thanks for all the response. I try the suggestions. I think I ll have to do it not with fftw then.
--- On Mon, 7/4/11, Mirco Wahab <mirco.wa...@chemie.tu-freiberg.de> wrote: From: Mirco Wahab <mirco.wa...@chemie.tu-freiberg.de> Subject: Re: [gmx-users] On multi-core PCs and gromacs installation To: gmx-users@gromacs.org Date: Monday, July 4, 2011, 11:08 PM >> 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 + 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. -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
