IDRE-HPC Research Projects

As a convergence point for engineering, mathematics and computer science with the domain sciences, IDRE represents and supports research at UCLA where high performance computation, visualization, modeling and simulation play a key role.

IDRE staff and scientists are involved in two different types of computational research projects. Pilot projects are initiated by the IDRE Director and Executive Committee to address key computational needs for UCLA researchers. Focus projects are chosen through an annual IDRE solicitation for internal research proposals that involve one of IDRE's areas of expertise in high-performance computing. The purpose of this annual solicitation is to help faculty and research groups identify and solve their "bottlenecks' in high-performance computing. Successful proposals have access to expertise and resources of IDRE research staff, scientists, scholars, and post-doctoral researchers.

PILOT PROJECTS

Use of Cloud Computing Resources in an HPC Environment (2009)
Bill Labate (UCLA Office of Information Technology) and Prakashan Korambath (IDRE)

Investigation into use of configurable and scalable virtual networks for high-performance computing. Long-term use scenarios for cloud resources include applications for extending the existing UC Grid without building out additional IT infrastructure and linking the national supercomputing centers to provide a true on-demand HPC cloud environment.

Development of Particle-in-Cell Algorithms for Advanced Computer Architectures (2009)
Viktor Decyk (IDRE Research Physicist)

Design of a general algorithm for Particle-in-Cell (PIC) codes to run effectively on a variety of new computer architectures including multi-core processors, Cell processors, and graphical processing units (GPUs). The first test will be an implementation on GPUs.

Development of a Scientific Workflow using Kepler Software to Design Enzymes for Rection Catalysts in Protein Engineering (2009).
Prakashan Korambath (IDRE), Jianwu Wang (Scientific Workflow Automation Technologies (SWAT) Laboratory, SDSC), Kendall Houk (Professor, Chemistry & Biochemistry, UCLA), Seonah Kim (Post Doc, Chemistry & Biochemistry, UCLA), Scott Johnson (Graduate Student, Chemistry & Biochemistry, UCLA), Kejian Jin (IDRE), Ilkay Altinas (SWAT, SDSC), and Shava Smallen (SDSC)

In protein engineering, scientists have successfully designed new enzymes for reactions not catalyzed by naturally occurring biocatalysts. The design process is, however, computationally intensive. Implementation of Kepler workflow software will allow synchronization of the design process, the ability to distribute the job to multiple computational resources through UC Grid, and a reduction of the time required for future design processes from three years to three months.

FOCUS PROJECTS

Development of a Scalable Computational Tool for Simulation of Biomedical Flows with Complex Geometries (2009)
Jeff D. Eldredge (Associate Professor, Mechanical & Aerospace Engineering) and Shao-Ching Huang (IDRE)

Implementation of a scalable algorithm for massively-parallel simulations of biomedical flow systems involving complex geometry. Designed to facilitate the construction of the computational mesh by ‘immersing’ the geometry in a Cartesian mesh and utilizing distributed forcing functions to transfer information between mesh and geometry, the study focuses on the analysis of a vitreous cutter, a biomedical device used to extract the fluid in the eyeball during eye surgery.

Envisioning Climate with the UCLA Hydra Visualization Cluster (2009)
Alex Hall (Associate Professor, Department of Atmospheric and Oceanic Sciences) and Scott Friedman (IDRE)

Use of the UCLA Hydra Visualization Cluster for the analysis of high-resolution regional earth system models to study climate and the evolution of climate under anthropogenic forcing. The resultant interactive visualization of the climate data on the Hydra cluster will allow greater depth of data analysis and include optional layers of related variables such as atmospheric winds, ocean currents, and marine biological productivity.

Exact Many-Electron Simulation Method for Bond-Breaking Reactions in Liquids (2007)
Benjamin J. Schwartz (Professor, Chemistry & Biochemistry), William J. Glover (Student, Chemistry & Biochemistry), Prakashan Korambath (IDRE)

Research to solve eigenvalue problem for a Sparse Matrix using Implicitly Restarted Lancoz Method to exact many-electron simulation method for bond-breaking reactions in liquids.

High-Performance Image Processing for Cryo-Electron Microscopy (2007)
Z. Hong Zhou (Director, Electron Imaging Center for NanoMachines (EICN); Professor, Microbiology, Immunology & Molecular Genetics), Xhark Zhang (EICN, CNSI, and MIMG), Scott Friedman (IDRE) and Shao-Ching Huang (IDRE)

Peformance analysis and optimization to increase computing speed by performing FFT on the GPU for fast image processing and reconstruction utilizing the GPU.

RESEARCH PROJECTS ON THE IDRE SHARED CLUSTER

Evolution of our Solar System
Brad Hansen (Associate Professor, Astrophysics), Steve Berukoff and Elliot Koch (Students, Astrophysics)

Implementation of an 80-core cluster in the IDRE data center to research white dwarfs, extrasolar planets, neutron stars, and black holes in an effort to determine how our own solar system may have evolved. Funded in part with a grant from the Sloan Foundation.