[gmx-users] Installing Gromacs 4.6.3 using Cygwin

[chem grad]

Hello,

I am new to both Cygwin and Gromacs, so I apologize in advance if this error
is do to my computing ignorance. I downloaded the gromacs-4.6.3.tar.gz file
and tried to follow the 'Quick and Dirty Installation Instructions' to
install Gromacs 4.6.3 on my new Windows 8 machine, but encountered a couple
snags.

I started with $ tar xfz gromacs-4.6.3.tar.gz, then $ cd gromacs-4.6.3/, $
mkdir build, $ cd build, and then $ cmake .. -DGMX_BUILD_OWN_FFTW=ON and
everything went smoothly:
-- Configuring done
-- Generating done
-- Build files have been written to:
/cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/build

Then when I entered $ make I received the following from Cygwin:
Scanning dependencies of target gmxfftw
[  0%] Creating directories for 'gmxfftw'
[  0%] Performing download step (download, verify and extract) for 'gmxfftw'
-- downloading...
     src='http://www.fftw.org/fftw-3.3.2.tar.gz'
    
dst='/cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
     timeout='none'
-- [download 0% complete]
-- [download 2% complete]
-- [download 26% complete]
-- [download 57% complete]
-- [download 84% complete]
-- [download 100% complete]
-- downloading... done
-- verifying file...
    
file='/cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
-- verifying file... done
-- extracting...
    
src='/cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz'
    
dst='/cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/src/gmxfftw'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done

... and so on until it stopped with the following error message:

[ 17%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o
[ 17%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o
In file included from
/cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0:
/cygdrive/c/Cygwin/home/kelly/Gromacs/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
'src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1
CMakeFiles/Makefile2:1238: recipe for target
'src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2

I found a fix for this error on the forum and entered  #define
HAVE_SYS_TIME_H into the impl.h file, then tried make again and it got
farther this time before I received the following error message:

[ 39%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_single.c.o
[ 39%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_single.c.o
make[2]: *** No rule to make target
'//cygdrive/c/Cygwin/home/kelly/Gromacs/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a',
needed by 'src/gmxlib/cyggmx-8.dll'.  Stop.
CMakeFiles/Makefile2:1238: recipe for target
'src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2

Any help you can provide is much appreciated!

Thank you,
Kelly

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