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gpuncfunctions.cpp
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gpuncfunctions.cpp
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//#include"nctest.h"
#include "gpuuebpgdecls.h"
//read multiple slubs (y,x arrays) along the time dim (for interval between tstart --- tend)
__host__ __device__ int readNC_yxSlub(const char* FILE_NAME, const char* VAR_NAME, const char* tcor_NAME, int &tStart, int tEnd,
float*** &pvar_in, int &nrecords, int &numNc, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//float* pvarin_temp = NULL;
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0; // pxid = 0, pyid = 0, ndims = 0;
//variable data type
nc_type varType;
size_t pdim_sizes;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error message otherwise
//dimension names
char pdim_Names[80];
size_t start[3], count[3];
//Open the netcdf file.
if ((retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid)))
ERR(retncval);
//var information, checking the dimension array
if ((retncval = nc_inq_var(ncid, pvarid, NULL, &varType, NULL, pdimids, NULL)))
ERR(retncval);
//parallel access mode
if (retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE))
ERR(retncval);
//check dimension info and set start and count arrays;
//int yxDim = 1;
for (int i = 0; i < 3; i++) {
if (retncval = nc_inq_dim(ncid, pdimids[i], pdim_Names, &pdim_sizes))
ERR(retncval);
if (strcmp(pdim_Names, tcor_NAME) == 0){
start[i] = tStart;
if (tEnd < pdim_sizes){
count[i] = tEnd - tStart;
tStart += count[i]; //new start point
}
else{
count[i] = pdim_sizes - tStart; //take the lower of the tEnd/count[i] to guarantee against going out of bounds
numNc++; //next time go to the next netcdf file
tStart = 0;
}
nrecords = count[i];
}
else{
start[i] = 0;
count[i] = pdim_sizes;
//yxDim *= count[i];
}
}
if (pvar_in != NULL)
delete3DArrayblock_Contiguous(pvar_in);
pvar_in = create3DArrayblock_Contiguous(count[0], count[1], count[2]);
//read var data
if (retncval = nc_get_vara_float(ncid, pvarid, start, count, &pvar_in[0][0][0]))
ERR(retncval);
//close netcdf file
if (retncval = nc_close(ncid))
ERR(retncval);
return 0;
}
//read multiple slubs (y,x arrays) along the time dim for data with t, y, x config---time as slowely varying array; and pvar_in already allocated
__host__ __device__ int readNC_yxSlub_givenT(const char* FILE_NAME, const char* VAR_NAME, const char* tcor_NAME, const char* ycor_NAME, const char* xcor_NAME, int &tStart, int tEnd,
int Nydim, int Nxdim, float*** pvar_in, int &nrecords, int &numNc, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//float* pvarin_temp = NULL;
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0; // pxid = 0, pyid = 0, ndims = 0;
//variable data type
nc_type varType;
size_t pdim_sizes;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error message otherwise
//dimension names
char pdim_Names[80];
size_t start[3], count[3];
//Open the netcdf file.
if ((retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid)))
ERR(retncval);
//var information, checking the dimension array
if ((retncval = nc_inq_var(ncid, pvarid, NULL, &varType, NULL, pdimids, NULL)))
ERR(retncval);
//check dimension info and set start and count arrays;
//int yxDim = 1;
int tDim = 24;
int tIndx = 0;
for (int i = 0; i < 3; i++) {
if (retncval = nc_inq_dim(ncid, pdimids[i], pdim_Names, &pdim_sizes))
ERR(retncval);
if (strcmp(pdim_Names, tcor_NAME) == 0){
tIndx = i;
start[i] = tStart;
if (tEnd < pdim_sizes){
count[i] = 1;
tDim = tEnd - tStart;
tStart += tDim; // count[i]; //new start point
}
else{
count[i] = 1;
tDim = pdim_sizes - tStart; //take the lower of the tEnd/count[i] to guarantee against going out of bounds
numNc++; //next time go to the next netcdf file
tStart = 0;
}
nrecords = tDim; // count[i];
}
else if (strcmp(pdim_Names, ycor_NAME) == 0){
start[i] = 0;
count[i] = Nydim;
}
else
{
start[i] = 0;
count[i] = Nxdim;
}
//start[i] = 0; count[i] = pdim_sizes;
//yxDim *= count[i]; }
}
/*if (pvar_in != NULL)
delete3DArrayblock_Contiguous(pvar_in);
pvar_in = create3DArrayblock_Contiguous(count[0], count[1], count[2]);*/
//parallel access mode
if ((retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE)))
ERR(retncval);
for (int tk = 0; tk < tDim; tk++)
{
start[tIndx] += tk;//read var data
if (retncval = nc_get_vara_float(ncid, pvarid, start, count, &pvar_in[tk][0][0]))
ERR(retncval);
}
//close netcdf file
if (retncval = nc_close(ncid))
ERR(retncval);
return 0;
}
//read whole nc array for a given variable to contiguous 1d array; the y,x,time order is irrelevant inside the function, but it is assumed known by caller,
__host__ __device__ int readNC_Contiguous(const char* FILE_NAME, const char* VAR_NAME, const char* tcor_NAME, int &Ntdim, float* &pvar_in, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0;
//size_t pdim_sizes;
//variable data type
nc_type varType;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error message otherwise
//dimension names
char pdim_Names[80];
size_t start[3], count[3];
//dimensions lengths
//size_t Ntdim = 0, Nxdim = 0, Nydim = 0;
//Open the file.
if (retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid)))
ERR(retncval);
//var information, checking the dimension array
if ((retncval = nc_inq_var(ncid, pvarid, NULL, &varType, NULL, pdimids, NULL)))
ERR(retncval);
//check dimension info and set start and count arrays;
for (int i = 0; i < 3; i++)
{
if (retncval = nc_inq_dim(ncid, pdimids[i], pdim_Names, &count[i]))
ERR(retncval);
//start[i] = 0;
if (strcmp(pdim_Names, tcor_NAME) == 0)
Ntdim = (int) count[i];
}
//free memory
if (pvar_in !=NULL)
delete[] pvar_in;
//create the output arrays
pvar_in = new float[count[0] * count[1] * count[2]]; // create3DArrayblock_Contiguous(count[0], count[1], count[2]); // (Ntdim, Nydim, Nxdim);
//parallel access mode
if (retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE))
ERR(retncval);
//read variable (input data)
if (retncval = nc_get_var_float(ncid, pvarid, &pvar_in[0]))
ERR(retncval);
//close netcdf file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//cout << "SUCCESS reading input file: " << FILE_NAME << endl;
return 0;
}
//read whole nc array for a given variable to contiguous 3d array; the y,x,time order is irrelevant inside the function, but it is assumed known by caller,
__host__ __device__ int read3DNC_Contiguous(const char* FILE_NAME, const char* VAR_NAME, const char* tcor_NAME, int &Ntdim, float*** &pvar_in, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0;
//size_t pdim_sizes;
//variable data type
nc_type varType;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error message otherwise
//dimension names
char pdim_Names[80];
size_t start[3], count[3];
//dimensions lengths
//size_t Ntdim = 0, Nxdim = 0, Nydim = 0;
//Open the file.
if (retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid))
ERR(retncval);
// get variable id
if (retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid))
ERR(retncval);
//var information, checking the dimension array
if (retncval = nc_inq_var(ncid, pvarid, NULL, &varType, NULL, pdimids, NULL))
ERR(retncval);
//check dimension info and set start and count arrays;
for (int i = 0; i < 3; i++)
{
if (retncval = nc_inq_dim(ncid, pdimids[i], pdim_Names, &count[i]))
ERR(retncval);
//start[i] = 0;
if (strcmp(pdim_Names, tcor_NAME) == 0)
Ntdim = (int)count[i];
}
//create the output arrays
//free existing memory
if (pvar_in != NULL)
delete3DArrayblock_Contiguous(pvar_in);
pvar_in = create3DArrayblock_Contiguous(count[0], count[1], count[2]); // (Ntdim, Nydim, Nxdim); new float(count[0] * count[1] * count[2]);
//parallel access mode
if (retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE))
ERR(retncval);
//read variable (input data)
if (retncval = nc_get_var_float(ncid, pvarid, &pvar_in[0][0][0]))
ERR(retncval);
//close netcdf file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//cout << "SUCCESS reading input file: " << FILE_NAME << endl;
return 0;
}
//read nc to contiguous 1d array; y,x,time coordinate names are same as index names
__host__ __device__ int readNC_Contiguous(const char* FILE_NAME, const char* VAR_NAME, const char* tcor_NAME, const char* ycor_NAME, const char* xcor_NAME,
float* tcorvar, float* ycorvar, float* xcorvar, size_t &Ntdim, size_t &Nydim, size_t &Nxdim, float* &pvar_in, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0, ptid = 0, ndims = 0;
size_t pdim_sizes;
//variable data type
nc_type varType;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error message otherwise
//dimension names
char pdim_Names[80];
size_t start[3], count[3];
//dimensions lengths
//size_t Ntdim = 0, Nxdim = 0, Nydim = 0;
//Open the file.
if (retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid))
ERR(retncval);
// get variable id
if (retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid))
ERR(retncval);
// Get the varids of the coordinate variables
if (retncval = nc_inq_varid(ncid, tcor_NAME, &ptid))
ERR(retncval);
if (retncval = nc_inq_varid(ncid, ycor_NAME, &pyid))
ERR(retncval);
if (retncval = nc_inq_varid(ncid, xcor_NAME, &pxid))
ERR(retncval);
//var information, checking the dimension array
if ((retncval = nc_inq_var(ncid, pvarid, NULL, &varType, NULL, pdimids, NULL)))
ERR(retncval);
//check dimension info and set start and count arrays;
for (int i = 0; i < 3; i++)
{
if ((retncval = nc_inq_dim(ncid, pdimids[i], pdim_Names, &pdim_sizes)))
ERR(retncval);
if (strcmp(pdim_Names, tcor_NAME) == 0)
{
start[i] = 0;
Ntdim = pdim_sizes;
count[i] = Ntdim;
tcorvar = new float[Ntdim];
}
else if (strcmp(pdim_Names, ycor_NAME) == 0)
{
start[i] = 0;
Nydim = pdim_sizes;
count[i] = Nydim;
ycorvar = new float[Nydim];
}
else
{
start[i] = 0;
Nxdim = pdim_sizes;
count[i] = Nxdim;
xcorvar = new float[Nxdim];
}
}
//create the output arrays
if (pvar_in != NULL)
delete[] pvar_in;
pvar_in = new float[count[0] * count[1] * count[2]]; // create3DArrayblock_Contiguous(count[0], count[1], count[2]); // (Ntdim, Nydim, Nxdim);
//parallel access mode
if (retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, ptid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, pyid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, pxid, NC_COLLECTIVE))
ERR(retncval);
// Read the coordinate (dimensions) variable data.
if (retncval = nc_get_var_float(ncid, ptid, &tcorvar[0]))
ERR(retncval);
if (retncval = nc_get_var_float(ncid, pyid, &ycorvar[0]))
ERR(retncval);
if (retncval = nc_get_var_float(ncid, pxid, &xcorvar[0]))
ERR(retncval);
//read variable (input data)
if (retncval = nc_get_var_float(ncid, pvarid, &pvar_in[0]))
ERR(retncval);
//close netcdf file
if (retncval = nc_close(ncid))
ERR(retncval);
//cout << "SUCCESS reading input file: " << FILE_NAME << endl;
return 0;
}
//read 3d nc to contiguous array; y,x,time coordinate names are same as index names
__host__ __device__ int read3DNC_Contiguous(const char* FILE_NAME, const char* VAR_NAME, const char* tcor_NAME, const char* ycor_NAME, const char* xcor_NAME,
float* tcorvar, float* ycorvar, float* xcorvar, size_t &Ntdim, size_t &Nydim, size_t &Nxdim, float*** &pvar_in, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0, ptid = 0, ndims = 0;
//dimensions lengths
size_t pdim_sizes;
//variable data type
nc_type varType;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error message otherwise
//dimension names
char pdim_Names[80];
size_t start[3], count[3];
//dimensions lengths
//size_t Ntdim = 0, Nxdim = 0, Nydim = 0;
//Open the file.
if ((retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, tcor_NAME, &ptid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, ycor_NAME, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xcor_NAME, &pxid)))
ERR(retncval);
//var information, checking the dimension array
if ((retncval = nc_inq_var(ncid, pvarid, NULL, &varType, NULL, pdimids, NULL)))
ERR(retncval);
//check dimension info and set start and count arrays;
for (int i = 0; i < 3; i++)
{
if ((retncval = nc_inq_dim(ncid, pdimids[i], pdim_Names, &pdim_sizes)))
ERR(retncval);
if (strcmp(pdim_Names, tcor_NAME) == 0)
{
start[i] = 0;
Ntdim = pdim_sizes;
count[i] = Ntdim;
tcorvar = new float[Ntdim];
}
else if (strcmp(pdim_Names, ycor_NAME) == 0)
{
start[i] = 0;
Nydim = pdim_sizes;
count[i] = Nydim;
ycorvar = new float[Nydim];
}
else
{
start[i] = 0;
Nxdim = pdim_sizes;
count[i] = Nxdim;
xcorvar = new float[Nxdim];
}
}
//free existing memory
if (pvar_in != NULL)
delete3DArrayblock_Contiguous(pvar_in);
//create the output arrays
pvar_in = create3DArrayblock_Contiguous(count[0], count[1], count[2]); // (Ntdim, Nydim, Nxdim);
//parallel access mode
if (retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, ptid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, pyid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, pxid, NC_COLLECTIVE))
ERR(retncval);
/* Read the coordinate (dimensions) variable data. */
if (retncval = nc_get_var_float(ncid, ptid, &tcorvar[0]))
ERR(retncval);
if (retncval = nc_get_var_float(ncid, pyid, &ycorvar[0]))
ERR(retncval);
if (retncval = nc_get_var_float(ncid, pxid, &xcorvar[0]))
ERR(retncval);
//read variable (input data)
if (retncval = nc_get_var_float(ncid, pvarid, &pvar_in[0][0][0]))
ERR(retncval);
//close netcdf file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//cout<<"SUCCESS reading input file: "<< FILE_NAME<<endl;
return 0;
}
//writes the 1D array (TS values) at specified location in the netcdf
__host__ __device__ int WriteTSto3DNC(const char* FileName, const char* VarName, int dimOrd, int y_dim, int x_dim, int Nt_dim, float* var_inp, MPI::Intracomm inpComm, MPI::Info inpInfo) //ydim, xdim =the coordinate point the data to be written; Nt_dim =the length of the TS
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if (retncval = nc_open_par(FileName, NC_WRITE | NC_MPIIO, inpComm, inpInfo, &ncid))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VarName, &v_varid)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch (dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = y_dim;
start[2] = x_dim;
count[0] = Nt_dim;
count[1] = 1;
count[2] = 1;
break;
case 1: //y,x,t
start[0] = y_dim;
start[1] = x_dim;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = Nt_dim;
break;
case 2: //x,t,y
start[0] = x_dim;
start[1] = 0;
start[2] = y_dim;
count[0] = 1;
count[1] = Nt_dim;
count[2] = 1;
break;
default:
cout << "the dim order has to be between 0 and 2" << endl;
getchar();
break;
}
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid, NC_COLLECTIVE)))
ERR(retncval);
//put variable values
if ((retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[0])))
ERR(retncval);
//close file
if (retncval = nc_close(ncid))
ERR(retncval);
//fflush(stdout);
return 0;
}
//writes multiple 1D arrays (TS values) at specified locations in the netcdf
__host__ __device__ int WriteTSto3DNC_Block(const char* FileName, const char* VarName, int dimOrd, int *YindArr, int *XindArr, int bSize, int Nt_dim, float** var_inp, MPI::Intracomm inpComm, MPI::Info inpInfo) //ydim, xdim =the coordinate point the data to be written; Nt_dim =the length of the TS
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if (retncval = nc_open_par(FileName, NC_WRITE | NC_MPIIO, inpComm, inpInfo, &ncid))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VarName, &v_varid)))
ERR(retncval);
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid, NC_COLLECTIVE)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
for (int j = 0; j < bSize; j++)
{
switch (dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = YindArr[j]; // y_dim;
start[2] = XindArr[j]; // x_dim;
count[0] = Nt_dim;
count[1] = 1;
count[2] = 1;
break;
case 1: //y,x,t
start[0] = YindArr[j]; // y_dim;
start[1] = XindArr[j]; // x_dim;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = Nt_dim;
break;
case 2: //x,t,y
start[0] = XindArr[j]; // x_dim;
start[1] = 0;
start[2] = YindArr[j]; // y_dim;
count[0] = 1;
count[1] = Nt_dim;
count[2] = 1;
break;
default:
cout << "the dim order has to be between 0 and 2" << endl;
getchar();
break;
}
//put variable values
if (retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[j][0]))
ERR(retncval);
}
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//fflush(stdout);
return 0;
}
//aggregate outputs at specified zone in the netcdf
__host__ __device__ int Write_uebaggTS_toNC(const char* FileName, const char* VarName, int dimOrd, int z_dim, int Nt_dim, float* var_inp)
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if ((retncval = nc_open(FileName, NC_WRITE, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VarName, &v_varid)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch (dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = z_dim;
count[0] = Nt_dim;
count[1] = 1;
break;
case 1: //y,x,t
start[0] = z_dim;
start[1] = 0;
count[0] = 1;
count[1] = Nt_dim;
break;
default:
cout << "the dim order has to be 0 or 1" << endl;
getchar();
break;
}
//put variable values
if (retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[0]))
ERR(retncval);
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//fflush(stdout);
return 0;
}
//aggregate outputs at specified zone in the netcdf in parallel
__host__ __device__ int Write_uebaggTS_toNC_par(const char* FileName, const char* VarName, int dimOrd, int z_dim, int Nt_dim, float* var_inp, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if ((retncval = nc_open_par(FileName, NC_WRITE | NC_MPIIO, inpComm, inpInfo, &ncid))) //|NC_MPIIO, MPI::COMM_WORLD, MPI::INFO_NULL, &ncid)))
ERR(retncval);
// get variable id
if (retncval = nc_inq_varid(ncid, VarName, &v_varid))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch (dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = z_dim;
count[0] = Nt_dim;
count[1] = 1;
break;
case 1: //y,x,t
start[0] = z_dim;
start[1] = 0;
count[0] = 1;
count[1] = Nt_dim;
break;
default:
cout << "the dim order has to be 0 or 1" << endl;
getchar();
break;
}
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid, NC_INDEPENDENT)))
ERR(retncval);
//put variable values
if (retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[0]))
ERR(retncval);
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//fflush(stdout);
return 0;
}
//creates 2D netcdf and stores dimension variables for UEB aggregated outputs; some attributes are copied from the watershed netCDF
__host__ __device__ int create3DNC_uebAggregatedOutputs(const char* FileName, aggOutput *aggOut, int naggOut, const char* tName, const char* tUnits, const char* tlong_name, const char* tcalendar, int Nt_dim, int dimOrd,
float* t_inp, float *fillVal, const char* ws_FileName, const char* ws_VarName, const char* yName, const char* xName, int nZones, const char * zName, float* y_inp, float* x_inp)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0;
//info from watershed nc
if ((retncval = nc_open(ws_FileName, NC_NOWRITE, &ncid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, ws_VarName, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, yName, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xName, &pxid)))
ERR(retncval);
//dimensions lengths
size_t Nzdim = nZones;
//3D outputs nc
int ncid_out = 0, pzid_out = 0, ptid_out = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0, gridmap_id = 0;
//attributes
int natts = 0;
size_t att_len;
void * attValue;
nc_type attType;
char attName[256]; // = {}; // "grid_mapping_or_any_other_long_enough_name";
char grid_mappingValue[256] = {NULL}; // "grid_mapping_or_any_other_long_enough_name";
const char* fillValueName = "_FillValue";
//float missVal = -9999;
const int NDIMS = 2;
int dimids[NDIMS];
int oldFill = 0;
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Create netcdf file.
if ((retncval = nc_create(FileName, NC_NETCDF4 | NC_CLOBBER, &ncid_out)))
ERR(retncval);
//?? set fill on
if ((retncval = nc_set_fill(ncid_out, NC_FILL, &oldFill)))
ERR(retncval);
//copy global attributes from the ws nc
if (retncval = nc_inq_natts(ncid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, NC_GLOBAL, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, NC_GLOBAL, (const char*)attName, ncid_out, NC_GLOBAL))
ERR(retncval);
}
/* Define the dimensions. record dim can be unlimited*/
if (retncval = nc_def_dim(ncid_out, tName, Nt_dim, &ptid_out))
ERR(retncval);
if (retncval = nc_def_dim(ncid_out, zName, Nzdim, &pzid_out))
ERR(retncval);
switch (dimOrd)
{
case 0:
dimids[0] = ptid_out;
dimids[1] = pzid_out;
break;
case 1:
dimids[0] = pzid_out;
dimids[1] = ptid_out;
break;
default:
cout << "the dim order has to be either 0 or 1" << endl;
getchar();
break;
}
// Define variables
for (int ivar = 0; ivar < naggOut; ivar++)
{
if (retncval = nc_def_var(ncid_out, (const char*) aggOut[ivar].symbol, NC_FLOAT, NDIMS, dimids, &v_varid))
ERR(retncval);
//assign fill value
if (retncval = nc_put_att_float(ncid_out, v_varid, fillValueName, NC_FLOAT, 1, fillVal))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if (retncval = nc_put_att_text(ncid_out, v_varid, "units", strlen((const char*)aggOut[ivar].units), (const char*)aggOut[ivar].units))
ERR(retncval);
//grid mapping (projection) attribute
if (retncval = nc_copy_att(ncid, pvarid, "grid_mapping", ncid_out, v_varid))
ERR(retncval);
}
//variable containing info about projection / grid mapping
if (retncval = nc_get_att_text(ncid, pvarid, "grid_mapping", grid_mappingValue))
ERR(retncval);
if (retncval = nc_inq_varid(ncid, (const char*)grid_mappingValue, &gridmap_id))
ERR(retncval);
if (retncval = nc_copy_var(ncid, gridmap_id, ncid_out))
ERR(retncval);
//time variable
if (retncval = nc_def_var(ncid_out, tName, NC_FLOAT, 1, &ptid_out, &t_varid))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "units", strlen(tUnits), tUnits))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "long_name", strlen(tlong_name), tlong_name))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "calendar", strlen(tcalendar), tcalendar))
ERR(retncval);
// y and x vars
if (retncval = nc_def_var(ncid_out, yName, NC_FLOAT, 1, &pzid_out, &y_varid))
ERR(retncval);
if (retncval = nc_def_var(ncid_out, xName, NC_FLOAT, 1, &pzid_out, &x_varid))
ERR(retncval);
if (retncval = nc_inq_varnatts(ncid, pyid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pyid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pyid, (const char*)attName, ncid_out, y_varid))
ERR(retncval);
}
if (retncval = nc_inq_varnatts(ncid, pxid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pxid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pxid, (const char*)attName, ncid_out, x_varid))
ERR(retncval);
}
//put values to dim variables
if (retncval = nc_put_var_float(ncid_out, t_varid, &t_inp[0]))
ERR(retncval);
if (retncval = nc_put_var_float(ncid_out, y_varid, &y_inp[0]))
ERR(retncval);
if (retncval = nc_put_var_float(ncid_out, x_varid, &x_inp[0]))
ERR(retncval);
//close files
if (retncval = nc_close(ncid))
ERR(retncval);
if (retncval = nc_close(ncid_out))
ERR(retncval);
cout << "Sucess creating and storing dimension vars in: " << FileName << endl;
//fflush(stdout);
return 0;
}
//creates 3D netcdf in PARALLEL mode, and stores dimension variables for UEB aggregated outputs; some attributes are copied from the watershed netCDF
__host__ __device__ int create3DNC_uebAggregatedOutputs_par(const char* FileName, aggOutput *aggOut, int naggOut, const char* tName, const char* tUnits, const char* tlong_name, const char* tcalendar, int Nt_dim, int dimOrd,
float* t_inp, float *fillVal, const char* ws_FileName, const char* ws_VarName, const char* yName, const char* xName, int nZones, const char * zName, float* y_inp, float* x_inp, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0;
//info from watershed nc
if ((retncval = nc_open_par(ws_FileName, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, ws_VarName, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, yName, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xName, &pxid)))
ERR(retncval);
//dimensions lengths
size_t Nzdim = nZones;
//3D outputs nc
int ncid_out = 0, pzid_out = 0, ptid_out = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0, gridmap_id = 0;
//attributes
int natts = 0;
size_t att_len;
void * attValue;
nc_type attType;
char attName[256]; // = {}; // "grid_mapping_or_any_other_long_enough_name";
char grid_mappingValue[256] = { NULL }; // "grid_mapping_or_any_other_long_enough_name";
const char* fillValueName = "_FillValue";
//float missVal = -9999;
const int NDIMS = 2;
int dimids[NDIMS];
int oldFill = 0;
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Create netcdf file.
if ((retncval = nc_create_par(FileName, NC_NETCDF4 | NC_MPIIO | NC_CLOBBER, inpComm, inpInfo, &ncid_out)))
ERR(retncval);
//?? set fill on
if ((retncval = nc_set_fill(ncid_out, NC_FILL, &oldFill)))
ERR(retncval);
//copy global attributes from the ws nc
if (retncval = nc_inq_natts(ncid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, NC_GLOBAL, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, NC_GLOBAL, (const char*)attName, ncid_out, NC_GLOBAL))
ERR(retncval);
}
/* Define the dimensions. record dim can be unlimited*/
if (retncval = nc_def_dim(ncid_out, tName, Nt_dim, &ptid_out))
ERR(retncval);
if (retncval = nc_def_dim(ncid_out, zName, Nzdim, &pzid_out))
ERR(retncval);
switch (dimOrd)
{
case 0:
dimids[0] = ptid_out;
dimids[1] = pzid_out;
break;
case 1:
dimids[0] = pzid_out;
dimids[1] = ptid_out;
break;
default:
cout << "the dim order has to be either 0 or 1" << endl;
getchar();
break;
}
// Define variables
for (int ivar = 0; ivar < naggOut; ivar++)
{
if (retncval = nc_def_var(ncid_out, (const char*)aggOut[ivar].symbol, NC_FLOAT, NDIMS, dimids, &v_varid))
ERR(retncval);
//assign fill value
if (retncval = nc_put_att_float(ncid_out, v_varid, fillValueName, NC_FLOAT, 1, fillVal))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if (retncval = nc_put_att_text(ncid_out, v_varid, "units", strlen((const char*)aggOut[ivar].units), (const char*)aggOut[ivar].units))
ERR(retncval);
//grid mapping (projection) attribute
if (retncval = nc_copy_att(ncid, pvarid, "grid_mapping", ncid_out, v_varid))
ERR(retncval);
}
//variable containing info about projection / grid mapping
if (retncval = nc_get_att_text(ncid, pvarid, "grid_mapping", grid_mappingValue))
ERR(retncval);
if (retncval = nc_inq_varid(ncid, (const char*)grid_mappingValue, &gridmap_id))
ERR(retncval);
if (retncval = nc_copy_var(ncid, gridmap_id, ncid_out))
ERR(retncval);
//time variable
if (retncval = nc_def_var(ncid_out, tName, NC_FLOAT, 1, &ptid_out, &t_varid))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "units", strlen(tUnits), tUnits))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "long_name", strlen(tlong_name), tlong_name))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "calendar", strlen(tcalendar), tcalendar))
ERR(retncval);
// y and x vars
if (retncval = nc_def_var(ncid_out, yName, NC_FLOAT, 1, &pzid_out, &y_varid))
ERR(retncval);
if (retncval = nc_def_var(ncid_out, xName, NC_FLOAT, 1, &pzid_out, &x_varid))
ERR(retncval);
if (retncval = nc_inq_varnatts(ncid, pyid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pyid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pyid, (const char*)attName, ncid_out, y_varid))
ERR(retncval);
}
if (retncval = nc_inq_varnatts(ncid, pxid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pxid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pxid, (const char*)attName, ncid_out, x_varid))
ERR(retncval);
}
//parallel access mode
if ((retncval = nc_var_par_access(ncid_out, v_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, t_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, y_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, x_varid, NC_COLLECTIVE)))
ERR(retncval);
//put values to dim variables
if (retncval = nc_put_var_float(ncid_out, t_varid, &t_inp[0]))
ERR(retncval);
if (retncval = nc_put_var_float(ncid_out, y_varid, &y_inp[0]))
ERR(retncval);
if (retncval = nc_put_var_float(ncid_out, x_varid, &x_inp[0]))
ERR(retncval);
//close files
if (retncval = nc_close(ncid))
ERR(retncval);
if (retncval = nc_close(ncid_out))
ERR(retncval);
cout << "Sucess creating and storing dimension vars in: " << FileName << endl;
//fflush(stdout);
return 0;
}
//creates 3D netcdf and stores dimension variables for a given UEB output; called once for a given output netcdf
//attributes are copied from the 2D (watershed) netCDF which the 3D netCDF spatial dimension follow
__host__ __device__ int create3DNC_uebOutputs(const char* FileName, const char* VarName, const char *varUnits, const char* tName, const char* tUnits, const char* tlong_name,
const char* tcalendar, int Nt_dim, int dimOrd, float* t_inp, float *fillVal, const char* ws_FileName, const char* ws_VarName, const char* yName, const char* xName, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//const char* yUnits, const char* xUnits;
float* y_inp;
float* x_inp;
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0, ndims = 0;
//dimensions lengths
size_t Nxdim = 0, Nydim = 0;
//array of dimensions
int pdimids[2];
if ((retncval = nc_open_par(ws_FileName, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, ws_VarName, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, yName, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xName, &pxid)))
ERR(retncval);
//var information, checking the dimension array
if (retncval = nc_inq_vardimid(ncid, pvarid, pdimids))
ERR(retncval);
//check dimension sizes
if ((retncval = nc_inq_dim(ncid, pdimids[0], NULL, &Nydim)))
ERR(retncval);
if ((retncval = nc_inq_dim(ncid, pdimids[1], NULL, &Nxdim)))
ERR(retncval);
//create the output arrays
y_inp = new float[Nydim];
x_inp = new float[Nxdim];
//parallel access mode
/*if ((retncval = nc_var_par_access(ncid, pvarid,NC_INDEPENDENT)))
ERR(retncval);*/
if ((retncval = nc_var_par_access(ncid, pyid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, pxid, NC_COLLECTIVE)))
ERR(retncval);