The HDF Group’s HPC Program

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. Continue reading

Parallel I/O – Why, How, and Where to?

Mohamad Chaarawi, The HDF Group

First in a series: parallel HDF5

What costs applications a lot of time and resources rather than doing actual computation?  Slow I/O.  It is well known that I/O subsystems are very slow compared to other parts of a computing system.  Applications use I/O to store simulation output for future use by analysis applications, to checkpoint application memory to guard against system failure, to exercise out-of-core techniques for data that does not fit in a processor’s memory, and so on.  I/O middleware libraries, such as HDF5, provide application users with a rich interface for I/O access to organize their data and store it efficiently.  A lot of effort is invested by such I/O libraries to reduce or completely hide the cost of I/O from applications.

Parallel I/O is one technique used to access data on disk simultaneously from different application processes to maximize bandwidth and speed things up. There are several ways to do parallel I/O, and I will highlight the most popular methods that are in use today.  

Blue Waters supercomputer
Blue Waters supercomputer at the National Center for Supercomputing, University of Illinois, Urbana-Champaign campus.  Blue Waters is supported by the National Science Foundation and the University of Illinois.

First, to leverage parallel I/O, it is very important that you have a parallel file system; Continue reading

HDF at the 2015 Oil & Gas High Performance Computing Workshop

Quincey Koziol, The HDF Group

nasa.gov
photo from NASA.gov

Perhaps the original producers of “big data,” the oil & gas (O&G) industry held its eighth annual High-Performance Computing (HPC) workshop in early March.    Hosted by Rice University, the workshop brings in attendees from both the HPC and petroleum industries.  Jan Odegard, the workshop organizer, invited me to the workshop to give a tutorial and short update on HDF5.

2015-03-18 09_08_46-▶ Rice 2014 Oil & Gas High Performance Computing Workshop - YouTube snapshot
Rice University hosts 2015 O & G HPC Workshop

The workshop (#oghpc) has grown a great deal during the last few years and now has more than 500 people attending, with preliminary attendance numbers for this year’s workshop over 575 people (even in a “down” year for the industry).  In fact, Jan’s pushing it to a “conference” next year, saying, “any workshop with more attendees than Congress is really a conference.” But it’s still a small enough crowd and venue that most people know each other well, both on the Oil & Gas and HPC sides.

The workshop program had two main tracks, one on HPC-oriented technologies that support the industry, and one on oil & gas technologies and how they can leverage HPC.  The HPC track is interesting, but mostly “practical” and not research-oriented, unlike, for example, the SC technical track. The oil & gas track seems more research-focused, in ways that can enable the industry to be more productive.

I gave an hour and a half tutorial on developing and tuning parallel HDF5 applications, which Continue reading