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HDF5 1 8 merge of recent changes and tools (#353)

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* Update supported platforms

* Merge PR#3 changes from develop

* # WARNING: head commit changed in the meantime

Merge gcc 10 diagnostics option from develop

Merge CMake changes from develop
Merge warnings from develop
Merge #318 OSX changes from develop
Merge tools changes from develop
Merge test macros from develop

* Format updates

* Fix missing semicolon and format fix

* Format update

* Correct actions, remove java option

* Update autotools build files

* Add testfiles

* Fix configure issue with make flags

* Init fapls to default

* Update generated files and fix h5repack id closure

* update format
This commit is contained in:
Allen Byrne
2021-02-21 22:05:43 -06:00
committed by GitHub
parent 8896048960
commit df1a4af961
213 changed files with 8835 additions and 7960 deletions
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330
tools/h5diff/h5diff_common.c
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@@ -25,7 +25,7 @@ static int check_d_input(const char *);
* Command-line options: The user can specify short or long-named
* parameters.
*/
static const char * s_opts = "hVrv:qn:d:p:NcelxE:S";
static const char * s_opts = "hVrv*qn:d:p:NcelxE:A:S";
static struct long_options l_opts[] = {{"help", no_arg, 'h'},
{"version", no_arg, 'V'},
{"report", no_arg, 'r'},
@@ -40,6 +40,7 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},
{"follow-symlinks", no_arg, 'l'},
{"no-dangling-links", no_arg, 'x'},
{"exclude-path", require_arg, 'E'},
{"exclude-attribute", require_arg, 'A'},
{"enable-error-stack", no_arg, 'S'},
{NULL, 0, '\0'}};
@@ -47,7 +48,6 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},
* Function: check_options
*
* Purpose: parse command line input
*
*-------------------------------------------------------------------------
*/
static void
@@ -60,7 +60,7 @@ check_options(diff_opt_t *opts)
/* check between -d , -p, --use-system-epsilon.
* These options are mutually exclusive.
*/
if ((opts->d + opts->p + opts->use_system_epsilon) > 1) {
if ((opts->delta_bool + opts->percent_bool + opts->use_system_epsilon) > 1) {
HDprintf("%s error: -d, -p and --use-system-epsilon options are mutually-exclusive;\n", PROGRAMNAME);
HDprintf("use no more than one.\n");
HDprintf("Try '-h' or '--help' option for more information or see the %s entry in the 'HDF5 "
@@ -70,11 +70,128 @@ check_options(diff_opt_t *opts)
}
}
#if TRILABS_227
/*-------------------------------------------------------------------------
* Function: parse_hsize_list
*
* Purpose: Parse a list of comma or space separated integers and return
* them in a list. The string being passed into this function
* should be at the start of the list you want to parse. You are
* responsible for freeing the array returned from here.
*
* Lists in the so-called "terse" syntax are separated by
* semicolons (;). The lists themselves can be separated by
* either commas (,) or white spaces.
*
* Return: <none>
*-------------------------------------------------------------------------
*/
static void
parse_hsize_list(const char *h_list, subset_d *d)
{
hsize_t * p_list;
const char * ptr;
unsigned int size_count = 0;
unsigned int i = 0;
unsigned int last_digit = 0;
if (!h_list || !*h_list || *h_list == ';')
return;
H5TOOLS_START_DEBUG(" - h_list:%s", h_list);
/* count how many integers do we have */
for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
if (HDisdigit(*ptr)) {
if (!last_digit)
/* the last read character wasn't a digit */
size_count++;
last_digit = 1;
}
else
last_digit = 0;
if (size_count == 0) {
/* there aren't any integers to read */
H5TOOLS_ENDDEBUG("No integers to read");
return;
}
H5TOOLS_DEBUG("Number integers to read=%ld", size_count);
/* allocate an array for the integers in the list */
if ((p_list = (hsize_t *)HDcalloc(size_count, sizeof(hsize_t))) == NULL)
H5TOOLS_INFO("Unable to allocate space for subset data");
for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
if (HDisdigit(*ptr)) {
/* we should have an integer now */
p_list[i++] = (hsize_t)HDstrtoull(ptr, NULL, 0);
while (HDisdigit(*ptr))
/* scroll to end of integer */
ptr++;
}
d->data = p_list;
d->len = size_count;
H5TOOLS_ENDDEBUG("");
}
/*-------------------------------------------------------------------------
* Function: parse_subset_params
*
* Purpose: Parse the so-called "terse" syntax for specifying subsetting parameters.
*
* Return: Success: struct subset_t object
* Failure: NULL
*-------------------------------------------------------------------------
*/
static struct subset_t *
parse_subset_params(const char *dset)
{
struct subset_t *s = NULL;
char * brace;
H5TOOLS_START_DEBUG(" - dset:%s", dset);
if ((brace = HDstrrchr(dset, '[')) != NULL) {
*brace++ = '\0';
s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t));
parse_hsize_list(brace, &s->start);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
parse_hsize_list(brace, &s->stride);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
parse_hsize_list(brace, &s->count);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
parse_hsize_list(brace, &s->block);
}
H5TOOLS_ENDDEBUG("");
return s;
}
#endif
/*-------------------------------------------------------------------------
* Function: parse_command_line
*
* Purpose: parse command line input
*
*-------------------------------------------------------------------------
*/
@@ -85,9 +202,11 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
int i;
int opt;
struct exclude_path_list *exclude_head, *exclude_prev, *exclude_node;
struct exclude_path_list *exclude_attr_head, *exclude_attr_prev, *exclude_attr_node;
H5TOOLS_START_DEBUG("");
/* process the command-line */
memset(opts, 0, sizeof(diff_opt_t));
HDmemset(opts, 0, sizeof(diff_opt_t));
/* assume equal contents initially */
opts->contents = 1;
@@ -96,7 +215,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
opts->do_nans = 1;
/* not Listing objects that are not comparable */
opts->m_list_not_cmp = 0;
opts->mode_list_not_cmp = 0;
/* initially no not-comparable. */
/**this is bad in mixing option with results**/
@@ -105,6 +224,9 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
/* init for exclude-path option */
exclude_head = NULL;
/* init for exclude-attribute option */
exclude_attr_head = NULL;
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
@@ -124,45 +246,39 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
break;
case 'v':
opts->m_verbose = 1;
/* This for loop is for handling style like
* -v, -v1, --verbose, --verbose=1.
*/
opts->mode_verbose = 1;
for (i = 1; i < argc; i++) {
/*
* short opt
* special check for short opt
*/
if (!strcmp(argv[i], "-v")) { /* no arg */
opt_ind--;
opts->m_verbose_level = 0;
if (!strcmp(argv[i], "-v")) {
if (opt_arg != NULL)
opt_ind--;
opts->mode_verbose_level = 0;
break;
}
else if (!strncmp(argv[i], "-v", (size_t)2)) {
opts->m_verbose_level = atoi(&argv[i][2]);
if (opt_arg != NULL)
opt_ind--;
opts->mode_verbose_level = atoi(&argv[i][2]);
break;
}
/*
* long opt
*/
if (!strcmp(argv[i], "--verbose")) { /* no arg */
opts->m_verbose_level = 0;
break;
}
else if (!strncmp(argv[i], "--verbose", (size_t)9) && argv[i][9] == '=') {
opts->m_verbose_level = atoi(&argv[i][10]);
break;
else {
if (opt_arg != NULL)
opts->mode_verbose_level = HDatoi(opt_arg);
else
opts->mode_verbose_level = 0;
}
}
break;
case 'q':
/* use quiet mode; supress the message "0 differences found" */
opts->m_quiet = 1;
opts->mode_quiet = 1;
break;
case 'r':
opts->m_report = 1;
opts->mode_report = 1;
break;
case 'l':
@@ -188,7 +304,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
}
/* init */
exclude_node->obj_path = (char *)opt_arg;
exclude_node->obj_path = opt_arg;
exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
exclude_prev = exclude_head;
@@ -205,37 +321,62 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
}
break;
case 'A':
opts->exclude_attr_path = 1;
/* create linked list of excluding objects */
if ((exclude_attr_node =
(struct exclude_path_list *)HDmalloc(sizeof(struct exclude_path_list))) == NULL) {
HDprintf("Error: lack of memory!\n");
h5diff_exit(EXIT_FAILURE);
}
/* init */
exclude_attr_node->obj_path = opt_arg;
exclude_attr_node->obj_type = H5TRAV_TYPE_UNKNOWN;
exclude_attr_prev = exclude_attr_head;
if (NULL == exclude_attr_head) {
exclude_attr_head = exclude_attr_node;
exclude_attr_head->next = NULL;
}
else {
while (NULL != exclude_attr_prev->next)
exclude_attr_prev = exclude_attr_prev->next;
exclude_attr_node->next = NULL;
exclude_attr_prev->next = exclude_attr_node;
}
break;
case 'd':
opts->d = 1;
opts->delta_bool = 1;
if (check_d_input(opt_arg) == -1) {
HDprintf("<-d %s> is not a valid option\n", opt_arg);
usage();
h5diff_exit(EXIT_FAILURE);
}
opts->delta = atof(opt_arg);
/* -d 0 is the same as default */
if (H5_DBL_ABS_EQUAL(opts->delta, (double)0.0F))
opts->d = 0;
opts->delta = HDatof(opt_arg);
/* do not check against default, the DBL_EPSILON is being replaced by user */
break;
case 'p':
opts->p = 1;
opts->percent_bool = 1;
if (check_p_input(opt_arg) == -1) {
HDprintf("<-p %s> is not a valid option\n", opt_arg);
usage();
h5diff_exit(EXIT_FAILURE);
}
opts->percent = atof(opt_arg);
opts->percent = HDatof(opt_arg);
/* -p 0 is the same as default */
if (H5_DBL_ABS_EQUAL(opts->percent, (double)0.0F))
opts->p = 0;
opts->percent_bool = 0;
break;
case 'n':
opts->n = 1;
opts->count_bool = 1;
if (check_n_input(opt_arg) == -1) {
HDprintf("<-n %s> is not a valid option\n", opt_arg);
usage();
@@ -249,7 +390,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
break;
case 'c':
opts->m_list_not_cmp = 1;
opts->mode_list_not_cmp = 1;
break;
case 'e':
@@ -265,6 +406,10 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
if (opts->exclude_path)
opts->exclude = exclude_head;
/* if exclude-attribute option is used, keep the exclude attr list */
if (opts->exclude_attr_path)
opts->exclude_attr = exclude_attr_head;
/* check for file names to be processed */
if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
error_msg("missing file names\n");
@@ -275,11 +420,15 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
*fname1 = argv[opt_ind];
*fname2 = argv[opt_ind + 1];
*objname1 = argv[opt_ind + 2];
H5TOOLS_DEBUG("file1 = %s", *fname1);
H5TOOLS_DEBUG("file2 = %s", *fname2);
if (*objname1 == NULL) {
*objname2 = NULL;
H5TOOLS_ENDDEBUG("No obj names");
return;
}
H5TOOLS_DEBUG("objname1 = %s", *objname1);
if (argv[opt_ind + 3] != NULL) {
*objname2 = argv[opt_ind + 3];
@@ -287,33 +436,45 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
else {
*objname2 = *objname1;
}
H5TOOLS_DEBUG("objname2 = %s", *objname2);
/*
* TRILABS_227 is complete except for an issue with printing indices
* the following calls will enable subsetting
*/
#if TRILABS_227
opts->sset[0] = parse_subset_params(*objname1);
opts->sset[1] = parse_subset_params(*objname2);
#endif
H5TOOLS_ENDDEBUG("");
}
/*-------------------------------------------------------------------------
* Function: print_info
*
* Purpose: print several information messages after h5diff call
*
*-------------------------------------------------------------------------
*/
void
print_info(diff_opt_t *opts)
{
if (opts->m_quiet || opts->err_stat)
if (opts->mode_quiet || opts->err_stat)
return;
if (opts->cmn_objs == 0) {
HDprintf("No common objects found. Files are not comparable.\n");
if (!opts->m_verbose)
if (!opts->mode_verbose)
HDprintf("Use -v for a list of objects.\n");
}
if (opts->not_cmp == 1) {
if (opts->m_list_not_cmp == 0) {
if (opts->mode_list_not_cmp == 0) {
HDprintf("--------------------------------\n");
HDprintf("Some objects are not comparable\n");
HDprintf("--------------------------------\n");
if (opts->m_verbose)
if (opts->mode_verbose)
HDprintf("Use -c for a list of objects without details of differences.\n");
else
HDprintf("Use -c for a list of objects.\n");
@@ -327,15 +488,6 @@ print_info(diff_opt_t *opts)
* Purpose: check for valid input
*
* Return: 1 for ok, -1 for fail
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: May 9, 2003
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
@@ -362,13 +514,6 @@ check_n_input(const char *str)
* Purpose: check for a valid p option input
*
* Return: 1 for ok, -1 for fail
*
* Date: May 9, 2003
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
@@ -377,13 +522,13 @@ check_p_input(const char *str)
double x;
/*
the atof return value on a hexadecimal input is different
on some systems; we do a character check for this
*/
* the atof return value on a hexadecimal input is different
* on some systems; we do a character check for this
*/
if (HDstrlen(str) > 2 && str[0] == '0' && str[1] == 'x')
return -1;
x = atof(str);
x = HDatof(str);
if (x < 0)
return -1;
@@ -396,13 +541,6 @@ check_p_input(const char *str)
* Purpose: check for a valid d option input
*
* Return: 1 for ok, -1 for fail
*
* Date: November 11, 2007
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
@@ -411,13 +549,13 @@ check_d_input(const char *str)
double x;
/*
the atof return value on a hexadecimal input is different
on some systems; we do a character check for this
*/
* the atof return value on a hexadecimal input is different
* on some systems; we do a character check for this
*/
if (HDstrlen(str) > 2 && str[0] == '0' && str[1] == 'x')
return -1;
x = atof(str);
x = HDatof(str);
if (x < 0)
return -1;
@@ -430,7 +568,6 @@ check_d_input(const char *str)
* Purpose: print a usage message
*
* Return: void
*
*-------------------------------------------------------------------------
*/
@@ -458,10 +595,11 @@ usage(void)
" Verbose mode with level. Print differences and list of objects.\n");
PRINTVALSTREAM(rawoutstream, " Level of detail depends on value of N:\n");
PRINTVALSTREAM(rawoutstream, " 0 : Identical to '-v' or '--verbose'.\n");
PRINTVALSTREAM(rawoutstream, " 1 : All level 0 information plus one-line attribute\n");
PRINTVALSTREAM(rawoutstream, " status summary.\n");
PRINTVALSTREAM(rawoutstream, " 2 : All level 1 information plus extended attribute\n");
PRINTVALSTREAM(rawoutstream, " status report.\n");
PRINTVALSTREAM(rawoutstream,
" 1 : All level 0 information plus one-line attribute status summary.\n");
PRINTVALSTREAM(rawoutstream,
" 2 : All level 1 information plus extended attribute status report.\n");
PRINTVALSTREAM(rawoutstream, " 3 : All level 2 information plus file names.\n");
PRINTVALSTREAM(rawoutstream, " -q, --quiet\n");
PRINTVALSTREAM(rawoutstream, " Quiet mode. Do not produce output.\n");
PRINTVALSTREAM(rawoutstream, " --enable-error-stack\n");
@@ -574,7 +712,18 @@ usage(void)
PRINTVALSTREAM(rawoutstream, " excluded.\n");
PRINTVALSTREAM(rawoutstream, " This option can be used repeatedly to exclude multiple paths.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " --exclude-attribute \"path/to/object/with/attribute\"\n");
PRINTVALSTREAM(
rawoutstream,
" Exclude attributes on the specified path to an object when comparing files or groups.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream,
" If there are multiple paths to an object, only the specified path(s)\n");
PRINTVALSTREAM(rawoutstream,
" will be excluded; the comparison will include any path not explicitly\n");
PRINTVALSTREAM(rawoutstream, " excluded.\n");
PRINTVALSTREAM(rawoutstream, " This option can be used repeatedly to exclude multiple paths.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Modes of output:\n");
PRINTVALSTREAM(rawoutstream,
" Default mode: print the number of differences found and where they occured\n");
@@ -614,7 +763,22 @@ usage(void)
PRINTVALSTREAM(rawoutstream, " (The option --follow-symlinks overrides the default behavior when\n");
PRINTVALSTREAM(rawoutstream, " symbolic links are compared.).\n");
PRINTVALSTREAM(rawoutstream, "\n");
/*
* TRILABS_227 is complete except for an issue with printing indices
* the following will be needed for subsetting
PRINTVALSTREAM(rawoutstream, " Subsetting options:\n");
PRINTVALSTREAM(rawoutstream, " Subsetting is available by using the fcompact form of subsetting, as
follows:\n"); PRINTVALSTREAM(rawoutstream, " obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]\n");
PRINTVALSTREAM(rawoutstream, " It is not required to use all parameters, but until the last parameter
value used,\n"); PRINTVALSTREAM(rawoutstream, " all of the semicolons (;) are required, even when a
parameter value is not specified. Example:\n"); PRINTVALSTREAM(rawoutstream, " obj1
/foo/mydataset[START;;COUNT;BLOCK]\n"); PRINTVALSTREAM(rawoutstream, " obj1 /foo/mydataset[START]\n");
PRINTVALSTREAM(rawoutstream, " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1
in\n"); PRINTVALSTREAM(rawoutstream, " each dimension. START is optional and will default to 0 in each
dimension.\n"); PRINTVALSTREAM(rawoutstream, " Each of START, STRIDE, COUNT, and BLOCK must be a
comma-separated list of integers with\n"); PRINTVALSTREAM(rawoutstream, " one integer for each dimension
of the dataset.\n"); PRINTVALSTREAM(rawoutstream, "\n");
*/
PRINTVALSTREAM(rawoutstream, " Exit code:\n");
PRINTVALSTREAM(rawoutstream, " 0 if no differences, 1 if differences found, 2 if error\n");
PRINTVALSTREAM(rawoutstream, "\n");