PnetCDF/src/utils at master · Parallel-NetCDF/PnetCDF
ncmpigen(1) PnetCDF utilities ncmpigen(1)
NAME
ncmpigen - From a CDL file generate a netCDF file, a C program, or a
Fortran program
SYNOPSIS
ncmpigen [-b] [-c] [-f] [-n] [-o netcdf_filename] [-v file_format]
input_file
DESCRIPTION
ncmpigen generates either a netCDF file, or C or Fortran source code to
create a netCDF file. The input to ncmpigen is a description of a
netCDF file in a small language known as CDL (network Common Data form
Language), described below. If no options are specified in invoking
ncmpigen, it merely checks the syntax of the input CDL file, producing
error messages for any violations of CDL syntax. Other options can be
used to create the corresponding netCDF file, to generate a C program
that uses the netCDF C interface to create the netCDF file, or to gen-
erate a Fortran program that uses the netCDF Fortran interface to cre-
ate the same netCDF file.
ncmpigen may be used with the companion program ncmpidump to perform
some simple operations on netCDF files. For example, to rename a di-
mension in a netCDF file, use ncmpidump to get a CDL version of the
netCDF file, edit the CDL file to change the name of the dimensions,
and use ncmpigen to generate the corresponding netCDF file from the
edited CDL file.
OPTIONS
-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. If a file already exists with the speci-
fied name, it will be overwritten.
-c Generate C source code that will create a netCDF file matching
the netCDF specification. The C source code is written to stan-
dard output.
-f Generate Fortran source code that will create a netCDF file
matching the netCDF specification. The Fortran source code is
written to standard output.
-o netcdf_file
Name for the binary netCDF file created. If this option is
specified, it implies the "-b" option. (This option is neces-
sary because netCDF files cannot be written directly to standard
output, since standard output is not seekable.)
-n Like -b option, except creates netCDF file with the obsolete
`.cdf' extension instead of the `.nc' extension, in the absence
of an output filename specified by the -o option. This option
is only supported for backward compatibility.
-v file_format
File format of the output netCDF file. The value of file_format
can be: 1 or classic for CDF-1 format. 2 or 64-bit-offset is
CDF-2. 5 or 64-bit-variable for CDF-5. The default (if this
option is not given) is CDF-1, the classic format.
EXAMPLES
Check the syntax of the CDL file `foo.cdl':
ncmpigen foo.cdl
From the CDL file `foo.cdl', generate an equivalent binary netCDF file
named `x.nc':
ncmpigen -o x.nc foo.cdl
From the CDL file `foo.cdl', generate a C program containing the netCDF
function invocations necessary to create an equivalent binary netCDF
file named `x.nc':
ncmpigen -c -o x.nc foo.cdl
USAGE
CDL Syntax Summary
Below is an example of CDL syntax, describing a netCDF file with sever-
al named dimensions (lat, lon, and time), variables (Z, t, p, rh, lat,
lon, time), variable attributes (units, long_name, valid_range, _Fill-
Value), and some data. CDL keywords are in boldface. (This example is
intended to illustrate the syntax; a real CDL file would have a more
complete set of attributes so that the data would be more completely
self-describing.)
netcdf foo { // an example netCDF specification in CDL
dimensions:
lat = 10, lon = 5, time = unlimited ;
variables:
long lat(lat), lon(lon), time(time);
float Z(time,lat,lon), t(time,lat,lon);
double p(time,lat,lon);
long rh(time,lat,lon);
// variable attributes
lat:long_name = "latitude";
lat:units = "degrees_north";
lon:long_name = "longitude";
lon:units = "degrees_east";
time:units = "seconds since 1992-1-1 00:00:00";
Z:units = "geopotential 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
characters `//' on any line.
A CDL description consists of three optional parts: dimensions, vari-
ables, and data, beginning with the keyword dimensions:, variables:,
and data, respectively. The variable part may contain variable decla-
rations and attribute assignments.
A netCDF dimension is used to define the shape of one or more of the
multidimensional variables contained in the netCDF file. A netCDF di-
mension has a name and a size. At most one dimension in a netCDF file
can have the unlimited size, which means a variable using this dimen-
sion can grow to any length (like a record number in a 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 is one-dimensional and contains coordi-
nates of the dimension it names. Dimensions need not have correspond-
ing variables.
A netCDF attribute contains information about a netCDF variable or
about the whole netCDF dataset. Attributes are used to specify such
properties as units, special values, maximum and minimum valid values,
scaling factors, offsets, and parameters. Attribute information is
represented by single values or arrays of values. For example, "units"
is an attribute represented by a character array 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, at-
tributes are intended for metadata (data about data).
In CDL, an attribute is designated by a variable and attribute name,
separated by `:'. It is possible to assign global attributes not asso-
ciated with any variable to the netCDF as a whole by using `:' before
the attribute name. The data type of an attribute in CDL is derived
from the type of the value assigned to it. The length of an attribute
is the number of data values assigned to it, or the number of charac-
ters in the character string assigned to it. Multiple values are as-
signed to non-character attributes by separating the values with com-
mas. All values assigned to an attribute must be of the same type.
The names for CDL dimensions, variables, and attributes must begin with
an alphabetic character or `_', and subsequent characters may be al-
phanumeric or `_' or `-'.
The optional data section of a CDL specification is where netCDF vari-
ables may be initialized. The syntax of an initialization is simple: a
variable name, an equals sign, and a comma-delimited list of constants
(possibly separated by spaces, tabs and newlines) terminated with a
semicolon. For multi-dimensional 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 a type-dependent `fill value', which can be overridden by
supplying a value for a distinguished variable attribute named `_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. The constant `_' can be used to designate the fill value for
a variable.
Primitive Data Types
char characters
byte 8-bit data
short 16-bit signed integers
long 32-bit signed integers
int (synonymous with long)
float IEEE single precision floating point (32 bits)
real (synonymous with float)
double IEEE double precision floating point (64 bits)
Except for the added data-type byte and the lack of unsigned, CDL sup-
ports the same primitive data types as C. The names for the primitive
data types are reserved words in CDL, so the names of variables, dimen-
sions, and attributes must not be type names. In declarations, type
names may be specified in either upper or lower case.
Bytes differ from characters in that they are intended to hold a full
eight bits of data, and the zero byte has no special significance, as
it does for character data. ncmpigen converts byte declarations to
char declarations in the output C code and to the nonstandard BYTE dec-
laration in output Fortran code.
Shorts can hold values between -32768 and 32767. ncmpigen converts
short declarations to short declarations in the output C code and to
the nonstandard INTEGER*2 declaration in output Fortran code.
Longs can hold values between -2147483648 and 2147483647. ncmpigen
converts long declarations to long declarations in the output C code
and to INTEGER declarations in output Fortran code. int and integer
are accepted as synonyms for long in CDL declarations. Now that there
are platforms with 64-bit representations for C longs, it may be better
to use the int synonym to avoid confusion.
Floats can hold values between about -3.4+38 and 3.4+38. Their exter-
nal representation is as 32-bit IEEE normalized single-precision float-
ing point numbers. ncmpigen converts float declarations to float dec-
larations in the output C code and to REAL declarations in output For-
tran code. real is accepted as a synonym for float in CDL declara-
tions.
Doubles can hold values between about -1.7+308 and 1.7+308. Their ex-
ternal representation is as 64-bit IEEE standard normalized double-pre-
cision floating point numbers. ncmpigen converts double declarations
to double declarations in the output C code and to DOUBLE PRECISION
declarations in output Fortran code.
CDL Constants
Constants assigned to attributes or variables may be of any of the ba-
sic netCDF types. The syntax for constants is similar to C syntax, ex-
cept that type suffixes must be appended to shorts and floats to dis-
tinguish them from longs and doubles.
A byte constant is represented by a single character or multiple char-
acter 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)
'\377' // 377 octal = 255 decimal, non-ASCII
Character constants are enclosed in double quotes. A character array
may be represented as a string enclosed in double quotes. The usual C
string escape conventions are honored. For example
"a" // ASCII `a'
"Two\nlines\n" // a 10-character string with two embedded newlin es
"a bell:\007" // a string containing an ASCII bell
Note that the netCDF character array "a" would fit in a one-element
variable, since no terminating NULL character is assumed. However, a
zero byte in a character array is interpreted as the end of the signif-
icant characters by the ncmpidump program, following the C convention.
Therefore, a NULL byte should not be embedded in a character string un-
less at the end: use the byte data type instead for byte arrays that
contain the zero byte. NetCDF and CDL have no string type, but only
fixed-length character arrays, which may be multi-dimensional.
short integer constants are intended for representing 16-bit signed
quantities. 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 in-
terpreted as octal, except that if it begins with `0x', it is inter-
preted as a hexadecimal constant. For example:
-2s // a short -2
0123s // octal
0x7ffs //hexadecimal
Long integer constants are intended for representing 32-bit signed
quantities. The form of a long constant is an ordinary integer con-
stant, although it is acceptable to append an optional `l' or `L'. If
a long constant begins with `0', it is interpreted as octal, except
that if it begins with `0x', it is interpreted as a hexadecimal con-
stant. Examples of valid long constants include:
-2
1234567890L
0123i // octal
0x7ff // hexadecimal
Floating point constants of type float are appropriate for representing
floating point 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. For example the following are all accept-
able float constants:
-2.0f
3.14159265358979f // will be truncated to less precision
1.f
.1f
Floating point constants of type double are appropriate for represent-
ing floating point data with about sixteen significant digits of preci-
sion. The form of a double constant is the same as a C floating point
constant. An optional `d' or `D' may be appended. For example the
following are all acceptable double constants:
-2.0
3.141592653589793
1.0e-20
1.d
DATE
February 21, 2022
BUGS
The programs generated by ncmpigen when using the -c or -f use initial-
ization statements to store data in variables, and will fail to produce
compilable programs if you try to use them for large datasets, since
the resulting statements may exceed the line length or number of con-
tinuation statements permitted by the compiler.
The CDL syntax makes it easy to assign what looks like an array of
variable-length strings to a netCDF variable, but the strings will sim-
ply be concatenated into a single array of characters, since netCDF
cannot represent an array of variable-length strings in one netCDF
variable.
NetCDF and CDL do not yet support a type corresponding to a 64-bit in-
teger.