Setup Prerequisites

Setup Prerequisites #

To start with this course, you need the to install necessary programs and setup your system to allow programming. Depending on the platform and operating systems you are using the steps differ but eventually you should be able to use the course material independently of your platform.

Important

If you are working at a CIP pool computer in the Mulliken Center for Theoretical Chemistry we have taken care for you about the setup and you can immediately continue with the next chapter.

Windows 10 #

There are multiple ways to enable your Windows system for development. For this course we will present two methods, either running natively (see Install MSYS2) or with a virtualisation of a Linux subsystem (see Install WSL).

Install MSYS2 #

The MSYS2 project provides a package manager and makes many common Unix tools available for Windows. It comes with its own bash-like shell which allows to easily follow this course.

Download the msys2-x86_64-YYYYMMDD.exe installer from the MSYS2 webpage and run the installer. MSYS2 will create three new desktop shortcuts: MSYS terminal, MinGW64 terminal and MinGW32 terminal (more information on MSYS2 terminals is available here).

You can either use the MSYS terminal or the MinGW64 terminal for this course we recommend to use the latter.

Open a new terminal and update your installation with

pacman -Syu

You might have to update MSYS2 and pacman first, restart the terminal and run the above command again to update the installed packages.

If you are using the MinGW64 terminal you can install the required software with

pacman -S git mingw-w64-x86_64-gcc-fortran mingw-w64-x86_64-make mingw-w64-x86_64-fpm vim

If you use the MSYS terminal leave out the mingw-w64-x86_64 prefixes to install the required software.

After having installed the necessary software, you need to download the course material. Unzip the course-material.zip archive to your home directory and you are setup to start with the next chapter.

Note

Your home directories C:\Users\<name> will be accessible under /c/Users/<name> in the MSYS2 terminals, look there if you are searching for your downloaded files.

Tip

The content of the archive might be potentially important as a starting point for your SCF program later.

Install WSL #

With Windows 10 comes the possibility to integrate a Linux Console to your Windows PC via the Windows Subsystem for Linux (WSL). This is in particular useful for you as a Windows user to participate in our Linux based course from home. This guide will show you how to use WSL in order to install a Unix-based console that allows you to complete all the tasks of the course (it is basically a shortened version of the Microsoft documentation for installing WSL).

In order to install WSL, you first have to enable the optional WSL feature. Open the Windows PowerShell as administrator (for example by typing powershell in the search field of the taskbar).

Type the following command in PowerShell and press <Enter>:

Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

Afterwards please restart your computer if you are asked to.

Install Linux Distribution #

You can now install a Linux distribution of your choice to use with WSL. We recommend Ubuntu. You can install it from the Microsoft Store. Just type Ubuntu in the search field and download the application.

After the installation was successful, you can start the Linux distribution. Ubuntu will open a console and install itself. You will be ask to choose a username and a password. Those are equivalent to the ones you would choose on a real Ubuntu machine.

Your new console will now show linuxusername@hostname:/some/path$, similar to an Ubuntu console. linuxusername is your chosen username in the Linux distribution and hostname the name of your computer. The directory in which the window is opened (/some/path) will probably be your Linux home directory ~ (see Shell in a nutshell). Note that this home directory can not simply be accessed via the Windows explorer. But the other way around, you can find your Windows home directory in /mnt/c/Users/windowsusername, where windowsusername is your username on your Windows computer. If you want to open new files with some Windows program, we recommend to create and save all new files in the mentioned directory or subfolders of it.

You can now also access your Linux console through a Windows console such as CMD. To open CMD, just type cmd in the search field of the Windows taskbar and press Enter. By entering the command wsl or bash, you will change to the Linux console in your current directory which is your Windows home directory.

Note

If you feel advanced in handling the shown terminals of different distributions on your Windows computer, you can try the Windows Terminal. It allows you to manage your WSL terminals and may make your home office more comfortable. However, it is still a preview release and thus the installation might require some effort.

You have now successfully installed a Linux console on your Windows computer and can continue with the Ubuntu part of this documentation (see Ubuntu).

Ubuntu #

Starting with a fresh version of Ubuntu 18.04 we have to install a few programs first. You have to install the packages: git, gfortran, make, and vim. We will assume you are working with apt to install packages, in case you prefer another package manager, feel free to install the packages listed here with this one (see Ubuntu install & remove software).

sudo apt install git gfortran make vim

Note

Some packages, especially vim and make might already be installed on your system, but it does not harm to include them here again.

For the programming course we recommend to use the Fortran package manager (fpm), which can be downloaded from here. or setup from conda-forge as described in Fortran package manager from conda.

After having installed the necessary software, you need to download the course material. Unzip the course-material.zip archive to your home directory and you are setup to start with the next chapter.

Tip

The content of the archive might be potentially important as a starting point for your SCF program later.

Fortran package manager from conda #

You can install the Fortran package manager (fpm) easily from conda-forge, a large scientific software repository. To do so, download a mambaforge installer from the conda-forge project. For Ubuntu Mambaforge-Linux-x86_64.sh is the correct choice. Run the installer as user (no sudo required) to setup your conda base environment:

sh Mambaforge-Linux-x86_64.sh

Your prompt should now show a (base) label in front, which signals you that you now have access to the mamba package manager and the conda environment manager.

Note

Those two tools, mamba and conda, are very powerful to create reproducable development and production environments for scientific work. For this course they allow us to easily install software, that would be difficult to install otherwise or software which is not yet available in all Linux distributions. Many of our groups software is available over conda-forge as well.

To add Fortran package manager (fpm) to your base environment run

mamba install fpm

Tip

Alternatively, you can create a separate environment for fpm with

mamba create -n fpm fpm
conda activate fpm

When creating a separate environment, you will always have to activate it after starting a new shell, but it allows you more fine grained control over your installed software.

MacOS #

To setup your MacOS for the course follow this steps

Install Xcode from the the App Store
Open a terminal from /Applications/Utilities/
Install command line tools with
```
xcode-select --install
```
Install gfortran either by installing it from here or by using Homebrew (see Installing with Homebrew)
Install the Fortran package manager from conda (see Fortran package manager from conda) or homebrew (see Installing with Homebrew)

Important

The default shell on MacOS is not bash, but a zsh, but they should be mostly compatible. In case you want to follow the course with a bash start a new bash instance after opening your terminal with

exec bash

After having installed the necessary software, you need to download the course material. Unzip the course-material.zip archive to your home directory and you are setup to start with the next chapter.

Note

Some of the keyboard shortcuts in the next chapter are targeted at Linux OS, you probably have to use the cmd key instead of the ctrl key.

Installing with Homebrew #

You can manage packages for your Mac using homebrew. To install homebrew download the installation script from the official homebrew channel at GitHub:

curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh > install-homebrew.sh
/bin/bash install-homebrew.sh

The script will ask you a few questions to complete the installation process, for more information on the homebrew installation check their documentation.

To install gfortran we will install the gcc formula, where it is included, with

brew install gcc

Additionally, install the Fortran package manager (fpm) with

brew tap awvwgk/fpm
brew install fpm

Setup Prerequisites

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