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4.28 Nonblockingly Write a List of Subarrays: ncmpi_iput_varn_<type>

The ncmpi_iput_varn_<type> family of functions is the nonblocking version of ncmpi_put_varn_<type> family. The functions write, in a nonblocking fashion, a list of subarrays into a netCDF variable of an opened netCDF file.

A nonblocking put call indicates that the PnetCDF may start using (possible altering the contents of) the put buffer. The caller should not access any part of the put buffer after a nonblocking put is called, until the put completes.

The part of the netCDF variable to write is specified by giving a list of subarrays and each subarray is specified by a corner and a vector of edge lengths that refer to an array section of the netCDF variable. For each subarray, the values to be written are associated with the netCDF variable by assuming that the last dimension of the netCDF variable varies fastest in the C interface.

This API essentially has the same effect of making multiple calls to ncmpi_iput_vara_<type> with the same variable ID.

Data types

<type > for API names <C type> for API arguments
text char
schar signed char
short short
int int
float float
double double
uchar unsigned char
ushort unsigned short
uint unsigned int
longlong long long
ulonglong unsigned longlong

Operational Mode

Prior to version 1.7.0, nonblocking APIs must be called while the netCDF file is in data mode. Starting from 1.7.0, nonblocking APIs can be called in either define or data mode. This API family can be called in either collective or independent data mode.

Usage

int ncmpi_iput_varn_<type>     (int               ncid,
                                int               varid,
                                int               num,
                                const MPI_Offset  starts[num][],
                                const MPI_Offset  counts[num][],
                                const <C type>   *buf,
                                int              *request);

int ncmpi_iput_varn            (int               ncid,
                                int               varid,
                                int               num,
                                const MPI_Offset  starts[num][],
                                const MPI_Offset  counts[num][],
                                const void       *buf,
                                MPI_Offset        bufcount,
                                MPI_Datatype      buftype,
                                int              *request);
ncid

NetCDF ID, from a previous call to ncmpi_open or ncmpi_create.

varid

Variable ID. Different MPI processes may use different variable IDs.

num

Number of subarray requests.

starts

A double pointer that mimics a 2D array of size [num][ndims]. See below for example of how to allocate space and construct such a 2D array. Each starts[i] is a vector specifying the index in the variable where the first of the data values will be written. The indices are relative to 0, so for example, the first data value of a variable would have index (0, 0, ... , 0). The size of starts must be [num][ndims], where ndims is the number of dimensions of the specified variable. The elements of each starts[i] must correspond to the variable’s dimensions in order. Hence, if the variable is a record variable, the first index of each starts[i] would correspond to the starting record number for writing the data values.

counts

A double pointer that mimics a 2D array of size [num][ndims]. See below for example of how to allocate space and construct such a 2D array. Each counts[i] is a vector specifying the edge lengths along each dimension of the block of data values to be written. To write a single value, for example, specify count as (1, 1, ... , 1). The size of counts should be [num][ndims], where ndims is the number of dimensions of the specified variable. The elements of count correspond to the variable’s dimensions. Hence, if the variable is a record variable, the first element of each counts[i] corresponds to a count of the number of records to write. This argument can be NULL, in which case it is equivalent to providing counts[*][*]=(1, 1, ... , 1).

buf

A pointer to the memory address that contains the data values to be written. If the type of data values differs from the netCDF variable type, type conversion will occur.

bufcount

An integer indicates the number of MPI derived data type elements in the buffer pointed by buf to be written to the file.

buftype

An MPI derived data type that describes the memory layout of buf. Starting from PnetCDF version 1.6.0, buftype can be MPI_DATATYPE_NULL. In this case, bufcount is ignored and the buf’s data type must match the type of the variable defined in the file - no data conversion will be done.

request

The nonblocking request ID returned by PnetCDF. It is to be used in a successive call to ncmpi_wait_all() or ncmpi_wait() for the completion of the nonblocking operation.

Starting from 1.7.0, the request argument can be NULL, meaning the caller does not intend to track the requests IDs. In this case, a call to ncmpi_wait_all/ncmpi_wait must use NC_REQ_ALL in its second argument "num" to flush all pending nonblocking requests.

Return Error Codes

ncmpi_iput_varn_<type> returns the value NC_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include:

Example

This example shows how to use a single call of ncmpi_put_varn_float_all() to write a sequence of requests with arbitrary array indices. 

#include <pnetcdf.h>
    ...
#define MAX_NUM_REQS 6
#define NDIMS        2

int  i, j;
int  rank;                         /* MPI process rank ID */
int  err;                          /* error status */
int  ncid;                         /* netCDF ID */
int  varid;                        /* variable ID */
int  num_reqs;                     /* number of subarray requests */
int  dimid[2];                     /* dimension IDs */
int  request[1];                   /* nonblocking request ID */
int  st[1];                        /* nonblocking request status */
int  buf_len;                      /* number of elements in buffer */
float *buffer;                     /* write buffer to hold values */
MPI_Offset **starts, **counts;
    ...
MPI_Comm_rank(MPI_COMM_WORLD, &rank);

err = ncmpi_create(MPI_COMM_WORLD, "foo.nc", NC_CLOBBER, MPI_INFO_NULL, &ncid);

if (err != NC_NOERR) handle_error(err);

err = ncmpi_def_dim(ncid, "Y", 4,  &dimid[0]);
err = ncmpi_def_dim(ncid, "X", 10, &dimid[1]);
err = ncmpi_def_var(ncid, "var", NC_FLOAT, 2, dimid, &varid);
err = ncmpi_enddef(ncid);

/* allocate starts and counts */
starts    = (MPI_Offset**) malloc(MAX_NUM_REQS*       sizeof(MPI_Offset*));
starts[0] = (MPI_Offset*)  calloc(MAX_NUM_REQS*NDIMS, sizeof(MPI_Offset));
for (i=1; i<MAX_NUM_REQS; i++)
    starts[i] = starts[i-1] + NDIMS;

counts    = (MPI_Offset**) malloc(MAX_NUM_REQS*       sizeof(MPI_Offset*));
counts[0] = (MPI_Offset*)  calloc(MAX_NUM_REQS*NDIMS, sizeof(MPI_Offset));
for (i=1; i<MAX_NUM_REQS; i++)
    counts[i] = counts[i-1] + NDIMS;

if (rank == 0) {
    num_reqs = 4;
    starts[0][0] = 0; starts[0][1] = 5; counts[0][0] = 1; counts[0][1] = 2;
    starts[1][0] = 1; starts[1][1] = 0; counts[1][0] = 1; counts[1][1] = 1;
    starts[2][0] = 2; starts[2][1] = 6; counts[2][0] = 1; counts[2][1] = 2;
    starts[3][0] = 3; starts[3][1] = 0; counts[3][0] = 1; counts[3][1] = 3;
    /* rank 0 is writing the following locations: ("-" means skip)
              -  -  -  -  -  0  0  -  -  - 
              0  -  -  -  -  -  -  -  -  - 
              -  -  -  -  -  -  0  0  -  - 
              0  0  0  -  -  -  -  -  -  - 
     */
} else if (rank == 1) {
    num_reqs = 6;
    starts[0][0] = 0; starts[0][1] = 3; counts[0][0] = 1; counts[0][1] = 2;
    starts[1][0] = 0; starts[1][1] = 8; counts[1][0] = 1; counts[1][1] = 2;
    starts[2][0] = 1; starts[2][1] = 5; counts[2][0] = 1; counts[2][1] = 2;
    starts[3][0] = 2; starts[3][1] = 0; counts[3][0] = 1; counts[3][1] = 2;
    starts[4][0] = 2; starts[4][1] = 8; counts[4][0] = 1; counts[4][1] = 2;
    starts[5][0] = 3; starts[5][1] = 4; counts[5][0] = 1; counts[5][1] = 3;
    /* rank 1 is writing the following locations: ("-" means skip)
              -  -  -  1  1  -  -  -  1  1 
              -  -  -  -  -  1  1  -  -  - 
              1  1  -  -  -  -  -  -  1  1 
              -  -  -  -  1  1  1  -  -  - 
     */
} else if (rank == 2) {
    num_reqs = 5;
    starts[0][0] = 0; starts[0][1] = 7; counts[0][0] = 1; counts[0][1] = 1;
    starts[1][0] = 1; starts[1][1] = 1; counts[1][0] = 1; counts[1][1] = 3;
    starts[2][0] = 1; starts[2][1] = 7; counts[2][0] = 1; counts[2][1] = 3;
    starts[3][0] = 2; starts[3][1] = 2; counts[3][0] = 1; counts[3][1] = 1;
    starts[4][0] = 3; starts[4][1] = 3; counts[4][0] = 1; counts[4][1] = 1;
    /* rank 2 is writing the following locations: ("-" means skip)
              -  -  -  -  -  -  -  2  -  - 
              -  2  2  2  -  -  -  2  2  2 
              -  -  2  -  -  -  -  -  -  - 
              -  -  -  2  -  -  -  -  -  - 
     */
} else if (rank == 3) {
    num_reqs = 4;
    starts[0][0] = 0; starts[0][1] = 0; counts[0][0] = 1; counts[0][1] = 3;
    starts[1][0] = 1; starts[1][1] = 4; counts[1][0] = 1; counts[1][1] = 1;
    starts[2][0] = 2; starts[2][1] = 3; counts[2][0] = 1; counts[2][1] = 3;
    starts[3][0] = 3; starts[3][1] = 7; counts[3][0] = 1; counts[3][1] = 3;
    /* rank 3 is writing the following locations: ("-" means skip)
              3  3  3  -  -  -  -  -  -  - 
              -  -  -  -  3  -  -  -  -  - 
              -  -  -  3  3  3  -  -  -  - 
              -  -  -  -  -  -  -  3  3  3 
     */
} else {
    num_reqs = 0;
}

/* allocate write buffer */
buf_len = 0;
for (i=0; i<num_reqs; i++) {
    MPI_Offset w_req_len=1;
    for (j=0; j<NDIMS; j++)
        w_req_len *= counts[i][j];
    buf_len += w_req_len;
}
buffer = (float*) malloc(buf_len * sizeof(float));
for (i=0; i<buf_len; i++) buffer[i] = (float)rank;

 /* write values into netCDF variable */
 err = ncmpi_iput_varn_float(ncid, varid, num_reqs, starts, counts, buffer, &request[0]);
 if (err != NC_NOERR) handle_error(err);
    ...
 /* wait for the nonblocking operation to complete */
 status = ncmpi_wait_all(ncid, 1, request, st);
 if (status != NC_NOERR) handle_error(status);

 err = ncmpi_close(ncid);
 if (err != NC_NOERR) handle_error(err);

/*    % ncmpidump foo.nc
 *    netcdf foo {
 *    dimensions:
 *             Y = 4 ;
 *             X = 10 ;
 *    variables:
 *             float var(Y, X) ;
 *    data:
 *
 *     var =
 *       3, 3, 3, 1, 1, 0, 0, 2, 1, 1,
 *       0, 2, 2, 2, 3, 1, 1, 2, 2, 2,
 *       1, 1, 2, 3, 3, 3, 0, 0, 1, 1,
 *       0, 0, 0, 2, 1, 1, 1, 3, 3, 3 ;
 *    }
 */

Full example C program

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