BerkeleyGW Workshop: Set-up Instructions

Account set up

You should first check that you have an account on Cori, either from before the workshop or that we set up for you specially for this workshop. Jack Deslippe can help if you have issues with your account.

Logging in

To log in to Cori use the following command:

ssh -X <username>@cori.nersc.gov

We recommend that you keep two ssh connections to Cori: one to run the interactive jobs, and another to read the instructions stored in the README.md files.

Environment setup

When you first log in to Cori, open the file ~/.bashrc.ext and add the following line (anywhere is fine):

module load berkeleygw/2.1-beta

Then, log off and log in to Cori again.

Note: if you are using another shell, like csh, edit ~/.cshrc.ext instead.

Scratch directory and interactive jobs

Please, run all your calculations in the scratch space in an interactive job. After you log in to Cori (and after you modified your ~/.bashrc.ext file) start an interactive job with the special bgw_interactive script, and go to the $SCRATCH directory:

bgw_interactive

cd $SCRATCH

We have a limited reservation on Cori, so, please, do not start more than one interactive queue simultaneously with the bgw_interactive command!

Note: if you are logging in to Cori using your previous existing NERSC account, you won't be able to access the reservation, and you will need to manually start the interactive job with the command salloc -N 2 -q interactive -C haswell -t 02:00:00 , followed by export OMP_THREADS=1.

Working with tutorial examples

All example files are stored in the $BGW_TUTORIAL 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 1-silicon example files using the following commands:

# Start an interactive job and go to the scratch space.

# ** Do not start more than one interactive job! **

module load berkeleygw/2.1-beta

bgw_interactive

cd $SCRATCH

# List all examples available

ls $BGW_TUTORIAL

# Copy the desired example to your directory, e.g., 1a-silicon_mfs

cp -R $BGW_TUTORIAL/1a-silicon_mfs .

# Go to your local folder and follow instructions

cd 1a-silicon-mfs

less README.md

Important: Always read the README.md files before running anything! They contain the required steps for the calculations and questions to make sure you understand the process to run a GW-BSE calculation.

Make sure you also take a look into the Resources pages for useful documents, and the FAQ for solutions of common problems.

Jupyter

You can also use Jypiter to access the BerkeleyGW examples. This allows you easily browse through the instructions (README.md files) and display plots. We have put together a mini presentation if you would like to use Jupyter.