Out of curiosity, I installed cygwin 1.7.17-1 on my AMD/FX-8350 workplace box (W8Pro/x64). This is what I found out:
- Gromacs 4.6 compiles smooth but crashes w/native(AVX_128) on simulation start with loads of fp errors (non-reproducible, sometimes stops w/no error at all, just stops) - Gromacs 4.6 runs fine if compiled w/GMX_CPU_ACCELERATION=SSE2, even if PME involved (see below) - Gromacs shared executables (runtime-dlls) didn't start due to some erratic dlopen problems with I didn't understand. By using GMX_PREFER_STATIC_LIBS=ON, this was solved I testet a "Martini"-system of ~1 Mio particles (a 50^3nm water box with a vesicle). Performance comparison: VS2010(x64) - md/cut-off/Reaction-Field : 37.460 ns/day cygwin/gcc 4.5.3 - md/cut-off/Reaction-Field : 30.304 ns/day VS2010(x64) - md/cut-off/PME : 10.874 ns/day cygwin/gcc 4.5.3 - md/cut-off/PME : 9.283 ns/day The fftw3f used was installed before from source. I'll attach a recipe for both builds and some more hints below. Resumé: cygwin installation of Gromacs 4.6 is (still) cumbersome and may throw up suprising errors. For windows users, looks much more promising (imho!) to build Gromacs with the Visual Studio compiler (which is, through combination of VS2010 express + SDK 7.1, free of cost). "works on my machine"-instructions: =>
Install cygwin 1.7.17-1 and: gcc-4 g++-4 gfortran-4 make cmake automake autoconf lapack gsl vim procps binutils (and what you like) ####################### # 1. edit bash env ####################### cd ~ vi .bashrc # insert this at the stop of the file: # (a) PATH cleanup (don't interfere with other stuff installed on windows machine!) # and add /usr/local/lib (for gromacs dll files) export PATH=/usr/local/bin:/usr/bin:/usr/local/lib:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/ # (b) prepare for GROMACS environment if [ -e /usr/local/bin/GMXRC.bash ] ; then source /usr/local/bin/GMXRC.bash fi :x exit ###################### 2. install fftw3f ####################### cd ~ mkdir fftw3; cd fftw3 wget http://www.fftw.org/fftw-3.3.3.tar.gz tar xzf fftw-3.3.3.tar.gz rm -rf fftw3-build/; mkdir fftw3-build/; cd fftw3-build/ CC=gcc-4 CXX=g++-4 F77=gfortran-4 ../fftw-3.3.3/configure --enable-shared --enable-float --enable-sse2 --with-our-malloc make -j 8 install ####################### # 3. install gromacs ####################### cd ~ mkdir gromacs; cd gromacs wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz tar xzf gromacs-4.6.tar.gz rm -rf gromacs-build/; mkdir gromacs-build/; cd gromacs-build/ CC=gcc-4 CXX=g++-4 F77=gfortran-4 cmake -DGMX_OPENMP=ON -DGMX_CPU_ACCELERATION=SSE2 -DGMX_PREFER_STATIC_LIBS=ON -DFFTW3F_INCLUDE_DIR=/usr/local/include -DFFTW3F_LIBRARY=/usr/local/lib/libfftw3f.dll.a -DCMAKE_INSTALL_PREFIX=/usr/local -DGMX_GPU=OFF ../gromacs-4.6 make -j 8 install exit relogin
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