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
