[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin
shahid nayeem
msnayeem at gmail.com
Wed Sep 11 09:32:15 CEST 2013
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.abraham at 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 <msnayeem at 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.wahab at 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 at 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-request at 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 at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
More information about the gromacs.org_gmx-users
mailing list