[gmx-users] Installing 5.0 on Cygwin - Getting error

[Mirco Wahab]

On 22.07.2014 00:51, John Doe wrote:
> [  8%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o
> /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp: In function ‘int low_fflib_search_file_end(const char*, gmx_bool, const char*, gmx_bool, char***, char***)’:
> /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp:205:47: error: ‘strdup’ was not declared in this scope
>                           fns[n] = strdup(fn_dir);

clean up the build directory,

+ add -DBUILD_SHARED_LIBS=off to your cmake invocation

+ after cmake, look up the file "CMakeCache.txt" in the top build
   directory, find the line containing:
       CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
   change it to
       CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -std=gnu++11 -DNDEBUG
+ repeat your cmake command invocation and build with make.


other possible problems - "time-related header missing" (if it occurs):

+ edit gromacs file src/external/thread_mpi/src/impl.h
   add (as first line) above everything else:

   #define HAVE_SYS_TIME_H

+ rebuild



Regards

M.