Don't know, sorry. None of the devs use Cygwin. I suggest you follow the normal instructions to install FFTW manually, and then direct CMake to use it.
Mark On Wed, Sep 11, 2013 at 9:38 AM, shahid nayeem <msnay...@gmail.com> wrote: > 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 <msnay...@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.abra...@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 <msnay...@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.wa...@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. >>> >> >>> >> -- >>> >> gmx-users mailing list gmx-users@gromacs.org >>> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users< >>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> >> * Please search the archive at http://www.gromacs.org/** >>> >> Support/Mailing_Lists/Search< >>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! >>> >> * Please don't post (un)subscribe requests to the list. Use the www >>> >> interface or send it to gmx-users-requ...@gromacs.org. >>> >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< >>> http://www.gromacs.org/Support/Mailing_Lists> >>> >> >>> > -- >>> > gmx-users mailing list gmx-users@gromacs.org >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users >>> > * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> > * Please don't post (un)subscribe requests to the list. Use the >>> > www interface or send it to gmx-users-requ...@gromacs.org. >>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
