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

[shahid nayeem]

Thanks Wahab
I followed your instruction and added  #define HAVE_SYS_TIME_H

at the very top of the file gmxlib/thread_mpi/impl.h.
Then again in make command I got following errors.
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_avx_256_double.c.o
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomP1P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW3W3_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwLJ_GeomW4W4_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomP1P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3P1_avx_256_double.c.o
[ 55%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4P1_avx_256_double.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW4W4_avx_256_double.c.o
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-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

Please help me to compile gromacs 4.6.3 on cygwin

Shahid Nayeem


On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab <
mirco.wahab at chemie.tu-freiberg.de> wrote:

> 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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