won not five but six R&D 100 Awards in 2002. The October 2002
issue of this magazine described five awards for which Livermore
was the primary developer. But the Laboratory was also a key member
of a four-institution team that won a sixth R&D 100 Award for
a software project called Hierarchical Data Format 5 (HDF5). As
the primary developer, the National Center for Supercomputing Applications
(NCSA) at the University of Illinois (UrbanaChampaign) worked
in collaboration with Livermore, Los Alamos, and Sandia national
is the first widely used input/output (I/O) library specifically
designed for massively parallel computing systems. An I/O library
is a collection of programming routines that a computing code calls
on to write or read data to or from a file on disk.
early years of scientific computing, roughly 1959 to 1980, I/O libraries
took the form of little more than Fortran format statements to write
or read binary or ASCII (text) files. Between 1980 and 2000, an
important innovation emergedthe general purpose I/O library,
which has two variants working at slightly different levels of data
abstraction. One focused on computer science data structures, the
other on computational science mesh structures. In addition to providing
random access to named, abstract data objects, these libraries provided
data that could be written on one machine architecture and read
the advent of massively parallel computers, computer scientists
identified the need for a general-purpose I/O library that writes
data from multiple processors into a single file, that can handle
individual data structures larger than a gigabyte and individual
files larger than a terabyte, and whose performance scales to large
numbers of processors.
HDF5, we were also aiming at another big goalto lay the foundation
for solving the interoperability problem in scientific computing,
says Livermore computer scientist Linnea Cook. Many of the
major supercomputing centers around the worldincluding Livermore,
Los Alamos, and Sandiahad developed their own I/O libraries
to address requirements not satisfied by existing libraries. None
of these institutions could easily share data or software tools.
Mark Miller, a Livermore expert on data modeling, agrees. With
HDF5, we have the beginnings of a solution to the interoperability
problem. Plus we made an important contribution to the scientific
|Livermore members of the award-winning
HDF5 team are (from left) Robb Matzke, Mark Miller, Linnea Cook,
and Kim Yates.
HDF5 is the successor to HDF1 through HDF4, a
series of highly successful I/O libraries developed at NCSA and
used around the world. HDF software includes I/O tools for analyzing,
visualizing, and converting data between various numeric formats
and storage schemes. By the mid-1990s, however, HDF4 had begun to
show its limitations. It lacked the capacity to handle the enormous
amounts of data being generated by many scientific research programs,
and it was not designed to support parallel applications.
At about the same time,
the Department of Energy established its Accelerated Strategic Computing
Initiative (ASCI), now the National Nuclear Security Administrations
Advanced Simulation and Computing Program, to develop a massively
parallel computing capability. Livermore, Los Alamos, and Sandia
established a group to explore the possibilities of developing visualization
codes jointly. Cook served on this committee and initiated the effort
to develop a common, tri-laboratory, parallel I/O library. She believed
that the HDF group at NCSA might be part of the solution and invited
them to participate.
Throughout the late 1990s,
the three national laboratories worked with NCSA under ASCI auspices
to develop an improved version of HDF. Livermore computer scientist
Robb Matzke developed the majority of the first production versions
of HDF5, with colleague Kim Yates making substantial contributions
to the parallel version.
The teams primary goal
was to produce a high-performance, parallel I/O library that would
meet the requirements of all three laboratories. This meant that
HDF5 needed to be delivered quickly, with sufficient functionality,
robustness, and performance, before other libraries being built
at all three laboratories became entrenched. The second goal was
to develop a de facto standard library that would be widely used
throughout the international scientific computing community. Once
an I/O library becomes widely used, commercial software companies
and free tool developers begin developing codes to operate on data
stored in that format. Many users can then quickly and easily use
these tools. Likewise, Livermore-built tools that read HDF5 data
will be more easily used by other organizations that use HDF5.
Today, HDF5 can store, access,
manage, exchange, and archive not only massive amounts of complex
data but also any type of data suitable for digital storage, no
matter its origin or size. HDF5 is a completely portable file format.
A file can be written on any system and read on any other. Plus
its I/O libraries can run on virtually any scientific research computing
system, be it serial or parallel. The HDF5 file format and library
are designed to evolve as requirements emerge.
HDF5 can handle, for example,
trillions of bytes of computational modeling data or high-resolution
electronic images in a continuously evolving computing and storage
environment. With the help of lower-level libraries, HDF5 enables
thousands of processors to simultaneously write data to a single
file. Terabytes of remote-sensing data received from satellites,
computational results from weather or nuclear testing models, and
high-resolution magnetic resonance imaging brain scans can be stored
in HDF5 files along with additional information needed for efficient
data exchange, data processing, visualization, and archiving.
HDF5 can also write data
to a file on disk, to memory, across the network, or to any device
specified by using its Virtual File Layer. Applications can write
a virtually unlimited number of objects to a file, and the maximum
size of any object is limited only by the computer or the file systems
capacity. HDF5 provides simple data types, user-defined data types,
and compound data types of any degree of complexity, including nesting
to any number of levels. Through its grouping and linking mechanism,
the HDF5 data model supports complex data relationships and dependencies.
Multidimensional arrays can be extended in any dimension. In addition,
HDF5 provides partial I/O capabilities. For example, users may wish
to read only a subset of an array containing hundreds of millions
Work continues on HDF5as
well as on the broader interoperability problem it helps to address.
Groups that collaborated on this award-winning technology are also
working on higher level libraries to capture the mathematical and
physical abstractions of scientific data. In addition, the HDF group
is defining conventions for using HDF5, which will also improve
|A sample HDF5 file with groups
to provide structure, datasets, raster images, and a palette.
Interesting Uses for HDF5
is used by government, academic, and commercial institutions in
more than 60 countries. The three DOE laboratories are currently
the largest users of HDF5s parallel capabilities, but that
is beginning to change.
HDF5 is incorporated into
the Globus Project at Argonne National Laboratory, which focuses
on the fundamental technologies required to deploy computational
grids. Argonnes NeXus, which provides a standard data format
for work in neutron and synchrotron radiation internationally, is
converting to HDF5. FLASH, a product used to study thermonuclear
flashes on the surfaces of compact stars, is built on HDF5.
The big surprise of 2001
for the HDF group came when the Help Desk started getting e-mail
messages from a programmer in New Zealand. His questions were not
of the ordinary sort, and the technical support staff eventually
asked him how he was using the library. All he was free to say at
the time was that he was working on graphical special effects. Later
information revealed that his company was using HDF5 to generate
atmospheric effectssmoke, wind, and cloudsfor The Lord
of the Rings film trilogy.
Advanced Simulation and Computing (ASCI), Hierarchical Data Format
5 (HDF5), input/output (I/O) libraries, R&D 100 Award, supercomputing.
For further information contact Linnea Cook (925) 422-1686 (email@example.com).
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