[BUG] Compilation problem when installing python3.9 environment by anaconda #484

csqjxiao · 2024-06-25T00:11:01Z

I am a university researcher, and would like to develop several new graph mining algorithms based on mage. So I have to install mage from source code. The following compilation error is encoutered however.

In file included from /home/qingjunxiao.linux/mage/cpp/biconnected_components_module/biconnected_components_module.cpp:1:
/home/qingjunxiao.linux/mage/cpp/memgraph/include/mg_exceptions.hpp:79:44: error: expected ‘)’ before ‘identifier’
   79 |   explicit InvalidIDException(std::uint64_t identifier) : message_{StringSerialize("Invalid ID =", identifier)} {}
      |                              ~             ^~~~~~~~~~~
      |                                            )
/home/qingjunxiao.linux/mage/cpp/memgraph/include/mg_exceptions.hpp:79:113: error: expected unqualified-id before ‘{’ token
   79 |   explicit InvalidIDException(std::uint64_t identifier) : message_{StringSerialize("Invalid ID =", identifier)} {}
      |                                                                                                                 ^
In file included from /home/qingjunxiao.linux/mage/cpp/bipartite_matching_module/bipartite_matching_module.cpp:1:
/home/qingjunxiao.linux/mage/cpp/memgraph/include/mg_exceptions.hpp:79:44: error: expected ‘)’ before ‘identifier’
   79 |   explicit InvalidIDException(std::uint64_t identifier) : message_{StringSerialize("Invalid ID =", identifier)} {}
      |                              ~             ^~~~~~~~~~~
      |                                            )
/home/qingjunxiao.linux/mage/cpp/memgraph/include/mg_exceptions.hpp:79:113: error: expected unqualified-id before ‘{’ token
   79 |   explicit InvalidIDException(std::uint64_t identifier) : message_{StringSerialize("Invalid ID =", identifier)} {}
      |                                                                                                                 ^
make[2]: *** [biconnected_components_module/CMakeFiles/biconnected_components.dir/build.make:76: biconnected_components_module/CMakeFiles/biconnected_components.dir/biconnected_components_module.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1772: biconnected_components_module/CMakeFiles/biconnected_components.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
make[2]: *** [bipartite_matching_module/CMakeFiles/bipartite_matching.dir/build.make:76: bipartite_matching_module/CMakeFiles/bipartite_matching.dir/bipartite_matching_module.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:1824: bipartite_matching_module/CMakeFiles/bipartite_matching.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
2024-06-25 07:42:53,611 [ERROR]: [Terminal] Running command ['make', '-j4'] failed.
2024-06-25 07:42:53,611 [ERROR]: [Terminal] (1/8) Building C++ modules failed.
2024-06-25 07:42:53,611 [ERROR]: [Terminal] An error occurred while building. Check the output message for more information.

My platform is Ubuntu 24.04 (i.e., MacOS installed with lima and ubuntu-lts). The CPU chip on my computer is Apple M1 Pro with ARM instruction set.

Firstly, I cloned the v1.17-memgraph-2.17 branch of mage project.

git clone --recurse-submodules -b v1.17-memgraph-2.17 https://github.com/memgraph/mage

Then, I installed the project's dependencies by the following commands. Note that libpython3.9 is not availble on Ubuntu 24.04. So I have to install a python3.9 virtual environment by anaconda.

sudo apt install python3 python3-dev python3-setuptools python3-pip libcurl4 libssl-dev openssl build-essential make cmake curl g++ clang unixodbc
# this a must
sudo apt install unixodbc-dev

wget https://repo.anaconda.com/archive/Anaconda3-2024.02-1-Linux-aarch64.sh
bash Anaconda3-2024.02-1-Linux-aarch64.sh
source ~/.bashrc
conda update conda
conda update anaconda
conda create --name python39 python=3.9
conda activate python39

curl https://sh.rustup.rs -sSf | sh -s -- -y \
&& export PATH="/root/.cargo/bin:${PATH}"

cd ~/mage
pip3 install -r ./python/requirements.txt 
pip3 install -r ./python/tests/requirements.txt 
pip3 install torch-sparse torch-cluster torch-spline-conv torch-geometric torch-scatter -f https://data.pyg.org/whl/torch-1.12.0+cu102.html

I have also installed the toolchain.

$ source /opt/toolchain-vXYZ/activate
(toolchain-v5) (python39) $ which gcc
/opt/toolchain-v5/bin/gcc
(toolchain-v5) (python39) $ which g++
/opt/toolchain-v5/bin/g++
(toolchain-v5) (python39) $ which clang
/opt/toolchain-v5/bin/clang
(toolchain-v5) (python39) $ which clang++
/opt/toolchain-v5/bin/clang++

Everything was fine until this step.

Thirdly, I complied the probject by:

python3 setup build -p /usr/lib/memgraph/query_modules

The C++ compiliation error appeared as mentioned at the beginning.

[ 23%] Building CXX object biconnected_components_module/CMakeFiles/biconnected_components.dir/biconnected_components_module.cpp.o
In file included from /home/qingjunxiao.linux/mage/cpp/biconnected_components_module/biconnected_components_module.cpp:1:
/home/qingjunxiao.linux/mage/cpp/memgraph/include/mg_exceptions.hpp:79:44: error: expected ‘)’ before ‘identifier’
   79 |   explicit InvalidIDException(std::uint64_t identifier) : message_{StringSerialize("Invalid ID =", identifier)} {}
      |                              ~             ^~~~~~~~~~~
      |                                            )
/home/qingjunxiao.linux/mage/cpp/memgraph/include/mg_exceptions.hpp:79:113: error: expected unqualified-id before ‘{’ token
   79 |   explicit InvalidIDException(std::uint64_t identifier) : message_{StringSerialize("Invalid ID =", identifier)} {}
      |                                                                                                                 ^
make[2]: *** [biconnected_components_module/CMakeFiles/biconnected_components.dir/build.make:76: biconnected_components_module/CMakeFiles/biconnected_components.dir/biconnected_components_module.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1772: biconnected_components_module/CMakeFiles/biconnected_components.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

The text was updated successfully, but these errors were encountered:

csqjxiao · 2024-06-25T08:27:49Z

I fixed this cpp compilation problem by adding the following header include at the beginning of ~/mage/cpp/memgraph/include/mg_exceptions.hpp. The type std::uint64_t is defined in cstdint.h.

#include <cstdint>

Regretfully, after fixing this problem, more compilation errors appeared.

[ 63%] Building CXX object uuid_module/CMakeFiles/uuid_generator.dir/uuid_module.cpp.o
In file included from /usr/include/c++/13/bits/chrono_io.h:39,
                 from /usr/include/c++/13/chrono:3370,
                 from /home/qingjunxiao.linux/mage/cpp/build/uuid/include/uuid.h:15,
                 from /home/qingjunxiao.linux/mage/cpp/uuid_module/uuid_module.cpp:1:
/usr/include/c++/13/format:2404:7: error: ‘span’ does not name a type
 2404 |       span<_CharT> _M_span;
      |       ^~~~
/usr/include/c++/13/format:2405:16: error: expected nested-name-specifier before ‘span’
 2405 |       typename span<_CharT>::iterator _M_next;
      |                ^~~~
/usr/include/c++/13/format:2405:16: error: expected ‘;’ at end of member declaration
 2405 |       typename span<_CharT>::iterator _M_next;
      |                ^~~~
      |                    ;
/usr/include/c++/13/format:2405:20: error: expected unqualified-id before ‘<’ token
 2405 |       typename span<_CharT>::iterator _M_next;
      |                    ^
/usr/include/c++/13/format:2416:17: error: expected ‘)’ before ‘<’ token
 2416 |       _Sink(span<_CharT> __span) noexcept
      |            ~    ^
      |                 )
/usr/include/c++/13/format:2422:7: error: ‘span’ does not name a type
 2422 |       span<_CharT>
      |       ^~~~
/usr/include/c++/13/format:2428:17: error: ‘span’ does not name a type
 2428 |       constexpr span<_CharT>
      |                 ^~~~
/usr/include/c++/13/format:2440:16: error: ‘span’ is not a type
 2440 |       _M_reset(span<_CharT> __s, size_t __pos = 0) noexcept
      |                ^~~~
/usr/include/c++/13/format:2440:20: error: expected ‘,’ or ‘...’ before ‘<’ token
 2440 |       _M_reset(span<_CharT> __s, size_t __pos = 0) noexcept
      |                    ^
/usr/include/c++/13/format: In member function ‘constexpr void std::__format::_Sink<_CharT>::_M_rewind()’:
/usr/include/c++/13/format:2436:9: error: ‘_M_next’ was not declared in this scope; did you mean ‘next’?
 2436 |       { _M_next = _M_span.begin(); }
      |         ^~~~~~~
      |         next
/usr/include/c++/13/format:2436:19: error: ‘_M_span’ was not declared in this scope; did you mean ‘span’?
 2436 |       { _M_next = _M_span.begin(); }
      |                   ^~~~~~~
      |                   span
/usr/include/c++/13/format: In member function ‘void std::__format::_Sink<_CharT>::_M_reset(int)’:
/usr/include/c++/13/format:2442:9: error: ‘_M_span’ was not declared in this scope; did you mean ‘span’?
 2442 |         _M_span = __s;
      |         ^~~~~~~
      |         span
/usr/include/c++/13/format:2442:19: error: ‘__s’ was not declared in this scope
 2442 |         _M_span = __s;
      |                   ^~~
/usr/include/c++/13/format:2443:9: error: ‘_M_next’ was not declared in this scope; did you mean ‘next’?
 2443 |         _M_next = __s.begin() + __pos;
      |         ^~~~~~~
      |         next
/usr/include/c++/13/format:2443:33: error: ‘__pos’ was not declared in this scope; did you mean ‘__pow’?
 2443 |         _M_next = __s.begin() + __pos;
      |                                 ^~~~~
      |                                 __pow
/usr/include/c++/13/format: In member function ‘constexpr void std::__format::_Sink<_CharT>::_M_write(_CharT)’:
/usr/include/c++/13/format:2450:10: error: ‘_M_next’ was not declared in this scope; did you mean ‘next’?
 2450 |         *_M_next++ = __c;
      |          ^~~~~~~
      |          next
/usr/include/c++/13/format:2451:23: error: ‘_M_span’ was not declared in this scope; did you mean ‘span’?
 2451 |         if (_M_next - _M_span.begin() == std::ssize(_M_span)) [[unlikely]]
      |                       ^~~~~~~
      |                       span
/usr/include/c++/13/format: In member function ‘constexpr void std::__format::_Sink<_CharT>::_M_write(std::basic_string_view<_CharT>)’:
/usr/include/c++/13/format:2458:14: error: expected ‘;’ before ‘__to’
 2458 |         span __to = _M_unused();
      |              ^~~~
/usr/include/c++/13/format:2459:16: error: ‘__to’ was not declared in this scope
 2459 |         while (__to.size() <= __s.size())
      |                ^~~~
/usr/include/c++/13/format:2462:13: error: ‘_M_next’ was not declared in this scope; did you mean ‘next’?
 2462 |             _M_next += __to.size();
      |             ^~~~~~~
      |             next
/usr/include/c++/13/format:2465:20: error: there are no arguments to ‘_M_unused’ that depend on a template parameter, so a declaration of ‘_M_unused’ must be available [-fpermissive]
 2465 |             __to = _M_unused();
      |                    ^~~~~~~~~
/usr/include/c++/13/format:2465:20: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/usr/include/c++/13/format:2469:22: error: ‘__to’ was not declared in this scope
 2469 |             __s.copy(__to.data(), __s.size());
      |                      ^~~~
/usr/include/c++/13/format:2470:13: error: ‘_M_next’ was not declared in this scope; did you mean ‘next’?
 2470 |             _M_next += __s.size();
      |             ^~~~~~~
      |             next
/usr/include/c++/13/format: In member function ‘void std::__format::_Iter_sink<_CharT, _OutIter>::_M_overflow()’:
/usr/include/c++/13/format:2572:13: error: ‘span’ was not declared in this scope; did you mean ‘gsl::span’?
 2572 |             span<_CharT> __first;
      |             ^~~~
      |             gsl::span
In file included from /usr/include/c++/13/format:44:
/home/qingjunxiao.linux/mage/cpp/build/uuid/include/gsl/span:78:7: note: ‘gsl::span’ declared here
   78 | class span;
      |       ^~~~
/usr/include/c++/13/format:2572:24: error: expected primary-expression before ‘>’ token
 2572 |             span<_CharT> __first;
      |                        ^
/usr/include/c++/13/format:2572:26: error: ‘__first’ was not declared in this scope
 2572 |             span<_CharT> __first;
      |                          ^~~~~~~
/usr/include/c++/13/format: At global scope:
/usr/include/c++/13/format:2646:14: error: ‘span’ does not name a type
 2646 |       static span<_CharT>
      |              ^~~~
/usr/include/c++/13/format: In instantiation of ‘_Seq std::__format::_Seq_sink<_Seq>::get() && [with _Seq = std::__cxx11::basic_string<char>]’:
/usr/include/c++/13/format:3788:32:   required from here
/usr/include/c++/13/format:2538:19: error: ‘class std::__format::_Seq_sink<std::__cxx11::basic_string<char> >’ has no member named ‘_M_used’; did you mean ‘_M_seq’?
 2538 |         if (this->_M_used().size() != 0)
      |             ~~~~~~^~~~~~~
      |             _M_seq
/usr/include/c++/13/format: In instantiation of ‘_Seq std::__format::_Seq_sink<_Seq>::get() && [with _Seq = std::__cxx11::basic_string<wchar_t>]’:
/usr/include/c++/13/format:3797:32:   required from here
/usr/include/c++/13/format:2538:19: error: ‘class std::__format::_Seq_sink<std::__cxx11::basic_string<wchar_t> >’ has no member named ‘_M_used’; did you mean ‘_M_seq’?
 2538 |         if (this->_M_used().size() != 0)
      |             ~~~~~~^~~~~~~
      |             _M_seq
/usr/include/c++/13/format: In instantiation of ‘constexpr std::__format::_Buf_sink<_CharT>::_Buf_sink() [with _CharT = char]’:
/usr/include/c++/13/format:2527:7:   required from ‘std::__format::_Seq_sink<_Seq>::_Seq_sink() [with _Seq = std::__cxx11::basic_string<char>]’
/usr/include/c++/13/format:3786:31:   required from here
/usr/include/c++/13/format:2494:23: error: cannot convert ‘char [256]’ to ‘const std::__format::_Sink<char>&’
 2494 |       : _Sink<_CharT>(_M_buf)
      |                       ^~~~~~
      |                       |
      |                       char [256]
/usr/include/c++/13/format:2475:13: note:   initializing argument 1 of ‘std::__format::_Sink<_CharT>::_Sink(const std::__format::_Sink<_CharT>&) [with _CharT = char]’
 2475 |       _Sink(const _Sink&) = delete;
      |             ^~~~~~~~~~~~
/usr/include/c++/13/format: In instantiation of ‘constexpr std::__format::_Buf_sink<_CharT>::_Buf_sink() [with _CharT = wchar_t]’:
/usr/include/c++/13/format:2527:7:   required from ‘std::__format::_Seq_sink<_Seq>::_Seq_sink() [with _Seq = std::__cxx11::basic_string<wchar_t>]’
/usr/include/c++/13/format:3795:34:   required from here
/usr/include/c++/13/format:2494:23: error: cannot convert ‘wchar_t [64]’ to ‘const std::__format::_Sink<wchar_t>&’
 2494 |       : _Sink<_CharT>(_M_buf)
      |                       ^~~~~~
      |                       |
      |                       wchar_t [64]
/usr/include/c++/13/format:2475:13: note:   initializing argument 1 of ‘std::__format::_Sink<_CharT>::_Sink(const std::__format::_Sink<_CharT>&) [with _CharT = wchar_t]’
 2475 |       _Sink(const _Sink&) = delete;
      |             ^~~~~~~~~~~~
/usr/include/c++/13/format: In instantiation of ‘void std::__format::_Iter_sink<_CharT, _OutIter>::_M_overflow() [with _CharT = wchar_t; _OutIter = std::__format::_Sink_iter<wchar_t>]’:
/usr/include/c++/13/format:2564:7:   required from here
/usr/include/c++/13/format:2566:26: error: ‘class std::__format::_Iter_sink<wchar_t, std::__format::_Sink_iter<wchar_t> >’ has no member named ‘_M_used’
 2566 |         auto __s = this->_M_used();
      |                    ~~~~~~^~~~~~~
/usr/include/c++/13/format: In instantiation of ‘void std::__format::_Iter_sink<_CharT, _OutIter>::_M_overflow() [with _CharT = char; _OutIter = std::__format::_Sink_iter<char>]’:
/usr/include/c++/13/format:2564:7:   required from here
/usr/include/c++/13/format:2566:26: error: ‘class std::__format::_Iter_sink<char, std::__format::_Sink_iter<char> >’ has no member named ‘_M_used’
/usr/include/c++/13/format: In instantiation of ‘constexpr void std::__format::_Sink<_CharT>::_M_write(std::basic_string_view<_CharT>) [with _CharT = wchar_t]’:
/usr/include/c++/13/format:2379:19:   required from ‘constexpr std::__format::_Sink_iter<_CharT>& std::__format::_Sink_iter<_CharT>::operator=(std::basic_string_view<_CharT>) [with _CharT = wchar_t]’
/usr/include/c++/13/format:599:12:   required from ‘_Out std::__format::__write(_Out, std::basic_string_view<_CharT>) [with _Out = _Sink_iter<wchar_t>; _CharT = wchar_t]’
/usr/include/c++/13/format:3639:36:   required from ‘constexpr void std::__format::_Formatting_scanner<_Out, _CharT>::_M_on_chars(iterator) [with _Out = std::__format::_Sink_iter<wchar_t>; _CharT = wchar_t; iterator = const wchar_t*]’
/usr/include/c++/13/format:3636:7:   required from here
/usr/include/c++/13/format:2465:29: error: ‘_M_unused’ was not declared in this scope
 2465 |             __to = _M_unused();
      |                    ~~~~~~~~~^~
/usr/include/c++/13/format: In instantiation of ‘constexpr void std::__format::_Sink<_CharT>::_M_write(std::basic_string_view<_CharT>) [with _CharT = char]’:
/usr/include/c++/13/format:2379:19:   required from ‘constexpr std::__format::_Sink_iter<_CharT>& std::__format::_Sink_iter<_CharT>::operator=(std::basic_string_view<_CharT>) [with _CharT = char]’
/usr/include/c++/13/format:599:12:   required from ‘_Out std::__format::__write(_Out, std::basic_string_view<_CharT>) [with _Out = _Sink_iter<char>; _CharT = char]’
/usr/include/c++/13/format:3639:36:   required from ‘constexpr void std::__format::_Formatting_scanner<_Out, _CharT>::_M_on_chars(iterator) [with _Out = std::__format::_Sink_iter<char>; _CharT = char; iterator = const char*]’
/usr/include/c++/13/format:3636:7:   required from here
/usr/include/c++/13/format:2465:29: error: ‘_M_unused’ was not declared in this scope
make[2]: *** [uuid_module/CMakeFiles/uuid_generator.dir/build.make:76: uuid_module/CMakeFiles/uuid_generator.dir/uuid_module.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:2243: uuid_module/CMakeFiles/uuid_generator.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

katarinasupe · 2024-07-02T13:02:46Z

Hi @csqjxiao, thank you for reporting this! Did you try installing MAGE outside of Conda? To unblock you, is it okay for you to run Memgraph MAGE Docker image?

csqjxiao added the bug bug label Jun 25, 2024

csqjxiao assigned gitbuda Jun 25, 2024

katarinasupe added Severity - S2 Severity - S2 community community Frequency - Weekly Frequency - Weekly Reach - VeryFew Reach - VeryFew Effort - Unknown Effort - Unknown labels Jul 2, 2024

katarinasupe added this to community bugs and incremental features Jul 2, 2024

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[BUG] Compilation problem when installing python3.9 environment by anaconda #484

[BUG] Compilation problem when installing python3.9 environment by anaconda #484

[BUG] Compilation problem when installing python3.9 environment by anaconda #484

[BUG] Compilation problem when installing python3.9 environment by anaconda #484

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