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
include "pnetcdf.inc"
Most Systems:
mpif77 ... -lpnetcdf
CRAY PVP Systems:
f90 -dp -i64 ... -lnetcdf
Complete documentation for the PnetCDF libraries can be found at the PnetCDF website:
http://cucis.ece.northwestern.edu/projects/PnetCDF/.
LIBRARY VERSION
This document describes Parallel netCDF APIs for the FORTRAN programming language.
character*80 nfmpi_inq_libvers(void)
(Corresponds to nf_inq_libvers() in netCDF)
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".
RETURN VALUES
All PnetCDF functions (except nfmpi_inq_libvers() and nfmpi_strerror()) return an integer
status.
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 pnetcdf.inc.
character*80 nfmpi_strerror(integer status)
(Corresponds to nf_strerror() in netCDF)
Returns a string textual translation of the status value, like "Attribute or
variable name contains illegal characters" or "No such file or directory".
FILE OPERATIONS
integer function nfmpi_create(integer comm, character*(*) path, integer cmode, integer
info, integer ncid)
(Corresponds to nf_create() in netCDF)
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: NF_NOCLOBBER to protect existing datasets
(default is NF_CLOBBER, silently blows them away), NF_SHARE for stronger metadata
data consistency control, NF_64BIT_OFFSET to create a file in the 64-bit offset
format (CDF-2), as opposed to classic format, the default, or NF_64BIT_DATA to
create a file in the 64-bit data format (CDF-5). Use either NF_64BIT_OFFSET or
NF_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 NF_WRITE mode. When this
function returns, the new netCDF dataset is in define mode.
integer function nfmpi_open(integer comm, character*(*) path, integer mode, integer info,
integer ncid)
(Corresponds to nf_open() in netCDF)
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:
NF_WRITE for read-write access (default read-only), NF_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.
integer function nfmpi_redef(integer ncid)
(Corresponds to nf_redef() in netCDF)
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 nfmpi_enddef(integer ncid)
(Corresponds to nf_enddef() in netCDF)
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.
integer function nfmpi_sync(integer ncid)
(Corresponds to nf_sync() in netCDF)
Unless the NF_SHARE bit is set in nfmpi_open() or nfmpi_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.
integer function nfmpi_abort(integer ncid)
(Corresponds to nf_abort() in netCDF)
You don't need to call this function. This function is called automatically by
nfmpi_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 nfmpi_close(). If it is called after nfmpi_redef(), but before
nfmpi_enddef(), the new definitions are not committed and the dataset is closed.
If it is called after nfmpi_create() but before nfmpi_enddef(), the dataset
disappears.
integer function nfmpi_close(integer ncid)
(Corresponds to nf_close() in netCDF)
Closes an open netCDF dataset. If the dataset is in define mode, nfmpi_enddef()
will be called before closing. After a dataset is closed, its ID may be reassigned
to another dataset.
integer function nfmpi_inq(integer ncid, integer ndims, integer nvars, integer natts,
integer unlimdimid)
(Corresponds to nf_inq() in netCDF)
integer function nfmpi_inq_ndims(integer ncid, integer ndims)
(Corresponds to nf_inq_ndims() in netCDF)
integer function nfmpi_inq_nvars(integer ncid, integer nvars)
(Corresponds to nf_inq_nvars() in netCDF)
integer function nfmpi_inq_natts(integer ncid, integer natts)
(Corresponds to nf_inq_natts() in netCDF)
integer function nfmpi_inq_unlimdim(integer ncid, integer unlimdimid)
(Corresponds to nf_inq_unlimdim() in netCDF)
integer function nfmpi_inq_format(integer ncid, integer formatn)
(Corresponds to nf_inq_format() in netCDF)
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. formatn will contain the version number
of the dataset <format>, one of NF_FORMAT_CLASSIC, NF_FORMAT_64BIT, or
NF_FORMAT_64BIT_DATA.
integer function nfmpi_def_dim(integer ncid, character*(*) name, integer(kind=MPI_OFFSET)
len, integer dimid)
(Corresponds to nf_def_dim() in netCDF)
Adds a new dimension to an open netCDF dataset, which must be in define mode. name
is the dimension name. dimid will contain the dimension ID of the newly created
dimension.
DIMENSIONS
integer function nfmpi_inq_dimid(integer ncid, character*(*) name, integer dimid)
(Corresponds to nf_inq_dimid() in netCDF)
Given a dimension name, returns the ID of a netCDF dimension in dimid.
integer function nfmpi_inq_dim(integer ncid, integer dimid, character*(*) name,
integer(kind=MPI_OFFSET) len)
(Corresponds to nf_inq_dim() in netCDF)
integer function nfmpi_inq_dimname(integer ncid, integer dimid, character*(*) name)
(Corresponds to nf_inq_dimname() in netCDF)
integer function nfmpi_inq_dimlen(integer ncid, integer dimid, integer(kind=MPI_OFFSET)
len)
(Corresponds to nf_inq_dimlen() in netCDF)
Use these functions to find out about a dimension.
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 nfmpi_rename_dim(integer ncid, integer dimid, character*(*) name)
(Corresponds to nf_rename_dim() in netCDF)
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.
VARIABLES
integer function nfmpi_def_var(integer ncid, character*(*) name, integer xtype, integer
ndims, integer dimids(1), integer varid)
(Corresponds to nf_def_var() in netCDF)
Adds a new variable to a netCDF dataset. The netCDF must be in define mode. varid
will be set to the netCDF variable ID. ndims will be the number of dimensions for
the variable. name will be the name of the netCDF variable. xtype is the
external, netCDF type of the variable and should be one of NF_BYTE NF_CHAR,
NF_SHORT, NF_INT, NF_FLOAT, or NF_DOUBLE, for CDF-1 and CDF-2 file formats. CDF-5
defines additional external types: NF_UBYTE, NF_USHORT, NF_UINT, NF_INT64, and
NF_UINT64. dimids argument is a vector of ndims dimension IDs corresponding to the
variable dimensions.
integer function nfmpi_inq_varid(integer ncid, character*(*) name, integer varid)
(Corresponds to nf_inq_varid() in netCDF)
Returns the ID of a netCDF variable in varid given its name.
integer function nfmpi_inq_var(integer ncid, integer varid, character*(*) name, integer
xtype, integer ndims, integer dimids(1), integer natts)
(Corresponds to nf_inq_var() in netCDF)
integer function nfmpi_inq_varname(integer ncid, integer varid, character*(*) name)
(Corresponds to nf_inq_varname() in netCDF)
integer function nfmpi_inq_vartype(integer ncid, integer varid, integer xtype)
(Corresponds to nf_inq_vartype() in netCDF)
integer function nfmpi_inq_varndims(integer ncid, integer varid, integer ndims)
(Corresponds to nf_inq_varndims() in netCDF)
integer function nfmpi_inq_vardimid(integer ncid, integer varid, integer dimids(1))
(Corresponds to nf_inq_vardimid() in netCDF)
integer function nfmpi_inq_varnatts(integer ncid, integer varid, integer natts)
(Corresponds to nf_inq_varnatts() in netCDF)
Returns information about a netCDF variable, given its ID.
integer function nfmpi_rename_var(integer ncid, integer varid, character*(*) name)
(Corresponds to nf_rename_var() in netCDF)
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.
WRITING AND READING WHOLE VARIABLES
integer function nfmpi_put_var_text(integer ncid, integer varid, character*(*) out)
(Corresponds to nf_put_var_text() in netCDF)
integer function nfmpi_put_var_int1(integer ncid, integer varid, integer*1 out(1))
(Corresponds to nf_put_var_int1() in netCDF)
integer function nfmpi_put_var_int2(integer ncid, integer varid, integer*2 out(1))
(Corresponds to nf_put_var_int2() in netCDF)
integer function nfmpi_put_var_int(integer ncid, integer varid, integer out(1))
(Corresponds to nf_put_var_int() in netCDF)
integer function nfmpi_put_var_real(integer ncid, integer varid, real out(1))
(Corresponds to nf_put_var_real() in netCDF)
integer function nfmpi_put_var_double(integer ncid, integer varid, doubleprecision out(1))
(Corresponds to nf_put_var_double() in netCDF)
Writes an entire netCDF variable (i.e. all the values). The netCDF dataset must be
open and in data mode. The type of the data is specified in the function name, and
it is converted to the external type of the specified variable, if possible,
otherwise an NF_ERANGE error is returned. Note that rounding is not performed
during the conversion. Floating point numbers are truncated when converted to
integers.
integer function nfmpi_get_var_text(integer ncid, integer varid, character*(*) in)
(Corresponds to nf_get_var_text() in netCDF)
integer function nfmpi_get_var_int1(integer ncid, integer varid, integer*1 in(1))
(Corresponds to nf_get_var_int1() in netCDF)
integer function nfmpi_get_var_int2(integer ncid, integer varid, integer*2 in(1))
(Corresponds to nf_get_var_int2() in netCDF)
integer function nfmpi_get_var_int(integer ncid, integer varid, integer in(1))
(Corresponds to nf_get_var_int() in netCDF)
integer function nfmpi_get_var_real(integer ncid, integer varid, real in(1))
(Corresponds to nf_get_var_real() in netCDF)
integer function nfmpi_get_var_double(integer ncid, integer varid, doubleprecision in(1))
(Corresponds to nf_get_var_double() in netCDF)
Reads an entire netCDF variable (i.e. all the values). The netCDF dataset must be
open and in data mode. The data is converted from the external type of the
specified variable, if necessary, to the type specified in the function name. If
conversion is not possible, an NF_ERANGE error is returned.
WRITING AND READING ONE DATUM
integer function nfmpi_put_var1_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), character*1 *out)
(Corresponds to nf_put_var1_text() in netCDF)
integer function nfmpi_put_var1_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), integer*1 *out)
(Corresponds to nf_put_var1_int1() in netCDF)
integer function nfmpi_put_var1_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), integer*2 *out)
(Corresponds to nf_put_var1_int2() in netCDF)
integer function nfmpi_put_var1_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), integer *out)
(Corresponds to nf_put_var1_int() in netCDF)
integer function nfmpi_put_var1_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), real *out)
(Corresponds to nf_put_var1_real() in netCDF)
integer function nfmpi_put_var1_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) index(1), doubleprecision *out)
(Corresponds to nf_put_var1_double() in netCDF)
Puts a single data value into a variable at the position index of an open netCDF
dataset that is in data mode. The type of the data is specified in the function
name, and it is converted to the external type of the specified variable, if
possible, otherwise an NF_ERANGE error is returned.
integer function nfmpi_get_var1_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), character*1 in)
(Corresponds to nf_get_var1_text() in netCDF)
integer function nfmpi_get_var1_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), integer*1 in)
(Corresponds to nf_get_var1_int1() in netCDF)
integer function nfmpi_get_var1_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), integer*2 in)
(Corresponds to nf_get_var1_int2() in netCDF)
integer function nfmpi_get_var1_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), integer in)
(Corresponds to nf_get_var1_int() in netCDF)
integer function nfmpi_get_var1_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
index(1), real in)
(Corresponds to nf_get_var1_real() in netCDF)
integer function nfmpi_get_var1_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) index(1), doubleprecision in)
(Corresponds to nf_get_var1_double() in netCDF)
Gets a single data value from a variable at the position index of an open netCDF
dataset that is in data mode. The data is converted from the external type of the
specified variable, if necessary, to the type specified in the function name. If
conversion is not possible, an NF_ERANGE error is returned.
WRITING AND READING AN ARRAY
integer function nfmpi_put_vara_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), character*(*) out)
(Corresponds to nf_put_vara_text() in netCDF)
integer function nfmpi_put_vara_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer*1 out(1))
(Corresponds to nf_put_vara_int1() in netCDF)
integer function nfmpi_put_vara_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer*2 out(1))
(Corresponds to nf_put_vara_int2() in netCDF)
integer function nfmpi_put_vara_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer out(1))
(Corresponds to nf_put_vara_int() in netCDF)
integer function nfmpi_put_vara_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), real out(1))
(Corresponds to nf_put_vara_real() in netCDF)
integer function nfmpi_put_vara_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) start(1), integer(kind=MPI_OFFSET) count(1),
doubleprecision out(1))
(Corresponds to nf_put_vara_double() in netCDF)
Writes an array section of values into a netCDF variable of an open netCDF dataset,
which must be in data mode. The array section is specified by the start and count
vectors, which give the starting index and count of values along each dimension of
the specified variable. The type of the data is specified in the function name and
is converted to the external type of the specified variable, if possible, otherwise
an NF_ERANGE error is returned.
integer function nfmpi_get_vara_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), character*(*) in)
(Corresponds to nf_get_vara_text() in netCDF)
integer function nfmpi_get_vara_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer*1 in(1))
(Corresponds to nf_get_vara_int1() in netCDF)
integer function nfmpi_get_vara_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer*2 in(1))
(Corresponds to nf_get_vara_int2() in netCDF)
integer function nfmpi_get_vara_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer in(1))
(Corresponds to nf_get_vara_int() in netCDF)
integer function nfmpi_get_vara_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), real in(1))
(Corresponds to nf_get_vara_real() in netCDF)
integer function nfmpi_get_vara_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) start(1), integer(kind=MPI_OFFSET) count(1),
doubleprecision in(1))
(Corresponds to nf_get_vara_double() in netCDF)
Reads an array section of values from a netCDF variable of an open netCDF dataset,
which must be in data mode. The array section is specified by the start and count
vectors, which give the starting index and count of values along each dimension of
the specified variable. The data is converted from the external type of the
specified variable, if necessary, to the type specified in the function name. If
conversion is not possible, an NF_ERANGE error is returned.
WRITING AND READING A SLICED ARRAY
integer function nfmpi_put_vars_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
character*(*) out)
(Corresponds to nf_put_vars_text() in netCDF)
integer function nfmpi_put_vars_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer*1 out(1))
(Corresponds to nf_put_vars_int1() in netCDF)
integer function nfmpi_put_vars_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer*2 out(1))
(Corresponds to nf_put_vars_int2() in netCDF)
integer function nfmpi_put_vars_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer out(1))
(Corresponds to nf_put_vars_int() in netCDF)
integer function nfmpi_put_vars_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
real out(1))
(Corresponds to nf_put_vars_real() in netCDF)
integer function nfmpi_put_vars_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) start(1), integer(kind=MPI_OFFSET) count(1),
integer(kind=MPI_OFFSET) stride(1), doubleprecision out(1))
(Corresponds to nf_put_vars_double() in netCDF)
These functions are used for strided output, which is like the array section output
described above, except that the sampling stride (the interval between accessed
values) is specified for each dimension. For an explanation of the sampling stride
vector, see COMMON ARGUMENTS DESCRIPTIONS below.
integer function nfmpi_get_vars_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
character*(*) in)
(Corresponds to nf_get_vars_text() in netCDF)
integer function nfmpi_get_vars_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer*1 in(1))
(Corresponds to nf_get_vars_int1() in netCDF)
integer function nfmpi_get_vars_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer*2 in(1))
(Corresponds to nf_get_vars_int2() in netCDF)
integer function nfmpi_get_vars_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer in(1))
(Corresponds to nf_get_vars_int() in netCDF)
integer function nfmpi_get_vars_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
real in(1))
(Corresponds to nf_get_vars_real() in netCDF)
integer function nfmpi_get_vars_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) start(1), integer(kind=MPI_OFFSET) count(1),
integer(kind=MPI_OFFSET) stride(1), doubleprecision in(1))
(Corresponds to nf_get_vars_double() in netCDF)
These functions are used for strided input, which is like the array section input
described above, except that the sampling stride (the interval between accessed
values) is specified for each dimension. For an explanation of the sampling stride
vector, see COMMON ARGUMENTS DESCRIPTIONS below.
WRITING AND READING A MAPPED ARRAY
integer function nfmpi_put_varm_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), character*(*) out)
(Corresponds to nf_put_varm_text() in netCDF)
integer function nfmpi_put_varm_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), integer*1 out(1))
(Corresponds to nf_put_varm_int1() in netCDF)
integer function nfmpi_put_varm_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), integer*2 out(1))
(Corresponds to nf_put_varm_int2() in netCDF)
integer function nfmpi_put_varm_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), integer out(1))
(Corresponds to nf_put_varm_int() in netCDF)
integer function nfmpi_put_varm_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), real out(1))
(Corresponds to nf_put_varm_real() in netCDF)
integer function nfmpi_put_varm_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) start(1), integer(kind=MPI_OFFSET) count(1),
integer(kind=MPI_OFFSET) stride(1), integer(kind=MPI_OFFSET) imap(1),
doubleprecision out(1))
(Corresponds to nf_put_varm_double() in netCDF)
These functions are used for mapped output, which is like strided output described
above, except that an additional index mapping vector is provided to specify the
in-memory arrangement of the data values. For an explanation of the index mapping
vector, see COMMON ARGUMENTS DESCRIPTIONS below.
integer function nfmpi_get_varm_text(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), character*(*) in)
(Corresponds to nf_get_varm_text() in netCDF)
integer function nfmpi_get_varm_int1(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), integer*1 in(1))
(Corresponds to nf_get_varm_int1() in netCDF)
integer function nfmpi_get_varm_int2(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), integer*2 in(1))
(Corresponds to nf_get_varm_int2() in netCDF)
integer function nfmpi_get_varm_int(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), integer in(1))
(Corresponds to nf_get_varm_int() in netCDF)
integer function nfmpi_get_varm_real(integer ncid, integer varid, integer(kind=MPI_OFFSET)
start(1), integer(kind=MPI_OFFSET) count(1), integer(kind=MPI_OFFSET) stride(1),
integer(kind=MPI_OFFSET) imap(1), real in(1))
(Corresponds to nf_get_varm_real() in netCDF)
integer function nfmpi_get_varm_double(integer ncid, integer varid,
integer(kind=MPI_OFFSET) start(1), integer(kind=MPI_OFFSET) count(1),
integer(kind=MPI_OFFSET) stride(1), integer(kind=MPI_OFFSET) imap(1),
doubleprecision in(1))
(Corresponds to nf_get_varm_double() in netCDF)
These functions are used for mapped input, which is like strided input described
above, except that an additional index mapping vector is provided to specify the
in-memory arrangement of the data values. For an explanation of the index mapping
vector, see COMMON ARGUMENTS DESCRIPTIONS below.
ATTRIBUTES
integer function nfmpi_put_att_text(integer ncid, integer varid, character*(*) name,
integer xtype, integer(kind=MPI_OFFSET) len, character*(*) out)
(Corresponds to nf_put_att_text() in netCDF)
integer function nfmpi_put_att_int1(integer ncid, integer varid, character*(*) name,
integer xtype, integer(kind=MPI_OFFSET) len, integer*1 out(1))
(Corresponds to nf_put_att_int1() in netCDF)
integer function nfmpi_put_att_int2(integer ncid, integer varid, character*(*) name,
integer xtype, integer(kind=MPI_OFFSET) len, integer*2 out(1))
(Corresponds to nf_put_att_int2() in netCDF)
integer function nfmpi_put_att_int(integer ncid, integer varid, character*(*) name,
integer xtype, integer(kind=MPI_OFFSET) len, integer out(1))
(Corresponds to nf_put_att_int() in netCDF)
integer function nfmpi_put_att_real(integer ncid, integer varid, character*(*) name,
integer xtype, integer(kind=MPI_OFFSET) len, real out(1))
(Corresponds to nf_put_att_real() in netCDF)
integer function nfmpi_put_att_double(integer ncid, integer varid, character*(*) name,
integer xtype, integer(kind=MPI_OFFSET) len, doubleprecision out(1))
(Corresponds to nf_put_att_double() in netCDF)
integer function nfmpi_put_att(integer ncid, integer varid, character*(*) name, integer
xtype, integer(kind=MPI_OFFSET) len, void * ip)
(Corresponds to nf_put_att() in netCDF)
integer function nfmpi_get_att(integer ncid, integer varid, character*(*) name, void * ip)
(Corresponds to nf_get_att() in netCDF)
Unlike variables, attributes do not have separate functions for defining and
writing values. This family of functions 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. The parameter len is the number of values from out
to transfer. It is often one, except that for nfmpi_put_att_text() it will usually
be len_trim(out).
For these functions, the type component of the function name refers to the in-
memory type of the value, whereas the xtype argument refers to the external type
for storing the value. An NF_ERANGE error results if a conversion between these
types is not possible. In this case the value is represented with the appropriate
fill-value for the associated external type.
integer function nfmpi_inq_attname(integer ncid, integer varid, integer attnum,
character*(*) name)
(Corresponds to nf_inq_attname() in netCDF)
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, since attributes are accessed by name rather
than number in all other attribute functions. The number of an attribute is more
volatile than the name, since 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 nvatts, where nvatts is the number of attributes for the
variable, as returned from a call to nfmpi_inq_varnatts().
integer function nfmpi_inq_att(integer ncid, integer varid, character*(*) name, integer
xtype, integer(kind=MPI_OFFSET) len)
(Corresponds to nf_inq_att() in netCDF)
integer function nfmpi_inq_attid(integer ncid, integer varid, character*(*) name, integer
attnum)
(Corresponds to nf_inq_attid() in netCDF)
integer function nfmpi_inq_atttype(integer ncid, integer varid, character*(*) name,
integer xtype)
(Corresponds to nf_inq_atttype() in netCDF)
integer function nfmpi_inq_attlen(integer ncid, integer varid, character*(*) name,
integer(kind=MPI_OFFSET) len)
(Corresponds to nf_inq_attlen() in netCDF)
These functions return information about a netCDF attribute, given its variable ID
and name. The information returned is the external type in xtype and the number of
elements in the attribute as len.
integer function nfmpi_copy_att(integer ncid, integer varid_in, character*(*) name,
integer ncid_out, integer varid_out)
(Corresponds to nf_copy_att() in netCDF)
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. 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 NF_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 NF_GLOBAL to copy to a global attribute.
integer function nfmpi_rename_att(integer ncid, integer varid, character*(*) name,
character*(*) newname)
(Corresponds to nf_rename_att() in netCDF)
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.
integer function nfmpi_del_att(integer ncid, integer varid, character*(*) name)
(Corresponds to nf_del_att() in netCDF)
Deletes an attribute from a netCDF dataset. The dataset must be in define mode.
integer function nfmpi_get_att_text(integer ncid, integer varid, character*(*) name,
character*(*) in)
(Corresponds to nf_get_att_text() in netCDF)
integer function nfmpi_get_att_int1(integer ncid, integer varid, character*(*) name,
integer*1 in(1))
(Corresponds to nf_get_att_int1() in netCDF)
integer function nfmpi_get_att_int2(integer ncid, integer varid, character*(*) name,
integer*2 in(1))
(Corresponds to nf_get_att_int2() in netCDF)
integer function nfmpi_get_att_int(integer ncid, integer varid, character*(*) name,
integer in(1))
(Corresponds to nf_get_att_int() in netCDF)
integer function nfmpi_get_att_real(integer ncid, integer varid, character*(*) name, real
in(1))
(Corresponds to nf_get_att_real() in netCDF)
integer function nfmpi_get_att_double(integer ncid, integer varid, character*(*) name,
doubleprecision in(1))
(Corresponds to nf_get_att_double() in netCDF)
Gets the value(s) of a netCDF attribute, given its variable ID and name. Converts
from the external type to the type specified in the function name, if possible,
otherwise returns an NF_ERANGE error. All elements of the vector of attribute
values are returned, so you must allocate enough space to hold them. If you don't
know how much space to reserve, call nfmpi_inq_attlen() first to find out the
length of the attribute.
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 nfmpi_open() or
nfmpi_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 for CDF-1
and CDF-2 file formats. 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.
CDF-5 defines additional external types: NF_UBYTE, NF_USHORT, NF_UINT, NF_INT64,
and NF_UINT64.
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 nfmpi_inquire()
function or the number of attributes associated with a netCDF variable for the
nfmpi_varinq() function.
integer(kind=MPI_OFFSET) index(1)
specifies the 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(kind=MPI_OFFSET) 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(kind=MPI_OFFSET) 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(kind=MPI_OFFSET) 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.).
integer(kind=MPI_OFFSET) imap(1)
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).
VARIABLE PREFILLING
Prior to version 1.6.1, PnetCDF does not support data filling. The default fill mode in
PnetCDF is NF_NOFILL This contrary to netCDF library whose default is NF_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 nfmpi_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 nfmpi_fill_var_rec(). Note this fills only one record of a
variable.
The fill mode for the entire file can be set by nfmpi_set_fill(). Per-variable fill mode
setting is also available through nfmpi_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(3f).
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/.