Tutorial:BerkeleyGW

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NOTE: This tutorial page is set up for the Benasque TDDFT school 2016.

Interacting with Cori

The BerkeleyGW tutorial is done on the Cori supercomputer (at NERSC in California). There are a few key things you need to know about how to interact with the machine:

  • To log in, run ssh trainXXX@cori.nersc.gov in your terminal, substituting the actual name of your training account for XXX.
  • Be aware that since this machine is far away, you should not try running X-Windows programs.
  • We will work with "debug" jobs which can submitted via the provided scripts in each directory. We are using the SLURM queue manager on Cori.
  • To copy files from Cori to your local machine, in a terminal on your local machine, write scp trainXXX@cori.nersc.gov:FULL_PATH_TO_YOUR_FILE . (filling in the username and filename) and enter your password when prompted. For very small ASCII files, you may find cut and paste more convenient.
  • To see if you have jobs running, do squeue -u trainXXX. You should not have more than one in the queue; if you do, cancel them with scancel JOBID, filling in the number for JOBID from the output of squeue.
  • Accounts will expire on October 7.
  • Cori is actually down for an upgrade since Sept 19, but the files we were using are available if you login to edison.nersc.gov and go to $CSCRATCH.

Documentation and resources

Instructions

The first time you log in, execute these lines which will help you see color-coding for what is a link, executable, or directory:

echo 'alias ls="ls --color"' >> ~/.bashrc.ext
. ~/.bashrc

Each time you log in, you should do this:

# Load modules
module load berkeleygw/1.2 octopus/6.0
# Go to the scratch directory, where all runs should happen.
cd $SCRATCH

To begin with the examples,

# List all examples available
ls /project/projectdirs/mp149/Benasque2016
# Copy 1-silicon example to your directory
cp -R /project/projectdirs/mp149/Benasque2016/1-boron_nitride .
# Go to your local folder and follow instructions
cd 1-boron_nitride
less README

Schedule

  • Day 1
    • 1-boron_nitride, GW
  • Day 2
    • 2-benzene, GW and Bethe-Salpeter
    • 3-xct_LiCl, exciton visualization (copy to your local machine according to blackboard or from Cori, unpack the archive, and follow README)
    • 4-silicon, Bethe-Salpeter

For historical interest


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