PnetCDF(3f)

NAME
PnetCDF - Parallel library for accessing files in Network Common Data Form (CDF, CDF-2 and CDF-5 formats)

SYNOPSIS
use pnetcdf

  Most Systems:
mpif90 ... -lpnetcdf

  CRAY PVP Systems:
f90 -dp -i64 ... -lpnetcdf

LIBRARY VERSION

This document describes PnetCDF APIs for the Fortran-90 programming language.

character*80 nf90mpi_inq_libvers()
    character(len=80) :: nf90mpi_inq_libvers

Returns a string identifying the version of the PnetCDF library, and when it was built, like: "1.12.2 of 2021-01-15".

The RCS ident(1) command will find a string like "$Id: @(#) PnetCDF library version 1.12.2 of 2021-01-15 $" in the library. The SCCS what(1) command will find a string like "PnetCDF library version 1.12.2 of 2021-01-15".

ROUTINE DESCRIPTIONS

All PnetCDF functions (except nf90mpi_inq_libvers() and nf90mpi_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 nf90_noerr (zero), it indicates that an error occurred. The possible status values are defined in the module pnetcdf.

function nf90mpi_strerror(ncerr)
    integer, intent(in) :: ncerr
    character(len=80) :: nf90mpi_strerror

    Returns a string textual translation of the ncerr value, like "Attribute or variable name contains illegal characters" or "No such file or directory".

function nf90mpi_create(comm, path, cmode, info, ncid)
    integer, intent(in) :: comm
    character(len=*), intent(in) :: path
    integer, intent(in) :: cmode
    integer, intent(in) :: info
    integer, intent(out) :: ncid
    integer :: nf90mpi_create

    Creates a new netCDF dataset at path collectively by a group of MPI processes specified by comm, returning a netCDF ID in ncid. The argument cmode may include the bitwise-or of the following flags: nf90_noclobber to protect existing datasets (default is nf90_clobber, silently blows them away), nf90_share for stronger metadata data consistency control, nf90_64bit_offset to create a file in the 64-bit offset format (CDF-2), as opposed to classic format, the default, or nf90_64bit_data to create a file in the 64-bit data format (CDF-5). Use either nf90_64bit_offset or nf90_64bit_data. The 64-bit offset format allows the creation of very large files with far fewer restrictions than netCDF classic format, 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 format 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 format or 64-bit offset format. The 64-bit data format allows the creation of very large array variables. CDF-5 files currently will not be recognized by netCDF 3 or 4 library. The argument cmode must be consistent among all MPI processes that collectively create the file. The argument info is an MPI info object. Users can use it to supply the file access hints further performance improvement. The hints include existing MPI-IO hints as well as hints defined and used in PnetCDF.

    When a netCDF dataset is created, it is opened in nf90_write mode. When this function returns, the new netCDF dataset is in define mode.

function nf90mpi_open(comm, path, mode, info, ncid)
    integer, intent(in) :: comm
    character(len=*), intent(in) :: path
    integer, intent(in) :: mode
    integer, intent(in) :: info
    integer, intent(out) :: ncid
    integer :: nf90mpi_open

    Opens an existing netCDF dataset at path collectively by a group of MPI processes specified by comm, 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: nf90_write for read-write access (default read-only), nf90_share for stronger metadata data consistency control.

    The argument mode must be consistent among all MPI processes that collectively open the file. The argument info is an MPI info object. Users can use it to supply the file access hints further performance improvement. The hints include existing MPI-IO hints as well as hints defined and used in PnetCDF.

function nf90mpi_redef(ncid)
    integer, intent(in) :: ncid
    integer :: nf90mpi_redef

    Puts an open netCDF dataset into define mode, so dimensions, variables, and attributes can be added or renamed and attributes can be deleted.

function nf90mpi_enddef(ncid)
    integer, intent(in) :: ncid
    integer :: nf90mpi_enddef

    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. After a successful call, variable data can be read or written to the dataset.

function nf90mpi_sync(ncid)
    integer, intent(in) :: ncid
    integer :: nf90mpi_sync

    Unless the nf90_share bit is set in nf90mpi_open() or nf90mpi_create(), data written by PnetCDF APIs may be cached by local file system on each compute node. This API flushes cached data by calling MPI_File_sync.

function nf90mpi_flush(ncid)
    integer, intent(in) :: ncid
    integer :: nf90mpi_flush

    Flush the data in the buffer.

function nf90mpi_abort(ncid)
    integer, intent(in) :: ncid
    integer :: nf90mpi_abort

    You don't need to call this function. This function is called automatically by nf90mpi_close() if the netCDF dataset 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 nf90mpi_close(). If it is called after nf90mpi_redef(), but before nf90mpi_enddef(), the new definitions are not committed and the dataset is closed. If it is called after nf90mpi_create() but before nf90mpi_enddef(), the dataset disappears.

function nf90mpi_close(ncid)
    integer, intent(in) :: ncid
    integer :: nf90mpi_close

    Closes an open netCDF dataset. If the dataset is in define mode, nf90mpi_enddef() will be called before closing. After a dataset is closed, its ID may be reassigned to another dataset.

function nf90mpi_inquire(ncid, ndims, nvars, natts, unlimdimid, nformat)
    integer, intent(in) :: ncid
    integer, optional, intent(out) :: ndims, nvars
    integer, optional, intent(out) :: natts, unlimdimid
    integer, optional, intent(out) :: nformat
    integer :: nf90mpi_inquire

    Inquire about an open netCDF dataset. ncid is the netCDF ID of the open 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. nformat will contain the format version number, rarely needed because the library detects the format version and behaves appropriately.

function nf90mpi_def_dim(ncid, name, len, dimid)
    integer, intent(in) :: ncid
    character(len=*), intent(in) :: name
    integer, intent(in) :: len
    integer, intent(out) :: dimid
    integer :: nf90mpi_def_dim

    Adds a new dimension to an open netCDF dataset, which must be in define mode. name is the dimension name. len is the size of the new dimension or nf90mpi_unlimited to define the unlimited dimension. On return, dimid will contain the dimension ID of the newly created dimension.

function nf90mpi_inq_dimid(ncid, name, dimid)
    integer, intent(in) :: ncid
    character(len=*), intent(in) :: name
    integer, intent(out) :: dimid
    integer :: nf90mpi_inq_dimid

    Given an open netCDF dataset and dimension name, returns the dimension ID of the netCDF dimension in dimid.

function nf90mpi_inquire_dimension(ncid, dimid, name, len)
    integer, intent(in) :: ncid, dimid
    character(len=*), optional, intent(out) :: name
    integer, optional, intent(out) :: len
    integer :: nf90mpi_inquire_dimension

    Inquire about a dimension. name should be big enough (nf90_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.

function nf90mpi_rename_dim(ncid, dimid, name)
    integer, intent(in) :: ncid
    character(len=*), intent(in) :: name
    integer, intent(in) :: dimid
    integer :: nf90mpi_rename_dim

    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.

function nf90mpi_def_var(ncid, name, xtype, dimids, varid)
    integer, intent(in) :: ncid
    character(len=*), intent(in) :: name
    integer, intent(in) :: xtype
    integer, optional, dimension(:), intent(in) :: dimids
    integer :: nf90mpi_def_var

    Adds a new variable to a netCDF dataset. The netCDF must be in define mode. name will be the name of the netCDF variable. xtype is the external, netCDF type of the variable and should be one of nf90_byte, nf90_char, nf90_short, nf90_int, nf90_float, or nf90_double for CDF-1 and CDF-2 file formats. CDF-5 defines additional external types: nf90_ubyte, nf90_ushort, nf90_uint, nf90_int64, and nf90_uint64. The optional dimids argument contains the dimension ID-s of the domain of the netCDF variable and, consequently, determines the rank of the created variable: if dimids is omitted, then the netCDF variable will be a scalar; if dimids is a scalar, then the netCDF variable will be 1 dimensional; and if dimids is a vector, then the netCDF variable will have rank equal to the number of elements in dimids. varid will be set to the netCDF variable ID.

function nf90mpi_inq_varid(ncid, name, varid)
    integer, intent(in) :: ncid
    character(len=*), intent(in) :: name
    integer, intent(out) :: varid
    integer :: nf90mpi_inq_varid

    Returns the ID of a netCDF variable in varid given an open netCDF dataset and the name of the variable.

function nf90mpi_inquire_variable(ncid, varid, name, xtype, ndims, dimids, natts)
    integer, intent(in) :: ncid, varid
    character(len=*), optional, intent(out) :: name
    integer, optional, intent(out) :: xtype, ndims
    integer, dimension(*), optional, intent(out) :: dimids
    integer, optional, intent(out) :: natts
    integer :: nf90mpi_inquire_variable

    Inquire about a netCDF variable in an open netCDF dataset, given its variable ID. On return, name will contain the name of the variable and should be capacious enough (nf90_max_name). xtype will contain the external, netCDF type of the variable. ndims will contain the dimensionality of the netCDF variable: if the variable is a scalar, then size(ndims) will be zero; otherwise, size(ndims) will be the rank of the variable and ndims will contain the dimension ID-s of the netCDF dimensions that constitute the domain of the variable. natts will contain the number of attributes associated with the netCDF variable.

function nf90mpi_rename_var(ncid, varid, name)
    integer, intent9in) :: ncid, varid
    character(len=*), intent(in) :: newname
    integer :: nf90mpi_rename_var

    Changes the name of a netCDF variable. If the new name is longer than the old name, the netCDF must be in define mode. You cannot rename a variable to have the name of any existing variable.

function nf90mpi_put_var(ncid, varid, values, start, stride, imap)
    integer, intent(in) :: ncid, varid
    <<whatever>>, intent(in) :: values
    integer, dimension(:), optional, intent(in) :: start
    integer, dimension(:), optional, intent(in) ::  stride
    integer, dimension(:), optional, intent(in) ::  imap
    integer :: nf90mpi_put_var

    Writes a value or values to a netCDF variable. The netCDF dataset must be open and in data mode. values contains the value(s) what will be written to the netCDF variable identified by ncid and varid; it may be a scalar or an array and must be of type character, integer(kind=OneByteInt), integer(kind=TwoByteInt), integer(kind=FourByteInt), integer(kind=EightByteInt), real(kind=FourByteReal), or real(kind=EightByteReal). All values are converted to the external type of the netCDF variable, if possible; otherwise, an nf90_erange error is returned. The optional argument start specifies the starting index in the netCDF variable for writing for each dimension of the netCDF variable. The optional argument stride specifies the sampling stride (the interval between accessed values in the netCDF variable) for each dimension of the netCDF variable (see COMMON ARGUMENT DESCRIPTIONS below). The optional argument imap specifies the in-memory arrangement of the data values (see COMMON ARGUMENT DESCRIPTIONS below).

function nf90mpi_get_var(ncid, varid, values, start, stride, imap)
    integer, intent(in) :: ncid, varid
    <<whatever>>, intent(out) :: values
    integer, dimension(:), optional, intent(in) :: start
    integer, dimension(:), optional, intent(in) ::  stride
    integer, dimension(:), optional, intent(in) ::  imap
    integer :: nf90mpi_get_var

    Reads a value or values from a netCDF variable. The netCDF dataset must be open and in data mode. values will receive the value(s) what will be read from the netCDF
     variable identified by ncid and varid; it may be a scalar or an array and must be of type character, integer(kind=OneByteInt), integer(kind=TwoByteInt), integer(kind=FourByteInt), integer(kind=EightByteInt), real(kind=FourByteReal), or real(kind=EightByteReal). All values are converted from the external type of the netCDF variable, if possible; otherwise, an nf90_erange error is returned. The optional argument start specifies the starting index in the netCDF variable for reading for each dimension of the netCDF variable. The optional argument stride specifies the sampling stride (the interval between accessed values in the netCDF variable) for each dimension of the netCDF variable (see COMMON ARGUMENT DESCRIPTIONS below). The optional argument imap specifies the in-memory arrangement of the data values (see COMMON ARGUMENT DESCRIPTIONS below).

function nf90mpi_inquire_attribute(ncid, varid, name, xtype, len, attnum)
    integer, intent(in) :: ncid, varid
    character(len=*), intent(in) :: name
    integer, optional, intent(out) :: xtype, len, attnum
    integer :: nf90mpi_inquire_attribute

    Inquires about the netCDF attribute named name, of variable varid, in the open netCDF dataset ncid. xtype will contain the external, netCDF type of the variable. len will contain the number of elements in the attribute. attnum will contain the attribute number.

function nf90mpi_inq_attname(ncid, varid, attnum, name)
    integer, intent(in) :: ncid, varid, attnum
    character(len=*), intent(out) :: name
    integer :: nf90mpi_inq_attname

    Gets the name of an attribute, given its variable ID and attribute number. This function is useful in generic applications that need to get the names of all the attributes associated with a variable because attributes are accessed by name rather than number in all other attribute functions (the number of an attribute is more volatile than the name because it can change when other attributes of the same variable are deleted). The attributes for each variable are numbered from 1 (the first attribute) to natts, where natts is the number of attributes for the variable, as returned from a call to nf90mpi_inquire_variable().

function nf90mpi_put_att(ncid, varid, name, values)
    integer, intent(in) :: ncid, varid
    character(len=*), intent(in) :: name
    <<whatever>>, intent(in) :: values
    integer :: nf90mpi_put_att

    Unlike variables, attributes do not have separate functions for defining and writing values. This function defines a new attribute with a value or changes the value of an existing attribute. If the attribute is new, or if the space required to store the attribute value is greater than before, the netCDF dataset must be in define mode. values contains the attribute values to be written; it may be a scalar or a vector and must be of type character, integer(kind=OneByteInt), integer(kind=TwoByteInt), integer(kind=FourByteInt), integer(kind=EightByteInt), real(kind=FourByteReal), or real(kind=EightByteReal).

function nf90mpi_get_att(ncid, varid, name, fIvalues)
    integer, intent(in) :: ncid, varid
    character(len=*), intent(in) :: name
    <<whatever>>, intent(out) :: values
    integer :: nf90mpi_get_att

    Gets the value(s) of a netCDF attribute, given its variable ID and name. The values are returned in values, which must be of type character, integer(kind=OneByteInt), integer(kind=TwoByteInt), integer(kind=FourByteInt), integer(kind=EightByteInt), real(kind=FourByteReal), or real(kind=EightByteReal). Converts from the external type to the type of the receiving variable, if possible; otherwise returns an nf90_erange error. All values of the attribute are returned, so you must allocate enough space to hold them. If you don't know how much space to reserve, call nf90mpi_inquire_attribute() first to find out the length of the attribute.

function nf90mpi_copy_att(ncid_in, varid_in, name, ncid_out, varid_out)
    integer, intent(in) :: ncid_in, varid_in
    character(len=*), intent(in) :: name
    integer, intent(in) :: ncid_out, varid_out
    integer :: nf90mpi_copy_att

    Copies an attribute from one netCDF dataset to another. It can also be used to copy an attribute from one variable to another within the same netCDF dataset. ncid_in is the netCDF ID of an input netCDF dataset from which the attribute will be copied. varid_in is the ID of the variable in the input netCDF dataset from which the attribute will be copied, or nf90_global for a global attribute. name is the name of the attribute in the input netCDF dataset to be copied. ncid_out is the netCDF ID of the output netCDF dataset to which the attribute will be copied. It is permissible for the input and output netCDF ID's to be the same. The output netCDF dataset should be in define mode if the attribute to be copied does not already exist for the target variable, or if it would cause an existing target attribute to grow. varid_out is the ID of the variable in the output netCDF dataset to which the attribute will be copied, or nf90_global to copy to a global attribute.

function nf90mpi_rename_att(ncid, varid, name, newname)
    integer, intent(in) :: ncid, varid
    character(len=*), intent(in) :: name, newname
    integer :: nf90mpi_rename_att

    Changes the name of an attribute. If the new name is longer than the original name, the netCDF must be in define mode. You cannot rename an attribute to have the same name as another attribute of the same variable. name is the original attribute name. newname is the new name to be assigned to the specified attribute. If the new name is longer than the old name, the netCDF dataset must be in define mode.

function nf90mpi_del_att(ncid, varid, name)
    integer, intent(in) :: ncid, varid
    character(len=*), intent(in) :: name
    integer :: nf90mpi_del_att

    Deletes an attribute from a netCDF dataset. The dataset must be in define mode.

COMMON ARGUMENT DESCRIPTIONS

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 nf90mpi_open() or nf90mpi_create()

character(len=*) name
    is the name of a dimension, variable, or attribute. It shall begin with an alphabetic character, followed by zero or more alphanumeric characters including the underscore (_) or hyphen (-). Case is significant. The maximum allowable number of characters is nf90_max_name. Names that begin with an underscore (_) are reserved for use by the netCDF and PnetCDF interfaces.

integer xtype
    specifies the external data type of a netCDF variable or attribute and is one of the following: nf90_byte, nf90_char, nf90_short, nf90_int, nf90_float, or nf90_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
    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 nf90_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 nf90_max_var_dims.

integer varid
    is the ID of a netCDF variable or (for the attribute-access functions) the symbolic constant nf90_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 nf90mpi_inquire() function or the number of attributes associated with a netCDF variable for the nf90mpi_varinq() function.

integer(kind=MPI_OFFSET) start
    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(kind=MPI_OFFSET) stride
    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.).

integer(kind=MPI_OFFSET) 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 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).

VARIABLE PREFILLING

Prior to version 1.6.1, PnetCDF does not support data filling. The default fill mode in PnetCDF is NF90_NOFILL. This contrary to netCDF library whose default is NF90_FILL. When fill mode is enabled, PnetCDF 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 nf90mpi_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 not prefilled in PnetCDF. This is also contrary to netCDF, which does prefill record variables. In PnetCDF, filling a record variable must be done by calling nf90mpi_fill_var_rec(). Note this fills only one record of a variable.

The fill mode for the entire file can be set by nf90mpi_set_fill(). Per-variable fill mode setting is also available through nf90mpi_def_var_fill(). In PnetCDF, changing fill mode must be done in define mode. In netCDF, it is true only for fixed-size variables. For record variables, changing fill mode can be made at any time in netCDF.

ENVIRONMENT VARIABLES

PNETCDF_SAFE_MODE
    Set to 1 to enable metadata consistency check. Warning messages will be printed to stdout if any inconsistency is detected.

MAILING-LISTS

A mailing list is available for discussion of the PnetCDF interface and announcements about PnetCDF bugs, fixes, and enhancements. To subscribe or unsubscribe to the PnetCDF mailing list, visit https://lists.mcs.anl.gov/mailman/listinfo/parallel-netcdf

SEE ALSO

ncmpidump(1), ncmpigen(1), ncmpidiff(1), ncvalidator(1), pnetcdf(3).

DATE
January 15, 2021

PnetCDF User's Guide, published by Northwestern University and Argonne National Laboratory. This document is adopted from the netCDF User's Guide, developed at the Unidata Program Center, University Corporation for Atmospheric Research, located in Boulder, Colorado. PnetCDF home page at https://parallel-netcdf.github.io