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

[Mark Abraham]

Hi,

That's a cmake log for a different run (building fftw via GROMACS vs not).
But I can build and install the 5.1.4 tarball fine with the stock gcc 5.4.0
on ubuntu 16.04.02 and cuda 8.0, with or without building ffftw via GROMACS.

Mark

On Fri, Mar 3, 2017 at 9:26 PM Толстов Андрей <atolst at yandex.ru> wrote:

> HI,
>
> Thanks for yuor reply. Here is log of my cmake output. I can't find
> anything significantly wrong there.
>
> Andrey
>
> 03.03.2017, 10:39, "Mark Abraham" <mark.j.abraham at gmail.com>:
>
> 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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