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DOCUMENTATION: add docs for nc_create_par() and other functions #599

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Nov 15, 2017
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DOCUMENTATION: add docs for nc_create_par() and other functions #599

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6252d25
add docs for nc_create_par() and other functions
edhartnett Nov 8, 2017
02b66af
added more documentation
edhartnett Nov 8, 2017
a416f3e
Merge branch 'master' into ejh_more_docs_2
edhartnett Nov 10, 2017
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5 changes: 3 additions & 2 deletions include/netcdf_par.h
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@
*
* This header file is for the parallel I/O functions of netCDF.
*
* \author Ed Hartnett
*/
/* "$Id: netcdf_par.h,v 1.1 2010/06/01 15:46:49 ed Exp $" */

#ifndef NETCDF_PAR_H
#define NETCDF_PAR_H 1
Expand All @@ -19,8 +19,9 @@
extern "C" {
#endif

/* Use these with nc_var_par_access(). */
/** Use with nc_var_par_access() to set parallel access to independent. */
#define NC_INDEPENDENT 0
/** Use with nc_var_par_access() to set parallel access to collective. */
#define NC_COLLECTIVE 1

/* Create a file and enable parallel I/O. */
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170 changes: 149 additions & 21 deletions libdispatch/dparallel.c
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Original file line number Diff line number Diff line change
@@ -1,17 +1,89 @@
/** \file dparallel.c
This file has the parallel I/O functions which correspond to the serial I/O functions.
/** \file

This file has the parallel I/O functions which correspond to the
serial I/O functions.

Copyright 2010 University Corporation for Atmospheric
Research/Unidata. See COPYRIGHT file for more info.
*/

#include "config.h"
#include "ncdispatch.h"

/**
Create a netCDF file for parallel I/O.

This function creates a new netCDF file for parallel I/O access.

Parallel I/O access is only available in library build which support
parallel I/O. To support parallel I/O, netCDF must be built with
netCDF-4 enabled, and with a HDF5 library that supports parallel I/O,
or with support for the parallel-netcdf library via the
enable-pnetcdf option.

See nc_create() for a fuller discussion of file creation.

\note When opening a netCDF-4 file HDF5 error reporting is turned off,
if it is on. This doesn't stop the HDF5 error stack from recording the
errors, it simply stops their display to the user through stderr.

\param path The file name of the new netCDF dataset.

\param cmode The creation mode flag. The following flags are available:
NC_NOCLOBBER (do not overwrite existing file),
NC_NETCDF4 (create netCDF-4/HDF5 file),
NC_CLASSIC_MODEL (enforce netCDF classic mode on netCDF-4/HDF5 files),
NC_PNETCDF.

\param comm the MPI communicator to be used.

\param info MPI info or MPI_INFO_NULL.

\param ncidp Pointer to location where returned netCDF ID is to be
stored.

\returns ::NC_NOERR No error.
\returns ::NC_ENOPAR Library was not built with parallel I/O features.
\returns ::NC_EINVAL Invalid input parameters.
\returns ::NC_ENOMEM System out of memory.
\returns ::NC_ENOTNC Binary format could not be determined.
\returns ::NC_EHDFERR HDF5 error (netCDF-4 files only).
\returns ::NC_EFILEMETA Error writing netCDF-4 file-level metadata in
HDF5 file. (netCDF-4 files only).

<h1>Example</h1>

In this example from nc_test4/tst_parallel.c, a file is create for
parallel I/O.

\code
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
int ncid, v1id, dimids[NDIMS];
char file_name[NC_MAX_NAME + 1];

MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);

sprintf(file_name, "%s/%s", TEMP_LARGE, FILE);
if ((res = nc_create_par(file_name, NC_NETCDF4|NC_MPIIO, comm,
info, &ncid))) ERR;

if (nc_def_dim(ncid, "d1", DIMSIZE, dimids)) ERR;
if (nc_def_dim(ncid, "d2", DIMSIZE, &dimids[1])) ERR;
if (nc_def_dim(ncid, "d3", NUM_SLABS, &dimids[2])) ERR;

This function creates a file for use with parallel I/O.
if ((res = nc_def_var(ncid, "v1", NC_INT, NDIMS, dimids, &v1id))) ERR;

if ((res = nc_enddef(ncid))) ERR;

...

if ((res = nc_close(ncid))) ERR;
\endcode
\author Ed Hartnett, Dennis Heimbigner
\ingroup datasets
*/
int nc_create_par(const char *path, int cmode, MPI_Comm comm,
MPI_Info info, int *ncidp)
Expand All @@ -33,7 +105,7 @@ int nc_create_par(const char *path, int cmode, MPI_Comm comm,
#endif /* USE_PARALLEL */
}

/** \ingroup datasets
/**
Open an existing netCDF file for parallel I/O.

This function opens an existing netCDF dataset for parallel I/O
Expand All @@ -58,7 +130,7 @@ path will return the same ncid value.
if it is on. This doesn't stop the HDF5 error stack from recording the
errors, it simply stops their display to the user through stderr.

\param path File name for netCDF dataset to be opened.
\param path File name for netCDF dataset to be opened.

\param mode The mode flag may include NC_WRITE (for read/write
access), NC_MPIIO or NC_MPIPOSIX (not both) for parallel netCDF-4 I/O,
Expand All @@ -77,23 +149,18 @@ occurred. Otherwise, the returned status indicates an error. Possible
causes of errors include:

\returns ::NC_NOERR No error.

\returns ::NC_EINVAL Invalid parameters.

\returns ::NC_ENOTNC Not a netCDF file.

\returns ::NC_ENOMEM Out of memory.

\returns ::NC_EHDFERR HDF5 error. (NetCDF-4 files only.)

\returns ::NC_EDIMMETA Error in netCDF-4 dimension metadata. (NetCDF-4
files only.)

<h1>Examples</h1>

Here is an example using nc_open_par() from examples/C/parallel_vara.c.

@code
\code
#include <mpi.h>
#include <netcdf.h>
#include <netcdf_par.h>
Expand All @@ -103,7 +170,9 @@ Here is an example using nc_open_par() from examples/C/parallel_vara.c.
...
omode = NC_PNETCDF | NC_NOWRITE;
err = nc_open_par(filename, omode, MPI_COMM_WORLD, MPI_INFO_NULL, &ncid); FATAL_ERR
@endcode
\endcode
\author Ed Hartnett, Dennis Heimbigner
\ingroup datasets
*/
int
nc_open_par(const char *path, int mode, MPI_Comm comm,
Expand All @@ -130,10 +199,39 @@ nc_open_par(const char *path, int mode, MPI_Comm comm,
#endif /* USE_PARALLEL */
}

/*! \ingroup datasets
/**
This is the same as nc_open_par(), but accepts the MPI comm/info as
integers.

\param path File name for netCDF dataset to be opened.

\param mode The mode flag may include NC_WRITE (for read/write
access), NC_MPIIO or NC_MPIPOSIX (not both) for parallel netCDF-4 I/O,
or NC_PNETCDF for parallel-netcdf parallel I/O access for a netCDF
classic or CDF5 file.

\param comm the MPI communicator to be used.

\param info MPI info or MPI_INFO_NULL.

Fortran needs to pass MPI comm/info as integers.
\param ncidp Pointer to location where returned netCDF ID is to be
stored.

nc_open_par() returns the value NC_NOERR if no errors
occurred. Otherwise, the returned status indicates an error. Possible
causes of errors include:

\returns ::NC_NOERR No error.
\returns ::NC_EINVAL Invalid parameters.
\returns ::NC_ENOTNC Not a netCDF file.
\returns ::NC_ENOMEM Out of memory.
\returns ::NC_EHDFERR HDF5 error. (NetCDF-4 files only.)
\returns ::NC_EDIMMETA Error in netCDF-4 dimension metadata. (NetCDF-4
files only.)

\author Ed Hartnett
\ingroup datasets
\internal
*/
int
nc_open_par_fortran(const char *path, int mode, int comm,
Expand All @@ -159,7 +257,6 @@ nc_open_par_fortran(const char *path, int mode, int comm,
#endif
}

/* */
/**\ingroup datasets

This function will change the parallel access of a variable from
Expand All @@ -174,13 +271,9 @@ nc_inq_ncid().
\param par_access NC_COLLECTIVE or NC_INDEPENDENT.

\returns ::NC_NOERR No error.

\returns ::NC_EBADID Invalid ncid passed.

\returns ::NC_ENOTVAR Invalid varid passed.

\returns ::NC_ENOPAR LFile was not opened with nc_open_par/nc_create_var.

\returns ::NC_EINVAL Invalid par_access specified.

<h1>Example</h1>
Expand Down Expand Up @@ -222,6 +315,8 @@ parallel access of a variable and then writes to it.
err = nc_put_vara_int(ncid, varid, start, count, &buf[0][0]); ERR

\endcode
\author Ed Hartnett, Dennis Heimbigner
\ingroup datasets
*/
int
nc_var_par_access(int ncid, int varid, int par_access)
Expand All @@ -240,7 +335,40 @@ nc_var_par_access(int ncid, int varid, int par_access)
#endif
}

/* when calling from fortran: convert MPI_Comm and MPI_Info to C */
/**
Create a netCDF file for parallel access from the Fortran API.

This function calls nc_create_par() after converting the MPI comm and
info from Fortran to C, if necessary.

\param path The file name of the new netCDF dataset.

\param cmode The creation mode flag. The following flags are available:
NC_NOCLOBBER (do not overwrite existing file),
NC_NETCDF4 (create netCDF-4/HDF5 file),
NC_CLASSIC_MODEL (enforce netCDF classic mode on netCDF-4/HDF5 files),
NC_PNETCDF.

\param comm the MPI communicator to be used.

\param info MPI info or MPI_INFO_NULL.

\param ncidp Pointer to location where returned netCDF ID is to be
stored.

\returns ::NC_NOERR No error.
\returns ::NC_ENOPAR Library was not built with parallel I/O features.
\returns ::NC_EINVAL Invalid input parameters.
\returns ::NC_ENOMEM System out of memory.
\returns ::NC_ENOTNC Binary format could not be determined.
\returns ::NC_EHDFERR HDF5 error (netCDF-4 files only).
\returns ::NC_EFILEMETA Error writing netCDF-4 file-level metadata in
HDF5 file. (netCDF-4 files only).

\author Ed Hartnett, Dennis Heimbigner
\ingroup datasets
\internal
*/
int
nc_create_par_fortran(const char *path, int cmode, int comm,
int info, int *ncidp)
Expand Down