       libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_blas_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     accelerate_info:
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:690: UserWarning:
#0 7.308         Optimized (vendor) Blas libraries are not found.
#0 7.308         Falls back to netlib Blas library which has worse performance.
#0 7.308         A better performance should be easily gained by switching
#0 7.308         Blas library.
#0 7.308       self.calc_info()
#0 7.308     blas_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries blas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:690: UserWarning:
#0 7.308         Blas (http://www.netlib.org/blas/) libraries not found.
#0 7.308         Directories to search for the libraries can be specified in the
#0 7.308         numpy/distutils/site.cfg file (section [blas]) or by setting
#0 7.308         the BLAS environment variable.
#0 7.308       self.calc_info()
#0 7.308     blas_src_info:
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:690: UserWarning:
#0 7.308         Blas (http://www.netlib.org/blas/) sources not found.
#0 7.308         Directories to search for the sources can be specified in the
#0 7.308         numpy/distutils/site.cfg file (section [blas_src]) or by setting
#0 7.308         the BLAS_SRC environment variable.
#0 7.308       self.calc_info()
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     /bin/sh: 1: svnversion: not found
#0 7.308     non-existing path in 'numpy/distutils': 'site.cfg'
#0 7.308     lapack_opt_info:
#0 7.308     lapack_mkl_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     openblas_lapack_info:
#0 7.308     customize UnixCCompiler
#0 7.308     customize UnixCCompiler
#0 7.308       libraries openblas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     openblas_clapack_info:
#0 7.308     customize UnixCCompiler
#0 7.308     customize UnixCCompiler
#0 7.308       libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     flame_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries flame not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_3_10_threads_info:
#0 7.308     Setting PTATLAS=ATLAS
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries tatlas,tatlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries tatlas,tatlas not found in /usr/lib
#0 7.308     <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_3_10_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries satlas,satlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries satlas,satlas not found in /usr/lib
#0 7.308     <class 'numpy.distutils.system_info.atlas_3_10_info'>
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_threads_info:
#0 7.308     Setting PTATLAS=ATLAS
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries ptf77blas,ptcblas,atlas not found in /usr/lib
#0 7.308     <class 'numpy.distutils.system_info.atlas_threads_info'>
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     atlas_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries f77blas,cblas,atlas not found in /usr/local/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack_atlas not found in /usr/lib
#0 7.308     customize UnixCCompiler
#0 7.308       libraries f77blas,cblas,atlas not found in /usr/lib
#0 7.308     <class 'numpy.distutils.system_info.atlas_info'>
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     lapack_info:
#0 7.308     customize UnixCCompiler
#0 7.308       libraries lapack not found in ['/usr/local/lib', '/usr/lib']
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:1712: UserWarning:
#0 7.308         Lapack (http://www.netlib.org/lapack/) libraries not found.
#0 7.308         Directories to search for the libraries can be specified in the
#0 7.308         numpy/distutils/site.cfg file (section [lapack]) or by setting
#0 7.308         the LAPACK environment variable.
#0 7.308       if getattr(self, '_calc_info_{}'.format(lapack))():
#0 7.308     lapack_src_info:
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:1712: UserWarning:
#0 7.308         Lapack (http://www.netlib.org/lapack/) sources not found.
#0 7.308         Directories to search for the sources can be specified in the
#0 7.308         numpy/distutils/site.cfg file (section [lapack_src]) or by setting
#0 7.308         the LAPACK_SRC environment variable.
#0 7.308       if getattr(self, '_calc_info_{}'.format(lapack))():
#0 7.308       NOT AVAILABLE
#0 7.308   
#0 7.308     /usr/lib/python3.8/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
#0 7.308       warnings.warn(msg)
#0 7.308     running bdist_wheel
#0 7.308     running build
#0 7.308     running config_cc
#0 7.308     unifing config_cc, config, build_clib, build_ext, build commands --compiler options
#0 7.308     running config_fc
#0 7.308     unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
#0 7.308     running build_src
#0 7.308     build_src
#0 7.308     building py_modules sources
#0 7.308     creating build
#0 7.308     creating build/src.linux-aarch64-3.8
#0 7.308     creating build/src.linux-aarch64-3.8/numpy
#0 7.308     creating build/src.linux-aarch64-3.8/numpy/distutils
#0 7.308     building library "npymath" sources
#0 7.308     get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
#0 7.308     customize Gnu95FCompiler
#0 7.308     Could not locate executable gfortran
#0 7.308     Could not locate executable f95
#0 7.308     customize IntelFCompiler
#0 7.308     Could not locate executable ifort
#0 7.308     Could not locate executable ifc
#0 7.308     customize LaheyFCompiler
#0 7.308     Could not locate executable lf95
#0 7.308     customize PGroupFCompiler
#0 7.308     Could not locate executable pgfortran
#0 7.308     customize AbsoftFCompiler
#0 7.308     Could not locate executable f90
#0 7.308     Could not locate executable f77
#0 7.308     customize NAGFCompiler
#0 7.308     customize VastFCompiler
#0 7.308     customize CompaqFCompiler
#0 7.308     Could not locate executable fort
#0 7.308     customize IntelItaniumFCompiler
#0 7.308     Could not locate executable efort
#0 7.308     Could not locate executable efc
#0 7.308     customize IntelEM64TFCompiler
#0 7.308     customize GnuFCompiler
#0 7.308     Could not locate executable g77
#0 7.308     customize G95FCompiler
#0 7.308     Could not locate executable g95
#0 7.308     customize PathScaleFCompiler
#0 7.308     Could not locate executable pathf95
#0 7.308     customize NAGFORCompiler
#0 7.308     Could not locate executable nagfor
#0 7.308     don't know how to compile Fortran code on platform 'posix'
#0 7.308     C compiler: aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
#0 7.308   
#0 7.308     compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.8 -c'
#0 7.308     aarch64-linux-gnu-gcc: _configtest.c
#0 7.308     failure.
#0 7.308     removing: _configtest.c _configtest.o
#0 7.308     Traceback (most recent call last):
#0 7.308       File "<string>", line 1, in <module>
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/setup.py", line 443, in <module>
#0 7.308         setup_package()
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/setup.py", line 435, in setup_package
#0 7.308         setup(**metadata)
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/core.py", line 171, in setup
#0 7.308         return old_setup(**new_attr)
#0 7.308       File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 144, in setup
#0 7.308         return distutils.core.setup(**attrs)
#0 7.308       File "/usr/lib/python3.8/distutils/core.py", line 148, in setup
#0 7.308         dist.run_commands()
#0 7.308       File "/usr/lib/python3.8/distutils/dist.py", line 966, in run_commands
#0 7.308         self.run_command(cmd)
#0 7.308       File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
#0 7.308         cmd_obj.run()
#0 7.308       File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 223, in run
#0 7.308         self.run_command('build')
#0 7.308       File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
#0 7.308         self.distribution.run_command(command)
#0 7.308       File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
#0 7.308         cmd_obj.run()
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build.py", line 47, in run
#0 7.308         old_build.run(self)
#0 7.308       File "/usr/lib/python3.8/distutils/command/build.py", line 135, in run
#0 7.308         self.run_command(cmd_name)
#0 7.308       File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
#0 7.308         self.distribution.run_command(command)
#0 7.308       File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
#0 7.308         cmd_obj.run()
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 142, in run
#0 7.308         self.build_sources()
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 153, in build_sources
#0 7.308         self.build_library_sources(*libname_info)
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 286, in build_library_sources
#0 7.308         sources = self.generate_sources(sources, (lib_name, build_info))
#0 7.308       File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 369, in generate_sources
#0 7.308         source = func(extension, build_dir)
#0 7.308       File "numpy/core/setup.py", line 669, in get_mathlib_info
#0 7.308         raise RuntimeError("Broken toolchain: cannot link a simple C program")
#0 7.308     RuntimeError: Broken toolchain: cannot link a simple C program
#0 7.308     ----------------------------------------
#0 7.308     ERROR: Failed building wheel for numpy
#0 7.308     Running setup.py clean for numpy
#0 7.308     ERROR: Command errored out with exit status 1:
#0 7.308      command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
#0 7.308          cwd: /tmp/pip-install-46pmyfff/numpy
#0 7.308     Complete output (10 lines):
#0 7.308     Running from numpy source directory.
#0 7.308   
#0 7.308     `setup.py clean` is not supported, use one of the following instead:
#0 7.308   
#0 7.308       - `git clean -xdf` (cleans all files)
#0 7.308       - `git clean -Xdf` (cleans all versioned files, doesn't touch
#0 7.308                           files that aren't checked into the git repo)
#0 7.308   
#0 7.308     Add `--force` to your command to use it anyway if you must (unsupported).
#0 7.308   
#0 7.308     ----------------------------------------
#0 7.308     ERROR: Failed cleaning build dir for numpy
#0 7.308   Failed to build numpy
#0 7.308   Installing collected packages: setuptools, wheel, Cython, numpy
#0 7.308       Running setup.py install for numpy: started
#0 7.308       Running setup.py install for numpy: finished with status 'error'
#0 7.308       ERROR: Command errored out with exit status 1:
#0 7.308        command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-he1dm7ma/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-9i_hfnvd/overlay --compile --install-headers /tmp/pip-build-env-9i_hfnvd/overlay/include/python3.8/numpy
#0 7.308            cwd: /tmp/pip-install-46pmyfff/numpy/
#0 7.308       Complete output (271 lines):
#0 7.308       Running from numpy source directory.
#0 7.308   
#0 7.308       Note: if you need reliable uninstall behavior, then install
#0 7.308       with pip instead of using `setup.py install`:
#0 7.308   
#0 7.308         - `pip install .`       (from a git repo or downloaded source
#0 7.308                                  release)
#0 7.308         - `pip install numpy`   (last NumPy release on PyPi)
#0 7.308   
#0 7.308   
#0 7.308       blas_opt_info:
#0 7.308       blas_mkl_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       blis_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries blis not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       openblas_info:
#0 7.308       customize UnixCCompiler
#0 7.308       customize UnixCCompiler
#0 7.308         libraries openblas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_3_10_blas_threads_info:
#0 7.308       Setting PTATLAS=ATLAS
#0 7.308       customize UnixCCompiler
#0 7.308         libraries tatlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_3_10_blas_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries satlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_blas_threads_info:
#0 7.308       Setting PTATLAS=ATLAS
#0 7.308       customize UnixCCompiler
#0 7.308         libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_blas_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       accelerate_info:
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:690: UserWarning:
#0 7.308           Optimized (vendor) Blas libraries are not found.
#0 7.308           Falls back to netlib Blas library which has worse performance.
#0 7.308           A better performance should be easily gained by switching
#0 7.308           Blas library.
#0 7.308         self.calc_info()
#0 7.308       blas_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries blas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:690: UserWarning:
#0 7.308           Blas (http://www.netlib.org/blas/) libraries not found.
#0 7.308           Directories to search for the libraries can be specified in the
#0 7.308           numpy/distutils/site.cfg file (section [blas]) or by setting
#0 7.308           the BLAS environment variable.
#0 7.308         self.calc_info()
#0 7.308       blas_src_info:
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:690: UserWarning:
#0 7.308           Blas (http://www.netlib.org/blas/) sources not found.
#0 7.308           Directories to search for the sources can be specified in the
#0 7.308           numpy/distutils/site.cfg file (section [blas_src]) or by setting
#0 7.308           the BLAS_SRC environment variable.
#0 7.308         self.calc_info()
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       /bin/sh: 1: svnversion: not found
#0 7.308       non-existing path in 'numpy/distutils': 'site.cfg'
#0 7.308       lapack_opt_info:
#0 7.308       lapack_mkl_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       openblas_lapack_info:
#0 7.308       customize UnixCCompiler
#0 7.308       customize UnixCCompiler
#0 7.308         libraries openblas not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       openblas_clapack_info:
#0 7.308       customize UnixCCompiler
#0 7.308       customize UnixCCompiler
#0 7.308         libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       flame_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries flame not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_3_10_threads_info:
#0 7.308       Setting PTATLAS=ATLAS
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries tatlas,tatlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries tatlas,tatlas not found in /usr/lib
#0 7.308       <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_3_10_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries satlas,satlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries satlas,satlas not found in /usr/lib
#0 7.308       <class 'numpy.distutils.system_info.atlas_3_10_info'>
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_threads_info:
#0 7.308       Setting PTATLAS=ATLAS
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries ptf77blas,ptcblas,atlas not found in /usr/lib
#0 7.308       <class 'numpy.distutils.system_info.atlas_threads_info'>
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       atlas_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries f77blas,cblas,atlas not found in /usr/local/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack_atlas not found in /usr/lib
#0 7.308       customize UnixCCompiler
#0 7.308         libraries f77blas,cblas,atlas not found in /usr/lib
#0 7.308       <class 'numpy.distutils.system_info.atlas_info'>
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       lapack_info:
#0 7.308       customize UnixCCompiler
#0 7.308         libraries lapack not found in ['/usr/local/lib', '/usr/lib']
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:1712: UserWarning:
#0 7.308           Lapack (http://www.netlib.org/lapack/) libraries not found.
#0 7.308           Directories to search for the libraries can be specified in the
#0 7.308           numpy/distutils/site.cfg file (section [lapack]) or by setting
#0 7.308           the LAPACK environment variable.
#0 7.308         if getattr(self, '_calc_info_{}'.format(lapack))():
#0 7.308       lapack_src_info:
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       /tmp/pip-install-46pmyfff/numpy/numpy/distutils/system_info.py:1712: UserWarning:
#0 7.308           Lapack (http://www.netlib.org/lapack/) sources not found.
#0 7.308           Directories to search for the sources can be specified in the
#0 7.308           numpy/distutils/site.cfg file (section [lapack_src]) or by setting
#0 7.308           the LAPACK_SRC environment variable.
#0 7.308         if getattr(self, '_calc_info_{}'.format(lapack))():
#0 7.308         NOT AVAILABLE
#0 7.308   
#0 7.308       /usr/lib/python3.8/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
#0 7.308         warnings.warn(msg)
#0 7.308       running install
#0 7.308       running build
#0 7.308       running config_cc
#0 7.308       unifing config_cc, config, build_clib, build_ext, build commands --compiler options
#0 7.308       running config_fc
#0 7.308       unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
#0 7.308       running build_src
#0 7.308       build_src
#0 7.308       building py_modules sources
#0 7.308       building library "npymath" sources
#0 7.308       get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
#0 7.308       customize Gnu95FCompiler
#0 7.308       Could not locate executable gfortran
#0 7.308       Could not locate executable f95
#0 7.308       customize IntelFCompiler
#0 7.308       Could not locate executable ifort
#0 7.308       Could not locate executable ifc
#0 7.308       customize LaheyFCompiler
#0 7.308       Could not locate executable lf95
#0 7.308       customize PGroupFCompiler
#0 7.308       Could not locate executable pgfortran
#0 7.308       customize AbsoftFCompiler
#0 7.308       Could not locate executable f90
#0 7.308       Could not locate executable f77
#0 7.308       customize NAGFCompiler
#0 7.308       customize VastFCompiler
#0 7.308       customize CompaqFCompiler
#0 7.308       Could not locate executable fort
#0 7.308       customize IntelItaniumFCompiler
#0 7.308       Could not locate executable efort
#0 7.308       Could not locate executable efc
#0 7.308       customize IntelEM64TFCompiler
#0 7.308       customize GnuFCompiler
#0 7.308       Could not locate executable g77
#0 7.308       customize G95FCompiler
#0 7.308       Could not locate executable g95
#0 7.308       customize PathScaleFCompiler
#0 7.308       Could not locate executable pathf95
#0 7.308       customize NAGFORCompiler
#0 7.308       Could not locate executable nagfor
#0 7.308       don't know how to compile Fortran code on platform 'posix'
#0 7.308       C compiler: aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
#0 7.308   
#0 7.308       compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.8 -c'
#0 7.308       aarch64-linux-gnu-gcc: _configtest.c
#0 7.308       failure.
#0 7.308       removing: _configtest.c _configtest.o
#0 7.308       Traceback (most recent call last):
#0 7.308         File "<string>", line 1, in <module>
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/setup.py", line 443, in <module>
#0 7.308           setup_package()
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/setup.py", line 435, in setup_package
#0 7.308           setup(**metadata)
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/core.py", line 171, in setup
#0 7.308           return old_setup(**new_attr)
#0 7.308         File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 144, in setup
#0 7.308           return distutils.core.setup(**attrs)
#0 7.308         File "/usr/lib/python3.8/distutils/core.py", line 148, in setup
#0 7.308           dist.run_commands()
#0 7.308         File "/usr/lib/python3.8/distutils/dist.py", line 966, in run_commands
#0 7.308           self.run_command(cmd)
#0 7.308         File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
#0 7.308           cmd_obj.run()
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/install.py", line 62, in run
#0 7.308           r = self.setuptools_run()
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/install.py", line 36, in setuptools_run
#0 7.308           return distutils_install.run(self)
#0 7.308         File "/usr/lib/python3.8/distutils/command/install.py", line 589, in run
#0 7.308           self.run_command('build')
#0 7.308         File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
#0 7.308           self.distribution.run_command(command)
#0 7.308         File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
#0 7.308           cmd_obj.run()
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build.py", line 47, in run
#0 7.308           old_build.run(self)
#0 7.308         File "/usr/lib/python3.8/distutils/command/build.py", line 135, in run
#0 7.308           self.run_command(cmd_name)
#0 7.308         File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
#0 7.308           self.distribution.run_command(command)
#0 7.308         File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
#0 7.308           cmd_obj.run()
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 142, in run
#0 7.308           self.build_sources()
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 153, in build_sources
#0 7.308           self.build_library_sources(*libname_info)
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 286, in build_library_sources
#0 7.308           sources = self.generate_sources(sources, (lib_name, build_info))
#0 7.308         File "/tmp/pip-install-46pmyfff/numpy/numpy/distutils/command/build_src.py", line 369, in generate_sources
#0 7.308           source = func(extension, build_dir)
#0 7.308         File "numpy/core/setup.py", line 669, in get_mathlib_info
#0 7.308           raise RuntimeError("Broken toolchain: cannot link a simple C program")
#0 7.308       RuntimeError: Broken toolchain: cannot link a simple C program
#0 7.308       ----------------------------------------
#0 7.308   ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-46pmyfff/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-he1dm7ma/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-9i_hfnvd/overlay --compile --install-headers /tmp/pip-build-env-9i_hfnvd/overlay/include/python3.8/numpy Check the logs for full command output.
#0 7.308   ----------------------------------------
#0 7.332 ERROR: Command errored out with exit status 1: /usr/bin/python3 /usr/lib/python3/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-9i_hfnvd/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.29.21,<3' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.5; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy; python_version>='"'"'3.9'"'"'' Check the logs for full command output.
------
Dockerfile:16
--------------------
  14 |         rm -fr /var/lib/apt/lists/*
  15 |     
  16 | >>> RUN python3 -m pip install pandas==1.2.3
  17 |     
--------------------
error: failed to solve: process "/bin/sh -c python3 -m pip install pandas==1.2.3" did not complete successfully: exit code: 1
@kidmose
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kidmose commented Apr 21, 2023

I can reproduce the error with a simpler Dockerfile and lima/nerdctl in the same setup:

FROM ubuntu:20.04

ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && \
    apt-get -y upgrade && \
    apt-get -y install --no-install-recommends \
    ca-certificates \
    curl \
    python3 \
    python3-pip \
    python3-setuptools \
    python3-venv \
    python3-wheel && \
    rm -fr /var/lib/apt/lists/*

RUN python3 -m pip install pandas==1.2.3

@kidmose
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kidmose commented Apr 21, 2023 •
edited
Loading

I tested various version of pandas on my setup (major=1, minor>=2, patch=latest, and then patch+1 compared to the currently pinned). It seems that the one closest to the current pinned version which installs without failure is pandas==1.2.5, so I'll play arround some more and do a PR if i get that to work.

FROM ubuntu:20.04

ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && \
    apt-get -y upgrade && \
    apt-get -y install --no-install-recommends \
    ca-certificates \
    curl \
    python3 \
    python3-pip \
    python3-setuptools \
    python3-venv \
    python3-wheel && \
    rm -fr /var/lib/apt/lists/*

# RUN python3 -m pip install pandas==1.5.3 # OK
# RUN python3 -m pip install pandas==1.4.4 # OK
# RUN python3 -m pip install pandas==1.3.5 # OK
RUN python3 -m pip install pandas==1.2.5 # OK
# RUN python3 -m pip install pandas==1.2.4 # NOT OK
# RUN python3 -m pip install pandas==1.2.3 # NOT OK

kidmose pushed a commit to kidmose/tram that referenced this issue Apr 24, 2023
Bump pandas to 1.2.5. Fixes center-for-threat-informed-defense#192 (s…
d56ea68 
…upport for arm64/Apple M2)
@kidmose kidmose linked a pull request Apr 24, 2023 that will close this issue
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Bump pandas to 1.2.5. Fixes #192 (support for arm64/Apple M2) kidmose/tram
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@kidmose