// Traj_NcEnsemble::readArray() //TODO RemdValues
int Traj_NcEnsemble::readArray(int set, FrameArray& f_ensemble) {
# ifdef HAS_PNETCDF
MPI_Offset pstart_[4];
MPI_Offset pcount_[4];
# define start_ pstart_
# define count_ pcount_
# endif
start_[0] = set; // Frame
start_[2] = 0; // Atoms
start_[3] = 0; // XYZ
count_[0] = 1; // Frame
count_[1] = 1; // Ensemble
count_[3] = 3; // XYZ
//rprintf("DEBUG: Reading frame %i\n", set+1);
for (int member = ensembleStart_; member != ensembleEnd_; member++) {
# ifdef MPI
Frame& frm = f_ensemble[0];
# else
Frame& frm = f_ensemble[member];
# endif
start_[1] = member; // Ensemble
count_[2] = Ncatom(); // Atoms
// Read Coords
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, coordVID_, start_, count_, Coord_)))
# else
if (NC::CheckErr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)))
# endif
{
rprinterr("Error: Getting coordinates for frame %i\n", set+1);
return 1;
}
FloatToDouble(frm.xAddress(), Coord_);
//mprintf("Frm=%8i Rep=%8i ", set+1, member+1); // DEBUG
//frm.printAtomCoord(0); // DEBUG
// Read Velocities
if (velocityVID_ != -1) {
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, velocityVID_, start_, count_, Coord_)))
# else
if (NC::CheckErr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)))
# endif
{
rprinterr("Error: Getting velocities for frame %i\n", set+1);
return 1;
}
FloatToDouble(frm.vAddress(), Coord_);
}
// Read Box
if (cellLengthVID_ != -1) {
count_[2] = 3;
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
# else
if (NC::CheckErr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
# endif
{
rprinterr("Error: Getting cell lengths for frame %i.\n", set+1);
return 1;
}
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
# else
if (NC::CheckErr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
# endif
{
rprinterr("Error: Getting cell angles for frame %i.\n", set+1);
return 1;
}
}
// Read Temperature
if (TempVID_!=-1) {
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, TempVID_, start_, count_, frm.tAddress())))
# else
if (NC::CheckErr(nc_get_vara_double(ncid_, TempVID_, start_, count_, frm.tAddress())))
# endif
{
rprinterr("Error: Getting replica temperature for frame %i.\n", set+1);
return 1;
}
//fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
}
// Read indices
if (indicesVID_!=-1) {
count_[2] = remd_dimension_;
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_int_all(ncid_, indicesVID_, start_, count_, frm.iAddress())))
# else
if (NC::CheckErr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, frm.iAddress())))
# endif
{
rprinterr("Error: Getting replica indices for frame %i.\n", set+1);
return 1;
}
// DEBUG
//char buffer[128];
//char* ptr = buffer;
//ptr += sprintf(buffer,"DEBUG:\tReplica indices:");
//for (int dim=0; dim < remd_dimension_; dim++) ptr += sprintf(ptr, " %i", frm.RemdIndices()[dim]);
//sprintf(ptr,"\n");
//rprintf("%s", buffer);
}
}
# ifdef HAS_PNETCDF
// DEBUG
# undef start_
# undef count_
# endif
return 0;
}
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];
int isRecvar;
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 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_float.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:
;
/* TODO: 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, i, j, name);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_inq_att (ncid1, 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, 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, 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, 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, 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, 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:
; /* TODO: 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
* (ONLY DEAL WITH: NC_INT, NC_FLOAT, NC_DOUBLE for now)
* 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: collective
*/
for (i = 0; i < NC_MAX_VAR_DIMS; i++)
start[i] = 0;
for (i = 0; i < nvars; i++) {
isRecvar = 0;
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];
if (vardims[i][j] == unlimdimid)
isRecvar = 1;
}
switch (vartypes[i]) {
case NC_CHAR:
break;
case NC_SHORT:
valuep = (void *)malloc(varsize * sizeof(short));
status = ncmpi_get_vara_short_all(ncid1, i, start, shape, (short *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_short_all(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_all(ncid1, i, start, shape, (int *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_int_all(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_all(ncid1, i, start, shape, (float *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_float_all(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_all(ncid1, i, start, shape, (double *)valuep);
if (status != NC_NOERR) handle_error(status);
status = ncmpi_put_vara_double_all(ncid2, varids[i],
start, shape, (double *)valuep);
if (status != NC_NOERR) handle_error(status);
free(valuep);
break;
default:
; /* TODO: handle unexpected types */
}
}
/**
* 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;
}
