[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
shahid nayeem
msnayeem at gmail.com
Wed Sep 11 09:38:17 CEST 2013
Thanks Mark
$ make
[ 0%] Built target gmxfftw
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
I checked in folder
/cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
, this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
locate it.
Please help me
shahid Nayeem
On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem <msnayeem at gmail.com> wrote:
> Thanks. But when I ran make again I am getting this error
> [ 0%] Built target gmxfftw
> 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
> shahid Nayeem
>
>
> On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
>> this problem. Run make a second time and it will work.
>>
>> Mark
>>
>> On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem <msnayeem at gmail.com>
>> wrote:
>> > 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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>
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