Installation Instructions

Version 1

#These INSTALLATION INSTRUCTIONS belong to work by Gygli and Pleiss

#'Simulation Foundry: scalable and FAIR molecular modelling'

# This code is released under a GNU GPL license
# https://www.gnu.org/licenses/gpl-3.0.html

# This is free software; you are free to change and redistribute it.
# There is NO WARRANTY, to the extent permitted by law.

# Gudrun Gygli October 19 gudrungygli@gmail.com
###############################################################################

###############################################################################
# Read the manual for the Simulation Foundry before using it!
###############################################################################

This file details steps needed to ensure the Simulation Foundry works:


*******************************************************************************

get UBUNTU, e.g. Ubuntu 18.04.2. 
Install Ubuntu as your main OS, 
or as a dual boot system alongside your preferred OS 
(e.g. https://www.tecmint.com/install-ubuntu-alongside-with-windows-dual-boot/ )

*******************************************************************************

use bash (e.g. versions 4.1.2, 4.2.46 or 4.4.20)

check with 

	echo "${BASH_VERSION}"
	
*******************************************************************************

setup SSH KEYS and ALIAS for Supercomputer:

	ssh-keygen

accept default/ do not set a passphrase 


create config file in .ssh:

	cd .ssh
	touch config
	gedit config

insert details, example below:

Host test
    HostName 192.168.145.111
    User gug


copy to remote-host (replace with your supercomputer name or IP)

	ssh-copy-id -i ~/.ssh/id_rsa.pub test

Are you sure...?
Type yes

give password for supercomputer

login with simply ssh test without giving a password from now on :)

*******************************************************************************

update your system:

	sudo apt update


and upgrade:

	sudo apt upgrade
	
*******************************************************************************

You can manually install the required python packages, 
or check your python packages using 

	pip freeze

you need python (version 2.7.15)
o	os (backports.os, version 0.1.1)
o	argparse
o	math (mpmath, version1.1.0)
o	sys
o	csv (unicodecsv, version 0.14.1)
o	matplotlib (version 2.2.3)
o	xml.etree.cElementTree
o	pandas (version 0.23.3)
o	seaborn (version 0.9.0)
o	numpy (version 1.15.4)
o	scipy (version 1.1.0)

the Simulation Foundry was alos tested with Python 3, and should work as well
Please contact me if it does not work for you with Python 3!

install python:

	sudo apt install python  

or python 3

	sudo apt install python3

install pip

	sudo apt install python-pip

get python packages

	pip install matplotlib==2.2.3
    pip install numpy==1.15.4
	pip install pandas==0.23.3
	pip install scipy==1.1.0
	pip install seaborn==0.9.0

	sudo apt-get install python-tk

uninstall numpy 
(until you see the red error message that numpy does not exist on your machine)
this is needed because numpy is updated by the other packages and then you 
have multiple versions, which python does not like...

	pip uninstall numpy
	pip uninstall numpy

re-install the numpy version we want

    pip install numpy==1.15.4

*******************************************************************************
Other stuff you will need: 

get grace 
	sudo apt install grace

get latex
	sudo apt install texlive-latex-base

# if enough diskspace is available, install full texlive 
- this is recommended and typically more robust:

	sudo apt install texlive-full

otherwise install only the required packages (e.g. for caption.sty etc)

*******************************************************************************

set the input in all the csv files in the directory (SIMULATION_V1.5/INPUT)
and (ANALYSIS_V1.5/INPUT)

!!!! Please read the manual carefully, hopefully it is 
!!!! clear enough to make sense

*******************************************************************************

go to the SIMULATIONFOUNDRY directory

make .sh scripts executable with

	chmod +x SIMULATIONS_V1.5.sh

*******************************************************************************

run the simulation foundry

	./SIMULATIONS_V1.5.sh

and, once all simulations are done:

	./ANALYSIS_V1.5.sh