HDF5 Pioneer Joins NERSC Data Analytics Team

Quincey Koziol, who has spent more than two decades helping develop and refine the Hierarchical Data Format (HDF) I/O library used by thousands of organizations across government, academia and industry to manage large scientific data files, recently left the HDF Group to join NERSC as principal data architect in the Data and Analytics Services group.

As director of core software and high performance computing at the HDF Group, Koziol spent the last 11 years developing the HDF5 I/O middleware package and overseeing the group’s HPC development efforts. In his new position, Koziol will help lead NERSC’s data management efforts, including investigating object storage technologies and participating in defining the storage subsystem for the NERSC-9 system. He will also continue to provide technical leadership for the HDF5 project.

CrossConnects Bioinformatics Workshop Tomorrow: Registration Still Available

ESnet’s CrossConnects Bioinformatics Workshop starts tomorrow, and it’s not too late to attend, either virtually or in person. Registration for the on-site workshop, held at Berkeley Lab’s Advanced Light Source, is still open. For those who can’t make it to the ALS, ESnet will be hosting a live video stream of the event. A full agenda is available on ESnet’s site.

The workshop will bring together leaders in the bioinformatics, computing, and networking communities to discuss the resources, partners and tools needed to support high-performance data transfers, distributed data analysis and global collaboration in precision medicine and precision agriculture and their relevant ties to human and plant microbiomic and metagenomic research.

‘Navigating Conflict of Interest’ Next BLIC Topic

Tomorrow, Tuesday, April 12, at noon in Perseverance Hall, the next Berkeley Lab Innovation Corps (BLIC) meeting addresses conflict of interest (COI) issues. Molly Stoufer, the Lab’s COI coordinator and Innovation and Partnerships Office staff will lead the discussion and answer questions. New BLIC members are welcome. Join your fellow innovators and entrepreneurial researchers and claim a coveted BLIC T-shirt. Email techoutreach@lbl.gov to be added to the mailing list for future BLIC announcements.

This Week’s CS Seminars

Tuesday, April 12

Island Avatars: Simulating Social-Ecological Systems
11 a.m. to 12 p.m., 190 Doe Library, UC Berkeley
George Roderick, UC Berkeley, ESPM
Matthias Troyer, ETH Zurich
Neil Davies, UC Berkeley, BIDS/GUMP
Sally Holbrock, UC Santa Barbara, MCR-LTER
Matt Münnich, ETH Zurich

We will present how ETH Zurich and the University of California are working together to build the first full-scale simulation of a complex social-ecological system. The Island Digital Ecosystem Avatar (IDEA) is an open science initiative to build use-oriented simulations (avatars) of entire systems starting with the island of Moorea, French Polynesia. The Moorea IDEA is a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. The resulting knowledge and tools will help predict human and natural change at scales relevant to management/conservation actions. We will present progress to date in building this powerful new tool for scenario-based planning, education, and local population engagement. The lecture is one of series of events presented by ETH Zurich and San Francisco Bay area institutions. Free registration required.

Wednesday, April 13

Tensor Networks and Hierachcial Tensors for Quantum Physics and More
3:30 to 4:30 p.m., 939 Evans Hall, UC Berkeley
Reinhold Schneider, TU Berlin

Approximation by sum of products (of uni-variate functions) is a widely used, e.g. in statistics and physics, concept to approximate high dimensional functions, and high-dimensional problems, e.g. PDE’s are cast into optimzation problems. However, the non-linear parametrization leads to problems, where the most simplest are shown to be NP hard (Hillard-Lim 2012). For a particular class of multi-linear parametrizations, namely hierarchical tensor representations (Hackbusch et al. 2009) or tree tensor networks, these difficulties can be resolved to a fairely wide extent, and provide a mathematically sound concept for tensor product approximation. Hierarchcial tensors will be introduced by a hierarchy of optimal subspace approximations, and demostrated by tensor trains (TT), resp. matrix products states (MPS).

We treat different applications ranging from quantum chemistry, Langevin dynamics of biomolecules, uncertainty quantification to tensor completion by variant of DMRG (density matrix renormalization group) and improved algorithm.

Friday, April 15

Exploring New and Upcoming Technologies for Exascale
10 to 11 a.m., Bldg 59 (Wang Hall) Room 4101
Manu Shantharam, Performance Modeling and Characterization (PMaC) Laboratory, San Diego Supercomputer Center

New and upcoming technologies are being proposed for peta-to-exascale systems to address important concerns such as scalability, power, and performance. These technologies span different areas including algorithms, programming models, proce›dispatch from the data science frontier, Dr. Nick Adams shares his vision of a future where social science’s long under-tested meso-level theories of symbolic interaction and social psychology meet the big complex text and sensor data needed to give them new life and constructive power. Highlighting innovative methods scaling qualitative explanation to quantitative analysis, Adams sounds a bold call for the kind of social science this moment requires.

Link of the Week: White House Proposes Open-Sourcing More Software

“While the government has long used open-source software and tools, a new proposal out of the White House last weekend suggests that government-written or commissioned software should be released under free and open-source licenses,” reports the SD Times.” The paper, titled “Federal Source Code Policy — Achieving Efficiency, Transparency, and Innovation through Reusable and Open Source Software,” specifically calls for all governmental agencies to begin open-sourcing and sharing their code starting this July.”