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)

NERSC (Perlmutter)BRC (Savio)LRC (Lawrencium)

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=27017 --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:

• Savio deletes data older than 6 months

• Lawrencium does not back-up the scratch directory but backs up other types of directories

• Cori has a purging policy on the scratch directory

For NERSC users, the data archive system HPSS is an excellent resource for putting your data long-term. There are command line tools for you to directly compress your large directory and send to HPSS in your scratch nodes. Alternatively, you could also use Globus (listed below) to transfer your data, but note that you have to compress your folders first rather than moving thousands of small documents over. This could be an alternatvie to moving data to /project directory under matgen nodes, because the latter would use up lots of inodes and NERSC will complain. The only downside is that others couldn't access your easily in HPSS.

You can use one of the following popular tools for backing up raw data in our group:

• Rclone

• Globus

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, [e-mail]

• HPC Consulting = menu option 3, or [e-mail]

Special thanks to the original authors of this page: Kara Fong, Eric Sivonxay, and John Dagdelen