mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-01-12 15:04:59 +08:00
11dfa25910
* Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
701 lines
20 KiB
C
701 lines
20 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the COPYING file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* This tests the performance of the H5Dwrite_chunk() function.
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*
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*/
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#include "hdf5.h"
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#ifdef H5_HAVE_FILTER_DEFLATE
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#include <zlib.h>
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#if !defined(WIN32) && !defined(__MINGW32__)
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#include <errno.h>
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#include <fcntl.h>
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <time.h>
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#ifdef H5_HAVE_SYS_STAT_H
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#include <sys/stat.h>
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#endif
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#ifdef H5_HAVE_SYS_TIME_H
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#include <sys/time.h>
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#endif
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#ifdef H5_HAVE_SYS_TYPES_H
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#include <sys/types.h>
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#endif
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#ifdef H5_HAVE_UNISTD_H
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#include <unistd.h>
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#endif
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const char *FILENAME[] = {"direct_write", "unix.raw", NULL};
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/*
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* Print the current location on the standard output stream.
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*/
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#define AT() printf(" at %s:%d in %s()...\n", __FILE__, __LINE__, __func__);
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#define H5_FAILED() \
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{ \
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puts("*FAILED*"); \
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fflush(stdout); \
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}
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#define TEST_ERROR \
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{ \
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H5_FAILED(); \
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AT(); \
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goto error; \
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}
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#define TESTING(WHAT) \
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{ \
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printf("Testing %-62s", WHAT); \
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fflush(stdout); \
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}
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#define PASSED() \
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{ \
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puts(" PASSED"); \
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fflush(stdout); \
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}
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#define DIRECT_UNCOMPRESSED_DSET "direct_uncompressed_dset"
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#define DIRECT_COMPRESSED_DSET "direct_compressed_dset"
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#define REG_COMPRESSED_DSET "reg_compressed_dset"
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#define REG_NO_COMPRESS_DSET "reg_no_compress_dset"
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#define RANK 3
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#define NX 100
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#define NY 1000
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#define NZ 250
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#define CHUNK_NX 1
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#define CHUNK_NY 1000
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#define CHUNK_NZ 250
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#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s)) * 1.001) + 12)
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char filename[1024];
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unsigned int *outbuf[NX];
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size_t data_size[NX];
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double total_size = 0.0;
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unsigned int *direct_buf[NX];
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double MB = 1048576.0;
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/*--------------------------------------------------
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* Function to report IO rate
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*--------------------------------------------------
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*/
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void
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reportTime(struct timeval start, double mbytes)
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{
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struct timeval timeval_stop, timeval_diff;
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/*end timing*/
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gettimeofday(&timeval_stop, NULL);
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/* Calculate the elapsed gettimeofday time */
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timeval_diff.tv_usec = timeval_stop.tv_usec - start.tv_usec;
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timeval_diff.tv_sec = timeval_stop.tv_sec - start.tv_sec;
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if (timeval_diff.tv_usec < 0) {
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timeval_diff.tv_usec += 1000000;
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timeval_diff.tv_sec--;
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} /* end if */
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/*printf("mbytes=%lf, sec=%lf, usec=%lf\n", mbytes, (double)timeval_diff.tv_sec,
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* (double)timeval_diff.tv_usec);*/
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printf("MBytes/second: %lf\n", (double)mbytes / ((double)timeval_diff.tv_sec +
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((double)timeval_diff.tv_usec / (double)1000000.0)));
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}
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/*--------------------------------------------------
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* Create file, datasets, and initialize data
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*--------------------------------------------------
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*/
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int
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create_file(hid_t fapl_id)
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{
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hid_t file; /* handles */
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hid_t fapl;
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hid_t cparms;
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hid_t dataspace, dataset;
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hsize_t dims[RANK] = {NX, NY, NZ};
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hsize_t chunk_dims[RANK] = {CHUNK_NX, CHUNK_NY, CHUNK_NZ};
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unsigned int aggression = 9; /* Compression aggression setting */
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int ret;
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int i, j, n;
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int flag;
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int unix_file;
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unsigned int *p;
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size_t buf_size = CHUNK_NY * CHUNK_NZ * sizeof(unsigned int);
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const Bytef *z_src;
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Bytef *z_dst; /*destination buffer */
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uLongf z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
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uLong z_src_nbytes = (uLong)buf_size;
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TESTING("Create a file and dataset");
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/*
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* Create the data space with unlimited dimensions.
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*/
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if ((dataspace = H5Screate_simple(RANK, dims, NULL)) < 0)
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TEST_ERROR;
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/*
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* Create a new file. If file exists its contents will be overwritten.
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*/
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if ((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id)) < 0)
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TEST_ERROR;
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/*
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* Modify dataset creation properties, i.e. enable chunking and compression
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*/
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if ((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
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TEST_ERROR;
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if (H5Pset_chunk(cparms, RANK, chunk_dims) < 0)
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TEST_ERROR;
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/*
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* Create a new dataset within the file using cparms
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* creation properties.
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*/
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if ((dataset = H5Dcreate2(file, DIRECT_UNCOMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms,
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H5P_DEFAULT)) < 0)
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TEST_ERROR;
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if (H5Dclose(dataset) < 0)
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TEST_ERROR;
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if ((dataset = H5Dcreate2(file, REG_NO_COMPRESS_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms,
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H5P_DEFAULT)) < 0)
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TEST_ERROR;
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if (H5Dclose(dataset) < 0)
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TEST_ERROR;
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/* Set compression */
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if (H5Pset_deflate(cparms, aggression) < 0)
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TEST_ERROR;
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if ((dataset = H5Dcreate2(file, DIRECT_COMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms,
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H5P_DEFAULT)) < 0)
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TEST_ERROR;
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if (H5Dclose(dataset) < 0)
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TEST_ERROR;
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if ((dataset = H5Dcreate2(file, REG_COMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms,
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H5P_DEFAULT)) < 0)
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TEST_ERROR;
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if (H5Dclose(dataset) < 0)
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TEST_ERROR;
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if (H5Fclose(file) < 0)
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TEST_ERROR;
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if (H5Sclose(dataspace) < 0)
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TEST_ERROR;
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if (H5Pclose(cparms) < 0)
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TEST_ERROR;
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/* create a unix file*/
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flag = O_CREAT | O_TRUNC | O_WRONLY;
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if ((unix_file = open(FILENAME[1], flag, S_IRWXU)) == -1)
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TEST_ERROR;
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if (close(unix_file) < 0) {
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printf(" unable to close the file\n");
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TEST_ERROR;
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}
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/* Initialize data for chunks */
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for (i = 0; i < NX; i++) {
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p = direct_buf[i] = (unsigned int *)malloc(CHUNK_NY * CHUNK_NZ * sizeof(unsigned int));
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for (j = 0; j < CHUNK_NY * CHUNK_NZ; j++, p++)
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*p = rand() % 65000;
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z_src = (const Bytef *)direct_buf[i];
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z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
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/* Allocate output (compressed) buffer */
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outbuf[i] = (unsigned int *)malloc((size_t)z_dst_nbytes);
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z_dst = (Bytef *)outbuf[i];
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/* Perform compression from the source to the destination buffer */
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ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
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data_size[i] = (size_t)z_dst_nbytes;
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total_size += data_size[i];
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/* Check for various zlib errors */
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if (Z_BUF_ERROR == ret) {
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fprintf(stderr, "overflow");
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TEST_ERROR;
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}
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else if (Z_MEM_ERROR == ret) {
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fprintf(stderr, "deflate memory error");
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TEST_ERROR;
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}
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else if (Z_OK != ret) {
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fprintf(stderr, "other deflate error");
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TEST_ERROR;
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}
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}
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PASSED();
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error:
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H5E_BEGIN_TRY
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{
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H5Dclose(dataset);
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H5Sclose(dataspace);
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H5Pclose(cparms);
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H5Fclose(file);
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}
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H5E_END_TRY;
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return 1;
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}
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/*--------------------------------------------------
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* Benchmark the performance of the new function
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* with precompressed data.
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*--------------------------------------------------
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*/
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int
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test_direct_write_uncompressed_data(hid_t fapl_id)
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{
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hid_t file; /* handles */
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hid_t dataspace, dataset;
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hid_t dxpl;
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herr_t status;
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int i;
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unsigned filter_mask = 0;
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hsize_t offset[RANK] = {0, 0, 0};
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struct timeval timeval_start;
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TESTING("H5Dwrite_chunk for uncompressed data");
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if ((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
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TEST_ERROR;
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/* Start the timer */
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gettimeofday(&timeval_start, NULL);
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/* Reopen the file and dataset */
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if ((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
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TEST_ERROR;
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if ((dataset = H5Dopen2(file, DIRECT_UNCOMPRESSED_DSET, H5P_DEFAULT)) < 0)
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TEST_ERROR;
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/* Write the compressed chunk data repeatedly to cover all the chunks in the
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* dataset, using the direct writing function. */
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for (i = 0; i < NX; i++) {
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status = H5Dwrite_chunk(dataset, dxpl, filter_mask, offset,
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CHUNK_NY * CHUNK_NZ * sizeof(unsigned int), direct_buf[i]);
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(offset[0])++;
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}
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/*
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* Close/release resources.
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*/
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H5Dclose(dataset);
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H5Pclose(dxpl);
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H5Fclose(file);
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/* Report the performance */
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reportTime(timeval_start, (double)(NX * NY * NZ * sizeof(unsigned int) / MB));
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PASSED();
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return 0;
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error:
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H5E_BEGIN_TRY
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{
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H5Dclose(dataset);
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H5Pclose(dxpl);
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H5Fclose(file);
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}
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H5E_END_TRY;
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return 1;
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}
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/*--------------------------------------------------
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* Benchmark the performance of the new function
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* with precompressed data.
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*--------------------------------------------------
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*/
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int
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test_direct_write_compressed_data(hid_t fapl_id)
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{
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hid_t file; /* handles */
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hid_t dataspace, dataset;
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hid_t dxpl;
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herr_t status;
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int i;
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unsigned filter_mask = 0;
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hsize_t offset[RANK] = {0, 0, 0};
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struct timeval timeval_start;
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TESTING("H5DOwrite_chunk for pre-compressed data");
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if ((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
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TEST_ERROR;
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/* Start the timer */
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gettimeofday(&timeval_start, NULL);
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/* Reopen the file and dataset */
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if ((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
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TEST_ERROR;
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if ((dataset = H5Dopen2(file, DIRECT_COMPRESSED_DSET, H5P_DEFAULT)) < 0)
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TEST_ERROR;
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/* Write the compressed chunk data repeatedly to cover all the chunks in the
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* dataset, using the direct writing function. */
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for (i = 0; i < NX; i++) {
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status = H5Dwrite_chunk(dataset, dxpl, filter_mask, offset, data_size[i], outbuf[i]);
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(offset[0])++;
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}
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/*
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* Close/release resources.
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*/
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H5Dclose(dataset);
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H5Pclose(dxpl);
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H5Fclose(file);
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/* Report the performance */
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reportTime(timeval_start, (double)(total_size / MB));
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PASSED();
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return 0;
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error:
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H5E_BEGIN_TRY
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{
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H5Dclose(dataset);
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H5Pclose(dxpl);
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H5Fclose(file);
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}
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H5E_END_TRY;
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return 1;
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}
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/*--------------------------------------------------
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* Benchmark the performance of the regular H5Dwrite
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* with compression filter enabled.
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*--------------------------------------------------
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*/
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int
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test_compressed_write(hid_t fapl_id)
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{
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hid_t file; /* handles */
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hid_t dataspace, dataset;
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hid_t mem_space;
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hsize_t chunk_dims[RANK] = {CHUNK_NX, CHUNK_NY, CHUNK_NZ};
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hid_t dxpl;
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herr_t status;
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int i;
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hsize_t start[RANK]; /* Start of hyperslab */
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hsize_t stride[RANK]; /* Stride of hyperslab */
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hsize_t count[RANK]; /* Block count */
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hsize_t block[RANK]; /* Block sizes */
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struct timeval timeval_start;
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TESTING("H5Dwrite with compression enabled");
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if ((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
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TEST_ERROR;
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if ((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
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TEST_ERROR;
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/* Start the timer */
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gettimeofday(&timeval_start, NULL);
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/* Reopen the file and dataset */
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if ((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
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TEST_ERROR;
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if ((dataset = H5Dopen2(file, REG_COMPRESSED_DSET, H5P_DEFAULT)) < 0)
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TEST_ERROR;
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if ((dataspace = H5Dget_space(dataset)) < 0)
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TEST_ERROR;
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start[0] = start[1] = start[2] = 0;
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stride[0] = stride[1] = stride[2] = 1;
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count[0] = count[1] = count[2] = 1;
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block[0] = CHUNK_NX;
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block[1] = CHUNK_NY;
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block[2] = CHUNK_NZ;
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for (i = 0; i < NX; i++) {
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/*
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* Select hyperslab for one chunk in the file
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*/
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if ((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
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TEST_ERROR;
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(start[0])++;
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if ((status = H5Dwrite(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, direct_buf[i])) <
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0)
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TEST_ERROR;
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}
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/*
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* Close/release resources.
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*/
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H5Dclose(dataset);
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H5Sclose(dataspace);
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H5Sclose(mem_space);
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H5Pclose(dxpl);
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H5Fclose(file);
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/* Report the performance */
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reportTime(timeval_start, (double)(NX * NY * NZ * sizeof(unsigned int) / MB));
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PASSED();
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return 0;
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error:
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H5E_BEGIN_TRY
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{
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H5Dclose(dataset);
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H5Sclose(dataspace);
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H5Sclose(mem_space);
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H5Pclose(dxpl);
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H5Fclose(file);
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}
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H5E_END_TRY;
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return 1;
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}
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/*--------------------------------------------------
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* Benchmark the performance of the regular H5Dwrite
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* with compression
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*--------------------------------------------------
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*/
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int
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test_no_compress_write(hid_t fapl_id)
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{
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hid_t file; /* handles */
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hid_t dataspace, dataset;
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hid_t mem_space;
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hsize_t chunk_dims[RANK] = {CHUNK_NX, CHUNK_NY, CHUNK_NZ};
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hid_t dxpl;
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herr_t status;
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int i;
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hsize_t start[RANK]; /* Start of hyperslab */
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hsize_t stride[RANK]; /* Stride of hyperslab */
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hsize_t count[RANK]; /* Block count */
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hsize_t block[RANK]; /* Block sizes */
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struct timeval timeval_start;
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TESTING("H5Dwrite without compression");
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if ((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
|
|
TEST_ERROR;
|
|
|
|
if ((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
|
|
TEST_ERROR;
|
|
|
|
/* Start the timer */
|
|
gettimeofday(&timeval_start, NULL);
|
|
|
|
/* Reopen the file and dataset */
|
|
if ((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
|
|
TEST_ERROR;
|
|
|
|
if ((dataset = H5Dopen2(file, REG_NO_COMPRESS_DSET, H5P_DEFAULT)) < 0)
|
|
TEST_ERROR;
|
|
|
|
if ((dataspace = H5Dget_space(dataset)) < 0)
|
|
TEST_ERROR;
|
|
|
|
start[0] = start[1] = start[2] = 0;
|
|
stride[0] = stride[1] = stride[2] = 1;
|
|
count[0] = count[1] = count[2] = 1;
|
|
block[0] = CHUNK_NX;
|
|
block[1] = CHUNK_NY;
|
|
block[2] = CHUNK_NZ;
|
|
|
|
for (i = 0; i < NX; i++) {
|
|
/*
|
|
* Select hyperslab for one chunk in the file
|
|
*/
|
|
if ((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
|
|
TEST_ERROR;
|
|
(start[0])++;
|
|
|
|
if ((status = H5Dwrite(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, direct_buf[i])) <
|
|
0)
|
|
TEST_ERROR;
|
|
}
|
|
|
|
/*
|
|
* Close/release resources.
|
|
*/
|
|
H5Dclose(dataset);
|
|
H5Sclose(dataspace);
|
|
H5Sclose(mem_space);
|
|
H5Pclose(dxpl);
|
|
H5Fclose(file);
|
|
|
|
/* Report the performance */
|
|
reportTime(timeval_start, (double)(NX * NY * NZ * sizeof(unsigned int) / MB));
|
|
|
|
PASSED();
|
|
return 0;
|
|
|
|
error:
|
|
H5E_BEGIN_TRY
|
|
{
|
|
H5Dclose(dataset);
|
|
H5Sclose(dataspace);
|
|
H5Sclose(mem_space);
|
|
H5Pclose(dxpl);
|
|
H5Fclose(file);
|
|
}
|
|
H5E_END_TRY;
|
|
return 1;
|
|
}
|
|
|
|
/*--------------------------------------------------
|
|
* Benchmark the performance for writing compressed
|
|
* data to a Unix file
|
|
*--------------------------------------------------
|
|
*/
|
|
int
|
|
test_unix_write(void)
|
|
{
|
|
int file, flag;
|
|
ssize_t op_size;
|
|
int i;
|
|
struct timeval timeval_start;
|
|
|
|
TESTING("Write compressed data to a Unix file");
|
|
|
|
/* create file*/
|
|
flag = O_WRONLY;
|
|
|
|
/* Start the timer */
|
|
gettimeofday(&timeval_start, NULL);
|
|
|
|
if ((file = open(FILENAME[1], flag)) == -1)
|
|
TEST_ERROR;
|
|
|
|
/* Write the compressed chunk data repeatedly to cover all the chunks in the
|
|
* dataset, using the direct writing function. */
|
|
for (i = 0; i < NX; i++) {
|
|
op_size = write(file, outbuf[i], data_size[i]);
|
|
if (op_size < 0) {
|
|
printf(" Error in writing data to file because %s \n", strerror(errno));
|
|
TEST_ERROR;
|
|
}
|
|
else if (op_size == 0) {
|
|
printf(" unable to write sufficient data to file because %s \n", strerror(errno));
|
|
TEST_ERROR;
|
|
}
|
|
}
|
|
|
|
if (close(file) < 0) {
|
|
printf(" unable to close the file\n");
|
|
TEST_ERROR;
|
|
}
|
|
|
|
/* Report the performance */
|
|
reportTime(timeval_start, (double)(total_size / MB));
|
|
|
|
PASSED();
|
|
return 0;
|
|
|
|
error:
|
|
return 1;
|
|
}
|
|
|
|
/*--------------------------------------------------
|
|
* Main function
|
|
*--------------------------------------------------
|
|
*/
|
|
int
|
|
main(void)
|
|
{
|
|
hid_t fapl = H5P_DEFAULT;
|
|
int i;
|
|
|
|
snprintf(filename, sizeof(filename), "%s.h5", FILENAME[0]);
|
|
|
|
create_file(fapl);
|
|
test_direct_write_uncompressed_data(fapl);
|
|
test_direct_write_compressed_data(fapl);
|
|
test_no_compress_write(fapl);
|
|
test_compressed_write(fapl);
|
|
test_unix_write();
|
|
|
|
for (i = 0; i < NX; i++) {
|
|
free(outbuf[i]);
|
|
free(direct_buf[i]);
|
|
}
|
|
|
|
return 0;
|
|
}
|
|
|
|
#else /* WIN32 / MINGW32 */
|
|
|
|
int
|
|
main(void)
|
|
{
|
|
printf("Non-POSIX platform. Exiting.\n");
|
|
return EXIT_FAILURE;
|
|
} /* end main() */
|
|
|
|
#endif /* WIN32 / MINGW32 */
|
|
|
|
#else /* !H5_HAVE_FILTER_DEFLATE */
|
|
|
|
/*
|
|
* Function: main
|
|
* Purpose: Dummy main() function for if HDF5 was configured without
|
|
* zlib stuff.
|
|
* Return: EXIT_SUCCESS
|
|
*/
|
|
int
|
|
main(void)
|
|
{
|
|
HDfprintf(stdout, "No compression IO performance because zlib was not configured\n");
|
|
return EXIT_SUCCESS;
|
|
}
|
|
|
|
#endif /* !H5_HAVE_FILTER_DEFLATE */
|