Bug 887685 – sci-chemistry/gromacs-2023_rc1 - /.../ld: lib/libgromacs.so.8.0.0: undefined reference to mu::ParserBase::DefineVar(std::_cxx11::b

• Product: Gentoo Linux
• Status: RESOLVED UPSTREAM

[Description Toralf Förster 2022-12-21 10:21:03 UTC]

too long lines were shrinked:

[1144/1154] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -D_UNICODE -Dlibgromacs_EXPORTS -I/var/tmp/portage/sci-chemistry/gromacs-2023_rc1/work/gromacs-2023-rc1/src/include -I/var/tmp/portage/sci-chemistry/gromacs-2023_rc1/
[1145/1154] : && /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -pipe -march=native -fno-diagnostics-color -O2  -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -shared -Wl,-soname,libgromacs.so.8 -o lib/libgromacs.so.8.0.0 src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errh
[1146/1154] /usr/bin/cmake -E cmake_symlink_library lib/libgromacs.so.8.0.0  lib/libgromacs.so.8 lib/libgromacs.so && :
[1147/1154] : && /usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o src/programs/CMakeFiles/mdrun_o
FAILED: bin/gmx 
: && /usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o src/programs/CMakeFiles/mdrun_objlib.dir/md
/usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: lib/libgromacs.so.8.0.0: undefined reference to `mu::ParserBase::DefineVar(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double*)'
/usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: lib/libgromacs.so.8.0.0: undefined reference to `mu::ParserBase::SetExpr(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
collect2: error: ld returned 1 exit status

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1-j4-20221220-180004

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-12 *
clang/llvm (if any):
/usr/lib/llvm/15
15.0.6
Python 3.10.9
Available Ruby profiles:
  [1]   ruby27 *
Available Rust versions:
  [1]   rust-bin-1.66.0 *
The following VMs are available for generation-2:
*)	Eclipse Temurin JDK 17.0.5_p8 [openjdk-bin-17]
Available Java Virtual Machines:
  [1]   openjdk-bin-17  system-vm

The Glorious Glasgow Haskell Compilation System, version 9.0.2
php cli (if any):

  HEAD of ::gentoo
commit 339b86324729a2587fa61a1a15a8a27d316e1a4b
Author: Repository mirror & CI <[e-mail]>
Date:   Tue Dec 20 22:17:09 2022 +0000

    2022-12-20 22:17:08 UTC

emerge -qpvO sci-chemistry/gromacs
[ebuild  N    ] sci-chemistry/gromacs-2023_rc1  USE="custom-cflags doc fftw gmxapi gmxapi-legacy hwloc offensive openmp single-precision threads tng -blas -build-manual -clang -clang-cuda (-cuda) -double-precision -lapack -mkl -mpi -opencl (-python) -test" CPU_FLAGS_X86="avx avx2 sse2 sse4_1 -avx512f -fma4" PYTHON_SINGLE_TARGET="python3_10 -python3_8 -python3_9 -python3_11"

[Comment 1 Toralf Förster 2022-12-21 10:21:04 UTC]

Created attachment 844411 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2022-12-21 10:21:05 UTC]

Created attachment 844413 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2022-12-21 10:21:06 UTC]

Created attachment 844415 [details]
environment

[Comment 4 Toralf Förster 2022-12-21 10:21:08 UTC]

Created attachment 844417 [details]
etc.portage.tar.bz2

[Comment 5 Toralf Förster 2022-12-21 10:21:09 UTC]

Created attachment 844419 [details]
logs.tar.bz2

[Comment 6 Toralf Förster 2022-12-21 10:21:10 UTC]

Created attachment 844421 [details]
sci-chemistry:gromacs-2023_rc1:20221220-231709.log.bz2

[Comment 7 Toralf Förster 2022-12-21 10:21:11 UTC]

Created attachment 844423 [details]
temp.tar.bz2

[Comment 8 Alexey Shvetsov 2023-04-25 09:52:56 UTC]

Should be fixed upstream