Research

Quincey Koziol, The HDF Group

“A supercomputer is a device for turning compute-bound problems into I/O-bound problems.” – Ken Batcher, Prof. Emeritus, Kent State University.

HDF5 began out of a collaboration between the National Center for Supercomputing Applications (NCSA) and the US Department of Energy’s Advanced Simulation and Computing Program (ASC), so high-performance computing (HPC) I/O has been in our focus from the very beginning.  As we are starting our 20th year of development on HDF5, HPC I/O continues to be a critical driver of new features.

Los Alamos National Laboratory is home to two of the world’s most powerful supercomputers, each capable of performing more than 1,000 trillion operations per second. Here, ASC is examining the effects of a one-megaton nuclear energy source detonated on the surface of an asteroid. Image from ASC at http://www.lanl.gov/asci/

The HDF5 development team has focused on three things when serving the HPC community: performance, freedom of choice and ease of use.

David Dotson, doctoral student, Center for Biological Physics, Arizona State University; HDF Guest Blogger

Recently I had the pleasure of meeting Anthony Scopatz for the first time at SciPy 2015, and we talked shop. I was interested in his opinions on MDSynthesis, a Python package our lab has designed to help manage the complexity of raw and derived data sets from molecular dynamics simulations, about which I was

Mohamad Chaarawi, The HDF Group

Second in a series: Parallel HDF5

NERSC’s Cray Sonexion system provides data storage for its Mendel scientific computing cluster.

In my previous blog post, I discussed the need for parallel I/O and a few paradigms for doing parallel I/O from applications. HDF5 is an I/O middleware library that supports (or will support in the near future) most of the I/O paradigms we talked about.

In this blog post I will discuss how to use HDF5 to implement some of the parallel I/O methods and some of the ongoing research to support new I/O paradigms. I will not discuss pros and cons of each method since we discussed those in the previous blog post.

But before getting on with how HDF5 supports parallel I/O, let’s address a question that comes up often, which is,

“Why do I need Parallel HDF5 when the MPI standard already provides an interface for doing I/O?”

John Readey, The HDF Group

Editor’s Note: Since this post was written in 2015, The HDF Group has developed HDF Cloud, a new product that addresses the challenges of adapting large scale array-based computing to the cloud and object storage while intelligently handling the full data management life cycle. If this is something that interests you, we’d love to hear from you.

 

Interestingly enough, in addition to being known as the place to go for BBQ and live music, Austin, Texas is a major hub of Python development.  Each year, Austin is host to the annual confab of Python developers known as the SciPy Conference.  Enthought, a local Python-based company, was the major sponsor of the conference and did a great job of organizing the event.  By the way, Enthought is active in Python-based training, and I thought the tutorial sessions I attended were very well done.  If you would like to get some expert training on various aspects of Python, check out their offerings.

As a first-time conference attendee, I found attending the talks and tutorials very informative and entertaining.  The conference’s focus is the set of packages that form the core of the SciPy ecosystem (SciPy, iPython, NumPy, Pandas, Matplotlib, and SymPy) and the ever-increasing number of specialized packages around this core.     

Lindsay Powers - The HDF Group The HDF Group provides free, open-source software that is widely used in government, academia and industry. The goal of The HDF Group is to ensure the sustainable development of HDF (Hierarchical Data Format) technologies and the ongoing accessibility of HDF-stored data because users and organizations have mission-critical systems and archives relying on these technologies. These users and organizations are a critical element of the HDF community and an important source of new and innovative uses of, and sustainability for, the HDF platforms, libraries and tools. We want to create a sustainability model for the open access platforms and libraries that can serve these diverse communities in the future use and preservation of their data. As a...

  • 2