Gromacs and Plumed

This page documents the compilation of Gromac and Plumed in Xsede-supermic cluster

http://www.hpc.lsu.edu/docs/guides.php?system=SuperMIC

1, load the proper modules in supermic

Currently Loaded Modulefiles:

• INTEL/14.0.2
• intel/14.0.2
• mvapich2/2.0/INTEL-14.0.2
• cuda/6.5
• gcc/4.9.0
• cmake/2.8.12/INTEL-14.0.2

2, build fftw3.3.6 with the default Intel 14.0.2 compiler

• wget http://www.fftw.org/fftw-3.3.6-pl2.tar.gz
• tar -xvzf fftw-3.3.6-pl2.tar.gz
• cd fftw-3.3.6-pl2
• ./configure --prefix="/HOME_Directory/fftw-3.3.6" --enable-float --enable-sse2 --enable-shared --enable-avx CC=icc CXX=icpc FC=ifort F77=ifort
• make
• make check > check.log

remember to make sure your make works

• create a directory called fftw-3.3.6 under $HOME before make install.

• mkdir $HOME/fftw-3.3.6

• make install

• Add paths to .bash_profile under your $HOME, i.e. add the following lines:

#add path to fftw 3.3.6 
export PATH=$HOME/fftw-3.3.6/bin:$PATH
export LD_LIBRARY_PATH=$HOME/fftw-3.3.6/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=$HOME/fftw-3.3.6/lib:$LIBRARY_PATH
export PKG_CONFIG_PATH=$HOME/fftw-3.3.6/lib/pkgconfig:$PKG_CONFIG_PATH
export LD_INCLUDE_PATH=$HOME/fftw-3.3.6/include:$LD_INCLUDE_PATH

• source .bash_profile to take effect the change.

3, build gromacs 5.1.4

• tar xfz gromacs-5.1.4.tar.gz
• cd gromacs-5.1.4
• mkdir build
• cd build
• cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-5.1.4 -DCMAKE_PREFIX_PATH=$HOME/fftw-3.3.6:/usr/local/packages/cuda/6.5 -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/packages/cuda/6.5 -DGMX_MPI=on -DGMX_THREAD_MPI=off -DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256 -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON
• make
• make check
• make install

Additional comments from supermic admin：

Once make check looks good, as well as other tests with the gmx command under $HOME/gromacs-5.1.4/build/bin, I think there is no need to "make install" (it tried to make some file/directory under the system path and gave me the error of permission denied even I already specified my local directory in cmake). Instead, just add the path to your .bash_profile:

• add the path to your .bash_profile:

#add path to gromacs 5.1.4
export PATH=$HOME/gromacs-5.1.4/bin:$PATH
export LIBRARY_PATH=$HOME/gromacs-5.1.4/lib:$LIBRARY_PATH
export PKG_CONFIG_PATH=$HOME/gromacs-5.1.4/lib/pkgconfig:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=$HOME/gromacs-5.1.4/lib:$LD_LIBRARY_PATH
source $HOME/gromacs-5.1.4/bin/GMXRC

Additional comments from supermic admin:

The important thing is the installation of fftw and the cmake options in gromacs building. I will test my build more and keep you updated if I found I need correct anything. Please let me know if you have any questions.

Install Plumed

Patch Gromacs from Plumed