[gmx-users] Gromacs 2016 building issue

Mark Abraham mark.j.abraham at gmail.com
Mon Aug 22 10:04:02 CEST 2016 

Hi,

My guess is that these are dependencies of your system's hwloc library. If
I'm right, then a fresh GROMACS 2016 build with the cmake variable
GMX_HWLOC=off will have no problems.

But the proper solution seems to be to set up your dynamic linking
environment correctly. What is the origin of the set of packages in
/opt/pkg against which you are building?

Mark

On Mon, 22 Aug 2016 03:09 Quentin Kaas <q.kaas at imb.uq.edu.au> wrote:

> Hi,
>
> I finally succeeded to build gromacs 2016, there was indeed an issue with
> two zlib libraries installed in at different folder. I had to modify the
> link.txt to add a path to the more recent libraries (the path was set in
> environment variable but for some reason was not considered by cmake). Once
> again, when I compile 5.1.3 (or previous versions) I never encountered this
> issue.
>
> Regarding gromacs-2016 not using libxml2, running "ldd gmx" gives:
>
>     linux-vdso.so.1 =>  (0x00007fffa35ff000)
>     libhwloc.so.5 => /opt/pkg/2015Q2/lib/libhwloc.so.5 (0x00007f6604273000)
>     libz.so.1 => /opt/pkg/2015Q2/lib/libz.so.1 (0x00007f660405e000)
>     librt.so.1 => /lib64/librt.so.1 (0x00007f6603e42000)
>     libblas.so.4 => /opt/pkg/2015Q2/lib/libblas.so.4 (0x00007f6603bf2000)
>     liblapack.so.4 => /opt/pkg/2015Q2/lib/liblapack.so.4
> (0x00007f6603390000)
>     libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f6603173000)
>     libstdc++.so.6 =>
> /opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libstdc++.so.6
> (0x00007f6602e60000)
>     libm.so.6 => /lib64/libm.so.6 (0x00007f6602bdc000)
>     libgomp.so.1 =>
> /opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgomp.so.1
> (0x00007f66029c6000)
>     libgcc_s.so.1 =>
> /opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgcc_s.so.1
> (0x00007f66027af000)
>     libc.so.6 => /lib64/libc.so.6 (0x00007f660241b000)
>     libxml2.so.2 => /opt/pkg/2015Q2/lib/libxml2.so.2 (0x00007f66020be000)
>     libdl.so.2 => /lib64/libdl.so.2 (0x00007f6601eb9000)
>     liblzma.so.5 => /opt/pkg/2015Q2/lib/liblzma.so.5 (0x00007f6601c94000)
>     /lib64/ld-linux-x86-64.so.2 (0x00007f66044a0000)
>     libgfortran.so.3 =>
> /opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgfortran.so.3
> (0x00007f6601977000)
>     libquadmath.so.0 =>
> /opt/pkg/2015Q2/gcc49/lib/../lib64/libquadmath.so.0 (0x00007f6601739000)
>
> Note the reference to libxml2.so.2.
>
> Quentin
>
>
> On 19/08/16 21:45, Justin Lemkul wrote:
>
>
>
> On 8/18/16 8:44 PM, Victor Rosas Garcia wrote:
>
> I thought the "build" directory had to be *outside* the gromacs source
> directory.  Don't know for sure if that makes a difference.
>
>
> No, the build directory can be wherever you like, and building within
> source is fine (and recommended in the install guide).  One should not
> *install* within the source as that generates problems.
>
> The full CMake output would be helpful here, as clearly the build process
> is doing something it shouldn't, but that is probably specific to the
> system in question, because as Mark said, it is not anticipated that
> GROMACS should be throwing this sort of error.
>
> -Justin
>
> 2016-08-18 18:20 GMT-05:00 Quentin Kaas <q.kaas at imb.uq.edu.au>
> <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> <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
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> --
> *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/
>
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>
>
> --
> *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
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