Introduction to Work Environment

Access the cloud

We will use STFC cloud environment https://training.jupyter.stfc.ac.uk. It runs a custom baked docker image of Ubuntu Noble.

Use the username given at registration and following instructions to setup your instance.

Create account and login

  1. Go to training.jupyter.stfc.ac.uk

  2. Signup: click on Signup then use the username given and choose password and click Create User

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landing page screen

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Signup page

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Signup page

Authorization happens behind the scenes if successful you will see something like.

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success

  1. Login with the credentials from above

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login screen

You shall see something like this, if all ok, if you follow avanced course in Machine Learning inter-atomic potentials please use: (GPU) - CCP5 Summer School 2024 otherwise CCP5 Summer School 2024

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login success

Create instance

In the list you shall see CCP5 Summer school, select it and click start.

Once you click start will spawn the new VM machine, shall take 2 min or so but sometimes can be faster or slower, which exists for 24h by default and has a persistent home directory associated with your user.

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instance started success

If you click desktop you will get a minimalistic desktop environment

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desktop success

you can see a video of the process

Stop instance and update

if things go wrong or you need to create an instance with an updated image you need to follow the following steps.

  1. get the hub settings: File -> Hub Control Panel

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hub control panel settings

  1. stop the instance

    stop the instance by clicking on the “Stop My Server” button then once stopped you can click Logout.

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stop server and logout

  1. logout and create a new instance as above. This will use the latest version of the image.

a video of the process below

Obtain exercises

open a terminal

cd
git clone https://gitlab.com/ccp5/workshop.git WORKSHOP

a WORKSHOP folder will appear on the left hand side and now you can navigate inside it and find the relevant notebook of the day.

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checkout WORKSHOP

Word processors and spreadsheets

These are available as part of the LibreOffice suite of programs.

Browsers

Mozilla Firefox is installed on the machine.

Compilers

The GNU toolchain is used throughout the summer school and are available at the unix prompt.

  • gcc: the C/C++ compiler

  • gfortran: the fortran compiler (it assumes f77 and f95 for *.f and *.f90 respecively). Some of the codes may be in fixed format requiring the compiler flag -ffixed-form.

  • python3 is available on the machine, use python3, be aware that python will give you python2.

Plotting Packages

Two graphics packages are available for plotting graphs: gnuplot and xmgrace. You can also use matplotlib from python.

VMD is the basic viewer for use in the summer school. Jmol is also available. In order to use Jmol type jmol.sh on the command line.

DL_Visualizer is another graphical package that helps you visualising complex data usually coming from abinitio simulations. You will need this if you take the advanced option on first principles simulations.

Editors

There are several editors available. You should choose whichever you are confortable with.

  • vi the venerable UNIX screen mode editor.

  • vim the improved venerable UNIX screen mode editor.

  • emacs probably the commonest full-screen UNIX editor.

  • gedit gui editor

Terminals

When one refers to terminal, console or command line, usually means a shell window. Gnome Terminal, xterm and uxterm are available, You can click on the terminal icon to get one in the desktop or in the jupyter hub.