[gmx-users] Gromacs 2016 building issue

[Victor Rosas Garcia]

I thought the "build" directory had to be *outside* the gromacs source
directory.  Don't know for sure if that makes a difference.

2016-08-18 18:20 GMT-05:00 Quentin Kaas <q.kaas at imb.uq.edu.au>:

> Hi Mark,
>
> Thank you for your answer. I just have redone again everything but I get
> the same problem. I am not even compiling with MPI or GPU support and I
> have the same.
>
> Hereis my procedure:
> """
> tar xzvf gromacs-2016.tar.gz
> cd gromacs-2016
> mkdir build
> cd build/
> cmake -DGMX_GPU=OFF -DGMX_MPI=OFF -DCMAKE_INSTALL_PREFIX=/home/
> q.kaas/share/gromacs-2016_nompi/ -DGMX_BUILD_OWN_FFTW=ON
> -DBUILD_SHARED_LIBS=OFF -DGMX_SIMD=AVX_256 ..
> nice -20 make -j 2
> """
>
> And the answer is the same:
>
> """
> (...)
> [100%] Built target libgromacs
> Linking CXX executable ../../bin/template
> /opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error
> """
>
> What is this "template" doing? Could that be coming from this binary?
> There is no such thing in 5.1.3.
>
> Thank you
> Quentin
>
>
>
> On 18/08/16 22:17, Mark Abraham wrote:
>
> Hi,
>
> GROMACS 2016 doesn't use libxml2 at all, so it looks like there's something
> strange going on with how you've done that build, because there's no way
> the template can have such a linking dependency.
>
> Mark
>
> On Thu, Aug 18, 2016 at 2:43 AM Quentin Kaas <q.kaas at imb.uq.edu.au> <q.kaas at imb.uq.edu.au> wrote:
>
>
> Hello,
>
> I just tried building Gromacs2016. The build went fine until it reached
> the linking stage:
>
> linking CXX executable ../../bin/template
> /opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64'
> collect2: error: ld returned 1 exit status
> make[1]: *** [bin/template] Error 1
> make: *** [share/template/CMakeFiles/template.dir/all] Error 2
>
> Could someone help me tell cmake to tell ld where the zlib library is?
>
> I compiled Gromacs-5.1.3 about 10 min before trying the new 2016 version
> and it went without any complaint. There might be something to fix in the
> 2016 version?
>
> Best wishes
>
> Quentin
> --
> Gromacs Users mailing list
>
> * Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> --
> *Dr Quentin Kaas*
>
> Institute for Molecular Bioscience (IMB)
> Level 2 North, Building 80, The University of Queensland, Brisbane QLD
> 4072, Australia
> F: +61 7 3346 2021
>
> http://researchers.uq.edu.au/researcher/1804
> http://www.conoserver.org/
> http://cybase.org.au/
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>