[gmx-users] New beta release: 4.5-beta3

[Rossen Apostolov]

  Hi,
> > I can't compile using CMake - I get undefined references to GSL
> > functions when compiling do_dssp. -lgsl seems to be missing from the
> > linker line.
> >
GSL libraries support has been removed from the CMake system, you can 
use autoconf for now. The GSL and Gromacs licenses are not compatible 
for binary releases.
> > Another issue is that the CMake build scripts do not seem to honor
> > CFLAGS. The string "-fomit-frame-pointer -finline-functions
> > -funroll-all-loops  -O3 -DNDEBUG" is added to the end of
> > the flags,
> > which causes a problem since the optimization settings are overruled.
> >
Sander just commited a patch that will honour the CFLAGS/CXXFLAGS 
environmental variables, if they are set. However, the CMake system 
provides a few build types such as Debug and Release, and they come with 
predefined set of flags which will be appended to your custom settings. 
In Gromacs the default "Release" comes with -O3 etc.(what you see above).


If you want more control over the flags then you can use:
* cmake -i
* ccmake
* cmake-gui
* manually modify CMakeCache.txt (and run $ cmake /path/to/gromacs after 
without other arguments)

Pay attention that variables are called CMAKE_C_FLAGS, 
CMAKE_C_FLAGS_RELEASE, CMAKE_CXX_FLAGS etc., and those are the ones that 
you have to modify.

I'll extend the section on custom flags on the website.

> > Plus, I think there should be some kind of minimal readme for usage
> > with CMake.
>
> Agreed - I asked for that a while ago, and Rossen put some info here 
> http://www.gromacs.org/Developer_Zone/Cmake
I added a new INSTALL.cmake file in the source tree, it will be 
available in the next release.

Rossen