[gmx-users] Gromacs 2016 building issue

[Justin Lemkul]

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>:
>
>> 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
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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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================