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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* This verifies the correctness of parallel reading of a dataset that has been
* written serially using filters.
*
* Created by: Christian Chilan
* Date: 2007/05/15
*/
#include "testphdf5.h"
#ifdef H5_HAVE_SZLIB_H
# include "szlib.h"
#endif
static int mpi_size, mpi_rank;
/* Chunk sizes */
#define CHUNK_DIM1 7
#define CHUNK_DIM2 27
/* Sizes of the vertical hyperslabs. Total dataset size is
{HS_DIM1, HS_DIM2 * mpi_size } */
#define HS_DIM1 200
#define HS_DIM2 100
/*-------------------------------------------------------------------------
* Function: filter_read_internal
*
* Purpose: Tests parallel reading of a 2D dataset written serially using
* filters. During the parallel reading phase, the dataset is
* divided evenly among the processors in vertical hyperslabs.
*
* Programmer: Christian Chilan
* Tuesday, May 15, 2007
*
*-------------------------------------------------------------------------
*/
static void
filter_read_internal(const char *filename, hid_t dcpl,
hsize_t *dset_size)
{
hid_t file, dataset; /* HDF5 IDs */
hid_t access_plist; /* Access property list ID */
hid_t sid, memspace; /* Dataspace IDs */
hsize_t size[2]; /* Dataspace dimensions */
hsize_t hs_offset[2]; /* Hyperslab offset */
hsize_t hs_size[2]; /* Hyperslab size */
size_t i, j; /* Local index variables */
char name[32] = "dataset";
herr_t hrc; /* Error status */
int *points = NULL; /* Writing buffer for entire dataset */
int *check = NULL; /* Reading buffer for selected hyperslab */
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* set sizes for dataset and hyperslabs */
hs_size[0] = size[0] = HS_DIM1;
hs_size[1] = HS_DIM2;
size[1] = hs_size[1] * mpi_size;
hs_offset[0] = 0;
hs_offset[1] = hs_size[1] * mpi_rank;
/* Create the data space */
sid = H5Screate_simple(2, size, NULL);
VRFY(sid>=0, "H5Screate_simple");
/* Create buffers */
points = (int *)HDmalloc(size[0] * size[1] * sizeof(int));
VRFY(points!=NULL, "HDmalloc");
check = (int *)HDmalloc(hs_size[0] * hs_size[1] * sizeof(int));
VRFY(check!=NULL, "HDmalloc");
/* Initialize writing buffer with random data */
for(i = 0; i < size[0]; i++)
for(j = 0; j < size[1]; j++)
points[i * size[1]+j] = (int)(i+j+7);
VRFY(H5Pall_filters_avail(dcpl), "Incorrect filter availability");
/* Serial write phase */
if(MAINPROCESS) {
file = H5Fcreate(h5_rmprefix(filename), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
VRFY(file>=0, "H5Fcreate");
/* Create the dataset */
dataset = H5Dcreate2(file, name, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
VRFY(dataset>=0, "H5Dcreate2");
hrc = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, points);
VRFY(hrc>=0, "H5Dwrite");
*dset_size = H5Dget_storage_size(dataset);
VRFY(*dset_size>0, "H5Dget_storage_size");
hrc = H5Dclose (dataset);
VRFY(hrc>=0, "H5Dclose");
hrc = H5Fclose (file);
VRFY(hrc>=0, "H5Fclose");
}
MPI_Barrier(MPI_COMM_WORLD);
/* Parallel read phase */
/* Set up MPIO file access property lists */
access_plist = H5Pcreate(H5P_FILE_ACCESS);
VRFY((access_plist >= 0), "H5Pcreate");
hrc = H5Pset_fapl_mpio(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL);
VRFY((hrc >= 0), "H5Pset_fapl_mpio");
/* Open the file */
file = H5Fopen(filename, H5F_ACC_RDWR, access_plist);
VRFY((file >= 0), "H5Fopen");
dataset = H5Dopen2(file, name, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dopen2");
hrc = H5Sselect_hyperslab(sid, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL);
VRFY(hrc>=0, "H5Sselect_hyperslab");
memspace = H5Screate_simple(2, hs_size, NULL);
VRFY(memspace>=0, "H5Screate_simple");
hrc = H5Dread (dataset, H5T_NATIVE_INT, memspace, sid, H5P_DEFAULT, check);
VRFY(hrc>=0, "H5Dread");
/* Check that the values read are the same as the values written */
for (i=0; i<hs_size[0]; i++) {
for (j=0; j<hs_size[1]; j++) {
if(points[i*size[1]+(size_t)hs_offset[1]+j] !=
check[i*hs_size[1]+j]) {
fprintf(stderr," Read different values than written.\n");
fprintf(stderr," At index %lu,%lu\n",
(unsigned long)(i),
(unsigned long)(hs_offset[1]+j));
fprintf(stderr," At original: %d\n",
(int)points[i*size[1]+(size_t)hs_offset[1]+j]);
fprintf(stderr," At returned: %d\n",
(int)check[i*hs_size[1]+j]);
VRFY(FALSE, "");
}
}
}
/* Get the storage size of the dataset */
*dset_size=H5Dget_storage_size(dataset);
VRFY(*dset_size!=0, "H5Dget_storage_size");
/* Clean up objects used for this test */
hrc = H5Dclose (dataset);
VRFY(hrc>=0, "H5Dclose");
hrc = H5Sclose (sid);
VRFY(hrc>=0, "H5Sclose");
hrc = H5Sclose (memspace);
VRFY(hrc>=0, "H5Sclose");
hrc = H5Pclose (access_plist);
VRFY(hrc>=0, "H5Pclose");
hrc = H5Fclose (file);
VRFY(hrc>=0, "H5Fclose");
free(points);
free(check);
MPI_Barrier(MPI_COMM_WORLD);
}
/*-------------------------------------------------------------------------
* Function: test_filter_read
*
* Purpose: Tests parallel reading of datasets written serially using
* several (combinations of) filters.
*
* Programmer: Christian Chilan
* Tuesday, May 15, 2007
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
test_filter_read(void)
{
hid_t dc; /* HDF5 IDs */
const hsize_t chunk_size[2] = {CHUNK_DIM1, CHUNK_DIM2}; /* Chunk dimensions */
hsize_t null_size; /* Size of dataset without filters */
herr_t hrc;
const char *filename;
#ifdef H5_HAVE_FILTER_FLETCHER32
hsize_t fletcher32_size; /* Size of dataset with Fletcher32 checksum */
#endif /* H5_HAVE_FILTER_FLETCHER32 */
#ifdef H5_HAVE_FILTER_DEFLATE
hsize_t deflate_size; /* Size of dataset with deflate filter */
#endif /* H5_HAVE_FILTER_DEFLATE */
#ifdef H5_HAVE_FILTER_SZIP
hsize_t szip_size; /* Size of dataset with szip filter */
unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK;
unsigned szip_pixels_per_block=4;
#endif /* H5_HAVE_FILTER_SZIP */
#ifdef H5_HAVE_FILTER_SHUFFLE
hsize_t shuffle_size; /* Size of dataset with shuffle filter */
#endif /* H5_HAVE_FILTER_SHUFFLE */
#if(defined H5_HAVE_FILTER_DEFLATE | defined H5_HAVE_FILTER_SZIP) && defined H5_HAVE_FILTER_SHUFFLE && defined H5_HAVE_FILTER_FLETCHER32
hsize_t combo_size; /* Size of dataset with shuffle+deflate filter */
#endif /* H5_HAVE_FILTER_DEFLATE && H5_HAVE_FILTER_SHUFFLE && H5_HAVE_FILTER_FLETCHER32 */
filename = GetTestParameters();
if(VERBOSE_MED)
printf("Parallel reading of dataset written with filters %s\n", filename);
/*----------------------------------------------------------
* STEP 0: Test without filters.
*----------------------------------------------------------
*/
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0,"H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0,"H5Pset_chunk");
filter_read_internal(filename,dc,&null_size);
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0,"H5Pclose");
/*----------------------------------------------------------
* STEP 1: Test Fletcher32 Checksum by itself.
*----------------------------------------------------------
*/
#ifdef H5_HAVE_FILTER_FLETCHER32
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0,"H5Pset_filter");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0,"H5Pset_filter");
hrc = H5Pset_filter (dc,H5Z_FILTER_FLETCHER32,0,0,NULL);
VRFY(hrc>=0,"H5Pset_filter");
filter_read_internal(filename,dc,&fletcher32_size);
VRFY(fletcher32_size > null_size,"Size after checksumming is incorrect.");
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
#endif /* H5_HAVE_FILTER_FLETCHER32 */
/*----------------------------------------------------------
* STEP 2: Test deflation by itself.
*----------------------------------------------------------
*/
#ifdef H5_HAVE_FILTER_DEFLATE
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0, "H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0, "H5Pset_chunk");
hrc = H5Pset_deflate (dc, 6);
VRFY(hrc>=0, "H5Pset_deflate");
filter_read_internal(filename,dc,&deflate_size);
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
#endif /* H5_HAVE_FILTER_DEFLATE */
/*----------------------------------------------------------
* STEP 3: Test szip compression by itself.
*----------------------------------------------------------
*/
#ifdef H5_HAVE_FILTER_SZIP
if(h5_szip_can_encode() == 1) {
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0, "H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0, "H5Pset_chunk");
hrc = H5Pset_szip(dc, szip_options_mask, szip_pixels_per_block);
VRFY(hrc>=0, "H5Pset_szip");
filter_read_internal(filename,dc,&szip_size);
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
}
#endif /* H5_HAVE_FILTER_SZIP */
/*----------------------------------------------------------
* STEP 4: Test shuffling by itself.
*----------------------------------------------------------
*/
#ifdef H5_HAVE_FILTER_SHUFFLE
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0, "H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0, "H5Pset_chunk");
hrc = H5Pset_shuffle (dc);
VRFY(hrc>=0, "H5Pset_shuffle");
filter_read_internal(filename,dc,&shuffle_size);
VRFY(shuffle_size==null_size,"Shuffled size not the same as uncompressed size.");
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
#endif /* H5_HAVE_FILTER_SHUFFLE */
/*----------------------------------------------------------
* STEP 5: Test shuffle + deflate + checksum in any order.
*----------------------------------------------------------
*/
#if defined H5_HAVE_FILTER_DEFLATE && defined H5_HAVE_FILTER_SHUFFLE && defined H5_HAVE_FILTER_FLETCHER32
/* Testing shuffle+deflate+checksum filters (checksum first) */
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0, "H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0, "H5Pset_chunk");
hrc = H5Pset_fletcher32 (dc);
VRFY(hrc>=0, "H5Pset_fletcher32");
hrc = H5Pset_shuffle (dc);
VRFY(hrc>=0, "H5Pset_shuffle");
hrc = H5Pset_deflate (dc, 6);
VRFY(hrc>=0, "H5Pset_deflate");
filter_read_internal(filename,dc,&combo_size);
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
/* Testing shuffle+deflate+checksum filters (checksum last) */
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0, "H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0, "H5Pset_chunk");
hrc = H5Pset_shuffle (dc);
VRFY(hrc>=0, "H5Pset_shuffle");
hrc = H5Pset_deflate (dc, 6);
VRFY(hrc>=0, "H5Pset_deflate");
hrc = H5Pset_fletcher32 (dc);
VRFY(hrc>=0, "H5Pset_fletcher32");
filter_read_internal(filename,dc,&combo_size);
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
#endif /* H5_HAVE_FILTER_DEFLATE && H5_HAVE_FILTER_SHUFFLE && H5_HAVE_FILTER_FLETCHER32 */
/*----------------------------------------------------------
* STEP 6: Test shuffle + szip + checksum in any order.
*----------------------------------------------------------
*/
#if defined H5_HAVE_FILTER_SZIP && defined H5_HAVE_FILTER_SHUFFLE && defined H5_HAVE_FILTER_FLETCHER32
/* Testing shuffle+szip(with encoder)+checksum filters(checksum first) */
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0, "H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0, "H5Pset_chunk");
hrc = H5Pset_fletcher32 (dc);
VRFY(hrc>=0, "H5Pset_fletcher32");
hrc = H5Pset_shuffle (dc);
VRFY(hrc>=0, "H5Pset_shuffle");
/* Make sure encoding is enabled */
if(h5_szip_can_encode() == 1) {
hrc = H5Pset_szip(dc, szip_options_mask, szip_pixels_per_block);
VRFY(hrc>=0, "H5Pset_szip");
filter_read_internal(filename,dc,&combo_size);
}
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
/* Testing shuffle+szip(with encoder)+checksum filters(checksum last) */
/* Make sure encoding is enabled */
if(h5_szip_can_encode() == 1) {
dc = H5Pcreate(H5P_DATASET_CREATE);
VRFY(dc>=0, "H5Pcreate");
hrc = H5Pset_chunk (dc, 2, chunk_size);
VRFY(hrc>=0, "H5Pset_chunk");
hrc = H5Pset_shuffle (dc);
VRFY(hrc>=0, "H5Pset_shuffle");
hrc = H5Pset_szip(dc, szip_options_mask, szip_pixels_per_block);
VRFY(hrc>=0, "H5Pset_szip");
hrc = H5Pset_fletcher32 (dc);
VRFY(hrc>=0, "H5Pset_fletcher32");
filter_read_internal(filename,dc,&combo_size);
/* Clean up objects used for this test */
hrc = H5Pclose (dc);
VRFY(hrc>=0, "H5Pclose");
}
#endif /* H5_HAVE_FILTER_SZIP && H5_HAVE_FILTER_SHUFFLE && H5_HAVE_FILTER_FLETCHER32 */
}
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