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
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
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.
Regards
M.
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