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[netCDF #VRF-491011]: Malloc and nc_put_var___

Hi Edin,

> I am using netCDF library to save my data sets. I didn't have much trouble
> using it until I faced the problem of saving the multidimensional array of
> data which memory space was dynamically allocated during the process.
> When dynamic allocation of single variable array was performed in contiguous
> way, use of nc_put_var_ resulted in correct data set. However, when memory
> for structured array is dynamically allocated in non contiguous way (relying
> on pointers to guide me thru the data), then, as expected, simple use of
> nc_put_var_ was not successful.
>
> Could you please advise what are my potential solutions to storing a
> variable pointer array into netCDF data set.
> I included some portions of my code for your convenience.

If you are using netCDF-3, I suggest you store the data in pieces,
each Z_SIZE values of a single parameter, in a nested loop for X_SIZE
and Y_SIZE.  There is no way to store all the values scattered all
over memory with pointers returned from calloc using
nc_put_varm_TYPE() calls, as these only handle regular spacing in
memory determined by a linear function of the indices.

So the psuedocode for writing out all the data might be something
like:

for (x = 0; x < X_SIZE; x++) {
   for (y = 0; y < Y_SIZE; y++) {
      start[0] = x;
      start[1] = y;
      start[2] = 0;
      count[0] = 1;
      count[1] = 1;
      count[2] = Z_SIZE;
      stride[0] = 1;
      stride[1] = 1;
      stride[2] = 1;
      imap[0] = 1; /* doesn't matter, won't be used */
      imap[1] = 1; /* doesn't matter, won't be used */
      imap[2] = sizeof(NODE_STRUCT);
      /* write subsampled or mapped array of values into netCDF variable */
      nc_put_varm_float(ncid, Refl_id, start, count, stride, imap,
                        &cart_grid[x][y][0].Refl);
      nc_put_varm_float(ncid, Vel_id, start, count, stride, imap,
                        &cart_grid[x][y][0].Vel);
       ...
      nc_put_varm_int(ncid, Cnt_id, start, count, stride, imap,
                        &cart_grid[x][y][0].Cnt);
   }
}

Another suggestion is to consider using netCDF-4, which permits
writing all the values of a C struct at once into a netCDF variable of
user-defined type, where you define the type to correspond to your
NODE_STRUCT.  That would permit making only a single nc_put_var() call
within the nested loops above to replace the 14 calls for each struct
member individually, but you would still need the nested loops on x
and y.

--Russ

Russ Rew                                         UCAR Unidata Program
address@hidden                     http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: VRF-491011
Department: Support netCDF
Priority: Normal
Status: Closed