The NetCDF Users Guide

The NetCDF Users Guide
The NetCDF Users Guide
Data Model, Programming Interfaces, and Format for Self-Describing, Portable Data
NetCDF Version 4.1.1
March 2010
Russ Rew, Glenn Davis, Steve Emmerson, Harvey Davies, Ed
Hartnett, and Dennis Heimbigner Unidata Program Center
c 2005-2009 University Corporation for Atmospheric Research
Copyright Permission is granted to make and distribute verbatim copies of this manual provided that
the copyright notice and these paragraphs are preserved on all copies. The software and any
accompanying written materials are provided “as is” without warranty of any kind. UCAR
expressly disclaims all warranties of any kind, either expressed or implied, including but not
limited to the implied warranties of merchantability and fitness for a particular purpose.
The Unidata Program Center is managed by the University Corporation for Atmospheric
Research and sponsored by the National Science Foundation. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and
do not necessarily reflect the views of the National Science Foundation.
Mention of any commercial company or product in this document does not constitute an
endorsement by the Unidata Program Center. Unidata does not authorize any use of
information from this publication for advertising or publicity purposes.
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Table of Contents
Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.1
1.2
1.3
1.4
The NetCDF Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
NetCDF Is Not a Database Management System . . . . . . . . . . . . . . . 5
The netCDF File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
How to Select the Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4.1 NetCDF Classic Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4.2 NetCDF 64-bit Offset Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4.3 NetCDF-4 Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.5 What about Performance?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6 Is NetCDF a Good Archive Format? . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.7 Creating Self-Describing Data conforming to Conventions . . . . . . . 8
1.8 Background and Evolution of the NetCDF Interface . . . . . . . . . . . . 9
1.9 What’s New Since the Previous Release? . . . . . . . . . . . . . . . . . . . . . . 12
1.10 Limitations of NetCDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.11 Plans for NetCDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.12 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2
Components of a NetCDF Dataset . . . . . . . . . . 17
2.1
The NetCDF Data Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.1.1 Expanded Model in NetCDF-4 Files . . . . . . . . . . . . . . . . . . . . . .
2.1.2 Naming Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.1.3 Network Common Data Form Language (CDL) . . . . . . . . . . .
2.2 Dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3 Variables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.1 Coordinate Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.4 Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.5 Differences between Attributes and Variables . . . . . . . . . . . . . . . . . .
3
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Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1
3.2
3.3
NetCDF External Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Data Structures in Classic and 64-bit Offset Files . . . . . . . . . . . . . .
NetCDF-4 User Defined Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3.1 Compound Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3.2 VLEN Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3.3 Opaque Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3.4 Enum Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3.5 Groups. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.4 Data Access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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3.4.1 Forms of Data Access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.4.2 A C Example of Array-Section Access . . . . . . . . . . . . . . . . . . . .
3.4.3 More on General Array Section Access for C . . . . . . . . . . . . . .
3.4.4 A Fortran Example of Array-Section Access . . . . . . . . . . . . . .
3.4.5 More on General Array Section Access for Fortran . . . . . . . .
3.5 Type Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4
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30
31
32
33
33
File Structure and Performance . . . . . . . . . . . . . . 35
4.1
4.2
4.3
4.4
4.5
4.6
4.7
4.8
4.9
Parts of a NetCDF Classic File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Parts of a NetCDF-4 HDF5 File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The Extended XDR Layer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Large File Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
NetCDF 64-bit Offset Format Limitations . . . . . . . . . . . . . . . . . . . . .
NetCDF Classic Format Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . .
The NetCDF-3 I/O Layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
UNICOS Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Improving Performance With Chunking . . . . . . . . . . . . . . . . . . . . . . .
4.9.1 The Chunk Cache . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.9.2 The Default Chunking Scheme in version 4.1 (and 4.1.1) . .
4.9.3 The Default Chunking Scheme in version 4.0.1 . . . . . . . . . . . .
4.9.4 Chunking and Parallel I/O . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.9.5 A Utility to Help Benchmark Results: bm file . . . . . . . . . . . .
4.10 Parallel Access with NetCDF-4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.11 Interoperability with HDF5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12 DAP Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.1 Accessing OPeNDAP Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2 DAP to NetCDF Translation Rules . . . . . . . . . . . . . . . . . . . . . .
4.12.2.1 netCDF-3 Translation Rules . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.2 Variable Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.3 Variable Dimension Translation. . . . . . . . . . . . . . . . . . . . .
4.12.2.4 Dimension translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.5 Variable Name Translation . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.6 Translating DAP DDS Sequences . . . . . . . . . . . . . . . . . . .
4.12.2.7 netCDF-4 Translation Rules . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.8 Variable Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.9 Dimension Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.10 Type Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.11 Choosing a Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.12 Caching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.2.13 Defined Client Parameters . . . . . . . . . . . . . . . . . . . . . . . . .
4.12.3 Notes on Debugging OPeNDAP Access . . . . . . . . . . . . . . . . . .
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57
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5
NetCDF Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.1
5.2
5.3
5.4
5.5
5.6
CDL Syntax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
CDL Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
CDL Notation for Data Constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ncgen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ncdump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ncgen3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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61
62
63
65
68
Appendix A
Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Appendix B
Attribute Conventions . . . . . . . . . . . 71
Appendix C
File Format Specification . . . . . . . . 75
C.1 The NetCDF Classic Format Specification . . . . . . . . . . . . . . . . . . . .
The Format in Detail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Notes on Computing File Offsets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.2 The 64-bit Offset Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3 The NetCDF-4 Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.1 Creation Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.2 Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.3 Dimensions with HDF5 Dimension Scales . . . . . . . . . . . . . . . .
C.3.4 Dimensions without HDF5 Dimension Scales . . . . . . . . . . . . .
C.3.5 Dimension and Coordinate Variable Ordering . . . . . . . . . . . .
C.3.6 Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.7 Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.8 User-Defined Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.9 Compression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.4 The NetCDF-4 Classic Model Format . . . . . . . . . . . . . . . . . . . . . . . . .
C.5 HDF4 SD Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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87
88
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Foreword
1
Foreword
Unidata (http://www.unidata.ucar.edu) is a National Science Foundation-sponsored program empowering U.S. universities, through innovative applications of computers and networks, to make the best use of atmospheric and related data for enhancing education and
research. For analyzing and displaying such data, the Unidata Program Center offers universities several supported software packages developed by other organizations. Underlying
these is a Unidata-developed system for acquiring and managing data in real time, making
practical the Unidata principle that each university should acquire and manage its own data
holdings as local requirements dictate. It is significant that the Unidata program has no
data center–the management of data is a "distributed" function.
The Network Common Data Form (netCDF) software described in this guide was originally intended to provide a common data access method for the various Unidata applications. These deal with a variety of data types that encompass single-point observations,
time series, regularly-spaced grids, and satellite or radar images.
The netCDF software functions as an I/O library, callable from C, FORTRAN, C++,
Perl, or other language for which a netCDF library is available. The library stores and
retrieves data in self-describing, machine-independent datasets. Each netCDF dataset can
contain multidimensional, named variables (with differing types that include integers, reals,
characters, bytes, etc.), and each variable may be accompanied by ancillary data, such as
units of measure or descriptive text. The interface includes a method for appending data
to existing netCDF datasets in prescribed ways, functionality that is not unlike a (fixed
length) record structure. However, the netCDF library also allows direct-access storage and
retrieval of data by variable name and index and therefore is useful only for disk-resident
(or memory-resident) datasets.
NetCDF access has been implemented in about half of Unidata’s software, so far, and it
is planned that such commonality will extend across all Unidata applications in order to:
• Facilitate the use of common datasets by distinct applications.
• Permit datasets to be transported between or shared by dissimilar computers transparently, i.e., without translation.
• Reduce the programming effort usually spent interpreting formats.
• Reduce errors arising from misinterpreting data and ancillary data.
• Facilitate using output from one application as input to another.
• Establish an interface standard which simplifies the inclusion of new software into the
Unidata system.
A measure of success has been achieved. NetCDF is now in use on computing platforms
that range from personal computers to supercomputers and include most UNIX-based workstations. It can be used to create a complex dataset on one computer (say in FORTRAN)
and retrieve that same self-describing dataset on another computer (say in C) without intermediate translations–netCDF datasets can be transferred across a network, or they can
be accessed remotely using a suitable network file system or remote access protocols.
Because we believe that the use of netCDF access in non-Unidata software will benefit Unidata’s primary constituency–such use may result in more options for analyzing
and displaying Unidata information–the netCDF library is distributed without licensing or
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The NetCDF Users’ Guide
other significant restrictions, and current versions can be obtained via anonymous FTP.
Apparently the software has been well received by a wide range of institutions beyond the
atmospheric science community, and a substantial number of public domain and commercial
data analysis systems can now accept netCDF datasets as input.
Several organizations have adopted netCDF as a data access standard, and there is an
effort underway at the National Center for Supercomputer Applications (NCSA, which is
associated with the University of Illinois at Urbana-Champaign) to support the netCDF
programming interfaces as a means to store and retrieve data in "HDF files," i.e., in the
format used by the popular NCSA tools. We have encouraged and cooperated with these
efforts.
Questions occasionally arise about the level of support provided for the netCDF software.
Unidata’s formal position, stated in the copyright notice which accompanies the netCDF
library, is that the software is provided "as is". In practice, the software is updated from
time to time, and Unidata intends to continue making improvements for the foreseeable
future. Because Unidata’s mission is to serve geoscientists at U.S. universities, problems
reported by that community necessarily receive the greatest attention.
We hope the reader will find the software useful and will give us feedback on its application as well as suggestions for its improvement.
David Fulker, 1996
Unidata Program Center Director, University Corporation for Atmospheric Research
Summary
3
Summary
The purpose of the Network Common Data Form (netCDF) interface is to allow you to
create, access, and share array-oriented data in a form that is self-describing and portable.
"Self-describing" means that a dataset includes information defining the data it contains.
"Portable" means that the data in a dataset is represented in a form that can be accessed by
computers with different ways of storing integers, characters, and floating-point numbers.
Using the netCDF interface for creating new datasets makes the data portable. Using the
netCDF interface in software for data access, management, analysis, and display can make
the software more generally useful.
The netCDF software includes C, Fortran 77, Fortran 90, and C++ interfaces for accessing
netCDF data. These libraries are available for many common computing platforms.
The community of netCDF users has contributed ports of the software to additional
platforms and interfaces for other programming languages as well. Source code for netCDF
software libraries is freely available to encourage the sharing of both array-oriented data
and the software that makes the data useful.
This User’s Guide presents the netCDF data model. It explains how the netCDF data
model uses dimensions, variables, and attributes to store data. Language specific programming guides are available for C (see Section “Top” in The NetCDF C Interface Guide), C++
(see Section “Top” in The NetCDF C++ Interface Guide), Fortran 77 (see Section “Top”
in The NetCDF Fortran 77 Interface Guide), and Fortran 90 (see Section “Top” in The
NetCDF Fortran 90 Interface Guide).
Reference documentation for UNIX systems, in the form of UNIX ’man’ pages
for the C and FORTRAN interfaces is also available at the netCDF web site
(http://www.unidata.ucar.edu/netcdf), and with the netCDF distribution.
The latest version of this document, and the language specific guides, can be found at
the netCDF web site, http://www.unidata.ucar.edu/netcdf/docs, along with extensive
additional information about netCDF, including pointers to other software that works with
netCDF data.
Separate documentation of the Java netCDF library can be found at
http://www.unidata.ucar.edu/software/netcdf-java.
For installation and porting information See Section “Top” in The NetCDF Installation
and Porting Guide.
Chapter 1: Introduction
5
1 Introduction
1.1 The NetCDF Interface
The Network Common Data Form, or netCDF, is an interface to a library of data access
functions for storing and retrieving data in the form of arrays. An array is an n-dimensional
(where n is 0, 1, 2, . . . ) rectangular structure containing items which all have the same data
type (e.g., 8-bit character, 32-bit integer). A scalar (simple single value) is a 0-dimensional
array.
NetCDF is an abstraction that supports a view of data as a collection of self-describing,
portable objects that can be accessed through a simple interface. Array values may be
accessed directly, without knowing details of how the data are stored. Auxiliary information
about the data, such as what units are used, may be stored with the data. Generic utilities
and application programs can access netCDF datasets and transform, combine, analyze,
or display specified fields of the data. The development of such applications has led to
improved accessibility of data and improved re-usability of software for array-oriented data
management, analysis, and display.
The netCDF software implements an abstract data type, which means that all operations
to access and manipulate data in a netCDF dataset must use only the set of functions
provided by the interface. The representation of the data is hidden from applications that
use the interface, so that how the data are stored could be changed without affecting existing
programs. The physical representation of netCDF data is designed to be independent of
the computer on which the data were written.
Unidata supports the netCDF interfaces for C, (see Section “Top” in The NetCDF C
Interface Guide), FORTRAN 77 (see Section “Top” in The NetCDF Fortran 77 Interface
Guide), FORTRAN 90 (see Section “Top” in The NetCDF Fortran 90 Interface Guide),
and C++ (see Section “Top” in The NetCDF C++ Interface Guide).
The netCDF library is supported for various UNIX operating systems. A MS Windows
port is also available. The software is also ported and tested on a few other operating
systems, with assistance from users with access to these systems, before each major release.
Unidata’s netCDF software is freely available via FTP to encourage its widespread use.
(ftp://ftp.unidata.ucar.edu/pub/netcdf).
For detailed installation instructions, see the Porting and Installation Guide. See Section
“Top” in The NetCDF Installation and Porting Guide.
1.2 NetCDF Is Not a Database Management System
Why not use an existing database management system for storing array-oriented data?
Relational database software is not suitable for the kinds of data access supported by the
netCDF interface.
First, existing database systems that support the relational model do not support multidimensional objects (arrays) as a basic unit of data access. Representing arrays as relations
makes some useful kinds of data access awkward and provides little support for the abstractions of multidimensional data and coordinate systems. A quite different data model
is needed for array-oriented data to facilitate its retrieval, modification, mathematical manipulation and visualization.
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The NetCDF Users’ Guide
Related to this is a second problem with general-purpose database systems: their poor
performance on large arrays. Collections of satellite images, scientific model outputs and
long-term global weather observations are beyond the capabilities of most database systems
to organize and index for efficient retrieval.
Finally, general-purpose database systems provide, at significant cost in terms of both
resources and access performance, many facilities that are not needed in the analysis, management, and display of array-oriented data. For example, elaborate update facilities, audit
trails, report formatting, and mechanisms designed for transaction-processing are unnecessary for most scientific applications.
1.3 The netCDF File Format
Until version 3.6.0, all versions of netCDF employed only one binary data format, now
referred to as netCDF classic format. NetCDF classic is the default format for all versions
of netCDF.
In version 3.6.0 a new binary format was introduced, 64-bit offset format. Nearly identical to netCDF classic format, it uses 64-bit offsets (hence the name), and allows users to
create far larger datasets.
In version 4.0.0 a third binary format was introduced: the HDF5 format. Starting with
this version, the netCDF library can use HDF5 files as its base format. (Only HDF5 files
created with netCDF-4 can be understood by netCDF-4).
By default, netCDF uses the classic format. To use the 64-bit offset or netCDF-4/HDF5
format, set the appropriate constant when creating the file.
To achieve network-transparency (machine-independence), netCDF classic and 64-bit
offset formats are implemented in terms of an external representation much like XDR (eXternal Data Representation, see http://www.ietf.org/rfc/rfc1832.txt), a standard for
describing and encoding data. This representation provides encoding of data into machineindependent sequences of bits. It has been implemented on a wide variety of computers, by
assuming only that eight-bit bytes can be encoded and decoded in a consistent way. The
IEEE 754 floating-point standard is used for floating-point data representation.
Descriptions of the overall structure of netCDF classic and 64-bit offset files are provided
later in this manual. See Chapter 4 [Structure], page 35.
The details of the classic and 64-bit offset formats are described in an appendix. See
Appendix C [File Format], page 75. However, users are discouraged from using the format
specification to develop independent low-level software for reading and writing netCDF files,
because this could lead to compatibility problems if the format is ever modified.
1.4 How to Select the Format
With three different base formats, care must be taken in creating data files to choose the
correct base format.
The format of a netCDF file is determined at create time.
When opening an existing netCDF file the netCDF library will transparently detect
its format and adjust accordingly. However, netCDF library versions earlier than 3.6.0
Chapter 1: Introduction
7
cannot read 64-bit offset format files, and library versions before 4.0 can’t read netCDF4/HDF5 files. NetCDF classic format files (even if created by version 3.6.0 or later) remain
compatible with older versions of the netCDF library.
Users are encouraged to use netCDF classic format to distribute data, for maximum
portability.
To select 64-bit offset or netCDF-4 format files, C programmers should use flag
NC 64BIT OFFSET or NC NETCDF4 in function nc create. See Section “nc create” in
The NetCDF C Interface Guide.
In Fortran, use flag nf 64bit offset or nf format netcdf4 in function NF CREATE. See
Section “NF CREATE” in The NetCDF Fortran 77 Interface Guide.
It is also possible to change the default creation format, to convert a large
body of code without changing every create call.
C programmers see Section
“nc set default format” in The NetCDF C Interface Guide. Fortran programs see Section
“NF SET DEFAULT FORMAT” in The NetCDF Fortran 77 Interface Guide.
1.4.1 NetCDF Classic Format
The original netCDF format is identified using four bytes in the file header. All files in this
format have “CDF\001” at the beginning of the file. In this documentation this format is
referred to as “netCDF classic format.”
NetCDF classic format is identical to the format used by every previous version of
netCDF. It has maximum portability, and is still the default netCDF format.
For some users, the various 2 GiB format limitations of the classic format become a
problem. (see Section 4.6 [Classic Limitations], page 38).
1.4.2 NetCDF 64-bit Offset Format
For these users, 64-bit offset format is a natural choice. It greatly eases the size restrictions
of netCDF classic files (see Section 4.5 [64 bit Offset Limitations], page 38).
Files with the 64-bit offsets are identified with a “CDF\002” at the beginning of the file.
In this documentation this format is called “64-bit offset format.”
Since 64-bit offset format was introduced in version 3.6.0, earlier versions of the netCDF
library can’t read 64-bit offset files.
1.4.3 NetCDF-4 Format
In version 4.0, netCDF included another new underlying format: HDF5.
NetCDF-4 format files offer new features such as groups, compound types, variable length
arrays, new unsigned integer types, parallel I/O access, etc. None of these new features can
be used with classic or 64-bit offset files.
NetCDF-4 files can’t be created at all, unless the netCDF configure script is run with
–enable-netcdf-4. This also requires version 1.8.0 of HDF5.
For the netCDF-4.0 release, netCDF-4 features are only available from the C and Fortran
interfaces. We plan to bring netCDF-4 features to the CXX API in a future release of
netCDF.
NetCDF-4 files can’t be read by any version of the netCDF library previous to 4.0. (But
they can be read by HDF5, version 1.8.0 or better).
For more discussion of format issues see Section “Versions” in The NetCDF Tutorial.
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The NetCDF Users’ Guide
1.5 What about Performance?
One of the goals of netCDF is to support efficient access to small subsets of large datasets.
To support this goal, netCDF uses direct access rather than sequential access. This can
be much more efficient when the order in which data is read is different from the order in
which it was written, or when it must be read in different orders for different applications.
The amount of overhead for a portable external representation depends on many factors,
including the data type, the type of computer, the granularity of data access, and how well
the implementation has been tuned to the computer on which it is run. This overhead is
typically small in comparison to the overall resources used by an application. In any case,
the overhead of the external representation layer is usually a reasonable price to pay for
portable data access.
Although efficiency of data access has been an important concern in designing and implementing netCDF, it is still possible to use the netCDF interface to access data in inefficient
ways: for example, by requesting a slice of data that requires a single value from each
record. Advice on how to use the interface efficiently is provided in Chapter 4 [Structure],
page 35.
The use of HDF5 as a data format adds significant overhead in metadata operations,
less so in data access operations. We continue to study the challenge of implementing
netCDF-4/HDF5 format without compromising performance.
1.6 Is NetCDF a Good Archive Format?
NetCDF classic or 64-bit offset formats can be used as a general-purpose archive format for
storing arrays. Compression of data is possible with netCDF (e.g., using arrays of eightbit or 16-bit integers to encode low-resolution floating-point numbers instead of arrays of
32-bit numbers), or the resulting data file may be compressed before storage (but must be
uncompressed before it is read). Hence, using these netCDF formats may require more space
than special-purpose archive formats that exploit knowledge of particular characteristics of
specific datasets.
With netCDF-4/HDF5 format, the zlib library can provide compression on a per-variable
basis. That is, some variables may be compressed, others not. In this case the compression
and decompression of data happen transparently to the user, and the data may be stored,
read, and written compressed.
1.7 Creating Self-Describing Data conforming to
Conventions
The mere use of netCDF is not sufficient to make data "self-describing" and meaningful to
both humans and machines. The names of variables and dimensions should be meaningful
and conform to any relevant conventions. Dimensions should have corresponding coordinate
variables where sensible.
Attributes play a vital role in providing ancillary information. It is important to use all
the relevant standard attributes using the relevant conventions. For a description of reserved
attributes (used by the netCDF library) and attribute conventions for generic application
software, see Appendix B [Attribute Conventions], page 71.
Chapter 1: Introduction
9
A number of groups have defined their own additional conventions and
styles for netCDF data.
Descriptions of these conventions, as well as examples incorporating them can be accessed from the netCDF Conventions site,
http://www.unidata.ucar.edu/netcdf/conventions.html.
These conventions should be used where suitable. Additional conventions are often
needed for local use. These should be contributed to the above netCDF conventions site if
likely to interest other users in similar areas.
1.8 Background and Evolution of the NetCDF Interface
The development of the netCDF interface began with a modest goal related to Unidata’s
needs: to provide a common interface between Unidata applications and real-time meteorological data. Since Unidata software was intended to run on multiple hardware platforms
with access from both C and FORTRAN, achieving Unidata’s goals had the potential for
providing a package that was useful in a broader context. By making the package widely
available and collaborating with other organizations with similar needs, we hoped to improve the then current situation in which software for scientific data access was only rarely
reused by others in the same discipline and almost never reused between disciplines (Fulker,
1988).
Important concepts employed in the netCDF software originated in a paper (Treinish
and Gough, 1987) that described data-access software developed at the NASA Goddard
National Space Science Data Center (NSSDC). The interface provided by this software was
called the Common Data Format (CDF). The NASA CDF was originally developed as a
platform-specific FORTRAN library to support an abstraction for storing arrays.
The NASA CDF package had been used for many different kinds of data in an extensive
collection of applications. It had the virtues of simplicity (only 13 subroutines), independence from storage format, generality, ability to support logical user views of data, and
support for generic applications.
Unidata held a workshop on CDF in Boulder in August 1987. We proposed exploring
the possibility of collaborating with NASA to extend the CDF FORTRAN interface, to
define a C interface, and to permit the access of data aggregates with a single call, while
maintaining compatibility with the existing NASA interface.
Independently, Dave Raymond at the New Mexico Institute of Mining and Technology had developed a package of C software for UNIX that supported sequential access to
self-describing array-oriented data and a "pipes and filters" (or "data flow") approach to
processing, analyzing, and displaying the data. This package also used the "Common Data
Format" name, later changed to C-Based Analysis and Display System (CANDIS). Unidata
learned of Raymond’s work (Raymond, 1988), and incorporated some of his ideas, such as
the use of named dimensions and variables with differing shapes in a single data object,
into the Unidata netCDF interface.
In early 1988, Glenn Davis of Unidata developed a prototype netCDF package in C that
was layered on XDR. This prototype proved that a single-file, XDR-based implementation
of the CDF interface could be achieved at acceptable cost and that the resulting programs
could be implemented on both UNIX and VMS systems. However, it also demonstrated
that providing a small, portable, and NASA CDF-compatible FORTRAN interface with
10
The NetCDF Users’ Guide
the desired generality was not practical. NASA’s CDF and Unidata’s netCDF have since
evolved separately, but recent CDF versions share many characteristics with netCDF.
In early 1988, Joe Fahle of SeaSpace, Inc. (a commercial software development firm in
San Diego, California), a participant in the 1987 Unidata CDF workshop, independently
developed a CDF package in C that extended the NASA CDF interface in several important
ways (Fahle, 1989). Like Raymond’s package, the SeaSpace CDF software permitted variables with unrelated shapes to be included in the same data object and permitted a general
form of access to multidimensional arrays. Fahle’s implementation was used at SeaSpace
as the intermediate form of storage for a variety of steps in their image-processing system.
This interface and format have subsequently evolved into the Terascan data format.
After studying Fahle’s interface, we concluded that it solved many of the problems we
had identified in trying to stretch the NASA interface to our purposes. In August 1988, we
convened a small workshop to agree on a Unidata netCDF interface, and to resolve remaining
open issues. Attending were Joe Fahle of SeaSpace, Michael Gough of Apple (an author
of the NASA CDF software), Angel Li of the University of Miami (who had implemented
our prototype netCDF software on VMS and was a potential user), and Unidata systems
development staff. Consensus was reached at the workshop after some further simplifications
were discovered. A document incorporating the results of the workshop into a proposed
Unidata netCDF interface specification was distributed widely for comments before Glenn
Davis and Russ Rew implemented the first version of the software. Comparison with other
data-access interfaces and experience using netCDF are discussed in Rew and Davis (1990a),
Rew and Davis (1990b), Jenter and Signell (1992), and Brown, Folk, Goucher, and Rew
(1993).
In October 1991, we announced version 2.0 of the netCDF software distribution. Slight
modifications to the C interface (declaring dimension lengths to be long rather than int)
improved the usability of netCDF on inexpensive platforms such as MS-DOS computers,
without requiring recompilation on other platforms. This change to the interface required
no changes to the associated file format.
Release of netCDF version 2.3 in June 1993 preserved the same file format but added single call access to records, optimizations for accessing cross-sections involving non-contiguous
data, subsampling along specified dimensions (using ’strides’), accessing non-contiguous
data (using ’mapped array sections’), improvements to the ncdump and ncgen utilities, and
an experimental C++ interface.
In version 2.4, released in February 1996, support was added for new platforms and for
the C++ interface, significant optimizations were implemented for supercomputer architectures, and the file format was formally specified in an appendix to the User’s Guide.
FAN (File Array Notation), software providing a high-level interface to netCDF data,
was made available in May 1996. The capabilities of the FAN utilities include extracting
and manipulating array data from netCDF datasets, printing selected data from netCDF
arrays, copying ASCII data into netCDF arrays, and performing various operations (sum,
mean, max, min, product, and others) on netCDF arrays.
In 1996 and 1997, Joe Sirott implemented and made available the first implementation
of a read-only netCDF interface for Java, Bill Noon made a Python module available for
netCDF, and Konrad Hinsen contributed another netCDF interface for Python.
Chapter 1: Introduction
11
In May 1997, Version 3.3 of netCDF was released. This included a new type-safe interface
for C and Fortran, as well as many other improvements. A month later, Charlie Zender
released version 1.0 of the NCO (netCDF Operators) package, providing command-line
utilities for general purpose operations on netCDF data.
Version 3.4 of Unidata’s netCDF software, released in March 1998, included initial large
file support, performance enhancements, and improved Cray platform support. Later in
1998, Dan Schmitt provided a Tcl/Tk interface, and Glenn Davis provided version 1.0 of
netCDF for Java.
In May 1999, Glenn Davis, who was instrumental in creating and developing netCDF,
died in a small plane crash during a thunderstorm. The memory of Glenn’s passions and
intellect continue to inspire those of us who worked with him.
In February 2000, an experimental Fortran 90 interface developed by Robert Pincus was
released.
John Caron released netCDF for Java, version 2.0 in February 2001. This version incorporated a new high-performance package for multidimensional arrays, simplified the
interface, and included OpenDAP (known previously as DODS) remote access, as well as
remote netCDF access via HTTP contributed by Don Denbo.
In March 2001, NetCDF 3.5.0 was released. This release fully integrated the new Fortran
90 interface, enhanced portability, improved the C++ interface, and added a few new tuning
functions.
Also in 2001, Takeshi Horinouchi and colleagues made a netCDF interface for Ruby
available, as did David Pierce for the R language for statistical computing and graphics.
Charles Denham released WetCDF, an independent implementation of the netCDF interface
for Matlab, as well as updates to the popular netCDF Toolbox for Matlab.
In 2002, Unidata and collaborators developed NcML, an XML representation for netCDF
data useful for cataloging data holdings, aggregation of data from multiple datasets, augmenting metadata in existing datasets, and support for alternative views of data. The Java
interface currently provides access to netCDF data through NcML.
Additional developments in 2002 included translation of C and Fortran User Guides
into Japanese by Masato Shiotani and colleagues, creation of a “Best Practices” guide for
writing netCDF files, and provision of an Ada-95 interface by Alexandru Corlan.
In July 2003 a group of researchers at Northwestern University and Argonne National
Laboratory (Jianwei Li, Wei-keng Liao, Alok Choudhary, Robert Ross, Rajeev Thakur,
William Gropp, and Rob Latham) contributed a new parallel interface for writing and
reading netCDF data, tailored for use on high performance platforms with parallel I/O. The
implementation built on the MPI-IO interface, providing portability to many platforms.
In October 2003, Greg Sjaardema contributed support for an alternative format with
64-bit offsets, to provide more complete support for very large files. These changes, with
slight modifications at Unidata, were incorporated into version 3.6.0, released in December,
2004.
In 2004, thanks to a NASA grant, Unidata and NCSA began a collaboration to increase
the interoperability of netCDF and HDF5, and bring some advanced HDF5 features to
netCDF users.
In February, 2006, release 3.6.1 fixed some minor bugs.
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The NetCDF Users’ Guide
In March, 2007, release 3.6.2 introduced an improved build system that used automake
and libtool, and an upgrade to the most recent autoconf release, to support shared libraries
and the netcdf-4 builds. This release also introduced the NetCDF Tutorial and example
programs.
The first beta release of netCDF-4.0 was celebrated with a giant party at Unidata in
April, 2007. Over 2000 people danced ’til dawn at the NCAR Mesa Lab, listening to the
Flaming Lips and the Denver Gilbert & Sullivan repertory company.
In June, 2008, netCDF-4.0 was released. Version 3.6.3, the same code but with netcdf-4
features turned off, was released at the same time. The 4.0 release uses HDF5 1.8.1 as the
data storage layer for netcdf, and introduces many new features including groups and userdefined types. The 3.6.3/4.0 releases also introduced handling of UTF8-encoded Unicode
names.
1.9 What’s New Since the Previous Release?
This Guide documents the 4.1.1 release of netCDF, which introduces a new storage format,
netCDF-4/HDF5, while maintaining full backward compatibility.
New features available with netCDF-4/HDF5 files include:
• The use of groups to organize datasets.
• New unsigned integer data types, 64-bit integer types, and a string type.
• A user defined compound type, which can be constructed by users to match a C struct
or other arbitrary organization of types.
• A variable length array type.
• Multiple unlimited dimensions.
• Support for parallel I/O.
More information about netCDF-4 can be found at the netCDF web page
http://www.unidata.ucar.edu/netcdf/netcdf-4.
1.10 Limitations of NetCDF
The netCDF data model is widely applicable to data that can be organized into a collection
of named array variables with named attributes, but there are some important limitations
to the model and its implementation in software. Some of these limitations have been
removed or relaxed in netCDF-4 files, but still apply to netCDF classic and netCDF 64-bit
offset files.
Currently, netCDF classic and 64-bit offset formats offer a limited number of external
numeric data types: 8-, 16-, 32-bit integers, or 32- or 64-bit floating-point numbers. (The
netCDF-4 format adds 64-bit integer types and unsigned integer types.) This limited set
of sizes may use file space inefficiently compared to packing data in bit fields. For example,
arrays of 9-bit values must be stored in 16-bit short integers. Storing arrays of 1- or 2-bit
values in 8-bit values is even less optimal.
With the netCDF-4/HDF5 format, new unsigned integers (of various sizes), 64-bit integers, and the string type allow greater expression of scientific data. The new VLEN and
COMPOUND types allow users to organize data in new ways.
Chapter 1: Introduction
13
With the classic netCDF file format, there are constraints that limit how a dataset is
structured to store more than 2 GiBytes (2^30 or 1,073,741,824 bytes, as compared to a
Gbyte, which is 1,000,000,000 bytes.) of data in a single netCDF dataset. (see Section 4.6
[Classic Limitations], page 38). This limitation is a result of 32-bit offsets used for storing
relative offsets within a classic netCDF format file. Since one of the goals of netCDF is
portable data and some computing platforms still can’t deal with files larger than 2 GiB,
it is best to keep files that must be portable below this limit. Nevertheless, it is possible
to create and access netCDF files larger than 2 GiB on platforms that provide support for
such files (see Section 4.4 [Large File Support], page 37).
The new 64-bit offset format allows large files, and makes it easy to create to create fixed
variables of about 4 GiB, and record variables of about 4 GiB per record. (see Section 4.5
[64 bit Offset Limitations], page 38). However, old netCDF applications will not be able to
read the 64-bit offset files until they are upgraded to at least version 3.6.0 of netCDF (i.e.
the version in which 64-bit offset format was introduced).
With the netCDF-4/HDF5 format size limitations are further relaxed, and files can be
as large as the underlying file system supports. NetCDF-4/HDF5 files are unreadable to
the netCDF library before version 4.0.
Another limitation of the classic (and 64-bit offset) model is that only one unlimited
(changeable) dimension is permitted for each netCDF data set. Multiple variables can share
an unlimited dimension, but then they must all grow together. Hence the classic netCDF
model does not permit variables with several unlimited dimensions or the use of multiple
unlimited dimensions in different variables within the same dataset. Variables that have
non-rectangular shapes (for example, ragged arrays) cannot be represented conveniently.
In netCDF-4/HDF5 files, multiple unlimited dimensions are fully supported. Any variable can be defined with any combination of limited and unlimited dimensions.
The extent to which data can be completely self-describing is limited: there is always
some assumed context without which sharing and archiving data would be impractical.
NetCDF permits storing meaningful names for variables, dimensions, and attributes; units
of measure in a form that can be used in computations; text strings for attribute values that
apply to an entire data set; and simple kinds of coordinate system information. But for
more complex kinds of metadata (for example, the information necessary to provide accurate
georeferencing of data on unusual grids or from satellite images), it is often necessary to
develop conventions.
Specific additions to the netCDF data model might make some of these conventions
unnecessary or allow some forms of metadata to be represented in a uniform and compact
way. For example, adding explicit georeferencing to the netCDF data model would simplify
elaborate georeferencing conventions at the cost of complicating the model. The problem
is finding an appropriate trade-off between the richness of the model and its generality
(i.e., its ability to encompass many kinds of data). A data model tailored to capture the
shared context among researchers within one discipline may not be appropriate for sharing
or combining data from multiple disciplines.
The classic netCDF data model does not support nested data structures such as trees,
nested arrays, or other recursive structures. (This limitation also applies to 64-bit offset
files.) Through use of indirection and conventions it is possible to represent some kinds of
nested structures, but the result may fall short of the netCDF goal of self-describing data.
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The NetCDF Users’ Guide
In netCDF-4/HDF5 format files, the introduction of the compound type allows the
creation of complex data types, involving any combination of types. The VLEN type allows
efficient storage of ragged arrays, and the introduction of hierarchical groups allows users
to organize data.
Finally, for classic and 64-bit offset files, concurrent access to a netCDF dataset is limited.
One writer and multiple readers may access data in a single dataset simultaneously, but
there is no support for multiple concurrent writers.
NetCDF-4 supports parallel read/write access to netCDF-4/HDF5 files, using the underlying HDF5 library and parallel read/write access to classic and 64-bit offset files using
the parallel-netcdf library.
For more information about HDF5, see the HDF5 web site: http://hdfgroup.org/HDF5/.
For more information about parallel-netcdf, see their web site: http://www.mcs.anl.gov/parallel-netcdf
1.11 Plans for NetCDF
Future versions of NetCDF will include the following features:
1. Extensions of netCDF-4 features to C++ API and to tools ncgen/ncdump.
2. Better documentation and more examples.
1.12 References
1. Brown, S. A, M. Folk, G. Goucher, and R. Rew, "Software for Portable Scientific Data
Management," Computers in Physics, American Institute of Physics, Vol. 7, No. 3,
May/June 1993.
2. Davies, H. L., "FAN - An array-oriented query language," Second Workshop on Database Issues for Data Visualization (Visualization 1995), Atlanta, Georgia, IEEE, October 1995.
3. Fahle, J., TeraScan Applications Programming Interface, SeaSpace, San Diego, California, 1989.
4. Fulker, D. W., "The netCDF: Self-Describing, Portable Files—a Basis for
’Plug-Compatible’ Software Modules Connectable by Networks," ICSU Workshop on
Geophysical Informatics, Moscow, USSR, August 1988.
5. Fulker, D. W., "Unidata Strawman for Storing Earth-Referencing Data," Seventh International Conference on Interactive Information and Processing Systems for Meteorology, Oceanography, and Hydrology, New Orleans, La., American Meteorology Society,
January 1991.
6. Gough, M. L., NSSDC CDF Implementer’s Guide (DEC VAX/VMS) Version 1.1, National Space Science Data Center, 88-17, NASA/Goddard Space Flight Center, 1988.
7. Jenter, H. L. and R. P. Signell, "NetCDF: A Freely-Available Software-Solution to
Data-Access Problems for Numerical Modelers," Proceedings of the American Society
of Civil Engineers Conference on Estuarine and Coastal Modeling, Tampa, Florida,
1992.
8. Raymond, D. J., "A C Language-Based Modular System for Analyzing and Displaying
Gridded Numerical Data," Journal of Atmospheric and Oceanic Technology, 5, 501-511,
1988.
Chapter 1: Introduction
15
9. Rew, R. K. and G. P. Davis, "The Unidata netCDF: Software for Scientific Data Access," Sixth International Conference on Interactive Information and Processing Systems for Meteorology, Oceanography, and Hydrology, Anaheim, California, American
Meteorology Society, February 1990.
10. Rew, R. K. and G. P. Davis, "NetCDF: An Interface for Scientific Data Access,"
Computer Graphics and Applications, IEEE, pp. 76-82, July 1990.
11. Rew, R. K. and G. P. Davis, "Unidata’s netCDF Interface for Data Access: Status
and Plans," Thirteenth International Conference on Interactive Information and Processing Systems for Meteorology, Oceanography, and Hydrology, Anaheim, California,
American Meteorology Society, February 1997.
12. Treinish, L. A. and M. L. Gough, "A Software Package for the Data Independent
Management of Multi-Dimensional Data," EOS Transactions, American Geophysical
Union, 68, 633-635, 1987.
Chapter 2: Components of a NetCDF Dataset
17
2 Components of a NetCDF Dataset
2.1 The NetCDF Data Model
A netCDF dataset contains dimensions, variables, and attributes, which all have both a
name and an ID number by which they are identified. These components can be used
together to capture the meaning of data and relations among data fields in an array-oriented
dataset. The netCDF library allows simultaneous access to multiple netCDF datasets which
are identified by dataset ID numbers, in addition to ordinary file names.
2.1.1 Expanded Model in NetCDF-4 Files
Files created with the netCDF-4 format have access to an expanded data model, which
includes named groups. Groups, like directories in a Unix file system, are hierarchically
organized, to arbitrary depth. They can be used to organize large numbers of variables.
Each group acts as an entire netCDF dataset in the classic model. That is, each group
may have attributes, dimensions, and variables, as well as other groups.
The default root is the root group, which allows the classic netCDF data model to fit
neatly into the new model.
Dimensions are scoped such that they can be seen in all descendant groups. That is,
dimensions can be shared between variables in different groups, if they are defined in a
parent group.
In netCDF-4 files, the user may also define a type. For example a compound type may
hold information from an array of C structures, or a variable length array allows the user
to read and write arrays of variable length arrays.
Variables, groups, and types share a namespace. Within the same group, a variable,
groups, and types must have unique names. (That is, a type and variable may not have the
same name within the same group, and similarly for sub-groups of that group.)
Groups and user defined types are only available in files created in the NetCDF-4/HDF5
format. They are not available for classic or 64-bit offset format files.
2.1.2 Naming Conventions
The names of dimensions, variables and attributes (and, in netCDF-4 files, groups, userdefined types, compound member names, and enumeration symbols) consist of arbitrary
sequences of alphanumeric characters, underscore ’ ’, period ’.’, plus ’+’, hyphen ’-’, or at
sign ’@’, but beginning with a letter or underscore. However names commencing with underscore are reserved for system use. Case is significant in netCDF names. A zero-length
name is not allowed. Some widely used conventions restrict names to only alphanumeric
characters or underscores. Beginning with versions 3.6.3 and 4.0, names may also include
UTF-8 encoded Unicode characters as well as other special characters, except for the character ’/’, which may not appear in a name. Names that have trailing space characters are
also not permitted.
2.1.3 Network Common Data Form Language (CDL)
We will use a small netCDF example to illustrate the concepts of the netCDF data model.
This includes dimensions, variables, and attributes. The notation used to describe this simple netCDF object is called CDL (network Common Data form Language), which provides
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The NetCDF Users’ Guide
a convenient way of describing netCDF datasets. The netCDF system includes the ncdump
utility for producing human-oriented CDL text files from binary netCDF datasets and vice
versa. (The ncdump utility has recently been enhanced to accommodate netCDF-4 features
in the CDL output, but the example here is restricted to netCDF-3 CDL.)
netcdf example_1 {
// example of CDL notation for a netCDF dataset
dimensions:
// dimension names and lengths are declared first
lat = 5, lon = 10, level = 4, time = unlimited;
variables:
float
// variable types, names, shapes, attributes
temp(time,level,lat,lon);
temp:long_name
= "temperature";
temp:units
= "celsius";
float
rh(time,lat,lon);
rh:long_name = "relative humidity";
rh:valid_range = 0.0, 1.0;
// min and max
int
lat(lat), lon(lon), level(level);
lat:units
= "degrees_north";
lon:units
= "degrees_east";
level:units
= "millibars";
short
time(time);
time:units
= "hours since 1996-1-1";
// global attributes
:source = "Fictional Model Output";
data:
level
lat
lon
time
rh
// optional data assignments
= 1000, 850, 700, 500;
= 20, 30, 40, 50, 60;
= -160,-140,-118,-96,-84,-52,-45,-35,-25,-15;
= 12;
=.5,.2,.4,.2,.3,.2,.4,.5,.6,.7,
.1,.3,.1,.1,.1,.1,.5,.7,.8,.8,
.1,.2,.2,.2,.2,.5,.7,.8,.9,.9,
.1,.2,.3,.3,.3,.3,.7,.8,.9,.9,
0,.1,.2,.4,.4,.4,.4,.7,.9,.9;
}
The CDL notation for a netCDF dataset can be generated automatically by using ncdump, a utility program described later (see Section 5.5 [ncdump], page 65). Another
netCDF utility, ncgen, generates a netCDF dataset (or optionally C or FORTRAN source
code containing calls needed to produce a netCDF dataset) from CDL input (see Section 5.4
[ncgen], page 63). This version of ncgen can produce netcdf-3 or netcdf-4 files and can utilize CDL input that includes the netcdf-4 data model constructs. The older ncgen program
is still available under the name ncgen3.
The CDL notation is simple and largely self-explanatory. It will be explained more fully
as we describe the components of a netCDF dataset. For now, note that CDL statements
are terminated by a semicolon. Spaces, tabs, and newlines can be used freely for readability.
Chapter 2: Components of a NetCDF Dataset
19
Comments in CDL follow the characters ’//’ on any line. A CDL description of a netCDF
dataset takes the form
netCDF name {
types: [netcdf-4 only]
dimensions: ...
variables: ...
data: ...
}
where the name is used only as a default in constructing file names by the ncgen utility.
The CDL description consists of three optional parts, introduced by the keywords dimensions, variables, and data. NetCDF dimension declarations appear after the dimensions
keyword, netCDF variables and attributes are defined after the variables keyword, and
variable data assignments appear after the data keyword.
The ncgen utility provides a command line option which indicates the desired output
format. Limitations are enforced for the selected format - that is, some CDL files may be
expressible only in 64-bit offset or NetCDF-4 format.
For example, trying to create a file with very large variables in classic format may result
in an error because size limits are violated.
2.2 Dimensions
A dimension may be used to represent a real physical dimension, for example, time, latitude,
longitude, or height. A dimension might also be used to index other quantities, for example
station or model-run-number.
A netCDF dimension has both a name and a length.
A dimension length is an arbitrary positive integer, except that one dimension in a classic
or 64-bit offset netCDF dataset can have the length UNLIMITED. In a netCDF-4 dataset,
any number of unlimited dimensions can be used.
Such a dimension is called the unlimited dimension or the record dimension. A variable
with an unlimited dimension can grow to any length along that dimension. The unlimited
dimension index is like a record number in conventional record-oriented files.
A netCDF classic or 64-bit offset dataset can have at most one unlimited dimension, but
need not have any. If a variable has an unlimited dimension, that dimension must be the
most significant (slowest changing) one. Thus any unlimited dimension must be the first
dimension in a CDL shape and the first dimension in corresponding C array declarations.
A netCDF-4 dataset may have multiple unlimited dimensions, and there are no restrictions on their order in the list of a variables dimensions.
To grow variables along an unlimited dimension, write the data using any of the netCDF
data writing functions, and specify the index of the unlimited dimension to the desired
record number. The netCDF library will write however many records are needed (using the
fill value, unless that feature is turned off, to fill in any intervening records).
CDL dimension declarations may appear on one or more lines following the CDL keyword
dimensions. Multiple dimension declarations on the same line may be separated by commas.
Each declaration is of the form name = length. Use the “/” character to include group
information (netCDF-4 output only).
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There are four dimensions in the above example: lat, lon, level, and time (see Section 2.1
[Data Model], page 17). The first three are assigned fixed lengths; time is assigned the length
UNLIMITED, which means it is the unlimited dimension.
The basic unit of named data in a netCDF dataset is a variable. When a variable is
defined, its shape is specified as a list of dimensions. These dimensions must already exist.
The number of dimensions is called the rank (a.k.a. dimensionality). A scalar variable has
rank 0, a vector has rank 1 and a matrix has rank 2.
It is possible (since version 3.1 of netCDF) to use the same dimension more than once
in specifying a variable shape. For example, correlation(instrument, instrument) could
be a matrix giving correlations between measurements using different instruments. But
data whose dimensions correspond to those of physical space/time should have a shape
comprising different dimensions, even if some of these have the same length.
2.3 Variables
Variables are used to store the bulk of the data in a netCDF dataset. A variable represents
an array of values of the same type. A scalar value is treated as a 0-dimensional array. A
variable has a name, a data type, and a shape described by its list of dimensions specified
when the variable is created. A variable may also have associated attributes, which may be
added, deleted or changed after the variable is created.
A variable external data type is one of a small set of netCDF types. In classic and 64-bit
offset files, only the original six types are available (byte, character, short, int, float, and
double). Variables in netCDF-4 files may also use unsigned short, unsigned int, 64-bit int,
unsigned 64-bit int, or string. Or the user may define a type, as an opaque blob of bytes,
as an array of variable length arrays, or as a compound type, which acts like a C struct.
For more information on types for the C interface, see Section “Variable Types” in The
NetCDF C Interface Guide in The NetCDF C Interface Guide.
For more information on types for the Fortran interface, see Section “Variable Types”
in The NetCDF Fortran 77 Interface Guide in The NetCDF Fortran 77 Interface Guide.
In the CDL notation, classic and 64-bit offset type can be used. They are given the
simpler names byte, char, short, int, float, and double. The name real may be used as a
synonym for float in the CDL notation. The name long is a deprecated synonym for int.
For the exact meaning of each of the types see Section 3.1 [External Types], page 25. The
ncgen utility supports new primitive types with names ubyte, ushort, uint, int64, uint64,
and string.
CDL variable declarations appear after the variable keyword in a CDL unit. They have
the form
type variable_name ( dim_name_1, dim_name_2, ... );
for variables with dimensions, or
type variable_name;
for scalar variables.
In the above CDL example there are six variables. As discussed below, four of these
are coordinate variables. The remaining variables (sometimes called primary variables),
temp and rh, contain what is usually thought of as the data. Each of these variables has
the unlimited dimension time as its first dimension, so they are called record variables. A
Chapter 2: Components of a NetCDF Dataset
21
variable that is not a record variable has a fixed length (number of data values) given by
the product of its dimension lengths. The length of a record variable is also the product of
its dimension lengths, but in this case the product is variable because it involves the length
of the unlimited dimension, which can vary. The length of the unlimited dimension is the
number of records.
2.3.1 Coordinate Variables
It is legal for a variable to have the same name as a dimension. Such variables have no
special meaning to the netCDF library. However there is a convention that such variables
should be treated in a special way by software using this library.
A variable with the same name as a dimension is called a coordinate variable. It typically
defines a physical coordinate corresponding to that dimension. The above CDL example
includes the coordinate variables lat, lon, level and time, defined as follows:
int
short
lat(lat), lon(lon), level(level);
time(time);
level
lat
lon
time
=
=
=
=
...
data:
1000, 850, 700, 500;
20, 30, 40, 50, 60;
-160,-140,-118,-96,-84,-52,-45,-35,-25,-15;
12;
These define the latitudes, longitudes, barometric pressures and times corresponding to
positions along these dimensions. Thus there is data at altitudes corresponding to 1000,
850, 700 and 500 millibars; and at latitudes 20, 30, 40, 50 and 60 degrees north. Note that
each coordinate variable is a vector and has a shape consisting of just the dimension with
the same name.
A position along a dimension can be specified using an index. This is an integer with
a minimum value of 0 for C programs, 1 in Fortran programs. Thus the 700 millibar level
would have an index value of 2 in the example above in a C program, and 3 in a Fortran
program.
If a dimension has a corresponding coordinate variable, then this provides an alternative,
and often more convenient, means of specifying position along it. Current application
packages that make use of coordinate variables commonly assume they are numeric vectors
and strictly monotonic (all values are different and either increasing or decreasing).
2.4 Attributes
NetCDF attributes are used to store data about the data (ancillary data or metadata), similar in many ways to the information stored in data dictionaries and schema in conventional
database systems. Most attributes provide information about a specific variable. These are
identified by the name (or ID) of that variable, together with the name of the attribute.
Some attributes provide information about the dataset as a whole and are called global
attributes. These are identified by the attribute name together with a blank variable name
(in CDL) or a special null "global variable" ID (in C or Fortran).
In netCDF-4 file, attributes can also be added at the group level.
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An attribute has an associated variable (the null "global variable" for a global or grouplevel attribute), a name, a data type, a length, and a value. The current version treats all
attributes as vectors; scalar values are treated as single-element vectors.
Conventional attribute names should be used where applicable. New names should be
as meaningful as possible.
The external type of an attribute is specified when it is created. The types permitted for
attributes are the same as the netCDF external data types for variables. Attributes with
the same name for different variables should sometimes be of different types. For example,
the attribute valid max specifying the maximum valid data value for a variable of type int
should be of type int, whereas the attribute valid max for a variable of type double should
instead be of type double.
Attributes are more dynamic than variables or dimensions; they can be deleted and have
their type, length, and values changed after they are created, whereas the netCDF interface
provides no way to delete a variable or to change its type or shape.
The CDL notation for defining an attribute is
variable_name:attribute_name = list_of_values;
for a variable attribute, or
:attribute_name = list_of_values;
for a global attribute.
For the netCDF classic model, the type and length of each attribute are not explicitly
declared in CDL; they are derived from the values assigned to the attribute. All values of
an attribute must be of the same type. The notation used for constant values of the various
netCDF types is discussed later (see Section 5.3 [CDL Constants], page 62).
The extended CDL syntax for the enhanced data model supported by netCDF-4 allows optional type specifications, including user-defined types, for attributes of user-defined
types. See ncdump output or the reference documentation for ncgen4 for details of the
extended CDL systax.
In the netCDF example (see Section 2.1 [Data Model], page 17), units is an attribute
for the variable lat that has a 13-character array value ’degrees north’. And valid range is
an attribute for the variable rh that has length 2 and values ’0.0’ and ’1.0’.
One global attribute, called “source”, is defined for the example netCDF dataset. This is
a character array intended for documenting the data. Actual netCDF datasets might have
more global attributes to document the origin, history, conventions, and other characteristics
of the dataset as a whole.
Most generic applications that process netCDF datasets assume standard attribute
conventions and it is strongly recommended that these be followed unless there are good
reasons for not doing so. For information about units, long name, valid min, valid max,
valid range, scale factor, add offset, FillValue, and other conventional attributes, see
Appendix B [Attribute Conventions], page 71.
Attributes may be added to a netCDF dataset long after it is first defined, so you don’t
have to anticipate all potentially useful attributes. However adding new attributes to an
existing classic or 64-bit offset format dataset can incur the same expense as copying the
dataset. For a more extensive discussion see Chapter 4 [Structure], page 35.
Chapter 2: Components of a NetCDF Dataset
23
2.5 Differences between Attributes and Variables
In contrast to variables, which are intended for bulk data, attributes are intended for ancillary data, or information about the data. The total amount of ancillary data associated
with a netCDF object, and stored in its attributes, is typically small enough to be memoryresident. However variables are often too large to entirely fit in memory and must be split
into sections for processing.
Another difference between attributes and variables is that variables may be multidimensional. Attributes are all either scalars (single-valued) or vectors (a single, fixed dimension).
Variables are created with a name, type, and shape before they are assigned data values,
so a variable may exist with no values. The value of an attribute is specified when it is
created, unless it is a zero-length attribute.
A variable may have attributes, but an attribute cannot have attributes. Attributes
assigned to variables may have the same units as the variable (for example, valid range)
or have no units (for example, scale factor). If you want to store data that requires units
different from those of the associated variable, it is better to use a variable than an attribute.
More generally, if data require ancillary data to describe them, are multidimensional, require
any of the defined netCDF dimensions to index their values, or require a significant amount
of storage, that data should be represented using variables rather than attributes.
Chapter 3: Data
25
3 Data
This chapter discusses the primitive netCDF external data types, the kinds of data access
supported by the netCDF interface, and how data structures other than arrays may be
implemented in a netCDF dataset.
3.1 NetCDF External Data Types
The atomic external types supported by the netCDF interface are:
C name
storage
NC BYTE
Fortran
name
nf byte
NC CHAR
nf char
8-bit unsigned integer
NC SHORT
nf short
16-bit signed integer
8-bit signed integer
NC USHORT nf ushort
16-bit unsigned integer *
NC INT (or
NC LONG)
NC UINT
nf int
32-bit signed integer
nf uint
32-bit unsigned integer *
NC INT64
nf int64
64-bit signed integer *
NC UINT64
nf uint64
64-bit unsigned integer *
NC FLOAT
nf float
32-bit floating point
NC DOUBLE nf double
64-bit floating point
NC STRING
variable length character string *
nf string
* These types are available only for netCDF-4 format files. All the unsigned ints (except
NC CHAR), the 64-bit ints, and string type are for netCDF-4 files only.
These types were chosen to provide a reasonably wide range of trade-offs between data
precision and number of bits required for each value. These external data types are independent from whatever internal data types are supported by a particular machine and
language combination.
These types are called "external", because they correspond to the portable external representation for netCDF data. When a program reads external netCDF data into an internal
variable, the data is converted, if necessary, into the specified internal type. Similarly, if you
write internal data into a netCDF variable, this may cause it to be converted to a different
external type, if the external type for the netCDF variable differs from the internal type.
The separation of external and internal types and automatic type conversion have several
advantages. You need not be aware of the external type of numeric variables, since automatic
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The NetCDF Users’ Guide
conversion to or from any desired numeric type is available. You can use this feature to
simplify code, by making it independent of external types, using a sufficiently wide internal
type, e.g., double precision, for numeric netCDF data of several different external types.
Programs need not be changed to accommodate a change to the external type of a variable.
If conversion to or from an external numeric type is necessary, it is handled by the library.
Converting from one numeric type to another may result in an error if the target type is
not capable of representing the converted value. For example, an internal short integer type
may not be able to hold data stored externally as an integer. When accessing an array of
values, a range error is returned if one or more values are out of the range of representable
values, but other values are converted properly.
Note that mere loss of precision in type conversion does not return an error. Thus, if you
read double precision values into a single-precision floating-point variable, for example, no
error results unless the magnitude of the double precision value exceeds the representable
range of single-precision floating point numbers on your platform. Similarly, if you read a
large integer into a float incapable of representing all the bits of the integer in its mantissa,
this loss of precision will not result in an error. If you want to avoid such precision loss,
check the external types of the variables you access to make sure you use an internal type
that has adequate precision.
The names for the primitive external data types (byte, char, short, ushort, int, uint,
int64, uint64, float or real, double, string) are reserved words in CDL, so the names of
variables, dimensions, and attributes must not be type names.
It is possible to interpret byte data as either signed (-128 to 127) or unsigned (0 to 255).
However, when reading byte data to be converted into other numeric types, it is interpreted
as signed.
For the correspondence between netCDF external data types and the data types of a
language see Section 2.3 [Variables], page 20.
3.2 Data Structures in Classic and 64-bit Offset Files
The only kind of data structure directly supported by the netCDF classic (and 64-bit offset)
abstraction is a collection of named arrays with attached vector attributes. NetCDF is not
particularly well-suited for storing linked lists, trees, sparse matrices, ragged arrays or other
kinds of data structures requiring pointers.
It is possible to build other kinds of data structures in netCDF classic or 64-bit offset
formats, from sets of arrays by adopting various conventions regarding the use of data in
one array as pointers into another array. The netCDF library won’t provide much help or
hindrance with constructing such data structures, but netCDF provides the mechanisms
with which such conventions can be designed.
The following netCDF classic example stores a ragged array ragged mat using an attribute row index to name an associated index variable giving the index of the start of each
row. In this example, the first row contains 12 elements, the second row contains 7 elements
(19 - 12), and so on. (NetCDF-4 includes native support for variable length arrays. See
below.)
float
ragged_mat(max_elements);
ragged_mat:row_index = "row_start";
Chapter 3: Data
int
27
row_start(max_rows);
data:
row_start
= 0, 12, 19, ...
As another example, netCDF variables may be grouped within a netCDF classic or 64bit offset dataset by defining attributes that list the names of the variables in each group,
separated by a conventional delimiter such as a space or comma. Using a naming convention
for attribute names for such groupings permits any number of named groups of variables.
A particular conventional attribute for each variable might list the names of the groups
of which it is a member. Use of attributes, or variables that refer to other attributes or
variables, provides a flexible mechanism for representing some kinds of complex structures
in netCDF datasets.
3.3 NetCDF-4 User Defined Data Types
NetCDF supported six data types through version 3.6.0 (char, byte, short, int, float, and
double). Starting with version 4.0, many new data types are supported (unsigned int types,
strings, compound types, variable length arrays, enums, opaque).
In addition to the new atomic types the user may define types.
Types are defined in define mode, and must be fully defined before they are used. New
types may be added to a file by re-entering define mode.
Once defined the type may be used to create a variable or attribute.
Types may be nested in complex ways. For example, a compound type containing an
array of VLEN types, each containing variable length arrays of some other compound type,
etc. Users are cautioned to keep types simple. Reading data of complex types can be
challenging for Fortran users.
Types may be defined in any group in the data file, but they are always available globally
in the file.
Types cannot have attributes (but variables of the type may have attributes).
Only files created with the netCDF-4/HDF5 mode flag (NC NETCDF4, NF NETCDF4,
or NF90 NETCDF4), but without the classic model flag (NC CLASSIC MODEL,
NF CLASSIC MODEL, or NF90 CLASSIC MODEL.)
Once types are defined, use their ID like any other type ID when defining variables
or attributes. Each API has functions to read and write variables and attributes of any
type. Use these functions to read and write variables and attributes of user defined type.
In C use nc put att/nc get att and the nc put var/nc get var, nc put var1/nc get var1,
nc put vara/nc get vara, or nc put vars/nc get vars functons to access attribute and variable data of user defined type.
3.3.1 Compound Types
Compound types allow the user to combine atomic and user-defined types into C-like structs.
Since users defined types may be used within a compound type, they can contain nested
compound types.
Users define a compound type, and (in their C code) a corresponding C struct. They
can then use the nc put var[1asm] calls to write multi-dimensional arrays of these structs,
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and nc get var[1asm] calls to read them. (For example, the nc put varm function will write
mapped arrays of these structs.)
While structs, in general, are not portable from platform to platform, the HDF5 layer
(when installed) performs the magic required to figure out your platform’s idiosyncrasies,
and adjust to them. The end result is that HDF5 compound types (and therefore, netCDF-4
compound types), are portable.
For more information on creating and using compound types, see Section “Compound
Types” in The NetCDF C Interface Guide in The NetCDF C Interface Guide.
3.3.2 VLEN Types
Variable length arrays can be used to create a ragged array of data, in which one of the
dimensions varies in size from point to point.
An example of VLEN use would the to store a 1-D array of dropsonde data, in which
the data at each drop point is of variable length.
There is no special restriction on the dimensionality of VLEN variables. It’s possible to
have 2D, 3D, 4D, etc. data, in which each point contains a VLEN.
A VLEN has a base type (that is, the type that it is a VLEN of). This may be one of
the atomic types (forming, for example, a variable length array of NC INT), or it can be
another user defined type, like a compound type.
With VLEN data, special memory allocation and deallocation procedures must be followed, or memory leaks may occur.
Compression is permitted but may not be effective for VLEN data, because the compression is applied to structures containing lengths and pointers to the data, rather than
the actual data.
For more information on creating and using variable length arrays, see Section “Variable
Length Arrays” in The NetCDF C Interface Guide in The NetCDF C Interface Guide.
3.3.3 Opaque Types
Opaque types allow the user to store arrays of data blobs of a fixed size.
For more information on creating and using opaque types, see Section “Opaque Type”
in The NetCDF C Interface Guide in The NetCDF C Interface Guide.
3.3.4 Enum Types
Enum types allow the user to specify an enumeration.
For more information on creating and using enum types, see Section “Enum Type” in
The NetCDF C Interface Guide in The NetCDF C Interface Guide.
3.3.5 Groups
Although not a type of data, groups can help organize data within a dataset. Like a directory
structure on a Unix file-system, the grouping feature allows users to organize variables and
dimensions into distinct, named, hierarchical areas, called groups. For more information on
groups types, see Section “Groups” in The NetCDF C Interface Guide in The NetCDF C
Interface Guide.
Chapter 3: Data
29
3.4 Data Access
To access (read or write) netCDF data you specify an open netCDF dataset, a netCDF
variable, and information (e.g., indices) identifying elements of the variable. The name of
the access function corresponds to the internal type of the data. If the internal type has
a different representation from the external type of the variable, a conversion between the
internal type and external type will take place when the data is read or written.
Access to data in classic and 64-bit offset format is direct. Access to netCDF-4 data is
buffered by the HDF5 layer. In either case you can access a small subset of data from a
large dataset efficiently, without first accessing all the data that precedes it.
Reading and writing data by specifying a variable, instead of a position in a file, makes
data access independent of how many other variables are in the dataset, making programs
immune to data format changes that involve adding more variables to the data.
In the C and FORTRAN interfaces, datasets are not specified by name every time you
want to access data, but instead by a small integer called a dataset ID, obtained when the
dataset is first created or opened.
Similarly, a variable is not specified by name for every data access either, but by a
variable ID, a small integer used to identify each variable in a netCDF dataset.
3.4.1 Forms of Data Access
The netCDF interface supports several forms of direct access to data values in an open
netCDF dataset. We describe each of these forms of access in order of increasing generality:
• access to all elements;
• access to individual elements, specified with an index vector;
• access to array sections, specified with an index vector, and count vector;
• access to sub-sampled array sections, specified with an index vector, count vector, and
stride vector; and
• access to mapped array sections, specified with an index vector, count vector, stride
vector, and an index mapping vector.
The four types of vector (index vector, count vector, stride vector and index mapping
vector) each have one element for each dimension of the variable. Thus, for an n-dimensional
variable (rank = n), n-element vectors are needed. If the variable is a scalar (no dimensions),
these vectors are ignored.
An array section is a "slab" or contiguous rectangular block that is specified by two
vectors. The index vector gives the indices of the element in the corner closest to the origin.
The count vector gives the lengths of the edges of the slab along each of the variable’s
dimensions, in order. The number of values accessed is the product of these edge lengths.
A subsampled array section is similar to an array section, except that an additional
stride vector is used to specify sampling. This vector has an element for each dimension
giving the length of the strides to be taken along that dimension. For example, a stride of
4 means every fourth value along the corresponding dimension. The total number of values
accessed is again the product of the elements of the count vector.
A mapped array section is similar to a subsampled array section except that an additional
index mapping vector allows one to specify how data values associated with the netCDF
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The NetCDF Users’ Guide
variable are arranged in memory. The offset of each value from the reference location,
is given by the sum of the products of each index (of the imaginary internal array which
would be used if there were no mapping) by the corresponding element of the index mapping
vector. The number of values accessed is the same as for a subsampled array section.
The use of mapped array sections is discussed more fully below, but first we present an
example of the more commonly used array-section access.
3.4.2 A C Example of Array-Section Access
Assume that in our earlier example of a netCDF dataset (see Section 2.1 [Network Common
Data Form Language (CDL)], page 17), we wish to read a cross-section of all the data for
the temp variable at one level (say, the second), and assume that there are currently three
records (time values) in the netCDF dataset. Recall that the dimensions are defined as
lat = 5, lon = 10, level = 4, time = unlimited;
and the variable temp is declared as
float
temp(time, level, lat, lon);
in the CDL notation.
A corresponding C variable that holds data for only one level might be declared as
#define
#define
#define
#define
...
float
LATS 5
LONS 10
LEVELS 1
TIMES 3
/* currently */
temp[TIMES*LEVELS*LATS*LONS];
to keep the data in a one-dimensional array, or
...
float
temp[TIMES][LEVELS][LATS][LONS];
using a multidimensional array declaration.
To specify the block of data that represents just the second level, all times, all latitudes,
and all longitudes, we need to provide a start index and some edge lengths. The start index
should be (0, 1, 0, 0) in C, because we want to start at the beginning of each of the time,
lon, and lat dimensions, but we want to begin at the second value of the level dimension.
The edge lengths should be (3, 1, 5, 10) in C, (since we want to get data for all three time
values, only one level value, all five lat values, and all 10 lon values. We should expect to
get a total of 150 floating-point values returned (3 * 1 * 5 * 10), and should provide enough
space in our array for this many. The order in which the data will be returned is with the
last dimension, lon, varying fastest:
temp[0][1][0][0]
temp[0][1][0][1]
temp[0][1][0][2]
temp[0][1][0][3]
...
Chapter 3: Data
31
temp[2][1][4][7]
temp[2][1][4][8]
temp[2][1][4][9]
Different dimension orders for the C, FORTRAN, or other language interfaces do not
reflect a different order for values stored on the disk, but merely different orders supported
by the procedural interfaces to the languages. In general, it does not matter whether a
netCDF dataset is written using the C, FORTRAN, or another language interface; netCDF
datasets written from any supported language may be read by programs written in other
supported languages.
3.4.3 More on General Array Section Access for C
The use of mapped array sections allows non-trivial relationships between the disk addresses
of variable elements and the addresses where they are stored in memory. For example, a
matrix in memory could be the transpose of that on disk, giving a quite different order of
elements. In a regular array section, the mapping between the disk and memory addresses
is trivial: the structure of the in-memory values (i.e., the dimensional lengths and their
order) is identical to that of the array section. In a mapped array section, however, an
index mapping vector is used to define the mapping between indices of netCDF variable
elements and their memory addresses.
With mapped array access, the offset (number of array elements) from the origin of a
memory-resident array to a particular point is given by the inner product[1] of the index
mapping vector with the point’s coordinate offset vector. A point’s coordinate offset vector
gives, for each dimension, the offset from the origin of the containing array to the point.In
C, a point’s coordinate offset vector is the same as its coordinate vector.
The index mapping vector for a regular array section would have–in order from most
rapidly varying dimension to most slowly–a constant 1, the product of that value with the
edge length of the most rapidly varying dimension of the array section, then the product of
that value with the edge length of the next most rapidly varying dimension, and so on. In
a mapped array, however, the correspondence between netCDF variable disk locations and
memory locations can be different.
For example, the following C definitions
struct vel {
int flags;
float u;
float v;
} vel[NX][NY];
ptrdiff_t imap[2] = {
sizeof(struct vel),
sizeof(struct vel)*NY
};
where imap is the index mapping vector, can be used to access the memory-resident
values of the netCDF variable, vel(NY,NX), even though the dimensions are transposed
and the data is contained in a 2-D array of structures rather than a 2-D array of floatingpoint values.
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A detailed example of mapped array access is presented in the description of the interfaces
for mapped array access. See Section “nc put varm type” in The NetCDF C Interface
Guide.
Note that, although the netCDF abstraction allows the use of subsampled or mapped
array-section access there use is not required. If you do not need these more general forms
of access, you may ignore these capabilities and use single value access or regular array
section access instead.
3.4.4 A Fortran Example of Array-Section Access
Assume that in our earlier example of a netCDF dataset (see Section 2.1 [Data Model],
page 17), we wish to read a cross-section of all the data for the temp variable at one level
(say, the second), and assume that there are currently three records (time values) in the
netCDF dataset. Recall that the dimensions are defined as
lat = 5, lon = 10, level = 4, time = unlimited;
and the variable temp is declared as
float
temp(time, level, lat, lon);
in the CDL notation.
In FORTRAN, the dimensions are reversed from the CDL declaration with the first dimension varying fastest and the record dimension as the last dimension of a record variable.
Thus a FORTRAN declarations for a variable that holds data for only one level is
INTEGER LATS, LONS, LEVELS, TIMES
PARAMETER (LATS=5, LONS=10, LEVELS=1, TIMES=3)
...
REAL TEMP(LONS, LATS, LEVELS, TIMES)
To specify the block of data that represents just the second level, all times, all latitudes,
and all longitudes, we need to provide a start index and some edge lengths. The start index
should be (1, 1, 2, 1) in FORTRAN, because we want to start at the beginning of each of
the time, lon, and lat dimensions, but we want to begin at the second value of the level
dimension. The edge lengths should be (10, 5, 1, 3) in FORTRAN, since we want to get
data for all three time values, only one level value, all five lat values, and all 10 lon values.
We should expect to get a total of 150 floating-point values returned (3 * 1 * 5 * 10), and
should provide enough space in our array for this many. The order in which the data will
be returned is with the first dimension, LON, varying fastest:
TEMP( 1, 1, 2, 1)
TEMP( 2, 1, 2, 1)
TEMP( 3, 1, 2, 1)
TEMP( 4, 1, 2, 1)
...
TEMP( 8, 5, 2, 3)
TEMP( 9, 5, 2, 3)
TEMP(10, 5, 2, 3)
Different dimension orders for the C, FORTRAN, or other language interfaces do not
reflect a different order for values stored on the disk, but merely different orders supported
Chapter 3: Data
33
by the procedural interfaces to the languages. In general, it does not matter whether a
netCDF dataset is written using the C, FORTRAN, or another language interface; netCDF
datasets written from any supported language may be read by programs written in other
supported languages.
3.4.5 More on General Array Section Access for Fortran
The use of mapped array sections allows non-trivial relationships between the disk addresses
of variable elements and the addresses where they are stored in memory. For example, a
matrix in memory could be the transpose of that on disk, giving a quite different order of
elements. In a regular array section, the mapping between the disk and memory addresses
is trivial: the structure of the in-memory values (i.e., the dimensional lengths and their
order) is identical to that of the array section. In a mapped array section, however, an
index mapping vector is used to define the mapping between indices of netCDF variable
elements and their memory addresses.
With mapped array access, the offset (number of array elements) from the origin of a
memory-resident array to a particular point is given by the inner product[1] of the index
mapping vector with the point’s coordinate offset vector. A point’s coordinate offset vector
gives, for each dimension, the offset from the origin of the containing array to the point. In
FORTRAN, the values of a point’s coordinate offset vector are one less than the corresponding values of the point’s coordinate vector, e.g., the array element A(3,5) has coordinate
offset vector [2, 4].
The index mapping vector for a regular array section would have–in order from most
rapidly varying dimension to most slowly–a constant 1, the product of that value with the
edge length of the most rapidly varying dimension of the array section, then the product of
that value with the edge length of the next most rapidly varying dimension, and so on. In
a mapped array, however, the correspondence between netCDF variable disk locations and
memory locations can be different.
A detailed example of mapped array access is presented in the description of the interfaces
for mapped array access. See Section “nf put varm type” in The NetCDF Fortran 77
Interface Guide.
Note that, although the netCDF abstraction allows the use of subsampled or mapped
array-section access there use is not required. If you do not need these more general forms
of access, you may ignore these capabilities and use single value access or regular array
section access instead.
3.5 Type Conversion
Each netCDF variable has an external type, specified when the variable is first defined.
This external type determines whether the data is intended for text or numeric values, and
if numeric, the range and precision of numeric values.
If the netCDF external type for a variable is char, only character data representing text
strings can be written to or read from the variable. No automatic conversion of text data
to a different representation is supported.
If the type is numeric, however, the netCDF library allows you to access the variable
data as a different type and provides automatic conversion between the numeric data in
memory and the data in the netCDF variable. For example, if you write a program that
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deals with all numeric data as double-precision floating point values, you can read netCDF
data into double-precision arrays without knowing or caring what the external type of
the netCDF variables are. On reading netCDF data, integers of various sizes and singleprecision floating-point values will all be converted to double-precision, if you use the data
access interface for double-precision values. Of course, you can avoid automatic numeric
conversion by using the netCDF interface for a value type that corresponds to the external
data type of each netCDF variable, where such value types exist.
The automatic numeric conversions performed by netCDF are easy to understand, because they behave just like assignment of data of one type to a variable of a different type.
For example, if you read floating-point netCDF data as integers, the result is truncated towards zero, just as it would be if you assigned a floating-point value to an integer variable.
Such truncation is an example of the loss of precision that can occur in numeric conversions.
Converting from one numeric type to another may result in an error if the target type is
not capable of representing the converted value. For example, an integer may not be able to
hold data stored externally as an IEEE floating-point number. When accessing an array of
values, a range error is returned if one or more values are out of the range of representable
values, but other values are converted properly.
Note that mere loss of precision in type conversion does not result in an error. For
example, if you read double precision values into an integer, no error results unless the
magnitude of the double precision value exceeds the representable range of integers on your
platform. Similarly, if you read a large integer into a float incapable of representing all the
bits of the integer in its mantissa, this loss of precision will not result in an error. If you
want to avoid such precision loss, check the external types of the variables you access to
make sure you use an internal type that has a compatible precision.
Whether a range error occurs in writing a large floating-point value near the boundary
of representable values may be depend on the platform. The largest floating-point value
you can write to a netCDF float variable is the largest floating-point number representable
on your system that is less than 2 to the 128th power. The largest double precision value
you can write to a double variable is the largest double-precision number representable on
your system that is less than 2 to the 1024th power.
Chapter 4: File Structure and Performance
35
4 File Structure and Performance
This chapter describes the file structure of a netCDF classic or 64-bit offset dataset in
enough detail to aid in understanding netCDF performance issues.
NetCDF is a data abstraction for array-oriented data access and a software library that
provides a concrete implementation of the interfaces that support that abstraction. The
implementation provides a machine-independent format for representing arrays. Although
the netCDF file format is hidden below the interfaces, some understanding of the current
implementation and associated file structure may help to make clear why some netCDF
operations are more expensive than others.
Knowledge of the format is not needed for reading and writing netCDF data or understanding most efficiency issues. Programs that use only the documented interfaces and that
make no assumptions about the format will continue to work even if the netCDF format
is changed in the future, because any such change will be made below the documented
interfaces and will support earlier versions of the netCDF file format.
4.1 Parts of a NetCDF Classic File
A netCDF classic or 64-bit offset dataset is stored as a single file comprising two parts:
a header, containing all the information about dimensions, attributes, and variables
except for the variable data;
a data part, comprising fixed-size data, containing the data for variables that don’t have
an unlimited dimension; and variable-size data, containing the data for variables that have
an unlimited dimension.
Both the header and data parts are represented in a machine-independent form. This
form is very similar to XDR (eXternal Data Representation), extended to support efficient
storage of arrays of non-byte data.
The header at the beginning of the file contains information about the dimensions,
variables, and attributes in the file, including their names, types, and other characteristics.
The information about each variable includes the offset to the beginning of the variable’s
data for fixed-size variables or the relative offset of other variables within a record. The
header also contains dimension lengths and information needed to map multidimensional
indices for each variable to the appropriate offsets.
By default, this header has little usable extra space; it is only as large as it needs to be for
the dimensions, variables, and attributes (including all the attribute values) in the netCDF
dataset, with a small amount of extra space from rounding up to the nearest disk block
size. This has the advantage that netCDF files are compact, requiring very little overhead
to store the ancillary data that makes the datasets self-describing. A disadvantage of this
organization is that any operation on a netCDF dataset that requires the header to grow
(or, less likely, to shrink), for example adding new dimensions or new variables, requires
moving the data by copying it. This expense is incurred when the enddef function is called:
nc enddef in C (see Section “nc enddef” in The NetCDF C Interface Guide), NF ENDDEF
in Fortran (see Section “NF ENDDEF” in The NetCDF Fortran 77 Interface Guide), after
a previous call to the redef function: nc redef in C (see Section “nc redef” in The NetCDF
C Interface Guide) or NF REDEF in Fortran (see Section “NF REDEF” in The NetCDF
Fortran 77 Interface Guide). If you create all necessary dimensions, variables, and attributes
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before writing data, and avoid later additions and renamings of netCDF components that
require more space in the header part of the file, you avoid the cost associated with later
changing the header.
Alternatively, you can use an alternative version of the enddef function with two underbar
characters instead of one to explicitly reserve extra space in the file header when the file is
created: in C nc enddef (see Section “nc enddef” in The NetCDF C Interface Guide), in
Fortran NF ENDDEF (see Section “NF ENDDEF” in The NetCDF Fortran 77 Interface
Guide), after a previous call to the redef function. This avoids the expense of moving all
the data later by reserving enough extra space in the header to accommodate anticipated
changes, such as the addition of new attributes or the extension of existing string attributes
to hold longer strings.
When the size of the header is changed, data in the file is moved, and the location of
data values in the file changes. If another program is reading the netCDF dataset during
redefinition, its view of the file will be based on old, probably incorrect indexes. If netCDF
datasets are shared across redefinition, some mechanism external to the netCDF library
must be provided that prevents access by readers during redefinition, and causes the readers
to call nc sync/NF SYNC before any subsequent access.
The fixed-size data part that follows the header contains all the variable data for variables that do not employ an unlimited dimension. The data for each variable is stored
contiguously in this part of the file. If there is no unlimited dimension, this is the last part
of the netCDF file.
The record-data part that follows the fixed-size data consists of a variable number of
fixed-size records, each of which contains data for all the record variables. The record data
for each variable is stored contiguously in each record.
The order in which the variable data appears in each data section is the same as the
order in which the variables were defined, in increasing numerical order by netCDF variable
ID. This knowledge can sometimes be used to enhance data access performance, since the
best data access is currently achieved by reading or writing the data in sequential order.
For more detail see Appendix C [File Format], page 75.
4.2 Parts of a NetCDF-4 HDF5 File
NetCDF-4 files are created with the HDF5 library, and are HDF5 files in every way, and
can be read without the netCDF-4 interface. (Note that modifying these files with HDF5
will almost certainly make them unreadable to netCDF-4.)
Groups in a netCDF-4 file correspond with HDF5 groups (although the netCDF-4 tree
is rooted not at the HDF5 root, but in group “ netCDF”).
Variables in netCDF coo-respond with identically named datasets in HDF5. Attributes
similarly.
Since there is more metadata in a netCDF file than an HDF5 file, special datasets are
used to hold netCDF metadata.
The netcdf dim info dataset (in group netCDF) contains the ids of the shared dimensions, and their length (0 for unlimited dimensions).
The netcdf var info dataset (in group netCDF) holds an array of compound types
which contain the variable ID, and the associated dimension ids.
Chapter 4: File Structure and Performance
37
4.3 The Extended XDR Layer
XDR is a standard for describing and encoding data and a library of functions for external data representation, allowing programmers to encode data structures in a machineindependent way. Classic or 64-bit offset NetCDF employs an extended form of XDR for
representing information in the header part and the data parts. This extended XDR is used
to write portable data that can be read on any other machine for which the library has
been implemented.
The cost of using a canonical external representation for data varies according to the
type of data and whether the external form is the same as the machine’s native form for
that type.
For some data types on some machines, the time required to convert data to and from
external form can be significant. The worst case is reading or writing large arrays of floatingpoint data on a machine that does not use IEEE floating-point as its native representation.
4.4 Large File Support
It is possible to write netCDF files that exceed 2 GiByte on platforms that have "Large File
Support" (LFS). Such files are platform-independent to other LFS platforms, but trying to
open them on an older platform without LFS yields a "file too large" error.
Without LFS, no files larger than 2 GiBytes can be used. The rest of this section applies
only to systems with LFS.
The original binary format of netCDF (classic format) limits the size of data files by
using a signed 32-bit offset within its internal structure. Files larger than 2 GiB can be
created, with certain limitations. See Section 4.6 [Classic Limitations], page 38.
In version 3.6.0, netCDF included its first-ever variant of the underlying data format.
The new format introduced in 3.6.0 uses 64-bit file offsets in place of the 32-bit offsets.
There are still some limits on the sizes of variables, but the new format can create very
large datasets. See Section 4.5 [64 bit Offset Limitations], page 38.
NetCDF-4 variables and files can be any size supported by the underlying file system.
The original data format (netCDF classic), is still the default data format for the netCDF
library.
The following table summarizes the size limitations of various permutations of LFS
support, netCDF version, and data format. Note that 1 GiB = 2^30 bytes or about 1.07e+9
bytes, 1 EiB = 2^60 bytes or about 1.15e+18 bytes. Note also that all sizes are really 4
bytes less than the ones given below. For example the maximum size of a fixed variable in
netCDF 3.6 classic format is really 2 GiB - 4 bytes.
Limit
No LFS
v3.5
v4.0/netCDF4
8 EiB
v3.6/classic v3.6/64bit
offset
8 EiB
8 EiB
Max File Size
2 GiB
Max Number of Fixed
Vars > 2 GiB
0
1 (last)
1 (last)
??
2^32
??
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Max Record Vars w/
Rec Size > 2 GiB
Max
Size
of
Fixed/Record Size of
Record Var
Max Record Size
0
1 (last)
1 (last)
2^32
??
2 GiB
2 GiB
2 GiB
4 GiB
??
2
GiB/nrecs
4 GiB
8
EiB/nrecs
8
EiB/nrecs
??
For more information about the different file formats of netCDF See Section 1.4 [Which
Format], page 6.
4.5 NetCDF 64-bit Offset Format Limitations
Although the 64-bit offset format allows the creation of much larger netCDF files than was
possible with the classic format, there are still some restrictions on the size of variables.
It’s important to note that without Large File Support (LFS) in the operating system,
it’s impossible to create any file larger than 2 GiBytes. Assuming an operating system with
LFS, the following restrictions apply to the netCDF 64-bit offset format.
No fixed-size variable can require more than 2^32 - 4 bytes (i.e. 4GiB - 4 bytes, or
4,294,967,292 bytes) of storage for its data, unless it is the last fixed-size variable and there
are no record variables. When there are no record variables, the last fixed-size variable can
be any size supported by the file system, e.g. terabytes.
A 64-bit offset format netCDF file can have up to 2^32 - 1 fixed sized variables, each
under 4GiB in size. If there are no record variables in the file the last fixed variable can be
any size.
No record variable can require more than 2^32 - 4 bytes of storage for each record’s
worth of data, unless it is the last record variable. A 64-bit offset format netCDF file can
have up to 2^32 - 1 records, of up to 2^32 - 1 variables, as long as the size of one record’s
data for each record variable except the last is less than 4 GiB - 4.
Note also that all netCDF variables and records are padded to 4 byte boundaries.
4.6 NetCDF Classic Format Limitations
There are important constraints on the structure of large netCDF classic files that result
from the 32-bit relative offsets that are part of the netCDF classic file format:
The maximum size of a record in the classic format in versions 3.5.1 and earlier is 2^32
- 4 bytes, or about 4 GiB. In versions 3.6.0 and later, there is no such restriction on total
record size for the classic format or 64-bit offset format.
If you don’t use the unlimited dimension, only one variable can exceed 2 GiB in size,
but it can be as large as the underlying file system permits. It must be the last variable in
the dataset, and the offset to the beginning of this variable must be less than about 2 GiB.
The limit is really 2^31 - 4. If you were to specify a variable size of 2^31 -3, for example,
it would be rounded up to the nearest multiple of 4 bytes, which would be 2^31, which is
larger than the largest signed integer, 2^31 - 1.
For example, the structure of the data might be something like:
Chapter 4: File Structure and Performance
39
netcdf bigfile1 {
dimensions:
x=2000;
y=5000;
z=10000;
variables:
double x(x);
// coordinate variables
double y(y);
double z(z);
double var(x, y, z); // 800 Gbytes
}
If you use the unlimited dimension, record variables may exceed 2 GiB in size, as long
as the offset of the start of each record variable within a record is less than 2 GiB - 4. For
example, the structure of the data in a 2.4 Tbyte file might be something like:
netcdf bigfile2 {
dimensions:
x=2000;
y=5000;
z=10;
t=UNLIMITED;
variables:
double x(x);
double y(y);
double z(z);
double t(t);
// 1000 records, for example
// coordinate variables
// 3 record variables, 2400000000 bytes per record
double var1(t, x, y, z);
double var2(t, x, y, z);
double var3(t, x, y, z);
}
4.7 The NetCDF-3 I/O Layer
The following discussion applies only to netCDF classic and 64-bit offset files. For netCDF-4
files, the I/O layer is the HDF5 library.
For netCDF classic and 64-bit offset files, an I/O layer implemented much like the C
standard I/O (stdio) library is used by netCDF to read and write portable data to netCDF
datasets. Hence an understanding of the standard I/O library provides answers to many
questions about multiple processes accessing data concurrently, the use of I/O buffers, and
the costs of opening and closing netCDF files. In particular, it is possible to have one
process writing a netCDF dataset while other processes read it.
Data reads and writes are no more atomic than calls to stdio fread() and fwrite().
An nc sync/NF SYNC call is analogous to the fflush call in the C standard I/O library,
writing unwritten buffered data so other processes can read it; The C function nc sync (see
Section “nc sync” in The NetCDF C Interface Guide), or the Fortran function NF SYNC
(see Section “NF SYNC” in The NetCDF Fortran 77 Interface Guide), also brings header
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changes up-to-date (for example, changes to attribute values). Opening the file with the
NC SHARE (in C) or the NF SHARE (in Fortran) is analogous to setting a stdio stream
to be unbuffered with the IONBF flag to setvbuf.
As in the stdio library, flushes are also performed when "seeks" occur to a different area
of the file. Hence the order of read and write operations can influence I/O performance
significantly. Reading data in the same order in which it was written within each record
will minimize buffer flushes.
You should not expect netCDF classic or 64-bit offset format data access to work with
multiple writers having the same file open for writing simultaneously.
It is possible to tune an implementation of netCDF for some platforms by replacing
the I/O layer with a different platform-specific I/O layer. This may change the similarities between netCDF and standard I/O, and hence characteristics related to data sharing,
buffering, and the cost of I/O operations.
The distributed netCDF implementation is meant to be portable. Platform-specific ports
that further optimize the implementation for better I/O performance are practical in some
cases.
4.8 UNICOS Optimization
It should be noted that no UNICOS platform has been available at Unidata for netCDF
testing for some years. The following information is left here for historical reasons.
As was mentioned in the previous section, it is possible to replace the I/O layer in order
to increase I/O efficiency. This has been done for UNICOS, the operating system of Cray
computers similar to the Cray Y-MP.
Additionally, it is possible for the user to obtain even greater I/O efficiency through appropriate setting of the NETCDF FFIOSPEC environment variable. This variable specifies
the Flexible File I/O buffers for netCDF I/O when executing under the UNICOS operating
system (the variable is ignored on other operating systems). An appropriate specification
can greatly increase the efficiency of netCDF I/O–to the extent that it can surpass default
FORTRAN binary I/O. Possible specifications include the following:
bufa:336:2
2, asynchronous, I/O buffers of 336 blocks each (i.e., double buffering). This is
the default specification and favors sequential I/O.
cache:256:8
8, synchronous, 256-block buffers. This favors larger random accesses.
cachea:256:8:2
8, asynchronous, 256-block buffers with a 2 block read-ahead/write-behind factor. This also favors larger random accesses.
cachea:8:256:0
256, asynchronous, 8-block buffers without read-ahead/write-behind. This favors many smaller pages without read-ahead for more random accesses as typified by slicing netCDF arrays.
cache:8:256,cachea.sds:1024:4:1
This is a two layer cache. The first (synchronous) layer is composed of 256
8-block buffers in memory, the second (asynchronous) layer is composed of 4
Chapter 4: File Structure and Performance
41
1024-block buffers on the SSD. This scheme works well when accesses proceed
through the dataset in random waves roughly 2x1024-blocks wide.
All of the options/configurations supported in CRI’s FFIO library are available through
this mechanism. We recommend that you look at CRI’s I/O optimization guide for information on using FFIO to its fullest. This mechanism is also compatible with CRI’s EIE
I/O library.
Tuning the NETCDF FFIOSPEC variable to a program’s I/O pattern can dramatically
improve performance. Speedups of two orders of magnitude have been seen.
4.9 Improving Performance With Chunking
NetCDF may use HDF5 as a storage format (when files are created with
NC NETCDF4/NF NETCDF4/NF90 NETCDF4).
For those files, the writer may
control the size of the chunks of data that are written to the HDF5, along with
other aspects of the data, such as endianness, a shuffle and checksum filter, on-the-fly
compression/decompression of the data.
The chunk sizes of a variable are specified after the variable is defined, but before any
data are written. If chunk sizes are not specified for a variable, default chunk sizes are
chosen by the library.
The selection of good chunk sizes is a complex topic, and one that data writers must
grapple with. Once the data are written, there is no way to change the chunk sizes except
to copy the data to a new variable.
Chunks should match read access patterns; the best chunk performance can be achieved
by writing chunks which exactly match the size of the subsets of data that will be read.
When multiple read access patterns are to be used, there is no one way to best set the
chunk sizes.
Some good discussion of chunking can be found in the HDF5-EOS XIII workshop presentation (http://hdfeos.org/workshops/ws13/presentations/day1/HDF5-EOSXIII-Advanced-Chunking.ppt
4.9.1 The Chunk Cache
When data are first read or written to a netCDF-4/HDF5 variable, the HDF5 library opens
a cache for that variable. The default size of that cache (settable with the –with-chunkcache-size at netCDF build time).
For good performance your chunk cache must be larger than one chunk of your data preferably that it be large enough to hold multiple chunks of data.
In addition, when a file is opened (or a variable created in an open file), the netCDF-4
library checks to make sure the default chunk cache size will work for that variable. The
cache will be large enough to hold N chunks, up to a maximum size of M bytes. (Both N
and M are settable at configure time with the –with-default-chunks-in-cache and the –withmax-default-cache-size options to the configure script. Currently they are set to 10 and 64
MB.)
To change the default chunk cache size, use the set chunk cache function before opening the file. C programmers see Section “nc set chunk cache” in The NetCDF C Interface Guide, Fortran 77 programmers see Section “NF SET CHUNK CACHE” in The
NetCDF Fortran 77 Interface Guide). Fortran 90 programmers use the optional cache size,
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cache nelems, and cache preemption parameters to nf90 open/nf90 create to change the
chunk size before opening the file.
To change the per-variable cache size, use the set var chunk cache function at any time
on an open file. C programmers see Section “nc set var chunk cache” in The NetCDF C
Interface Guide, Fortran 77 programmers see Section “NF SET VAR CHUNK CACHE”
in The NetCDF Fortran 77 Interface Guide, ).
4.9.2 The Default Chunking Scheme in version 4.1 (and 4.1.1)
When the data writer does not specify chunk sizes for variable, the netCDF library has to
come up with some default values.
The C code below determines the default chunks sizes.
For unlimited dimensions, a chunk size of one is always used. Users are advised to set
chunk sizes for large data sets with one or more unlimited dimensions, since a chunk size of
one is quite inefficient.
For fixed dimensions, the algorithm below finds a size for the chunk sizes in each dimension which results in chunks of DEFAULT CHUNK SIZE (which can be modified in the
netCDF configure script).
/* Unlimited dim always gets chunksize of 1. */
if (dim->unlimited)
chunksize[d] = 1;
else
chunksize[d] = pow((double)DEFAULT_CHUNK_SIZE/type_size,
1/(double)(var->ndims - unlimdim));
4.9.3 The Default Chunking Scheme in version 4.0.1
In the 4.0.1 release, the default chunk sizes were chosen with a different scheme, as demonstrated in the following C code:
/* These are limits for default chunk sizes. (2^16 and 2^20). */
#define NC_LEN_TOO_BIG 65536
#define NC_LEN_WAY_TOO_BIG 1048576
/* Now we must determine the default chunksize. */
if (dim->unlimited)
chunksize[d] = 1;
else if (dim->len < NC_LEN_TOO_BIG)
chunksize[d] = dim->len;
else if (dim->len > NC_LEN_TOO_BIG && dim->len <= NC_LEN_WAY_TOO_BIG)
chunksize[d] = dim->len / 2 + 1;
else
chunksize[d] = NC_LEN_WAY_TOO_BIG;
As can be seen from this code, the default chunksize is 1 for unlimited dimensions,
otherwise it is the full length of the dimension (if it is under NC LEN TOO BIG), or half the
size of the dimension (if it is between NC LEN TOO BIG and NC LEN WAY TOO BIG),
and, if it’s longer than NC LEN WAY TOO BIG, it is set to NC LEN WAY TOO BIG.
Chapter 4: File Structure and Performance
43
Our experience is that these defaults work well for small data sets, but once variable size
reaches the GB range, the user is better off determining chunk sizes for their read access
patterns.
In particular, the idea of using 1 for the chunksize of an unlimited dimension works well
if the data are being read a record at a time. Any other read access patterns will result in
slower performance.
4.9.4 Chunking and Parallel I/O
When files are opened for read/write parallel I/O access, the chunk cache is not used.
Therefore it is important to open parallel files with read only access when possible, to
achieve the best performance.
4.9.5 A Utility to Help Benchmark Results: bm file
The bm file utility may be used to copy files, from one netCDF format to another, changing chunking, filter, parallel I/O, and other parameters. This program may be used for
benchmarking netCDF performance for user data files with a range of choices, allowing
data producers to pick settings that best serve their user base.
NetCDF must have been configured with –enable-benchmarks at build time for the
bm file program to be built. When built with –enable-benchmarks, netCDF will include
tests (run with “make check”) that will run the bm file program on sample data files.
Since data files and their access patterns vary from case to case, these benchmark tests
are intended to suggest further use of the bm file program for users.
Here’s an example of a call to bm file:
./bm_file -d -f 3 -o
tst_elena_out.nc -c 0:-1:0:1024:256:256 tst_elena_int_3D.nc
Generally a range of settings must be tested. This is best done with a shell script, which
calls bf file repeatedly, to create output like this:
*** Running benchmarking program bm_file for simple shorts test files, 1D to 6D...
input format, output_format, input size, output size, meta read time, meta write time,
1, 4, 200092, 207283, 1613, 1054, 409, 312, 0, 1208, 1551, 488.998, 641.026, 128.949, 0
1, 4, 199824, 208093, 1545, 1293, 397, 284, 0, 1382, 1563, 503.053, 703.211, 127.775, 0
1, 4, 194804, 204260, 1562, 1611, 390, 10704, 0, 1627, 2578, 499.159, 18.1868, 75.5128,
1, 4, 167196, 177744, 1531, 1888, 330, 265, 0, 12888, 1301, 506.188, 630.347, 128.395,
1, 4, 200172, 211821, 1509, 2065, 422, 308, 0, 1979, 1550, 473.934, 649.351, 129.032, 0
1, 4, 93504, 106272, 1496, 2467, 191, 214, 0, 32208, 809, 488.544, 436.037, 115.342, 0,
*** SUCCESS!!!
Such tables are suitable for import into spreadsheets, for easy graphing of results.
Several test scripts are run during the “make check” of the netCDF build, in the nc test4
directory. The following example may be found in nc test4/run bm elena.sh.
#!/bin/sh
# This shell runs some benchmarks that Elena ran as described here:
# http://hdfeos.org/workshops/ws06/presentations/Pourmal/HDF5_IO_Perf.pdf
# $Id: netcdf.texi,v 1.79 2010/03/30 15:08:17 ed Exp $
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set -e
echo ""
echo "***
./bm_file
./bm_file
./bm_file
./bm_file
./bm_file
./bm_file
echo ’***
Testing the benchmarking program bm_file for simple float file, no compressio
-h -d -f 3 -o tst_elena_out.nc -c 0:-1:0:1024:16:256 tst_elena_int_3D.nc
-d -f 3 -o tst_elena_out.nc -c 0:-1:0:1024:256:256 tst_elena_int_3D.nc
-d -f 3 -o tst_elena_out.nc -c 0:-1:0:512:64:256 tst_elena_int_3D.nc
-d -f 3 -o tst_elena_out.nc -c 0:-1:0:512:256:256 tst_elena_int_3D.nc
-d -f 3 -o tst_elena_out.nc -c 0:-1:0:256:64:256 tst_elena_int_3D.nc
-d -f 3 -o tst_elena_out.nc -c 0:-1:0:256:256:256 tst_elena_int_3D.nc
SUCCESS!!!’
exit 0
The reading that bm file does can be tailored to match the expected access pattern.
The bm file program is controlled with command line options.
./bm_file
bm_file -v [-s N]|[-t V:S:S:S -u V:C:C:C -r V:I:I:I] -o file_out -f N -h -c V:C:C,V:C:C
[-v]
Verbose
[-o file]
Output file name
[-f N]
Output format (1 - classic, 2 - 64-bit offset, 3 - netCDF-4, 4 - netCDF4/
[-h]
Print output header
[-c V:Z:S:C:C:C[,V:Z:S:C:C:C, etc.]] Deflate, shuffle, and chunking parameters for va
[-t V:S:S:S[,V:S:S:S, etc.]] Starts for reads/writes
[-u V:C:C:C[,V:C:C:C, etc.]] Counts for reads/writes
[-r V:I:I:I[,V:I:I:I, etc.]] Incs for reads/writes
[-d]
Doublecheck output by rereading each value
[-m]
Do compare of each data value during doublecheck (slow for large files!)
[-p]
Use parallel I/O
[-s N]
Denom of fraction of slowest varying dimension read.
[-i]
Use MPIIO (only relevant for parallel builds).
[-e 1|2]
Set the endianness of output (1=little 2=big).
file
Name of netCDF file
4.10 Parallel Access with NetCDF-4
Use the special parallel open (or create) calls to open (or create) a file, and then to use
parallel I/O to read or write that file. C programmers see Section “nc open par” in The
NetCDF C Interface Guide, Fortran 77 programmers see Section “NF OPEN PAR” in The
NetCDF Fortran 77 Interface Guide). Fortran 90 programmers use the optional comm and
info parameters to nf90 open/nf90 create to initiate parallel access.
Note that the chunk cache is turned off if a file is opened for parallel I/O in read/write
mode. Open the file in read-only mode to engage the chunk cache.
NetCDF uses the HDF5 parallel programming model for parallel I/O with netCDF4/HDF5 files. The HDF5 tutorial (http://hdfgroup.org/HDF5//HDF5/Tutor) is a good
reference.
Chapter 4: File Structure and Performance
For classic and 64-bit offset files, netCDF uses the
pnetcdf) library from Argonne National Labs/Nortwestern
access of classic and 64-bit offset files, netCDF must
–with-pnetcdf option at build time. See the parallel-netcdf
(http://www.mcs.anl.gov/parallel-netcdf).
45
parallel-netcdf (formerly
University. For parallel
be configured with the
site for more information
4.11 Interoperability with HDF5
To create HDF5 files that can be read by netCDF-4, use HDF5 1.8, which is not yet released.
However most (but not all) of the necessary features can be found in their latest development
snapshot.
HDF5 has some features that will not be supported by netCDF-4, and will cause problems for interoperability:
• HDF5 allows a Group to be both an ancestor and a descendant of another Group,
creating cycles in the subgroup graph. HDF5 also permits multiple parents for a Group.
In the netCDF-4 data model, Groups form a tree with no cycles, so each Group (except
the top-level unnamed Group) has a unique parent.
• HDF5 supports "references" which are like pointers to objects and data regions within
a file. The netCDF-4 data model omits references.
• HDF5 supports some primitive types that are not included in the netCDF-4 data model,
including H5T TIME and H5T BITFIELD.
• HDF5 supports multiple names for data objects like Datasets (netCDF-4 variables)
with no distinguished name. The netCDF-4 data model requires that each variable,
attribute, dimension, and group have a single distinguished name.
These are fairly easy requirements to meet, but there is one relating to shared dimensions
which is a little more challenging. Every HDF5 dataset must have a dimension scale attached
to each dimension.
Dimension scales are a new feature for HF 1.8, which allow specification of shared dimensions.
(In the future netCDF-4 will be able to deal with HDF5 files which do not have dimension
scales. However, this is not expected before netCDF 4.1.)
Finally, there is one feature which is missing from all current HDF5 releases, but which
will be in 1.8 - the ability to track object creation order. As you may know, netCDF keeps
track of the creation order of variables, dimensions, etc. HDF5 (currently) does not.
There is a bit of a hack in place in netCDF-4 files for this, but that hack will go away
when HDF5 1.8 comes out.
Without creation order, the files will still be readable to netCDF-4, it’s just that netCDF4 will number the variables in alphabetical, rather than creation, order.
Interoperability is a complex task, and all of this is in the alpha release stage. It is tested
in libsrc4/tst interops.c, which contains some examples of how to create HDF5 files, modify
them in netCDF-4, and then verify them in HDF5. (And vice versa).
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4.12 DAP Support
Beginning with NetCDF version 4.1, optional support is provided for accessing data through
OPeNDAP servers using the DAP protocol.
DAP support is automatically enabled if a usable curl library can be located using the
curl-config program or by the –with-curl-config flag. It can forcibly be enabled or disabled
using the –enable-dap flag or the –disable-dap flag, respectively. If enabled, then DAP
support requires access to the curl library. Refer to the installation manual for details
Section “Top” in The NetCDF Installation and Porting Guide.
DAP uses a data model that is different from that supported by netCDF, either classic
or enhanced. Generically, the DAP data model is encoded textually in a DDS (Dataset
Descriptor Structure). There is a second data model for DAP attributes, which is encoded
textually in a DAS (Dataset Attribute Structure). For detailed information about the DAP
DDS and DAS, refer to the OPeNDAP web site http://opendap.org.
4.12.1 Accessing OPeNDAP Data
In order to access an OPeNDAP data source through the netCDF API, the file name
normally used is replaced with a URL with a specific format. The URL is composed of four
parts.
1. Client parameters - these are prefixed to the front of the URL and are of the general
form [<name>] or [<name>=value]. Examples include [cache=1] and [netcdf3].
2. URL - this is a standard form URL such as http://test.opendap.org:8080/dods/dts/test.01
3. Constraints - these are suffixed to the URL and take the form “?<projections>&selections”. The meaning of the terms projection and selection is somewhat
complicated; and the OPeNDAP web site, http://www.opendap.or, should be
consulted. The interaction of DAP constraints with netCDF is complex and at the
moment requires an understanding of how DAP is translated to netCDF.
It is possible to see what the translation does to a particular DAP data source in either of
two ways. First, one can examine the DDS source through a web browser and then examine
the translation using the ncdump -h command to see the netCDF Classic translation. The
ncdump output will actually be the union of the DDS with the DAS, so to see the complete
translation, it is necessary to view both.
For example, if a web browser is given the following, the first URL will return the DDS
for the specified dataset, and the second URL will return the DAS for the specified dataset.
http://test.opendap.org:8080/dods/dts/test.01.dds
http://test.opendap.org:8080/dods/dts/test.01.das
Then by using the following ncdump command, it is possible to see the equivalent
netCDF Classic translation.
ncdump -h http://test.opendap.org:8080/dods/dts/test.01
The DDS output from the web server should look like this.
Dataset {
Byte b;
Int32 i32;
UInt32 ui32;
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47
Int16 i16;
UInt16 ui16;
Float32 f32;
Float64 f64;
String s;
Url u;
} SimpleTypes;
The DAS output from the web server should look like this.
Attributes {
Facility {
String
String
String
}
b {
String
String
}
i32 {
String
String
}
}
PrincipleInvestigator ‘‘Mark Abbott’’, ‘‘Ph.D’’;
DataCenter ‘‘COAS Environmental Computer Facility’’;
DrifterType ‘‘MetOcean WOCE/OCM’’;
Description ‘‘A test byte’’;
units ‘‘unknown’’;
Description ‘‘A 32 bit test server int’’;
units ‘‘unknown’’;
The output from ncdump should look like this.
netcdf test {
dimensions:
stringdim64 = 64 ;
variables:
byte b ;
b:Description = "A test byte" ;
b:units = "unknown" ;
int i32 ;
i32:Description = "A 32 bit test server int" ;
i32:units = "unknown" ;
int ui32 ;
short i16 ;
short ui16 ;
float f32 ;
double f64 ;
char s(stringdim64) ;
char u(stringdim64) ;
}
Note that the fields of type String and type URL have suddenly acquired a dimension.
This is because strings are translated to arrays of char, which requires adding an extra
dimension. The size of the dimension is determined in a variety of ways and can be specified.
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It defaults to 64 and when read, the underlying string is either padded or truncated to that
length.
Also note that the Facility attributes do not appear in the translation because they
are neither global nor associated with a variable in the DDS.
Alternately, one can get the text of the DDS as a global attribute by using the client
parameters mechanism . In this case, the parameter “[show=dds]” can be prefixed to the
URL and the data retrieved using the following command
ncdump -h [show=dds]http://test.opendap.org:8080/dods/dts/test.01.dds
The ncdump -h command will then show both the translation and the original DDS. In
the above example, the DDS would appear as the global attribute “ DDS” as follows.
netcdf test {
...
variables:
:_DDS = "Dataset { Byte b; Int32 i32; UInt32 ui32; Int16 i16;
UInt16 ui16; Float32 f32; Float64 f64;
Strings; Url u; } SimpleTypes;"
byte b ;
...
}
4.12.2 DAP to NetCDF Translation Rules
Two translations are currently available.
• DAP 2 Protocol to netCDF-3
• DAP 2 Protocol to netCDF-4
4.12.2.1 netCDF-3 Translation Rules
The current default translation code translates the OPeNDAP protocol to netCDF-3 (classic). This netCDF-3 translation converts an OPeNDAP DAP protocol version 2 DDS to
netCDF-3 and is designed to mimic as closely as possible the translation provided by the
libnc-dap system. In addition, a translation to netCDF-4 (enhanced) is provided that is
entirely new.
For illustrative purposes, the following example will be used.
Dataset {
Int32 f1;
Structure {
Int32 f11;
Structure {
Int32 f1[3];
Int32 f2;
} FS2[2];
} S1;
Structure {
Grid {
Array:
Chapter 4: File Structure and Performance
49
Float32 temp[lat=2][lon=2];
Maps:
Int32 lat[lat=2];
Int32 lon[lon=2];
} G1;
} S2;
Grid {
Array:
Float32 G2[lat=2][lon=2];
Maps:
Int32 lat[2];
Int32 lon[2];
} G2;
Int32 lat[lat=2];
Int32 lon[lon=2];
} D1;
4.12.2.2 Variable Definition
The set of netCDF variables is derived from the fields with primitive base types as they
occur in Sequences, Grids, and Structures. The field names are modified to be fully qualified
initially. For the above, the set of variables are as follows. The coordinate variables within
grids are left out in order to mimic the behavior of libnc-dap.
1. f1
2. S1.f11
3. S1.FS2.f1
4. S1.FS2.f2
5. S2.G1.temp
6. S2.G2.G2
7. lat
8. lon
4.12.2.3 Variable Dimension Translation
A variable’s rank is determined from three sources.
1. The variable has the dimensions associated with the field it represents (e.g. S1.FS2.f1[3]
in the above example).
2. The variable inherits the dimensions associated with any containing structure that has
a rank greater than zero. These dimensions precede those of case 1. Thus, we have in
our example, f1[2][3], where the first dimension comes from the containing Structure
FS2[2].
3. The variable’s set of dimensions are altered if any of its containers is a DAP DDS
Sequence. This is discussed more fully below.
4. If the type of the netCDF variable is char, then an extra string dimension is added as
the last dimension.
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4.12.2.4 Dimension translation
For dimensions, the rules are as follows.
1. Fields in dimensioned structures inherit the dimension of the structure; thus the above
list would have the following dimensioned variables.
• S1.FS2.f1 -> S1.FS2.f1[2][3]
• S1.FS2.f2 -> S1.FS2.f2[2]
• S2.G1.temp -> S2.G1.temp[lat=2][lon=2]
• S2.G1.lat -> S2.G1.lat[lat=2]
• S2.G1.lon -> S2.G1.lon[lon=2]
• S2.G2.G2 -> S2.G2.lon[lat=2][lon=2]
• S2.G2.lat -> S2.G2.lat[lat=2]
• S2.G2.lon -> S2.G2.lon[lon=2]
• lat -> lat[lat=2]
• lon -> lon[lon=2]
2. Collect all of the dimension specifications from the DDS, both named and anonymous
(unnamed) For each unique anonymous dimension with value NN create a netCDF
dimension of the form "XX <i>=NN", where XX is the fully qualified name of the
variable and i is the i’th (inherited) dimension of the array where the anonymous
dimension occurs. For our example, this would create the following dimensions.
• S1.FS2.f1 0 = 2 ;
• S1.FS2.f1 1 = 3 ;
• S1.FS2.f2 0 = 2 ;
• S2.G2.lat 0 = 2 ;
• S2.G2.lon 0 = 2 ;
3. If however, the anonymous dimension is the single dimension of a MAP vector in a
Grid then the dimension is given the same name as the map vector This leads to the
following.
• S2.G2.lat 0 -> S2.G2.lat
• S2.G2.lon 0 -> S2.G2.lon
4. For each unique named dimension "<name>=NN", create a netCDF dimension of the
form "<name>=NN", where name has the qualifications removed. If this leads to
duplicates (i.e. same name and same value), then the duplicates are ignored. This
produces the following.
• S2.G2.lat -> lat
• S2.G2.lon -> lon
Note that this produces duplicates that will be ignored later.
5. At this point the only dimensions left to process should be named dimensions with
the same name as some dimension from step number 3, but with a different value.
For those dimensions create a dimension of the form "<name>M=NN" where M is a
counter starting at 1. The example has no instances of this.
Chapter 4: File Structure and Performance
51
6. Finally and if needed, define a single UNLIMITED dimension named "unlimited" with
value zero. Unlimited will be used to handle certain kinds of DAP sequences (see
below).
This leads to the following set of dimensions.
dimensions:
unlimited =
lat = 2 ;
lon = 2 ;
S1.FS2.f1_0
S1.FS2.f1_1
S1.FS2.f2_0
UNLIMITED;
= 2 ;
= 3 ;
= 2 ;
4.12.2.5 Variable Name Translation
The steps for variable name translation are as follows.
1. Take the set of variables captured above. Thus for the above DDS, the following fields
would be collected.
• f1
• S1.f11
• S1.FS2.f1
• S1.FS2.f2
• S2.G1.temp
• S2.G2.G2
• lat
• lon
2. All grid array variables are renamed to be the same as the containing grid and the grid
prefix is removed. In the above DDS, this results in the following changes.
1. G1.temp -> G1
2. G2.G2 -> G2
It is important to note that this process could produce duplicate variables (i.e. with the
same name); in that case they are all assumed to have the same content and the duplicates
are ignored. If it turns out that the duplicates have different content, then the translation
will not detect this. YOU HAVE BEEN WARNED.
The final netCDF-3 schema (minus attributes) is then as follows.
netcdf t {
dimensions:
unlimited =
lat = 2 ;
lon = 2 ;
S1.FS2.f1_0
S1.FS2.f1_1
S1.FS2.f2_0
variables:
UNLIMITED ;
= 2 ;
= 3 ;
= 2 ;
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int f1 ;
int lat(lat) ;
int lon(lon) ;
int S1.f11 ;
int S1.FS2.f1(S1.FS2.f1_0, S1.FS2.f1_1) ;
int S1.FS2.f2(S1_FS2_f2_0) ;
float S2.G1(lat, lon) ;
float G2(lat, lon) ;
}
In actuality, the unlimited dimension is dropped because it is unused.
There are differences with the original libnc-dap here because libnc-dap technically was
incorrect. The original would have said this, for example.
int S1.FS2.f1(lat, lat) ;
Note that this is incorrect because it dimensions S1.FS2.f1(2,2) rather than
S1.FS2.f1(2,3).
4.12.2.6 Translating DAP DDS Sequences
Any variable (as determined above) that is contained directly or indirectly by a Sequence
is subject to revision of its rank using the following rules.
1. Let the variable be contained in Sequence Q1, where Q1 is the innermost containing
sequence. If Q1 is itself contained (directly or indirectly) in a sequence, or Q1 is contained (again directly or indirectly) in a structure that has rank greater than 0, then
the variable will have an initial UNLIMITED dimension. Further, all dimensions coming from "above" and including (in the containment sense) the innermost Sequence,
Q1, will be removed and replaced by that single UNLIMITED dimension. The size associated with that UNLIMITED is zero, which means that its contents are inaccessible
through the netCDF-3 API. Again, this differs from libnc-dap, which leaves out such
variables. Again, however, this difference is backward compatible.
2. If the variable is contained in a single Sequence (i.e. not nested) and all containing
structures have rank 0, then the variable will have an initial dimension whose size is
the record count for that Sequence. The name of the new dimension will be the name
of the Sequence.
Consider this example.
Dataset {
Structure {
Sequence {
Int32 f1[3];
Int32 f2;
} SQ1;
} S1[2];
Sequence {
Structure {
Int32 x1[7];
} S2[5];
} Q2;
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53
} D;
The corresponding netCDF-3 translation is pretty much as follows (the value for dimension Q2 may differ).
dimensions:
unlimited = UNLIMITED ; // (0 currently)
S1.SQ1.f1_0 = 2 ;
S1.SQ1.f1_1 = 3 ;
S1.SQ1.f2_0 = 2 ;
Q2.S2.x1_0 = 5 ;
Q2.S2.x1_1 = 7 ;
Q2 = 5 ;
variables:
int S1.SQ1.f1(unlimited, S1.SQ1.f1_1) ;
int S1.SQ1.f2(unlimited) ;
int Q2.S2.x1(Q2, Q2.S2.x1_0, Q2.S2.x1_1) ;
Note that for example S1.SQ1.f1 0 is not actually used because it has been folded into
the unlimited dimension.
Note that there is a performance cost because the translation code has to walk the
data to determine how many records are associated with the sequence. Since libnc-dap did
essentially the same thing, it can be assumed that the cost is not prohibitive.
4.12.2.7 netCDF-4 Translation Rules
A DAP to netCDF-4 translation also exists, but is not the default and in any case is only
available if the "–enable-netcdf-4" option is specified at configure time. This translation
includes some elements of the libnc-dap translation, but attempts to provide a simpler (but
not, unfortunately, simple) set of translation rules than is used for the netCDF-3 translation.
Please note that the translation is still experimental and will change to respond to unforeseen
problems or to suggested improvements.
This text will use this running example.
Dataset {
Int32 f1[fdim=10];
Structure {
Int32 f11;
Structure {
Int32 f1[3];
Int32 f2;
} FS2[2];
} S1;
Grid {
Array:
Float32 temp[lat=2][lon=2];
Maps:
Int32 lat[2];
Int32 lon[2];
} G1;
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Sequence {
Float64 depth;
} Q1;
} D
4.12.2.8 Variable Definition
The rule for choosing variables is relatively simple. Start with the names of the top-level
fields of the DDS. The term top-level means that the object is a direct subnode of the
Dataset object. In our example, this produces the set [f1, S1, G1, Q1].
4.12.2.9 Dimension Definition
The rules for choosing and defining dimensions is as follows.
1. Collect the set of dimensions (named and anonymous) directly associated with the
variables as defined above. This means that dimensions within user-defined types are
ignored. From our example, the dimension set is [fdim=10,lat=2,lon=2,2,2]. Note that
the unqualified names are used.
2. All remaining anonymous dimensions are given the name "<var> NN", where "<var>"
is the unqualified name of the variable in which the anonymous dimension appears and
NN is the relative position of that dimension in the dimensions associated with that
array. No instances of this rule occur in the running example.
3. Remove duplicate dimensions (those with same name and value). Our dimension set
now becomes [fdim=10,lat=2,lon=2].
4. The final case occurs when there are dimensions with the same name but with different
values. For this case, the size of the dimension is appended to the dimension name.
4.12.2.10 Type Definition
The rules for choosing user-defined types are as follows.
1. For every Structure, Grid, and Sequence, a netCDF-4 compound type is created whose
fields are the fields of the Structure, Sequence, or Grid. With one exception, the
name of the type is the same as the Structure or Grid name suffixed with " t". The
exception is that the compound types derived from Sequences are instead suffixed with
" record t".
The types of the fields are the types of the corresponding field of the Structure, Sequence, or Grid. Note that this type might be itself a user-defined type.
From the example, we get the following compound types.
compound FS2_t {
int f1(3);
int f2;
};
compound S1_t {
int f11;
FS2_t FS2(2);
};
compound G1_t {
float temp(2,2);
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55
int lat(2);
int lon(2);
}
compound Q1_record_t {
double depth;
};
2. For all sequences of name X, also create this type.
X_record_t (*) X_t
In our example, this produces the following type.
Q1_record_t (*) Q1_t
3. If a Sequence, Q has a single field F, whose type is a primitive type, T, (e.g., int, float,
string), then do not apply the previous rule, but instead replace the whole sequence
with the the following field.
T (*) Q.f
4.12.2.11 Choosing a Translation
The decision about whether to translate to netCDF-3 or netCDF-4 is determined by applying the following rules in order.
1. If the NC CLASSIC MODEL flag is set on nc open(), then netCDF-3 translation is
used.
2. If the NC NETCDF4 flag is set on nc open(), then netCDF-4 translation is used.
3. If the URL is prefixed with the client parameter "[netcdf3]" or "[netcdf-3]" then netCF3 translation is used.
4. If the URL is prefixed with the client parameter "[netcdf4]" or "[netcdf-4]" then netCF4 translation is used.
5. If none of the above holds, then default to netCDF-3 classic translation.
4.12.2.12 Caching
In an effort to provide better performance for some access patterns, client-side caching of
data is available. The default is no caching, but it may be enabled by prefixing the URL
with "[cache]".
Caching operates basically as follows.
1. When a URL is first accessed using nc open(), netCDF automatically does a pre-fetch
of selected variables. These include all variables smaller than a specified (and user
definable) size. This allows, for example, quick access to coordinate variables.
2. Whenever a request is made using some variant of the nc get var() API procedures, the
complete variable is fetched and stored in the cache as a new cache entry. Subsequence
requests for any part of that variable will access the cache entry to obtain the data.
3. The cache may become too full, either because there are too many entries or because it
is taking up too much disk space. In this case cache entries are purged until the cache
size limits are reached. The cache purge algorithm is LRU (least recently used) so that
variables that are repeatedly referenced will tend to stay in the cache.
4. The cache is completely purged when nc close() is invoked.
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In order to decide if you should enable caching, you will need to have some understanding
of the access patterns of your program.
• The ncdump program always dumps one or more whole variables so it turns on caching.
• If your program accesses only parts of a number of variables, then caching should
probably not be used since fetching whole variables will probably slow down your
program for no purpose.
Unfortunately, caching is currently an all or nothing proposition, so for more complex
access patterns, the decision to cache or not may not have an obvious answer. Probably
a good rule of thumb is to avoid caching initially and later turn it on to see its effect on
performance.
4.12.2.13 Defined Client Parameters
Currently, a limited set of client parameters is recognized. Parameters not listed here are
ignored, but no error is signalled.
Parameter Name Legal Values Semantics
[netcdf-3]|[netcdf-3]
Specify translation to netCDF-3.
[netcdf-4]|[netcdf-4]
Specify translation to netCDF-4.
"[log]|[log=<file>]" ""
Turn on logging and send the log output to the specified file. If no file is
specified, then output to standard error.
"[show=...]" das|dds|url
This causes information to appear as specific global attributes. The tags may
be combined using comma with no spaces (e.g. "show=dds,url"). The currently
recognized tags are "dds" to display the underlying DDS, "das" similarly, and
"url" to display the url used to retrieve the data.
"[show=fetch]"
This parameter causes the netCDF code to log a copy of the complete url for
every HTTP get request. If logging is enabled, then this can be helpful in
checking to see the access behavior of the netCDF code.
"[stringlength=NN]"
Specify the default string length to use for string dimensions. The default is
64.
"[stringlength <var>=NN]"
Specify the default string length to use for a string dimension for the specified
variable. The default is 64.
"[cache]"
This enables caching.
"[cachelimit=NN]"
Specify the maximum amount of space allowed for the cache.
"[cachecount=NN]"
Specify the maximum number of entries in the cache.
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4.12.3 Notes on Debugging OPeNDAP Access
The OPeNDAP support makes use of the logging facility of the underlying oc system. Note
that this is currently separate from the existing netCDF logging facility. Turning on this
logging can sometimes give important information. Logging can be enabled by prefixing
the url with the client parameter [log] or [log=filename], where the first case will send log
output to standard error and the second will send log output to the specified file.
Users should also be aware that the DAP subsystem creates temporary files of the name
dataddsXXXXXX, where XXXXX is some random string. If the program using the DAP
subsystem crashes, these files may be left around. It is perfectly safe to delete them. Also,
if you are accessing data over an NFS mount, you may see some .nfsxxxxx files; those can
be ignored as well.
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5 NetCDF Utilities
One of the primary reasons for using the netCDF interface for applications that deal with
arrays is to take advantage of higher-level netCDF utilities and generic applications for
netCDF data. Currently three netCDF utilities are available as part of the netCDF software
distribution:
ncdump
reads a netCDF dataset and prints a textual representation of the information
in the dataset
ncgen/ncgen4
reads a textual representation of a netCDF dataset and generates the corresponding binary netCDF file or a C or FORTRAN program to create the
netCDF dataset
nccopy
reads a netCDF dataset using the netCDF programming interface and copies
it, optionally to a different kind of netCDF dataset
Users have contributed other netCDF utilities, and various visualization and analysis
packages are available that access netCDF data. For an up-to-date list of freely-available
and commercial software that can access or manipulate netCDF data, see the NetCDF
Software list, http://www.unidata.ucar.edu/netcdf/software.html.
This chapter describes the ncgen, ncgen4, and ncdump utilities. These three tools convert
between binary netCDF datasets and a text representation of netCDF datasets. The output
of ncdump and the input to ncgen is a text description of a netCDF dataset in a tiny
language known as CDL (network Common data form Description Language).
5.1 CDL Syntax
Below is an example of CDL, describing a netCDF dataset with several named dimensions
(lat, lon, time), variables (z, t, p, rh, lat, lon, time), variable attributes (units, FillValue,
valid range), and some data.
netcdf foo {
// example netCDF specification in CDL
dimensions:
lat = 10, lon = 5, time = unlimited;
variables:
int
lat(lat), lon(lon), time(time);
float
z(time,lat,lon), t(time,lat,lon);
double p(time,lat,lon);
int
rh(time,lat,lon);
lat:units = "degrees_north";
lon:units = "degrees_east";
time:units = "seconds";
z:units = "meters";
z:valid_range = 0., 5000.;
p:_FillValue = -9999.;
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rh:_FillValue = -1;
data:
lat
lon
}
= 0, 10, 20, 30, 40, 50, 60, 70, 80, 90;
= -140, -118, -96, -84, -52;
All CDL statements are terminated by a semicolon. Spaces, tabs, and newlines can be
used freely for readability. Comments may follow the double slash characters ’//’ on any
line.
A CDL description for a classic model file consists of three optional parts: dimensions,
variables, and data. The variable part may contain variable declarations and attribute
assignments. For the enhanced model supported by netCDF-4, a CDL decription may also
includes groups, subgroups, and user-defined types.
A dimension is used to define the shape of one or more of the multidimensional variables
described by the CDL description. A dimension has a name and a length. At most one
dimension in a classic CDL description can have the unlimited length, which means a
variable using this dimension can grow to any length (like a record number in a file). Any
number of dimensions can be declared of unlimited length in CDL for an enhanced model
file.
A variable represents a multidimensional array of values of the same type. A variable
has a name, a data type, and a shape described by its list of dimensions. Each variable
may also have associated attributes (see below) as well as data values. The name, data
type, and shape of a variable are specified by its declaration in the variable section of a
CDL description. A variable may have the same name as a dimension; by convention such
a variable contains coordinates of the dimension it names.
An attribute contains information about a variable or about the whole netCDF dataset or
containing group. Attributes may be used to specify such properties as units, special values,
maximum and minimum valid values, and packing parameters. Attribute information is
represented by single values or one-dimensional arrays of values. For example, “units” might
be an attribute represented by a string such as “celsius”. An attribute has an associated
variable, a name, a data type, a length, and a value. In contrast to variables that are
intended for data, attributes are intended for ancillary data or metadata (data about data).
In CDL, an attribute is designated by a variable and attribute name, separated by a
colon (’:’). It is possible to assign global attributes to the netCDF dataset as a whole
by omitting the variable name and beginning the attribute name with a colon (’:’). The
data type of an attribute in CDL, if not explicitly specified, is derived from the type of
the value assigned to it. The length of an attribute is the number of data values or the
number of characters in the character string assigned to it. Multiple values are assigned to
non-character attributes by separating the values with commas (’,’). All values assigned to
an attribute must be of the same type. In the netCDF-4 enhanced model, attributes may
be declared to be of user-defined type, like variables.
In CDL, just as for netCDF, the names of dimensions, variables and attributes (and,
in netCDF-4 files, groups, user-defined types, compound member names, and enumeration
symbols) consist of arbitrary sequences of alphanumeric characters, underscore ’ ’, period
’.’, plus ’+’, hyphen ’-’, or at sign ’@’, but beginning with a letter or underscore. However
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61
names commencing with underscore are reserved for system use. Case is significant in
netCDF names. A zero-length name is not allowed. Some widely used conventions restrict
names to only alphanumeric characters or underscores. Names that have trailing space
characters are also not permitted.
Beginning with versions 3.6.3 and 4.0, names may also include UTF-8 encoded Unicode
characters as well as other special characters, except for the character ’/’, which may not
appear in a name (because it is reserved for path names of nested groups). In CDL, most
special characters are escaped with a backslash ’\’ character, but that character is not
actually part of the netCDF name. The special characters that do not need to be escaped
in CDL names are underscore ’ ’, period ’.’, plus ’+’, hyphen ’-’, or at sign ’@’. For the
formal specification of CDL name syntax See Section 1.3 [Format], page 6. Note that by
using special characters in names, you may make your data not compliant with conventions
that have more stringent requirements on valid names for netCDF components, for example
the CF Conventions.
The names for the primitive data types are reserved words in CDL, so names of variables,
dimensions, and attributes must not be primitive type names.
The optional data section of a CDL description is where netCDF variables may be
initialized. The syntax of an initialization is simple:
variable = value_1, value_2, ...;
The comma-delimited list of constants may be separated by spaces, tabs, and newlines.
For multidimensional arrays, the last dimension varies fastest. Thus, row-order rather than
column order is used for matrices. If fewer values are supplied than are needed to fill a
variable, it is extended with the fill value. The types of constants need not match the type
declared for a variable; coercions are done to convert integers to floating point, for example.
All meaningful type conversions among primitive types are supported.
A special notation for fill values is supported: the ‘_’ character designates a fill value for
variables.
5.2 CDL Data Types
The CDL primitive data types for the classic model are:
char
Characters.
byte
Eight-bit integers.
short
16-bit signed integers.
int
32-bit signed integers.
long
(Deprecated, synonymous with int)
float
IEEE single-precision floating point (32 bits).
real
(Synonymous with float).
double
IEEE double-precision floating point (64 bits).
NetCDF-4 supports the additional primitive types:
ubyte
Unsigned eight-bit integers.
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ushort
Unsigned 16-bit integers.
uint
Unsigned 32-bit integers.
int64
64-bit singed integers.
uint64
Unsigned 64-bit singed integers.
string
Variable-length string of characters
Except for the added data-type byte, CDL supports the same primitive data types as C.
For backward compatibility, in declarations primitive type names may be specified in either
upper or lower case.
The byte type differs from the char type in that it is intended for numeric data, and
the zero byte has no special significance, as it may for character data. The short type
holds values between -32768 and 32767. The ushort type holds values between 0 and
65536. The int type can hold values between -2147483648 and 2147483647. The uint
type holds values between 0 and 4294967296. The int64 type can hold values between 9223372036854775808 and 9223372036854775807. The uint64 type can hold values between
0 and 18446744073709551616.
The float type can hold values between about -3.4+38 and 3.4+38, with external representation as 32-bit IEEE normalized single-precision floating-point numbers. The double
type can hold values between about -1.7+308 and 1.7+308, with external representation as
64-bit IEEE standard normalized double-precision, floating-point numbers. The string type
holds variable length strings.
5.3 CDL Notation for Data Constants
This section describes the CDL notation for constants.
Attributes are initialized in the variables section of a CDL description by providing a list
of constants that determines the attribute’s length and type (if primitive and not explicitly
declared). CDL defines a syntax for constant values that permits distinguishing among
different netCDF primitive types. The syntax for CDL constants is similar to C syntax,
with type suffixes appended to bytes, shorts, and floats to distinguish them from ints and
doubles.
A byte constant is represented by a single character or multiple character escape sequence
enclosed in single quotes. For example:
’a’
’\0’
’\n’
’\33’
’\x2b’
’\376’
//
//
//
//
//
//
ASCII a
a zero byte
ASCII newline character
ASCII escape character (33 octal)
ASCII plus (2b hex)
377 octal = -127 (or 254) decimal
Character constants are enclosed in double quotes. A character array may be represented
as a string enclosed in double quotes. Multiple strings are concatenated into a single array
of characters, permitting long character arrays to appear on multiple lines. To support
multiple variable-length string values, a conventional delimiter such as ’,’ may be used, but
interpretation of any such convention for a string delimiter must be implemented in software
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63
above the netCDF library layer. The usual escape conventions for C strings are honored.
For example:
"a"
"Two\nlines\n"
"a bell:\007"
"ab","cde"
//
//
//
//
ASCII ’a’
a 10-character string with two embedded newlines
a string containing an ASCII bell
the same as "abcde"
The form of a short constant is an integer constant with an ’s’ or ’S’ appended. If a
short constant begins with ’0’, it is interpreted as octal. When it begins with ’0x’, it is
interpreted as a hexadecimal constant. For example:
2s
0123s
0x7ffs
// a short 2
// octal
// hexadecimal
The form of an int constant is an ordinary integer constant. If an int constant begins with
’0’, it is interpreted as octal. When it begins with ’0x’, it is interpreted as a hexadecimal
constant. Examples of valid int constants include:
-2
0123
0x7ff
1234567890L
// octal
// hexadecimal
// deprecated, uses old long suffix
The float type is appropriate for representing data with about seven significant digits of
precision. The form of a float constant is the same as a C floating-point constant with an
’f’ or ’F’ appended. A decimal point is required in a CDL float to distinguish it from an
integer. For example, the following are all acceptable float constants:
-2.0f
3.14159265358979f
1.f
.1f
// will be truncated to less precision
The double type is appropriate for representing floating-point data with about 16 significant digits of precision. The form of a double constant is the same as a C floating-point
constant. An optional ’d’ or ’D’ may be appended. A decimal point is required in a CDL
double to distinguish it from an integer. For example, the following are all acceptable double
constants:
-2.0
3.141592653589793
1.0e-20
1.d
5.4 ncgen
The ncgen tool generates a netCDF file or a C or FORTRAN program that creates a netCDF
dataset. If no options are specified in invoking ncgen, the program merely checks the syntax
of the CDL input, producing error messages for any violations of CDL syntax.
The ncgen tool is now is capable of producing netcdf-4 files. It operates essentially
identically to the original ncgen.
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The CDL input to ncgen may include data model constructs from the netcdf- data model.
In particular, it includes new primitive types such as unsigned integers and strings, opaque
data, enumerations, and user-defined constructs using vlen and compound types. The ncgen
man page should be consulted for more detailed information.
UNIX syntax for invoking ncgen:
ncgen [-b] [-o netcdf-file] [-c] [-f] [-k<kind>] [-l<language>] [-x] [input-file]
where:
-b
Create a (binary) netCDF file. If the ’-o’ option is absent, a default file name
will be constructed from the netCDF name (specified after the netcdf keyword
in the input) by appending the ’.nc’ extension. Warning: if a file already exists
with the specified name it will be overwritten.
-o netcdf-file
Name for the netCDF file created. If this option is specified, it implies the ’-b’
option. (This option is necessary because netCDF files are direct-access files
created with seek calls, and hence cannot be written to standard output.)
-c
Generate C source code that will create a netCDF dataset matching the netCDF
specification. The C source code is written to standard output. This is only
useful for relatively small CDL files, since all the data is included in variable
initializations in the generated program. The -c flag is deprecated and the -lc
flag should be used intstead.
-f
Generate FORTRAN source code that will create a netCDF dataset matching
the netCDF specification. The FORTRAN source code is written to standard
output. This is only useful for relatively small CDL files, since all the data
is included in variable initializations in the generated program. The -f flag is
deprecated and the -lf77 flag should be used intstead.
-k
The -k file specifies the kind of netCDF file to generate. The arguments to the
-k flag can be as follows.
• 1, classic – Produce a netcdf classic file format file."
• 2, 64-bit-offset, ’64-bit offset’ – Produce a netcdf 64 bit classic file format
file.
• 3, hdf5, netCDF-4, enhanced – Produce a netcdf-4 format file.
• 4, hdf5-nc3, ’netCDF-4 classic model’, enhanced-nc3 – Produce a netcdf-4
file format, but restricted to netcdf-3 classic CDL intput.
Note that the -v flag is a deprecated alias for -k.
-l
The -l file specifies that ncgen should output (to standard output) the text of
a program that, when compiled and executed, will produce the corresponding
binary .nc file. The arguments to the -l flag can be as follows.
• c|C => C language output.
• f77|fortran77 => FORTRAN 77 language output; note that currently only
the classic model is supported for fortran output.
• cml|CML => (experimental) NcML language output
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65
• j|java => (experimental) Java language output; the generated java code
targets the existing Unidata Java interface, which means that only the
classic model is supported.
-x
Use “no fill” mode, omitting the initialization of variable values with fill values.
This can make the creation of large files much faster, but it will also eliminate
the possibility of detecting the inadvertent reading of values that haven’t been
written.
Examples
Check the syntax of the CDL file foo.cdl:
ncgen foo.cdl
From the CDL file foo.cdl, generate an equivalent binary netCDF file named bar.nc:
ncgen -o bar.nc foo.cdl
From the CDL file foo.cdl, generate a C program containing netCDF function invocations
that will create an equivalent binary netCDF dataset:
ncgen -c foo.cdl > foo.c
5.5 ncdump
The ncdump tool generates the CDL text representation of a netCDF dataset on standard
output, optionally excluding some or all of the variable data in the output. The output from
ncdump is intended to be acceptable as input to ncgen. Thus ncdump and ncgen can be
used as inverses to transform data representation between binary and text representations.
As of NetCDF version 4.1, ncdump can also access DAP data sources if DAP support is
enabled in the underlying NetCDF library. Instead of specifying a file name as argument
to ncdump, the user specifies a URL to a DAP source.
ncdump may also be used as a simple browser for netCDF datasets, to display the
dimension names and lengths; variable names, types, and shapes; attribute names and
values; and optionally, the values of data for all variables or selected variables in a netCDF
dataset.
ncdump defines a default format used for each type of netCDF variable data, but this
can be overridden if a C format attribute is defined for a netCDF variable. In this case,
ncdump will use the C format attribute to format values for that variable. For example,
if floating-point data for the netCDF variable Z is known to be accurate to only three
significant digits, it might be appropriate to use this variable attribute:
Z:C_format = "%.3g"
ncdump uses ’ ’ to represent data values that are equal to the FillValue attribute for
a variable, intended to represent data that has not yet been written. If a variable has no
FillValue attribute, the default fill value for the variable type is used unless the variable is
of byte type.
UNIX syntax for invoking ncdump:
ncdump [ -c | -h] [-v var1,...] [-b lang] [-f lang]
[-l len] [ -p fdig[,ddig]] [ -s ] [ -n name] [input-file]
where:
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-c
Show the values of coordinate variables (variables that are also dimensions) as
well as the declarations of all dimensions, variables, and attribute values. Data
values of non-coordinate variables are not included in the output. This is often
the most suitable option to use for a brief look at the structure and contents of
a netCDF dataset.
-h
Show only the header information in the output, that is, output only the declarations for the netCDF dimensions, variables, and attributes of the input file,
but no data values for any variables. The output is identical to using the ’-c’
option except that the values of coordinate variables are not included. (At most
one of ’-c’ or ’-h’ options may be present.)
-v var1,...
The output will include data values for the specified variables, in addition to the
declarations of all dimensions, variables, and attributes. One or more variables
must be specified by name in the comma-delimited list following this option.
The list must be a single argument to the command, hence cannot contain
blanks or other white space characters. The named variables must be valid
netCDF variables in the input-file. The default, without this option and in the
absence of the ’-c’ or ’-h’ options, is to include data values for all variables in
the output.
-b lang
A brief annotation in the form of a CDL comment (text beginning with the
characters ’//’) will be included in the data section of the output for each
’row’ of data, to help identify data values for multidimensional variables. If
lang begins with ’C’ or ’c’, then C language conventions will be used (zerobased indices, last dimension varying fastest). If lang begins with ’F’ or ’f’,
then FORTRAN language conventions will be used (one-based indices, first
dimension varying fastest). In either case, the data will be presented in the
same order; only the annotations will differ. This option may be useful for
browsing through large volumes of multidimensional data.
-f lang
Full annotations in the form of trailing CDL comments (text beginning with the
characters ’//’) for every data value (except individual characters in character
arrays) will be included in the data section. If lang begins with ’C’ or ’c’, then
C language conventions will be used (zero-based indices, last dimension varying
fastest). If lang begins with ’F’ or ’f’, then FORTRAN language conventions
will be used (one-based indices, first dimension varying fastest). In either case,
the data will be presented in the same order; only the annotations will differ.
This option may be useful for piping data into other filters, since each data
value appears on a separate line, fully identified. (At most one of ’-b’ or ’-f’
options may be present.)
-l len
Changes the default maximum line length (80) used in formatting lists of noncharacter data values.
-p float_digits[,double_digits]
Specifies default precision (number of significant digits) to use in displaying
floating-point or double precision data values for attributes and variables. If
specified, this value overrides the value of the C format attribute, if any, for
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a variable. Floating-point data will be displayed with float digits significant
digits. If double digits is also specified, double-precision values will be displayed
with that many significant digits. In the absence of any ’-p’ specifications,
floating-point and double-precision data are displayed with 7 and 15 significant
digits respectively. CDL files can be made smaller if less precision is required.
If both floating-point and double precisions are specified, the two values must
appear separated by a comma (no blanks) as a single argument to the command.
-n name
CDL requires a name for a netCDF dataset, for use by ’ncgen -b’ in generating
a default netCDF dataset name. By default, ncdump constructs this name from
the last component of the file name of the input netCDF dataset by stripping off
any extension it has. Use the ’-n’ option to specify a different name. Although
the output file name used by ’ncgen -b’ can be specified, it may be wise to have
ncdump change the default name to avoid inadvertently overwriting a valuable
netCDF dataset when using ncdump, editing the resulting CDL file, and using
’ncgen -b’ to generate a new netCDF dataset from the edited CDL file.
-s
Specifies that special virtual attributes should be output for the file format
variant and for variable properties such as compression, chunking, and other
properties specific to the format implementation that are primarily related to
performance rather than the logical schema of the data. All the special virtual
attributes begin with ’ ’ followed by an upper-case letter. Currently they include the global attribute “ Format” and the variable attributes “ Fletcher32”,
“ ChunkSizes”, “ Endianness”, “ DeflateLevel”, “ Shuffle”, “ Storage”, and
“ NoFill”. The ncgen4 utility currently handles these correctly, as will the
ncgen utility in a future release.
Examples
Look at the structure of the data in the netCDF dataset foo.nc:
ncdump -c foo.nc
Produce an annotated CDL version of the structure and data in the netCDF dataset
foo.nc, using C-style indexing for the annotations:
ncdump -b c foo.nc > foo.cdl
Output data for only the variables uwind and vwind from the netCDF dataset foo.nc,
and show the floating-point data with only three significant digits of precision:
ncdump -v uwind,vwind -p 3 foo.nc
Produce a fully-annotated (one data value per line) listing of the data for the variable
omega, using FORTRAN conventions for indices, and changing the netCDF dataset name
in the resulting CDL file to omega:
ncdump -v omega -f fortran -n omega foo.nc > Z.cdl
Examine the translated DDS for the DAP source from the specified URL.
ncdump -h http://test.opendap.org:8080/dods/dts/test.01
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5.6 ncgen3
The ncgen3 tool is the new name for the older, original ncgen utility.
The ncgen3 tool generates a netCDF file or a C or FORTRAN program that creates a
netCDF dataset. If no options are specified in invoking ncgen3, the program merely checks
the syntax of the CDL input, producing error messages for any violations of CDL syntax.
The ncgen3 utility can only generate classic-model netCDF-4 files or programs.
UNIX syntax for invoking ncgen3:
ncgen3 [-b] [-o netcdf-file] [-c] [-f] [-v2|-v3] [-x] [input-file]
where:
-b
Create a (binary) netCDF file. If the ’-o’ option is absent, a default file name
will be constructed from the netCDF name (specified after the netcdf keyword
in the input) by appending the ’.nc’ extension. Warning: if a file already exists
with the specified name it will be overwritten.
-o netcdf-file
Name for the netCDF file created. If this option is specified, it implies the ’-b’
option. (This option is necessary because netCDF files are direct-access files
created with seek calls, and hence cannot be written to standard output.)
-c
Generate C source code that will create a netCDF dataset matching the netCDF
specification. The C source code is written to standard output. This is only
useful for relatively small CDL files, since all the data is included in variable
initializations in the generated program.
-f
Generate FORTRAN source code that will create a netCDF dataset matching
the netCDF specification. The FORTRAN source code is written to standard
output. This is only useful for relatively small CDL files, since all the data is
included in variable initializations in the generated program.
-v2
The generated netCDF file or program will use the version of the format with
64-bit offsets, to allow for the creation of very large files. These files are not as
portable as classic format netCDF files, because they require version 3.6.0 or
later of the netCDF library.
-v3
The generated netCDF file will be in netCDF-4/HDF5 format. These files are
not as portable as classic format netCDF files, because they require version 4.0
or later of the netCDF library.
-x
Use “no fill” mode, omitting the initialization of variable values with fill values.
This can make the creation of large files much faster, but it will also eliminate
the possibility of detecting the inadvertent reading of values that haven’t been
written.
Appendix A: Units
69
Appendix A Units
The Unidata Program Center has developed a units library to convert between formatted
and binary forms of units specifications and perform unit algebra on the binary form.
Though the units library is self-contained and there is no dependency between it and
the netCDF library, it is nevertheless useful in writing generic netCDF programs and
we suggest you obtain it. The library and associated documentation is available from
http://www.unidata.ucar.edu/packages/udunits/.
The following are examples of units strings that can be interpreted by the utScan()
function of the Unidata units library:
10 kilogram.meters/seconds2
10 kg-m/sec2
10 kg m/s^2
10 kilogram meter second-2
(PI radian)2
degF
100rpm
geopotential meters
33 feet water
milliseconds since 1992-12-31 12:34:0.1 -7:00
A unit is specified as an arbitrary product of constants and unit-names raised to arbitrary
integral powers. Division is indicated by a slash ’/’. Multiplication is indicated by white
space, a period ’.’, or a hyphen ’-’. Exponentiation is indicated by an integer suffix or
by the exponentiation operators ’^’ and ’**’. Parentheses may be used for grouping and
disambiguation. The time stamp in the last example is handled as a special case.
Arbitrary Galilean transformations (i.e., y = ax + b) are allowed. In particular, temperature conversions are correctly handled. The specification:
degF
32
indicates a Fahrenheit scale with the origin shifted to thirty-two degrees Fahrenheit (i.e.,
to zero Celsius). Thus, the Celsius scale is equivalent to the following unit:
1.8 degF
32
Note that the origin-shift operation takes precedence over multiplication. In order of
increasing precedence, the operations are division, multiplication, origin-shift, and exponentiation.
utScan() understands all the SI prefixes (e.g. "mega" and "milli") plus their abbreviations (e.g. "M" and "m")
The function utPrint() always encodes a unit specification one way. To reduce misunderstandings, it is recommended that this encoding style be used as the default. In general, a
unit is encoded in terms of basic units, factors, and exponents. Basic units are separated by
spaces, and any exponent directly appends its associated unit. The above examples would
be encoded as follows:
10 kilogram meter second-2
9.8696044 radian2
0.555556 kelvin 255.372
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10.471976 radian second-1
9.80665 meter2 second-2
98636.5 kilogram meter-1 second-2
0.001 seconds since 1992-12-31 19:34:0.1000 UTC
(Note that the Fahrenheit unit is encoded as a deviation, in fractional kelvins, from an
origin at 255.372 kelvin, and that the time in the last example has been referenced to UTC.)
The database for the units library is a formatted file containing unit definitions and is
used to initialize this package. It is the first place to look to discover the set of valid names
and symbols.
The format for the units-file is documented internally and the file may be modified by
the user as necessary. In particular, additional units and constants may be easily added
(including variant spellings of existing units or constants).
utScan() is case-sensitive. If this causes difficulties, you might try making appropriate
additional entries to the units-file.
Some unit abbreviations in the default units-file might seem counter-intuitive. In particular, note the following:
For
Use
Not
Which
Means
Instead
Celsius
Celsius
C
coulomb
gram
gram
g
<standard free fall>
gallon
gallon
gal
<acceleration>
radian
radian
rad
<absorbed dose>
Newton
newton or N
nt
nit (unit of photometry)
For additional information on this units library, please consult the manual pages that
come with its distribution.
Appendix B: Attribute Conventions
71
Appendix B Attribute Conventions
Names commencing with underscore (’ ’) are reserved for use by the netCDF library. Most
generic applications that process netCDF datasets assume standard attribute conventions
and it is strongly recommended that these be followed unless there are good reasons for not
doing so. Below we list the names and meanings of recommended standard attributes that
have proven useful. Note that some of these (e.g. units, valid range, scale factor) assume
numeric data and should not be used with character data.
units
A character string that specifies the units used for the variable’s data. Unidata
has developed a freely-available library of routines to convert between character
string and binary forms of unit specifications and to perform various useful operations on the binary forms. This library is used in some netCDF applications.
Using the recommended units syntax permits data represented in conformable
units to be automatically converted to common units for arithmetic operations.
For more information see Appendix A [Units], page 69.
long_name
A long descriptive name. This could be used for labeling plots, for example. If
a variable has no long name attribute assigned, the variable name should be
used as a default.
_FillValue
The FillValue attribute specifies the fill value used to pre-fill disk space allocated to the variable. Such pre-fill occurs unless nofill mode is set using
nc set fill in C (see Section “nc set fill” in The NetCDF C Interface Guide)
or NF SET FILL in Fortran (see Section “NF SET FILL” in The NetCDF
Fortran 77 Interface Guide). The fill value is returned when reading values
that were never written. If FillValue is defined then it should be scalar and of
the same type as the variable. If the variable is packed using scale factor and
add offset attributes (see below), the FillValue attribute should have the data
type of the packed data.
It is not necessary to define your own FillValue attribute for a variable if the
default fill value for the type of the variable is adequate. However, use of the
default fill value for data type byte is not recommended. Note that if you change
the value of this attribute, the changed value applies only to subsequent writes;
previously written data are not changed.
Generic applications often need to write a value to represent undefined or missing values. The fill value provides an appropriate value for this purpose because
it is normally outside the valid range and therefore treated as missing when read
by generic applications. It is legal (but not recommended) for the fill value to
be within the valid range.
For more information for C programmers see Section “Fill Values” in The
NetCDF C Interface Guide. For more information for Fortran programmers
see Section “Fill Values” in The NetCDF Fortran 77 Interface Guide.
missing_value
This attribute is not treated in any special way by the library or conforming
generic applications, but is often useful documentation and may be used by
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specific applications. The missing value attribute can be a scalar or vector
containing values indicating missing data. These values should all be outside
the valid range so that generic applications will treat them as missing.
When scale factor and add offset are used for packing, the value(s) of the missing value attribute should be specified in the domain of the data in the file (the
packed data), so that missing values can be detected before the scale factor and
add offset are applied.
valid_min
A scalar specifying the minimum valid value for this variable.
valid_max
A scalar specifying the maximum valid value for this variable.
valid_range
A vector of two numbers specifying the minimum and maximum valid values for this variable, equivalent to specifying values for both valid min and
valid max attributes. Any of these attributes define the valid range. The
attribute valid range must not be defined if either valid min or valid max is
defined.
Generic applications should treat values outside the valid range as missing. The
type of each valid range, valid min and valid max attribute should match the
type of its variable (except that for byte data, these can be of a signed integral
type to specify the intended range).
If neither valid min, valid max nor valid range is defined then generic applications should define a valid range as follows. If the data type is byte and
FillValue is not explicitly defined, then the valid range should include all possible values. Otherwise, the valid range should exclude the FillValue (whether
defined explicitly or by default) as follows. If the FillValue is positive then
it defines a valid maximum, otherwise it defines a valid minimum. For integer
types, there should be a difference of 1 between the FillValue and this valid
minimum or maximum. For floating point types, the difference should be twice
the minimum possible (1 in the least significant bit) to allow for rounding error.
If the variable is packed using scale factor and add offset attributes (see below),
the FillValue, missing value, valid range, valid min, or valid max attributes
should have the data type of the packed data.
scale_factor
If present for a variable, the data are to be multiplied by this factor after the
data are read by the application that accesses the data.
If valid values are specified using the valid min, valid max, valid range, or
FillValue attributes, those values should be specified in the domain of the
data in the file (the packed data), so that they can be interpreted before the
scale factor and add offset are applied.
add_offset
If present for a variable, this number is to be added to the data after it is read
by the application that accesses the data. If both scale factor and add offset
attributes are present, the data are first scaled before the offset is added. The
Appendix B: Attribute Conventions
73
attributes scale factor and add offset can be used together to provide simple
data compression to store low-resolution floating-point data as small integers in
a netCDF dataset. When scaled data are written, the application should first
subtract the offset and then divide by the scale factor, rounding the result to
the nearest integer to avoid a bias caused by truncation towards zero.
When scale factor and add offset are used for packing, the associated variable
(containing the packed data) is typically of type byte or short, whereas the
unpacked values are intended to be of type float or double. The attributes
scale factor and add offset should both be of the type intended for the unpacked
data, e.g. float or double.
signedness
Deprecated attribute, originally designed to indicate whether byte values should
be treated as signed or unsigned. The attributes valid min and valid max may
be used for this purpose. For example, if you intend that a byte variable store
only non-negative values, you can use valid min = 0 and valid max = 255. This
attribute is ignored by the netCDF library.
C_format
A character array providing the format that should be used by C applications
to print values for this variable. For example, if you know a variable is only accurate to three significant digits, it would be appropriate to define the C format
attribute as "%.3g". The ncdump utility program uses this attribute for variables for which it is defined. The format applies to the scaled (internal) type
and value, regardless of the presence of the scaling attributes scale factor and
add offset.
FORTRAN_format
A character array providing the format that should be used by FORTRAN
applications to print values for this variable. For example, if you know a variable
is only accurate to three significant digits, it would be appropriate to define the
FORTRAN format attribute as "(G10.3)".
title
A global attribute that is a character array providing a succinct description of
what is in the dataset.
history
A global attribute for an audit trail. This is a character array with a line
for each invocation of a program that has modified the dataset. Well-behaved
generic netCDF applications should append a line containing: date, time of
day, user name, program name and command arguments.
Conventions
If present, ’Conventions’ is a global attribute that is a character array for the
name of the conventions followed by the dataset. Originally, these conventions were named by a string that was interpreted as a directory name relative
to the directory /pub/netcdf/Conventions/ on the host ftp.unidata.ucar.edu.
The web page http://www.unidata.ucar.edu/netcdf/conventions.html is now
the preferred and authoritative location for registering a URI reference to a
set of conventions maintained elsewhere. The FTP site will be preserved for
compatibility with existing references, but authors of new conventions should
submit a request to support-netcdf@unidata.ucar.edu for listing on the Unidata
conventions web page.
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It may be convenient for defining institutions and groups to use a hierarchical
structure for general conventions and more specialized conventions. For example, if a group named NUWG agrees upon a set of conventions for dimension
names, variable names, required attributes, and netCDF representations for
certain discipline-specific data structures, they may store a document describing the agreed-upon conventions in a dataset in the NUWG/ subdirectory of the
Conventions directory. Datasets that followed these conventions would contain
a global Conventions attribute with value "NUWG".
Later, if the group agrees upon some additional conventions for a specific subset of NUWG data, for example time series data, the description of the additional conventions might be stored in the NUWG/Time series/ subdirectory,
and datasets that adhered to these additional conventions would use the global
Conventions attribute with value "NUWG/Time series", implying that this
dataset adheres to the NUWG conventions and also to the additional NUWG
time-series conventions.
It is possible for a netCDF file to adhere to more than one set of conventions,
even when there is no inheritance relationship among the conventions. In this
case, the value of the ‘Conventions’ attribute may be a single text string containing a list of the convention names separated by blank space (recommended)
or commas (if a convention name contains blanks).
Typical conventions web sites will include references to documents in some form
agreed upon by the community that supports the conventions and examples of
netCDF file structures that follow the conventions.
Appendix C: File Format Specification
75
Appendix C File Format Specification
In different contexts, “netCDF” may refer to an abstract data model, a software implementation with associated application program interfaces (APIs), or a data format. Confusion
may easily arise in discussions of different versions of the data models, software, and formats, because the relationships among versions of these entities is more complex than a
simple one-to-one correspondence by version. For example, compatibility commitments require that new versions of the software support all previous variants of the format and data
model.
To avoid this potential confusion, we assign distinct names to versions of the formats,
data models, and software releases that will be used consistently in the remainder of this
appendix.
In this appendix, two format variants are specified formally, the classic format and the
64-bit offset format for netCDF data. Two additional format variants are discussed less
formally, the netCDF-4 format and the netCDF-4 classic model format.
The classic format was the only format for netCDF data created between 1989 and
2004 by various versions of the reference software from Unidata. In 2004, the 64-bit offset
format variant was introduced for creation of and access to much larger files. The reference
software, available for C-based and Java-based programs, supported use of the same APIs
for accessing either classic or 64-bit offset files, so programs reading the files would not have
to depend on which format was used.
There are only two netCDF data models, the classic model and the enhanced model.
The classic model is the simpler of the two, and is used for all data stored in classic format,
64-bit offset format, or netCDF-4 classic model format. The enhanced model (also referred
to as the netCDF- 4 data model) was introduced in 2008 as an extension of the classic
model that adds more powerful forms of data representation and data types at the expense
of some additional complexity. Although data represented with the classic model can also
be represented using the enhanced model, datasets that use features of the enhanced model,
such as user-defined nested data types, cannot be represented with the classic model. Use of
added features of the enhanced model requires that data be stored in the netCDF-4 format.
Versions 1.0 through 3.5 of the Unidata C-based reference software, released between
1989 and 2000, supported only the classic data model and classic format. Version 3.6,
released in late 2004, first provided support for the 64-bit offset format, but still used
the classic data model. With version 4.0, released in 2008, the enhanced data model was
introduced along with the two new HDF5-based format variants, the netCDF-4 format
and the netCDF-4 classic model format. Evolution of the data models, formats, and APIs
will continue the commitment to support all previous netCDF data models, data format
variants, and APIs in future software releases.
Use of the HDF5 storage layer in netCDF-4 software provides features for improved
performance, independent of the data model used, for example compression and dynamic
schema changes. Such performance improvements are available for data stored in the
netCDF-4 classic model format, even when accessed by programs that only support the
classic model.
Related formats not discussed in this appendix include CDL (“Common Data Language”,
the original ASCII form of binary netCDF data), and NcML (NetCDF Markup Language,
an XML-based representation for netCDF metadata and data).
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Knowledge of format details is not required to read or write netCDF datasets. Software
that reads netCDF data using the reference implementation automatically detects and uses
the correct version of the format for accessing data. Understanding details may be helpful
for understanding performance issues related to disk or server access.
The netCDF reference library, developed and supported by Unidata, is written in C,
with Fortran77, Fortran90, and C++ interfaces. A number of community and commercially
supported interfaces to other languages are also available, including IDL, Matlab, Perl,
Python, and Ruby. An independent implementation, also developed and supported by
Unidata, is written entirely in Java.
C.1 The NetCDF Classic Format Specification
To present the format more formally, we use a BNF grammar notation. In this notation:
• Non-terminals (entities defined by grammar rules) are in lower case.
• Terminals (atomic entities in terms of which the format specification is written) are
in upper case, and are specified literally as US-ASCII characters within single-quote
characters or are described with text between angle brackets (‘<’ and ‘>’).
• Optional entities are enclosed between braces (‘[’ and ‘]’).
• A sequence of zero or more occurrences of an entity is denoted by ‘[entity ...]’.
• A vertical line character (‘|’) separates alternatives. Alternation has lower precedence
than concatenation.
• Comments follow ‘//’ characters.
• A single byte that is not a printable character is denoted using a hexadecimal number
with the notation ‘\xDD’, where each D is a hexadecimal digit.
• A literal single-quote character is denoted by ‘\’’, and a literal back-slash character is
denoted by ‘\\’.
Following the grammar, a few additional notes are included to specify format characteristics that are impractical to capture in a BNF grammar, and to note some special cases for
implementers. Comments in the grammar point to the notes and special cases, and help to
clarify the intent of elements of the format.
The Format in Detail
netcdf_file
header
magic
VERSION
=
=
=
=
numrecs
dim_list
gatt_list
att_list
var_list
ABSENT
ZERO
NC_DIMENSION
=
=
=
=
=
=
=
=
header data
magic numrecs dim_list gatt_list var_list
’C’ ’D’ ’F’ VERSION
\x01 |
// classic format
\x02
// 64-bit offset format
NON_NEG | STREAMING
// length of record dimension
ABSENT | NC_DIMENSION nelems [dim ...]
att_list
// global attributes
ABSENT | NC_ATTRIBUTE nelems [attr ...]
ABSENT | NC_VARIABLE
nelems [var ...]
ZERO ZERO
// Means list is not present
\x00 \x00 \x00 \x00
// 32-bit zero
\x00 \x00 \x00 \x0A
// tag for list of dimensions
Appendix C: File Format Specification
NC_VARIABLE
NC_ATTRIBUTE
nelems
dim
name
=
=
=
=
=
namestring
ID1
IDN
alphanumeric
lowercase
=
=
=
=
=
uppercase
=
numeric
=
special1
=
special2
=
MUTF8
dim_length
=
=
attr
nc_type
=
=
var
=
dimid
=
vatt_list
=
77
\x00 \x00 \x00 \x0B
// tag for list of variables
\x00 \x00 \x00 \x0C
// tag for list of attributes
NON_NEG
// number of elements in following sequence
name dim_length
nelems namestring
// Names a dimension, variable, or attribute.
// Names should match the regular expression
// ([a-zA-Z0-9_]|{MUTF8})([^\x00-\x1F/\x7F-\xFF]|{MUTF8})*
// For other constraints, see "Note on names", below.
ID1 [IDN ...] padding
alphanumeric | ’_’
alphanumeric | special1 | special2
lowercase | uppercase | numeric | MUTF8
’a’|’b’|’c’|’d’|’e’|’f’|’g’|’h’|’i’|’j’|’k’|’l’|’m’|
’n’|’o’|’p’|’q’|’r’|’s’|’t’|’u’|’v’|’w’|’x’|’y’|’z’
’A’|’B’|’C’|’D’|’E’|’F’|’G’|’H’|’I’|’J’|’K’|’L’|’M’|
’N’|’O’|’P’|’Q’|’R’|’S’|’T’|’U’|’V’|’W’|’X’|’Y’|’Z’
’0’|’1’|’2’|’3’|’4’|’5’|’6’|’7’|’8’|’9’
// special1 chars have traditionally been
// permitted in netCDF names.
’_’|’.’|’@’|’+’|’-’
// special2 chars are recently permitted in
// names (and require escaping in CDL).
// Note: ’/’ is not permitted.
’ ’ | ’!’ | ’"’ | ’#’ | ’$’ | ’%’ | ’&’ | ’\’’ |
’(’ | ’)’ | ’*’ | ’,’ | ’:’ | ’;’ | ’<’ | ’=’ |
’>’ | ’?’ | ’[’ | ’\\’ | ’]’ | ’^’ | ’‘’ | ’{’ |
’|’ | ’}’ | ’~’
<multibyte UTF-8 encoded, NFC-normalized Unicode character>
NON_NEG
// If zero, this is the record dimension.
// There can be at most one record dimension.
name nc_type nelems [values ...]
NC_BYTE
|
NC_CHAR
|
NC_SHORT |
NC_INT
|
NC_FLOAT |
NC_DOUBLE
name nelems [dimid ...] vatt_list nc_type vsize begin
// nelems is the dimensionality (rank) of the
// variable: 0 for scalar, 1 for vector, 2
// for matrix, ...
NON_NEG
// Dimension ID (index into dim_list) for
// variable shape. We say this is a "record
// variable" if and only if the first
// dimension is the record dimension.
att_list
// Variable-specific attributes
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vsize
= NON_NEG
// Variable size. If not a record variable,
// the amount of space in bytes allocated to
// the variable’s data. If a record variable,
// the amount of space per record. See "Note
// on vsize", below.
OFFSET
// Variable start location. The offset in
// bytes (seek index) in the file of the
// beginning of data for this variable.
non_recs recs
[vardata ...] // The data for all non-record variables,
// stored contiguously for each variable, in
// the same order the variables occur in the
// header.
[values ...] // All data for a non-record variable, as a
// block of values of the same type as the
// variable, in row-major order (last
// dimension varying fastest).
[record ...] // The data for all record variables are
// stored interleaved at the end of the
// file.
[varslab ...] // Each record consists of the n-th slab
// from each record variable, for example
// x[n,...], y[n,...], z[n,...] where the
// first index is the record number, which
// is the unlimited dimension index.
[values ...] // One record of data for a variable, a
// block of values all of the same type as
// the variable in row-major order (last
// index varying fastest).
bytes | chars | shorts | ints | floats | doubles
nelems [chars]
[BYTE ...] padding
[CHAR ...] padding
[SHORT ...] padding
[INT ...]
[FLOAT ...]
[DOUBLE ...]
<0, 1, 2, or 3 bytes to next 4-byte boundary>
// Header padding uses null (\x00) bytes. In
// data, padding uses variable’s fill value.
// See "Note on padding", below, for a special
// case.
<non-negative INT>
\xFF \xFF \xFF \xFF
// Indicates indeterminate record
// count, allows streaming data
<non-negative INT> | // For classic format or
<non-negative INT64> // for 64-bit offset format
begin
=
data
non_recs
=
=
vardata
=
recs
=
record
=
varslab
=
values
string
bytes
chars
shorts
ints
floats
doubles
padding
=
=
=
=
=
=
=
=
=
NON_NEG
STREAMING
=
=
OFFSET
=
Appendix C: File Format Specification
BYTE
CHAR
SHORT
INT
INT64
FLOAT
DOUBLE
=
=
=
=
=
=
=
NC_BYTE
NC_CHAR
NC_SHORT
NC_INT
NC_FLOAT
NC_DOUBLE
=
=
=
=
=
=
FILL_CHAR
FILL_BYTE
FILL_SHORT
FILL_INT
FILL_FLOAT
FILL_DOUBLE
=
=
=
=
=
=
79
<8-bit byte>
// See "Note on byte data", below.
<8-bit byte>
// See "Note on char data", below.
<16-bit signed integer, Bigendian, two’s complement>
<32-bit signed integer, Bigendian, two’s complement>
<64-bit signed integer, Bigendian, two’s complement>
<32-bit IEEE single-precision float, Bigendian>
<64-bit IEEE double-precision float, Bigendian>
// following type tags are 32-bit integers
\x00 \x00 \x00 \x01
// 8-bit signed integers
\x00 \x00 \x00 \x02
// text characters
\x00 \x00 \x00 \x03
// 16-bit signed integers
\x00 \x00 \x00 \x04
// 32-bit signed integers
\x00 \x00 \x00 \x05
// IEEE single precision floats
\x00 \x00 \x00 \x06
// IEEE double precision floats
// Default fill values for each type, may be
// overridden by variable attribute named
// ‘_FillValue’. See "Note on fill values",
// below.
\x00
// null byte
\x81
// (signed char) -127
\x80 \x01
// (short) -32767
\x80 \x00 \x00 \x01
// (int) -2147483647
\x7C \xF0 \x00 \x00
// (float) 9.9692099683868690e+36
\x47 \x9E \x00 \x00 \x00 \x00 //(double)9.9692099683868690e+36
Note on vsize: This number is the product of the dimension lengths (omitting the record
dimension) and the number of bytes per value (determined from the type), increased to the
next multiple of 4, for each variable. If a record variable, this is the amount of space per
record. The netCDF “record size” is calculated as the sum of the vsize’s of all the record
variables.
The vsize field is actually redundant, because its value may be computed from other
information in the header. The 32-bit vsize field is not large enough to contain the size of
variables that require more than 23 2 − 4 bytes, so 23 2 − 1 is used in the vsize field for such
variables.
Note on names: Earlier versions of the netCDF C-library reference implementation enforced a more restricted set of characters in creating new names, but permitted reading
names containing arbitrary bytes. This specification extends the permitted characters in
names to include multi-byte UTF-8 encoded Unicode and additional printing characters
from the US-ASCII alphabet. The first character of a name must be alphanumeric, a multibyte UTF-8 character, or ’ ’ (reserved for special names with meaning to implementations,
such as the “ FillValue” attribute). Subsequent characters may also include printing special
characters, except for ’/’ which is not allowed in names. Names that have trailing space
characters are also not permitted.
Implementations of the netCDF classic and 64-bit offset format must ensure that names
are normalized according to Unicode NFC normalization rules during encoding as UTF-8
for storing in the file header. This is necessary to ensure that gratuitous differences in the
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representation of Unicode names do not cause anomalies in comparing files and querying
data objects by name.
Note on streaming data: The largest possible record count, 23 2−1, is reserved to indicate
an indeterminate number of records. This means that the number of records in the file must
be determined by other means, such as reading them or computing the current number of
records from the file length and other information in the header. It also means that the
numrecs field in the header will not be updated as records are added to the file. [This
feature is not yet implemented].
Note on padding: In the special case of only a single record variable of character, byte,
or short type, no padding is used between data values.
Note on byte data: It is possible to interpret byte data as either signed (-128 to 127)
or unsigned (0 to 255). When reading byte data through an interface that converts it
into another numeric type, the default interpretation is signed. There are various attribute
conventions for specifying whether bytes represent signed or unsigned data, but no standard
convention has been established. The variable attribute “ Unsigned” is reserved for this
purpose in future implementations.
Note on char data: Although the characters used in netCDF names must be encoded
as UTF-8, character data may use other encodings. The variable attribute “ Encoding” is
reserved for this purpose in future implementations.
Note on fill values: Because data variables may be created before their values are written,
and because values need not be written sequentially in a netCDF file, default “fill values”
are defined for each type, for initializing data values before they are explicitly written. This
makes it possible to detect reading values that were never written. The variable attribute
“ FillValue”, if present, overrides the default fill value for a variable. If FillValue is defined
then it should be scalar and of the same type as the variable.
Fill values are not required, however, because netCDF libraries have traditionally supported a “no fill” mode when writing, omitting the initialization of variable values with fill
values. This makes the creation of large files faster, but also eliminates the possibility of
detecting the inadvertent reading of values that haven’t been written.
Notes on Computing File Offsets
The offset (position within the file) of a specified data value in a classic format or 64bit offset data file is completely determined by the variable start location (the offset in the
begin field), the external type of the variable (the nc_type field), and the dimension indices
(one for each of the variable’s dimensions) of the value desired.
The external size in bytes of one data value for each possible netCDF type, denoted
extsize below, is:
NC BYTE 1 NC CHAR 1 NC SHORT 2 NC INT 4 NC FLOAT 4 NC DOUBLE 8
The record size, denoted by recsize below, is the sum of the vsize fields of record
variables (variables that use the unlimited dimension), using the actual value determined
by dimension sizes and variable type in case the vsize field is too small for the variable
size.
To compute the offset of a value relative to the beginning of a variable, it is helpful
to precompute a “product vector” from the dimension lengths. Form the products of the
Appendix C: File Format Specification
81
dimension lengths for the variable from right to left, skipping the leftmost (record) dimension
for record variables, and storing the results as the product vector for each variable.
For example:
Non-record variable:
dimension lengths: [ 5 3 2 7] product vector: [210 42 14 7]
Record variable:
dimension lengths: [0 2 9 4] product vector: [0 72 36 4]
At this point, the leftmost product, when rounded up to the next multiple of 4, is the
variable size, vsize, in the grammar above. For example, in the non-record variable above,
the value of the vsize field is 212 (210 rounded up to a multiple of 4). For the record
variable, the value of vsize is just 72, since this is already a multiple of 4.
Let coord be the array of coordinates (dimension indices, zero-based) of the desired data
value. Then the offset of the value from the beginning of the file is just the file offset of the
first data value of the desired variable (its begin field) added to the inner product of the
coord and product vectors times the size, in bytes, of each datum for the variable. Finally,
if the variable is a record variable, the product of the record number, ’coord[0]’, and the
record size, recsize, is added to yield the final offset value.
A special case: Where there is exactly one record variable, we drop the requirement that
each record be four-byte aligned, so in this case there is no record padding.
Examples
By using the grammar above, we can derive the smallest valid netCDF file, having no
dimensions, no variables, no attributes, and hence, no data. A CDL representation of the
empty netCDF file is
netcdf empty { }
This empty netCDF file has 32 bytes. It begins with the four-byte “magic number”
that identifies it as a netCDF version 1 file: ‘C’, ‘D’, ‘F’, ‘\x01’. Following are seven 32-bit
integer zeros representing the number of records, an empty list of dimensions, an empty list
of global attributes, and an empty list of variables.
Below is an (edited) dump of the file produced using the Unix command
od -xcs empty.nc
Each 16-byte portion of the file is displayed with 4 lines. The first line displays the bytes
in hexadecimal. The second line displays the bytes as characters. The third line displays
each group of two bytes interpreted as a signed 16-bit integer. The fourth line (added by
human) presents the interpretation of the bytes in terms of netCDF components and values.
4344
4601
0000
0000
0000
0000
0000
0000
C
D
F 001 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0
17220
17921
00000
00000
00000
00000
00000
00000
[magic number ] [ 0 records ] [ 0 dimensions
(ABSENT)
]
0000
0000
0000
0000
0000
0000
\0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0
00000
00000
00000
00000
00000
00000
[ 0 global atts (ABSENT)
] [ 0 variables
0000
0000
\0 \0 \0 \0
00000
00000
(ABSENT)
]
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As a less trivial example, consider the CDL
netcdf tiny {
dimensions:
dim = 5;
variables:
short vx(dim);
data:
vx = 3, 1, 4, 1, 5 ;
}
which corresponds to a 92-byte netCDF file. The following is an edited dump of this file:
4344
4601
0000
0000
0000
000a
0000
0001
C
D
F 001 \0 \0 \0 \0 \0 \0 \0 \n \0 \0 \0 001
17220
17921
00000
00000
00000
00010
00000
00001
[magic number ] [ 0 records ] [NC_DIMENSION ] [ 1 dimension ]
0000
0003
6469
\0 \0 \0 003
d
i
00000
00003
25705
[ 3 char name = "dim"
6d00
0000
0005
0000
0000
m \0 \0 \0 \0 005 \0 \0 \0 \0
27904
00000
00005
00000
00000
] [ size = 5
] [ 0 global atts
0000
0000
0000
000b
0000
0001
0000
0002
\0 \0 \0 \0 \0 \0 \0 013 \0 \0 \0 001 \0 \0 \0 002
00000
00000
00000
00011
00000
00001
00000
00002
(ABSENT)
] [NC_VARIABLE ] [ 1 variable ] [ 2 char name =
7678
v
x
30328
"vx"
0000
0000
0001
0000
0000
0000
0000
\0 \0 \0 \0 \0 001 \0 \0 \0 \0 \0 \0 \0 \0
00000
00000
00001
00000
00000
00000
00000
] [1 dimension ] [ with ID 0
] [ 0 attributes
0000
0000
0000
0003
0000
000c
0000
0050
\0 \0 \0 \0 \0 \0 \0 003 \0 \0 \0 \f \0 \0 \0
P
00000
00000
00000
00003
00000
00012
00000
00080
(ABSENT)
] [type NC_SHORT] [size 12 bytes] [offset:
80]
0003
0001
0004
0001
0005
8001
\0 003 \0 001 \0 004 \0 001 \0 005 200 001
00003
00001
00004
00001
00005 -32767
[
3] [
1] [
4] [
1] [
5] [fill ]
C.2 The 64-bit Offset Format
The netCDF 64-bit offset format differs from the classic format only in the VERSION byte,
‘\x02’ instead of ‘\x01’, and the OFFSET entity, a 64-bit instead of a 32-bit offset from
the beginning of the file. This small format change permits much larger files, but there are
still some practical size restrictions. Each fixed-size variable and the data for one record’s
worth of each record variable are still limited in size to a little less that 4 GiB. The rationale
Appendix C: File Format Specification
83
for this limitation is to permit aggregate access to all the data in a netCDF variable (or a
record’s worth of data) on 32-bit platforms.
C.3 The NetCDF-4 Format
The netCDF-4 format implements and expands the netCDF-3 data model by using an
enhanced version of HDF5 as the storage layer. Use is made of features that are only
available in HDF5 version 1.8 and later.
Using HDF5 as the underlying storage layer, netCDF-4 files remove many of the restrictions for classic and 64-bit offset files. The richer enhanced model supports user-defined
types and data structures, hierarchical scoping of names using groups, additional primitive types including strings, larger variable sizes, and multiple unlimited dimensions. The
underlying HDF5 storage layer also supports per-variable compression, multidimensional
tiling, and efficient dynamic schema changes, so that data need not be copied when adding
new variables to the file schema.
Creating a netCDF-4/HDF5 file with netCDF-4 results in an HDF5 file. The features
of netCDF-4 are a subset of the features of HDF5, so the resulting file can be used by any
existing HDF5 application.
Although every file in netCDF-4 format is an HDF5 file, there are HDF5 files that are
not netCDF-4 format files, because the netCDF-4 format intentionally uses a limited subset
of the HDF5 data model and file format features. Some HDF5 features not supported in the
netCDF enhanced model and netCDF-4 format include non-hierarchical group structures,
HDF5 reference types, multiple links to a data object, user-defined atomic data types, stored
property lists, more permissive rules for data object names, the HDF5 date/time type, and
attributes associated with user-defined types.
A complete specification of HDF5 files is beyond the scope of this document. For more
information about HDF5, see the HDF5 web site: http://hdf.ncsa.uiuc.edu/HDF5/.
The specification that follows is sufficient to allow HDF5 users to create files that will
be accessable from netCDF-4.
C.3.1 Creation Order
The netCDF API maintains the creation order of objects that are created in the file. The
same is not true in HDF5, which maintains the objects in alphabetical order. Starting
in version 1.8 of HDF5, the ability to maintain creation order was added. This must be
explicitly turned on in the HDF5 data file in several ways.
Each group must have link and attribute creation order set. The following code (from
libsrc4/nc4hdf.c) shows how the netCDF-4 library sets these when creating a group.
/* Create group, with link_creation_order set in the group
* creation property list. */
if ((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0)
return NC_EHDFERR;
if (H5Pset_link_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEX
BAIL(NC_EHDFERR);
if (H5Pset_attr_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEX
BAIL(NC_EHDFERR);
if ((grp->hdf_grpid = H5Gcreate2(grp->parent->hdf_grpid, grp->name,
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H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
if (H5Pclose(gcpl_id) < 0)
BAIL(NC_EHDFERR);
Each dataset in the HDF5 file must be created with a property list for which the attribute
creation order has been set to creation ordering. The H5Pset attr creation order funtion
is used to set the creation ordering of attributes of a variable.
The following example code (from libsrc4/nc4hdf.c) shows how the creation ordering is
turned on by the netCDF library.
/* Turn on creation order tracking. */
if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
C.3.2 Groups
NetCDF-4 groups are the same as HDF5 groups, but groups in a netCDF-4 file must be
strictly hierarchical. In general, HDF5 permits non-hierarchical structuring of groups (for
example, a group that is its own grandparent). These non-hierarchical relationships are not
allowed in netCDF-4 files.
In the netCDF API, the global attribute becomes a group-level attribute. That is, each
group may have its own global attributes.
The root group of a file is named “/” in the netCDF API, where names of groups are
used. It should be noted that the netCDF API (like the HDF5 API) makes little use of
names, and refers to entities by number.
C.3.3 Dimensions with HDF5 Dimension Scales
Until version 1.8, HDF5 did not have any capability to represent shared dimensions. With
the 1.8 release, HDF5 introduced the dimension scale feature to allow shared dimensions in
HDF5 files.
The dimension scale is unfortunately not exactly equivilent to the netCDF shared dimension, and this leads to a number of compromises in the design of netCDF-4.
A netCDF shared dimension consists solely of a length and a name. An HDF5 dimension
scale also includes values for each point along the dimension, information that is (optionally)
included in a netCDF coordinate variable.
To handle the case of a netCDF dimension without a coordinate variable, netCDF-4
creates dimension scales of type char, and leaves the contents of the dimension scale empty.
Only the name and length of the scale are significant. To distinguish this case, netCDF-4
takes advantage of the NAME attribute of the dimension scale. (Not to be confused with
the name of the scale itself.) In the case of dimensions without coordinate data, the HDF5
dimension scale NAME attribute is set to the string: "This is a netCDF dimension but not
a netCDF variable."
In the case where a coordinate variable is defined for a dimension, the HDF5 dimscale
matches the type of the netCDF coordinate variable, and contains the coordinate data.
A further difficulty arrises when an n-dimensional coordinate variable is defined, where
n is greater than one. NetCDF allows such coordinate variables, but the HDF5 model does
Appendix C: File Format Specification
85
not allow dimension scales to be attached to other dimension scales, making it impossible
to completely represent the multi-dimensional coordinate variables of the netCDF model.
To capture this information, multidimensional coordinate variables have an attribute
named Netcdf4Coordinates. The attribute is an array of H5T NATIVE INT, with the
netCDF dimension IDs of each of its dimensions.
The Netcdf4Coordinates attribute is otherwise hidden by the netCDF API. It does not
appear as one of the attributes for the netCDF variable involved, except through the HDF5
API.
C.3.4 Dimensions without HDF5 Dimension Scales
Starting with the netCDF-4.1 release, netCDF can read HDF5 files which do not use dimension scales. In this case the netCDF library assigns dimensions to the HDF5 dataset as
needed, based on the length of the dimension.
When an HDF5 file is opened, each dataset is examined in turn. The lengths of all the
dimensions involved in the shape of the dataset are determined. Each new (i.e. previously
unencountered) length results in the creation of a phony dimension in the netCDF API.
This will not accurately detect a shared, unlimited dimension in the HDF5 file, if different
datasets have different lengths along this dimension (possible in HDF5, but not in netCDF).
Note that this is a read-only capability for the netCDF library. When the netCDF
library writes HDF5 files, they always use a dimension scale for every dimension.
Datasets must have either dimension scales for every dimension, or no dimension scales
at all. Partial dimension scales are not, at this time, understood by the netCDF library.
C.3.5 Dimension and Coordinate Variable Ordering
In order to preserve creation order, the netCDF-4 library writes variables in their creation
order. Since some variables are also dimension scales, their order reflects both the order of
the dimensions and the order of the coordinate variables.
However, these may be different. Consider the following code:
/* Create a test file. */
if (nc_create(FILE_NAME, NC_CLASSIC_MODEL|NC_NETCDF4, &ncid)) ERR;
/* Define dimensions in order. */
if (nc_def_dim(ncid, DIM0, NC_UNLIMITED, &dimids[0])) ERR;
if (nc_def_dim(ncid, DIM1, 4, &dimids[1])) ERR;
/* Define coordinate variables in a different order. */
if (nc_def_var(ncid, DIM1, NC_DOUBLE, 1, &dimids[1], &varid[1])) ERR;
if (nc_def_var(ncid, DIM0, NC_DOUBLE, 1, &dimids[0], &varid[0])) ERR;
In this case the order of the coordinate variables will be different from the order of the
dimensions.
In practice, this should make little difference in user code, but if the user is writing code
that depends on the ordering of dimensions, the netCDF library was updated in version 4.1
to detect this condition, and add the attribute Netcdf4Dimid to the dimension scales in
the HDF5 file. This attribute holds a scalar H5T NATIVE INT which is the (zero-based)
dimension ID for this dimension.
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If this attribute is present on any dimension scale, it must be present on all dimension
scales in the file.
C.3.6 Variables
Variables in netCDF-4/HDF5 files exactly correspond to HDF5 datasets. The data types
match naturally between netCDF and HDF5.
In netCDF classic format, the problem of endianness is solved by writing all data in
big-endian order. The HDF5 library allows data to be written as either big or little endian,
and automatically reorders the data when it is read, if necessary.
By default, netCDF uses the native types on the machine which writes the data. Users
may change the endianness of a variable (before any data are written). In that case the
specified endian type will be used in HDF5 (for example, a H5T STD I16LE will be used
for NC SHORT, if little-endian has been specified for that variable.)
NC_BYTE
H5T NATIVE SCHAR
NC_UBYTE
H5T NATIVE SCHAR
NC_CHAR
H5T C S1
NC_STRING
variable length array of H5T C S1
NC_SHORT
H5T NATIVE SHORT
NC_USHORT
H5T NATIVE USHORT
NC_INT
H5T NATIVE INT
NC_UINT
H5T NATIVE UINT
NC_INT64
H5T NATIVE LLONG
NC_UINT64
H5T NATIVE ULLONG
NC_FLOAT
H5T NATIVE FLOAT
NC_DOUBLE
H5T NATIVE DOUBLE
The NC CHAR type represents a single character, and the NC STRING an array of
characters. This can be confusing because a one-dimensional array of NC CHAR is used
to represent a string (i.e. a scalar NC STRING).
An odd case may arise in which the user defines a variable with the same name as a
dimension, but which is not intended to be the coordinate variable for that dimension. In
this case the string " nc4 non coord " is pre-pended to the name of the HDF5 dataset, and
stripped from the name for the netCDF API.
Appendix C: File Format Specification
87
C.3.7 Attributes
Attributes in HDF5 and NetCDF-4 correspond very closely. Each attribute in an HDF5
file is represented as an attribute in the netCDF-4 file, with the exception of the attributes
below, which are ignored by the netCDF-4 API.
_Netcdf4Coordinates
An integer array containing the dimension IDs of a variable which is a multidimensional coordinate variable.
_nc3_strict
When this (scalar, H5T NATIVE INT) attribute exists in the root group of
the HDF5 file, the netCDF API will enforce the netCDF classic model on the
data file.
REFERENCE_LIST
This attribute is created and maintained by the HDF5 dimension scale API.
CLASS
This attribute is created and maintained by the HDF5 dimension scale API.
DIMENSION_LIST
This attribute is created and maintained by the HDF5 dimension scale API.
NAME
This attribute is created and maintained by the HDF5 dimension scale API.
C.3.8 User-Defined Data Types
Each user-defined data type in an HDF5 file exactly corresponds to a user-defined data type
in the netCDF-4 file. Only base data types which correspond to netCDF-4 data types may
be used. (For example, no HDF5 reference data types may be used.)
C.3.9 Compression
The HDF5 library provides data compression using the zlib library and the szlib library.
NetCDF-4 only allows users to create data with the zlib library (due to licensing restrictions on the szlib library). Since HDF5 supports the transparent reading of the data with
either compression filter, the netCDF-4 library can read data compressed with szlib (if the
underlying HDF5 library is built to support szlib), but has no way to write data with szlib
compression.
With zlib compression (a.k.a. deflation) the user may set a deflation factor from 0 to 9.
In our measurements the zero deflation level does not compress the data, but does incur the
performance penalty of compressing the data. The netCDF API does not allow the user
to write a variable with zlib deflation of 0 - when asked to do so, it turns off deflation for
the variable instead. NetCDF can read an HDF5 file with deflation of zero, and correctly
report that to the user.
C.4 The NetCDF-4 Classic Model Format
Every classic and 64-bit offset file can be represented as a netCDF-4 file, with no loss of
information. There are some significant benefits to using the simpler netCDF classic model
with the netCDF-4 file format. For example, software that writes or reads classic model
data can write or read netCDF-4 classic model format data by recompiling/relinking to
a netCDF-4 API library, with no or only trivial changes needed to the program source
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code. The netCDF-4 classic model format supports this usage by enforcing rules on what
functions may be called to store data in the file, to make sure its data can be read by older
netCDF applications (when relinked to a netCDF-4 library).
Writing data in this format prevents use of enhanced model features such as groups,
added primitive types not available in the classic model, and user-defined types. However performance features of the netCDF-4 formats that do not require additional features
of the enhanced model, such as per-variable compression and chunking, efficient dynamic
schema changes, and larger variable size limits, offer potentially significant performance
improvements to readers of data stored in this format, without requiring program changes.
When a file is created via the netCDF API with a CLASSIC MODEL mode flag, the
library creates an attribute ( nc3 strict) in the root group. This attribute is hidden by the
netCDF API, but is read when the file is later opened, and used to ensure that no enhanced
model features are written to the file.
C.5 HDF4 SD Format
Starting with version 4.1, the netCDF libraries can read HDF4 SD (Scientific Dataset) files.
Access is limited to those HDF4 files created with the Scientific Dataset API. Access is
read-only.
Dataset types are translated between HDF4 and netCDF in a straighforward manner.
DFNT_CHAR
NC CHAR
DFNT_UCHAR, DFNT_UINT8
NC UBYTE
DFNT_INT8
NC BYTE
DFNT_INT16
NC SHORT
DFNT_UINT16
NC USHORT
DFNT_INT32
NC INT
DFNT_UINT32
NC UINT
DFNT_FLOAT32
NC FLOAT
DFNT_FLOAT64
NC DOUBLE
Index
89
Index
attributes, operations on . . . . . . . . . . . . . . . . . . . . . . . 21
_FillValue. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
IONBF flag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
6
64-bit
64-bit
64-bit
64-bit
offset file format . . . . . . . . . . . . . . . . . . . . . . . . 35
offset format, introduction. . . . . . . . . . . . . . . 37
offset format, limitations . . . . . . . . . . . . . . . . 38
offsets, history . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
B
buffers, I/O . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
byte . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
byte array vs. text string . . . . . . . . . . . . . . . . . . . . . .
byte CDL constant . . . . . . . . . . . . . . . . . . . . . . . . . . . .
byte, CDL data type . . . . . . . . . . . . . . . . . . . . . . . . . .
byte, signed vs. unsigned . . . . . . . . . . . . . . . . . . . . . .
39
61
33
62
61
25
A
C
access C example of array section . . . . . . . . . . . . . . 30
access Fortran example of array section . . . . . . . . 32
access random . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
access shared dataset I/O . . . . . . . . . . . . . . . . . . . . . . 39
ADA API, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
add_offset. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
ancillary data as attributes . . . . . . . . . . . . . . . . . . . . 23
ancillary data, storing . . . . . . . . . . . . . . . . . . . . . . . . . 21
API, C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
API, C++ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
API, F90 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
API, Fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
API, Java . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
appending data along unlimited dimension . . . . . 19
applications, generic . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
applications, generic, conventions . . . . . . . . . . . . 8, 71
applications, generic, reasons for netCDF . . . . . . 59
applications, generic, units . . . . . . . . . . . . . . . . . . . . . 69
archive format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Argonne National Laboratory . . . . . . . . . . . . . . . . . . . 9
array section, C example . . . . . . . . . . . . . . . . . . . . . . . 30
array section, corner . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
array section, definition . . . . . . . . . . . . . . . . . . . . . . . . 29
array section, edges . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
array section, Fortran example . . . . . . . . . . . . . . . . . 32
array section, mapped . . . . . . . . . . . . . . . . . . . . . . . . . 29
arrays, ragged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
ASCII characters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
attribute conventions . . . . . . . . . . . . . . . . . . . . . . . . . . 71
attributes associated with a variable . . . . . . . . . . . 20
attributes vs. variables . . . . . . . . . . . . . . . . . . . . . . . . . 23
attributes, adding to existing dataset . . . . . . . . . . 21
attributes, CDL, defining . . . . . . . . . . . . . . . . . . . . . . 59
attributes, CDL, global . . . . . . . . . . . . . . . . . . . . . . . . 59
attributes, CDL, initializing. . . . . . . . . . . . . . . . . . . . 62
attributes, data type . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
attributes, data types, CDL . . . . . . . . . . . . . . . . . . . . 62
attributes, defined . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
attributes, defining in CDL . . . . . . . . . . . . . . . . . . . . 21
attributes, global . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
attributes, length, CDL . . . . . . . . . . . . . . . . . . . . . . . . 62
C API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
C code via ncgen, generating. . . . . . . . . . . . . . . . . . . 63
C code via ncgen3, generating . . . . . . . . . . . . . . . . . 68
C++ API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
C_format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
CANDIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
CDF1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
CDF2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
CDL attributes, defining . . . . . . . . . . . . . . . . . . . . . . . 59
CDL constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
CDL data types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
CDL dimensions, defining . . . . . . . . . . . . . . . . . . . . . . 59
CDL syntax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
CDL variables, defining . . . . . . . . . . . . . . . . . . . . . . . . 59
CDL, defining attributes . . . . . . . . . . . . . . . . . . . . . . . 21
CDL, defining global attributes . . . . . . . . . . . . . . . . 21
CDL, example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
char . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
char, CDL data type. . . . . . . . . . . . . . . . . . . . . . . . . . . 61
chunking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
classic file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
classic format, introduction . . . . . . . . . . . . . . . . . . . . 37
classic format, limitations . . . . . . . . . . . . . . . . . . . . . . 38
classic netCDF format . . . . . . . . . . . . . . . . . . . . . . . . . 12
common data form language . . . . . . . . . . . . . . . . . . . 17
compound type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
compression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
conventions, attributes . . . . . . . . . . . . . . . . . . . . . . . . . 71
conventions, introduction . . . . . . . . . . . . . . . . . . . . . . . 8
conventions, naming . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
conversion of data types, introduction . . . . . . . . . . 25
coordinate variables . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
D
DAP support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
data base . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
data model, netCDF . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
data structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
data types, conversion . . . . . . . . . . . . . . . . . . . . . . . . . 33
90
The NetCDF Users’ Guide
data types, external . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
data, reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
data, writing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
DBMS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
deflation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
differences between attributes and variables . . . . 23
dimensions, CDL, defining . . . . . . . . . . . . . . . . . . . . . 59
dimensions, CDL, initializing . . . . . . . . . . . . . . . . . . 62
dimensions, introduction . . . . . . . . . . . . . . . . . . . . . . . 19
dimensions, length, CDL . . . . . . . . . . . . . . . . . . . . . . . 62
dimensions, unlimited. . . . . . . . . . . . . . . . . . . . . . . . . . 19
DODS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
double . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
double, CDL data type . . . . . . . . . . . . . . . . . . . . . . . . 61
E
enum type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
external data types . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
F
F90 API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
FAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
fflush . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
file format, 64-bit offset . . . . . . . . . . . . . . . . . . . . . . . . 35
file format, classic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
file format, netcdf-4. . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
file structure, overview . . . . . . . . . . . . . . . . . . . . . . . . . 35
float . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
float, CDL data type . . . . . . . . . . . . . . . . . . . . . . . . . . 61
flushing buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
format selection advice. . . . . . . . . . . . . . . . . . . . . . . . . . 6
Fortran API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
FORTRAN_format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
future plans for netCDF . . . . . . . . . . . . . . . . . . . . . . . 14
G
GBytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
generating C code via ncgen . . . . . . . . . . . . . . . . . . .
generating C code via ncgen3 . . . . . . . . . . . . . . . . . .
generic applications . . . . . . . . . . . . . . . . . . . . . . . . . . . .
GiBytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
global attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
groups. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
12
63
68
21
12
21
17
H
history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
I
I/O layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
initializing CDL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
int . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
int, CDL data type . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
int64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
interoperability with HDF5 . . . . . . . . . . . . . . . . . . . . 45
J
Java API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Java API, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
L
large file support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
LFS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
limitations of netCDF . . . . . . . . . . . . . . . . . . . . . . . . .
long . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
long, CDL data type . . . . . . . . . . . . . . . . . . . . . . . . . . .
long_name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
37
37
12
61
61
71
M
Matlab API, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
missing_value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
multiple unlimited dimensions . . . . . . . . . . . . . . . . . 19
N
naming conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
NASA CDF format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
NC BYTE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC CHAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC DOUBLE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC FLOAT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC INT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC INT64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC LONG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC SHARE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
NC SHORT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC STRING . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
nc sync . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
NC UBYTE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC UINT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC UINT64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NC USHORT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
ncdump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
ncdump, introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 17
ncdump, overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
ncgen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
ncgen and ncgen3, overview . . . . . . . . . . . . . . . . . . . . 59
ncgen3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
NcML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
NCO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
netCDF 5.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
netCDF data model . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
netCDF data types . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
netcdf-4 file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
NETCDF FFIOSPEC . . . . . . . . . . . . . . . . . . . . . . . . . 40
New Mexico Institute of Mining . . . . . . . . . . . . . . . . . 9
new netCDF features in 4.0 . . . . . . . . . . . . . . . . . . . . 12
Index
nf byte . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
nf char . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
nf double . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
nf float . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
nf int1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
nf int2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
nf real . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NF SHARE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
nf short . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
NF SYNC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Northwestern University . . . . . . . . . . . . . . . . . . . . . . . . 9
O
opaque type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
OpenDAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
operations on attributes . . . . . . . . . . . . . . . . . . . . . . . 21
P
parallel access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
performance of NetCDF . . . . . . . . . . . . . . . . . . . . . . . 35
performance, introduction. . . . . . . . . . . . . . . . . . . . . . . 8
plans for netCDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
pong . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
primary variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
python API, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
R
real . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
real, CDL data type . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
ruby API, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
S
scale_factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
SeaSpace, Inc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
share flag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
shared dataset I/O access . . . . . . . . . . . . . . . . . . . . . . 39
short . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
short, CDL data type . . . . . . . . . . . . . . . . . . . . . . . . . . 61
shuffle filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
signedness. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
SNIDE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
software list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
storing ancillary data . . . . . . . . . . . . . . . . . . . . . . . . . . 21
string . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
structures, data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
91
supported programming languages . . . . . . . . . . . . . . 3
T
Tcl/Tk API, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Terascan data format . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
type conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
U
ubyte . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
udunits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
uint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
uint64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
UNICOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
units library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
University of Miami . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
unlimited dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . 19
user defined types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
ushort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
V
valid_max . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
valid_min . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
valid_range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
variable length array type. . . . . . . . . . . . . . . . . . . . . .
variable types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
variables vs. attributes . . . . . . . . . . . . . . . . . . . . . . . . .
variables, CDL, defining . . . . . . . . . . . . . . . . . . . . . . .
variables, CDL, initializing . . . . . . . . . . . . . . . . . . . . .
variables, coordinate . . . . . . . . . . . . . . . . . . . . . . . . . . .
variables, data types, CDL . . . . . . . . . . . . . . . . . . . . .
variables, defined . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
variables, primary . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
vlen type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
72
72
72
27
20
23
59
62
20
62
20
20
27
W
WetCDF, history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
workshop, CDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
writers, multiple . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
X
XDR format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
XDR layer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
XDR, introduction into netCDF . . . . . . . . . . . . . . . . 9
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