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; }