<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">thanks for all the response. I try the suggestions. I think I ll have to do it not with fftw then.<BR><BR>--- On <B>Mon, 7/4/11, Mirco Wahab <I><mirco.wahab@chemie.tu-freiberg.de></I></B> wrote:<BR>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Mirco Wahab <mirco.wahab@chemie.tu-freiberg.de><BR>Subject: Re: [gmx-users] On multi-core PCs and gromacs installation<BR>To: gmx-users@gromacs.org<BR>Date: Monday, July 4, 2011, 11:08 PM<BR><BR>
<DIV class=plainMail>>> 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.<BR>>> ... Do I still need to install MPI using cygwin?<BR>> <BR>> Probably not, but I haven't tested threading on Cygwin.<BR><BR>I just did a test for fun and it worked remarkably good,<BR>even on Cygwin 1.7 + Win7/x64U box. I'ts very simple<BR>using 'make', didn't check cmake (seems more complicated<BR>here).<BR><BR>The following sequence will lead to success for<BR>fully functional Gromacs 4.5.4 for the CYGWIN_i686<BR>target on windows:<BR><BR>Install Cygwin 1.7.9 from its page, add<BR>+ gcc/g++ 4.x and 3.x (but not mingw-gcc variants)<BR>+ make/cmake<BR>+ lapack, lapack-devel, lapack-libs<BR>+ fftw3, *-devel, *-libs<BR>+ gsl, *-devel, *-libs<BR>+ wget, tar, vim<BR>+ bash, rxvt<BR>(do not install the 'pthread library stub' entry)<BR><BR>Open a cygwin bash shell, create a
gromacs base directory<BR>and change to it(!):<BR>$> mkdir gromacs; cd gromacs<BR><BR>Download source and unpack it:<BR>$> wget <A href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz" target=_blank>ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz</A><BR>$> tar xzf gromacs-4.5.4.tar.gz<BR><BR>Write a fancy build control file:<BR>$> cat > mk_gromacs.sh<BR>#!/bin/sh<BR>../gromacs-4.5.4/configure CC=gcc CXX=g++ \<BR> LDFLAGS="-L/usr/lib64 -llapack -lblas -lpthread" \<BR> --prefix=/usr/local/gromacs454 \<BR> --with-fft=fftw3 \<BR> --with-external-blas \<BR> --with-external-lapack \<BR> --with-gsl<BR><BR> if [ $? -eq 0 ]; then<BR> make -j
4<BR> if [ $? -eq 0 ]; then<BR> echo "********************"<BR> echo "Success!"<BR> echo "********************"<BR> echo "now: ==> make install (as root) / exit"<BR> fi<BR> fi<BR><BR>Modify the number in 'make -j 4' to match the number of<BR>your processor cores, which is the output of:<BR>$> echo $NUMBER_OF_PROCESSORS<BR><BR>Create a build directory and change to it(!):<BR>$> mkdir build; cd build<BR><BR>Run your control script (see above):<BR>$> sh ../mk_gromacs.sh<BR><BR>Wait and check error messages during configuration (if any),<BR>otherwise: go and get a large cup of coffee and lay back.<BR><BR>If its ready (without errors), install it by:<BR>$> make install<BR><BR>Initialize Gromacs environment variables in<BR>your shell by modifying your .bashrc
file:<BR><BR>$> vi .bashrc<BR>- go some lines down, at the start of an empty line<BR>- press 'i' (insert)<BR>- insert the following text<BR><BR> # GROMACS<BR> if [ -e /usr/local/gromacs454/bin/GMXRC.bash ] ; then<BR> source /usr/local/gromacs454/bin/GMXRC.bash<BR> fi<BR><BR>- press 'Escape' ':' 'x' (to write and close the file)<BR><BR>After leaving the shell and opening a new one,<BR>mdrun, grommp and friends should be available<BR>and working fine.<BR><BR>> Nothing will do MPI for you. Threading and MPI are complementary approaches to achieving parallelism, and which is better depends on your execution environment.<BR><BR>On Cygwin, OpenMPI would't even work anymore as<BR>they require MS Visual Studio Library linkage<BR>nowadays. One could try MPICH2 which compiled<BR>on Cygwin last time I tried (2 years ago?),<BR>but why? Gromacs threading works perfectly<BR>on Cygwin.<BR><BR>Regards<BR><BR>M.<BR>-- gmx-users
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