Gromacs on Future Grid

As noted by Vivek, by default there is not much consistency regarding Gromacs on Future Grid:

• Hotel - module is available but pdb2gmx or grompp commands dont get recognized
• Alamo - could not find the module
• India - got a fatal error
• Sierra - module is available but pdb2gmx or grompp commands dont get recognized

(Also the version that is installed is old, so its not useful anyway ...)

Therefore, we just compile it ourselves.

Sierra

mkdir -p proj/gromacs
cd proj/gromacs
wget http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz
tar -xvzf cmake-2.8.12.1.tar.gz
cd cmake-2.8.12.1
./bootstrap
gmake
cd
mkdir bin
export PATH=$PATH:$HOME/bin
cd bin
ln -s ../proj/gromacs/cmake-2.8.12.1/bin/cmake
cd ../proj/gromacs
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz
tar -xvzf gromacs-4.6.5.tar.gz
cd gromacs-4.6.5
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_CPU_ACCELERATION=SSE2
make
cd
cd bin
ln -s ../proj/gromacs/gromacs-4.6.5/build/src/kernel/grompp
ln -s ../proj/gromacs/gromacs-4.6.5/build/src/kernel/mdrun 
ln -s ../proj/gromacs/gromacs-4.6.5/build/src/kernel/pdb2gmx

Hotel

module load cmake
mkdir -p proj/gromacs
cd proj/gromacs
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz
tar -xvzf gromacs-4.6.5.tar.gz 
cd gromacs-4.6.5
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_CPU_ACCELERATION=SSE2
make
export PATH=$PATH:$HOME/bin
cd
mkdir bin
cd bin
ln -s ../proj/gromacs/gromacs-4.6.5/build/src/kernel/mdrun  
ln -s ../proj/gromacs/gromacs-4.6.5/build/src/kernel/grompp
ln -s ../proj/gromacs/gromacs-4.6.5/build/src/kernel/pdb2gmx

India

module load cmake
<build gromacs as above>

Alamo

<build cmake as above>
<build gromacs as above>