int Traj_AmberNetcdf::parallelWriteFrame(int set, Frame const& frameOut) {
MPI_Offset pstart_[3];
MPI_Offset pcount_[3];
pstart_[0] = set;
pstart_[1] = 0;
pstart_[2] = 0;
pcount_[0] = 1;
pcount_[1] = Ncatom();
pcount_[2] = 3;
// TODO check error better
DoubleToFloat(Coord_, frameOut.xAddress());
//int err = ncmpi_put_vara_float_all(ncid_, coordVID_, pstart_, pcount_, Coord_);
int err = ncmpi_put_vara_float(ncid_, coordVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
if (velocityVID_ != -1) {
DoubleToFloat(Coord_, frameOut.vAddress());
//err = ncmpi_put_vara_float_all(ncid_, velocityVID_, pstart_, pcount_, Coord_);
err = ncmpi_put_vara_float(ncid_, velocityVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
}
if (frcVID_ != -1) {
DoubleToFloat(Coord_, frameOut.fAddress());
err = ncmpi_put_vara_float(ncid_, frcVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
}
pcount_[2] = 0;
if (cellLengthVID_ != -1) {
pcount_[1] = 3;
//err = ncmpi_put_vara_double_all(ncid_, cellLengthVID_, pstart_, pcount_, frameOut.bAddress());
err = ncmpi_put_vara_double(ncid_, cellLengthVID_, pstart_, pcount_, frameOut.bAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
//err = ncmpi_put_vara_double_all(ncid_, cellAngleVID_, pstart_, pcount_, frameOut.bAddress()+3);
err = ncmpi_put_vara_double(ncid_, cellAngleVID_, pstart_, pcount_, frameOut.bAddress()+3);
}
if (TempVID_ != -1) {
//err = ncmpi_put_vara_double_all(ncid_, TempVID_, pstart_, pcount_, frameOut.tAddress());
err = ncmpi_put_vara_double(ncid_, TempVID_, pstart_, pcount_, frameOut.tAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
}
if (timeVID_ != -1) {
float tVal = (float)frameOut.Time();
err = ncmpi_put_vara_float(ncid_, timeVID_, pstart_, pcount_, &tVal);
if (checkPNCerr(err)) return Parallel::Abort(err);
}
if (indicesVID_ != -1) {
pcount_[1] = remd_dimension_;
//err = ncmpi_put_vara_int_all(ncid_, indicesVID_, pstart_, pcount_, frameOut.iAddress());
err = ncmpi_put_vara_int(ncid_, indicesVID_, pstart_, pcount_, frameOut.iAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
}
return 0;
}
FORTRAN_API int FORT_CALL nfmpi_put_vara_double_ ( int *v1, int *v2, MPI_Offset v3[], MPI_Offset v4[], double*v5 ){
int ierr;
int l2 = *v2 - 1;
MPI_Offset *l3 = 0;
MPI_Offset *l4 = 0;
{ int ln = ncmpixVardim(*v1,*v2-1);
if (ln > 0) {
int li;
l3 = (MPI_Offset *)malloc( ln * sizeof(MPI_Offset) );
for (li=0; li<ln; li++)
l3[li] = v3[ln-1-li] - 1;
}
else if (ln < 0) {
/* Error return */
ierr = ln;
return ierr;
}
}
{ int ln = ncmpixVardim(*v1,*v2-1);
if (ln > 0) {
int li;
l4 = (MPI_Offset *)malloc( ln * sizeof(MPI_Offset) );
for (li=0; li<ln; li++)
l4[li] = v4[ln-1-li];
}
else if (ln < 0) {
/* Error return */
ierr = ln;
return ierr;
}
}
ierr = ncmpi_put_vara_double( *v1, l2, l3, l4, v5 );
if (l3) { free(l3); }
if (l4) { free(l4); }
return ierr;
}
int main(int argc, char **argv) {
int i, j;
int status;
int ncid1, ncid2;
int ndims, nvars, ngatts, unlimdimid;
char name[NC_MAX_NAME];
nc_type type, vartypes[NC_MAX_VARS];
MPI_Offset attlen;
MPI_Offset dimlen, shape[NC_MAX_VAR_DIMS], varsize, start[NC_MAX_VAR_DIMS];
void *valuep;
int dimids[NC_MAX_DIMS], varids[NC_MAX_VARS];
int vardims[NC_MAX_VARS][NC_MAX_VAR_DIMS/16]; /* divided by 16 due to my memory limitation */
int varndims[NC_MAX_VARS], varnatts[NC_MAX_VARS];
params opts;
int rank;
int nprocs;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (rank == 0)
fprintf(stderr, "Testing independent read ... ");
parse_read_args(argc, argv, rank, &opts);
/********** START OF NETCDF ACCESS **************/
/* Read a netCDF file and write it out to another file */
/**
* Open the input dataset - ncid1:
* File name: "../data/test_int.nc"
* Dataset API: Collective
* And create the output dataset - ncid2:
* File name: "testread.nc"
* Dataset API: Collective
*/
status = ncmpi_open(comm, opts.infname, 0, MPI_INFO_NULL, &ncid1);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_create(comm, opts.outfname, NC_CLOBBER, MPI_INFO_NULL, &ncid2);
if (status != NC_NOERR) handle_error(status);
/**
* Inquire the dataset definitions of input dataset AND
* Add dataset definitions for output dataset.
*/
status = ncmpi_inq(ncid1, &ndims, &nvars, &ngatts, &unlimdimid);
if (status != NC_NOERR) handle_error(status);
/* Inquire global attributes, assume CHAR attributes. */
for (i = 0; i < ngatts; i++) {
status = ncmpi_inq_attname(ncid1, NC_GLOBAL, i, name);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_inq_att (ncid1, NC_GLOBAL, name, &type, &attlen);
if (status != NC_NOERR) handle_error(status);
switch (type) {
case NC_CHAR:
valuep = (void *)malloc(attlen * sizeof(char));
status = ncmpi_get_att_text(ncid1, NC_GLOBAL, name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_text (ncid2, NC_GLOBAL, name, attlen, (char *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_SHORT:
valuep = (void *)malloc(attlen * sizeof(short));
status = ncmpi_get_att_short(ncid1, NC_GLOBAL, name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_short (ncid2, NC_GLOBAL, name, type, attlen, (short *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_INT:
valuep = (void *)malloc(attlen * sizeof(int));
status = ncmpi_get_att_int(ncid1, NC_GLOBAL, name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_int (ncid2, NC_GLOBAL, name, type, attlen, (int *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_FLOAT:
valuep = (void *)malloc(attlen * sizeof(float));
status = ncmpi_get_att_float(ncid1, NC_GLOBAL, name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_float (ncid2, NC_GLOBAL, name, type, attlen, (float *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_DOUBLE:
valuep = (void *)malloc(attlen * sizeof(double));
status = ncmpi_get_att_double(ncid1, NC_GLOBAL, name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_double (ncid2, NC_GLOBAL, name, type, attlen, (double *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
default:
;
/* handle unexpected types */
}
}
/* Inquire dimension */
for (i = 0; i < ndims; i++) {
status = ncmpi_inq_dim(ncid1, i, name, &dimlen);
if (status != NC_NOERR) handle_error(status);
if (i == unlimdimid)
dimlen = NC_UNLIMITED;
status = ncmpi_def_dim(ncid2, name, dimlen, dimids+i);
if (status != NC_NOERR) handle_error(status);
}
/* Inquire variables */
for (i = 0; i < nvars; i++) {
status = ncmpi_inq_var (ncid1, i, name, vartypes+i, varndims+i, vardims[i], varnatts+i);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_def_var(ncid2, name, vartypes[i], varndims[i], vardims[i], varids+i);
if (status != NC_NOERR) handle_error(status);
/* var attributes, assume CHAR attributes */
for (j = 0; j < varnatts[i]; j++) {
status = ncmpi_inq_attname(ncid1, varids[i], j, name);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_inq_att (ncid1, varids[i], name, &type, &attlen);
if (status != NC_NOERR) handle_error(status);
switch (type) {
case NC_CHAR:
valuep = (void *)malloc(attlen * sizeof(char));
status = ncmpi_get_att_text(ncid1, varids[i], name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_text (ncid2, varids[i], name, attlen, (char *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_SHORT:
valuep = (void *)malloc(attlen * sizeof(short));
status = ncmpi_get_att_short(ncid1, varids[i], name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_short (ncid2, varids[i], name, type, attlen, (short *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_INT:
valuep = (void *)malloc(attlen * sizeof(int));
status = ncmpi_get_att_int(ncid1, varids[i], name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_int (ncid2, varids[i], name, type, attlen, (int *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_FLOAT:
valuep = (void *)malloc(attlen * sizeof(float));
status = ncmpi_get_att_float(ncid1, varids[i], name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_float (ncid2, varids[i], name, type, attlen, (float *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_DOUBLE:
valuep = (void *)malloc(attlen * sizeof(double));
status = ncmpi_get_att_double(ncid1, varids[i], name, valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_att_double (ncid2, varids[i], name, type, attlen, (double *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
default:
;
/* handle unexpected types */
}
}
}
/**
* End Define Mode (switch to data mode) for output dataset
* Dataset API: Collective
*/
status = ncmpi_enddef(ncid2);
if (status != NC_NOERR) handle_error(status);
/**
* Read data of variables from input dataset (assume INT variables)
* Write the data out to the corresponding variables in the output dataset
*
* Data Partition (Assume 4 processors):
* square: 2-D, (Block, *), 25*100 from 100*100
* cube: 3-D, (Block, *, *), 25*100*100 from 100*100*100
* xytime: 3-D, (Block, *, *), 25*100*100 from 100*100*100
* time: 1-D, Block-wise, 25 from 100
*
* Data Mode API: non-collective
*/
status = ncmpi_begin_indep_data(ncid1);
if (status != NC_NOERR) handle_error(status);
status =ncmpi_begin_indep_data(ncid2);
if (status != NC_NOERR) handle_error(status);
for (i = 0; i < NC_MAX_VAR_DIMS; i++)
start[i] = 0;
for (i = 0; i < nvars; i++) {
varsize = 1;
for (j = 0; j < varndims[i]; j++) {
status = ncmpi_inq_dim(ncid1, vardims[i][j], name, shape + j);
if (status != NC_NOERR) handle_error(status);
if (j == 0) {
shape[j] /= nprocs;
start[j] = shape[j] * rank;
}
varsize *= shape[j];
}
switch (vartypes[i]) {
case NC_CHAR:
break;
case NC_SHORT:
valuep = (void *)malloc(varsize * sizeof(short));
status = ncmpi_get_vara_short(ncid1, i, start, shape, (short *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_short(ncid2, varids[i],
start, shape, (short *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_INT:
valuep = (void *)malloc(varsize * sizeof(int));
status = ncmpi_get_vara_int(ncid1, i, start, shape, (int *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_int(ncid2, varids[i],
start, shape, (int *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_FLOAT:
valuep = (void *)malloc(varsize * sizeof(float));
status = ncmpi_get_vara_float(ncid1, i, start, shape, (float *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_float(ncid2, varids[i],
start, shape, (float *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
case NC_DOUBLE:
valuep = (void *)malloc(varsize * sizeof(double));
status = ncmpi_get_vara_double(ncid1, i, start, shape, (double *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_double(ncid2, varids[i],
start, shape, (double *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
default:
;
/* handle unexpected types */
}
}
status = ncmpi_end_indep_data(ncid1);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_end_indep_data(ncid2);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_sync(ncid1);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_sync(ncid2);
if (status != NC_NOERR) handle_error(status);
/**
* Close the datasets
* Dataset API: collective
*/
status = ncmpi_close(ncid1);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_close(ncid2);
if (status != NC_NOERR) handle_error(status);
/******************* END OF NETCDF ACCESS ****************/
if (rank == 0)
fprintf(stderr, "OK\nInput file %s copied to: %s!\n", opts.infname, opts.outfname);
MPI_Finalize();
return 0;
}
int main(int argc, char **argv) {
int i, j, k;
int status;
int ncid;
int dimid1, dimid2, dimid3, udimid;
int square_dim[2], cube_dim[3], xytime_dim[3], time_dim[1];
MPI_Offset square_start[2], cube_start[3] = {0, 0, 0};
MPI_Offset square_count[2] = {50, 50}, cube_count[3] = {100, 50, 50};
MPI_Offset xytime_start[3] = {0, 0, 0};
MPI_Offset xytime_count[3] = {100, 50, 50};
MPI_Offset time_start[1], time_count[1] = {25};
int square_id, cube_id, xytime_id, time_id;
static char title[] = "example netCDF dataset";
static char description[] = "2-D integer array";
double data[100][50][50], buffer[100];
int rank;
int nprocs;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info;
params opts;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (rank == 0)
fprintf(stderr, "Testing independent write ... ");
parse_write_args(argc, argv, rank, &opts);
/********** START OF NETCDF ACCESS **************/
MPI_Info_create(&info);
MPI_Info_set(info, "striping_factor", "4");
MPI_Info_set(info, "striping_unit", "20000");
MPI_Info_set(info, "start_iodevice", "0");
/**
* Create the dataset
* File name: "testwrite.nc"
* Dataset API: Collective
*/
status = ncmpi_create(comm, opts.outfname, NC_CLOBBER, info, &ncid);
if (status != NC_NOERR) handle_error(status);
/**
* Create a global attribute:
* :title = "example netCDF dataset";
*/
status = ncmpi_put_att_text (ncid, NC_GLOBAL, "title",
strlen(title), title);
if (status != NC_NOERR) handle_error(status);
/**
* Add 4 pre-defined dimensions:
* x = 100, y = 100, z = 100, time = NC_UNLIMITED
*/
status = ncmpi_def_dim(ncid, "x", 100L, &dimid1);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_def_dim(ncid, "y", 100L, &dimid2);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_def_dim(ncid, "z", 100L, &dimid3);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_def_dim(ncid, "time", NC_UNLIMITED, &udimid);
if (status != NC_NOERR) handle_error(status);
/**
* Define the dimensionality and then add 4 variables:
* square(x, y), cube(x,y,z), time(time), xytime(time, x, y)
*/
square_dim[0] = cube_dim[0] = xytime_dim[1] = dimid1;
square_dim[1] = cube_dim[1] = xytime_dim[2] = dimid2;
cube_dim[2] = dimid3;
xytime_dim[0] = udimid;
time_dim[0] = udimid;
status = ncmpi_def_var (ncid, "square", NC_DOUBLE, 2, square_dim, &square_id);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_def_var (ncid, "cube", NC_DOUBLE, 3, cube_dim, &cube_id);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_def_var (ncid, "time", NC_DOUBLE, 1, time_dim, &time_id);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_def_var (ncid, "xytime", NC_DOUBLE, 3, xytime_dim, &xytime_id);
if (status != NC_NOERR) handle_error(status);
/**
* Add an attribute for variable:
* square: decsription = "2-D integer array"
*/
status = ncmpi_put_att_text (ncid, square_id, "description",
strlen(description), description);
if (status != NC_NOERR) handle_error(status);
/**
* End Define Mode (switch to data mode)
* Dataset API: Collective
*/
status = ncmpi_enddef(ncid);
if (status != NC_NOERR) handle_error(status);
/**
* Data Partition (Assume 4 processors):
* square: 2-D, (Block, Block), 50*50 from 100*100
* cube: 3-D, (*, Block, Block), 100*50*50 from 100*100*100
* xytime: 3-D, (*, Block, Block), 100*50*50 from 100*100*100
* time: 1-D, Block-wise, 25 from 100
*/
square_start[0] = cube_start[1] = xytime_start[1] = (rank/2) * 50;
square_start[1] = cube_start[2] = xytime_start[2] = (rank%2) * 50;
time_start[0] = (rank%4) * 25;
/**
* Packing data in the buffer
*/
/* Data for variable: time */
for ( i = time_start[0]; i < time_start[0] + time_count[0]; i++ )
buffer[i - time_start[0]] = i;
/* Data for variable: square, cube and xytime */
for ( i = 0; i < 100; i++ )
for ( j = square_start[0]; j < square_start[0]+square_count[0]; j++ )
for ( k = square_start[1]; k < square_start[1]+square_count[1]; k++ )
data[i][j-square_start[0]][k-square_start[1]] = i*100*100 + j*100 + k;
/**
* Write data into variables: square, cube, time and xytime
* Access Method: subarray
* Data Mode API: non-collective
*/
status = ncmpi_begin_indep_data(ncid);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_double(ncid, square_id,
square_start, square_count,
&data[0][0][0]);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_double(ncid, cube_id,
cube_start, cube_count,
&data[0][0][0]);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_double(ncid, time_id,
time_start, time_count,
(double *)buffer);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_double(ncid, xytime_id,
xytime_start, xytime_count,
&data[0][0][0]);
if (status != NC_NOERR) handle_error(status);
{
/**
* Change a single element and then change it back
* Access Method: single value
* Data Mode API: non-collective
*/
double singlevalue = 0;
ncmpi_sync(ncid);
status = ncmpi_put_var1_double(ncid, square_id,
square_start, &singlevalue);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_var1_double(ncid, time_id,
time_start, &singlevalue);
if (status != NC_NOERR) handle_error(status);
ncmpi_sync(ncid);
singlevalue = square_start[0]*100 + square_start[1];
status = ncmpi_put_var1_double(ncid, square_id,
square_start, &singlevalue);
if (status != NC_NOERR) handle_error(status);
singlevalue = time_start[0];
status = ncmpi_put_var1_double(ncid, time_id,
time_start, &singlevalue);
if (status != NC_NOERR) handle_error(status);
}
{
/**
* Change the whole array for time[] and then change it back
* Access Method: whole array
* Data Mode API: non-collective
*/
ncmpi_sync(ncid);
for (i = 0; i < 100; i++ )
buffer[i] = 0;
if (rank == 0) {
status = ncmpi_put_var_double(ncid, time_id, buffer);
if (status != NC_NOERR) handle_error(status);
}
ncmpi_sync(ncid);
for (i=0; i<100; i++)
buffer[i] = i;
if (rank == 1) {
status = ncmpi_put_var_double(ncid, time_id, buffer);
if (status != NC_NOERR) handle_error(status);
}
}
status = ncmpi_end_indep_data(ncid);
if (status != NC_NOERR) handle_error(status);
/**
* Close the dataset
* Dataset API: collective
*/
status = ncmpi_close(ncid);
if (status != NC_NOERR) handle_error(status);
MPI_Info_free(&info);
/******************* END OF NETCDF ACCESS ****************/
if (rank == 0)
fprintf(stderr, "OK\nFile written to: %s!\n", opts.outfname);
MPI_Finalize();
return 0;
}
