#! /bin/bash

# This script installs mylammps automatically in an invidual user's home directory. It is specially designed to work for Rocks Linux 5.4.3. It should theoretically work for Rocks of other version, and presumably for CENTOS 5. 

## It is assumed that fftw3 and mpich2 are already properly installed
 
# This script will create a folder mylamps in ~/ (home directory of current user).
# Choose either scp from www2 (not current version) or git (current/latest version) or wget. By default, wget is used.
# Make sure you have git installed, or yum install git.x86_64 as root, if you wish to download with git clone (instead of scp)


######### begin downloading ###########################
cd ~/

# Use either Option 1 or Option 2, but not both to download the mylammps. By default, Option 2 is used. Option 2 is faster but it does not contains the lastest version of mylammps. Option 1 is slower but it downloads directly the latest version from the source in the web.

## Option 1. Uncomment if want to use this option.
# git clone http://git.icms.temple.edu/lammps-ro.git mylammps 
## End of Option 1

## Option 2. Default option.
wget -r -l1 --no-parent -A.tar.gz http://www2.fizik.usm.my/configrepo/howto/mylammps/
cp www2.fizik.usm.my/configrepo/howto/mylammps/*.tar.gz .
mv *.tar.gz  lammps-icms.tar.gz
tar -zxvf lammps-icms.tar.gz
rm -rf www2.fizik.usm.my lammps-icms.tar.gz 
#mkdir mylammps
mv lammps-* mylammps
## End of Option 2
 
####### begin installation ####################################################

# atc #
cd ~/mylammps
cd lib
cd atc
wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.g++.mylammps.atc.fedora13
mv Makefile.g++ Makefile.g++.bk
cp Makefile.g++.mylammps.atc.fedora13 Makefile.g++
make -f Makefile.g++

# linalg #
cd ~/mylammps/lib
cd linalg
make -f Makefile.gfortran

# mean #
cd ~/mylammps/lib
cd meam
wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.lammps.ubuntu
mv Makefile.lammps Makefile.lammps.orig
mv Makefile.lammps.ubuntu Makefile.lammps 
make -f Makefile.gfortran

# reax #
cd ~/mylammps/lib
cd reax
wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.lammps.ubuntu
mv Makefile.lammps Makefile.lammps.orig
mv Makefile.lammps.ubuntu Makefile.lammps
make -f Makefile.gfortran

# peom #
cd ~/mylammps/lib
cd poems
make -f Makefile.g++

# Now exit /lib 
cd ~/mylammps/src/MAKE

wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.g++.mylammps.src.MAKE.Rocks543
cp Makefile.g++ Makefile.g++.bk
cp Makefile.g++.mylammps.src.MAKE.Rocks543 Makefile.g++
cd  ~/mylammps/src/
make yes-all
make no-user-cuda
make no-gpu
make no-user-awpmd
make no-kim
make g++

### Post-installation ####

### Add the following aliases into ~/.bashrc
#echo 'alias mmpiexec="/opt/mpich2/gnu/bin/mpiexec"' >> ~/.bashrc
echo 'alias mmpiexec="/usr/local/bin/mpiexec"' >> ~/.bashrc
#echo 'alias lg++="~/mylammps/src/lmp_g++"' >> ~/.bashrc
### End of Post-installation ####

# To run an mylammps calclation, you must prepare an input file named as 'in.XXXX'. For example, to run the calculation 'colloid', which is kept in the folder ~/mylammps/examples/in.colloid, issue the command:
# 'mmpiexec -f ~/hosts -np NP lg++ < ~/mylammps/examples/colloid/in.colloid'
# where NP = number of processors, NP = 1, 2, 3, ...

# Note that the executable 'mmpiexec', 'lg++' must be ready before issuing the above command. 'mmpiexec' and 'lg++' are aliases that are to be defined in ~/.bashrc. 

# Note also that to run lammps in mpi mode, a ~/hosts file must be created. It should contain the list of nodes to be used to run a lammps calculation, e.g.,

#anicca.usm.my
#compute-0-0
#compute-0-1
#compute-0-2
# ...

# Alternatively, you can also specify the node's using their private IP addresses, e.g.,
# 10.1.1.1
# 10.1.255.245 
# 10.1.255.246 
# 10.1.255.247
# ...
# To check the private IP address of the nodes, just issue the command '/sbin/ifconfig'


# How to set the number of 'NP':

# anicca.usm.my, is a Rocks 5.4.3 cluster comprised of 30 nodes, where each node contains 4 cores. So the total number of cores available is 4 x 30. If the list as appear in ~/hosts contains only 20 nodes, then NP = 20 x 4 = 80 is the optimal number to use. If NP is set to be more than 80, non-optimal mpi performance may result. To run only a calculation in a single machine, set NP = 4, and list only 1 node in ~/hosts.