a. ciocioitsd/csac retreat march 3, 2004 1 scientific cluster support program scs steering committee...

A. Ciocio ITSD/CSAC Retreat March 3, 2004

1

Scientific Cluster Support Program

SCS Steering CommitteeReport


2

Overview

• Growing interest in the use of Linux clusters for scientific research at Berkeley Lab

• Hard to efficiently manage a multi-node compute cluster

• Findings from the Berkeley Lab Midrange Computing Workshop (March 2002) and subsequent discussions with scientists identified a need for affordable centralized support

• The ultimate goal: to increase the use of scientific computing to Lab research projects to introduce parallel computing to Berkeley Lab researchers to develop efficient, cost-effective methods for managing production clusters.

Four year program started 1/03


3

Mid Range Computing Gap


4

Scientific Cluster Support Program

Ten research projects from seven of the Lab's scientific Divisions were selected to participate in the 4 year Laboratory-funded program after a Lab-wide application process that was completed in September 2002.

These projects are eligible to receive the following services:

• Pre-purchase consulting • Procurement assistance • Setup and configuration • Ongoing systems administration and cyber security • Computer room space with networking and cooling


5

Chemical Sciences

PI: MillerContact: Michele

Semiclassical Molecular Reaction Dynamics: Methodological Development and Application to Complex Systems

New 30 Node Linux Cluster

Chemical Sciences

PI/Contact: M. Head-Gordon Parallel electronic structure theory New 15-25 Node Linux Cluster

Chemical Sciences

PI: LesterContact: Aspuru-Guzik

Quantum Monte Carlo for electronic structure Existing 19 Node Linux Cluster

Materials Sciences

PI: Arup ChakrabortyContact: Hagan, Dinner

Signaling and Mechanical Responses Due to Biomolecular Binding New 50 Node Linux Cluster

Physical Bioscience

PI/Contact: Kim/Adams/ Brenner/Holbrook

Structural Genomics of a Minimal GenomeComputational Structural & Functional GenomicsA Structural Classification of RNANudix DNA Repair Enzymes from Deinococcus radiodurans

Existing 32 Node IBM Linux Cluster to be expanded to 64 Nodes

Environmental Energy Technologies

PI: Gadgil/BrownContact: Finlayson/Tonse

Airflow and Pollutant Transport in BuildingsRegional Air Quality ModelingCombustion Modeling

New 20 Node Linux Cluster

Earth Sciences PI: Hoversten/MajerContact: Daley Geophysical Imaging Existing 16 Node Linux Cluster

to be expanded to 24 nodes

Life Sciences PI/Contact: Eisen Computational Analysis of cis-Regulatory Content of Animal Genomes

Existing 6 node Linux Cluster to be expanded to ~ 20 nodes

Life Sciences PI: Cooper/TainerContact: Frankel

Protein Crystallography and SAXS data Analysis for Sibyls/SBDR New 16 Node Linux Cluster

Physics PI/Contact: White Computing the Universe Existing 10 Node Linux Cluster to be expanded


6

SCSC• The SCS Steering Committee is a working group of CSAC. As such, it informs CSAC

of SCS project status and issues on a quarterly basis, or as needed, and solicits input from CSAC members as needed to aid in decision making and priority setting. In turn, CSAC members, as representatives of their divisions and CSAC, have the responsibility to communicate information to the Steering Committee that is important to its role in governance of the SCS Project.

• The SCS Steering Committee chartered by this document will work with the full CSAC committee and the ITSD project team to ensure success and visibility of the first phase (implementation phase) of the SCS Project. This phase will conclude once all of the clusters have been purchased or integrated into the project, and the support activities for the clusters have become routine, anticipated March 2004. The Steering Committee will meet bi-monthly or as-needed during this first period.

• The Steering Committee is responsible for governance of the implementation phase of the project. ITSD is responsible for day-to-day management. This governance includes the following activities:

- Provide oversight to ensure accountability - Participate in decision making - Participate in priority setting


7

SCSC Members

Committee Chair - Alessandra Ciocio - Physics, CSAC and MRC Working GroupPaul D. Adams - PBD, CSAC and MRC Working GroupShane Canon - NERSCTom Daley - ESDDamir Sudar - LSD, CSACGary Jung - SCS Project ManagerTammy Welcome - SCS Project DirectorJim Triplett (advisor)


8

Status

• SCS Program progressing well despite complexity of project scheduling due to availability of each project's procurement funds and differences in readiness.

• 6 of 10 clusters in production (Chakraborty, Gadgill/Brown, Hoversten/Majer, Miller, Lester, Eisen)

• 2 clusters in progress (Adams/Kim/Holbrook/Brenner, Cooper/Tainer)

• 1 cluster upcoming (Head-Gordon)

• 1 cluster opting out (White)


9

Progress

• Development of Linux cluster expertise has encouraged the use of Linux clusters at Berkeley Lab.

• These are funded on recharge and include: • PBD Berkeley Structural Genomics Center (14 processors) • LANL Tuberculosis Structural Genomics Consortium (24 processors) • Yucca Mountain Project (12 processors) • Yucca Mountain Project (32 processors)


10

Developments

• ITSD has developed high quality cost-effective Linux cluster support for Berkeley Lab - Development of standard toolsets and procedures Warewulf Cluster Implementation Toolkit

Developed locally by Greg Kurtzer GPL licensed through Lab Tech Transfer Showcased at Supercomputing 2003 Used widely outside the Lab (Univ of Kentucky supercomputer)

- Higher level of cybersecurity (SecureID cards) - Continual review of support costs

Summary: 360 processors in production (278 SCS, 82 Non-SCS)


11

Past and present Issues for the SCS Steering Committee

• Conforming to developed standards (cluster distribution, architecture)

• US Export Controls (deemed export)

• How do we select SCS replacements or additions?

- What to do beyond SCS program? - Extensibility - Many other projects are interested - Revisit institutional computing resource - What about GRIDs?

a. ciocioitsd/csac retreat march 3, 2004 1 scientific cluster support program scs steering committee...

Documents