CGRL Vector and Rosalind¶

This page provides a high-level overview for Computational Genomics Resource Laboratory (CGRL) users, but in most cases we simply link to pages that provide information for both CGRL and non-CGRL users.

The CGRL provides access to two computing clusters colocated within the larger Savio system administered by Berkeley Research Computing at the University of California, Berkeley. Vector is a heterogeneous cluster that is accessed through the Savio login nodes, but it is independent from the rest of Savio and exclusively used by the CGRL. Rosalind is a condo within Savio. Through the condo model of access, CGRL users can utilize a number of Savio nodes equal to those contributed by Rosalind.

Account requests¶

You can request new accounts through the CGRL by emailing cgrl@berkeley.edu.

Logging in¶

Vector and Rosalind (Savio) use One Time Passwords (OTPs) for login authentication. For details, please see Logging into BRC Clusters.

Use SSH to log into: hpc.brc.berkeley.edu

Transferring data¶

To transfer data to/from Vector and Rosalind (Savio), please follow these procedures.

Storage and backup¶

A variety of storage systems are available to CGRL users.

Hardware and scheduler configuration¶

Vector and Rosalind are heterogeneous, with a mix of several different types of nodes. Please be aware of these various hardware configurations, along with their associated scheduler configurations when specifying options for running your jobs.

Note that as of November 2023, the savio1 partition has been retired and is no longer available through Rosalind.

Running jobs¶

The settings for a job in Vector (Note: you don't need to set the "account"): --partition=vector --qos=vector_batch
The settings for a job in Rosalind (Savio2 HTC): --partition=savio2_htc --account=co_rosalind --qos=rosalind_htc2_normal

Low priority jobs¶

Because CGRL is a condo contributor, all CGRL users are entitled to use the extra resources that are available on the SAVIO cluster (across all partitions) through the low priority QoS.

Software configuration¶

Please see our pages on accessing software already installed and on installing your own software. All users have access to a variety of bioinformatics software installed system-wide and available via the module system. Type module avail and look for modules named bio/XYZ (e.g., bio/bowtie2) in the /global/software/rocky-8.x86_64/modfiles/app section of the results.

Getting help¶

For inquiries or service requests regarding the cluster systems, please see BRC's Getting Help page or send email to brc-hpc-help@berkeley.edu.

For questions about new accounts or installing new biology software please contact the Computational Genomics Resource Laboratory (CGRL) by emailing cgrl@berkeley.edu