mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-11-27 02:10:55 +08:00
36561530ce
To test MPI derived datatype Description: A very simple irregular hyperslab selection in parallel. Will not be tested when testing HDF5 library. Check in only for debugging purpose. This code will be tested in the future. Solution: Platforms tested: AIX 5.1, Linux 2.4+mpich 1.2.6 Misc. update:
309 lines
9.6 KiB
C
309 lines
9.6 KiB
C
|
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
|
* Copyright by the Board of Trustees of the University of Illinois. *
|
|
* All rights reserved. *
|
|
* *
|
|
* This file is part of HDF5. The full HDF5 copyright notice, including *
|
|
* terms governing use, modification, and redistribution, is contained in *
|
|
* the files COPYING and Copyright.html. COPYING can be found at the root *
|
|
* of the source code distribution tree; Copyright.html can be found at the *
|
|
* root level of an installed copy of the electronic HDF5 document set and *
|
|
* is linked from the top-level documents page. It can also be found at *
|
|
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
|
|
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
|
|
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
|
|
|
|
/*
|
|
* This program shows how the H5Sselect_hyperslab and H5Sselect_elements
|
|
* functions are used to write selected data from memory to the file.
|
|
* Program takes 48 elements from the linear buffer and writes them into
|
|
* the matrix using 3x2 blocks, (4,3) stride and (2,4) count.
|
|
* Then four elements of the matrix are overwritten with the new values and
|
|
* file is closed. Program reopens the file and selects the union of two
|
|
* hyperslabs in the dataset in the file. Then it reads the selection into the
|
|
* memory dataset preserving the shape of the selection.
|
|
*/
|
|
|
|
#include "hdf5.h"
|
|
#include "H5private.h"
|
|
#include "testphdf5.h"
|
|
|
|
|
|
void t_span_tree()
|
|
{
|
|
|
|
char *filename;
|
|
hid_t acc_plist,xfer_plist;
|
|
hid_t file, dataset; /* File and dataset identifiers */
|
|
hid_t mid1, mid2, mid, fid; /* Dataspace identifiers */
|
|
hid_t plist; /* Dataset property list identifier */
|
|
|
|
hsize_t dim1[] = {MSPACE1_DIM}; /* Dimension size of the first dataset
|
|
(in memory) */
|
|
hsize_t dim2[] = {MSPACE2_DIM}; /* Dimension size of the second dataset
|
|
(in memory */
|
|
hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2};
|
|
/* Dimension sizes of the dataset (on disk) */
|
|
hsize_t mdim[] = {MSPACE_DIM1, MSPACE_DIM2}; /* Dimension sizes of the
|
|
dataset in memory when we
|
|
read selection from the
|
|
dataset on the disk */
|
|
|
|
hssize_t start[2]; /* Start of hyperslab */
|
|
hsize_t stride[2]; /* Stride of hyperslab */
|
|
hsize_t count[2]; /* Block count */
|
|
hsize_t block[2]; /* Block sizes */
|
|
|
|
hssize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points
|
|
from the file dataspace */
|
|
herr_t ret;
|
|
unsigned i,j;
|
|
int fillvalue = 0; /* Fill value for the dataset */
|
|
|
|
int matrix_out[MSPACE_DIM1][MSPACE_DIM2]; /* Buffer to read from the
|
|
dataset */
|
|
int vector[MSPACE1_DIM];
|
|
int values[] = {53, 59, 61, 67}; /* New values to be written */
|
|
|
|
int mpi_size,mpi_rank;
|
|
hsize_t testdims[2];
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
/*set up MPI parameters */
|
|
MPI_Comm_size(comm,&mpi_size);
|
|
MPI_Comm_rank(comm,&mpi_rank);
|
|
|
|
printf("mpi_size %d\n",mpi_size);
|
|
printf("mpi_rank %d\n",mpi_rank);
|
|
|
|
/* Obtain file name */
|
|
filename = (char *) GetTestParameters();
|
|
|
|
|
|
/*
|
|
* Buffers' initialization.
|
|
*/
|
|
vector[0] = vector[MSPACE1_DIM - 1] = -1;
|
|
for (i = 1; i < MSPACE1_DIM - 1; i++) vector[i] = i;
|
|
|
|
acc_plist = H5Pcreate(H5P_FILE_ACCESS);
|
|
ret = H5Pset_fapl_mpio(acc_plist,comm,info);
|
|
|
|
/*
|
|
* Create a file.
|
|
*/
|
|
file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_plist);
|
|
|
|
/*
|
|
* Create property list for a dataset and set up fill values.
|
|
*/
|
|
plist = H5Pcreate(H5P_DATASET_CREATE);
|
|
ret = H5Pset_fill_value(plist, H5T_NATIVE_INT, &fillvalue);
|
|
|
|
/*
|
|
* Create dataspace for the dataset in the file.
|
|
*/
|
|
fid = H5Screate_simple(FSPACE_RANK, fdim, NULL);
|
|
|
|
/*
|
|
* Create dataset in the file. Notice that creation
|
|
* property list plist is used.
|
|
*/
|
|
dataset = H5Dcreate(file, "Matrix in file", H5T_NATIVE_INT, fid, plist);
|
|
|
|
|
|
/*
|
|
* Select hyperslab for the dataset in the file, using 3x2 blocks,
|
|
* (4,3) stride and (1,4) count starting at the position (0,1)
|
|
for the first selection
|
|
*/
|
|
start[0] = 0; start[1] = 1;
|
|
stride[0] = 4; stride[1] = 3;
|
|
count[0] = 1; count[1] = 4;
|
|
block[0] = 3; block[1] = 2;
|
|
ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block);
|
|
|
|
if(ret < 0) printf("hyperslab selection is wrong. \n");
|
|
|
|
/*
|
|
* Select hyperslab for the dataset in the file, using 3x2*4 blocks,
|
|
* stride 1 and (1,1) count starting at the position (4,0).
|
|
*/
|
|
/* start[0] = 4; start[1] = 0;
|
|
stride[0] = 1; stride[1] = 1;
|
|
count[0] = 1; count[1] = 1;
|
|
block[0] = 3; block[1] = 8;*/
|
|
|
|
start[0] = 4; start[1] = 0;
|
|
stride[0] = 1; stride[1] = 1;
|
|
count[0] = 1; count[1] = 1;
|
|
block[0] = 3; block[1] = 8;
|
|
ret = H5Sselect_hyperslab(fid, H5S_SELECT_OR, start, stride, count, block);
|
|
|
|
if(ret < 0) printf("hyperslab selection is wrong with or selection. \n");
|
|
/*
|
|
* Create dataspace for the first dataset.
|
|
*/
|
|
mid1 = H5Screate_simple(MSPACE1_RANK, dim1, NULL);
|
|
|
|
/*
|
|
* Select hyperslab.
|
|
* We will use 48 elements of the vector buffer starting at the second element.
|
|
* Selected elements are 1 2 3 . . . 48
|
|
*/
|
|
start[0] = 1;
|
|
stride[0] = 1;
|
|
count[0] = 48;
|
|
block[0] = 1;
|
|
ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block);
|
|
|
|
/*
|
|
* Write selection from the vector buffer to the dataset in the file.
|
|
*
|
|
* File dataset should look like this:
|
|
* 0 1 2 0 3 4 0 5 6 0 7 8
|
|
* 0 9 10 0 11 12 0 13 14 0 15 16
|
|
* 0 17 18 0 19 20 0 21 22 0 23 24
|
|
* 0 0 0 0 0 0 0 0 0 0 0 0
|
|
* 0 25 26 0 27 28 0 29 30 0 31 32
|
|
* 0 33 34 0 35 36 0 37 38 0 39 40
|
|
* 0 41 42 0 43 44 0 45 46 0 47 48
|
|
* 0 0 0 0 0 0 0 0 0 0 0 0
|
|
*/
|
|
|
|
xfer_plist = H5Pcreate(H5P_DATASET_XFER);
|
|
|
|
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
|
|
for (i = 0; i < MSPACE_DIM1; i++) {
|
|
for (j = 0; j < MSPACE_DIM2; j++)
|
|
matrix_out[i][j] = 3;
|
|
}
|
|
|
|
/* ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, xfer_plist, vector);*/
|
|
ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector);
|
|
if(ret < 0) printf("failing to write data .\n");
|
|
|
|
/*
|
|
* Initialize data buffer.
|
|
*/
|
|
for (i = 0; i < MSPACE_DIM1; i++) {
|
|
for (j = 0; j < MSPACE_DIM2; j++)
|
|
matrix_out[i][j] = 1;
|
|
}
|
|
|
|
for (i=0; i < MSPACE_DIM1; i++) {
|
|
for(j=0; j < MSPACE_DIM2; j++) printf("%3d ", matrix_out[i][j]);
|
|
printf("\n");
|
|
}
|
|
|
|
|
|
#if 0
|
|
|
|
/* for dataset reading */
|
|
xfer_plist = H5Pcreate(H5P_DATASET_XFER);
|
|
|
|
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
ret = H5Dread(dataset, H5T_NATIVE_INT, fid, fid,
|
|
xfer_plist, matrix_out);
|
|
|
|
|
|
/* ret = H5Dread(dataset, H5T_NATIVE_INT, fid, fid,
|
|
H5P_DEFAULT, matrix_out);*/
|
|
|
|
if(ret < 0) printf("fail to read the dataset afterwards.\n");
|
|
for (i=0; i < MSPACE_DIM1; i++) {
|
|
for(j=0; j < MSPACE_DIM2; j++) printf("%3d ", matrix_out[i][j]);
|
|
printf("\n");
|
|
}
|
|
#endif
|
|
|
|
ret = H5Sclose(mid1);
|
|
ret = H5Sclose(fid);
|
|
|
|
/*
|
|
* Close dataset.
|
|
*/
|
|
ret = H5Dclose(dataset);
|
|
|
|
/*
|
|
* Close the file.
|
|
*/
|
|
ret = H5Fclose(file);
|
|
|
|
/*
|
|
* Close property list
|
|
*/
|
|
|
|
ret = H5Pclose(acc_plist);
|
|
|
|
ret = H5Pclose(xfer_plist);
|
|
ret = H5Pclose(plist);
|
|
|
|
#if 0
|
|
/*
|
|
* Open the file.
|
|
*/
|
|
file = H5Fopen(filename, H5F_ACC_RDONLY, acc_plist);
|
|
if(file <0) printf("fail to open the file.\n");
|
|
|
|
/*
|
|
* Open the dataset.
|
|
*/
|
|
dataset = H5Dopen(file,"Matrix in file");
|
|
if(dataset < 0) printf("fail to open the dataset.\n");
|
|
|
|
/*
|
|
* Get dataspace of the open dataset.
|
|
*/
|
|
fid = H5Dget_space(dataset);
|
|
if(fid < 0) printf("cannot obtain the correct file space.\n");
|
|
H5Sget_simple_extent_dims(fid,testdims,NULL);
|
|
HDfprintf(stdout,"testdims[0] %Hu\n",testdims[0]);
|
|
HDfprintf(stdout, "testdims[1] %Hu\n",testdims[1]);
|
|
|
|
/*
|
|
* Initialize data buffer.
|
|
*/
|
|
for (i = 0; i < MSPACE_DIM1; i++) {
|
|
for (j = 0; j < MSPACE_DIM2; j++)
|
|
matrix_out[i][j] = 1;
|
|
}
|
|
|
|
ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
|
|
H5P_DEFAULT, matrix_out);
|
|
|
|
if(ret < 0) printf("fail to read the dataset.\n");
|
|
for (i=0; i < MSPACE_DIM1; i++) {
|
|
for(j=0; j < MSPACE_DIM2; j++) printf("%3d ", matrix_out[i][j]);
|
|
printf("\n");
|
|
}
|
|
|
|
/*
|
|
* Close memory file and memory dataspaces.
|
|
*/
|
|
ret = H5Sclose(mid);
|
|
ret = H5Sclose(fid);
|
|
|
|
/*
|
|
* Close dataset.
|
|
*/
|
|
ret = H5Dclose(dataset);
|
|
|
|
/*
|
|
* Close property list
|
|
*/
|
|
ret = H5Pclose(plist);
|
|
ret = H5Pclose(acc_plist);
|
|
|
|
ret = H5Pclose(xfer_plist);
|
|
|
|
/*
|
|
* Close the file.
|
|
*/
|
|
ret = H5Fclose(file);
|
|
#endif
|
|
return ;
|
|
}
|