netcdf - Unidata Network Common Data Form (netCDF) library, version 3 interface

include netcdf.inc

Most Systems:

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This document describes version 3 of Unidata netCDF data-access interface for the FORTRAN programming language. character*80 nf_inq_libvers(void) Returns a string identifying the version of the netCDF library, and when it was built, like: "3.1a of Aug 22 1996 12:57:47 $".

The RCS ident(1) command will find a string like "$Id: @(#) netcdf library version 3.1a of Sep 6 1996 15:56:26 $" in the library. The SCCS what(1) command will find a string like "netcdf library version 3.1a of Aug 23 1996 16:07:40 $".

All netCDF functions (except nf_inq_libvers() and nf_strerror()) return an integer status. This behavior replaces the rcode argument used in previous versions of the library. If this returned status value is not equal to NF_NOERR (zero), it indicates that an error occurred. The possible status values are defined in netcdf.inc. character*80 nf_strerror(integer status) Returns a string textual translation of the status value, like "Attribute or variable name contains illegal characters" or "No such file or directory". integer function nf_create(character*(*) path, integer cmode, integer ncid) (Corresponds to nccre() in version 2) Creates a new netCDF dataset at path, returning a netCDF ID in ncid. The argument cmode may include the bitwise-or of the following flags: NF_NOCLOBBER to protect existing datasets (default silently blows them away), NF_SHARE for synchronous dataset updates (default is to buffer accesses), and NF_LOCK (not yet implemented). When a netCDF dataset is created, is is opened NF_WRITE. The new netCDF dataset is in define mode. NF_64BIT_OFFSET. to create a file in the 64-bit offset (as opposed to classic , the default). 64-bit offset allows the creation of very large files with far fewer restrictions than netCDF classic , but can only be read by the netCDF library version 3.6 or greater. Users are cautioned that files that use the 64-bit offset will not be recognized by netCDF applications linked to an earlier version of the netCDF library than 3.6. Applications linked to version 3.6 or later will be able to transparently access either the classic or 64-bit offset . HP integer function nf__create(character*(*) path, integer cmode, integer initialsize, integer chunksize, integer ncid) Like nf_create() but has additional performance tuning parameters. The argument initialsize sets the initial size of the file at creation time. See nf__open() below for an explanation of the chunksize parameter. integer function nf_open(character*(*) path, integer mode, integer ncid) (Corresponds to ncopn() in version 2) Opens a existing netCDF dataset at path returning a netCDF ID in ncid. The type of access is described by the mode parameter, which may include the bitwise-or of the following flags: NF_WRITE for read-write access (default read-only), NF_SHARE for synchronous dataset updates (default is to buffer accesses), and NF_LOCK (not yet implemented). integer function nf__open(character*(*) path, integer mode, integer chunksize, integer ncid) Like nf_open() but has an additional performance tuning parameter. The argument referenced by chunksize controls a space versus time tradeoff, memory allocated in the netcdf library versus number of system calls. Because of internal requirements, the value may not be set to exactly the value requested. The actual value chosen is returned by reference. Using the value NF_SIZEHINT_DEFAULT causes the library to choose a default. How the system choses the default depends on the system. On many systems, the "preferred I/O block size" is available from the stat() system call, struct stat member st_blksize. If this is available it is used. Lacking that, twice the system pagesize is used. Lacking a call to discover the system pagesize, we just set default chunksize to 8192. The chunksize is a property of a given open netcdf descriptor ncid, it is not a persistent property of the netcdf dataset. integer function nf_redef(integer ncid) (Corresponds to ncredf() in version 2) Puts an open netCDF dataset into define mode, so dimensions, variables, and attributes can be added or renamed and attributes can be deleted. integer function nf_enddef(integer ncid) (Corresponds to ncendf() in version 2) Takes an open netCDF dataset out of define mode. The changes made to the netCDF dataset while it was in define mode are checked and committed to disk if no problems occurred. Some data values may be written as well, see "VARIABLE PREFILLING" below. After a successful call, variable data can be read or written to the dataset. integer function nf__enddef(integer ncid, integer h_minfree, integer v_align, integer v_minfree, integer r_align) Like nf_enddef() but has additional performance tuning parameters. Caution: this function exposes internals of the netcdf version 1 file format. It may not be available on future netcdf implementations. The current netcdf file format has three sections, the "header" section, the data section for fixed size variables, and the data section for variables which have an unlimited dimension (record variables). The header begins at the beginning of the file. The index (offset) of the beginning of the other two sections is contained in the header. Typically, there is no space between the sections. This causes copying overhead to accrue if one wishes to change the size of the sections, as may happen when changing names of things, text attribute values, adding attributes or adding variables. Also, for buffered i/o, there may be advantages to aligning sections in certain ways. The minfree parameters allow one to control costs of future calls to nf_redef(), nf_enddef() by requesting that minfree bytes be available at the end of the section. The h_minfree parameter sets the pad at the end of the "header" section. The v_minfree parameter sets the pad at the end of the data section for fixed size variables. The align parameters allow one to set the alignment of the beginning of the corresponding sections. The beginning of the section is rounded up to an index which is a multiple of the align parameter. The flag value NF_ALIGN_CHUNK tells the library to use the chunksize (see above) as the align parameter. The v_align parameter controls the alignment of the beginning of the data section for fixed size variables. The r_align parameter controls the alignment of the beginning of the data section for variables which have an unlimited dimension (record variables). The file format requires mod 4 alignment, so the align parameters are silently rounded up to multiples of 4. The usual call, nf_enddef(ncid) is equivalent to nf__enddef(ncid, 0, 4, 0, 4). The file format does not contain a "record size" value, this is calculated from the sizes of the record variables. This unfortunate fact prevents us from providing minfree and alignment control of the "records" in a netcdf file. If you add a variable which has an unlimited dimension, the third section will always be copied with the new variable added. integer function nf_sync(integer ncid) (Corresponds to ncsnc() in version 2) Unless the NF_SHARE bit is set in nf_open() or nf_create(), accesses to the underlying netCDF dataset are buffered by the library. This function synchronizes the state of the underlying dataset and the library. This is done automatically by nf_close() and nf_enddef(). integer function nf_abort(integer ncid) (Corresponds to ncabor() in version 2) You don't need to call this function. This function is called automatically by nf_close() if the netCDF was in define mode and something goes wrong with the commit. If the netCDF dataset isn't in define mode, then this function is equivalent to nf_close(). If it is called after nf_redef(), but before nf_enddef(), the new definitions are not committed and the dataset is closed. If it is called after nf_create() but before nf_enddef(), the dataset disappears. integer function nf_close(integer ncid) (Corresponds to ncclos() in version 2) Closes an open netCDF dataset. If the dataset is in define mode, nf_enddef() will be called before closing. After a dataset is closed, its ID may be reassigned to another dataset. integer function nf_inq(integer ncid, integer ndims, integer nvars, integer natts, integer unlimdimid) integer function nf_inq_ndims(integer ncid, integer ndims) integer function nf_inq_nvars(integer ncid, integer nvars) integer function nf_inq_natts(integer ncid, integer natts) integer function nf_inq_unlimdim(integer ncid, integer unlimdimid) (Replace ncinq() in version 2) Use these functions to find out what is in a netCDF dataset. Upon successful return, ndims will contain the number of dimensions defined for this netCDF dataset, nvars will contain the number of variables, natts will contain the number of attributes, and unlimdimid will contain the dimension ID of the unlimited dimension if one exists, or 0 otherwise.

name should be big enough (NF_MAX_NAME) to hold the dimension name as the name will be copied into your storage. The length return parameter, len will contain the size of the dimension. For the unlimited dimension, the returned length is the current maximum value used for writing into any of the variables which use the dimension. integer function nf_rename_dim(integer ncid, integer dimid, character*(*) name) (Corresponds to ncdren() in version 2) Renames an existing dimension in an open netCDF dataset. If the new name is longer than the old name, the netCDF dataset must be in define mode. You cannot rename a dimension to have the same name as another dimension. integer function nf_def_var(integer ncid, character*(*) name, integer xtype, integer ndims, integer dimids(1), integer varid) (Corresponds to ncvdef() in version 2) Adds a new variable to a netCDF dataset. The netCDF must be in define mode. varid will be set to the netCDF variable ID. integer function nf_inq_varid(integer ncid, character*(*) name, integer varid) (Corresponds to ncvid() in version 2) Returns the ID of a netCDF variable in varid given its name. integer function nf_inq_var(integer ncid, integer varid, character*(*) name, integer xtype, integer ndims, integer dimids(1), integer natts) integer function nf_inq_varname(integer ncid, integer varid, character*(*) name) integer function nf_inq_vartype(integer ncid, integer varid, integer xtype) integer function nf_inq_varndims(integer ncid, integer varid, integer ndims) integer function nf_inq_vardimid(integer ncid, integer varid, integer dimids(1)) integer function nf_inq_varnatts(integer ncid, integer varid, integer natts) (Replace ncvinq() in version 2) Returns information about a netCDF variable, given its ID.

In this section we define some common arguments which are used in the "FUNCTION DESCRIPTIONS" section.

integer ncid

is the netCDF ID returned from a previous, successful call to nf_open() or nf_create()

character*(*) name

is the name of a dimension, variable, or attribute. The names of dimensions, variables and attributes consist of arbitrary sequences of alphanumeric characters (as well as underscore '_', period '.' and hyphen '-'), 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.

The maximum allowable number of characters is NF_MAX_NAME.

integer xtype

specifies the external data type of a netCDF variable or attribute and is one of the following: NF_BYTE, NF_CHAR, NF_SHORT, NF_INT, NF_FLOAT, or NF_DOUBLE. These are used to specify 8-bit integers, characters, 16-bit integers, 32-bit integers, 32-bit IEEE floating point numbers, and 64-bit IEEE floating-point numbers, respectively.

integer dimids(1)

is a vector of dimension ID's and defines the shape of a netCDF variable. The size of the vector shall be greater than or equal to the rank (i.e. the number of dimensions) of the variable (ndims). The vector shall be ordered by the speed with which a dimension varies: dimids(1) shall be the dimension ID of the most rapidly varying dimension and dimids(ndims) shall be the dimension ID of the most slowly varying dimension. The maximum possible number of dimensions for a variable is given by the symbolic constant NF_MAX_VAR_DIMS.

integer dimid

is the ID of a netCDF dimension. netCDF dimension ID's are allocated sequentially from the positive integers beginning with 1.

integer ndims

is either the total number of dimensions in a netCDF dataset or the rank (i.e. the number of dimensions) of a netCDF variable. The value shall not be negative or greater than the symbolic constant NF_MAX_VAR_DIMS.

integer varid

is the ID of a netCDF variable or (for the attribute-access functions) the symbolic constant NF_GLOBAL, which is used to reference global attributes. netCDF variable ID's are allocated sequentially from the positive integers beginning with 1.

integer natts

is the number of global attributes in a netCDF dataset for the nf_inquire() function or the number of attributes associated with a netCDF variable for the nf_varinq() function.

integer index(1)

specifies the indicial coordinates of the netCDF data value to be accessed. The indices start at 1; thus, for example, the first data value of a two-dimensional variable is (1,1). The size of the vector shall be at least the rank of the associated netCDF variable and its elements shall correspond, in order, to the variable's dimensions.

integer start(1)

specifies the starting point for accessing a netCDF variable's data values in terms of the indicial coordinates of the corner of the array section. The indices start at 1; thus, the first data value of a variable is (1, 1, ..., 1). The size of the vector shall be at least the rank of the associated netCDF variable and its elements shall correspond, in order, to the variable's dimensions.

integer count(1)

specifies the number of indices selected along each dimension of the array section. Thus, to access a single value, for example, specify count as (1, 1, ..., 1). Note that, for strided I/O, this argument must be adjusted to be compatible with the stride and start arguments so that the interaction of the three does not attempt to access an invalid data co-ordinate. The elements of the count vector correspond, in order, to the variable's dimensions.

integer stride(1)

specifies the sampling interval along each dimension of the netCDF variable. The elements of the stride vector correspond, in order, to the netCDF variable's dimensions (stride(1)) gives the sampling interval along the most rapidly varying dimension of the netCDF variable). Sampling intervals are specified in type-independent units of elements (a value of 1 selects consecutive elements of the netCDF variable along the corresponding dimension, a value of 2 selects every other element, etc.).

imap

specifies the mapping between the dimensions of a netCDF variable and the in-memory structure of the internal data array. The elements of the index mapping vector correspond, in order, to the netCDF variable's dimensions (imap(1) gives the distance between elements of the internal array corresponding to the most rapidly varying dimension of the netCDF variable). Distances between elements are specified in type-independent units of elements (the distance between internal elements that occupy adjacent memory locations is 1 and not the element's byte-length as in netCDF 2).

By default, the netCDF interface sets the values of all newly-defined variables of finite length (i.e. those that do not have an unlimited, dimension) to the type-dependent fill-value associated with each variable. This is done when nf_enddef() is called. The fill-value for a variable may be changed from the default value by defining the attribute `_FillValue' for the variable. This attribute must have the same type as the variable and be of length one.

Variables with an unlimited dimension are also prefilled, but on an `as needed' basis. For example, if the first write of such a variable is to position 5, then positions 1 through 4 (and no others) would be set to the fill-value at the same time.

This default prefilling of data values may be disabled by or'ing the NF_NOFILL flag into the mode parameter of nf_open() or nf_create(), or, by calling the function nf_set_fill() with the argument NF_NOFILL. For variables that do not use the unlimited dimension, this call must be made before nf_enddef(). For variables that use the unlimited dimension, this call may be made at any time.

One can obtain increased performance of the netCDF interface by using this feature, but only at the expense of requiring the application to set every single data value. The performance enhancing behavior of this function is dependent on the particulars of the implementation and dataset format. The flag value controlled by nf_set_fill() is per netCDF ID, not per variable or per write. Allowing this to change affects the degree to which a program can be effectively parallelized. Given all of this, we state that the use of this feature may not be available (or even needed) in future releases. Programmers are cautioned against heavy reliance upon this feature. integer function nf_setfill(integer ncid, integer fillmode, integer old_fillemode)

Determines whether or not variable prefilling will be done (see above). The netCDF dataset shall be writable. fillmode is either NF_FILL to enable prefilling (the default) or NF_NOFILL to disable prefilling. This function returns the previous setting in old_fillmode.

Additional functions for use on SGI/Cray MPP machines (_CRAYMPP). These are used to set and inquire which PE is the base for MPP for a particular netCDF. These are only relevant when using the SGI/Cray ``global'' Flexible File I/O layer and desire to have only a subset of PEs to open the specific netCDF file. For technical reasons, these functions are available on all platforms. On a platform other than SGI/Cray MPP, it is as if only processor available were processor 0.

To use this feature, you need to specify a communicator group and call glio_group_mpi() or glio_group_shmem() prior to the netCDF nf_open() and nf_create() calls. integer function nf__create_mp(character*(*) path, integer cmode, integer initialsize, integer pe, integer chunksize, integer ncid) Like nf__create() but allows the base PE to be set. The argument pe sets the base PE at creation time. In the MPP environment, nf__create() and nf_create() set the base PE to processor zero by default. integer function nf__open_mp(character*(*) path, integer mode, integer pe, integer chunksize, integer ncid) Like nf__open() but allows the base PE to be set. The argument pe sets the base PE at creation time. In the MPP environment, nf__open() and nf_open() set the base PE to processor zero by default. integer function nf_inq_base_pe(integer ncid, integer pe) Inquires of the netCDF dataset which PE is being used as the base for MPP use. This is safe to use at any time. integer function nf_set_base_pe(integer ncid, integer pe) Resets the base PE for the netCDF dataset. Only perform this operation when the affected communicator group synchronizes before and after the call. This operation is very risky and should only be contemplated under only the most extreme cases.

NETCDF_FFIOSPEC

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 actually surpass FORTRAN binary I/O. This environment variable has been made a little more generalized, such that other FFIO option specifications can now be added. The default specification is bufa:336:2, unless a current FFIO specification is in operation, which will be honored. See UNICOS Flexible File I/O for more information.

Both a mailing list and a digest are available for discussion of the netCDF interface and announcements about netCDF bugs, fixes, and enhancements. To begin or change your subscription to either the mailing-list or the digest, send one of the following in the body (not the subject line) of an email message to "majordomo@unidata.ucar.edu". Use your email address in place of jdoe@host.inst.domain. To subscribe to the netCDF mailing list: subscribe netcdfgroup jdoe@host.inst.domain To unsubscribe from the netCDF mailing list: unsubscribe netcdfgroup jdoe@host.inst.domain To subscribe to the netCDF digest: subscribe netcdfdigest jdoe@host.inst.domain To unsubscribe from the netCDF digest: unsubscribe netcdfdigest jdoe@host.inst.domain To retrieve the general introductory information for the mailing list: info netcdfgroup To get a synopsis of other majordomo commands: help

ncdump(1), ncgen(1), netcdf(3f).

netCDF User's Guide, published by the Unidata Program Center, University Corporation for Atmospheric Research, located in Boulder, Colorado.