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