NAME¶

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

SYNOPSIS¶

include "pnetcdf.inc"

LIBRARY VERSION¶

This document describes PnetCDF 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: "1.12.3 of 2022-02-21".

The RCS ident(1) command will find a string like "$Id: @(#) PnetCDF library version 1.12.3 of 2022-02-21 $" in the library. The SCCS what(1) command will find a string like "PnetCDF library version 1.12.3 of 2022-02-21".

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 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(3f).

DATE¶

February 21, 2022

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