[gmx-users] On multi-core PCs and gromacs installation

[Mark Abraham]

On 5/07/2011 1:08 AM, Mirco Wahab wrote:
>>> I will be installing gromacs 4.5.x in another computer but this time 
>>> with four cores. The PC runs in windows and I will be using cygwin.
>>> ... Do I still need to install MPI using cygwin?
>>
>> Probably not, but I haven't tested threading on Cygwin.
>
> I just did a test for fun and it worked remarkably good,
> even on Cygwin 1.7 +  Win7/x64U box. I'ts very simple
> using 'make', didn't check cmake (seems more complicated
> here).
>
> The following sequence will lead to success for
> fully functional Gromacs 4.5.4 for the CYGWIN_i686
> target on windows:
>
> Install Cygwin 1.7.9 from its page, add
>  + gcc/g++ 4.x and 3.x (but not mingw-gcc variants)
>  + make/cmake
>  + lapack, lapack-devel, lapack-libs
>  + fftw3, *-devel, *-libs

Thanks for your detailed instructions, but I would note that this part 
is not effective - the fftw3 package is compiled in double precision, 
and your GROMACS install is not. See Cygwin build instructions on the 
GROMACS webpage.

Mark

>  + gsl, *-devel, *-libs
>  + wget, tar, vim
>  + bash, rxvt
> (do not install the 'pthread library stub' entry)
>
> Open a cygwin bash shell, create a gromacs base directory
> and change to it(!):
> $> mkdir gromacs; cd gromacs
>
> Download source and unpack it:
> $> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz
> $> tar xzf gromacs-4.5.4.tar.gz
>
> Write a fancy build control file:
> $> cat > mk_gromacs.sh
> #!/bin/sh
> ../gromacs-4.5.4/configure CC=gcc CXX=g++ \
>             LDFLAGS="-L/usr/lib64 -llapack -lblas -lpthread" \
>             --prefix=/usr/local/gromacs454 \
>         --with-fft=fftw3     \
>             --with-external-blas  \
>             --with-external-lapack \
>         --with-gsl
>
>   if [ $? -eq 0 ]; then
>      make -j 4
>      if [ $? -eq 0 ]; then
>      echo "********************"
>      echo "Success!"
>      echo "********************"
>      echo "now: ==>  make install (as root) / exit"
>      fi
>   fi
>
> Modify the number in 'make -j 4' to match the number of
> your processor cores, which is the output of:
> $> echo $NUMBER_OF_PROCESSORS
>
> Create a build directory and change to it(!):
> $> mkdir build; cd build
>
> Run your control script (see above):
> $> sh ../mk_gromacs.sh
>
> Wait and check error messages during configuration (if any),
> otherwise: go and get a large cup of coffee and lay back.
>
> If its ready (without errors), install it by:
> $> make install
>
> Initialize Gromacs environment variables in
> your shell by modifying your .bashrc file:
>
> $> vi .bashrc
>  - go some lines down, at the start of an empty line
>  - press 'i' (insert)
>  - insert the following text
>
>   # GROMACS
>   if [ -e /usr/local/gromacs454/bin/GMXRC.bash ] ; then
>    source /usr/local/gromacs454/bin/GMXRC.bash
>   fi
>
>  - press 'Escape' ':' 'x' (to write and close the file)
>
> After leaving the shell and opening a new one,
> mdrun, grommp and friends should be available
> and working fine.
>
>> Nothing will do MPI for you. Threading and MPI are complementary 
>> approaches to achieving parallelism, and which is better depends on 
>> your execution environment.
>
> On Cygwin, OpenMPI would't even work anymore as
> they require MS Visual Studio Library linkage
> nowadays. One could try MPICH2 which compiled
> on Cygwin last time I tried (2 years ago?),
> but why? Gromacs threading works perfectly
> on Cygwin.
>
> Regards
>
> M.