Tutorial:BerkeleyGW

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NOTE: This tutorial page is set up for the Benasque TDDFT school 2018.

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, running X-Windows programs will be very slow.
  • We submit jobs using the SLURM queue manager, using a "reservation" for Aug 22 (benasque2018_1), 23 (benasque2018_2), and 24 (benasque2018_3). If you want to run before or after that, use the debug queue.

To use a reservation, you need to add the --reservation=<reservation name> flag into your submission. So for example for the second day you could either put the following line in your batch script:

#SBATCH --reservation=benasque2018_2

or add the flag on the command line when you submit your script:

sbatch --reservation=benasque2018_2 ./myscript.sl

It also works with interactive jobs:

salloc --reservation=benasque2018_2 <other arguments>
  • Here is an example script using 32 cores (though the BerkeleyGW examples contain ones you can use):
#!/bin/bash

#SBATCH -J test_pulpo
#SBATCH -N 1
#SBATCH -C haswell
#SBATCH -p debug
#SBATCH -t 00:30:00
#SBATCH --export=ALL

module load octopus/8.2
srun -n 32 octopus &> output
  • 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 September 11. Feel free to copy the files off the machine before that to somewhere else for your future reference.

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/2.0 octopus/8.2
# 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/Benasque2018
# Copy 1-boron_nitride example to your directory
cp -R /project/projectdirs/mp149/Benasque2018/1-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 (download here or from Cori, unpack the archive, and follow README)
    • 4-silicon, Bethe-Salpeter

For historical interest


Back to Tutorials