diff options
| -rw-r--r-- | tools/h5recover/h5recover.c | 705 |
1 files changed, 689 insertions, 16 deletions
diff --git a/tools/h5recover/h5recover.c b/tools/h5recover/h5recover.c index d2b1c87..e989bee 100644 --- a/tools/h5recover/h5recover.c +++ b/tools/h5recover/h5recover.c @@ -13,26 +13,699 @@ * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/* - * Programmer: Albert Cheng - * March 25, 2008 +#include "hdf5.h" +#include "h5tools.h" +#include "h5tools_utils.h" +#include "H5private.h" +#include <unistd.h> +#include <fcntl.h> +#include <string.h> +#include <stdlib.h> + +const char * progname="h5recover"; +int d_status; + +/* Define valid command line options. */ +static const char *s_opts = "hb:j:vnV"; +static struct long_options l_opts[] = { + { "help", no_arg, 'h' }, + { "backup", require_arg, 'b' }, + { "journal", require_arg, 'j' }, + { "verbose", no_arg, 'v' }, + { "nocopy", no_arg, 'n' }, + { "version", no_arg, 'V' }, + { NULL, 0, '\0' } +}; + +/*------------------------------------------------------------------------- + * Function: usage() + * + * Purpose: Prints a usage message and then returns. + * + * Return: void + * + * Programmer: Mike McGreevy <mcgreevy@hdfgroup.org> + * Monday, March 10, 2008 + * + *------------------------------------------------------------------------- */ +static void +usage (void) +{ + fprintf(stdout, "\ +usage: h5recover [OPTIONS] [OBJECTS] [HDF5_FILE]\n\ + OBJECTS\n\ + -j, --journal [JOURNAL_FILE] journal file name\n\ + OPTIONS\n\ + -b, --backup [BACKUP_NAME] Specify a name for the backup copy\n\ + of the HDF5 file.\n\ + default = '[HDF5_FILE].backup'\n\ + -n, --nocopy Do not create a backup copy.\n\ + -h, --help Print a usage message and exit\n\ + -v, --verbose Generate more verbose output\n\ + -V, --version Print version number and exit\n"); +} -/* - * Just a dummy program to provide a real executable. +/*------------------------------------------------------------------------- + * Function: leave + * + * Purpose: Shutdown MPI & HDF5 and call exit() + * + * Return: Does not return + * + * Programmer: Quincey Koziol + * Saturday, 31. January 2004 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static void +leave(int ret) +{ + h5tools_close(); + + exit(ret); +} + +/*------------------------------------------------------------------------- + * Function: file_copy() + * + * Purpose: Makes a back up copy of a file. + * + * Return: 0 on success + * + * Programmer: Mike McGreevy <mcgreevy@hdfgroup.org> + * Monday, March 10, 2008 + * + *------------------------------------------------------------------------- + */ +int +file_copy(char * file_from, char * file_to){ + + FILE * from; + FILE * to; + char ch; + + /* open source file */ + if((from = fopen(file_from, "rb")) == NULL) { + error_msg(progname, "Could not open source file\n"); + leave( EXIT_FAILURE ); + } + + /* open destination file */ + if((to = fopen(file_to, "wb")) == NULL) { + error_msg(progname, "Could not open destination file\n"); + leave( EXIT_FAILURE ); + } + + /* copy the file */ + while( !feof(from) ) { + + ch = fgetc(from); + + if( ferror(from) ) { + error_msg(progname, "Error reading source file\n"); + leave( EXIT_FAILURE ); + } /* end if */ + + if( !feof(from) ) + fputc(ch, to); + + if( ferror(to) ) { + error_msg(progname, "Error writing destination file\n"); + leave( EXIT_FAILURE ); + } /* end if */ + + } /* end while */ + + /* close source file */ + if( fclose(from) == EOF ) { + error_msg(progname, "Error closing source file\n"); + leave( EXIT_FAILURE ); + } /* end if */ + + /* close destination file */ + if( fclose(to) == EOF ) { + error_msg(progname, "Error closing destination file\n"); + leave( EXIT_FAILURE ); + } /* end if */ + + return 0; + +} + +/*------------------------------------------------------------------------- + * Function: main() + * + * Purpose: main h5recover program. + * + * Programmer: Mike McGreevy <mcgreevy@hdfgroup.org> + * Monday, March 10, 2008 + * + *------------------------------------------------------------------------- */ -#include "H5private.h" -#include "h5tools.h" -#include "h5tools_utils.h" - int -main(int argc, const char *argv[]) +main (int argc, const char *argv[]) { - printf("h5recover is here.\n"); - printf("Command arguments are:\n"); - while (--argc > 0) - printf("%s\n", *++argv); - return(0); -} + + /*********************** + * Variable declarations + ***********************/ + + hid_t fid = -1; /* file id number */ + hid_t fapl = -1; /* file access property list */ + char * file_name = NULL; /* file name */ + char * file_name_backup = NULL; /* name of backup file */ + char * journal_name = NULL; /* journal name */ + unsigned verbose = 0; /* verbose boolean */ + int opt; /* option number */ + FILE * journal_fp; /* journal file pointer */ + int hdf5_fd; /* hdf5 file descriptor */ + char * readback; /* array to read into from journal */ + char * last_trans_msg; /* array to keep last end_trans msg */ + int last_trans_found = 0; /* bool */ + char * tok[9]; /* string tokens */ + int i; /* iterator */ + haddr_t address; /* address to write to */ + uint8_t * body; /* body of journal entry */ + size_t size; /* size of journal entry body */ + size_t max_size; /* maximum size of journal entry body */ + char * p; /* pointer */ + hbool_t custom_name = 0; /* bool indicating custom backup name */ + hbool_t no_copy = 0; /* bool indicating not to make backup */ + H5AC_cache_config_t config; /* cache configuration */ + hbool_t check_file = 1; /* boolean indicating whether to check */ + uint8_t * compare_buf; /* buffer to read into from hdf5 file */ + hid_t status = -1; /* status indicator for retval checking */ + char c_old,c_new; /* temporary storage for single characters */ + long pos; /* file descriptor position indicator */ + long pos_end; /* file descriptor position indicator */ + char temp[100]; /* temporary buffer */ + + /********************** + * Command line parsing + **********************/ + + /* initialize h5tools lib */ + h5tools_init(); + + /* Check for no command line parameters */ + if ( argc == 1 ) { + + usage(); + leave( EXIT_SUCCESS ); + + } /* end if */ + + /* parse command line options */ + while ( (opt = get_option(argc, argv, s_opts, l_opts) ) != EOF) { + + switch ((char)opt) { + + case 'h': + usage(); + leave( EXIT_SUCCESS ); + break; + + case 'b': + custom_name = 1; + file_name_backup = strdup ( opt_arg ); + break; + + case 'n': + no_copy = 1; + break; + + case 'j': + journal_name = strdup( opt_arg ); + break; + + case 'V': + print_version(progname); + leave( EXIT_SUCCESS ); + break; + + case 'v': + verbose = 1; + break; + + default: + usage(); + leave( EXIT_FAILURE ); + + } /* end switch */ + + } /* end while */ + + /* check for missing file name */ + if (argc <= opt_ind) { + error_msg(progname, "HDF5 file name missing\n"); + usage(); + leave( EXIT_FAILURE ); + } + + file_name = HDstrdup(argv[opt_ind]); + + /* check for missing journal name */ + if ( journal_name == NULL ) { + + error_msg(progname, "Journal file name missing\n"); + usage(); + leave( EXIT_FAILURE ); + + } /* end if */ + + /* check for missing backup file name */ + if ( custom_name == 1) { + + if ( file_name_backup == NULL ) { + + error_msg(progname, "Journal file backup name missing\n"); + usage(); + leave( EXIT_FAILURE ); + + } /* end if */ + + } /* end if */ + + /* =================== */ + /* Main H5recover code */ + /* =================== */ + + + if ( verbose ) printf("\n==============================================\n"); + + if (no_copy == 0) { + + /* make a backup copy of HDF5 file before recovery */ + if (custom_name == 1) { + + if ( verbose ) printf("Copying HDF5 file <%s> into file <%s>\n", file_name, file_name_backup); + + file_copy( /* from */ file_name, /* to */ file_name_backup); + + } /* end if */ + + else { + file_name_backup = HDmalloc(HDstrlen(file_name) + (size_t)10); + + HDsnprintf(file_name_backup, HDstrlen(file_name) + (size_t)8, "%s.backup", file_name); + if ( verbose ) printf("Copying HDF5 file <%s> into file <%s>\n", file_name, file_name_backup); + file_copy( /* from */ file_name, /* to */ file_name_backup); + + } /* end else */ + + } /* end if */ + + /* open the journal file for reading */ + journal_fp = fopen(journal_name, "r"); + + if (journal_fp == NULL) { + + error_msg(progname, "Could not open specified journal file\n"); + usage(); + leave( EXIT_FAILURE ); + + } /* end if */ + + /* open hdf5 file for reading and writing */ + hdf5_fd = open(file_name, O_RDWR); + + if (hdf5_fd == -1) { + + error_msg(progname, "Could not open specified hdf5 file\n"); + usage(); + leave( EXIT_FAILURE ); + + } /* end if */ + + /* allocate temporary space to store end transaction messages */ + last_trans_msg = HDmalloc((size_t)50); + if (last_trans_msg == NULL) { + + error_msg(progname, "Could not allocate space\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + if ( verbose ) printf("Recovering file <%s> from journal <%s>\n\n", + file_name, journal_name); + + /* ====================================================== */ + /* Find the last complete transaction in the journal file */ + /* ====================================================== */ + fseek(journal_fp, 0, SEEK_END); + + while (last_trans_found == 0) { + + while (fgetc(journal_fp) != '\n') { + + if (ftell(journal_fp) <= 1) { + + error_msg(progname, "Journal has no complete transactions\n"); + usage(); + leave( EXIT_FAILURE ); + + } /* end if */ + + fseek(journal_fp, -2, SEEK_CUR); + + } /* end while */ + + if ( fgetc(journal_fp) == '3' ) { + + last_trans_found = 1; + fseek(journal_fp, -1, SEEK_CUR); + fgets(last_trans_msg, 50, journal_fp); + + } /* end if */ + + else { + + fseek(journal_fp, -3, SEEK_CUR); + + } /* end else */ + + } /* end while */ + + /* ======================================= */ + /* determine size of biggest journal entry */ + /* ======================================= */ + fseek(journal_fp, 0, SEEK_END); + pos_end = ftell(journal_fp); + + fseek(journal_fp, 0, SEEK_SET); + + c_new = 0; + c_old = 0; + max_size = 0; + + /* while journal is not at end of file */ + while (ftell(journal_fp) != pos_end) { + + c_old = c_new; + c_new = fgetc(journal_fp); + + /* if position is at the start of a line */ + if (c_old == '\n') { + + /* if the line starts with a '2', find out size of entry */ + if (c_new == '2') { + + pos = ftell(journal_fp); + + fgets(temp, 100, journal_fp); + tok[0] = HDstrtok(temp, " "); + if (tok[0] == NULL) { + + error_msg(progname, "Could not tokenize entry\n"); + leave( EXIT_FAILURE); + + } /* end if */ + for (i=1; i<8; i++) { + + tok[i] = HDstrtok(NULL, " "); + if (tok[i] == NULL) { + + error_msg(progname, "Could not tokenize entry\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + } /* end for */ + + size = HDstrtod(tok[3], NULL); + + if (max_size < size) { + + max_size = size; + + } /* end if */ + + /* jump back to start of line */ + fseek(journal_fp, pos, SEEK_SET); + + } /* end if */ + + } /* end if */ + + } /* end while */ + + /* ================================================= */ + /* Tokenize each journal entry in order to grab data */ + /* ================================================= */ + + max_size = max_size * 3 + 200; + + /* allocate space large enough to hold largest journal entry */ + readback = HDmalloc( max_size ); + if (readback == NULL) { + + error_msg(progname, "Could not allocate space to hold entries\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + /* read through journal file. recover any journal entries found, up + * through the last transaction number */ + fseek(journal_fp, 0, SEEK_SET); + + while ( fgets(readback, max_size, journal_fp) != NULL ) { + + if (HDstrcmp(readback, last_trans_msg) == 0) { + + /* done reading from file */ + break; + + } /* end if */ + + if ( readback[0] == '2') { /* journal entry found */ + + if ( verbose ) printf("Journal entry found.\n"); + if ( verbose ) printf("Tokenizing journal entry.\n"); + + /* divide the journal entry into tokens */ + tok[0] = HDstrtok(readback, " "); + if (tok[0] == NULL) { + + error_msg(progname, "Could not tokenize journal entry\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + /* if ( verbose ) printf(" token[0] : <%s>\n", tok[0]); */ + + for (i=1; i<8; i++) { + + tok[i] = HDstrtok(NULL, " "); + if (tok[i] == NULL) { + + error_msg(progname, "Could not tokenize journal entry\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + /* if ( verbose ) printf(" token[%d] : <%s>\n", i, tok[i]); */ + + } /* end for */ + + /* put all remaining data into last token. */ + /* This contains all of the journal entry body */ + tok[8] = HDstrtok(NULL, "\n"); + if (tok[8] == NULL) { + + error_msg(progname, "Could not tokenize journal entry\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + /* if ( verbose ) printf(" token[8] : <%s>\n", tok[8]); */ + + /* ================================== */ + /* Convert Items from Character Array */ + /* ================================== */ + + if ( verbose ) printf("Converting data from character strings.\n"); + + /* convert address from character character string */ + address = HDstrtod(tok[6], NULL); + if (address == 0) { + + error_msg(progname, "Could not convert address to integer\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + /* if ( verbose ) printf(" address: %llx\n", address); */ + + /* convert size from character string*/ + size = HDstrtod(tok[4], NULL); + if (size == 0) { + + error_msg(progname, "Could not convert size to double\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + /* if ( verbose ) printf(" size: %d\n", size); */ + + /* transform body out of hexadecimal character string */ + body = HDmalloc(size); + if (body == NULL) { + + error_msg(progname, "Could not allocate space for body\n"); + leave( EXIT_FAILURE); + + } /* end if */ + + p = &(tok[8])[0]; + + for (i = 0; i < size; i++) { + + body[i] = HDstrtoul(p, NULL, 16); + p = &p[3]; + + } /* end for */ + + body[i] = 0; + + /* if ( verbose ) printf(" body: %s\n", body); */ + + /* ================================================ */ + /* Write into HDF5 file the recovered journal entry */ + /* ================================================ */ + + if ( verbose ) printf("Writing entry to HDF5 file.\n"); + + /* perform a write */ + status = pwrite(hdf5_fd, body, size, address); + + if (status == -1) { + error_msg(progname, "pwrite failed\n"); + leave( EXIT_FAILURE ); + } + + if (status == 0) { + error_msg(progname, "pwrite did not write anything!\n"); + leave( EXIT_FAILURE); + } + + /* Verify that write occurred correctly */ + if ( check_file == 1) { + + if ( verbose ) printf("Verifying success of write"); + + compare_buf = HDmalloc(size); + + if (compare_buf == NULL) { + error_msg(progname, "Could not allocate space\n"); + leave( EXIT_FAILURE); + } /* end if */ + + pread(hdf5_fd, compare_buf, size, address); + + /* do a quick string compare on two items */ + if (HDstrcmp(body, compare_buf) != 0) { + error_msg(progname, "Entry incorrectly written into HDF5 file. Exiting.\n"); + printf("Address %llx:\n", address); + printf(" -- from journal: %llx\n", body); + printf(" -- from HDF5 file: %llx\n", compare_buf); + leave( EXIT_FAILURE ); + } /* end if */ + + /* compare each individual value of entry */ + for (i=0; i<size; i++) { + if (body[i] != compare_buf[i]) { + error_msg(progname, "Entry incorrectly written into HDF5 file. Exiting.\n"); + printf("Address %d\n", address + i); + printf(" -- from journal: %d\n", body[i]); + printf(" -- from HDF5 file: %d\n", compare_buf[i]); + leave( EXIT_FAILURE ); + } + } + + if ( verbose ) printf(" .... SUCCESS!\n"); + free(compare_buf); + + } + + free(body); + + } /* end if */ + + } /* end while */ + + fclose(journal_fp); + close(hdf5_fd); + free(last_trans_msg); + free(readback); + free(journal_name); + + /************************ + * Mark HDF5 File as Recoverd * + ************************/ + + if ( verbose ) printf("Marking HDF5 File as recovered.\n"); + if ( verbose ) printf("==============================================\n\n"); + + /* set up appropriate fapl */ + fapl = H5Pcreate(H5P_FILE_ACCESS); + + if ( fapl == -1 ) { + + error_msg(progname, "Could not create FAPL.\n"); + leave( EXIT_FAILURE ); + + } /* end if */ + + config.version = 1; /* should be H5C2__CURR_AUTO_SIZE_CTL_VER */ + + /* get H5AC_cache_config_t configuration from fapl */ + if ( H5Pget_mdc_config(fapl, &config) == -1) { + + error_msg(progname, "Could not get mdc config from FAPL.\n"); + leave( EXIT_FAILURE ); + + } + + /* make sure journal recovered field is set to TRUE in mdc_config */ + config.journal_recovered = TRUE; + + /* set H5AC_cache_config_t configuration with file recovered */ + if ( H5Pset_mdc_config(fapl, &config) == -1) { + + error_msg(progname, "Could not set mdc config on FAPL.\n"); + leave( EXIT_FAILURE ); + + } /* end if */ + + /* open HDF5 file with provided fapl */ + fid = H5Fopen(file_name, H5F_ACC_RDWR, H5P_DEFAULT /*fapl */); + + if ( fid == -1 ) { + + error_msg(progname, "Could not open recovered HDF5 file.\n"); + leave( EXIT_FAILURE ); + + } /* end if */ + + /* close HDF5 file */ + if ( H5Fclose(fid) == -1 ) { + + error_msg(progname, "Could not close recovered HDF5 file.\n"); + leave( EXIT_FAILURE ); + + } /* end if */ + + printf("HDF5 file successfuly recovered.\n"); + + free(file_name); + + return 1; + +} /* end main */ + + |