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HDF5 Users

Some organizations who use HDF5

(For user-developed tools, see Software Using HDF5.)

AER, Inc
Using HDF5 in satellite meteorology (NPOESS).

Aberdeen Test Center
Uses HDF5 to store test data collected at the Aberdeen Test Center (ATC) at Aberdeen Proving Ground (APG) in Maryland, USA.

APAC National Facility and Australian National Facility

Aqualinc Research Ltd., New Zealand
Using HDF5 in field of groundwater hydrology.

Aquaveo, LLC
Aquaveo is a water resources engineering consulting firm and the developer of the Groundwater, Surface-water, and Watershed Modeling Systems. HDF5 is the foundation of a standard format for the geometry data storage of river cross-sections, 2D/3D structured grids, 2D/3D unstructured meshes, geometric paths through space, and associated time data.

Argonne National Laboratory
Using HDF5 in field of Accelerator/Plasma Science.

Argonne National Laboratory Globus Project
The Globus Project at Argonne National Laboratory develops fundamental technologies needed to build computational grids.

ASCI/Alliances Center for Astrophysical Thermonuclear Flashes

Australian Nuclear Science and Technology Organisation
Using HDF5 in field of Neutron and X-Ray Scattering.

BALTRAD
BALTRAD is a sustainable weather radar network for the Baltic Sea Region, operating in real-time, with high-quality data.

Baylor College of Medicine
The National Center for Macromolecular Imaging (NCMI) is a national facility supported mainly by the NIH National Center for Research Resources. Other support includes the National Institute of Allergy and Infectious Disease, the National Library of Medicine, the National Science Foundation, the R. Welch Foundation, the Agouron Institute and the WM Keck Foundation.

The long-term goal of the NCMI is to establish the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy and computer reconstruction. Our emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography. The ultimate outcome of our research is a three-dimensional image of the complex that we can use for design of drugs and vaccines for a variety of diseases.

Boston Collaborative Drug Surveillance Program
Using HDF5 in field of Pharmacoepidemiology. HDF5 is used to monitor and analyze drug usage for purposes of drug safety, using Python (through the PyTables module) to access HDF5.

Cactus
Supports HDF5 in the Cactus code, which is an open source problem solving environment designed for scientists and engineers.

California Air Resources Board
Uses HDF5 for their Aircraft Emissions Database

CalTech
The Bhattacharya group, ME, Division of Engineering at CalTech, is using HDF5 in the field of Ferroelectric materials.

Canada Centre for Remote Sensing, Ontario, Canada
Using HDF5 in Atmospheric radiation.

Cardiff University
Using HDF5 in problem solving environments/grid computing.

CAREERI, CAS, China
Using HDF and HDF5 in field of desertification.

Ceemple
Ceemple is an innovative solution enabling rapid C++ based technical computing. It features the productivity of MATLAB and Python, combined with the performance and power of standard C++. Ceemple also enables rapid development using the HDF library, greatly simplifying writing HDF based C++ code.

CEI
CEI offers a suite of tools for engineering and scientific simulation, including meshing, plotting, animation and data visualization. The company's software can be run on every type of computer, from laptops to clusters to supercomputers. It interfaces seamlessly to all popular CAE software and most scientific research codes, and can drive the most advanced VR displays. CEI has corporate headquarters in Apex, N.C., and authorized distributors around the world.

Center for Computation and Technology, Louisiana State
Using HDF5 in numerical relativity.

Center for Space Science and Applied Research, China

Centre de Suivi Ecologique, Senegal
Using HDF5 for land use and land cover maps in Senegal.

CESBIO Unite Mixte CNES-CNRS-UPS-IRD, France
Develop software functions to process ASTER, VEGETATION and other satellite data within the "Sud-Ouest" project, dealing with carbon and water fluxes modeling at meso-scale.

CINECA, Italy

C.I.R.A. - Italian Aerospace Research Center
Using HDF5 in field of Computational AeroAcoustics.

CIRAD
Using HDF5 for GIS and remote sensing applications in Guinean Research Institute Support.

CSIC-Institute of Earth Sciences, Spain
Using HDF5 in field of geophysics.

CONABIO, Mexico
Using HDF5 in MODIS fire detection.

CONAE - Comision Nacional De Actividades Espaciales, Argentina
Using HDF5 in remote sensing.

Department of Energy's ASC project
ASC (Advanced Simulation and Computing) is a Department of Energy program involving the Lawrence Livermore, Los Alamos and Sandia National Laboratories. ASC's goal is "to shift promptly from nuclear test-based methods to computational-based methods of ensuring the safety, reliability, and performance of our nuclear weapons stockpile." These methods must achieve high-resolution, three-dimensional calculations of full-systems using high-fidelity physical models. The ASCI Data Models and Formats group (ASCI DMF) is working closely with NCSA on the development of HDF5 to address I/O and data sharability issues, to replace existing mesh data management software with a unified mesh API, and to replace storage formats with HDF5. This involves not only supporting ASC data requirements in the new HDF5 format, but also implementing the HDF5 IO library on the three multi-teraflop ASC machines.

Deutsche Bank
Using HDF5 in field of Financial Engineering.

Deutscher Wetterdienst, Germany
Using HDF5 in Satellite Climate Monitoring.

Diamond Light Source
Using HDF5 in Synchrotron Science (using NeXus)

Duke University Nicholas School of the Environment
Using HDF5 in Antarctic Biological Oceanography.

Dynamics Research Corporation, CA
Using HDF5 in electronics (Alliance/NPACI user).

Edith Cowan University, Australia
Using HDF5 in field of photonics.

ESI Group
The ESI Group is using HDF5 as the data container for their new solver result database format, called ERF (ESI Result Database Format). ERF will be supported by all PAM-CSM FEM-solvers (PAM-CRASH and derivatives, explicit and implicit solution schemes) from version v2009.

European Southern Observatory (ESO)
Using HDF5 in numerical modeling of optical fibers.

EWRE, ltd., Israel
Using HDF5 if field of groundwater flow and transport modeling - visualization.

Freiburg Materials Research Center
The service group Scientific Information Processing of the Freiburg Materials Research Center (FMF) uses HDF for its Open Source Data Analysis Framework Pyphant, which uses HDF as native file format for saving scientific data and flow based data analysis algorithms.

Gazi University, Turkey
Using HDF5 in field of mechanical engineering.

Gemini Observatory
Using HDF5 in field of Adaptive Optics / Astronomy.

Geological Institute, Univ. of Copenhagen, Denmark
Using HDF5 in field of Hydrogeology.

Geological Survey Of Austria
Using HDF5 in interpretation of Aeroelectromagnetic Data.

GLOBE Claritas (GNS Science), New Zealand
Using HDF5 in seismic processing software (Geophysics).

Grassland Institute of CAAS, China
Using HDF5 for grassland monitoring.

Hankyong National University, Korea
Using HDF4 and HDF5 in air pollution modeling.

Hydrometeorological Research Centre Of Russia (RHMC)
Using HDF5 in Atmospheric Physics & Dynamical Meteorology.

IBAMA, Brazil
Using HDF5 in remote sensing.

INEL
Using HDF5 in the Advanced Fuel Cycle program.

Ifremer, France
CERSAT, the processing and archiving facility for satellite data at Ifremer (French Research Institute for Exploitation of the Sea), is using HDF5.

Innovative Management & Technology Services (IMTS)
Using HDF5 in Scientific Data Visualization.

Institut Laue-Langevin, Grenoble, France
Using HDF5 in neutron scattering simulation/NeXus format.

Institute of Mineralogy and Geochemistry, University Karlsruhe, Germany
Using HDF5 on project to study arsenic groundwater contamination.

International Space Station

ISRO, India

Istanbul Technical University, Aerospace Department
Using HDF5 in field of Gas Dynamics.

IWR, University of Heidelberg
Using HDF5 in Advanced Parallel Numerical Simulation (scalable I/O on Linux clusters).

Japan Aerospace Exploration Agency (JAXA)
The ACOS (Atmospheric CO2 Observations from Space) Team, in collaboration with the Japan Aerospace Exploration Agency (JAXA), is participating in the analyses of GOSAT "IBUKI" observation data.

The Joannopoulos Research Group at MIT
Physics department at MIT head by Professor John D. Joannopoulos. See MIT Photonic-Bands and Software for HDF5

Johns Hopkins University Applied Physics Lab
Using HDF5 in Aerospace Engineering.

Kell S.R.L.
Uses HDF5 in GIS and Remote Sensing.

KITWARE Inc.
Using HDF5 in medical image processing.

Kongsberg Spacetec AS
Using HDF4 and HDF5 in remote sensing applications.

Korea Ocean Satellite Center (KOSC)
GOCI is one of three payloads on the COMS satellite, and GOCI L1B and L2 data is stored in HDF-EOS5.

Kyushu University
Using HDF5 in field of oceanography.

Laboratory for Computational Astrophysics
See LCA Vision.

Laboratory of Theoretical Physics and Modelization, Universite de Cergy-Pontoise, France
Using HDF5 in the study of the propagation of light and different phenomena about light in photonic crystals.

Laboratory for Neural Computation
Uses HDF5 in field of bioengineering.

Lamont-Doherty Earth Observatory of Columbia University
Trying to parallellize (in MPI) the I/O of their ocean and atmosphere models, which is in sequential mode mostly using UNIDATA/UCAR's netCDF.

LandSAF
The Instituto de Meteorologia in Portugal is using HDF5 to store LandSAF products derived from METEOSAT SECOND GENERATION & EUMETSAT POLAR SYSTEM satellite images.

Lawrence Berkeley National Laboratory, Applied Numerical Algorithms and Visualization Group
The Applied Numerical Algorithms Group and Visualization Group at Lawrence Berkeley National Laboratory have developed the ChomboVis application, which uses HDF5. ChomboVis is a visualization tool for 2D and 3D AMR data sets. It is layered on top of the Visualization Toolkit (VTK) and provides a simple graphical user interface for interacting with a 2D or 3D data set.

Lawrence Berkeley National Laboratory, Free-electron lasers, light sources

LENS, Italy
Using HDF5 in field of physics.

Limnological Institute SD RAS Irkutsk, Russia
Using HDF5 in hydrology and hydrophysics.

Linac Coherent Light Source - Xray Free-Electron Laser
The LCLS is a multi-institutional proposal for a single-pass x-ray Free Electron Laser (FEL) operating in the 1-15 wavelength region, using electron beams.

LITA - POLITECNICO of Milan, Italy
Uses HDF5 in Water Resources Management - Computer Science.

LOFAR
Astronomy data from the LOFAR (Low Frequency Array) telescope is stored in HDF5.

Los Alamos National Laboratory (Parallel Architectures and Performance Team)
The Parallel Architectures and Performance Team investigates the issues that contribute to optimal application and computer system performance on extreme-scale advanced architectures.

Lupine Logic, Inc.
Lupine Logic, Inc. is a commercial firm working within the NASA EOS program (primarily land data products) developing EOS operational ECS MODIS algorithms as well as exploring commercial applications of NASA EOS data products. They use both HDF4 and HDF5.

Machine Learning Data Set Repositiory (mldata.org)
This is a repository for Machine Learning (ML) data, which uses HDF5 internally. Machine Learning (ML) is a branch of artificial intelligence concerned with the design and development of algorithms that allow computers to evolve behaviors based on empirical data.

The MathWorks
The MathWorks is a developer and supplier of software for technical computing and Model-Based Design. MATLAB, one of the core products from The Mathworks, stores its data in the HDF5 format.

Matrix Metals Limited
Matrix Metals Limited is an Australian copper producer that uses both HDF4 and HDF5 in earth science applications.

MeerKAT
Astronomy data from the MeerKAT Array is stored in HDF5.

MEPhI, Russia
Using HDF5 in Astroparticle Physics, PAMELA.

mosaik
Mosaik is an open-source flexible smart Grid co-simulation framework, written in Python. It uses existing simulators in a common context to perform a coordinated simulation of a given (Smart Grid) scenario.

NASA Earth Science Enterprise
See the HDF-EOS Tools and Information Center.

NASA Glenn Research Center
Use HDF as a platform-independent binary file format to store massive amounts of airplane engine simulation data for later analysis. Our tool, NPSS, or Numerical Propulsion Simulation System, allows multi-user, distributed simulations with the ability to hide proprietary codes. These simulations are then distributed to airframe manufacturers and other customers to link into their simulations. The storage of 0-D, 1-D, 2-D, and 3-D geometry data and engine parameters in a platform-independent data format is crucial to the ability to perform analyses and make use of this data in various applications, at various sites on various platforms.

NASA LaRC
Using HDF5 in Aerospace Engineering.

National Centre for Medium Range Weather Forecasting (NCMRWF), Govt. of India
Use HDF5 for some of meteorological and satellite data.

National Energy Research Scientific Computing Center

National Ignition Facility
Target Diagnostics computer software development, gathering of data for NIF experiments.

National Oceanographic Data Center (NOAA)
Using HDF5 in oceanography.

National Oceanography Centre, Southampton, UK  
NOCS has several large scale ocean modelling projects using low to high resolution global ocean and sea-ice models to investigate the physics underlying the ocean circulation and to understand its impact on biological systems and climate.

The high resolution ocean models, in particular, make good use of HDF5's chunking and compression facilities to store model output efficiently. They are able to use HDF5 with Ferret, by deriving "Ferret external functions", which can read HDF5 data directly. Helpful tips on doing this can be found at:

   http://www.noc.soton.ac.uk/JRD/OCCAM/OME/?page=ferret

National Renewable Energy Laboratory
Using HDF5 in Solid State Physics.

National Satellite Meteorological Center, Beijing, China
Uses HDF in satellite remote sensing.

NCSR "Demokritos", Greece
Using HDF5 for neutron scattering data aqcuisition and analysis.

NeXus Format
NeXus is a common data format for neutron, x-ray, and muon science. It is being developed as an international standard by scientists and programmers representing major scientific facilities in Europe, Asia, Australia, and North America in order to facilitate greater cooperation in the analysis and visualization of neutron, x-ray, and muon data. The NeXus API provides a unified interface for writing hierarchical data files in HDF4, HDF5, and XML formats.

Northwestern University, IL
Uses HDF5 in the field of astrophysics.

Norwegian Defence Research Establishment
Using HDF5 with regards to radar.

NPL, India
Using HDF5 in Atmospheric dispersion modeling.

NPOESS
The National Polar-orbiting Operational Environmental Satellite System (NPOESS) is a satellite system used to monitor global environmental conditions, and collect and disseminate data related to: weather, atmosphere, oceans, land and near-space environment.

OpenMSI
Advanced visualization, analysis and management of mass spectrometry imaging data via the web.

Open Navigation Surface Working Group
The Open Navigation Surface Working Group has collaborated on the Bathymetric Attributed Grid data format, which relies on HDF5 for the underlying file structure. We also provide an API for interacting with this data, driven by the needs of the community. In the tradition of open source, the code base is openly available.

ORNL
Using HDF5 in magnetohydrodynamics.

Pacific Biosciences
Pacific Biosciences is a biotechnology company which produces third-generation DNA sequencing instruments. It uses HDF5 for raw data storage and provides conversion tools to extract the data into common bioinformatics formats.

Photon Research Associates, Inc.
A mission planning software application has been developed using HDF files to store all mission planning parameters. HDF was chosen because performance, storage precision, and portability were primary requirements. Mission planning scripts are developed on users' laptop computers (Windows/NT/95). The mission scripts are then uploaded to the aircraft-based control computer (Sun/Solaris). The mission planning application was developed to support the USAF Advanced Remote Earth Sensing (ARES) project. See

The R Project for Statistical Computing
See R.

Exelis Visual Information Solutions
Exelis Visual Information Solutions is a leading developer of data analysis and visualization software. Its flagship product is IDL (the Interactive Data Language), an advanced fourth-generation language used to build visualization applications for science, medical, financial, and engineering data analysis. RSI also markets ENVI (written in IDL), the industry-leading remote sensing software.

SMAP (Soil Moisture Active & Passive)
SMAP is one of four Tier-1 missions recommended by the U.S. National Research Council Committee on Earth Science and Applications from Space. It will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles and extend the capabilities of weather and climate prediction models. SMAP data will also be used to quantify net carbon flux in boreal landscapes and improve flood prediction and drought monitoring capabilities. SMAP Data Products are stored in the HDF5 format.

Southern California Earthquake Center
Using HDF5 in predictive earthquake simulations for seismic hazard analysis.

S J College o f Engineering, Mysore, India
Using HDF5 in Electrical & Electronics Engineering.

Sony Pictures Imageworks and Lucasfilm
The Alembic open computer graphics interchange framework, which uses HDF5, was co-developed by Sony Imageworks and Lucasfilm.

Supercomputing Center, Chinese Academy of Science
Using HDF5 in scientific visualization.

SSAI
SSAI is using HDF-EOS5 as the standard file format for SIPS on the Ozone Monitoring Instrument project.

Swedish Meteorilogical and Hydrological Institute
See HL-HDF5.

Technical University of Lisbon, Portugal
Uses MOHID, a three-dimensional water modelling system, developed at MARETEC (Marine and Environmental Technology Research Center) from the Technical Superior Institute (IST) which belongs to Technical University of Lisbon. The output from MOHID is stored in HDF files and can be analyzed with a post processor able to browse the HDF files.

UESC, Brazil
Using HDF5 in bioinformatics.

Unidata
The NetCDF-4 format from Unidata is stored using the HDF5 format.

The University of Alabama (Huntsville) ESIPFED project

University of Alabama, Information Technology and Systems Center (ITSC)
The ITSC uses HDF and HDF5 primarily in conjunction with HDF-EOS (v2 and v5). They have generated software for subsetting HDF-EOS (v2.x) datasets, and are working on a version for HDF-EOS-5.

University of Antioquia, Institute of Physics, Medellin, Colombia
The Computational Physics and Astrophysics group is using HDF5 in the field of Galactic Astronomy. They are doing N-body simulations to study the dynamics of stellar systems.

The University of California, Berkeley
The Chemistry Department at UC Berkeley has developed Zori, a quantum Monte Carlo program (soon-to-be-released as open source). It uses a combination of XML files and HDF5 for checkpoint/restart.

The University of California, Davis, Compact Torus Injection Experiment (CTIX)
CTIX studies basic plasma phenomena of the acceleration and formation of spheromak like compact toroids (CT or SCT). The HDF5 format is used for the experimental data.

The University of California, Los Angeles, Basic Plasma Science Facility
The HDF5 format was adopted by the Basic Plasma Science Facility at UCLA to store time-series data as well as diagnostic information about the twenty-meter experimental device.

As a national facility for basic plasma science research, multi-gigabyte datasets are routinely acquired by groups from around the country which dictates the use of a widely supported, portable, and scalable means to store and analyze data. HDF5 best fulfilled our requirements.

University of Sannio at Benevento, Italy
Using HDF4 and HDF5 in field of Electromagnetics, Gravitational Waves, and Remote Sensing:
  • We work extensively in applied electromagnetics (antennas, special and meta materials, scattering).
  • We work in gravitational wave detection experiments (e.g. LIGO), with special reference to data analysis.
  • We work on remote sensing (we have access to two direct-broadcast X-band and L-S band groundstations, in Salerno and Benevento).

Universite de Technologie Troyes, France
Using HDF5 in Scanning Near Field Optical Microscopy.

University of Washington
Using HDF5 in field of Upper Atmospheric/Ionospheric Physics

U.S. Environmental Protection Agency
Using MODIS data in HDF EOS5 for evaluating air quality model especially aerosol optical depth for the CONUS.


- - Last modified: 04 August 2014