High Performance Computing (HPC)
This section and its subpages describe how to set up and run calculations on various computing resources that our group has access to, as well as how to backup your data.

Overview

Our group’s main computing resources are:
  • NERSC (the LBNL supercomputing center, one of the biggest in the world)
  • Savio / Berkeley Research Computing (BRC)
  • Lawrencium / Berkeley Lab Research Computing (LRC)
  • Peregrine (the NREL supercomputing center)
  • Argonne Leadership Computing Facility (sometimes)
  • Oak Ridge Leadership Computing Facility (sometimes)
At any time, if you feel you are computing-limited, please contact Kristin so she can work with you on finding solutions.

Setup Guides (see subpages)

Back-Up Data Frequently

Mongo DB

You should back-up your Mongo DB data frequently. The Mongo DB NERSC offers is not backed-up automatically. It's important to run regular backups during the course of your research. For Mongo DB you can:
  • Get a free education license for Studio 3T, right click your database, and click export or,
  • use the “mongodump” command line tool, tutorials available online — it’s a one line command
module load mongodb; mongodump --host=<host e.g. mongo01.nersc.gov> --port=20717 --username=<username> --password="<password>" --db="<db_name>" --authenticationDatabase="<db_name (same as --db flag)>" --out="<path to directory>"

NERSC Cori, BRC Savio, LRC Lawrencium

You should back-up your "scratch" directory data frequently.
Each cluster has different methods of deleting old data on your scratch directory:
You can use one of the following popular tools for backing up raw data in our group:
Both of these tools can help backup your raw calculation files to your Google Drive, or Box Drive, or even external hard drives.

Additional resources

Other Persson group members and the NERSC website are both excellent resources for getting additional help. If that fails, you can reach out to the NERSC Operations staff:
  • 1-800-666-3772 (or 1-510-486-8600)
  • Computer Operations = menu option 1 (24/7)
  • Account Support = menu option 2, [email protected]
  • HPC Consulting = menu option 3, or [email protected]
Special thanks to the original authors of this page: Kara Fong, Eric Sivonxay, and John Dagdelen
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On this page
Overview
Setup Guides (see subpages)
Back-Up Data Frequently
Mongo DB
NERSC Cori, BRC Savio, LRC Lawrencium
Additional resources