PnetCDF(3)

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

SYNOPSIS
#include <pnetcdf.h>

mpicc ... -lpnetcdf

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 PnetCDF APIs for the C programming language.

const char* ncmpi_inq_libvers()

(Corresponds to nc_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 ncmpi_inq_libvers() and ncmpi_strerror()) return an integer status.

If this returned status value is not equal to NC_NOERR (zero), it indicates that an error occurred. The possible status values are defined in system include file <errno.h> and in "pnetcdf.h".

const char* ncmpi_strerror(int status)

(Corresponds to nc_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

int ncmpi_create(MPI_Comm comm, const char path[], int cmode, MPI_Info info, int* ncid)

(Corresponds to nc_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: NC_NOCLOBBER to protect existing datasets (default is NC_CLOBBER, silently blows them away), NC_SHARE for stronger metadata data consistency control, NC_64BIT_OFFSET to create a file in the 64-bit offset format (CDF-2), as opposed to classic format, the default, or NC_64BIT_DATA to create a file in the 64-bit data format (CDF-5). Use either NC_64BIT_OFFSET or NC_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 NC_WRITE mode. When this function returns, the new netCDF dataset is in define mode.

int ncmpi_open(MPI_Comm comm, const char path[], int mode, MPI_Info info, int* ncid)

(Corresponds to nc_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: NC_WRITE for read-write access (default read-only), NC_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.

int ncmpi_redef(int ncid)

(Corresponds to nc_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.

int ncmpi_enddef(int ncid)

(Corresponds to nc_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.

int ncmpi_sync(int ncid)

(Corresponds to nc_sync() in netCDF)

Unless the NC_SHARE bit is set in ncmpi_open() or ncmpi_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.

int ncmpi_abort(int ncid)

(Corresponds to nc_abort() in netCDF)

You don't need to call this function. This function is called automatically by ncmpi_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 ncmpi_close(). If it is called after ncmpi_redef(), but before ncmpi_enddef(), the new definitions are not committed and the dataset is closed. If it is called after ncmpi_create() but before ncmpi_enddef(), the dataset disappears.

int ncmpi_close(int ncid)

(Corresponds to nc_close() in netCDF)

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

int ncmpi_inq(int ncid, int* ndims, int* nvars, int* natts, int* unlimdimid)

(Corresponds to nc_inq() in netCDF)

int ncmpi_inq_ndims(int ncid, int* ndims)

(Corresponds to nc_inq_ndims() in netCDF)

int ncmpi_inq_nvars(int ncid, int* nvars)

(Corresponds to nc_inq_nvars() in netCDF)

int ncmpi_inq_natts(int ncid, int* natts)

(Corresponds to nc_inq_natts() in netCDF)

int ncmpi_inq_unlimdim(int ncid, int* unlimdimid)

(Corresponds to nc_inq_unlimdim() in netCDF)

int ncmpi_inq_format(int ncid, int* formatn)

(Corresponds to nc_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 -1 otherwise. formatn will contain the version number of the dataset <format>, one of NC_FORMAT_CLASSIC, NC_FORMAT_64BIT, or NC_FORMAT_64BIT_DATA. If any of the return parameters is a NULL pointer, then the corresponding information will not be returned; hence, no space need be allocated for it.

int ncmpi_def_dim(int ncid, const char name[], MPI_Offset len, int* dimid)

(Corresponds to nc_def_dim() in netCDF)

Adds a new dimension to an open netCDF dataset, which must be in define mode. name is the dimension name. If dimid is not a NULL pointer then upon successful completion dimid will contain the dimension ID of the newly created dimension.

DIMENSIONS

int ncmpi_inq_dimid(int ncid, const char name[], int* dimid)

(Corresponds to nc_inq_dimid() in netCDF)

Given a dimension name, returns the ID of a netCDF dimension in dimid.

int ncmpi_inq_dim(int ncid, int dimid, char name[], MPI_Offset* len)

(Corresponds to nc_inq_dim() in netCDF)

int ncmpi_inq_dimname(int ncid, int dimid, char name[])

(Corresponds to nc_inq_dimname() in netCDF)

int ncmpi_inq_dimlen(int ncid, int dimid, MPI_Offset* len)

(Corresponds to nc_inq_dimlen() in netCDF)

Use these functions to find out about a dimension. If either the name argument or len argument is a NULL pointer, then the associated information will not be returned. Otherwise, name should be big enough (NC_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.

int ncmpi_rename_dim(int ncid, int dimid, const char name[])

(Corresponds to nc_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

int ncmpi_def_var(int ncid, const char name[], nc_type xtype, int ndims, const int dimids[], int* varid)

(Corresponds to nc_def_var() in netCDF)

Adds a new variable to a netCDF dataset. The netCDF must be in define mode. If not NULL, then 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 NC_BYTE NC_CHAR, NC_SHORT, NC_INT, NC_FLOAT, or NC_DOUBLE, for CDF-1 and CDF-2 file formats. CDF-5 defines additional external types: NC_UBYTE, NC_USHORT, NC_UINT, NC_INT64, and NC_UINT64. dimids argument is a vector of ndims dimension IDs corresponding to the variable dimensions.

int ncmpi_inq_varid(int ncid, const char name[], int* varid)

(Corresponds to nc_inq_varid() in netCDF)

Returns the ID of a netCDF variable in varid given its name.

int ncmpi_inq_var(int ncid, int varid, char name[], nc_type* xtype, int* ndims, int dimids[], int* natts)

(Corresponds to nc_inq_var() in netCDF)

int ncmpi_inq_varname(int ncid, int varid, char name[])

(Corresponds to nc_inq_varname() in netCDF)

int ncmpi_inq_vartype(int ncid, int varid, nc_type* xtype)

(Corresponds to nc_inq_vartype() in netCDF)

int ncmpi_inq_varndims(int ncid, int varid, int* ndims)

(Corresponds to nc_inq_varndims() in netCDF)

int ncmpi_inq_vardimid(int ncid, int varid, int dimids[])

(Corresponds to nc_inq_vardimid() in netCDF)

int ncmpi_inq_varnatts(int ncid, int varid, int* natts)

(Corresponds to nc_inq_varnatts() in netCDF)

Returns information about a netCDF variable, given its ID. If any of the return parameters (name, xtype, ndims, dimids, or natts) is a NULL pointer, then the corresponding information will not be returned; hence, no space need be allocated for it.

int ncmpi_rename_var(int ncid, int varid, const char name[])

(Corresponds to nc_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

int ncmpi_put_var_text(int ncid, int varid, const char out[])

(Corresponds to nc_put_var_text() in netCDF)

int ncmpi_put_var_uchar(int ncid, int varid, const unsigned char out[])

(Corresponds to nc_put_var_uchar() in netCDF)

int ncmpi_put_var_schar(int ncid, int varid, const signed char out[])

(Corresponds to nc_put_var_schar() in netCDF)

int ncmpi_put_var_short(int ncid, int varid, const short out[])

(Corresponds to nc_put_var_short() in netCDF)

int ncmpi_put_var_int(int ncid, int varid, const int out[])

(Corresponds to nc_put_var_int() in netCDF)

int ncmpi_put_var_long(int ncid, int varid, const long out[])

(Corresponds to nc_put_var_long() in netCDF)

int ncmpi_put_var_float(int ncid, int varid, const float out[])

(Corresponds to nc_put_var_float() in netCDF)

int ncmpi_put_var_double(int ncid, int varid, const double out[])

(Corresponds to nc_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 NC_ERANGE error is returned. Note that rounding is not performed during the conversion. Floating point numbers are truncated when converted to integers.

int ncmpi_get_var_text(int ncid, int varid, char in[])

(Corresponds to nc_get_var_text() in netCDF)

int ncmpi_get_var_uchar(int ncid, int varid, unsigned char in[])

(Corresponds to nc_get_var_uchar() in netCDF)

int ncmpi_get_var_schar(int ncid, int varid, signed char in[])

(Corresponds to nc_get_var_schar() in netCDF)

int ncmpi_get_var_short(int ncid, int varid, short in[])

(Corresponds to nc_get_var_short() in netCDF)

int ncmpi_get_var_int(int ncid, int varid, int in[])

(Corresponds to nc_get_var_int() in netCDF)

int ncmpi_get_var_long(int ncid, int varid, long in[])

(Corresponds to nc_get_var_long() in netCDF)

int ncmpi_get_var_float(int ncid, int varid, float in[])

(Corresponds to nc_get_var_float() in netCDF)

int ncmpi_get_var_double(int ncid, int varid, double in[])

(Corresponds to nc_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 NC_ERANGE error is returned.

WRITING AND READING ONE DATUM

int ncmpi_put_var1_text(int ncid, int varid, const MPI_Offset index[], char *out)

(Corresponds to nc_put_var1_text() in netCDF)

int ncmpi_put_var1_uchar(int ncid, int varid, const MPI_Offset index[], unsigned char *out)

(Corresponds to nc_put_var1_uchar() in netCDF)

int ncmpi_put_var1_schar(int ncid, int varid, const MPI_Offset index[], signed char *out)

(Corresponds to nc_put_var1_schar() in netCDF)

int ncmpi_put_var1_short(int ncid, int varid, const MPI_Offset index[], short *out)

(Corresponds to nc_put_var1_short() in netCDF)

int ncmpi_put_var1_int(int ncid, int varid, const MPI_Offset index[], int *out)

(Corresponds to nc_put_var1_int() in netCDF)

int ncmpi_put_var1_long(int ncid, int varid, const MPI_Offset index[], long *out)

(Corresponds to nc_put_var1_long() in netCDF)

int ncmpi_put_var1_float(int ncid, int varid, const MPI_Offset index[], float *out)

(Corresponds to nc_put_var1_float() in netCDF)

int ncmpi_put_var1_double(int ncid, int varid, const MPI_Offset index[], double *out)

(Corresponds to nc_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 NC_ERANGE error is returned.

int ncmpi_get_var1_text(int ncid, int varid, const MPI_Offset index[], char* in)

(Corresponds to nc_get_var1_text() in netCDF)

int ncmpi_get_var1_uchar(int ncid, int varid, const MPI_Offset index[], unsigned char* in)

(Corresponds to nc_get_var1_uchar() in netCDF)

int ncmpi_get_var1_schar(int ncid, int varid, const MPI_Offset index[], signed char* in)

(Corresponds to nc_get_var1_schar() in netCDF)

int ncmpi_get_var1_short(int ncid, int varid, const MPI_Offset index[], short* in)

(Corresponds to nc_get_var1_short() in netCDF)

int ncmpi_get_var1_int(int ncid, int varid, const MPI_Offset index[], int* in)

(Corresponds to nc_get_var1_int() in netCDF)

int ncmpi_get_var1_long(int ncid, int varid, const MPI_Offset index[], long* in)

(Corresponds to nc_get_var1_long() in netCDF)

int ncmpi_get_var1_float(int ncid, int varid, const MPI_Offset index[], float* in)

(Corresponds to nc_get_var1_float() in netCDF)

int ncmpi_get_var1_double(int ncid, int varid, const MPI_Offset index[], double* in)

(Corresponds to nc_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 NC_ERANGE error is returned.

WRITING AND READING AN ARRAY

int ncmpi_put_vara_text(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const char out[])

(Corresponds to nc_put_vara_text() in netCDF)

int ncmpi_put_vara_uchar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const unsigned char out[])

(Corresponds to nc_put_vara_uchar() in netCDF)

int ncmpi_put_vara_schar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const signed char out[])

(Corresponds to nc_put_vara_schar() in netCDF)

int ncmpi_put_vara_short(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const short out[])

(Corresponds to nc_put_vara_short() in netCDF)

int ncmpi_put_vara_int(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const int out[])

(Corresponds to nc_put_vara_int() in netCDF)

int ncmpi_put_vara_long(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const long out[])

(Corresponds to nc_put_vara_long() in netCDF)

int ncmpi_put_vara_float(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const float out[])

(Corresponds to nc_put_vara_float() in netCDF)

int ncmpi_put_vara_double(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const double out[])

(Corresponds to nc_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 NC_ERANGE error is returned.

int ncmpi_get_vara_text(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], char in[])

(Corresponds to nc_get_vara_text() in netCDF)

int ncmpi_get_vara_uchar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], unsigned char in[])

(Corresponds to nc_get_vara_uchar() in netCDF)

int ncmpi_get_vara_schar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], signed char in[])

(Corresponds to nc_get_vara_schar() in netCDF)

int ncmpi_get_vara_short(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], short in[])

(Corresponds to nc_get_vara_short() in netCDF)

int ncmpi_get_vara_int(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], int in[])

(Corresponds to nc_get_vara_int() in netCDF)

int ncmpi_get_vara_long(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], long in[])

(Corresponds to nc_get_vara_long() in netCDF)

int ncmpi_get_vara_float(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], float in[])

(Corresponds to nc_get_vara_float() in netCDF)

int ncmpi_get_vara_double(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], double in[])

(Corresponds to nc_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 NC_ERANGE error is returned.

WRITING AND READING A SLICED ARRAY

int ncmpi_put_vars_text(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const char out[])

(Corresponds to nc_put_vars_text() in netCDF)

int ncmpi_put_vars_uchar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const unsigned char out[])

(Corresponds to nc_put_vars_uchar() in netCDF)

int ncmpi_put_vars_schar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const signed char out[])

(Corresponds to nc_put_vars_schar() in netCDF)

int ncmpi_put_vars_short(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const short out[])

(Corresponds to nc_put_vars_short() in netCDF)

int ncmpi_put_vars_int(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const int out[])

(Corresponds to nc_put_vars_int() in netCDF)

int ncmpi_put_vars_long(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const long out[])

(Corresponds to nc_put_vars_long() in netCDF)

int ncmpi_put_vars_float(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const float out[])

(Corresponds to nc_put_vars_float() in netCDF)

int ncmpi_put_vars_double(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const double out[])

(Corresponds to nc_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.

int ncmpi_get_vars_text(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], char in[])

(Corresponds to nc_get_vars_text() in netCDF)

int ncmpi_get_vars_uchar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], unsigned char in[])

(Corresponds to nc_get_vars_uchar() in netCDF)

int ncmpi_get_vars_schar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], signed char in[])

(Corresponds to nc_get_vars_schar() in netCDF)

int ncmpi_get_vars_short(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], short in[])

(Corresponds to nc_get_vars_short() in netCDF)

int ncmpi_get_vars_int(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], int in[])

(Corresponds to nc_get_vars_int() in netCDF)

int ncmpi_get_vars_long(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], long in[])

(Corresponds to nc_get_vars_long() in netCDF)

int ncmpi_get_vars_float(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], float in[])

(Corresponds to nc_get_vars_float() in netCDF)

int ncmpi_get_vars_double(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], double in[])

(Corresponds to nc_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

int ncmpi_put_varm_text(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const char out[])

(Corresponds to nc_put_varm_text() in netCDF)

int ncmpi_put_varm_uchar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const unsigned char out[])

(Corresponds to nc_put_varm_uchar() in netCDF)

int ncmpi_put_varm_schar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const signed char out[])

(Corresponds to nc_put_varm_schar() in netCDF)

int ncmpi_put_varm_short(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const short out[])

(Corresponds to nc_put_varm_short() in netCDF)

int ncmpi_put_varm_int(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const int out[])

(Corresponds to nc_put_varm_int() in netCDF)

int ncmpi_put_varm_long(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const long out[])

(Corresponds to nc_put_varm_long() in netCDF)

int ncmpi_put_varm_float(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const float out[])

(Corresponds to nc_put_varm_float() in netCDF)

int ncmpi_put_varm_double(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], const double out[])

(Corresponds to nc_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.

int ncmpi_get_varm_text(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], char in[])

(Corresponds to nc_get_varm_text() in netCDF)

int ncmpi_get_varm_uchar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], unsigned char in[])

(Corresponds to nc_get_varm_uchar() in netCDF)

int ncmpi_get_varm_schar(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], signed char in[])

(Corresponds to nc_get_varm_schar() in netCDF)

int ncmpi_get_varm_short(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], short in[])

(Corresponds to nc_get_varm_short() in netCDF)

int ncmpi_get_varm_int(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], int in[])

(Corresponds to nc_get_varm_int() in netCDF)

int ncmpi_get_varm_long(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], long in[])

(Corresponds to nc_get_varm_long() in netCDF)

int ncmpi_get_varm_float(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], float in[])

(Corresponds to nc_get_varm_float() in netCDF)

int ncmpi_get_varm_double(int ncid, int varid, const MPI_Offset start[], const MPI_Offset count[], const MPI_Offset stride[], const MPI_Offset imap[], double in[])

(Corresponds to nc_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

int ncmpi_put_att_text(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const char out[])

(Corresponds to nc_put_att_text() in netCDF)

int ncmpi_put_att_uchar(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const unsigned char out[])

(Corresponds to nc_put_att_uchar() in netCDF)

int ncmpi_put_att_schar(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const signed char out[])

(Corresponds to nc_put_att_schar() in netCDF)

int ncmpi_put_att_short(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const short out[])

(Corresponds to nc_put_att_short() in netCDF)

int ncmpi_put_att_int(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const int out[])

(Corresponds to nc_put_att_int() in netCDF)

int ncmpi_put_att_long(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const long out[])

(Corresponds to nc_put_att_long() in netCDF)

int ncmpi_put_att_float(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const float out[])

(Corresponds to nc_put_att_float() in netCDF)

int ncmpi_put_att_double(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, const double out[])

(Corresponds to nc_put_att_double() in netCDF)

int ncmpi_put_att(int ncid, int varid, const char name[], nc_type xtype, MPI_Offset len, void * ip)

(Corresponds to nc_put_att() in netCDF)

int ncmpi_get_att(int ncid, int varid, const char name[], void ** ip)

(Corresponds to nc_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 ncmpi_put_att_text() it will usually be strlen(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 NC_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.

int ncmpi_inq_attname(int ncid, int varid, int attnum, char name[])

(Corresponds to nc_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 0 (the first attribute) to nvatts-1, where nvatts is the number of attributes for the variable, as returned from a call to ncmpi_inq_varnatts(). If the name parameter is a NULL pointer, no name will be returned and no space need be allocated.

int ncmpi_inq_att(int ncid, int varid, const char name[], nc_type* xtype, MPI_Offset* len)

(Corresponds to nc_inq_att() in netCDF)

int ncmpi_inq_attid(int ncid, int varid, const char name[], int* attnum)

(Corresponds to nc_inq_attid() in netCDF)

int ncmpi_inq_atttype(int ncid, int varid, const char name[], nc_type* xtype)

(Corresponds to nc_inq_atttype() in netCDF)

int ncmpi_inq_attlen(int ncid, int varid, const char name[], MPI_Offset* len)

(Corresponds to nc_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. If any of the return arguments is a NULL pointer, the specified information will not be returned.

int ncmpi_copy_att(int ncid, int varid_in, const char name[], int ncid_out, int varid_out)

(Corresponds to nc_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 NC_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 NC_GLOBAL to copy to a global attribute.

int ncmpi_rename_att(int ncid, int varid, const char name[], const char newname[])

(Corresponds to nc_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.

int ncmpi_del_att(int ncid, int varid, const char name[])

(Corresponds to nc_del_att() in netCDF)

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

int ncmpi_get_att_text(int ncid, int varid, const char name[], char in[])

(Corresponds to nc_get_att_text() in netCDF)

int ncmpi_get_att_uchar(int ncid, int varid, const char name[], unsigned char in[])

(Corresponds to nc_get_att_uchar() in netCDF)

int ncmpi_get_att_schar(int ncid, int varid, const char name[], signed char in[])

(Corresponds to nc_get_att_schar() in netCDF)

int ncmpi_get_att_short(int ncid, int varid, const char name[], short in[])

(Corresponds to nc_get_att_short() in netCDF)

int ncmpi_get_att_int(int ncid, int varid, const char name[], int in[])

(Corresponds to nc_get_att_int() in netCDF)

int ncmpi_get_att_long(int ncid, int varid, const char name[], long in[])

(Corresponds to nc_get_att_long() in netCDF)

int ncmpi_get_att_float(int ncid, int varid, const char name[], float in[])

(Corresponds to nc_get_att_float() in netCDF)

int ncmpi_get_att_double(int ncid, int varid, const char name[], double in[])

(Corresponds to nc_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 NC_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 ncmpi_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.

int ncid
    is the netCDF ID returned from a previous, successful call to ncmpi_open() or ncmpi_create()

char 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. As an input argument, it shall be a pointer to a 0-terminated string; as an output argument, it shall be the address of a buffer in which to hold such a string. The maximum allowable number of characters (excluding the terminating 0) is NC_MAX_NAME.

nc_type xtype
    specifies the external data type of a netCDF variable or attribute and is one of the following: NC_BYTE, NC_CHAR, NC_SHORT, NC_INT, NC_FLOAT, or NC_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. (NC_LONG in netCDF version 2 is now obsolete and set to NC_INT). CDF-5 defines additional external types: NC_UBYTE, NC_USHORT, NC_UINT, NC_INT64, and NC_UINT64.

int 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[ndims-1] shall be the dimension ID of the most rapidly varying dimension and dimids[0] 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 NC_MAX_VAR_DIMS.

int dimid
    is the ID of a netCDF dimension. netCDF dimension ID's are allocated sequentially from the non-negative integers beginning with 0.

int 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 NC_MAX_VAR_DIMS.

int varid
    is the ID of a netCDF variable or (for the attribute-access functions) the symbolic constant NC_GLOBAL, which is used to reference global attributes. netCDF variable ID's are allocated sequentially from the non-negative integers beginning with 0.

int* natts
    is the number of global attributes in a netCDF dataset for the ncmpi_inquire() function or the number of attributes associated with a netCDF variable for the ncmpi_varinq() function.

const MPI_Offset index[]
    specifies the coordinates of the netCDF data value to be accessed. The indices start at 0; thus, for example, the first data value of a two-dimensional variable is (0,0). 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.

const 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 0; thus, the first data value of a variable is (0, 0, ..., 0). 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.

const MPI_Offset count[]
    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.

const 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[0]) gives the sampling interval along the most slowly 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.). A NULL stride argument is treated as (1, 1, ... , 1).

const 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[0] gives the distance between elements of the internal array corresponding to the most slowly 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). A NULL pointer means the memory-resident values have the same structure as the associated netCDF variable.

VARIABLE PREFILLING

Prior to version 1.6.1, PnetCDF does not support data filling. The default fill mode in PnetCDF is NC_NOFILL This contrary to netCDF library whose default is NC_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 ncmpi_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 ncmpi_fill_var_rec(). Note this fills only one record of a variable.

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

ENVIRONMENT VARIABLES

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

MAILING-LISTS

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

SEE ALSO

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

DATE
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