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INFO-DIR-SECTION netCDF scientific data format
START-INFO-DIR-ENTRY
* netcdf: (netcdf). The NetCDF Users Guide
END-INFO-DIR-ENTRY
File: netcdf.info, Node: Top, Next: Foreword, Prev: (dir), Up: (dir)
NetCDF Users Guide
******************
This guide describes the netCDF object model. This document applies to
netCDF version 4.1.1, and was last updated on 30 March 2010.
Interface guides are available for C (*note The NetCDF C Interface
Guide: (netcdf-c)Top.), C++ (*note The NetCDF C++ Interface Guide:
(netcdf-cxx)Top.), Fortran 77 (*note The NetCDF Fortran 77 Interface
Guide: (netcdf-f77)Top.), and Fortran 90 (*note The NetCDF Fortran 90
Interface Guide: (netcdf-f90)Top.).
Separate documentation for the netCDF Java library can be found at
the netCDF-Java website,
`http://www.unidata.ucar.edu/software/netcdf-java'.
For installation and porting information, see *note The NetCDF
Installation and Porting Guide: (netcdf-install)Top.
* Menu:
* Foreword:: Foreword from 1996 Manual
* Summary:: Orientation
* Introduction:: What is NetCDF?
* Dataset Components:: What's in a NetCDF File?
* Data:: How to Store Data
* Structure:: Behind the Scenes
* NetCDF Utilities:: Ncdump and ncgen and ncgen3
* Units:: Using UDUNITS
* Attribute Conventions:: Creating Human-Readable Files
* File Format:: Description of NetCDF Binary Formats
* Combined Index:: Index of Concepts and Functions
--- The Detailed Node Listing ---
Introduction
* Interface:: The NetCDF Interface
* Not DBMS:: NetCDF is not a Database
* Format:: The NetCDF File Format
* Which Format:: Selecting the Underlying NetCDF Format
* Performance:: What about Performance?
* Archival:: Is NetCDF a Good Archive Format?
* Conventions:: Creating Self-Describing Data Conforming to Conventions
* Background:: The Evolution of the NetCDF Interface
* Whats New:: Latest Developments in NetCDF
* Limitations:: Limitations of NetCDF
* Future :: Plans for Future Development
* References:: Papers Relating to Scientific Data
Components of a NetCDF Dataset
* Data Model:: How NetCDF Sees Data
* Dimensions:: Specifying Data Shape
* Variables:: Storing Data
* Attributes:: Storing Metadata
* Attributes and Variables:: Attributes vs. Variables
Data
* External Types:: Integers, Floats, and so on
* Classic Data Structures:: Complex Data in Classic Format
* User Defined Types:: Complex Data in NetCDF-4/HDF5 Format
* Data Access:: Reading and Writing Data
* Type Conversion:: Changing Type of Numeric Data
Forms of Data Access
* C Section Access:: A C Example
* Fortran Section Access:: A Fortran Example
File Structure and Performance
* Classic File Parts:: The Classic and 64-bit Offset File
* NetCDF-4 File Parts:: The NetCDF-4/HDF5 File
* XDR Layer:: Classic Machine Interoperability
* Large File Support:: Files that Exceed 2 GiBytes
* 64 bit Offset Limitations:: Limitations on File and Data Size
* Classic Limitations:: Limitations on File and Data Size
* The NetCDF-3 IO Layer:: Classic I/O Described
* UNICOS Optimization:: Some Cray Optimizations
* Chunking:: NetCDF-4/HDF5 Files Read/Write Chunks
* Parallel Access:: Parallel I/O with NetCDF-4
* Interoperability with HDF5:: Using HDF5 with NetCDF-4
* DAP Support::
Improving Performance With Chunking
* Chunk Cache::
* Default Chunking::
* Default Chunking 4_0_1::
* Parallel Chunking::
* bm_file::
NetCDF Utilities
* CDL Syntax:: Creating a File without Code
* CDL Data Types:: Describing Types in CDL
* CDL Constants:: Constant Values in CDL
* ncgen:: Turning CDL into Classic or Enhanced Data Files
* ncdump:: Turning Data Files into CDL (or XML)
* ncgen3:: Turning CDL into Classic Data Files
File Format Specification
* NetCDF Classic Format:: The Original Binary Format
* 64-bit Offset Format:: Supporting Larger Variables
* NetCDF-4 Format:: Uses HDF5
* NetCDF-4 Classic Model Format:: HDF5 with NetCDF Limitations
* HDF4 SD Format::
The NetCDF Classic Format Specification
* Classic Format Spec:: Detailed Format Information
* Computing Offsets:: How to Get the Data You Want
* Examples:: The Binary Layout of some Simple Files
File: netcdf.info, Node: Foreword, Next: Summary, Prev: Top, Up: Top
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
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
File: netcdf.info, Node: Summary, Next: Introduction, Prev: Foreword, Up: Top
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 (*note
The NetCDF C Interface Guide: (netcdf-c)Top.), C++ (*note The NetCDF
C++ Interface Guide: (netcdf-cxx)Top.), Fortran 77 (*note The NetCDF
Fortran 77 Interface Guide: (netcdf-f77)Top.), and Fortran 90 (*note
The NetCDF Fortran 90 Interface Guide: (netcdf-f90)Top.).
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 *Note The NetCDF
Installation and Porting Guide: (netcdf-install)Top.
File: netcdf.info, Node: Introduction, Next: Dataset Components, Prev: Summary, Up: Top
1 Introduction
**************
* Menu:
* Interface:: The NetCDF Interface
* Not DBMS:: NetCDF is not a Database
* Format:: The NetCDF File Format
* Which Format:: Selecting the Underlying NetCDF Format
* Performance:: What about Performance?
* Archival:: Is NetCDF a Good Archive Format?
* Conventions:: Creating Self-Describing Data Conforming to Conventions
* Background:: The Evolution of the NetCDF Interface
* Whats New:: Latest Developments in NetCDF
* Limitations:: Limitations of NetCDF
* Future :: Plans for Future Development
* References:: Papers Relating to Scientific Data
File: netcdf.info, Node: Interface, Next: Not DBMS, Prev: Introduction, Up: 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, (*note Top:
(netcdf-c)Top.), FORTRAN 77 (*note Top: (netcdf-f77)Top.), FORTRAN 90
(*note Top: (netcdf-f90)Top.), and C++ (*note Top: (netcdf-cxx)Top.).
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. *Note Top: (netcdf-install)Top.
File: netcdf.info, Node: Not DBMS, Next: Format, Prev: Interface, Up: Introduction
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.
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.
File: netcdf.info, Node: Format, Next: Which Format, Prev: Not DBMS, Up: Introduction
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
machine-independent 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. *Note Structure::.
The details of the classic and 64-bit offset formats are described in
an appendix. *Note File Format::. 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.
File: netcdf.info, Node: Which Format, Next: Performance, Prev: Format, Up: Introduction
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 cannot read 64-bit offset format
files, and library versions before 4.0 can't read netCDF-4/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.
*Note nc_create: (netcdf-c)nc_create.
In Fortran, use flag nf_64bit_offset or nf_format_netcdf4 in function
NF_CREATE. *Note NF_CREATE: (netcdf-f77)NF_CREATE.
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 *note nc_set_default_format: (netcdf-c)nc_set_default_format.
Fortran programs see *note NF_SET_DEFAULT_FORMAT:
(netcdf-f77)NF_SET_DEFAULT_FORMAT.
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. (*note Classic Limitations::).
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 (*note 64 bit
Offset Limitations::).
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 *note The NetCDF Tutorial:
(netcdf-tutorial)Versions.
File: netcdf.info, Node: Performance, Next: Archival, Prev: Which Format, Up: Introduction
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
*note Structure::.
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.
File: netcdf.info, Node: Archival, Next: Conventions, Prev: Performance, Up: Introduction
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 eight-bit 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.
File: netcdf.info, Node: Conventions, Next: Background, Prev: Archival, Up: Introduction
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 *note Attribute Conventions::.
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.
File: netcdf.info, Node: Background, Next: Whats New, Prev: Conventions, Up: Introduction
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 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.
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.
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 user-defined
types. The 3.6.3/4.0 releases also introduced handling of UTF8-encoded
Unicode names.
File: netcdf.info, Node: Whats New, Next: Limitations, Prev: Background, Up: Introduction
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'.
File: netcdf.info, Node: Limitations, Next: Future, Prev: Whats New, Up: Introduction
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.
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. (*note Classic
Limitations::). 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 (*note Large File Support::).
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. (*note 64 bit Offset Limitations::).
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.
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'.
File: netcdf.info, Node: Future, Next: References, Prev: Limitations, Up: Introduction
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.
File: netcdf.info, Node: References, Prev: Future, Up: Introduction
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.
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.
File: netcdf.info, Node: Dataset Components, Next: Data, Prev: Introduction, Up: Top
2 Components of a NetCDF Dataset
********************************
* Menu:
* Data Model:: How NetCDF Sees Data
* Dimensions:: Specifying Data Shape
* Variables:: Storing Data
* Attributes:: Storing Metadata
* Attributes and Variables:: Attributes vs. Variables
File: netcdf.info, Node: Data Model, Next: Dimensions, Prev: Dataset Components, Up: Dataset Components
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, 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 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 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: // variable types, names, shapes, attributes
float 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: // optional data assignments
level = 1000, 850, 700, 500;
lat = 20, 30, 40, 50, 60;
lon = -160,-140,-118,-96,-84,-52,-45,-35,-25,-15;
time = 12;
rh =.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 (*note ncdump::).
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 (*note ncgen::). 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. 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.
File: netcdf.info, Node: Dimensions, Next: Variables, Prev: Data Model, Up: Dataset Components
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).
There are four dimensions in the above example: lat, lon, level, and
time (*note Data Model::). 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.
File: netcdf.info, Node: Variables, Next: Attributes, Prev: Dimensions, Up: Dataset Components
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 *note
Variable Types: (netcdf-c)Variable Types. in The NetCDF C Interface
Guide.
For more information on types for the Fortran interface, see *note
Variable Types: (netcdf-f77)Variable Types. 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 *note External Types::. 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 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 lat(lat), lon(lon), level(level);
short time(time);
...
data:
level = 1000, 850, 700, 500;
lat = 20, 30, 40, 50, 60;
lon = -160,-140,-118,-96,-84,-52,-45,-35,-25,-15;
time = 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).
File: netcdf.info, Node: Attributes, Next: Attributes and Variables, Prev: Variables, Up: Dataset Components
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.
An attribute has an associated variable (the null "global variable"
for a global or group-level 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 (*note CDL Constants::).
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 (*note Data Model::), 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 *note Attribute Conventions::.
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 *note Structure::.
File: netcdf.info, Node: Attributes and Variables, Prev: Attributes, Up: Dataset Components
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
memory-resident. 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.
File: netcdf.info, Node: Data, Next: Structure, Prev: Dataset Components, Up: Top
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.
* Menu:
* External Types:: Integers, Floats, and so on
* Classic Data Structures:: Complex Data in Classic Format
* User Defined Types:: Complex Data in NetCDF-4/HDF5 Format
* Data Access:: Reading and Writing Data
* Type Conversion:: Changing Type of Numeric Data
File: netcdf.info, Node: External Types, Next: Classic Data Structures, Prev: Data, Up: Data
3.1 NetCDF External Data Types
==============================
The atomic external types supported by the netCDF interface are:
C name Fortran storage
name
NC_BYTE nf_byte 8-bit signed integer
NC_CHAR nf_char 8-bit unsigned integer
NC_SHORT nf_short 16-bit signed integer
NC_USHORT nf_ushort 16-bit unsigned integer *
NC_INT (or nf_int 32-bit signed integer
NC_LONG)
NC_UINT 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 nf_string variable length character 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 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 *note Variables::.
File: netcdf.info, Node: Classic Data Structures, Next: User Defined Types, Prev: External Types, Up: Data
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";
int row_start(max_rows);
data:
row_start = 0, 12, 19, ...
As another example, netCDF variables may be grouped within a netCDF
classic or 64-bit 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.
File: netcdf.info, Node: User Defined Types, Next: Data Access, Prev: Classic Data Structures, Up: Data
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, 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 *note
Compound Types: (netcdf-c)Compound Types. 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 *note Variable Length Arrays: (netcdf-c)Variable Length Arrays. 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 *note
Opaque Type: (netcdf-c)Opaque Type. 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 *note
Enum Type: (netcdf-c)Enum Type. 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 *note Groups: (netcdf-c)Groups. in
The NetCDF C Interface Guide.
File: netcdf.info, Node: Data Access, Next: Type Conversion, Prev: User Defined Types, Up: Data
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 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.
* Menu:
* C Section Access:: A C Example
* Fortran Section Access:: A Fortran Example
File: netcdf.info, Node: C Section Access, Next: Fortran Section Access, Prev: Data Access, Up: Data Access
3.4.2 A C Example of Array-Section Access
-----------------------------------------
Assume that in our earlier example of a netCDF dataset (*note Network
Common Data Form Language (CDL): Data Model.), 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 LATS 5
#define LONS 10
#define LEVELS 1
#define TIMES 3 /* currently */
...
float 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]
...
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 floating-point values.
A detailed example of mapped array access is presented in the
description of the interfaces for mapped array access. *Note Write a
Mapped Array of Values - nc_put_varm_ type: (netcdf-c)nc_put_varm_ type.
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.
File: netcdf.info, Node: Fortran Section Access, Prev: C Section Access, Up: Data Access
3.4.4 A Fortran Example of Array-Section Access
-----------------------------------------------
Assume that in our earlier example of a netCDF dataset (*note Data
Model::), 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 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. *Note
nf_put_varm_ type: (netcdf-f77)nf_put_varm_ type.
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.
File: netcdf.info, Node: Type Conversion, Prev: Data Access, Up: Data
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 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 single-precision 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.
File: netcdf.info, Node: Structure, Next: NetCDF Utilities, Prev: Data, Up: Top
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.
* Menu:
* Classic File Parts:: The Classic and 64-bit Offset File
* NetCDF-4 File Parts:: The NetCDF-4/HDF5 File
* XDR Layer:: Classic Machine Interoperability
* Large File Support:: Files that Exceed 2 GiBytes
* 64 bit Offset Limitations:: Limitations on File and Data Size
* Classic Limitations:: Limitations on File and Data Size
* The NetCDF-3 IO Layer:: Classic I/O Described
* UNICOS Optimization:: Some Cray Optimizations
* Chunking:: NetCDF-4/HDF5 Files Read/Write Chunks
* Parallel Access:: Parallel I/O with NetCDF-4
* Interoperability with HDF5:: Using HDF5 with NetCDF-4
* DAP Support::
File: netcdf.info, Node: Classic File Parts, Next: NetCDF-4 File Parts, Prev: Structure, Up: Structure
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 (*note
nc_enddef: (netcdf-c)nc_enddef.), NF_ENDDEF in Fortran (*note
NF_ENDDEF: (netcdf-f77)NF_ENDDEF.), after a previous call to the redef
function: nc_redef in C (*note nc_redef: (netcdf-c)nc_redef.) or
NF_REDEF in Fortran (*note NF_REDEF: (netcdf-f77)NF_REDEF.). If you
create all necessary dimensions, variables, and attributes 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 (*note nc__enddef: (netcdf-c)nc__enddef.), in Fortran
NF__ENDDEF (*note NF__ENDDEF: (netcdf-f77)NF__ENDDEF.), 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 *note File Format::.
File: netcdf.info, Node: NetCDF-4 File Parts, Next: XDR Layer, Prev: Classic File Parts, Up: Structure
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.
File: netcdf.info, Node: XDR Layer, Next: Large File Support, Prev: NetCDF-4 File Parts, Up: Structure
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 machine-independent 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 floating-point data on a machine
that does not use IEEE floating-point as its native representation.
File: netcdf.info, Node: Large File Support, Next: 64 bit Offset Limitations, Prev: XDR Layer, Up: Structure
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. *Note Classic Limitations::.
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. *Note 64 bit Offset Limitations::.
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 v3.6/classicv3.6/64-bit v4.0/netCDF-4
offset
Max File Size 2 GiB 8 EiB 8 EiB 8 EiB ??
Max Number of 0 1 (last) 1 (last) 2^32 ??
Fixed Vars > 2
GiB
Max Record Vars 0 1 (last) 1 (last) 2^32 ??
w/ Rec Size > 2
GiB
Max Size of 2 GiB 2 GiB 2 GiB 4 GiB ??
Fixed/Record Size
of Record Var
Max Record Size 2 4 GiB 8 EiB/nrecs 8 ??
GiB/nrecs EiB/nrecs
For more information about the different file formats of netCDF
*Note Which Format::.
File: netcdf.info, Node: 64 bit Offset Limitations, Next: Classic Limitations, Prev: Large File Support, Up: Structure
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.
File: netcdf.info, Node: Classic Limitations, Next: The NetCDF-3 IO Layer, Prev: 64 bit Offset Limitations, Up: Structure
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:
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; // 1000 records, for example
variables:
double x(x); // coordinate variables
double y(y);
double z(z);
double t(t);
// 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);
}
File: netcdf.info, Node: The NetCDF-3 IO Layer, Next: UNICOS Optimization, Prev: Classic Limitations, Up: Structure
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 (*note nc_sync:
(netcdf-c)nc_sync.), or the Fortran function NF_SYNC (*note NF_SYNC:
(netcdf-f77)NF_SYNC.), also brings header 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.
File: netcdf.info, Node: UNICOS Optimization, Next: Chunking, Prev: The NetCDF-3 IO Layer, Up: Structure
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 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.
File: netcdf.info, Node: Chunking, Next: Parallel Access, Prev: UNICOS Optimization, Up: Structure
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').
* Menu:
* Chunk Cache::
* Default Chunking::
* Default Chunking 4_0_1::
* Parallel Chunking::
* bm_file::
File: netcdf.info, Node: Chunk Cache, Next: Default Chunking, Prev: Chunking, Up: Chunking
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-chunk-cache-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 -with-max-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 *note
nc_set_chunk_cache: (netcdf-c)nc_set_chunk_cache, Fortran 77
programmers see *note NF_SET_CHUNK_CACHE:
(netcdf-f77)NF_SET_CHUNK_CACHE.). Fortran 90 programmers use the
optional cache_size, 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 *note
nc_set_var_chunk_cache: (netcdf-c)nc_set_var_chunk_cache, Fortran 77
programmers see *note NF_SET_VAR_CHUNK_CACHE:
(netcdf-f77)NF_SET_VAR_CHUNK_CACHE, ).
File: netcdf.info, Node: Default Chunking, Next: Default Chunking 4_0_1, Prev: Chunk Cache, Up: Chunking
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));
File: netcdf.info, Node: Default Chunking 4_0_1, Next: Parallel Chunking, Prev: Default Chunking, Up: Chunking
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.
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.
File: netcdf.info, Node: Parallel Chunking, Next: bm_file, Prev: Default Chunking 4_0_1, Up: Chunking
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.
File: netcdf.info, Node: bm_file, Prev: Parallel Chunking, Up: Chunking
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, data read time, data write time, enddianness, metadata reread time, data reread time, read rate, write rate, reread rate, deflate, shuffle, chunksize[0], chunksize[1], chunksize[2], chunksize[3]
1, 4, 200092, 207283, 1613, 1054, 409, 312, 0, 1208, 1551, 488.998, 641.026, 128.949, 0, 0, 100000, 0, 0, 0
1, 4, 199824, 208093, 1545, 1293, 397, 284, 0, 1382, 1563, 503.053, 703.211, 127.775, 0, 0, 316, 316, 0, 0
1, 4, 194804, 204260, 1562, 1611, 390, 10704, 0, 1627, 2578, 499.159, 18.1868, 75.5128, 0, 0, 46, 46, 46, 0
1, 4, 167196, 177744, 1531, 1888, 330, 265, 0, 12888, 1301, 506.188, 630.347, 128.395, 0, 0, 17, 17, 17, 17
1, 4, 200172, 211821, 1509, 2065, 422, 308, 0, 1979, 1550, 473.934, 649.351, 129.032, 0, 0, 10, 10, 10, 10
1, 4, 93504, 106272, 1496, 2467, 191, 214, 0, 32208, 809, 488.544, 436.037, 115.342, 0, 0, 6, 6, 6, 6
*** 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 $
set -e
echo ""
echo "*** Testing the benchmarking program bm_file for simple float file, no compression..."
./bm_file -h -d -f 3 -o tst_elena_out.nc -c 0:-1:0:1024:16:256 tst_elena_int_3D.nc
./bm_file -d -f 3 -o tst_elena_out.nc -c 0:-1:0:1024:256:256 tst_elena_int_3D.nc
./bm_file -d -f 3 -o tst_elena_out.nc -c 0:-1:0:512:64:256 tst_elena_int_3D.nc
./bm_file -d -f 3 -o tst_elena_out.nc -c 0:-1:0:512:256:256 tst_elena_int_3D.nc
./bm_file -d -f 3 -o tst_elena_out.nc -c 0:-1:0:256:64:256 tst_elena_int_3D.nc
./bm_file -d -f 3 -o tst_elena_out.nc -c 0:-1:0:256:256:256 tst_elena_int_3D.nc
echo '*** 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:C -d -m -p -i -e 1|2 file
[-v] Verbose
[-o file] Output file name
[-f N] Output format (1 - classic, 2 - 64-bit offset, 3 - netCDF-4, 4 - netCDF4/CLASSIC)
[-h] Print output header
[-c V:Z:S:C:C:C[,V:Z:S:C:C:C, etc.]] Deflate, shuffle, and chunking parameters for vars
[-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
File: netcdf.info, Node: Parallel Access, Next: Interoperability with HDF5, Prev: Chunking, Up: Structure
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 *note nc_open_par: (netcdf-c)nc_open_par, Fortran 77
programmers see *note NF_OPEN_PAR: (netcdf-f77)NF_OPEN_PAR.). 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 netCDF-4/HDF5 files. The HDF5 tutorial
(`http://hdfgroup.org/HDF5//HDF5/Tutor') is a good reference.
For classic and 64-bit offset files, netCDF uses the parallel-netcdf
(formerly pnetcdf) library from Argonne National Labs/Nortwestern
University. For parallel access of classic and 64-bit offset files,
netCDF must be configured with the -with-pnetcdf option at build time.
See the parallel-netcdf site for more information
(`http://www.mcs.anl.gov/parallel-netcdf').
File: netcdf.info, Node: Interoperability with HDF5, Next: DAP Support, Prev: Parallel Access, Up: Structure
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 netCDF-4 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).
File: netcdf.info, Node: DAP Support, Prev: Interoperability with HDF5, Up: Structure
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 *note The NetCDF Installation and Porting Guide:
(netcdf-install)Top.
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;
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 PrincipleInvestigator ``Mark Abbott'', ``Ph.D'';
String DataCenter ``COAS Environmental Computer Facility'';
String DrifterType ``MetOcean WOCE/OCM'';
}
b {
String Description ``A test byte'';
String units ``unknown'';
}
i32 {
String Description ``A 32 bit test server int'';
String 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. 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:
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.
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.
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 = UNLIMITED;
lat = 2 ;
lon = 2 ;
S1.FS2.f1_0 = 2 ;
S1.FS2.f1_1 = 3 ;
S1.FS2.f2_0 = 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 = UNLIMITED ;
lat = 2 ;
lon = 2 ;
S1.FS2.f1_0 = 2 ;
S1.FS2.f1_1 = 3 ;
S1.FS2.f2_0 = 2 ;
variables:
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;
} 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;
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);
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 netCF-3 translation is used.
4. If the URL is prefixed with the client parameter "[netcdf4]" or
"[netcdf-4]" then netCF-4 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.
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.
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.
File: netcdf.info, Node: NetCDF Utilities, Next: Units, Prev: Structure, Up: Top
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).
* Menu:
* CDL Syntax:: Creating a File without Code
* CDL Data Types:: Describing Types in CDL
* CDL Constants:: Constant Values in CDL
* ncgen:: Turning CDL into Classic or Enhanced Data Files
* ncdump:: Turning Data Files into CDL (or XML)
* ncgen3:: Turning CDL into Classic Data Files
File: netcdf.info, Node: CDL Syntax, Next: CDL Data Types, Prev: NetCDF Utilities, Up: NetCDF Utilities
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.;
rh:_FillValue = -1;
data:
lat = 0, 10, 20, 30, 40, 50, 60, 70, 80, 90;
lon = -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 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 *Note Format::. 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.
File: netcdf.info, Node: CDL Data Types, Next: CDL Constants, Prev: CDL Syntax, Up: NetCDF Utilities
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.
`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.
File: netcdf.info, Node: CDL Constants, Next: ncgen, Prev: CDL Data Types, Up: NetCDF Utilities
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' // ASCII a
'\0' // a zero byte
'\n' // ASCII newline character
'\33' // ASCII escape character (33 octal)
'\x2b' // ASCII plus (2b hex)
'\376' // 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 above the netCDF library
layer. The usual escape conventions for C strings are honored. For
example:
"a" // ASCII 'a'
"Two\nlines\n" // a 10-character string with two embedded newlines
"a bell:\007" // a string containing an ASCII bell
"ab","cde" // 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 // a short 2
0123s // octal
0x7ffs // 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 // octal
0x7ff // hexadecimal
1234567890L // 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 // will be truncated to less precision
1.f
.1f
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
File: netcdf.info, Node: ncgen, Next: ncdump, Prev: CDL Constants, Up: NetCDF Utilities
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.
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
* 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
File: netcdf.info, Node: ncdump, Next: ncgen3, Prev: ncgen, Up: NetCDF Utilities
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:
`-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 (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 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 non-character 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 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
File: netcdf.info, Node: ncgen3, Prev: ncdump, Up: NetCDF Utilities
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.
File: netcdf.info, Node: Units, Next: Attribute Conventions, Prev: NetCDF Utilities, Up: Top
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
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 Instead
Means
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.
File: netcdf.info, Node: Attribute Conventions, Next: File Format, Prev: Units, Up: Top
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 *note Units::.
`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 (*note nc_set_fill:
(netcdf-c)nc_set_fill.) or NF_SET_FILL in Fortran (*note
NF_SET_FILL: (netcdf-f77)NF_SET_FILL.). 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 *note Fill Values:
(netcdf-c)Fill Values. For more information for Fortran
programmers see *note Fill Values: (netcdf-f77)Fill Values.
`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 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 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.
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.
File: netcdf.info, Node: File Format, Next: Combined Index, Prev: Attribute Conventions, Up: Top
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).
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.
* Menu:
* NetCDF Classic Format:: The Original Binary Format
* 64-bit Offset Format:: Supporting Larger Variables
* NetCDF-4 Format:: Uses HDF5
* NetCDF-4 Classic Model Format:: HDF5 with NetCDF Limitations
* HDF4 SD Format::
File: netcdf.info, Node: NetCDF Classic Format, Next: 64-bit Offset Format, Prev: File Format, Up: File Format
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.
* Menu:
* Classic Format Spec:: Detailed Format Information
* Computing Offsets:: How to Get the Data You Want
* Examples:: The Binary Layout of some Simple Files
File: netcdf.info, Node: Classic Format Spec, Next: Computing Offsets, Prev: NetCDF Classic Format, Up: NetCDF Classic Format
The Format in Detail
--------------------
netcdf_file = header data
header = magic numrecs dim_list gatt_list var_list
magic = 'C' 'D' 'F' VERSION
VERSION = \x01 | // classic format
\x02 // 64-bit offset format
numrecs = NON_NEG | STREAMING // length of record dimension
dim_list = ABSENT | NC_DIMENSION nelems [dim ...]
gatt_list = att_list // global attributes
att_list = ABSENT | NC_ATTRIBUTE nelems [attr ...]
var_list = ABSENT | NC_VARIABLE nelems [var ...]
ABSENT = ZERO ZERO // Means list is not present
ZERO = \x00 \x00 \x00 \x00 // 32-bit zero
NC_DIMENSION = \x00 \x00 \x00 \x0A // tag for list of dimensions
NC_VARIABLE = \x00 \x00 \x00 \x0B // tag for list of variables
NC_ATTRIBUTE = \x00 \x00 \x00 \x0C // tag for list of attributes
nelems = NON_NEG // number of elements in following sequence
dim = name dim_length
name = 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.
namestring = ID1 [IDN ...] padding
ID1 = alphanumeric | '_'
IDN = alphanumeric | special1 | special2
alphanumeric = lowercase | uppercase | numeric | MUTF8
lowercase = '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'
uppercase = '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'
numeric = '0'|'1'|'2'|'3'|'4'|'5'|'6'|'7'|'8'|'9'
// special1 chars have traditionally been
// permitted in netCDF names.
special1 = '_'|'.'|'@'|'+'|'-'
// special2 chars are recently permitted in
// names (and require escaping in CDL).
// Note: '/' is not permitted.
special2 = ' ' | '!' | '"' | '#' | '$' | '%' | '&' | '\'' |
'(' | ')' | '*' | ',' | ':' | ';' | '<' | '=' |
'>' | '?' | '[' | '\\' | ']' | '^' | '`' | '{' |
'|' | '}' | '~'
MUTF8 = <multibyte UTF-8 encoded, NFC-normalized Unicode character>
dim_length = NON_NEG // If zero, this is the record dimension.
// There can be at most one record dimension.
attr = name nc_type nelems [values ...]
nc_type = NC_BYTE |
NC_CHAR |
NC_SHORT |
NC_INT |
NC_FLOAT |
NC_DOUBLE
var = 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, ...
dimid = 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.
vatt_list = att_list // Variable-specific attributes
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.
begin = OFFSET // Variable start location. The offset in
// bytes (seek index) in the file of the
// beginning of data for this variable.
data = non_recs recs
non_recs = [vardata ...] // The data for all non-record variables,
// stored contiguously for each variable, in
// the same order the variables occur in the
// header.
vardata = [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).
recs = [record ...] // The data for all record variables are
// stored interleaved at the end of the
// file.
record = [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.
varslab = [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).
values = bytes | chars | shorts | ints | floats | doubles
string = nelems [chars]
bytes = [BYTE ...] padding
chars = [CHAR ...] padding
shorts = [SHORT ...] padding
ints = [INT ...]
floats = [FLOAT ...]
doubles = [DOUBLE ...]
padding = <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_NEG = <non-negative INT>
STREAMING = \xFF \xFF \xFF \xFF // Indicates indeterminate record
// count, allows streaming data
OFFSET = <non-negative INT> | // For classic format or
<non-negative INT64> // for 64-bit offset format
BYTE = <8-bit byte> // See "Note on byte data", below.
CHAR = <8-bit byte> // See "Note on char data", below.
SHORT = <16-bit signed integer, Bigendian, two's complement>
INT = <32-bit signed integer, Bigendian, two's complement>
INT64 = <64-bit signed integer, Bigendian, two's complement>
FLOAT = <32-bit IEEE single-precision float, Bigendian>
DOUBLE = <64-bit IEEE double-precision float, Bigendian>
// following type tags are 32-bit integers
NC_BYTE = \x00 \x00 \x00 \x01 // 8-bit signed integers
NC_CHAR = \x00 \x00 \x00 \x02 // text characters
NC_SHORT = \x00 \x00 \x00 \x03 // 16-bit signed integers
NC_INT = \x00 \x00 \x00 \x04 // 32-bit signed integers
NC_FLOAT = \x00 \x00 \x00 \x05 // IEEE single precision floats
NC_DOUBLE = \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.
FILL_CHAR = \x00 // null byte
FILL_BYTE = \x81 // (signed char) -127
FILL_SHORT = \x80 \x01 // (short) -32767
FILL_INT = \x80 \x00 \x00 \x01 // (int) -2147483647
FILL_FLOAT = \x7C \xF0 \x00 \x00 // (float) 9.9692099683868690e+36
FILL_DOUBLE = \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 2^32 - 4 bytes, so 2^32 - 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 multi-byte 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 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, 2^32 - 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.
File: netcdf.info, Node: Computing Offsets, Next: Examples, Prev: Classic Format Spec, Up: NetCDF Classic Format
Notes on Computing File Offsets
-------------------------------
The offset (position within the file) of a specified data value in a
classic format or 64-bit 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 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.
File: netcdf.info, Node: Examples, Prev: Computing Offsets, Up: NetCDF Classic Format
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 0000 0000
\0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0
00000 00000 00000 00000 00000 00000 00000 00000
[ 0 global atts (ABSENT) ] [ 0 variables (ABSENT) ]
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 6d00 0000 0005 0000 0000
\0 \0 \0 003 d i m \0 \0 \0 \0 005 \0 \0 \0 \0
00000 00003 25705 27904 00000 00005 00000 00000
[ 3 char name = "dim" ] [ 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 0000 0000 0001 0000 0000 0000 0000
v x \0 \0 \0 \0 \0 001 \0 \0 \0 \0 \0 \0 \0 \0
30328 00000 00000 00001 00000 00000 00000 00000
"vx" ] [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 ]
File: netcdf.info, Node: 64-bit Offset Format, Next: NetCDF-4 Format, Prev: NetCDF Classic Format, Up: File Format
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 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.
File: netcdf.info, Node: NetCDF-4 Format, Next: NetCDF-4 Classic Model Format, Prev: 64-bit Offset Format, Up: File Format
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_INDEXED) < 0)
BAIL(NC_EHDFERR);
if (H5Pset_attr_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
if ((grp->hdf_grpid = H5Gcreate2(grp->parent->hdf_grpid, grp->name,
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 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.
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.
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 multi-dimensional 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.
File: netcdf.info, Node: NetCDF-4 Classic Model Format, Next: HDF4 SD Format, Prev: NetCDF-4 Format, Up: File Format
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 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.
File: netcdf.info, Node: HDF4 SD Format, Prev: NetCDF-4 Classic Model Format, Up: File Format
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
File: netcdf.info, Node: Combined Index, Prev: File Format, Up: Top
Index
*****
孩湤數
* Menu:
* 64-bit offset file format: Classic File Parts. (line 6)
* 64-bit offset format, introduction: Large File Support. (line 6)
* 64-bit offset format, limitations: 64 bit Offset Limitations.
(line 6)
* 64-bit offsets, history: Background. (line 6)
* _FillValue: Attribute Conventions.
(line 30)
* _IONBF flag: The NetCDF-3 IO Layer.
(line 6)
* access C example of array section: C Section Access. (line 6)
* access Fortran example of array section: Fortran Section Access.
(line 6)
* access random: Data Access. (line 6)
* access shared dataset I/O: The NetCDF-3 IO Layer.
(line 6)
* ADA API, history: Background. (line 6)
* add_offset: Attribute Conventions.
(line 122)
* ancillary data as attributes: Attributes and Variables.
(line 6)
* ancillary data, storing: Attributes. (line 6)
* API, C <1>: Summary. (line 6)
* API, C: Top. (line 6)
* API, C++ <1>: Summary. (line 6)
* API, C++: Top. (line 6)
* API, F90: Summary. (line 6)
* API, Fortran: Summary. (line 6)
* API, Fortran 77: Top. (line 6)
* API, Fortran 90: Top. (line 6)
* API, Java: Summary. (line 6)
* appending data along unlimited dimension: Dimensions. (line 6)
* applications, generic: Attributes. (line 6)
* applications, generic, conventions <1>: Attribute Conventions.
(line 6)
* applications, generic, conventions: Conventions. (line 6)
* applications, generic, reasons for netCDF: NetCDF Utilities.
(line 6)
* applications, generic, units: Units. (line 6)
* archive format: Archival. (line 6)
* Argonne National Laboratory: Background. (line 6)
* array section, C example: C Section Access. (line 6)
* array section, corner: Data Access. (line 36)
* array section, definition: Data Access. (line 36)
* array section, edges: Data Access. (line 36)
* array section, Fortran example: Fortran Section Access.
(line 6)
* array section, mapped: Data Access. (line 36)
* arrays, ragged: Limitations. (line 6)
* ASCII characters: External Types. (line 6)
* attribute conventions: Attribute Conventions.
(line 6)
* attributes associated with a variable: Variables. (line 6)
* attributes vs. variables: Attributes and Variables.
(line 6)
* attributes, adding to existing dataset: Attributes. (line 6)
* attributes, CDL, defining: CDL Syntax. (line 6)
* attributes, CDL, global: CDL Syntax. (line 6)
* attributes, CDL, initializing: CDL Constants. (line 6)
* attributes, data type: Attributes. (line 6)
* attributes, data types, CDL: CDL Constants. (line 6)
* attributes, defined: Attributes. (line 6)
* attributes, defining in CDL: Attributes. (line 6)
* attributes, global: Attributes. (line 6)
* attributes, length, CDL: CDL Constants. (line 6)
* attributes, operations on: Attributes. (line 6)
* buffers, I/O: The NetCDF-3 IO Layer.
(line 6)
* byte: CDL Data Types. (line 11)
* byte array vs. text string: Type Conversion. (line 6)
* byte CDL constant: CDL Constants. (line 6)
* byte, CDL data type: CDL Data Types. (line 6)
* byte, signed vs. unsigned: External Types. (line 6)
* C API <1>: Summary. (line 6)
* C API: Top. (line 6)
* C code via ncgen, generating: ncgen. (line 6)
* C code via ncgen3, generating: ncgen3. (line 6)
* C++ API <1>: Summary. (line 6)
* C++ API: Top. (line 6)
* C_format: Attribute Conventions.
(line 149)
* CANDIS: Background. (line 6)
* CDF1: Large File Support. (line 6)
* CDF2: Large File Support. (line 6)
* CDL attributes, defining: CDL Syntax. (line 6)
* CDL constants: CDL Constants. (line 6)
* CDL data types: CDL Data Types. (line 6)
* CDL dimensions, defining: CDL Syntax. (line 6)
* CDL syntax: CDL Syntax. (line 6)
* CDL variables, defining: CDL Syntax. (line 6)
* CDL, defining attributes: Attributes. (line 6)
* CDL, defining global attributes: Attributes. (line 6)
* CDL, example: Data Model. (line 6)
* char: CDL Data Types. (line 8)
* char, CDL data type: CDL Data Types. (line 6)
* chunking: Chunking. (line 6)
* classic file format: Classic File Parts. (line 6)
* classic format, introduction: Large File Support. (line 6)
* classic format, limitations: Classic Limitations. (line 6)
* classic netCDF format: Limitations. (line 6)
* common data form language: Data Model. (line 6)
* compound type: User Defined Types. (line 6)
* compression: Archival. (line 6)
* Conventions: Attribute Conventions.
(line 177)
* conventions, attributes: Attribute Conventions.
(line 6)
* conventions, introduction: Conventions. (line 6)
* conventions, naming: Data Model. (line 6)
* conversion of data types, introduction: External Types. (line 6)
* coordinate variables: Variables. (line 6)
* DAP support: DAP Support. (line 6)
* data base: Not DBMS. (line 6)
* data model, netCDF: Data Model. (line 6)
* data structures: Classic Data Structures.
(line 6)
* data types, conversion: Type Conversion. (line 6)
* data types, external: External Types. (line 6)
* data, reading: Data Access. (line 6)
* data, writing: Data Access. (line 6)
* DBMS: Not DBMS. (line 6)
* deflation: Chunking. (line 6)
* differences between attributes and variables: Attributes and Variables.
(line 6)
* dimensions, CDL, defining: CDL Syntax. (line 6)
* dimensions, CDL, initializing: CDL Constants. (line 6)
* dimensions, introduction: Dimensions. (line 6)
* dimensions, length, CDL: CDL Constants. (line 6)
* dimensions, unlimited: Dimensions. (line 6)
* DODS: Background. (line 6)
* double: CDL Data Types. (line 29)
* double, CDL data type: CDL Data Types. (line 6)
* enum type: User Defined Types. (line 6)
* external data types: External Types. (line 6)
* F90 API: Summary. (line 6)
* FAN: Background. (line 6)
* fflush: The NetCDF-3 IO Layer.
(line 6)
* file format: File Format. (line 6)
* file format, 64-bit offset: Classic File Parts. (line 6)
* file format, classic: Classic File Parts. (line 6)
* file format, netcdf-4: NetCDF-4 File Parts. (line 6)
* file structure, overview: Structure. (line 6)
* float: CDL Data Types. (line 23)
* float, CDL data type: CDL Data Types. (line 6)
* flushing buffers: The NetCDF-3 IO Layer.
(line 6)
* format selection advice: Which Format. (line 6)
* Fortran 77 API: Top. (line 6)
* Fortran 90 API: Top. (line 6)
* Fortran API: Summary. (line 6)
* FORTRAN_format: Attribute Conventions.
(line 159)
* future plans for netCDF: Future. (line 6)
* GBytes: Limitations. (line 6)
* generating C code via ncgen: ncgen. (line 6)
* generating C code via ncgen3: ncgen3. (line 6)
* generic applications: Attributes. (line 6)
* GiBytes: Limitations. (line 6)
* global attributes: Attributes. (line 6)
* groups: Data Model. (line 6)
* history: Attribute Conventions.
(line 170)
* I/O layer: The NetCDF-3 IO Layer.
(line 6)
* initializing CDL: CDL Constants. (line 6)
* int: CDL Data Types. (line 17)
* int, CDL data type: CDL Data Types. (line 6)
* int64: CDL Data Types. (line 43)
* Interface Guide, C: Top. (line 6)
* Interface Guide, C++: Top. (line 6)
* Interface Guide, Fortran 77: Top. (line 6)
* Interface Guide, Fortran 90: Top. (line 6)
* interoperability with HDF5: Interoperability with HDF5.
(line 6)
* Java API: Summary. (line 6)
* Java API, history: Background. (line 6)
* large file support: Large File Support. (line 6)
* LFS: Large File Support. (line 6)
* limitations of netCDF: Limitations. (line 6)
* long: CDL Data Types. (line 20)
* long, CDL data type: CDL Data Types. (line 6)
* long_name: Attribute Conventions.
(line 25)
* Matlab API, history: Background. (line 6)
* missing_value: Attribute Conventions.
(line 60)
* multiple unlimited dimensions: Dimensions. (line 6)
* naming conventions: Data Model. (line 6)
* NASA CDF format: Background. (line 6)
* NC_BYTE: Variables. (line 6)
* NC_CHAR: Variables. (line 6)
* NC_DOUBLE: Variables. (line 6)
* NC_FLOAT: Variables. (line 6)
* NC_INT: Variables. (line 6)
* NC_INT64: Variables. (line 6)
* NC_LONG: Variables. (line 6)
* NC_SHARE: The NetCDF-3 IO Layer.
(line 6)
* NC_SHORT: Variables. (line 6)
* NC_STRING: Variables. (line 6)
* nc_sync: The NetCDF-3 IO Layer.
(line 6)
* NC_UBYTE: Variables. (line 6)
* NC_UINT: Variables. (line 6)
* NC_UINT64: Variables. (line 6)
* NC_USHORT: Variables. (line 6)
* ncdump: ncdump. (line 6)
* ncdump, introduction: Data Model. (line 6)
* ncdump, overview: NetCDF Utilities. (line 6)
* ncgen: ncgen. (line 6)
* ncgen and ncgen3, overview: NetCDF Utilities. (line 6)
* ncgen3: ncgen3. (line 6)
* NcML: Background. (line 6)
* NCO: Background. (line 6)
* netCDF 5.0: Future. (line 6)
* netCDF data model: Data Model. (line 6)
* netCDF data types: Variables. (line 6)
* netcdf-4 file format: NetCDF-4 File Parts. (line 6)
* NETCDF_FFIOSPEC: UNICOS Optimization. (line 6)
* New Mexico Institute of Mining: Background. (line 6)
* new netCDF features in 4.0: Whats New. (line 6)
* nf_byte: Variables. (line 6)
* nf_char: Variables. (line 6)
* nf_double: Variables. (line 6)
* nf_float: Variables. (line 6)
* nf_int1: Variables. (line 6)
* nf_int2: Variables. (line 6)
* nf_real: Variables. (line 6)
* NF_SHARE: The NetCDF-3 IO Layer.
(line 6)
* nf_short: Variables. (line 6)
* NF_SYNC: The NetCDF-3 IO Layer.
(line 6)
* Northwestern University: Background. (line 6)
* opaque type: User Defined Types. (line 6)
* OpenDAP: Background. (line 6)
* operations on attributes: Attributes. (line 6)
* parallel access: Parallel Access. (line 6)
* performance of NetCDF: Structure. (line 6)
* performance, introduction: Performance. (line 6)
* plans for netCDF: Future. (line 6)
* pong: Future. (line 6)
* primary variables: Variables. (line 6)
* python API, history: Background. (line 6)
* real: CDL Data Types. (line 26)
* real, CDL data type: CDL Data Types. (line 6)
* references: References. (line 6)
* ruby API, history: Background. (line 6)
* scale_factor: Attribute Conventions.
(line 111)
* SeaSpace, Inc: Background. (line 6)
* share flag: The NetCDF-3 IO Layer.
(line 6)
* shared dataset I/O access: The NetCDF-3 IO Layer.
(line 6)
* short: CDL Data Types. (line 14)
* short, CDL data type: CDL Data Types. (line 6)
* shuffle filter: Chunking. (line 6)
* signedness: Attribute Conventions.
(line 141)
* SNIDE: Background. (line 6)
* software list: NetCDF Utilities. (line 6)
* storing ancillary data: Attributes. (line 6)
* string: CDL Data Types. (line 49)
* structures, data: Classic Data Structures.
(line 6)
* supported programming languages: Summary. (line 6)
* Tcl/Tk API, history: Background. (line 6)
* Terascan data format: Background. (line 6)
* title: Attribute Conventions.
(line 166)
* type conversion: Type Conversion. (line 6)
* ubyte: CDL Data Types. (line 34)
* udunits: Units. (line 6)
* uint: CDL Data Types. (line 40)
* uint64: CDL Data Types. (line 46)
* UNICOS: UNICOS Optimization. (line 6)
* units: Attribute Conventions.
(line 15)
* units library: Units. (line 6)
* University of Miami: Background. (line 6)
* unlimited dimensions: Dimensions. (line 6)
* user defined types: Data Model. (line 6)
* ushort: CDL Data Types. (line 37)
* utilities: NetCDF Utilities. (line 6)
* valid_max: Attribute Conventions.
(line 77)
* valid_min: Attribute Conventions.
(line 74)
* valid_range: Attribute Conventions.
(line 80)
* variable length array type: User Defined Types. (line 6)
* variable types: Variables. (line 6)
* variables vs. attributes: Attributes and Variables.
(line 6)
* variables, CDL, defining: CDL Syntax. (line 6)
* variables, CDL, initializing: CDL Constants. (line 6)
* variables, coordinate: Variables. (line 6)
* variables, data types, CDL: CDL Constants. (line 6)
* variables, defined: Variables. (line 6)
* variables, primary: Variables. (line 6)
* vlen type: User Defined Types. (line 6)
* WetCDF, history: Background. (line 6)
* workshop, CDF: Background. (line 6)
* writers, multiple: Limitations. (line 6)
* XDR format: Format. (line 6)
* XDR layer: XDR Layer. (line 6)
* XDR, introduction into netCDF: Background. (line 6)
Tag Table:
Node: Top1368
Node: Foreword6125
Node: Summary11202
Node: Introduction13675
Node: Interface14570
Node: Not DBMS16969
Node: Format18551
Node: Which Format20567
Node: Performance24029
Node: Archival25618
Node: Conventions26655
Node: Background27990
Node: Whats New38874
Node: Limitations39764
Node: Future45720
Node: References46051
Node: Dataset Components48770
Node: Data Model49197
Node: Dimensions56188
Node: Variables59206
Node: Attributes63822
Node: Attributes and Variables67857
Node: Data69508
Node: External Types70141
Node: Classic Data Structures74208
Node: User Defined Types76379
Node: Data Access81281
Node: C Section Access85321
Node: Fortran Section Access90613
Node: Type Conversion95457
Node: Structure98906
Node: Classic File Parts100818
Node: NetCDF-4 File Parts105490
Node: XDR Layer106555
Node: Large File Support107639
Node: 64 bit Offset Limitations110421
Node: Classic Limitations112046
Node: The NetCDF-3 IO Layer114337
Node: UNICOS Optimization116730
Node: Chunking119219
Node: Chunk Cache120747
Node: Default Chunking122436
Node: Default Chunking 4_0_1123513
Node: Parallel Chunking125153
Node: bm_file125534
Node: Parallel Access130172
Node: Interoperability with HDF5131449
Node: DAP Support134076
Node: NetCDF Utilities157336
Node: CDL Syntax159264
Node: CDL Data Types165543
Node: CDL Constants167539
Node: ncgen170928
Node: ncdump175214
Node: ncgen3183374
Node: Units186031
Node: Attribute Conventions190369
Node: File Format201806
Node: NetCDF Classic Format206502
Node: Classic Format Spec208268
Node: Computing Offsets221024
Node: Examples223701
Node: 64-bit Offset Format227268
Node: NetCDF-4 Format228058
Node: NetCDF-4 Classic Model Format241422
Node: HDF4 SD Format243149
Node: Combined Index243832
End Tag Table
