[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

[Mark Abraham]

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.
>>
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