[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Tue Sep 10 17:43:35 CEST 2013

On 10.09.2013 08:20, shahid nayeem wrote:
> I am installing gromacs -4.6.3 on cygwin with following commands
> tar -xvzf gramcs-4.6.3.tar.gz
> cd gromacs-4.6.3
> mkdir build
> cd build
> It runs fine and write file in build directory.
> when I run make command it gives following error.
> /cygdrive/c/packages/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20:
> error: field ‘timer_init’ has incomplete type
>       struct timeval timer_init;
>                      ^
> src/gmxlib/CMakeFiles/gmx.dir/build.make:3070: recipe for target

The Gromacs-file "gmxlib/thread_mpi/impl.h" is missing the
correct #define for the "unixish" Cygwin pseudo-os. You can
add it by inserting

  #define HAVE_SYS_TIME_H

at the very top of the file gmxlib/thread_mpi/impl.h

Then the package will probably compile and link, but
mdrun's thread-mpi (tMPI) will not work on Cygwin
(didn't work last time I tried).

So you could do the following: 1) install the Gromacs
package with "normal" compilation, and 2) build and
install the openmpi-version of mdrun (mdrun_mpi).

(1) cmake-options for package:
       -DGMX_GPU=OFF                         \
       -DGMX_PREFER_STATIC_LIBS=ON           \

make -j4 install

(delete all files from the build path)

(2) cmake options for mdrun_mpi
       -DGMX_GPU=OFF                        \
       -DGMX_MPI=ON                         \
       -DGMX_PREFER_STATIC_LIBS=ON          \

make -j4 install-mdrun

The openmpi-version (mdrun_mpi) runs reasonable on
Cygwin/64 1.7.25, but not as fast as the native
windows version (compiled with visual studio 10 or 12).
The windows-compiled version of 4.6.3 is very robust and
allows to link mdrun against CUDA 5.0 (but not 5.5(+VC12)
for unknown reasons). Then, you'll have full gpu support
under windows.



More information about the gromacs.org_gmx-users mailing list