[gmx-users] problem compiling gromacs 5.1

[Ana Marija]

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/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
-DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/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
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall
-DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
-DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
-DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF

on the and of the installation it was reported that:
GMX_FORCE_CXX
 MPI_LIBRARY

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?

also gmx_mpi is there:

ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build/bin> ls
gmx_mpi  template

On Sat, Oct 24, 2015 at 11:39 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Sat, Oct 24, 2015 at 6:32 PM Ana Marija <sokovic.anamarija at gmail.com>
> wrote:
>
>> Hay Mark,
>>
>> is it -DSPHINX_EXECUTABLE=OFF
>>
>
> They're equivalent - cmake regards both of them as equivalent to "not
> found."
>
>
>> also just curious would commenting out that 62 line in
>> /lustre/beagle2/ams/new/gromacs/gromacs-5.1/docs/CMakeLists.txt
>> solve the problem as well?
>>
>
> Looks like it, but not touching the source code is generally a good
> strategy. It's much easier to record a cmake command than to record how the
> source code was patched.
>
>
>> can you please tell me what other flags I need in cmake or you are saying
>> that I just have some redundant stuff there?
>>
>
> I can't tell what you need, that's between you, the machine, the sysadmins
> and their docs. I've said you have a bunch of things that don't exist /
> don't exist any more and that makes your life more complex than you want it
> to be.
>
> Mark
>
>
>> Ana
>>
>> On Sat, Oct 24, 2015 at 11:29 AM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> That one's our fault, sorry :-( It'll be fixed in 5.1.1 out shortly, but
>>> you can work around it by adding
>>>
>>> -DSPHINX_EXECUTABLE=no
>>>
>>> to your cmake call (which, by the way, still has a lot of stuff in it
>>> that I've said you don't want to have)
>>>
>>> Mark
>>>
>>> On Sat, Oct 24, 2015 at 6:14 PM Ana Marija <sokovic.anamarija at gmail.com>
>>> wrote:
>>>
>>>> HI,
>>>>
>>>> I tried to configure gromacs 5.1 via:
>>>>
>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake ..
>>>> -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>>>
>>>> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
>>>> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/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
>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall
>>>> -DGMX_X11=OFF -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF
>>>>
>>>>
>>>> But I am getting this error:
>>>> -- Found PythonInterp: /usr/bin/python (found version "2.6.9")
>>>> CMake Error at cmake/FindSphinx.cmake:52 (string):
>>>>   string sub-command REGEX, mode REPLACE needs at least 6 arguments
>>>> total to
>>>>   command.
>>>> Call Stack (most recent call first):
>>>>   docs/CMakeLists.txt:62 (find_package)
>>>>
>>>> line 62 in
>>>> /lustre/beagle2/ams/new/gromacs/gromacs-5.1/docs/CMakeLists.txt
>>>> looks like this:
>>>>
>>>>  find_package(Sphinx 1.2.3 QUIET COMPONENTS pygments)
>>>>
>>>> can you please advise me on what to do?
>>>>
>>>> Thanks
>>>> Ana
>>>> --
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>>>
>>