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linuxmint-17, ubuntu-trusty: scipy build error with pybind11 #32515

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mkoeppe opened this issue Sep 14, 2021 · 25 comments
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linuxmint-17, ubuntu-trusty: scipy build error with pybind11 #32515

mkoeppe opened this issue Sep 14, 2021 · 25 comments
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c: packages: standard p: critical / 2 t: bug
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sage-9.5

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@mkoeppe
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mkoeppe commented Sep 14, 2021

On linuxmint-17-minimal (https://github.com/sagemath/sage/runs/3593003595)

  gcc -pthread -shared -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -L. -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -shared -Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib build/temp.linux-x86_64-3.9/scipy/cluster/_optimal_leaf_ordering.o -L/sage/local/lib -Lbuild/temp.linux-x86_64-3.9 -o build/lib.linux-x86_64-3.9/scipy/cluster/_optimal_leaf_ordering.cpython-39-x86_64-linux-gnu.so -Wl,--version-script=build/temp.linux-x86_64-3.9/link-version-scipy.cluster._optimal_leaf_ordering.map
  C compiler: g++ -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -fPIC

  creating /tmp/tmpif5aglmi/tmp
  creating /tmp/tmpif5aglmi/tmp/tmpif5aglmi
  compile options: '-I/sage/local/include/python3.9 -c'
  extra options: '-std=c++14'
  g++: /tmp/tmpif5aglmi/main.cpp
  g++: error: unrecognized command line option '-std=c++14'
  C compiler: g++ -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -fPIC

  creating /tmp/tmpjrgp9vmy/tmp
  creating /tmp/tmpjrgp9vmy/tmp/tmpjrgp9vmy
  compile options: '-I/sage/local/include/python3.9 -c'
  extra options: '-std=c++11'
  g++: /tmp/tmpjrgp9vmy/main.cpp
  C compiler: g++ -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -fPIC

  creating /tmp/tmpik_q_vbd/tmp
  creating /tmp/tmpik_q_vbd/tmp/tmpik_q_vbd
  compile options: '-I/sage/local/include/python3.9 -c'
  g++: /tmp/tmpik_q_vbd/main.c
  C compiler: g++ -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -fPIC

  creating /tmp/tmpv4ojh26z/tmp
  creating /tmp/tmpv4ojh26z/tmp/tmpv4ojh26z
  compile options: '-I/sage/local/include/python3.9 -c'
  extra options: '-pthread'
  g++: /tmp/tmpv4ojh26z/main.c
  C compiler: g++ -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -fPIC

   creating build/temp.linux-x86_64-3.9/scipy/fft
  creating build/temp.linux-x86_64-3.9/scipy/fft/_pocketfft
  compile options: '-DPOCKETFFT_PTHREADS -I/sage/local/lib/python3.9/site-packages/pybind11/include -I/sage/local/lib/python3.9/site-packages/pybind11/include -I/sage/local/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/distutils/include -I/sage/local/include/python3.9 -c'
  extra options: '-std=c++11 -pthread -fvisibility=hidden -msse -msse2 -msse3'
  g++: scipy/fft/_pocketfft/pypocketfft.cxx
  In file included from scipy/fft/_pocketfft/pypocketfft.cxx:16:0:
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:328:5: error: 'is_trivially_copyable' is not a member of 'std'
       std::is_trivially_copyable<T>,
       ^
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:328:5: error: 'is_trivially_copyable' is not a member of 'std'
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:328:33: error: template argument 2 is invalid
       std::is_trivially_copyable<T>,
                                   ^
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:968:49: error: 'is_pod_struct' is not a member of 'pybind11::detail'
   struct format_descriptor<T, detail::enable_if_t<detail::is_pod_struct<T>::value>> {
                                                   ^
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:968:49: error: 'is_pod_struct' is not a member of 'pybind11::detail'
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:968:72: error: template argument 1 is invalid
   struct format_descriptor<T, detail::enable_if_t<detail::is_pod_struct<T>::value>> {
                                                                          ^
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:968:75: error: template argument 2 is invalid
   struct format_descriptor<T, detail::enable_if_t<detail::is_pod_struct<T>::value>> {
                                                                             ^
  /sage/local/lib/python3.9/site-packages/pybind11/include/pybind11/numpy.h:968:80: error: expected unqualified-id before '>' token
   struct format_descriptor<T, detail::enable_if_t<detail::is_pod_struct<T>::value>> {


error: Command "g++ -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O2 -g -fPIC -DPOCKETFFT_PTHREADS -I/sage/local/lib/python3.9/site-packages/pybind11/include -I/sage/local/lib/python3.9/site-packages/pybind11/include -I/sage/local/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/distutils/include -I/sage/local/include/python3.9 -c scipy/fft/_pocketfft/pypocketfft.cxx -o build/temp.linux-x86_64-3.9/scipy/fft/_pocketfft/pypocketfft.o -MMD -MF build/temp.linux-x86_64-3.9/scipy/fft/_pocketfft/pypocketfft.o.d -std=c++11 -pthread -fvisibility=hidden -msse -msse2 -msse3" failed with exit status 1

Likely caused by the pybind11 update (from 2.6.0 to 2.7.1; https://pybind11.readthedocs.io/en/stable/changelog.html) done as part of the Jupyter upgrade in #31280.

Broken:

  • linuxmint-17 (gcc 4.8.4-2ubuntu1~14.04.3, __GLIBCXX__ = 20150426),
  • ubuntu-trusty (4.8.4-2ubuntu1~14.04.4, __GLIBCXX__ = 20150426)

OK:

  • centos-7 4.8.5 20150623 (Red Hat 4.8.5-44, __GLIBCXX__ = 20150623)
  • debian-jessie (gcc 4.9.2-10+deb8u2),
  • linuxmint-18 (gcc 5.4.0-6ubuntu1~16.04.6),
  • fedora-26 (7.3.1 20180130 (Red Hat 7.3.1-2))

Opened pybind11 upstream issue: pybind/pybind11#3269, PR pybind/pybind11#3270 (merged in the 2.7 maintenance branch)

CC: @dimpase @orlitzky @jhpalmieri @kliem

Component: packages: standard

Author: Matthias Koeppe

Branch/Commit: d0e1e95

Reviewer: Jonathan Kliem

Issue created by migration from https://trac.sagemath.org/ticket/32515
@mkoeppe mkoeppe added this to the sage-9.5 milestone Sep 14, 2021
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mkoeppe commented Sep 15, 2021

comment:4

I don't see anything in the pybind11 changelog nor in https://pybind11.readthedocs.io/en/stable/upgrade.html that indicates that C++14 would now be needed

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mkoeppe commented Sep 15, 2021

comment:6

OK, C++14 is irrelevant. Looks like the failing compilers do not implement C++11 completely.
https://stackoverflow.com/questions/25123458/is-trivially-copyable-is-not-a-member-of-std

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mkoeppe commented Sep 15, 2021

comment:8

Relevant: pybind/pybind11#2956 (pybind/pybind11@e08a581#diff-32496cc1f174bae1792ee91e0228cb198995509d66c039d64a3739f9c777cf10)

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mkoeppe commented Sep 15, 2021

Branch: u/mkoeppe/linuxmint_17__ubuntu_trusty__scipy_build_error_with_pybind11

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mkoeppe commented Sep 15, 2021

Author: Matthias Koeppe

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mkoeppe commented Sep 15, 2021

New commits:

d7a2ef3build/pkgs/pybind11/patches: Add fix for linuxmint-17, ubuntu-trusty

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mkoeppe commented Sep 15, 2021

Commit: d7a2ef3

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sagetrac-git mannequin commented Sep 15, 2021

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

dc418ddbuild/pkgs/pybind11/patches: Add fix for linuxmint-17, ubuntu-trusty
d0e1e95build/pkgs/pybind11/package-version.txt: Adjust patch for layout of the sdist

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sagetrac-git mannequin commented Sep 15, 2021

Changed commit from d7a2ef3 to d0e1e95

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mkoeppe commented Sep 15, 2021

comment:15

Tested successfully using tox -e docker-ubuntu-trusty-standard -- scipy

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mkoeppe commented Sep 23, 2021

comment:18

Let's get this in please

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kliem commented Sep 23, 2021

Reviewer: Jonathan Kliem

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kliem commented Sep 23, 2021

comment:19

LGTM.

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mkoeppe commented Sep 23, 2021

comment:20

Thank you!

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vbraun commented Oct 9, 2021

Changed branch from u/mkoeppe/linuxmint_17__ubuntu_trusty__scipy_build_error_with_pybind11 to d0e1e95

@vbraun vbraun closed this as completed in 686e5c2 Oct 9, 2021
@dimpase dimpase mentioned this issue Jan 6, 2023
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