[gmx-users] linking error while trying to build gromacs

[Mark Abraham]

Hi,

The simplest explanation would be that your C compiler and your C++
compiler are somehow incompatible. But we'd have to see eg the terminal log
from cmake to know.

Mark

On Thu, 2 Mar 2017 22:44 Andrey Tolstov <atolst at yandex.ru> wrote:

> Hello!
>
> I'm trying to install gromacs 5.1.4 on my Ubuntu 16.04. I've unpacked
> sources, made build dir, launched from it "cmake ..
> -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DGMX_DOUBLE=off" - it worked fine,
> then ran "make". Compilation was ok, but linker returned an error
> "collect2: error: ld returned 1 exit status" and a lot of undefined
> references, like that:
>
> [ 98%] Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_avx_256_single'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn'
> ../../lib/libgromacs.so.1.4.0: undefined reference to
> `nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_single'
>
> After that I've tried to build and use fftw3, switch from avx to sse4.1,
> switch from gcc-5 to gcc-4.9, but these (or very similar) errors didn't
> disappear. Also I've tried gromacs versions 5.1.3 and 5.0.4 but I've got
> the same problem.
> For more information see the full make log by link
> http://pastebin.com/UeyfPdgA or tail of it with all the errors in
> attached file.
> Can you please help me finding the reason of this problem?
>
> Thanks in advance,
> Andrey
> --
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