===General Info===

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.  It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.  [[http://www.gromacs.org/About_Gromacs|source]]

===Useful Links===

HPCAC Guide [[http://www.hpcadvisorycouncil.com/pdf/GROMACS_Best_Practices.pdf]] \\
Acceleration and parallelization [[http://www.gromacs.org/Documentation/Acceleration_and_parallelization]]

===Installation Guide===

  cd ~
  mkdir GROMACS
  cd GROMACS

Create a source file:

  vim bashrc

  source /data/opt/intel/bin/compilervars.sh intel64
  source /data/opt/intel/mkl/bin/mklvars.sh intel64
  export PATH=/data/opt/openmpi-1.8.7-ics2013/bin:$PATH
  export LD_LIBRARY_PATH=/data/opt/openmpi-1.8.7-ics2013/lib:$LD_LIBRARY_PATH
  export PATH=/home/$USER/GROMACS/libs/binutils/bin:$PATH
  export LD_LIBRARY_PATH=/home/$USER/GROMACS/libs/binutils/lib:$LD_LIBRARY_PATH
  export PATH=/home/$USER/GROMACS/libs/cmake/bin:$PATH
  export CC=icc
  export CXX=icpc
  export CFLAGS='-O3'
  export CXXFLAGS='-O3'
  export F77=ifort
  export FC=ifort
  export F90=ifort
  export FFLAGS='-O3'
  export CPP='icc -E'
  export CXXCPP='icpc -E'

  source bashrc

  mkdir tars
  mkidr libs
  mkdir tests
  cd tars

Install dependencies from repository:

  sudo yum install blas-devel lapack-devel atlas-devel libxml2-devel

==CMAKE==

  cd ~/GROMACS/tars
  wget http://www.cmake.org/files/v3.0/cmake-3.0.2.tar.gz
  tar -xf cmake-3.0.2.tar.gz
  cd cmake-3.0.2
  ./configure --prefix=/home/$USER/GROMACS/libs/cmake
  make -j4
  make install

==BINUTILS==

  cd ~/GROMACS/tars
  wget https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.gz
  tar -xf binutils-2.25.tar.gz
  cd binutils-2.25
  ./configure --prefix=/home/$USER/GROMACS/libs/binutils
  make -j4
  make install

==GROMACS==

  cd ~/GROMACS/tars
  wget https://kth.box.com/shared/static/7uwctwj33h4uo2f8d1tmdyj9afaj3hzy.gz
  tar -xf 7uwctwj33h4uo2f8d1tmdyj9afaj3hzy.gz
  cd gromacs-5.0.6
  mkdir build
  cd build

==x86 build==

  cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_GPU=off -DGMX_MPI=on -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/$USER/GROMACS/gromacs-x86/ -DGMX_BUILD_OWN_FFTW=ON -DGMX_BUILD_UNITTESTS=ON
  make -j10
  make install

==CUDA build==
The CUDA version requires a CUDA SDK of at least version 4.0, however the latest is recommended (version 7.0 was used for testing).  If the SDK in not found in the default /usr/local/cuda directory, then source it.

  cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_GPU=on -DGMX_MPI=on -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/$USER/GROMACS/gromacs-cuda/ -DGMX_BUILD_UNITTESTS=ON
  make -j10
  make install

===Test Installation===

Source the GROMACS installation:
  export PATH=/home/$USER/GROMACS/gromacs-x86/bin:$PATH

Test the installation by using the regression tests which ship with the release, available here: [[http://www.ace.chpc.ac.za/tars/regressiontests.tar.gz|regressiontests.tar.gz]]
  cd ~/GROMACS/tests
  tar -xf Regressiontests.tar.gz
  cd regressiontests
  ./gmxtest.pl -suffix _mpi all
  
===Benchmark===