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