High Performance Computing at Berkeley Lab

LABORATORY RESEARCH COMPUTING
Berkeley Lab provides Lawrencium, a 524-node (5376 computational cores) Linux cluster, equipped with a high performance, low latency Infiniband interconnect, to Berkeley Lab researchers needing access to scientific computational resources. The system, which consists of shared core nodes and PI-contributed Condo nodes, has a theoretical peak performance rating of 79 teraflops and delivers over 33M processor hours to researchers every year.

SCIENTIFIC CLUSTER SUPPORT

With over 35 clusters in production, HPC Services also offers comprehensive Linux cluster support, including data center resource planning, pre-purchase consulting, procurement assistance, installation, and ongoing support, for PI-owned clusters. Our HPC User Services consultants can help you to get your application running well to make best use of your new cluster. UC Berkeley PIs can also make use of our services through the Cal HPC program available through IST.


NEWS

March 14, 2014 HPCS presenting at GlobusWorld 2014
LBL HPC consultant Krishna Muriki and HPCS systems engineer Karen Fernsler will be presenting at GlobusWorld 2014 on April 15-17, 2014 at Argonne National Laboratory.Their talk "Globus for Big Data and Science Gateways at LBL" will highlight some of our projects, including the Sloan Digital Sky Survey III and the X-Ray Diffraction and Microtomography Beamlines at the Advanced Light Source user facility, which benefit from Globus endpoints to construct Data Pipelines.

Feb 3, 2014 - NHC Talk at Stanford Exascale Conference
LBL HPCS senior engineer Michael Jennings will be giving a talk on the "Node Health Check (NHC)" on Feb 4, 2014 at the Stanford Conference and Exascale Workshop 2014 sponsored by the HPC Advisory Council. NHC, developed by Jennings, provides the framework and implementation for a highly reliable, flexible, extensible node health check solution. It is now widely recommended by major HPC job scheduler vendors and is in use at many large HPC sites and research institutions.

Sept 6, 2013 - Monitoring with Ganglia book released
HPC Services cluster expert Bernard Li's new book "Monitoring with Ganglia - Tracking Dynamic Host and Application Metrics at Scale" has been recently published by O'Reilly media. His book shows how to use Ganglia to collect and visualize metrics from clusters, grids, and cloud infrastructures at any scale.

Mar 21, 2013 - Supporting Science with HPC
HPC Services manager Gary Jung gave a presentation on "Supporting Science with HPC" at the "Enabling Discovery and Production Innovation with Dell HPC Solutions" workshop held in Santa Clara where he talked about how different Berkeley Lab researchers from EETD, ESD, NSD, and Physics are using HPC data pipelines to accomplish their science.

Mar 18, 2013 - GPU Accelerated Synchrotron Radiation Calculation
Today, HPC Services consultant Yong Qin will be presenting his work during a poster session at this week's GPU Technology Conference, GTC 2013, in San Jose, California. Yong's work demonstrates how data parallelism can be applied to spectrum calculation of undulator radiation, which is widely used at synchrotron light facilities across the world. More

Mar 13, 2013 - The Science of Clouds computed on Lawrencium
The climate models that scientists use to understand and project climate change are improving constantly; however the largest source of uncertainty in today’s climate models are clouds. As the source of rain and wind, clouds are important in modeling climate. Berkeley Lab scientist David Romps discusses his work to develop better cloud resolution models. More

Nov 13, 2012 - Node Health Check
HPCS staffers Jackie Scoggins and Michael Jennings gave a well-attended presentation on Jenning's Node Health Check (NHC) software today at the Adaptive Computing booth at SC12. NHC works in conjunction with the job scheduler and resource manager to ensure clean job runs on large HPC systems.

Nov 12, 2012 - Warewulf wins Intel Cluster Ready "Explorer" award
The Berkeley Lab Warewulf Cluster Toolkit development team has been honored with the 'Explorer Award' from the Intel(R) Cluster Ready team at Intel, which recognizes organizations who have continued to explore and implement Intel Cluster Ready (ICR) certified systems. The award was presented to lead developer Greg Kurtzer, and co-developers Michael Jennings, and Bernard Li of the IT Division's HPC Services Group at the annual Intel Partners meeting.

Oct 24, 2012 - HPCS at 2012 Data Center Efficiency Summit
HPCS staff member Yong Qin will be part of a panel, along with other Berkeley Lab scientists, at the 2012 Data Center Efficiency Summit today in San Jose talking about Berkeley Lab's recently released study to understand the feasibility of implementing Demand Response and control strategies in Data Centers. Yong will discuss the issues and our experiences related to reducing or geographically shifting computational workload to a remote datacenter as a response to a demand to lower electrical usage.

Sept 18, 2012 - Warewulf featured in HPC Admin Magazine
This month's issue of HPC Admin Magazine features the last in a 4-part series on how to best use the latest version of the Warewulf Cluster Toolkit. Warewulf, developed by LBNL's Greg Kurtzer and recently certified as Intel Cluster Ready, is a zero-cost, open source solution that guarantees integration and compatibility with Intel products as well as 3rd-party hardware and software solutions. Read this article to learn how to use it.

May 21, 2012 - Cloud Bursting for Particle Tracking
ALS physicists Changchun Sun and Hiroshi Nishimura along with HPCS staff Kai Song, Susan James, Krishna Muriki, Gary Jung, Bernard Li and Yong Qin recently explored the use of Amazon's VPC service to transparently extend the ALS compute cluster and software environment, into the public Cloud to provide on-demand compute resources for particle tracking and NGLS APEX development. Their work was presented during the poster session at the International Particle Accelerator Conference (IPAC12) in New Orleans this week.

Jan 24, 2012 - Bootstrapping Institutional Capability
HPC Services Manager Gary Jung talks about the issues institutions may encounter when developing new or enhancing existing infrastructure to support data intensive science at the Winter 2012 ESCC/Internet2 Joint Techs Conference in Baton Rouge, LA this week.


Nov 3, 2011 - Supercomputers Accelerate Development of Advanced Materials

Researchers from Berkeley Lab and MIT have teamed up to develop a new tool,as part of the Materials Project, to speed up the development for new materials. The project incorporates the use of supercomputing resources including Lawrencium to characterize the properties of inorganic compounds. More

Oct 25, 2011 - Supercomputing As A Service
LBL CIO Rosio Alvarez and HPC Services Manager Gary Jung present their experiences using cloud services for HPC at InformationWeek's GovCloud 2011 conference in Washington DC. More

Sep 19, 2011 - Lawrencium LR1 relocated to SDSC
Did you know that the Lawrencium LR1 compute nodes have been relocated to the San Diego Supercomputing Center? This was done as part of the IT Division's quest to best optimize data center space. The LR1 nodes are connected via a dedicated 10 gigabit ESNET virtual circuit into the Lab's HPC infrastructure here in Berkeley. The impact of having LR1 remote should be minimal for most users.


PROJECTS

Green Computing now available to users
Together with researchers in EETD, we are evaluating the use of hot-water, direct-to-chip liquid cooling on a 800-core Intel IvyBridge cluster. Help us test this system by running your code on it. Contact us for more info.

Chemical Science Division One of our current projects is a Dell 720-core Intel IvyBridge processor cluster for DOE early career award winner Dan Haxton of the Atomic, Molecular, and Optical Theory Group

Material Science Division We recently completed a dedicated 1824-core Intel SandyBridge processor cluster, Catamount, for MSD researchers. The system will be used to investigate the development of advanced materials.

Joint Center for Artificial Photosynthesis (JCAP) We recently completed a dedicated 2944-core AMD Interlagos cluster for the researchers at JCAP, which is the nation's largest research program dedicated to the development of an artificial solar-fuel generation technology

Geologic Carbon Sequestration
A 64-node, 768-core, Condo expansion has been added to Lawrencium for PIs Quanlin Zhou and Curt Oldenburg in ESD. It will be used for modeling of geo carbon sequestration which is a major measure for climate change mitigation, and an important component of LBNL's Carbon Cycle 2.0 Initiative.