[gmx-users] problem compiling gromacs 5.1
sokovic.anamarija at gmail.com
Thu Oct 29 03:52:54 CET 2015
I was able to compile gromacs 5.1 via:
cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/18.104.22.168/abudhabi/include
-DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_DOUBLE=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
-DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF
Thank you for all your help and patience with mine somewhat basic questions!
On Sat, Oct 24, 2015 at 9:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
> The purpose of using a wrapper compiler is that it handles linking all the
> right stuff. MPI_LIBRARY was a thing from a cmake module we used only in
> Gromacs 4.5, before we removed it when we decided that wrapper compilers do
> a better job. So there's nothing that replaces it. That the recent
> installation guides make zero mention of linking MPI libraries is a big
> On Sat, 24 Oct 2015 22:05 Ana Marija <sokovic.anamarija at gmail.com> wrote:
>> For 4.6.7 gromacs MPI_Library flag was necessary as well as for 4.5.5.
>> What I am asking here is not weather my admins are doing a good job,and
>> also as you know some things you just got with machine,and sometimes things
>> are not great,so you have to make a workaround. What I am asking here is
>> what is the function and is there is a function of mpi_Library flag in
>> gromacs 5.1 and was that flag replaced with a different one in that version?
>> On Oct 24, 2015 2:07 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>>> On Sat, Oct 24, 2015 at 8:22 PM Ana Marija <sokovic.anamarija at gmail.com>
>>>> so I managed to install gromacs via:
>>>> #in ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build>
>>>> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/22.214.171.124/abudhabi/include
>>>> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
>>>> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
>>>> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
>>>> -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF
>>>> on the and of the installation it was reported that:
>>>> flags were not used. What I am worried about is MPI_LIBRARY flag. Does
>>>> this means that gromacs just found on it's own MPI libraries or?
>>> What's more likely? That I said earlier that the point of the modules
>>> you loaded is that you are using the magic wrapper compilers Cray provides
>>> to handle MPI for you, or that I'm wrong about that *and* about my
>>> assertion that MPI_LIBRARY was useless? :-)
>>> Not needing to know about such garbage is why you should be asking your
>>> system administators to do these infrastructure things for you...
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