pip install scikit-fmm failing on mac

[Eric Hester]

Hello,

I am trying to install scikit-fmm.

When I run "pip install scikit-fmm" I get the following error message:

Collecting scikit-fmm

  Using cached scikit-fmm-2021.10.29.tar.gz (423 kB)

  Installing build dependencies ... done

  Getting requirements to build wheel ... done

  Preparing metadata (pyproject.toml) ... done

Requirement already satisfied: numpy>=1.0.2 in /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/lib/python3.8/site-packages (from scikit-fmm) (1.21.2)

Building wheels for collected packages: scikit-fmm

  Building wheel for scikit-fmm (pyproject.toml) ... error

  ERROR: Command errored out with exit status 1:

   command: /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/python3.8 /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /var/folders/qg/0036tg3d5pz15ggfrgj_m2z00000gn/T/tmpxo3ohjzm

       cwd: /private/var/folders/qg/0036tg3d5pz15ggfrgj_m2z00000gn/T/pip-install-qimrwh7d/scikit-fmm_48050be06a214e808e712314482cbeab

  Complete output (82 lines):

  running bdist_wheel

  running build

  running config_cc

  unifing config_cc, config, build_clib, build_ext, build commands --compiler options

  running config_fc

  unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options

  running build_src

  build_src

  building extension "skfmm.cfmm" sources

  building extension "skfmm.pheap" sources

  build_src: building npy-pkg config files

  running build_py

  creating build

  creating build/lib.macosx-10.9-x86_64-3.8

  creating build/lib.macosx-10.9-x86_64-3.8/skfmm

  copying skfmm/heap.py -> build/lib.macosx-10.9-x86_64-3.8/skfmm

  copying skfmm/pfmm.py -> build/lib.macosx-10.9-x86_64-3.8/skfmm

  copying skfmm/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/skfmm

  copying skfmm/setup.py -> build/lib.macosx-10.9-x86_64-3.8/skfmm

  running build_ext

  customize UnixCCompiler

  customize UnixCCompiler using build_ext

  customize UnixCCompiler

  #### ['x86_64-apple-darwin13.4.0-clang', '-fno-strict-aliasing', '-Wsign-compare', '-Wunreachable-code', '-DNDEBUG', '-fwrapv', '-O3', '-Wall', '-Wstrict-prototypes', '-march=core2', '-mtune=haswell', '-mssse3', '-ftree-vectorize', '-fPIC', '-fPIE', '-fstack-protector-strong', '-O3', '-pipe', '-fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION}', '-fdebug-prefix-map=/Users/ericwilliamhester/opt/anaconda3/envs/dedalus=/usr/local/src/conda-prefix', '-flto', '-Wl,-export_dynamic', '-march=core2', '-mtune=haswell', '-mssse3', '-ftree-vectorize', '-fPIC', '-fPIE', '-fstack-protector-strong', '-O3', '-march=core2', '-mtune=haswell', '-mssse3', '-ftree-vectorize', '-fPIC', '-fPIE', '-fstack-protector-strong', '-O2', '-pipe', '-isystem', '/Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include', '-D_FORTIFY_SOURCE=2', '-isystem', '/Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include'] #######

  customize UnixCCompiler using build_ext

  building 'skfmm.cfmm' extension

  compiling C++ sources

  C compiler: x86_64-apple-darwin13.4.0-clang++ -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/ericwilliamhester/opt/anaconda3/envs/dedalus=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include -D_FORTIFY_SOURCE=2 -isystem /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include

  

  creating build/temp.macosx-10.9-x86_64-3.8/skfmm

  compile options: '-Iskfmm -I/private/var/folders/qg/0036tg3d5pz15ggfrgj_m2z00000gn/T/pip-build-env-vuxw4ohz/overlay/lib/python3.8/site-packages/numpy/core/include -I/Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include/python3.8 -c'

  x86_64-apple-darwin13.4.0-clang++: skfmm/fmm.cpp

  x86_64-apple-darwin13.4.0-clang++: skfmm/heap.cpp

  x86_64-apple-darwin13.4.0-clang++: skfmm/base_marcher.cpp

  x86_64-apple-darwin13.4.0-clang++: skfmm/distance_marcher.cpp

  x86_64-apple-darwin13.4.0-clang++: skfmm/travel_time_marcher.cpp

  x86_64-apple-darwin13.4.0-clang++: skfmm/extension_velocity_marcher.cpp

  clang-11: warning: clang-11-Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]

  : warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]

  clang-11: clang-11: warningwarning: : -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]

  -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]

  clang-11: clang-11: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]warning

  : -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]

  In file included from skfmm/heap.cpp:30:

  /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/stdio.h:107:15: fatal error: 'stdio.h' file not found

  #include_next <stdio.h>

                ^~~~~~~~~

  In file included from skfmm/fmm.cpp:4:

  In file included from /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include/python3.8/Python.h:25:

  /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/stdio.h:107:15: fatal error: 'stdio.h' file not found

  #include_next <stdio.h>

                ^~~~~~~~~

  In file included from skfmm/extension_velocity_marcher.cpp:5:

  In file included from /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/stdexcept:45:

  In file included from /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/cstdlib:85:

  /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/stdlib.h:93:15: fatal error: 'stdlib.h' file not found

  #include_next <stdlib.h>

                ^~~~~~~~~~

  In file included from skfmm/distance_marcher.cpp:2:

  /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/math.hIn file included from skfmm/base_marcher.cpp:8:

  :/Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/math.h:300:15: 300fatal error:: 15'math.h' file not found:

   fatal error: 'math.h' file not found

  #include_next <math.h>

                ^~~~~~~~#include_next <math.h>

                ^~~~~~~~

  

  In file included from skfmm/travel_time_marcher.cpp:3:

  In file included from skfmm/travel_time_marcher.h:3:

  In file included from /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/set:429:

  In file included from /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/__tree:14:

  In file included from /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/iterator:418:

  In file included from /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/iosfwd:95:

  /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/bin/../include/c++/v1/wchar.h:119:15: fatal error: 'wchar.h' file not found

  #include_next <wchar.h>

                ^~~~~~~~~

  1 error generated.

  1 error generated.

  1 error generated.

  1 error generated.

  1 error generated.

  1 error generated.

  error: Command "x86_64-apple-darwin13.4.0-clang++ -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/ericwilliamhester/opt/anaconda3/envs/dedalus=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include -D_FORTIFY_SOURCE=2 -isystem /Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include -Iskfmm -I/private/var/folders/qg/0036tg3d5pz15ggfrgj_m2z00000gn/T/pip-build-env-vuxw4ohz/overlay/lib/python3.8/site-packages/numpy/core/include -I/Users/ericwilliamhester/opt/anaconda3/envs/dedalus/include/python3.8 -c skfmm/heap.cpp -o build/temp.macosx-10.9-x86_64-3.8/skfmm/heap.o -MMD -MF build/temp.macosx-10.9-x86_64-3.8/skfmm/heap.o.d" failed with exit status 1

  ----------------------------------------

  ERROR: Failed building wheel for scikit-fmm

Failed to build scikit-fmm

ERROR: Could not build wheels for scikit-fmm, which is required to install pyproject.toml-based projects

I am running python 3.8.10 on a MacBook Pro with OS 11.6. I can provide any other information needed to figure out the issue.

What do I need to do to install scikit-fmm?

Thanks,

Eric

[Makki Karim]

The best way in your case is to install the package via conda: https://anaconda.org/conda-forge/scikit-fmm

Also you can try via pip3 as you use python 3 as a second alternative.

Hope this will solve the problem.

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[Eric Hester]

Perfect! Thanks for the tip, it works great now.

Best,

Eric

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