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TitleTypeExcerpt
Software Available on Savio Page Overview Savio provides a variety of software installed by the system administrators and BRC consultants, ranging from compilers and interpreters to statistical analysis and visualization software, bioinformatics and computational biology software, and much more. To access much of the software available on the Savio cluster, you'll use <a...
CGRL Accounts Page The Computational Genomics Resource Laboratory (CGRL) provides access to two computing clusters collocated 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...
CGRL (Vector/Rosalind) User Guide Page 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 collocated within the larger Savio system administered by <a...
Condo Cluster Service Page Overview BRC manages Savio, the new high-performance computational cluster for research computing. Designed as a turnkey computing resource, it features flexible usage and business models, and professional system administration. Unlike traditional clusters, Savio is a collaborative system wherein the majority of nodes are purchased and shared by the...
BRC Condo Storage Service for Savio Page Berkeley Research Computing (BRC) offers a Condo Storage service for researchers who are Savio Condo Cluster contributors and need additional persistent storage to hold their data sets while using the Savio cluster. Researchers pay a one-time upfront cost for this storage, which is available in 42 TB increments at a...
Community Contributions Guide Page Overview This site is generated using Jekyll and was forked from the Jekyll Documentation Theme. It is hosted on GitLab using GitLab Pages. We welcome your help with to make these docs as accurate as possible. You can submit an...
Faculty Computing Allowance Page Download the Faculty Computing Allowance info packet. The Faculty Computing Allowance (FCA) provides up to 300K Service Units (SUs) of free compute time per academic year to all qualified UC Berkeley faculty/PIs, where one SU is equivalent to one compute cycle on the latest standard hardware. (Allowances are prorated based...
Frequently Asked Questions Page Q. How can I access the Faculty Computing Allowance application (Requirements Survey) and Additional User Request forms? I'm seeing a "You need permission" error. A. You need to authenticate via CalNet to access the online forms for applying for a Faculty Computing Allowance, and for requesting additional user...
GNU parallel Page GNU Parallel is a shell tool for executing jobs in parallel on one or multiple computers. It’s a helpful tool for automating the parallelization of multiple (often serial) jobs, in particular allowing one to group jobs into a single SLURM submission to take advantage of the multiple cores on a...
Savio User Guide Page Savio Hardware Configuration The following table details the hardware configuration of each partition of nodes. Each partition corresponds to a combination of a generation and type of node. Partition Nodes Node List CPU Model # Cores/Node Memory/Node <th...
ht_helper script Page Overview Note: in the past we have recommended the use of Savio's HT Helper to bundle together multiple tasks into a single job to better take advantage of the fact the Savio schedules most partitions on a per node bases. We now recommend use of the more widely-used, community-supported <a...
Getting Help Page Getting help by email To get help - to ask questions about the BRC clusters (Savio and Vector) report a problem, or provide suggestions - please email us at brc-hpc-help@berkeley.edu. Doing so will create an issue ticket, and you’ll receive email responses whenever the ticket’s status changes. Support...
Condo Partner Access Page By becoming a Condo Partner, through purchasing and contributing compute nodes to the Savio cluster via the Condo Cluster Service, researchers and their groups obtain priority - and hence nearly unlimited - access to resources equivalent to their contribution. In addition, Condo partners can access any of the other...
Getting an Account Page The Savio cluster is open to all UC Berkeley PIs who need access to high performance computing. Multi-institutional research collaborations involving at least one UC Berkeley PI are also welcome. PIs can then designate researchers (including those not affiliated with UC Berkeley) working on the project to be users on...
Transferring Data Page This is an overview of how to transfer data to or from the Berkeley Research Computing (BRC) supercluster, consisting of the Savio and Vector high-performance computing clusters, at the University of California, Berkeley. When transferring data using file transfer software, you should connect only to the supercluster's...
Using MATLAB on Savio Page This document describes how to use MATLAB, a matrix-based, technical computing language and environment for solving engineering and scientific problems, on the Savio high-performance computing cluster at the University of California, Berkeley. Getting access to MATLAB on Savio As of summer 2019, you no longer need...
Using Software on Savio Page This page provides links to introductory guides on the use of various software applications, on the Savio high performance computing cluster at the University of California, Berkeley. Using Python on Savio An introduction to using Python, a programming language widely used in scientific computing, on Savio....
Running Your Jobs Page Overview To submit and run jobs, cancel jobs, and check the status of jobs on the Savio cluster, you’ll use the Simple Linux Utility for Resource Management (SLURM), an open-source resource manager and job scheduling system. (SLURM manages jobs, job steps, nodes, partitions (groups of nodes), and other entities...
Using Jupyter Notebooks and JupyterHub on Savio Page The Jupyter Notebook is a web application that enables you to create and share documents (called "notebooks") that can contain a mix of live code, equations, visualizations, and explanatory text. This is an introduction to using these notebooks on Savio. Before getting started, make sure you have access to...
High Performance Computing Page This provides an overview of how to use the Savio and CGRL clusters. For details please click on the links below or in the sidebar. Passwords. You'll need...
High Performance Computing Page In recognition of the increasing importance of research computing across many disciplines, UC Berkeley has made a significant investment in developing the BRC High Performance Computing service, as a way to grow and sustain high performance computing for UC Berkeley. This service, offering and supporting access to the Savio Institutional/Condo...
Accessing and Installing Software Page In addition to the software provided on the cluster, you are welcome to install your own software. Before installing software yourself, first check if it is already provided on the cluster by running module avail and looking to see if the software is listed. Please note that some modules...
Instructional Computing Allowance Page Instructional Computing Allowances (ICAs) provide a no-cost allocation on the Savio high-performance computing cluster to instructors who need significant computational resources for their courses. Instructional Computing Allowances are intended for any instructor of record of an official UC Berkeley course. Each Instructional Computing Allowance is based upon a partnership agreement...
Logging into BRC Clusters Page This document provides instructions on how to log into the Berkeley Research Computing (BRC) high performance computing (HPC) clusters - Savio and Vector - at the University of California, Berkeley. Unlike most remote computer systems that you may have encountered to date, when logging into the BRC clusters...
Making files accessible to group members and other Savio users Page This page documents some aspects of file permissions on Linux and some tools you can use to make files accessible to your group members or more broadly to other Savio users. Back to top Background on Linux file permissions and file ownership We'll start by briefly...
Migrating from Torque/PBS to SLURM Page Table 1 lists the common tasks that you can perform in Torque/PBS and the equivalent ways to perform those tasks in SLURM. Task Torque/PBS SLURM Submit a job qsub myjob.sh sbatch myjob.sh ...
Options When a Faculty Computing Allowance Is Exhausted Page When you’ve used up your Faculty Computing Allowance of computing time on the campus’s Savio high performance computing cluster, but still need more time on Savio (or an equivalent computing resource) to complete your project, here are some of the options that you might now consider: Purchase...
Parallelization in JupyterHub on Savio Page This document shows how to use IPython Clusters, which allow you to use parallelization in a Jupyter IPython notebook. We’ll first show an example of how to use IPython Clusters to use the parallelization capabilities of the IPython Parallel package, both using the default parallel profile for use on a...
Authenticating rclone to Transfer Data Between Savio and Your UC Berkeley bDrive Account Page Here are the steps for setting up a bDrive account for access via rclone from Savio. Research IT strongly recommends that rclone be used with a Special Purpose Account (SPA), and not with the bDrive storage owned by (and accessible via) your personal CalNet ID. Separating this third-party...
Authenticating rclone to Transfer Data Between Savio and Your UC Berkeley Box Account Page Here are the steps for setting up a Box account for access via rclone from Savio. Research IT strongly recommends that rclone be used with a Special Purpose Account (SPA), and not with the Box storage owned by (and accessible via) your personal CalNet ID. Separating this third-party...
Transferring Data Between Savio and Box or bDrive Page Berkeley Research Computing recommends the use of rclone to transfer files between Savio and either Box and bDrive. We'll first describe how to set up rclone so it can access your Box or bDrive account, then how to transfer files via rclone, and then various tips and tricks for...
Running MATLAB jobs across multiple Savio nodes Page The MATLAB Distributed Computing Server (DCS) toolbox allows one to run MATLAB jobs across multiple nodes. There are a few things you need to do to get it set up, but once you do, the parallel code you use in MATLAB will be the same as discussed in the previous...
Scheduler configuration Page Savio scheduler configuration Savio partitions Partition Nodes Node Features Nodes shared? SU/core hour ratio savio 160 savio exclusive 0.75 savio_bigmem 4 savio_bigmem or savio_m512 exclusive 1.67 savio2 163 savio2...
SLURM job script and syntax examples Page Here we show some example job scripts that allow for various kinds of parallelization, jobs that use fewer cores than available on a node, GPU jobs, low-priority condo jobs, and long-running FCA jobs. 1. Threaded/OpenMP job script #!/bin/bash # Job name: #SBATCH --job-name=test...
Accounts for sensitive data Page As of 2019, Savio users can set up projects to work with moderately-sensitive data. Moderately-sensitive data includes the P2 and P3 (as well as NIH dbGap data) data security classifications as defined by UC Policy (IS-3) and documented by the campus Information Security Office....
Working with Sensitive Data on Savio Page Establishing a Moderately Sensitive (P2/P3) Project on Savio Researchers can use Savio to work with moderately sensitive data - what campus classifies as P2/P3 data. To do so, you must create a special project, which uses separate memory, storage and scratch resources than other Savio jobs. You must set...
Service Units on Savio Page Tracking usage of computing time, on the UC Berkeley campus's Savio high-performance computing cluster, is done via abstract measurement units called "Service Units." Note that this tracking does not apply to computing done using a condo. A Service Unit (abbreviated as "SU") is equivalent to one “core hour”: that is,...
Setting Up One-Time Passwords Page Setting up your mobile device to generate these one-time passwords, so you can log into the BRC clusters, is fairly straightforward. It typically takes between 10 and 30 minutes, and you only need to do it once. Here's an overview of that process: Submit a form to receive a linking...
Storing Data Page Overview By default, each user on Savio is entitled to a 10 GB home directory which receives regular backups; in addition, each Faculty Computing Allowance-using research group receives 30 GB of project space and each Condo-using research group receives 200 GB of project space to hold research specific application software...
System Overview Page The Savio institutional cluster forms the foundation of the Berkeley Research Computing (BRC) Institutional/Condo Cluster. As of April 2020, the system consists of 600 compute nodes in various configurations to support a wide diversity of research applications, with a total of over 15,300 cores and a peak performance of 540...
Training and Tutorials Page This page provides links to training and tutorial materials pertaining to the BRC high performance computing clusters (Savio and Vector) at the University of California, Berkeley. Savio - Introductory Training Training materials from an introductory-level Savio training session in September 2019. These materials provide an overview of the cluster and its basic...
User Access Agreement Form Page Every prospective user of the Savio high-performance computing cluster and other clusters managed by Berkeley Research Computing (BRC) must first complete and (electronically) sign a BRC User Access Agreement form, in order to obtain credentials to access the cluster.   If you have a UC Berkeley CalNet ID, please complete...
Using Authy on a desktop computer to generate one-time passwords for Savio Page Authy, a free app from Twilio, can generate one-time passwords (OTPs) on your laptop or desktop computer, which you can use when logging into the Savio high-performance computing cluster at UC Berkeley. We recommend using the Authy app if you do not have a mobile...
Using the BRC Visualization Node with RealVNC Page The purpose of this document is to explain how to set up and use a graphical user interface (GUI) desktop environment on Savio. Overview The remote desktop allows users to run a real desktop within the cluster environment. This is very useful for users who require to run scientific applications...
Using Globus Connect with the BRC Supercluster Page This document describes how to use Globus Connect (formerly Globus Online) to transfer data between your computer (or any other computer on the Internet that is acting as a Globus "endpoint" and to which you have access) and the Berkeley Research Computing (BRC) supercluster, consisting of the Savio, Vector, and...
Using Hadoop and Spark on Savio Page This document describes how to run jobs that use Hadoop and Spark, on the Savio high-performance computing cluster at the University of California, Berkeley, via auxiliary scripts provided on the cluster. Running Hadoop Jobs on Savio The Hadoop framework and an auxiliary script are provided to help users to...
Using Mathematica on Savio Page # Using Mathematica on Savio This document describes how to use Mathematica on the Savio high-performance computing cluster at the University of California, Berkeley. ## Loading Mathematica To load Mathematica into your current software environment on Savio, at any shell prompt, enter: ``` module load mathematica ``` To launch the...
Using Perl on Savio Page # Using Perl on Savio This document describes how to use Perl on the Savio high-performance computing cluster at the University of California, Berkeley. ## Running Perl Unlike most software on Savio, to use Perl, you do not need to load a module. Just call `perl` from the shell prompt....
Using Python on Savio Page This document describes how to use Python, a programming language widely used in scientific computing, on the Savio high-performance computing cluster at the University of California, Berkeley. Loading Python and accessing Python packages To run Python 3 code, load Python into your current software environment. To do...
Using R on Savio Page # Using R on Savio This document describes how to use R, a language and environment for statistical computing and graphics, on the Savio high-performance computing cluster at the University of California, Berkeley. ## Loading R and accessing R packages To load R into your current software environment on Savio,...
Using SCP with the BRC Supercluster Page This document describes how to use SCP to transfer data between your computer and the Berkeley Research Computing (BRC) supercluster, consisting of the Savio, Vector, and Cortex high-performance computing clusters, at the University of California, Berkeley. This video walks through the process of using SCP: <iframe width="560" height="315" src="https://www.youtube.com/embed/ScBho4OkyJI?rel=0"...
Using SFTP with the BRC Supercluster via FileZilla Page This document describes how to use SFTP (via the open source FileZilla application) to transfer data between your computer and the Berkeley Research Computing (BRC) supercluster, consisting of the Savio, Vector, and Cortex high-performance computing clusters, at the University of California, Berkeley. If you don't already have FileZilla,...
Using Singularity on Savio Page This document describes how to use Singularity, a software tool that facilitates the movement of software applications and workflows between various computational environments, on the Savio high-performance computing cluster at the University of California, Berkeley. Overview Singularity is a software tool provided on the Savio cluster....

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