Provided by: libpnetcdf-dev_1.9.0-2_amd64 
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 Parallel netCDF 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: "1.9.0 of 19 Dec 2017".
The RCS ident(1) command will find a string like "$Id: @(#) PnetCDF library version 1.9.0
of 19 Dec 2017 $" in the library. The SCCS what(1) command will find a string like
"PnetCDF library version 1.9.0 of 19 Dec 2017".
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_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 fix-sized 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(3f90).
DATE
2017-12-19
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 http://cucis.ece.northwestern.edu/projects/PnetCDF/.