/*! \file The tutorial document. \page tutorial Tutorial Background and Further Reading: - \ref what_is_netcdf - \ref netcdf_documentation NetCDF Data Model: - \ref netcdf_data_model - \ref classic_model - \ref enhanced_model - \ref unlimited_dims - \ref groups - \ref user_defined_types - \ref string_type Important Conventions: - \ref fill_values Tools for NetCDF: - \ref netcdf_utilities - \ref netcdf_tools Programming with NetCDF: - \ref netcdf_apis - \ref error_handling - \ref interoperability_hdf5 - \ref parallel_io Example Programs: - \ref examples1 \page what_is_netcdf What is NetCDF? NetCDF is a set of data formats, programming interfaces, and software libraries that help read and write scientific data files. NetCDF was developed and is maintained at Unidata. Unidata provides data and software tools for use in geoscience education and research. Unidata is part of the University Corporation for Atmospheric Research (UCAR) Community Programs (UCP). Unidata is funded primarily by the National Science Foundation. \page netcdf_utilities The NetCDF Utilities The ncdump command reads a netCDF file and outputs text in a format called CDL. The ncgen command reads a text file in CDL format, and generates a netCDF data file. The nccopy command copies a netCDF file from one binary format to another, optionally changing compression and chunksize settings. \section ncdump ncdump The utility ncdump can be used to show the contents of netCDF files. By default, ncdump shows the CDL description of the file. This CDL description can be fed into ncgen to create the data file. \section ncgen ncgen The ncgen utility can take an ASCII input file, in CDL format, and generate a binary netCDF file. It is the opposite of ncdump. \section nccopy nccopy The nccopy utility can copy a netCDF file, changing binary format, chunk sizes, compression, and other storage settings. \page netcdf_tools Tools for Manipulating NetCDF Files Many existing software applications can read and manipulate netCDF files. Before writing your own program, check to see if any existing programs meet your needs. Three utilities come with the netCDF distribution: ncdump, ncgen, and nccopy. (See \ref netcdf_utilities). The following general-purpose tools have been found to be useful in many situations. Some of the tools on this list are developed at Unidata. The others are developed elsewhere, and we can make no guarantees about their continued availability or success. All of these tools are open-source. - UDUNITS - Unidata library to help with scientific units. - IDV - Unidata's Integrated Data Viewer, a 3D visualization and analysis package (Java based). - NCL - NCAR Command Language, a graphics and data manipulation package. - GrADS - The Grid Analysis and Display System package. - NCO - NetCDF Command line Operators, tools to manipulate netCDF files. A list of netCDF tools that we know about can be found on the website. If you know of any that should be added to this list, send email to support-netcdf@unidata.ucar.edu. \page netcdf_apis The NetCDF Programming APIs Unidata supports netCDF APIs in C, C++, Fortran 77, Fortran 90, and Java. The netCDF Java API is a complete implementation of netCDF in Java. It is distributed independently of the other APIs. If you are writing web server software, you should certainly be doing so in Java. The main netCDF distribution contains the C library and the netCDF utilities, ncgen/ncdump/nccopy. The C++, Fortran 77 and Fortran 90 APIs are distributed separately from the C library. The C library must be installed before any of these APIs may be built. They depend on the C API. Due to the nature of C++ and Fortran 90, users of those languages can also use the C and Fortran 77 APIs (respectively) directly. Full documentation exists for each API (see \ref netcdf_documentation). In addition, many other language APIs exist, including Perl, Python, and Ruby. Most of these APIs were written and supported by netCDF users. Some of them are listed on the netCDF software page. Since these generally use the C API, they should work well with netCDF-4/HDF5 files, but the maintainers of the APIs must add support for netCDF-4 advanced features. In addition to the main netCDF-3 C API, there is an additional (older) C API, the netCDF-2 API. This API produces exactly the same files as the netCDF-3 API - only the API is different. (That is, users can create either classic format files, the default, or 64-bit offset files, or netCDF-4/HDF5 files.) The version 2 API was the API before netCDF-3.0 came out. It is still fully supported, however. Programs written to the version 2 API will continue to work. The version 2 API is built with the netCDF library by default. Users writing new programs should use the netCDF-3 API, which contains better type checking, better error handling, and better documentation. The netCDF-2 API is provided for backward compatibility. Documentation for the netCDF-2 API can be found on the netCDF website, see http://www.unidata.ucar.edu/netcdf/old_docs/really_old/guide_toc.html. \page netcdf_documentation NetCDF Documentation Language specific programming guides are available for netCDF for the C, C++, Fortran 77, Fortran 90, and Java APIs: - C - The NetCDF C Interface Guide. - C++ - The NetCDF C++ Interface Guide. - Fortran 77 - The NetCDF Fortran 77 Interface Guide. - Fortran 90 - The NetCDF Fortran 90 Interface Guide. - Java The netCDF-Java Users Guide. Man pages for the C, F77, and F90 interfaces, and ncgen and ncdump, are available on the documentation page of the netCDF web site (http://www.unidata.ucar.edu/netcdf/docs), and are installed with the libraries. The latest version of all netCDF documentation can always be found at the netCDF documentation page. \page netcdf_data_model The netCDF data model is the way that we think about data. The data model of dimensions, variables, and attributes, which define the \ref classic_model, was extended starting with netCDF-4.0. The new \ref enhanced_model supports the classic model in a completely backward-compatible way, while allowing access to new features such as groups, multiple unlimited dimensions, and new types, including user-defined types. For maximum interoparability with existing code, new data should be created with the \ref classic_model.
\image html nc4-model.png "The NetCDF Enhanced Data Model" \page classic_model The Classic Model The classic netCDF data model consists of variables, dimensions, and attributes. This way of thinking about data was introduced with the very first netCDF release, and is still the core of all netCDF files.
\image html nc-classic-uml.png "NetCDF Classic Data Model" In version 4.0, the netCDF data model has been expanded. See \ref enhanced_model.
Variables | N-dimensional arrays of data. Variables in netCDF files can be one of six types (char, byte, short, int, float, double). |
Dimensions | describe the axes of the data arrays. A dimension has a name and a length. An unlimited dimension has a length that can be expanded at any time, as more data are written to it. NetCDF files can contain at most one unlimited dimension. |
Attributes | annotate variables or files with small notes or supplementary metadata. Attributes are always scalar values or 1D arrays, which can be associated with either a variable or the file as a whole. Although there is no enforced limit, the user is expected to keep attributes small. |
\image html nc4-model.png
With netCDF-4/HDF5 files, the user may define groups, which may
contain variables, dimensions, and attributes. In this way, a group
acts as a container for the classic netCDF dataset. But netCDF-4/HDF5
files can have many groups, organized hierarchically.
Each file begins with at least one group, the root group. The user may
then add more groups, receiving a new ncid for each group created.
Since each group functions as a complete netCDF classic dataset, it is
possible to have variables with the same name in two or more different
groups, within the same netCDF-4/HDF5 data file.
Dimensions have a special scope: they may be seen by all variables in
their group, and all descendant groups. This allows the user to define
dimensions in a top-level group, and use them in many sub-groups.
Since it may be necessary to write code which works with all types of
netCDF data files, we also introduce the ability to create
netCDF-4/HDF5 files which follow all the rules of the classic netCDF
model. That is, these files are in HDF5, but will not support multiple
unlimited dimensions, user-defined types, groups, etc. They act just
like a classic netCDF file.
\page fill_values Fill Values
Sometimes there are missing values in the data, and some value is
needed to represent them.
For example, what value do you put in a sea-surface temperature
variable for points over land?
In netCDF, you can create an attribute for the variable (and of the
same type as the variable) called “_FillValue” that contains a value
that you have used for missing data. Applications that read the data
file can use this to know how to represent these values.
Using attributes it is possible to capture metadata that would
otherwise be separated from the data. Various conventions have been
established. By using a set of conventions, a data producer is more
likely to produce files that can be easily shared within the research
community, and that contain enough details to be useful as a long-term
archive. Conventions also make it easier to develop software that
interprets information represented in data, because a convention
selects one conventional way to represent information when multiple
equivalent representations are possible.
For more information on _FillValue and other attribute conventions,
see \ref attribute_conventions.
Climate and meteorological users are urged to follow the Climate and
Forecast (CF) metadata conventions when producing data files. For more
information about the CF conventions, see http://cf-pcmdi.llnl.gov.
\page error_handling Error Handling
Each netCDF function in the C, Fortran 77, and Fortran 90 APIs returns
0 on success, in the tradition of C.
When programming with netCDF in these languages, always check return
values of every netCDF API call. The return code can be looked up in
netcdf.h (for C programmers) or netcdf.inc (for Fortran programmers),
or you can use the strerror function to print out an error
message. (See nc_strerror/NF_STRERROR/NF90_STRERROR).
In general, if a function returns an error code, you can assume it
didn't do what you hoped it would. The exception is the NC_ERANGE
error, which is returned by any of the reading or writing functions
when one or more of the values read or written exceeded the range for
the type. (For example if you were to try to read 1000 into an
unsigned byte.)
In the case of NC_ERANGE errors, the netCDF library completes the
read/write operation, and then returns the error. The type conversion
is handled like a C type conversion, whether or not it is within
range. This may yield bad data, but the netCDF library just returns
NC_ERANGE and leaves it up to the user to handle. (For more
information about type conversion see Type Conversion).
\page unlimited_dims Unlimited Dimensions
Sometimes you don't know the size of all dimensions when you create a
file, or you would like to arbitrarily extend the file along one of
the dimensions.
For example, model output usually has a time dimension. Rather than
specifying that there will be forty-two output times when creating the
file, you might like to create it with one time, and then add data for
additional times, until you wanted to stop.
For this purpose netCDF provides the unlimited dimension. By
specifying a length of “unlimited” when defining a dimension, you
indicate to netCDF that the dimension may be extended, and its length
may increase.
In netCDF classic files, there can only be one unlimited dimension,
and it must be declared first in the list of dimensions for a
variable.
For programmers, the unlimited dimension will correspond with the
slowest-varying dimension. In C this is the first dimension of an
array, in Fortran, the last.
The third example in this tutorial, pres_temp_4D, demonstrates how to
write and read data one time step at a time along an unlimited
dimension in a classic netCDF file. See pres_temp_4D.
In netCDF-4/HDF5 files, any number of unlimited dimensions may be
used, and there is no restriction as to where they appear in a
variable's list of dimension IDs.
\page examples1 NetCDF Example Programs
The netCDF example programs show how to use netCDF.
In the netCDF distribution, the “examples” directory contains examples
in C and CDL. The examples create, and then read, example data files
of increasing complexity.
There are three sets of netCDF classic example programs; corresponding
examples are included with the netCDF Fortran and C++ APIs.
- \ref example_simple_xy
- \ref example_sfc_pres_temp
- \ref example_pres_temp_4D
Any existing netCDF applications can be converted to generate
netCDF-4/HDF5 files. Simply change the file creation call to include
the correct mode flag.
In one of the netCDF classic examples which write a data file, change
the nc_create() call so that ::NC_NETCDF4 is one of the flags set on
the create.
The corresponding read example will work without modification; netCDF
will notice that the file is a NetCDF-4/HDF5 file, and will read it
automatically, just as if it were a netCDF classic format file.
In the example in this section we show some of the advanced features
of netCDF-4.
- \ref example_simple_nc4
- \ref example_simple_xy_nc4
The examples are built and run with the “make check” command. (See
\ref building).
The corresponding examples in each language create identical netCDF
data files. For example, the C program sfc_pres_temp_wr.c produces the
same data file as the Fortran 77 program sfc_pres_temp_wr.f.
\page example_simple_xy The simple_xy Example
This example is an unrealistically simple netCDF file, to demonstrate
the minimum operation of the netCDF APIs. Users should seek to make
their netCDF files more self-describing than this primitive example.
- simple_xy_wr.c
- simple_xy_rd.c
As in all the netCDF tutorial examples, this example file can be
created by C and by ncgen, which creates it from a CDL script. Both
ncgen and the C example create identical files, “simple_xy.nc.”
The simple_xy.nc data file contains two dimensions, “x” and “y”, and
one netCDF variable, “data.”
The CDL for this example is shown below. For more information on
ncdump and ncgen see NetCDF Utilities.
\code
netcdf simple_xy {
dimensions:
x = 6 ;
y = 12 ;
variables:
int data(x, y) ;
data:
data =
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 ;
}
\endcode
\page example_sfc_pres_temp The sfc_pres_temp Example
This example has been constructed for the meteorological mind.
Suppose you have some data you want to write to a netCDF file. For
example, you have one time step of surface temperature and surface
pressure, on a 6 x 12 latitude longitude grid.
To store this in netCDF, create a file, add two dimensions (latitude
and longitude) and two variables (pressure and temperature).
- sfc_pres_temp_wr.c
- sfc_pres_temp_rd.c
In this example we add some netCDF attributes, as is typical in
scientific applications, to further describe the data. In this case we
add a units attribute to every netCDF variable.
In this example we also add additional netCDF variables to describe
the coordinate system. These “coordinate variables” allow us to
specify the latitudes and longitudes that describe the data grid.
The CDL version of the data file, generated by ncdump, is shown below
(see \ref netcdf_utilities).
\code
netcdf sfc_pres_temp {
dimensions:
latitude = 6 ;
longitude = 12 ;
variables:
float latitude(latitude) ;
latitude:units = "degrees_north" ;
float longitude(longitude) ;
longitude:units = "degrees_east" ;
float pressure(latitude, longitude) ;
pressure:units = "hPa" ;
float temperature(latitude, longitude) ;
temperature:units = "celsius" ;
data:
latitude = 25, 30, 35, 40, 45, 50 ;
longitude = -125, -120, -115, -110, -105, -100, -95, -90, -85, -80, -75, -70 ;
pressure =
900, 906, 912, 918, 924, 930, 936, 942, 948, 954, 960, 966,
901, 907, 913, 919, 925, 931, 937, 943, 949, 955, 961, 967,
902, 908, 914, 920, 926, 932, 938, 944, 950, 956, 962, 968,
903, 909, 915, 921, 927, 933, 939, 945, 951, 957, 963, 969,
904, 910, 916, 922, 928, 934, 940, 946, 952, 958, 964, 970,
905, 911, 917, 923, 929, 935, 941, 947, 953, 959, 965, 971 ;
temperature =
9, 10.5, 12, 13.5, 15, 16.5, 18, 19.5, 21, 22.5, 24, 25.5,
9.25, 10.75, 12.25, 13.75, 15.25, 16.75, 18.25, 19.75, 21.25, 22.75, 24.25,
25.75,
9.5, 11, 12.5, 14, 15.5, 17, 18.5, 20, 21.5, 23, 24.5, 26,
9.75, 11.25, 12.75, 14.25, 15.75, 17.25, 18.75, 20.25, 21.75, 23.25, 24.75,
26.25,
10, 11.5, 13, 14.5, 16, 17.5, 19, 20.5, 22, 23.5, 25, 26.5,
10.25, 11.75, 13.25, 14.75, 16.25, 17.75, 19.25, 20.75, 22.25, 23.75,
25.25, 26.75 ;
}
\endcode
\page example_pres_temp_4D The pres_temp_4D Example
This example expands on the previous example by making our
two-dimensional data into four-dimensional data, adding a vertical
level axis and an unlimited time step axis.
- pres_temp_4D_wr.c
- pres_temp_4D_rd.c
Additionally, in this example the data are written and read one time
step at a time, as is typical in scientific applications that use the
unlimited dimension.
The sample data file created by pres_temp_4D_wr can be examined with
the utility ncdump (see \ref netcdf_utilities).
\code
netcdf pres_temp_4D {
dimensions:
level = 2 ;
latitude = 6 ;
longitude = 12 ;
time = UNLIMITED ; // (2 currently)
variables:
float latitude(latitude) ;
latitude:units = "degrees_north" ;
float longitude(longitude) ;
longitude:units = "degrees_east" ;
float pressure(time, level, latitude, longitude) ;
pressure:units = "hPa" ;
float temperature(time, level, latitude, longitude) ;
temperature:units = "celsius" ;
data:
latitude = 25, 30, 35, 40, 45, 50 ;
longitude = -125, -120, -115, -110, -105, -100, -95, -90, -85, -80, -75, -70 ;
pressure =
900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911,
912, 913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923,
924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935,
936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947,
948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959,
960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 971,
972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983,
984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995,
996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007,
1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019,
1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031,
1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043,
900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911,
912, 913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923,
924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935,
936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947,
948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959,
960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 971,
972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983,
984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995,
996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007,
1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019,
1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031,
1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043 ;
temperature =
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,
57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,
105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,
129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140,
141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,
57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,
105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,
129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140,
141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152 ;
}
\endcode
\page example_simple_nc4 The simple_nc4 Example
This example, like the simple_xy netCDF-3 example above, is an overly simplified example which demonstrates how to use groups in a netCDF-4 file.
This example is only available in C for this version of netCDF-4. The example creates and then reads the file “simple_nc4.nc.”
The simple_xy.nc data file contains two dimensions, “x” and “y”, two groups, “grp1” and “grp2”, and two data variables, one in each group, both named: “data.” One data variable is an unsigned 64-bit integer, the other a user-defined compound type.
The example program simple_nc4_wr.c creates the example data file simple_nc4.nc. The example program simple_nc4_rd.c reads the data file.
- simple_nc4_wr.c
- simple_nc4_rd.c
\page example_simple_xy_nc4 The simple_xy_nc4 Example
This example, like the simple_xy netCDF-3 example above, is an overly simplified example. It is based on the simple_xy example, but used data chunking, compression, and the fletcher32 filter.
(These are all HDF5 features. For more information see http://hdfgroup.org/HDF5/).
This example is not yet available in C++. We hope to have the C++ example in a future release of netCDF.
The example creates and then reads the file “simple_xy_nc4.nc.”
The example program simple_xy_nc4_wr.c creates the example data file
simple_xy_nc4.nc. The example program simple_xy_nc4_rd.c reads the
data file.
- simple_xy_nc4_wr.c
- simple_xy_nc4_rd.c
\page interoperability_hdf5 Interoperability with HDF5
NetCDF-4 allows some interoperability with HDF5.
\section reading_with_hdf5 Reading and Editing NetCDF-4 Files with HDF5
The HDF5 Files produced by netCDF-4 are perfectly respectable HDF5
files, and can be read by any HDF5 application.
NetCDF-4 relies on several new features of HDF5, including dimension
scales. The HDF5 dimension scales feature adds a bunch of attributes
to the HDF5 file to keep track of the dimension information.
It is not just wrong, but wrong-headed, to modify these attributes
except with the HDF5 dimension scale API. If you do so, then you will
deserve what you get, which will be a mess.
Additionally, netCDF stores some extra information for dimensions
without dimension scale information. (That is, a dimension without an
associated coordinate variable). So HDF5 users should not write data
to a netCDF-4 file which extends any unlimited dimension.
Also there are some types allowed in HDF5, but not allowed in netCDF-4
(for example the time type). Using any such type in a netCDF-4 file
will cause the file to become unreadable to netCDF-4. So don't do it.
NetCDF-4 ignores all HDF5 references. Can't make head nor tail of
them. Also netCDF-4 assumes a strictly hierarchical group
structure. No looping, you weirdo!
Attributes can be added (they must be one of the netCDF-4 types),
modified, or even deleted, in HDF5.
\section accessing_hdf5 Reading and Editing HDF5 Files with NetCDF-4
Assuming a HDF5 file is written in accordance with the netCDF-4 rules
(i.e. no strange types, no looping groups), and assuming that *every*
dataset has a dimension scale attached to each dimension, the netCDF-4
API can be used to read and edit the file, quite easily.
In HDF5 (version 1.8.0 and later), dimension scales are (generally) 1D
datasets, that hold dimension data. A multi-dimensional dataset can
then attach a dimension scale to any or all of its dimensions. For
example, a user might have 1D dimension scales for lat and lon, and a
2D dataset which has lat attached to the first dimension, and lon to
the second.
If dimension scales are not used, then netCDF-4 can still edit the
file, and will invent anonymous dimensions for each variable shape.
\page groups Groups
NetCDF-4 files can store attributes, variables, and dimensions in
hierarchical groups.
This allows the user to create a structure much like a Unix file
system. In netCDF, each group gets an ncid. Opening or creating a file
returns the ncid for the root group (which is named “/”). Groups can
be added with the nc_def_grp() function. Get the number of groups, and
their ncids, with the nc_inq_grps() function.
Dimensions are scoped such that they are visible to all child
groups. For example, you can define a dimension in the root group, and
use its dimension id when defining a variable in a sub-group.
Attributes defined as ::NC_GLOBAL apply to the group, not the entire
file.
The degenerate case, in which only the root group is used, corresponds
exactly with the classic data mode, before groups were introduced.
\page user_defined_types User Defined Types
\section compound_types Compound Types
In netCDF-4 files it's possible to create a data type which
corresponds to a C struct. These are known as “compound” types
(following HDF5 nomenclature).
That is, a netCDF compound type is a data structure which contains an
arbitrary collection of other data types, including other compound
types.
To define a new compound type, use nc_def_compound(). Then call
nc_insert_compound() for each type within the compound type.
Read and write arrays of compound data with the nc_get_vara() and
nc_put_vara() functions. These functions were actually part of the
netCDF-2 API, brought out of semi-retirement to handle user-defined
types in netCDF-4.
\section opaque_types Opaque Types
Store blobs of bits in opaque types. Create an opaque type with
nc_def_opaque. Read and write them with nc_get_vara()/nc_put_vara().
\section vlen_type Variable Length Arrays (VLEN)
Create a VLEN type to store variable length arrays of a known base
type. Use nc_def_vlen() to define a VLEN type, read and write them with
nc_get_vara()/nc_put_vara().
\page string_type Strings
Use the ::NC_STRING type to store arrays of strings. Read and write them
with nc_get_vara()/nc_put_vara().
\page parallel_io Parallel I/O with NetCDF-4
NetCDF-4 provides access to HDF5 parallel I/O features for
netCDF-4/HDF5 files. NetCDF classic and 64-bit offset format may not
be opened or created for use with parallel I/O. (They may be opened
and created, but parallel I/O is not available.)
A few functions have been added to the netCDF C API to handle parallel
I/O.
You must build netCDF-4 properly to take advantage of parallel
features (see \ref build_parallel).
The nc_open_par() and nc_create_par() functions are used to
create/open a netCDF file with parallel access.
The parallel access associated with these functions is not a
characteristic of the data file, but the way it was opened.
\section collective_independent Collective/Independent Access
Parallel file access is either collective (all processors must
participate) or independent (any processor may access the data without
waiting for others).
All netCDF metadata writing operations are collective. That is, all
creation of groups, types, variables, dimensions, or attributes.
Data reads and writes (ex. calls to nc_put_vara_int() and
nc_get_vara_int()) may be independent (the default) or collective. To
make writes to a variable collective, call nc_var_par_access().
\page tutorial_ncids Numbering of NetCDF IDs
In C, Fortran 77, and Fortran 90, netCDF objects are identified by an
integer: the ID. NetCDF functions use this ID to identify the
object. It's helpful for the programmer to understand these IDs.
Open data files, dimensions, variables, and attributes, and
used-defined types are each numbered independently, and are always
numbered in the order in which they were defined. (They also appear in
this order in ncdump output.) Numbering starts with 0 in C, and 1 in
Fortran 77/90.
For example, the first variable defined in a file will have an ID of 0
in C programs, and 1 in Fortran programs, and functions that apply to
a variable will need to know the ID of the variable you mean.
IDs for netCDF dimensions and variables are persistent, but deleting
an attribute changes subsequent attribute numbers.
Although netCDF refers to everything by an integer id (varid, dimid,
attnum), there are inquiry functions which, given a name, will return
an ID. For example, nc_inq_varid() will take a character
string (the name), and give back the ID of the variable of that
name. The variable ID is then used in subsequent calls (to read the
data, for example).
The ncid used to identify a file in the classic model, or a group
within that file in the enhanced model (see \ref netcdf_data_model), or a
user-defined type, are not permanently associated with the file. They
may change the next time the file is opened.
\page creating Creating New Files and Metadata, an Overview
To construct a netCDF file you need to:
- create the file - Specify the name, optionally the format: classic
(the default) or 64bit-offset.
- define metadata - Specify the names and types of dimensions, data
variables, and attributes.
- write data - Write arrays of data from program variables to the
netCDF file. Arrays of data may be written all at once, or in subsets.
- close the file - Close the file to flush all buffers to the disk and
free all resources allocated for this file.
\page reading_known Reading NetCDF Files of Known Structure
To read a netCDF file of known structure, you need to:
- open the file - Specify the file name and whether you want
read-write or read-only access.
- read variable or attribute data - Read the data or attributes of
interest.
- close the file - Release all resources associated with this file.
Use ncdump to learn the structure of a file (use the -h option).
\page reading_unknown Reading NetCDF Files of Unknown Structure
Perhaps you would like to write your software to handle more general
cases, so that you don't have to adjust your source every time the
grid size changes, or a variable is added to the file.
There are inquiry functions that let you find out everything you need
to know about a file. These functions contain “inq” or “INQ” in their
names.
Using the inquiry functions, it is possible to write code that will
read and understand any netCDF file, whatever its contents. (For
example, ncdump does just that.)
First use nc_inq(), which will tell you how many variables and global
attributes there are in the file.
Start with global attribute 0, and proceed to natts - 1, the number of
global attributes minus one. The nc_inq_att() function will tell you
the name, type, and length of each global attribute.
Then start with dimid 0, and proceed to dimid ndims - 1, calling
nc_inq_dim(). This will tell you the name and length of each
dimension, and whether it is unlimited.
Then start with varid 0, and proceed to varid nvars - 1, calling
nc_inq_var(). This will tell you the number of dimensions of this
variable, and their associated IDs. It will also get the name and type
of this variable, and whether there are any attributes attached. If
there are attributes attached, use the nc_inq_att() function to get
their names, types, and lengths.
(To read an attribute, use the appropriate nc_get_att_