Issues with Eigen array header during make

[svolk19-stanford]

Issue summary

Hello,

When I follow the standard instructions to build gnina on Ubuntu 20.04 (windows WSL) everything goes smoothly until the make command. Then, I receive the following error when building atom_constants.cpp:

[ 48%] Building CXX object gninasrc/CMakeFiles/gninalib.dir/lib/atom_constants.cpp.o
In file included from /usr/include/c++/9/tuple:39,
from /usr/include/c++/9/functional:54,
from /usr/include/c++/9/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/9/algorithm:71,
from /mnt/c/Users/[usr]/Desktop/gnina/gnina/gninasrc/lib/common.h:30,
from /mnt/c/Users/[usr]/Desktop/gnina/gnina/gninasrc/lib/atom_constants.h:26,
from /mnt/c/Users/[usr]/Desktop/gnina/gnina/gninasrc/lib/atom_constants.cpp:1:
/mnt/c/Users/[usr]/Desktop/gnina/gnina/gninasrc/../Eigen/array:8:4: error: #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.
8 | #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.
| ^~~~~
In file included from /usr/include/c++/9/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/9/algorithm:71,
from /mnt/c/Users/[usr]/Desktop/gnina/gnina/gninasrc/lib/common.h:30,
from /mnt/c/Users/[usr]/Desktop/gnina/gnina/gninasrc/lib/atom_constants.h:26,
from /mnt/c/Users/[usr]/Desktop/gnina/gnina/gninasrc/lib/atom_constants.cpp:1:
/usr/include/c++/9/functional:1111:29: error: ‘array’ is not a member of ‘std’
1111 | tuple<_GLIBCXX_STD_C::array<_Tp, _Len>, _Pred> _M_bad_char;
| ^~~~~
/usr/include/c++/9/functional:63:1: note: ‘std::array’ is defined in header ‘’; did you forget to ‘#include ’?
62 | # include
+++ |+#include
63 | # include
/usr/include/c++/9/functional:1111:44: error: template argument 1 is invalid
1111 | tuple<_GLIBCXX_STD_C::array<_Tp, _Len>, _Pred> _M_bad_char;
| ^
/usr/include/c++/9/functional:1111:44: error: template argument 2 is invalid
/usr/include/c++/9/functional:1111:45: error: expected unqualified-id before ‘,’ token
1111 | tuple<_GLIBCXX_STD_C::array<_Tp, _Len>, _Pred> _M_bad_char;
| ^
/usr/include/c++/9/functional: In constructor ‘std::__boyer_moore_array_base<_Tp, _Len, _Pred>::__boyer_moore_array_base(_RAIter, std::size_t, _Unused&&, _Pred&&)’:
/usr/include/c++/9/functional:1083:4: error: class ‘std::__boyer_moore_array_base<_Tp, _Len, _Pred>’ does not have any field named ‘_M_bad_char’
1083 | : _M_bad_char{ _GLIBCXX_STD_C::array<_Tp, _Len>{}, std::move(__pred) }
| ^~~~~~~~~~~
/usr/include/c++/9/functional:1083:33: error: ‘array’ is not a member of ‘std’
1083 | : _M_bad_char{ _GLIBCXX_STD_C::array<_Tp, _Len>{}, std::move(__pred) }
| ^~~~~
/usr/include/c++/9/functional:1083:33: note: ‘std::array’ is defined in header ‘’; did you forget to ‘#include ’?
/usr/include/c++/9/functional:1083:42: error: expected primary-expression before ‘,’ token
1083 | : _M_bad_char{ _GLIBCXX_STD_C::array<_Tp, _Len>{}, std::move(__pred) }
| ^
/usr/include/c++/9/functional:1083:49: error: expected primary-expression before ‘{’ token
1083 | : _M_bad_char{ _GLIBCXX_STD_C::array<_Tp, _Len>{}, std::move(__pred) }
| ^
/usr/include/c++/9/functional:1083:49: error: expected ‘}’ before ‘{’ token
/usr/include/c++/9/functional: In member function ‘std::__boyer_moore_array_base<_Tp, _Len, _Pred>::__diff_type std::__boyer_moore_array_base<_Tp, _Len, _Pred>::_M_lookup(_Key, std::__boyer_moore_array_base<_Tp, _Len, _Pred>::__diff_type) const’:
/usr/include/c++/9/functional:1105:23: error: ‘_M_bad_char’ was not declared in this scope; did you mean ‘__is_char’?
1105 | return std::get<0>(_M_bad_char)[__ukey];
| ^~~~~~~~~~~
| __is_char
/usr/include/c++/9/functional: In member function ‘const _Pred& std::__boyer_moore_array_base<_Tp, _Len, _Pred>::_M_pred() const’:
/usr/include/c++/9/functional:1109:44: error: ‘_M_bad_char’ was not declared in this scope; did you mean ‘__is_char’?
1109 | _M_pred() const { return std::get<1>(_M_bad_char); }
| ^~~~~~~~~~~
| __is_char
make[2]: *** [gninasrc/CMakeFiles/gninalib.dir/build.make:97: gninasrc/CMakeFiles/gninalib.dir/lib/atom_constants.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1729: gninasrc/CMakeFiles/gninalib.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

Steps to reproduce

git clone https://github.com/gnina/gnina.git
cd gnina
mkdir build
cd build
cmake ..
make

system configuration

Operating system: Ubuntu 20.04 (windows WSL)
nvcc: V12.2.91

[dkoes]

I've added a 20.04 Dockerfile to illustrate building on 20.04: https://github.com/gnina/gnina/blob/master/docker/ubuntu-20.04/Dockerfile

This doesn't do anything special, so I suspect the issue is with your setup. To me this seems like a problem with the standard libraries not providing array.

[mainguyenanhvu]

I faced the same issue when running make command on WSL2. Please show me the way to address it.

[dkoes]

Instructions for WSL2 Ubuntu 22.04 have been added to the readme.

[mainguyenanhvu]

@dkoes I tried your instruction, however, it does not work. Please help me. I created a new issue #255

[mainguyenanhvu]

@dkoes why do you use cmake 3.18 in dockerfile although your instruction requires cmake 3.25?

[dkoes]

That's for Ubuntu 18.04. The newer versions (and compat) use newer cmake. I've removed the 18.04 since it is out of support.