The pilot is a collaborative effort of the UC CIOs and VCRs to identify a limited set of projects that will benefit from shared compute resources to demonstrate how greater research capacity and capability can be provided in a shared environment. UC will be among the first to do this as a public university system.
The pilot project name, ShaRCS pronounced sharks, is a play on an acronym for Shared Research Computing Services pilot. The pronunciation of this word inspired the names of the northern and southern cluster, Mako and Thresher, respectively. Mako and Thresher are both types of shark species.
This pilot project has been designed to define, demonstrate and measure how shared research computing and storage clusters residing in regional data centers can provide computing services to principal investigators (PIs). The Pilot needs to show that these research computing services provide better capabilities than can be individually developed, reduce the overall cost to UC, and retain low-barrier-to-access service to the PIs. In particular, the pilot will determine how best to deploy and sustain an economies-of-scale alternative to current costly and performance-inefficient campus facilities.
UC as a whole will benefit by learning how to create research cyber-infrastructure that works effectively at the UC-wide level and leverages existing resources. In addition, researchers will benefit by having privileged access to specialized services and systems designed for the type of research computing projects already in progress on the campuses and the best available computing technology to develop and enhance scientific software tools, gaining recognition and exposure for their projects and the university. Fostering collaboration among researchers at all UC campuses as well as recruiting and retaining outstanding researchers are also significant benefits to having this shared cluster computing service.
The ShaRCS pilot project is deploying two 272-node, dual-socket, quad-core Nehalem processor Linux clusters with a Quad Data Rate Infiniband interconnect; the clusters are managed by the San Diego Supercomputer Center (SDSC), a research unit of UCSD; and Lawrence Berkeley National Laboratory (LBNL), a DOE-funded national laboratory managed by UC. Both north (LBNL) and south (SDSC) centers have a long history of delivering state-of-the-art high-productivity compute facilities, and this high standard continues in the deployment of the ShaRCS high-performance computing clusters.
Participation in this pilot project includes LBNL and nine of the 10 UC campuses. Thirteen research projects will utilize the North Cluster and 10 will utilize the South Cluster.
Campuses represented in the North Cluster:
Campuses represented in the South Cluster:
The roughly two dozen projects proposed by teams from across UC were selected on the basis of their capacity to
The following projects across the University of California were selected for the initial phase of ShaRCS.
| Project | Campus | Principal Investigator(s) |
|---|---|---|
| Climate Modeling Capacity | Berkeley | John Chiang, Thomas Zach Powell, Inez Fung, Ron Cohen |
| Comparative Genomics Cyberinfrastructure Needs; Understanding Diversity in Microbial Community Sequencing | Berkeley | Steven Brenner |
| Phylogenomics Cyberinfrastructure for Biological Discovery | Berkeley | Kimmen Sjolander, Steven Brenner, Jasper Rine |
| Optimized Materials and Nanostructures from Predictive Computer Simulations | Davis | Giulia Galli, Francois Gygi |
| Hydrology Analysis Cyber-infrastructure Proposal | Irvine | Soroosh Sorooshian, Sue Bryant, Bisher Imam |
| Simulation and Modeling of biological molecules | Irvine | Doug Tobias |
| Speeding the Annotation and Analysis of Genomic Data for Biofuels and Biology Research | LBNL | Adam Arkin, Dylan Chivian, Paramvir Dehal, Paul Adams |
| CCSM to Study New Biofuels with Carbon Cycles | LBNL, Berkeley | Bill Collins |
| Research in the Physics of Real Materials at the Most Fundamental Level Using Atomistic First Principles (or ab initio) Quantum-Mechanical Calculations | LBNL, Berkeley | Steven Louie, Jeffrey Neaton |
| Universe-Scale Simulations for Dark Energy Experiments | LBNL, Berkeley | Martin White, David Schlegel |
| Nano-system Modeling and Design of Advanced Materials | Los Angeles | Nasr Ghoniem |
| Organic Reaction Mechanisms and Selectivities, Enzyme Design, and Material and Molecular Devices | Los Angeles | K.N. Houk |
| Particle-in-cell Simulations of Plasmas | Los Angeles | W.B.Mori, V.K.Decyk, F.S.Tsung, P.Pritchett, J.Tonge |
| Space Plasma Simulations | Los Angeles | Maha Ashour-Abdalla |
| Oceanic Simulation of Surface Waves and Currents | Los Angeles, Santa Barbara | J.C. McWilliams, A.F. Shchepetkin, and Yusuke Uchiyama |
| Dynamics and Allosteric Regulation of Enzyme Complex | Riverside | Chia-en Angelina Chang |
| Functional Theory for Multi-Scaling of Complex Molecular Systems and Processes | Riverside | Jianzhong Wu |
| Establishing CI Capable of Capture and Analysis of Next-Generation Sequencing Data | San Diego | Trey Ideker |
| Physics-Based Protein Structure Prediction | San Francisco | Ken Dill |
| Computational Chemistry and Chemical Engineering Projects | Santa Barbara | Joan Shea, Baron Peters |
| Development and Mathematical Analysis of Computational Methods | Santa Barbara | Paul Atzberger |
| California Current System | Santa Cruz | Christopher Edwards |
| Convection and Magnetic Field Generation | Santa Cruz | Gary Glatzmaier |
These are the PIs currently in production on the clusters. Some changes have been made based on the original 24 pilot PI projects.
