[gmx-users] gromacs build options

[Mark Abraham]

Hi,

On Sat, Oct 8, 2016 at 5:31 PM Mahmood Naderan <mahmood.nt at gmail.com> wrote:

> I got an error regarding fftw3. Maybe not related to GMX itself, but I
>
> appreciate any comment for that.
>
>
>
>
>
> root at cluster:build#


Do not configure software as root, unless your preferred hobby is
reinstalling operating systems. Particularly do not do so when you're using
unfamiliar configuration systems to configure unfamiliar software, so
you're not sure what the consequences of any action might be...

Only "make install" to a destination that needs root privileges needs root
privileges.


> /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake
>
> .. -DCMAKE_C_COMPILER=/share/ap
>
> ps/computer/openmpi-2.0.1/bin/mpicc
>
> -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++
>
> -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1
>
> -DBUILD_SHARED_LIBS=off
>
> -DFFTWF_LIBRARY=/share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a
>
> -DFFTWF_INCLUDE_DIR=/share/apps/computer/fftw-3.3.5/include
>

If you would like to manage this manually, then you're going to have to
read the .log file that cmake mentioned and work out what the problem is.

Or just follow
http://manual.gromacs.org/documentation/2016/install-guide/index.html#helping-cmake-find-the-right-libraries-headers-or-programs
and
let cmake do its job of working out what your toolchain can do, if it's
possible.

Mark


> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
>
> acceleration
>
> -- Looking for fftwf_plan_r2r_1d in
>
> /share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a
>
> -- Looking for fftwf_plan_r2r_1d in
>
> /share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a - not found
>
> CMake Error at cmake/FindFFTW.cmake:100 (message):
>
>   Could not find fftwf_plan_r2r_1d in
>
>   /share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a, take a look at the
>
>   error message in
>
>   /share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeError.log to find
>
>   out what went wrong.  If you are using a static lib (.a) make sure you
>
> have
>
>   specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
>
>   -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
>
> Call Stack (most recent call first):
>
>
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>
> I don't understand the last message. Should I use shared libs only?
>
>
>
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>
>
>
> Regards,
>
> Mahmood
>
> --
>
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