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spectralDNS / shenfun

High performance computational platform in Python for the spectral Galerkin method
http://shenfun.readthedocs.org
BSD 2-Clause "Simplified" License
204 stars 42 forks source link

Failed to install on Linux Mint #76

Closed yesint closed 3 years ago

yesint commented 3 years ago

I used shenfun before with great success but I can't install it on my new machine running pretty standard Linux Mint distro. Below is the error message. What should I do?

 pip3 install shenfun
Collecting shenfun
  Using cached shenfun-3.1.2.tar.gz (174 kB)
Requirement already satisfied: cython in /usr/lib/python3/dist-packages (from shenfun) (0.29.14)
Requirement already satisfied: mpi4py in /usr/lib/python3/dist-packages (from shenfun) (3.0.3)
Requirement already satisfied: mpi4py-fft in /home/semen/.local/lib/python3.8/site-packages (from shenfun) (2.0.3)
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from shenfun) (1.17.4)
Requirement already satisfied: scipy in /usr/lib/python3/dist-packages (from shenfun) (1.3.3)
Building wheels for collected packages: shenfun
  Building wheel for shenfun (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-zotpvdlq/shenfun/setup.py'"'"'; __file__='"'"'/tmp/pip-install-zotpvdlq/shenfun/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-cwo1m0fk
       cwd: /tmp/pip-install-zotpvdlq/shenfun/
  Complete output (175 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/shenfun
  copying shenfun/matrixbase.py -> build/lib.linux-x86_64-3.8/shenfun
  copying shenfun/tensorproductspace.py -> build/lib.linux-x86_64-3.8/shenfun
  copying shenfun/spectralbase.py -> build/lib.linux-x86_64-3.8/shenfun
  copying shenfun/coordinates.py -> build/lib.linux-x86_64-3.8/shenfun
  copying shenfun/la.py -> build/lib.linux-x86_64-3.8/shenfun
  copying shenfun/__init__.py -> build/lib.linux-x86_64-3.8/shenfun
  creating build/lib.linux-x86_64-3.8/shenfun/optimization
  copying shenfun/optimization/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/optimization
  creating build/lib.linux-x86_64-3.8/shenfun/optimization/cython
  copying shenfun/optimization/cython/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/cython
  creating build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/biharmonic.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/helmholtz.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/tdma.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/pdma.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/chebyshev.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/fdma.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  copying shenfun/optimization/numba/legendre.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
  creating build/lib.linux-x86_64-3.8/shenfun/legendre
  copying shenfun/legendre/lobatto.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
  copying shenfun/legendre/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
  copying shenfun/legendre/la.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
  copying shenfun/legendre/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
  copying shenfun/legendre/bases.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
  package init file 'shenfun/legendre/fastgl/__init__.py' not found (or not a regular file)
  creating build/lib.linux-x86_64-3.8/shenfun/laguerre
  copying shenfun/laguerre/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/laguerre
  copying shenfun/laguerre/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/laguerre
  copying shenfun/laguerre/bases.py -> build/lib.linux-x86_64-3.8/shenfun/laguerre
  creating build/lib.linux-x86_64-3.8/shenfun/hermite
  copying shenfun/hermite/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/hermite
  copying shenfun/hermite/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/hermite
  copying shenfun/hermite/bases.py -> build/lib.linux-x86_64-3.8/shenfun/hermite
  creating build/lib.linux-x86_64-3.8/shenfun/chebyshev
  copying shenfun/chebyshev/quasi.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
  copying shenfun/chebyshev/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
  copying shenfun/chebyshev/la.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
  copying shenfun/chebyshev/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
  copying shenfun/chebyshev/bases.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
  creating build/lib.linux-x86_64-3.8/shenfun/fourier
  copying shenfun/fourier/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/fourier
  copying shenfun/fourier/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/fourier
  copying shenfun/fourier/bases.py -> build/lib.linux-x86_64-3.8/shenfun/fourier
  creating build/lib.linux-x86_64-3.8/shenfun/jacobi
  copying shenfun/jacobi/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
  copying shenfun/jacobi/la.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
  copying shenfun/jacobi/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
  copying shenfun/jacobi/bases.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
  creating build/lib.linux-x86_64-3.8/shenfun/forms
  copying shenfun/forms/arguments.py -> build/lib.linux-x86_64-3.8/shenfun/forms
  copying shenfun/forms/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/forms
  copying shenfun/forms/project.py -> build/lib.linux-x86_64-3.8/shenfun/forms
  copying shenfun/forms/operators.py -> build/lib.linux-x86_64-3.8/shenfun/forms
  copying shenfun/forms/inner.py -> build/lib.linux-x86_64-3.8/shenfun/forms
  creating build/lib.linux-x86_64-3.8/shenfun/utilities
  copying shenfun/utilities/lagrangian_particles.py -> build/lib.linux-x86_64-3.8/shenfun/utilities
  copying shenfun/utilities/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/utilities
  copying shenfun/utilities/integrators.py -> build/lib.linux-x86_64-3.8/shenfun/utilities
  creating build/lib.linux-x86_64-3.8/shenfun/io
  copying shenfun/io/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/io
  running build_ext
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.cpp
  warning: shenfun/optimization/cython/Matvec.pyx:1656:14: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined
  warning: shenfun/optimization/cython/Matvec.pyx:1656:22: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.cpp
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.cpp
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.cpp

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
  # distutils: language = c++
  #cython: boundscheck=False
  #cython: wraparound=False
  #cython: language_level=3

  cimport fastgl_wrap
         ^
  ------------------------------------------------------------

  shenfun/legendre/fastgl/fastgl_wrap.pyx:6:8: 'fastgl_wrap.pxd' not found

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      N : int
          The total number of quadrature points
      k : int
          The k'th point in the N-point quadrature rule
      """
      f = fastgl_wrap.GLPair(N, k)
                    ^
  ------------------------------------------------------------

  shenfun/legendre/fastgl/fastgl_wrap.pyx:19:19: cimported module has no attribute 'GLPair'

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
      N : int
          The total number of quadrature points
      k : int
          The k'th point in the N-point quadrature rule
      """
      f = fastgl_wrap.GLPair(N, k)
                    ^
  ------------------------------------------------------------

  shenfun/legendre/fastgl/fastgl_wrap.pyx:19:19: Compiler crash in AnalyseExpressionsTransform

  ModuleNode.body = StatListNode(fastgl_wrap.pyx:6:0)
  StatListNode.stats[2] = StatListNode(fastgl_wrap.pyx:9:0)
  StatListNode.stats[0] = DefNode(fastgl_wrap.pyx:9:0,
      doc = "Return point and weight k for N-point Gauss-Legendre rule\n\n    Parameters\n    ----------\n    N : int\n        The total number of quadrature points\n    k : int\n        The k'th point in the N-point quadrature rule\n    ",
      modifiers = [...]/0,
      name = 'getGLPair',
      np_args_idx = [...]/0,
      num_required_args = 2,
      outer_attrs = [...]/2,
      py_wrapper_required = True,
      reqd_kw_flags_cname = '0',
      used = True)
  File 'ExprNodes.py', line 5344, in infer_type: SimpleCallNode(fastgl_wrap.pyx:19:26,
      result_is_used = True,
      use_managed_ref = True)
  File 'ExprNodes.py', line 6832, in infer_type: AttributeNode(fastgl_wrap.pyx:19:19,
      attribute = 'GLPair',
      is_attribute = 1,
      needs_none_check = True,
      result_is_used = True,
      use_managed_ref = True)

  Compiler crash traceback from this point on:
    File "/usr/lib/python3/dist-packages/Cython/Compiler/ExprNodes.py", line 6832, in infer_type
      return node.entry.type
  AttributeError: 'NoneType' object has no attribute 'type'
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Cheb.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Cheb.c
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Cheb.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/convolve.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/convolve.c
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/convolve.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/outer.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/outer.c
  cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/applymask.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/applymask.c
  building 'shenfun.optimization.cython.Matvec' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/tmp
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython
  x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.o -g0 -O3 -w -Ofast -ffast-math -march=native
  x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.o -lm -o build/lib.linux-x86_64-3.8/shenfun/optimization/cython/Matvec.cpython-38-x86_64-linux-gnu.so -std=c++11
  building 'shenfun.optimization.cython.la' extension
  x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.o -g0 -O3 -w -Ofast -ffast-math -march=native
  x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.o -lm -o build/lib.linux-x86_64-3.8/shenfun/optimization/cython/la.cpython-38-x86_64-linux-gnu.so -std=c++11
  building 'shenfun.optimization.cython.evaluate' extension
  x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.o -g0 -O3 -w -Ofast -ffast-math -march=native
  x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.o -lm -o build/lib.linux-x86_64-3.8/shenfun/optimization/cython/evaluate.cpython-38-x86_64-linux-gnu.so -std=c++11
  building 'shenfun.legendre.fastgl.fastgl_wrap' extension
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl
  x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.o -g0 -O3 -w -Ofast -ffast-math -march=native
  /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.cpp:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
      1 | #error Do not use this file, it is the result of a failed Cython compilation.
        |  ^~~~~
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for shenfun
  Running setup.py clean for shenfun
Failed to build shenfun
Installing collected packages: shenfun
    Running setup.py install for shenfun ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-zotpvdlq/shenfun/setup.py'"'"'; __file__='"'"'/tmp/pip-install-zotpvdlq/shenfun/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-ptiffp84/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/semen/.local/include/python3.8/shenfun
         cwd: /tmp/pip-install-zotpvdlq/shenfun/
    Complete output (169 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.8
    creating build/lib.linux-x86_64-3.8/shenfun
    copying shenfun/matrixbase.py -> build/lib.linux-x86_64-3.8/shenfun
    copying shenfun/tensorproductspace.py -> build/lib.linux-x86_64-3.8/shenfun
    copying shenfun/spectralbase.py -> build/lib.linux-x86_64-3.8/shenfun
    copying shenfun/coordinates.py -> build/lib.linux-x86_64-3.8/shenfun
    copying shenfun/la.py -> build/lib.linux-x86_64-3.8/shenfun
    copying shenfun/__init__.py -> build/lib.linux-x86_64-3.8/shenfun
    creating build/lib.linux-x86_64-3.8/shenfun/optimization
    copying shenfun/optimization/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/optimization
    creating build/lib.linux-x86_64-3.8/shenfun/optimization/cython
    copying shenfun/optimization/cython/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/cython
    creating build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/biharmonic.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/helmholtz.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/tdma.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/pdma.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/chebyshev.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/fdma.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    copying shenfun/optimization/numba/legendre.py -> build/lib.linux-x86_64-3.8/shenfun/optimization/numba
    creating build/lib.linux-x86_64-3.8/shenfun/legendre
    copying shenfun/legendre/lobatto.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
    copying shenfun/legendre/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
    copying shenfun/legendre/la.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
    copying shenfun/legendre/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
    copying shenfun/legendre/bases.py -> build/lib.linux-x86_64-3.8/shenfun/legendre
    package init file 'shenfun/legendre/fastgl/__init__.py' not found (or not a regular file)
    creating build/lib.linux-x86_64-3.8/shenfun/laguerre
    copying shenfun/laguerre/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/laguerre
    copying shenfun/laguerre/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/laguerre
    copying shenfun/laguerre/bases.py -> build/lib.linux-x86_64-3.8/shenfun/laguerre
    creating build/lib.linux-x86_64-3.8/shenfun/hermite
    copying shenfun/hermite/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/hermite
    copying shenfun/hermite/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/hermite
    copying shenfun/hermite/bases.py -> build/lib.linux-x86_64-3.8/shenfun/hermite
    creating build/lib.linux-x86_64-3.8/shenfun/chebyshev
    copying shenfun/chebyshev/quasi.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
    copying shenfun/chebyshev/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
    copying shenfun/chebyshev/la.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
    copying shenfun/chebyshev/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
    copying shenfun/chebyshev/bases.py -> build/lib.linux-x86_64-3.8/shenfun/chebyshev
    creating build/lib.linux-x86_64-3.8/shenfun/fourier
    copying shenfun/fourier/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/fourier
    copying shenfun/fourier/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/fourier
    copying shenfun/fourier/bases.py -> build/lib.linux-x86_64-3.8/shenfun/fourier
    creating build/lib.linux-x86_64-3.8/shenfun/jacobi
    copying shenfun/jacobi/matrices.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
    copying shenfun/jacobi/la.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
    copying shenfun/jacobi/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
    copying shenfun/jacobi/bases.py -> build/lib.linux-x86_64-3.8/shenfun/jacobi
    creating build/lib.linux-x86_64-3.8/shenfun/forms
    copying shenfun/forms/arguments.py -> build/lib.linux-x86_64-3.8/shenfun/forms
    copying shenfun/forms/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/forms
    copying shenfun/forms/project.py -> build/lib.linux-x86_64-3.8/shenfun/forms
    copying shenfun/forms/operators.py -> build/lib.linux-x86_64-3.8/shenfun/forms
    copying shenfun/forms/inner.py -> build/lib.linux-x86_64-3.8/shenfun/forms
    creating build/lib.linux-x86_64-3.8/shenfun/utilities
    copying shenfun/utilities/lagrangian_particles.py -> build/lib.linux-x86_64-3.8/shenfun/utilities
    copying shenfun/utilities/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/utilities
    copying shenfun/utilities/integrators.py -> build/lib.linux-x86_64-3.8/shenfun/utilities
    creating build/lib.linux-x86_64-3.8/shenfun/io
    copying shenfun/io/__init__.py -> build/lib.linux-x86_64-3.8/shenfun/io
    running build_ext
    skipping '/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.cpp' Cython extension (up-to-date)
    skipping '/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.cpp' Cython extension (up-to-date)
    skipping '/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.cpp' Cython extension (up-to-date)
    cythoning /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.pyx to /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.cpp

    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    # distutils: language = c++
    #cython: boundscheck=False
    #cython: wraparound=False
    #cython: language_level=3

    cimport fastgl_wrap
           ^
    ------------------------------------------------------------

    shenfun/legendre/fastgl/fastgl_wrap.pyx:6:8: 'fastgl_wrap.pxd' not found

    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        N : int
            The total number of quadrature points
        k : int
            The k'th point in the N-point quadrature rule
        """
        f = fastgl_wrap.GLPair(N, k)
                      ^
    ------------------------------------------------------------

    shenfun/legendre/fastgl/fastgl_wrap.pyx:19:19: cimported module has no attribute 'GLPair'

    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        N : int
            The total number of quadrature points
        k : int
            The k'th point in the N-point quadrature rule
        """
        f = fastgl_wrap.GLPair(N, k)
                      ^
    ------------------------------------------------------------

    shenfun/legendre/fastgl/fastgl_wrap.pyx:19:19: Compiler crash in AnalyseExpressionsTransform

    ModuleNode.body = StatListNode(fastgl_wrap.pyx:6:0)
    StatListNode.stats[2] = StatListNode(fastgl_wrap.pyx:9:0)
    StatListNode.stats[0] = DefNode(fastgl_wrap.pyx:9:0,
        doc = "Return point and weight k for N-point Gauss-Legendre rule\n\n    Parameters\n    ----------\n    N : int\n        The total number of quadrature points\n    k : int\n        The k'th point in the N-point quadrature rule\n    ",
        modifiers = [...]/0,
        name = 'getGLPair',
        np_args_idx = [...]/0,
        num_required_args = 2,
        outer_attrs = [...]/2,
        py_wrapper_required = True,
        reqd_kw_flags_cname = '0',
        used = True)
    File 'ExprNodes.py', line 5344, in infer_type: SimpleCallNode(fastgl_wrap.pyx:19:26,
        result_is_used = True,
        use_managed_ref = True)
    File 'ExprNodes.py', line 6832, in infer_type: AttributeNode(fastgl_wrap.pyx:19:19,
        attribute = 'GLPair',
        is_attribute = 1,
        needs_none_check = True,
        result_is_used = True,
        use_managed_ref = True)

    Compiler crash traceback from this point on:
      File "/usr/lib/python3/dist-packages/Cython/Compiler/ExprNodes.py", line 6832, in infer_type
        return node.entry.type
    AttributeError: 'NoneType' object has no attribute 'type'
    skipping '/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Cheb.c' Cython extension (up-to-date)
    skipping '/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/convolve.c' Cython extension (up-to-date)
    skipping '/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/outer.c' Cython extension (up-to-date)
    skipping '/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/applymask.c' Cython extension (up-to-date)
    building 'shenfun.optimization.cython.Matvec' extension
    creating build/temp.linux-x86_64-3.8
    creating build/temp.linux-x86_64-3.8/tmp
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython
    x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.o -g0 -O3 -w -Ofast -ffast-math -march=native
    x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/Matvec.o -lm -o build/lib.linux-x86_64-3.8/shenfun/optimization/cython/Matvec.cpython-38-x86_64-linux-gnu.so -std=c++11
    building 'shenfun.optimization.cython.la' extension
    x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.o -g0 -O3 -w -Ofast -ffast-math -march=native
    x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/la.o -lm -o build/lib.linux-x86_64-3.8/shenfun/optimization/cython/la.cpython-38-x86_64-linux-gnu.so -std=c++11
    building 'shenfun.optimization.cython.evaluate' extension
    x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.o -g0 -O3 -w -Ofast -ffast-math -march=native
    x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/optimization/cython/evaluate.o -lm -o build/lib.linux-x86_64-3.8/shenfun/optimization/cython/evaluate.cpython-38-x86_64-linux-gnu.so -std=c++11
    building 'shenfun.legendre.fastgl.fastgl_wrap' extension
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl
    x86_64-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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.o -g0 -O3 -w -Ofast -ffast-math -march=native
    /tmp/pip-install-zotpvdlq/shenfun/shenfun/legendre/fastgl/fastgl_wrap.cpp:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
        1 | #error Do not use this file, it is the result of a failed Cython compilation.
          |  ^~~~~
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-zotpvdlq/shenfun/setup.py'"'"'; __file__='"'"'/tmp/pip-install-zotpvdlq/shenfun/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-ptiffp84/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/semen/.local/include/python3.8/shenfun Check the logs for full command output.
mikaem commented 3 years ago

Looks like the fastgl directory is simply missing an __init__.py file.

yesint commented 3 years ago

This problem vanishes if latest git version is used.