You should first check that you have an account on Discovery, if you do not, you can request access here.
General Resources
Introduction to Discovery Cluster: slides
Code Academy intro to the command line: Tutorial
Discovery Cluster guide and tutorials for Python, Spark, Keras and Pyro provided by the Ioannidis Group: Wiki
Logging in to the server will require a ssh client
To log into Discovery use the following command:
ssh -X <username>@login.discovery.neu.edu
We recommend that you keep two ssh connections to Discovery:
one to run the interactive jobs, and another to read the instructions stored in the README files.
Environment setup
When you first log in to Discovery, run following command:
source /scratch/DFTPrimer/DFTPRIMERENVIRONMENT
You will need to do this each time you logon.
Working with tutorial examples
All example files are stored in the /scratch/DFTPrimer directory. For each tutorial session,
you will need to copy the files associated to each example into your own scratch space and then
follow the corresponding instructions. For example, in the first hands-on session, you will copy
the Practical-1 example files using the following commands:
# List all examples available
ls /scratch/DFTPrimer/workshop_materials
# Copy Practical-1 example to your directory
cp -R /scratch/DFTPrimer/workshop_materials/Practical-1 /scratch/<username>
# Go to your local folder and follow instructions
cd /scratch/<username>/Practical-1
less README
Important: Always read the README files before running anything! They contain the required
steps for the calculations and questions to make sure you understand the process to run a DFT calculation.
Installing Pymatgen
To enable the band structure and density of states plots, install the following python module:
pip install pymatgen --user
SSH Clients
SSH (Secure Shell) is a network protocol that provides administrators with a
secure way to access a remote computer. SSH is typically used to log in to a
remote machine and execute commands.
Common SSH clients by OS:
Linux:
built-in, use the terminal
Mac:
ssh built-in, use the terminal
X11 forwarding needs to be set up independently
Windows:
MobaXterm
WinSCP
Learning the Basics of the Command Line
The command line interface is a really fundamental and powerfull way to move about a
computer system. From the command line one can navigate directories, edit files,
execute programs and script complex processes. Since most of the hands-on session for DFT,
and possiblly later sessions, will require a basic understanding of the commandline interface,
we will be providing a basic primer at the beginning of the first session. Below we have also posted
a link to a good introductory tutorial.