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author | Dana Robinson <derobins@hdfgroup.org> | 2015-12-15 09:48:59 (GMT) |
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committer | Dana Robinson <derobins@hdfgroup.org> | 2015-12-15 09:48:59 (GMT) |
commit | 4fe9d56f786f1f43e06655fa238ac7b11a194ba1 (patch) | |
tree | 7b1d0a0d729a2fe508efb0c46360d5204edec7b1 /tools/h5format_convert/h5format_convert.c | |
parent | e9da1c3460abdb32496f9271edf2a2dbbaa4e72b (diff) | |
download | hdf5-4fe9d56f786f1f43e06655fa238ac7b11a194ba1.zip hdf5-4fe9d56f786f1f43e06655fa238ac7b11a194ba1.tar.gz hdf5-4fe9d56f786f1f43e06655fa238ac7b11a194ba1.tar.bz2 |
[svn-r28658] Manual merge of revise_chunks and alpha branch.
Tested on: Unbuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
Autotools serial (C++ Fortran)
Autotools parallel (MPICH 3.1.4, Fortran)
CMake serial (CMake 3.3.2)
Diffstat (limited to 'tools/h5format_convert/h5format_convert.c')
-rw-r--r-- | tools/h5format_convert/h5format_convert.c | 438 |
1 files changed, 438 insertions, 0 deletions
diff --git a/tools/h5format_convert/h5format_convert.c b/tools/h5format_convert/h5format_convert.c new file mode 100644 index 0000000..7686acc --- /dev/null +++ b/tools/h5format_convert/h5format_convert.c @@ -0,0 +1,438 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Programmer: Vailin Choi; Feb 2015 + */ + + +/* + * We include the private header file so we can get to the uniform + * programming environment it declares. + * HDF5 API functions (except for H5G_basename()) + */ +#include "H5private.h" +#include "h5tools.h" +#include "h5tools_utils.h" +#include "h5trav.h" + +/* Name of tool */ +#define PROGRAMNAME "h5format_convert" + +static char *fname_g = NULL; +static char *dname_g = NULL; +static int dset_g = FALSE; +static int noop_g = FALSE; +static int verbose_g = 0; + +/* + * Command-line options: The user can specify short or long-named + * parameters. + */ +static const char *s_opts = "hVvd:n"; +static struct long_options l_opts[] = { + { "help", no_arg, 'h' }, + { "hel", no_arg, 'h'}, + { "he", no_arg, 'h'}, + { "version", no_arg, 'V' }, + { "version", no_arg, 'V' }, + { "versio", no_arg, 'V' }, + { "versi", no_arg, 'V' }, + { "vers", no_arg, 'V' }, + { "verbose", no_arg, 'v' }, + { "verbos", no_arg, 'v' }, + { "verbo", no_arg, 'v' }, + { "verb", no_arg, 'v' }, + { "dname", require_arg, 'd' }, + { "dnam", require_arg, 'd' }, + { "dna", require_arg, 'd' }, + { "dn", require_arg, 'd' }, + { "noop", no_arg, 'n' }, + { "noo", no_arg, 'n' }, + { "no", no_arg, 'n' }, + { NULL, 0, '\0' } +}; + + +/*------------------------------------------------------------------------- + * Function: usage + * + * Purpose: print usage + * + * Return: void + * + *------------------------------------------------------------------------- + */ +static void usage(const char *prog) +{ + printf("usage: %s [OPTIONS] file_name\n", prog); + printf(" OPTIONS\n"); + printf(" -h, --help Print a usage message and exit\n"); + printf(" -V, --version Print version number and exit\n"); + printf(" -v, --verbose Turn on verbose mode\n"); + printf(" -d dname, --dname=dataset_name Pathname for the dataset\n"); + printf(" -n, --noop Perform all the steps except the actual conversion\n"); + printf("\n"); + printf("Examples of use:\n"); + printf("\n"); + printf("h5format_convert -d /group/dataset file_name\n"); + printf(" Convert the chunk indexing type to version 1 B-tree\n"); + printf(" for the chunked dataset </group/dataset> in the HDF5 file <file_name>.\n"); + printf("\n"); + printf("h5format_convert file_name\n"); + printf(" Convert the chunk indexing type to version 1 B-tree\n"); + printf(" for all the chunked datasets in the HDF5 file <file_name>.\n"); + printf("\n"); + printf("h5format_convert -n -d /group/dataset file_name\n"); + printf(" Go through all the steps except the actual conversion when \n"); + printf(" converting the chunked dataset </group/dataset> in the HDF5 file <file_name>.\n"); +} /* usage() */ + +/*------------------------------------------------------------------------- + * Function: parse_command_line + * + * Purpose: parse command line input + * + * Return: Success: 0 + * Failure: 1 + * + *------------------------------------------------------------------------- + */ +static int +parse_command_line(int argc, const char **argv) +{ + int opt; + + /* no arguments */ + if (argc == 1) { + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + goto error; + } + + /* parse command line options */ + while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { + switch((char) opt) { + case 'h': + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_SUCCESS); + goto error; + + case 'V': + print_version(h5tools_getprogname()); + h5tools_setstatus(EXIT_SUCCESS); + goto error; + + case 'v': + verbose_g = TRUE; + break; + + case 'd': /* -d dname */ + if(opt_arg != NULL && *opt_arg) + /* if(opt_arg != NULL)*/ + dname_g = HDstrdup(opt_arg); + if(dname_g == NULL) { + h5tools_setstatus(EXIT_FAILURE); + error_msg("No dataset name\n", opt_arg); + usage(h5tools_getprogname()); + goto error; + } + dset_g = TRUE; + break; + + case 'n': /* -n */ + noop_g = TRUE; + break; + + default: + h5tools_setstatus(EXIT_FAILURE); + usage(h5tools_getprogname()); + goto error; + break; + } /* switch */ + } /* while */ + + if (argc <= opt_ind) { + error_msg("missing file name\n"); + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + goto error; + } + + fname_g = HDstrdup(argv[opt_ind]); + + return(0); + +error: + return(-1); ; +} /* parse_command_line() */ + + +/*------------------------------------------------------------------------- + * Function: leave + * + * Purpose: Close HDF5 + * + * Return: Does not return + * + *------------------------------------------------------------------------- + */ +static void +leave(int ret) +{ + h5tools_close(); + + HDexit(ret); +} /* leave() */ + +/*------------------------------------------------------------------------- + * Function: convert() + * + * Purpose: To change the chunk indexing type for the dataset to version 1 B-tree. + * -- the dataset has to be chunked + * -- the dataset's chunk indexing type is not already version 1 B-tree. + * If the above conditions are not fulfilled, the tool will not perform + * the conversion but will exit with success. + * + * Return: Success: 0 + * Failure: 1 + * + *------------------------------------------------------------------------- + */ +static int +convert(hid_t fid, const char *dname) +{ + hid_t dcpl = -1; + hid_t did = -1; + H5D_layout_t layout_type; + H5D_chunk_index_t idx_type; + + /* Open the dataset */ + if((did = H5Dopen2(fid, dname, H5P_DEFAULT)) < 0) { + error_msg("unable to open dataset \"%s\"\n", dname); + h5tools_setstatus(EXIT_FAILURE); + goto error; + + } else if(verbose_g) + printf("Open the dataset\n"); + + /* Get the dataset's creation property list */ + if((dcpl = H5Dget_create_plist(did)) < 0) { + error_msg("unable to get the dataset creation property list\n"); + h5tools_setstatus(EXIT_FAILURE); + goto error; + } + + /* Get the dataset's layout */ + if((layout_type = H5Pget_layout(dcpl)) < 0) { + error_msg("unable to get the dataset layout type\n"); + h5tools_setstatus(EXIT_FAILURE); + goto error; + + } else if(verbose_g) + printf("Retrieve the dataset's layout\n"); + + /* No further action if not a chunked dataset */ + if(layout_type != H5D_CHUNKED) { + if(verbose_g) + printf("Dataset is not chunked: no further action\n"); + h5tools_setstatus(EXIT_SUCCESS); + goto done; + + } else if(verbose_g) + printf("Verify the dataset is a chunked dataset\n"); + + /* Get the dataset's chunk indexing type */ + if(H5Dget_chunk_index_type(did, &idx_type) < 0) { + error_msg("unable to get the chunk indexing type for \"%s\"\n", dname); + h5tools_setstatus(EXIT_FAILURE); + goto error; + + } else if(verbose_g) + printf("Retrieve the dataset's chunk indexing type\n"); + + /* No further action if the chunk indexing type is already version 1 B-tree */ + if(idx_type == H5D_CHUNK_IDX_BTREE) { + if(verbose_g) + printf("Chunk indexing type is already version 1 B-tree: no further action\n"); + h5tools_setstatus(EXIT_SUCCESS); + goto done; + + } else if (verbose_g) + printf("Verify the dataset's chunk indexing type is not version 1 B-tree\n"); + + /* No further action if it is a noop */ + if(noop_g) { + if(verbose_g) + printf("Not converting the dataset\n"); + h5tools_setstatus(EXIT_SUCCESS); + goto done; + } + + if(verbose_g) + printf("Converting the dataset...\n"); + + /* Convert the dataset's chunk indexing type to version 1 B-tree */ + if(H5Dformat_convert(did) < 0) { + error_msg("unable to convert chunk indexing for \"%s\"\n", dname); + h5tools_setstatus(EXIT_FAILURE); + goto error; + + } else if(verbose_g) + printf("Done\n"); + +done: + /* Close the dataset */ + if(H5Dclose(did) < 0) { + error_msg("unable to close dataset \"%s\"\n", dname); + h5tools_setstatus(EXIT_FAILURE); + goto error; + } else if(verbose_g) + printf("Close the dataset\n"); + + /* Close the dataset creation property list */ + if(H5Pclose(dcpl) < 0) { + error_msg("unable to close dataset creation property list\n"); + h5tools_setstatus(EXIT_FAILURE); + goto error; + } else if(verbose_g) + printf("Close the dataset creation property list\n"); + + return(0); + +error: + if(verbose_g) + printf("Error encountered\n"); + + H5E_BEGIN_TRY { + H5Pclose(dcpl); + H5Dclose(did); + } H5E_END_TRY; + + return(-1); + +} /* convert() */ + +/*------------------------------------------------------------------------- + * Function: convert_dsets_cb() + * + * Purpose: The callback routine from the traversal to convert the + * chunk indexing type of the dataset object. + * + * Return: Success: 0 + * Failure: 1 + *------------------------------------------------------------------------- + */ +static int +convert_dsets_cb(const char *path, const H5O_info_t *oi, const char *already_visited, void *_fid) +{ + hid_t fid = *(hid_t *)_fid; + + /* If the object has already been seen then just return */ + if(NULL == already_visited) { + + if(oi->type == H5O_TYPE_DATASET) { + if(verbose_g) + printf("Going to process dataset:%s...\n", path); + if(convert(fid, path) < 0) + goto error; + } + + } /* end if */ + + return 0; + +error: + return -1; + +} /* end convert_dsets_cb() */ + + +/*------------------------------------------------------------------------- + * Function: main + * + * Purpose: To convert the chunk indexing type of a dataset in a file to + * version 1 B-tree. + * + * Return: Success: 0 + * Failure: 1 + * + *------------------------------------------------------------------------- + */ +int +main(int argc, const char *argv[]) +{ + H5E_auto2_t func; + void *edata; + hid_t fid = -1; + + h5tools_setprogname(PROGRAMNAME); + h5tools_setstatus(EXIT_SUCCESS); + + /* Disable error reporting */ + H5Eget_auto2(H5E_DEFAULT, &func, &edata); + H5Eset_auto2(H5E_DEFAULT, NULL, NULL); + + /* Initialize h5tools lib */ + h5tools_init(); + + /* Parse command line options */ + if(parse_command_line(argc, argv) < 0) + goto done; + else if(verbose_g) + printf("Process command line options\n"); + + if(noop_g && verbose_g) + printf("It is noop...\n"); + + /* Open the HDF5 file */ + if((fid = h5tools_fopen(fname_g, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0)) < 0) { + error_msg("unable to open file \"%s\"\n", fname_g); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } else if(verbose_g) + printf("Open the file %s\n", fname_g); + + if(dset_g) { /* Convert a specified dataset in the file */ + if(verbose_g) + printf("Going to process dataset: %s...\n", dname_g); + if(convert(fid, dname_g) < 0) + goto done; + } else { /* Convert all datasets in the file */ + if(verbose_g) + printf("Processing all datasets in the file...\n"); + if(h5trav_visit(fid, "/", TRUE, TRUE, convert_dsets_cb, NULL, &fid) < 0) + goto done; + } + +done: + /* Close the file */ + if(fid >= 0) { + if(H5Fclose(fid) < 0) { + error_msg("unable to close file \"%s\"\n", fname_g); + h5tools_setstatus(EXIT_FAILURE); + } else if(verbose_g) + printf("Close the file\n"); + } + + if(fname_g) + HDfree(fname_g); + if(dname_g) + HDfree(dname_g); + + H5Eset_auto2(H5E_DEFAULT, func, edata); + leave(h5tools_getstatus()); + +} /* end main() */ |