mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-12-27 08:01:04 +08:00
f859cb732b
* fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
550 lines
19 KiB
C
550 lines
19 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 is copied from use_append_chunk.c with modifications to show
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* the usage of H5Odisable_mdc_flushes/H5Oenable_mdc_flushes/H5Oare_mdc_flushes_disabled public routines.
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*/
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#include "h5test.h"
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/* This test uses many POSIX things that are not available on
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* Windows.
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*/
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#ifdef H5_HAVE_UNISTD_H
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#define H5D_FRIEND /*suppress error about including H5Dpkg */
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#define H5D_TESTING
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#include "H5Dpkg.h"
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/* Global Variable definitions */
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const char *progname_g = "use_disable_mdc_flushes"; /* program name */
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/* these two definitions must match each other */
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#define UC_DATATYPE H5T_NATIVE_SHORT /* use case HDF5 data type */
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#define UC_CTYPE short /* use case C data type */
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#define UC_RANK 3 /* use case dataset rank */
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#define Chunksize_DFT 256 /* chunksize default */
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#define Hgoto_error(val) \
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{ \
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ret_value = val; \
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goto done; \
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}
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char * filename_g;
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hsize_t nplanes_g;
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int use_swmr_g;
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int chunkplanes_g;
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int chunksize_g;
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hsize_t dims_g[UC_RANK];
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hsize_t max_dims_g[UC_RANK];
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hsize_t chunkdims_g[UC_RANK];
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static void usage(const char *prog);
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static int parse_option(int argc, char *const argv[]);
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static void show_parameters(void);
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static int create_file(void);
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static int setup_parameters(int argc, char *const argv[]);
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/*
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* Note: Long options are not yet implemented.
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*
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* usage: use_disable_mdc_flushes [OPTIONS]
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* OPTIONS
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* -h, --help Print a usage message and exit
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* -f FN Test file name [default: use_disable_mdc_flushes.h5]
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* -n N, --nplanes=N Number of planes to write. [default: 1000]
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* -s N, --swmr=N Use SWMR mode (0: no, non-0: yes) default is yes
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* -z N, --chunksize=N Chunk size [default: 256]
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* -y N, --chunkplanes=N Number of planes per chunk [default: 1]
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*/
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static void
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usage(const char *prog)
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{
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HDfprintf(stderr, "usage: %s [OPTIONS]\n", prog);
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HDfprintf(stderr, " OPTIONS\n");
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HDfprintf(stderr, " -h Print a usage message and exit\n");
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HDfprintf(stderr, " -f FN Test file name [default: %s.h5]\n", prog);
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HDfprintf(stderr, " -n N Number of planes to write. [default: 1000]\n");
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HDfprintf(stderr, " -s N Use SWMR mode (0: no, non-0: yes) default is yes\n");
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HDfprintf(stderr, " -z N Chunk size [default: %d]\n", Chunksize_DFT);
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HDfprintf(stderr, " -y N Number of planes per chunk [default: 1]\n");
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HDfprintf(stderr, "\n");
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} /* usage() */
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/*
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* Setup Use Case parameters by parsing command line options.
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* Setup default values if not set by options. */
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static int
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parse_option(int argc, char *const argv[])
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{
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int ret_value = 0;
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int c;
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/* command line options: See function usage for a description */
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const char *cmd_options = "f:hn:s:y:z:";
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/* suppress getopt from printing error */
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opterr = 0;
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while (1) {
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c = getopt(argc, argv, cmd_options);
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if (-1 == c)
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break;
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switch (c) {
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case 'h':
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usage(progname_g);
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HDexit(EXIT_SUCCESS);
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break;
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case 'f': /* usecase data file name */
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filename_g = optarg;
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break;
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case 'n': /* number of planes to write/read */
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if ((nplanes_g = (hsize_t)HDatoi(optarg)) <= 0) {
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HDfprintf(stderr, "bad number of planes %s, must be a positive integer\n", optarg);
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usage(progname_g);
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Hgoto_error(-1);
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};
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break;
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case 's': /* use swmr file open mode */
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if ((use_swmr_g = HDatoi(optarg)) < 0) {
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HDfprintf(stderr, "swmr value should be 0(no) or 1(yes)\n");
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usage(progname_g);
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Hgoto_error(-1);
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};
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break;
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case 'y': /* Number of planes per chunk */
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if ((chunkplanes_g = HDatoi(optarg)) <= 0) {
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HDfprintf(stderr, "bad number of planes per chunk %s, must be a positive integer\n",
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optarg);
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usage(progname_g);
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Hgoto_error(-1);
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};
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break;
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case 'z': /* size of chunk=(z,z) */
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if ((chunksize_g = HDatoi(optarg)) <= 0) {
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HDfprintf(stderr, "bad chunksize %s, must be a positive integer\n", optarg);
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usage(progname_g);
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Hgoto_error(-1);
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};
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break;
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case '?':
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HDfprintf(stderr, "getopt returned '%c'.\n", c);
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Hgoto_error(-1);
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default:
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HDfprintf(stderr, "getopt returned unexpected value.\n");
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HDfprintf(stderr, "Unexpected value is %d\n", c);
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Hgoto_error(-1);
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}
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}
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/* set test file name if not given */
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if (!filename_g) {
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/* default data file name is <progname>.h5 */
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if ((filename_g = (char *)HDmalloc(HDstrlen(progname_g) + 4)) == NULL) {
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HDfprintf(stderr, "malloc: failed\n");
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Hgoto_error(-1);
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};
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HDstrcpy(filename_g, progname_g);
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HDstrcat(filename_g, ".h5");
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}
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done:
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/* All done. */
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return (ret_value);
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} /* parse_option() */
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/* Show parameters used for this use case */
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static void
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show_parameters(void)
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{
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HDprintf("===Parameters used:===\n");
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HDprintf("chunk dims=(%llu, %llu, %llu)\n", (unsigned long long)chunkdims_g[0],
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(unsigned long long)chunkdims_g[1], (unsigned long long)chunkdims_g[2]);
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HDprintf("dataset max dims=(%llu, %llu, %llu)\n", (unsigned long long)max_dims_g[0],
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(unsigned long long)max_dims_g[1], (unsigned long long)max_dims_g[2]);
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HDprintf("number of planes to write=%llu\n", (unsigned long long)nplanes_g);
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HDprintf("using SWMR mode=%s\n", use_swmr_g ? "yes(1)" : "no(0)");
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HDprintf("data filename=%s\n", filename_g);
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HDprintf("===Parameters shown===\n");
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} /* show_parameters() */
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/*
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* Setup parameters for the use case.
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* Return: 0 succeed; -1 fail.
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*/
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static int
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setup_parameters(int argc, char *const argv[])
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{
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/* use case defaults */
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chunksize_g = Chunksize_DFT;
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use_swmr_g = 1; /* use swmr open */
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chunkplanes_g = 1;
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/* parse options */
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if (parse_option(argc, argv) < 0) {
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return (-1);
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}
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/* set chunk dims */
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chunkdims_g[0] = (hsize_t)chunkplanes_g;
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chunkdims_g[1] = chunkdims_g[2] = (hsize_t)chunksize_g;
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/* set dataset initial and max dims */
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dims_g[0] = 0;
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max_dims_g[0] = H5S_UNLIMITED;
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dims_g[1] = dims_g[2] = max_dims_g[1] = max_dims_g[2] = (hsize_t)chunksize_g;
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/* set nplanes */
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if (nplanes_g == 0)
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nplanes_g = (hsize_t)chunksize_g;
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/* show parameters and return */
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show_parameters();
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return (0);
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} /* setup_parameters() */
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/*
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* Create the skeleton use case file for testing.
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* It has one 3d dataset using chunked storage.
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* The dataset is (unlimited, chunksize, chunksize).
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* Dataset type is 2 bytes integer.
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* It starts out "empty", i.e., first dimension is 0.
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*
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* Return: 0 succeed; -1 fail.
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*/
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static int
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create_file(void)
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{
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hsize_t dims[3]; /* Dataset starting dimensions */
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hid_t fid; /* File ID for new HDF5 file */
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hid_t dcpl; /* Dataset creation property list */
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hid_t sid; /* Dataspace ID */
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hid_t dsid; /* Dataset ID */
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hid_t fapl; /* File access property list */
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H5D_chunk_index_t idx_type; /* Chunk index type */
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/* Create the file */
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if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
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return -1;
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if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
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return -1;
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if ((fid = H5Fcreate(filename_g, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
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return -1;
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/* Set up dimension sizes */
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dims[0] = 0;
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dims[1] = dims[2] = max_dims_g[1];
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/* Create dataspace for creating datasets */
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if ((sid = H5Screate_simple(3, dims, max_dims_g)) < 0)
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return -1;
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/* Create dataset creation property list */
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if ((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
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return -1;
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if (H5Pset_chunk(dcpl, 3, chunkdims_g) < 0)
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return -1;
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/* create dataset of progname */
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if ((dsid = H5Dcreate2(fid, progname_g, UC_DATATYPE, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
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return -1;
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/* Check that the chunk index type is not version 1 B-tree.
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* Version 1 B-trees are not supported under SWMR.
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*/
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if (H5D__layout_idx_type_test(dsid, &idx_type) < 0)
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return -1;
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if (idx_type == H5D_CHUNK_IDX_BTREE) {
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HDfprintf(stderr, "ERROR: Chunk index is version 1 B-tree: aborting.\n");
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return -1;
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}
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/* Close everything */
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if (H5Dclose(dsid) < 0)
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return -1;
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if (H5Pclose(fapl) < 0)
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return -1;
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if (H5Pclose(dcpl) < 0)
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return -1;
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if (H5Sclose(sid) < 0)
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return -1;
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if (H5Fclose(fid) < 0)
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return -1;
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return 0;
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} /* create_file() */
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/*
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* Append planes, each of (1,2*chunksize,2*chunksize) to the dataset.
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* In other words, 4 chunks are appended to the dataset at a time.
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* Fill each plane with the plane number and then write it at the nth plane.
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* Increase the plane number and repeat till the end of dataset, when it
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* reaches chunksize long. End product is a (2*chunksize)^3 cube.
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*
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* Return: 0 succeed; -1 fail.
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*/
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static int
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write_file(void)
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{
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hid_t fid; /* File ID for new HDF5 file */
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hid_t dsid; /* dataset ID */
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hid_t fapl; /* File access property list */
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hid_t dcpl; /* Dataset creation property list */
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char * name;
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UC_CTYPE *buffer, *bufptr; /* data buffer */
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hsize_t cz = (hsize_t)chunksize_g; /* Chunk size */
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hid_t f_sid; /* dataset file space id */
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hid_t m_sid; /* memory space id */
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int rank; /* rank */
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hsize_t chunk_dims[3]; /* Chunk dimensions */
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hsize_t dims[3]; /* Dataspace dimensions */
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hsize_t memdims[3]; /* Memory space dimensions */
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hsize_t start[3] = {0, 0, 0}, count[3]; /* Hyperslab selection values */
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hbool_t disabled; /* Object's disabled status */
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hsize_t i, j, k;
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name = filename_g;
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/* Open the file */
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if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
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return -1;
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if (use_swmr_g)
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if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
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return -1;
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if ((fid = H5Fopen(name, H5F_ACC_RDWR | (use_swmr_g ? H5F_ACC_SWMR_WRITE : 0), fapl)) < 0) {
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HDfprintf(stderr, "H5Fopen failed\n");
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return -1;
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}
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/* Open the dataset of the program name */
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if ((dsid = H5Dopen2(fid, progname_g, H5P_DEFAULT)) < 0) {
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HDfprintf(stderr, "H5Dopen2 failed\n");
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return -1;
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}
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/* Disabled mdc flushed for the dataset */
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if (H5Odisable_mdc_flushes(dsid) < 0) {
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HDfprintf(stderr, "H5Odisable_mdc_flushes failed\n");
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return -1;
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}
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/* Get mdc disabled status of the dataset */
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if (H5Oare_mdc_flushes_disabled(dsid, &disabled) < 0) {
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HDfprintf(stderr, "H5Oare_mdc_flushes_disabled failed\n");
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return -1;
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}
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else if (disabled)
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HDprintf("Dataset has disabled mdc flushes.\n");
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else
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HDprintf("Dataset should have disabled its mdc flushes.\n");
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/* Find chunksize used */
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if ((dcpl = H5Dget_create_plist(dsid)) < 0) {
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HDfprintf(stderr, "H5Dget_create_plist failed\n");
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return -1;
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}
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if (H5D_CHUNKED != H5Pget_layout(dcpl)) {
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HDfprintf(stderr, "storage layout is not chunked\n");
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return -1;
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}
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if ((rank = H5Pget_chunk(dcpl, 3, chunk_dims)) != 3) {
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HDfprintf(stderr, "storage rank is not 3\n");
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return -1;
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}
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/* verify chunk_dims against set parameters */
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if (chunk_dims[0] != chunkdims_g[0] || chunk_dims[1] != cz || chunk_dims[2] != cz) {
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HDfprintf(stderr, "chunk size is not as expected. Got dims=(%llu,%llu,%llu)\n",
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(unsigned long long)chunk_dims[0], (unsigned long long)chunk_dims[1],
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(unsigned long long)chunk_dims[2]);
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return -1;
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}
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/* allocate space for data buffer 1 X dims[1] X dims[2] of UC_CTYPE */
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memdims[0] = 1;
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memdims[1] = dims_g[1];
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memdims[2] = dims_g[2];
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if ((buffer = (UC_CTYPE *)HDmalloc((size_t)memdims[1] * (size_t)memdims[2] * sizeof(UC_CTYPE))) == NULL) {
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HDfprintf(stderr, "malloc: failed\n");
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return -1;
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};
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/*
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* Get dataset rank and dimension.
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*/
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f_sid = H5Dget_space(dsid); /* Get filespace handle first. */
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rank = H5Sget_simple_extent_ndims(f_sid);
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if (rank != UC_RANK) {
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HDfprintf(stderr, "rank(%d) of dataset does not match\n", rank);
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return -1;
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}
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if (H5Sget_simple_extent_dims(f_sid, dims, NULL) < 0) {
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HDfprintf(stderr, "H5Sget_simple_extent_dims got error\n");
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return -1;
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}
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HDprintf("dataset rank %d, dimensions %llu x %llu x %llu\n", rank, (unsigned long long)(dims[0]),
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(unsigned long long)(dims[1]), (unsigned long long)(dims[2]));
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/* verify that file space dims are as expected and are consistent with memory space dims */
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if (dims[0] != 0 || dims[1] != memdims[1] || dims[2] != memdims[2]) {
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HDfprintf(stderr, "dataset is not empty. Got dims=(%llu,%llu,%llu)\n", (unsigned long long)dims[0],
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(unsigned long long)dims[1], (unsigned long long)dims[2]);
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return -1;
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}
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/* setup mem-space for buffer */
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if ((m_sid = H5Screate_simple(rank, memdims, NULL)) < 0) {
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HDfprintf(stderr, "H5Screate_simple for memory failed\n");
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return -1;
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};
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/* write planes */
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count[0] = 1;
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count[1] = dims[1];
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count[2] = dims[2];
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for (i = 0; i < nplanes_g; i++) {
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/* fill buffer with value i+1 */
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bufptr = buffer;
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for (j = 0; j < dims[1]; j++)
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for (k = 0; k < dims[2]; k++) {
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if (i > SHRT_MAX) {
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HDfprintf(stderr, "rank(%d) of dataset overflow\n", rank);
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return -1;
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}
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*bufptr++ = (short)i;
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}
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/* extend the dataset by one for new plane */
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dims[0] = i + 1;
|
|
if (H5Dset_extent(dsid, dims) < 0) {
|
|
HDfprintf(stderr, "H5Dset_extent failed\n");
|
|
return -1;
|
|
}
|
|
|
|
/* Get the dataset's dataspace */
|
|
if ((f_sid = H5Dget_space(dsid)) < 0) {
|
|
HDfprintf(stderr, "H5Dset_extent failed\n");
|
|
return -1;
|
|
}
|
|
|
|
start[0] = i;
|
|
/* Choose the next plane to write */
|
|
if (H5Sselect_hyperslab(f_sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0) {
|
|
HDfprintf(stderr, "Failed H5Sselect_hyperslab\n");
|
|
return -1;
|
|
}
|
|
|
|
/* Write plane to the dataset */
|
|
if (H5Dwrite(dsid, UC_DATATYPE, m_sid, f_sid, H5P_DEFAULT, buffer) < 0) {
|
|
HDfprintf(stderr, "Failed H5Dwrite\n");
|
|
return -1;
|
|
}
|
|
|
|
/* Flush the dataset for every "chunkplanes_g" planes */
|
|
if (!((i + 1) % (hsize_t)chunkplanes_g)) {
|
|
if (H5Dflush(dsid) < 0) {
|
|
HDfprintf(stderr, "Failed to H5Dflush dataset\n");
|
|
return -1;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (H5Dflush(dsid) < 0) {
|
|
HDfprintf(stderr, "Failed to H5Dflush dataset\n");
|
|
return -1;
|
|
}
|
|
|
|
/* Enable mdc flushes for the dataset */
|
|
/* Closing the dataset later will enable mdc flushes automatically if this is not done */
|
|
if (disabled)
|
|
if (H5Oenable_mdc_flushes(dsid) < 0) {
|
|
HDfprintf(stderr, "Failed to H5Oenable_mdc_flushes\n");
|
|
return -1;
|
|
}
|
|
|
|
/* Done writing. Free/Close all resources including data file */
|
|
HDfree(buffer);
|
|
|
|
if (H5Dclose(dsid) < 0) {
|
|
HDfprintf(stderr, "Failed to close datasete\n");
|
|
return -1;
|
|
}
|
|
if (H5Sclose(m_sid) < 0) {
|
|
HDfprintf(stderr, "Failed to close memory space\n");
|
|
return -1;
|
|
}
|
|
if (H5Sclose(f_sid) < 0) {
|
|
HDfprintf(stderr, "Failed to close file space\n");
|
|
return -1;
|
|
}
|
|
if (H5Pclose(fapl) < 0) {
|
|
HDfprintf(stderr, "Failed to property list\n");
|
|
return -1;
|
|
}
|
|
if (H5Fclose(fid) < 0) {
|
|
HDfprintf(stderr, "Failed to close file id\n");
|
|
return -1;
|
|
}
|
|
|
|
return 0;
|
|
} /* write_file() */
|
|
|
|
/* Overall Algorithm:
|
|
* Parse options from user;
|
|
* Generate/pre-created test files needed and close it;
|
|
* Write to the file.
|
|
*/
|
|
int
|
|
main(int argc, char *argv[])
|
|
{
|
|
int ret_value = 0;
|
|
|
|
/* initialization */
|
|
if (setup_parameters(argc, argv) < 0)
|
|
Hgoto_error(1);
|
|
|
|
/* ============*/
|
|
/* Create file */
|
|
/* ============*/
|
|
HDprintf("Creating skeleton data file for testing H5Odisable_mdc_flushes()...\n");
|
|
if (create_file() < 0) {
|
|
HDfprintf(stderr, "***encounter error\n");
|
|
Hgoto_error(1);
|
|
} /* end if */
|
|
else
|
|
HDprintf("File created.\n");
|
|
|
|
HDprintf("writing to the file\n");
|
|
if (write_file() < 0) {
|
|
HDfprintf(stderr, "write_file encountered error\n");
|
|
Hgoto_error(1);
|
|
}
|
|
|
|
done:
|
|
/* Print result and exit */
|
|
if (ret_value != 0)
|
|
HDprintf("Error(s) encountered\n");
|
|
else
|
|
HDprintf("All passed\n");
|
|
|
|
return (ret_value);
|
|
}
|
|
|
|
#else /* H5_HAVE_UNISTD_H */
|
|
|
|
int
|
|
main(void)
|
|
{
|
|
HDfprintf(stderr, "Non-POSIX platform. Skipping.\n");
|
|
HDexit(EXIT_SUCCESS);
|
|
} /* end main() */
|
|
|
|
#endif /* H5_HAVE_UNISTD_H */
|