Install_gromacs

Install GROMACS and all the other dependecy

GROMACS has been a most used Molecular dynamics simulation engine in the last couple of years. Thanks to the increasing power of computer. When I staret doing simnulation GROMACS was installe on our computing cluster and I had started right way to do the simulation. Later when I need to used some recent version of it, I was perplexed. I have included here how to install GROMACS so we can make most of it and patch GROMACS with PLUMED. PLUMED is a PLUmed MolEcular Dynamics simulation package which is very useful in estimating free energy. It has both Umbrella Sampling and Metadynamics techniques. All this installation tutorial is intended for HPC but it also works for a personal machine too

Depencency (latest version will be better)

• gcc compiler
• fftw
• OpenMPI (for parallelization)
• cmake

Start with compiling gcc

I prefer to download all the software and compiler in the source folder. Download the gcc compiler directly to your machine

wget http://mirror.rit.edu/gnu/gcc/gcc-8.5.0/gcc-8.5.0.tar.gz

Extract the files

tar -xvf gcc-8.5.0/gcc-8.5.0.tar.gz

Go to gcc-8.5.0 folder

cd gcc-8.5.0

Download all the prerequisite for gcc to compile

 sh contrib/download_prerequisites
 

make a new directory inside gcc-8.5.0 and go to that folder

mkdir build
cd build

Configure

../configure --prefix=/lscratch/apps/gcc/8.5.0 --enable-languages=c,c++,fortran,go --disable-multilib

Compile (this will take a little while ~20 mins

make- j 10 bootstrap

Install

make install

CONGRATULATIONS!!! gcc is now installed

If you are working in a HPC it is always helpful to make a modulefiles for all the software that you installed. Lets make a module file for gcc. Make a folder called modulesfiles in your home directory and make a gcc folder inside modulefiles

mkdir modulefiles
cd modulefiles
mkdir gcc

Make module files with in it. I named this module file according to version of the software because it will be easier if I have to installed the updated one again.

touch 8.5.0

paste this lines to the 8.5.0 file

#%Module1.0 
set root_dir /lscratch/apps/gcc/8.5.0 
prepend-path LD_LIBRARY_PATH $root_dir/lib:$root_dir/lib64 
prepend-path MANPATH $root_dir/share/man 
prepend-path PATH $root_dir/bin 
prepend-path CMAKE_PREFIX_PATH $root_dir 
setenv CC   gcc 
setenv CXX  g++ 
setenv FC   gfortran 
setenv F77  gfortran 
setenv F90  gfortran 
setenv F95  gfortran

NOTE: To specify a default module within a modulefiles folder (In case if you have multiple version) , create a file called .version and paste the lines below

#%Module1.0# 
set ModulesVersion  "gcc-8.5.0" 

Now you can import the gcc compiler in you machine

module load gcc-8.5.0

Now install FFTW, will come back later and complete it.