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hdf5/test/set_extent.c
Quincey Koziol 43e3b45021 [svn-r6825] Purpose: 
New feature/enhancement

Description:
    Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.

Solution:
    Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.

    There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.


Platforms tested:
    h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
2003-05-07 16:52:24 -05:00

482 lines
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Pedro Vicente <pvn@ncsa.uiuc.edu>
* April 12, 2002
*
* Purpose: Tests the H5Dset_extent call
*/
#include "hdf5.h"
#include "h5test.h"
/*-------------------------------------------------------------------------
*
* Tests the function H5Dset_extent. In the current version of the library
* the dataset MUST be chunked.
*
*-------------------------------------------------------------------------
*/
#define RANK 2
int main( void )
{
hid_t file_id;
hid_t dataset_id=(-1);
hid_t space_id=(-1);
hid_t plist_id=(-1);
hsize_t dims[RANK] = { 90, 90 };
hsize_t dims_new[RANK] = { 70, 70 };
hsize_t dims_chunk[RANK] = { 20, 20 };
hsize_t dims_out[RANK];
hsize_t maxdims[RANK] = { H5S_UNLIMITED, H5S_UNLIMITED };
int data[ 90 ][ 90 ];
int buf1[ 70 ][ 70 ];
int buf2[ 90 ][ 90 ];
int i, j, n = 0;
int fillvalue = 1; /* Fill value for the dataset */
for( i = 0; i < 90; i++ )
for( j = 0; j < 90; j++ )
data[i][j] = n++;
/*-------------------------------------------------------------------------
* Test H5Dset_extent with chunks on the raw data cache
*-------------------------------------------------------------------------
*/
/* Create a new file using default properties. */
if ((file_id = H5Fcreate( "set_extent_create.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT ))<0) goto out;
TESTING("extend dataset create with fill value");
/* Create the data space with unlimited dimensions. */
if ((space_id = H5Screate_simple( RANK, dims, maxdims ))<0) goto out;
/* Modify dataset creation properties, i.e. enable chunking. */
if ((plist_id = H5Pcreate (H5P_DATASET_CREATE ))<0) goto out;
if (H5Pset_chunk( plist_id, RANK, dims_chunk )<0) goto out;
if (H5Pset_fill_value( plist_id, H5T_NATIVE_INT, &fillvalue )<0) goto out;
/*-------------------------------------------------------------------------
* Create and write one dataset
*-------------------------------------------------------------------------
*/
/* Create a new dataset */
if ((dataset_id = H5Dcreate( file_id , "Dataset1", H5T_NATIVE_INT, space_id, plist_id ))<0) goto out;
/* Write the data. */
if (H5Dwrite( dataset_id , H5T_NATIVE_INT, space_id, H5S_ALL, H5P_DEFAULT, data )<0) goto out;
/*-------------------------------------------------------------------------
* Set new dimensions for the array; shrink it
*-------------------------------------------------------------------------
*/
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id , dims_new )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims_new[0] ) goto out;
/*-------------------------------------------------------------------------
* Read
*-------------------------------------------------------------------------
*/
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf1 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ )
for( j = 0; j < (int)dims_out[1]; j++ )
if ( buf1[i][j] != data[i][j] ) goto out;
/*-------------------------------------------------------------------------
* Set new dimensions for the array; expand it again
*-------------------------------------------------------------------------
*/
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id , dims )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims[0] ) goto out;
/*-------------------------------------------------------------------------
* Read
*-------------------------------------------------------------------------
*/
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf2 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ ) {
for( j = 0; j < (int)dims_out[1]; j++ ) {
if ( i >= 70 || j >= 70 ) {
if ( buf2[i][j] != fillvalue ) goto out;
}
else {
if ( buf2[i][j] != data[i][j] ) goto out;
}
}
}
/*-------------------------------------------------------------------------
* Close/release resources
*-------------------------------------------------------------------------
*/
H5Dclose( dataset_id );
H5Sclose( space_id );
H5Pclose( plist_id );
PASSED();
TESTING("extend dataset create without fill value");
/* Create the data space with unlimited dimensions. */
if ((space_id = H5Screate_simple( RANK, dims, maxdims ))<0) goto out;
/* Modify dataset creation properties, i.e. enable chunking. */
if ((plist_id = H5Pcreate (H5P_DATASET_CREATE ))<0) goto out;
if (H5Pset_chunk( plist_id, RANK, dims_chunk )<0) goto out;
/*-------------------------------------------------------------------------
* Create and write one dataset
*-------------------------------------------------------------------------
*/
/* Create a new dataset */
if ((dataset_id = H5Dcreate( file_id , "Dataset2", H5T_NATIVE_INT, space_id, plist_id ))<0) goto out;
/* Write the data. */
if (H5Dwrite( dataset_id , H5T_NATIVE_INT, space_id, H5S_ALL, H5P_DEFAULT, data )<0) goto out;
/*-------------------------------------------------------------------------
* Set new dimensions for the array; shrink it
*-------------------------------------------------------------------------
*/
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id , dims_new )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims_new[0] ) goto out;
/*-------------------------------------------------------------------------
* Read
*-------------------------------------------------------------------------
*/
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf1 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ )
for( j = 0; j < (int)dims_out[1]; j++ )
if ( buf1[i][j] != data[i][j] ) goto out;
/*-------------------------------------------------------------------------
* Set new dimensions for the array; expand it again
*-------------------------------------------------------------------------
*/
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id , dims )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims[0] ) goto out;
/*-------------------------------------------------------------------------
* Read
*-------------------------------------------------------------------------
*/
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf2 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ ) {
for( j = 0; j < (int)dims_out[1]; j++ ) {
if ( i >= 70 || j >= 70 ) {
if ( buf2[i][j] != 0 ) goto out;
}
else {
if ( buf2[i][j] != data[i][j] ) goto out;
}
}
}
/*-------------------------------------------------------------------------
* Close/release resources
*-------------------------------------------------------------------------
*/
H5Dclose( dataset_id );
H5Sclose( space_id );
H5Pclose( plist_id );
H5Fclose( file_id );
PASSED();
/*-------------------------------------------------------------------------
* Test H5Dset_extent with chunks written to file
*-------------------------------------------------------------------------
*/
/* Create a new file using default properties. */
if ((file_id = H5Fcreate( "set_extent_read.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT ))<0) goto out;
TESTING("extend dataset read with fill value");
/* Create the data space with unlimited dimensions. */
if ((space_id = H5Screate_simple( RANK, dims, maxdims ))<0) goto out;
/* Modify dataset creation properties, i.e. enable chunking. */
if ((plist_id = H5Pcreate (H5P_DATASET_CREATE ))<0) goto out;
if (H5Pset_chunk( plist_id, RANK, dims_chunk )<0) goto out;
if (H5Pset_fill_value( plist_id, H5T_NATIVE_INT, &fillvalue )<0) goto out;
/* Create a new dataset within the file using cparms creation properties. */
if ((dataset_id = H5Dcreate( file_id , "Dataset1", H5T_NATIVE_INT, space_id, plist_id ))<0) goto out;
/* Write the data. */
if (H5Dwrite( dataset_id , H5T_NATIVE_INT, space_id, H5S_ALL, H5P_DEFAULT, data )<0) goto out;
/* Close/release resources. */
H5Dclose( dataset_id );
H5Sclose( space_id );
H5Pclose( plist_id );
H5Fclose( file_id );
/* Open the file */
if ((file_id = H5Fopen( "set_extent_read.h5", H5F_ACC_RDWR, H5P_DEFAULT ))<0) goto out;
/* Open the dataset */
if ((dataset_id = H5Dopen( file_id , "Dataset1" ))<0) goto out;
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id, dims_new )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims_new[0] ) goto out;
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf1 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ )
for( j = 0; j < (int)dims_out[1]; j++ )
if ( buf1[i][j] != data[i][j] ) goto out;
/*-------------------------------------------------------------------------
* Set new dimensions for the array; expand it again
*-------------------------------------------------------------------------
*/
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id , dims )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims[0] ) goto out;
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf2 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ ) {
for( j = 0; j < (int)dims_out[1]; j++ ) {
if ( i >= 70 || j >= 70 ) {
if ( buf2[i][j] != fillvalue ) goto out;
}
else {
if ( buf2[i][j] != data[i][j] ) goto out;
}
}
}
/*-------------------------------------------------------------------------
* Close/release resources
*-------------------------------------------------------------------------
*/
H5Dclose( dataset_id );
H5Sclose( space_id );
PASSED();
TESTING("extend dataset read without fill value");
/* Create the data space with unlimited dimensions. */
if ((space_id = H5Screate_simple( RANK, dims, maxdims ))<0) goto out;
/* Modify dataset creation properties, i.e. enable chunking. */
if ((plist_id = H5Pcreate (H5P_DATASET_CREATE ))<0) goto out;
if (H5Pset_chunk( plist_id, RANK, dims_chunk )<0) goto out;
/* Create a new dataset within the file using cparms creation properties. */
if ((dataset_id = H5Dcreate( file_id , "Dataset2", H5T_NATIVE_INT, space_id, plist_id ))<0) goto out;
/* Write the data. */
if (H5Dwrite( dataset_id , H5T_NATIVE_INT, space_id, H5S_ALL, H5P_DEFAULT, data )<0) goto out;
/* Close/release resources. */
H5Dclose( dataset_id );
H5Sclose( space_id );
H5Pclose( plist_id );
H5Fclose( file_id );
/* Open the file */
if ((file_id = H5Fopen( "set_extent_read.h5", H5F_ACC_RDWR, H5P_DEFAULT ))<0) goto out;
/* Open the dataset */
if ((dataset_id = H5Dopen( file_id , "Dataset2" ))<0) goto out;
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id, dims_new )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims_new[0] ) goto out;
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf1 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ )
for( j = 0; j < (int)dims_out[1]; j++ )
if ( buf1[i][j] != data[i][j] ) goto out;
/*-------------------------------------------------------------------------
* Set new dimensions for the array; expand it again
*-------------------------------------------------------------------------
*/
/* Set new dimensions for the array. */
if (H5Dset_extent( dataset_id , dims )<0) goto out;
/* Get the space. */
if ((space_id = H5Dget_space( dataset_id ))<0) goto out;
/* Get dimensions. */
if (H5Sget_simple_extent_dims( space_id, dims_out, NULL )<0) goto out;
if ( dims_out[0] != dims[0] ) goto out;
/* Read the new dataset. */
if (H5Dread( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf2 )<0) goto out;
/* Compare the read array with the original array */
for( i = 0; i < (int)dims_out[0]; i++ ) {
for( j = 0; j < (int)dims_out[1]; j++ ) {
if ( i >= 70 || j >= 70 ) {
if ( buf2[i][j] != 0 ) goto out;
}
else {
if ( buf2[i][j] != data[i][j] ) goto out;
}
}
}
/*-------------------------------------------------------------------------
* Close/release resources
*-------------------------------------------------------------------------
*/
H5Dclose( dataset_id );
H5Sclose( space_id );
H5Fclose( file_id );
PASSED();
return 0;
out:
H5Dclose( dataset_id );
H5Sclose( space_id );
H5Pclose( plist_id );
H5Fclose( file_id );
H5_FAILED();
return 1;
}
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