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
