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Fix for HDFFV-10333:

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1) Check for valid object header version for a refcount messge
2) Check for invalid fill value size
3) Check for invalid dimension size in a layout message
4) Add --enable-error-stack option to h5stat
5) Add error checks to h5stat.c
6) Add tests to h5stat and h5dump
This commit is contained in:
Vailin Choi 2018-07-10 22:00:14 -05:00
parent 832aced6c1
commit cf38292064
20 changed files with 458 additions and 144 deletions
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28
src/H5Ocache.c
View File

@ -1430,9 +1430,10 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
/* Check for combining two adjacent 'null' messages */
if((udata->file_intent & H5F_ACC_RDWR) &&
H5O_NULL_ID == id && oh->nmesgs > 0 &&
H5O_NULL_ID == oh->mesg[oh->nmesgs - 1].type->id &&
oh->mesg[oh->nmesgs - 1].chunkno == chunkno) {
H5O_NULL_ID == id && oh->nmesgs > 0 &&
H5O_NULL_ID == oh->mesg[oh->nmesgs - 1].type->id &&
oh->mesg[oh->nmesgs - 1].chunkno == chunkno) {
size_t mesgno; /* Current message to operate on */
/* Combine adjacent null messages */
@ -1467,13 +1468,13 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
/* Point unknown messages at 'unknown' message class */
/* (Usually from future versions of the library) */
if(id >= H5O_UNKNOWN_ID ||
if(id >= H5O_UNKNOWN_ID ||
#ifdef H5O_ENABLE_BOGUS
id == H5O_BOGUS_VALID_ID ||
id == H5O_BOGUS_VALID_ID ||
#endif
NULL == H5O_msg_class_g[id]) {
NULL == H5O_msg_class_g[id]) {
H5O_unknown_t *unknown; /* Pointer to "unknown" message info */
H5O_unknown_t *unknown; /* Pointer to "unknown" message info */
/* Allocate "unknown" message info */
if(NULL == (unknown = H5FL_MALLOC(H5O_unknown_t)))
@ -1490,9 +1491,9 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
/* Check for "fail if unknown" message flags */
if(((udata->file_intent & H5F_ACC_RDWR) &&
(flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE))
|| (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS))
HGOTO_ERROR(H5E_OHDR, H5E_BADMESG, FAIL, "unknown message with 'fail if unknown' flag found")
(flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE))
|| (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS))
HGOTO_ERROR(H5E_OHDR, H5E_BADMESG, FAIL, "unknown message with 'fail if unknown' flag found")
/* Check for "mark if unknown" message flag, etc. */
else if((flags & H5O_MSG_FLAG_MARK_IF_UNKNOWN) &&
!(flags & H5O_MSG_FLAG_WAS_UNKNOWN) &&
@ -1543,7 +1544,8 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
H5O_refcount_t *refcount;
/* Decode ref. count message */
HDassert(oh->version > H5O_VERSION_1);
if(oh->version <= H5O_VERSION_1)
HGOTO_ERROR(H5E_OHDR, H5E_VERSION, FAIL, "object header version does not support reference count message")
refcount = (H5O_refcount_t *)(H5O_MSG_REFCOUNT->decode)(udata->f, NULL, 0, &ioflags, mesg->raw_size, mesg->raw);
/* Save 'native' form of ref. count message */
@ -1614,6 +1616,10 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
} /* end if */
done:
if(ret_value < 0 && udata->cont_msg_info->msgs) {
udata->cont_msg_info->msgs = (H5O_chunk_t *)H5FL_SEQ_FREE(H5O_cont_t, udata->cont_msg_info->msgs);
udata->cont_msg_info->alloc_nmsgs = 0;
}
FUNC_LEAVE_NOAPI(ret_value)
} /* H5O__chunk_deserialize() */

22
src/H5Ofill.c
View File

@ -19,6 +19,7 @@
*/
#include "H5Omodule.h" /* This source code file is part of the H5O module */
#define H5T_FRIEND /*prevent warning from including H5Tpkg */
#include "H5private.h" /* Generic Functions */
@ -31,6 +32,7 @@
#include "H5Pprivate.h" /* Property lists */
#include "H5Sprivate.h" /* Dataspaces */
#include "H5Tpkg.h" /* Datatypes */
static void *H5O_fill_old_decode(H5F_t *f, H5O_t *open_oh, unsigned mesg_flags,
unsigned *ioflags, size_t p_size, const uint8_t *p);
@ -307,11 +309,13 @@ done:
*-------------------------------------------------------------------------
*/
static void *
H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
H5O_fill_old_decode(H5F_t *f, H5O_t *open_oh,
unsigned H5_ATTR_UNUSED mesg_flags, unsigned H5_ATTR_UNUSED *ioflags,
size_t H5_ATTR_UNUSED p_size, const uint8_t *p)
{
H5O_fill_t *fill = NULL; /* Decoded fill value message */
htri_t exists = FALSE;
H5T_t *dt = NULL;
void *ret_value = NULL; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@ -332,6 +336,19 @@ H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
/* Only decode the fill value itself if there is one */
if(fill->size > 0) {
H5_CHECK_OVERFLOW(fill->size, ssize_t, size_t);
/* Get the datatype message */
if((exists = H5O_msg_exists_oh(open_oh, H5O_DTYPE_ID)) < 0)
HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, NULL, "unable to read object header")
if(exists) {
if((dt = H5O_msg_read_oh(f, open_oh, H5O_DTYPE_ID, NULL)) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTGET, NULL, "can't read DTYPE message")
/* Verify size */
if(fill->size != dt->shared->size)
HGOTO_ERROR(H5E_SYM, H5E_CANTGET, NULL, "inconsistent fill value size")
}
if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value")
HDmemcpy(fill->buf, p, (size_t)fill->size);
@ -344,6 +361,9 @@ H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
ret_value = (void*)fill;
done:
if(dt)
H5O_msg_free(H5O_DTYPE_ID, dt);
if(!ret_value && fill) {
if(fill->buf)
H5MM_xfree(fill->buf);

4
src/H5Olayout.c
View File

@ -125,8 +125,8 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh,
/* Dimensionality */
ndims = *p++;
if(ndims > H5O_LAYOUT_NDIMS)
HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large")
if(!ndims || ndims > H5O_LAYOUT_NDIMS)
HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is out of range")
/* Layout class */
mesg->type = (H5D_layout_t)*p++;

2
src/H5Sselect.c
View File

@ -160,7 +160,7 @@ H5S_select_release(H5S_t *ds)
HDassert(ds);
/* Call the selection type's release function */
if((ret_value = (*ds->select.type->release)(ds)) < 0)
if((ds->select.type) && ((ret_value = (*ds->select.type->release)(ds)) < 0))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection")
done:

284
tools/src/h5stat/h5stat.c
View File

@ -146,7 +146,7 @@ struct handler_t {
char **obj;
};
static const char *s_opts ="Aa:Ddm:FfhGgl:sSTO:V";
static const char *s_opts ="Aa:Ddm:EFfhGgl:sSTO:V";
/* e.g. "filemetadata" has to precede "file"; "groupmetadata" has to precede "group" etc. */
static struct long_options l_opts[] = {
{"help", no_arg, 'h'},
@ -224,6 +224,7 @@ static struct long_options l_opts[] = {
{ "attr", no_arg, 'A' },
{ "att", no_arg, 'A' },
{ "at", no_arg, 'A' },
{ "enable-error-stack", no_arg, 'E' },
{ "numattrs", require_arg, 'a' },
{ "numattr", require_arg, 'a' },
{ "numatt", require_arg, 'a' },
@ -293,6 +294,7 @@ static void usage(const char *prog)
HDfprintf(stdout, " than 0. The default threshold is 10.\n");
HDfprintf(stdout, " -s, --freespace Print free space information\n");
HDfprintf(stdout, " -S, --summary Print summary of file space information\n");
HDfprintf(stdout, " --enable-error-stack Prints messages from the HDF5 error stack as they occur\n");
}
@ -378,9 +380,8 @@ attribute_stats(iter_t *iter, const H5O_info_t *oi)
*
* Purpose: Gather statistics about the group
*
* Return: Success: 0
*
* Failure: -1
* Return: Success: 0
* Failure: -1
*
* Programmer: Quincey Koziol
* Tuesday, August 16, 2005
@ -402,9 +403,9 @@ attribute_stats(iter_t *iter, const H5O_info_t *oi)
static herr_t
group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
{
H5G_info_t ginfo; /* Group information */
unsigned bin; /* "bin" the number of objects falls in */
herr_t ret;
H5G_info_t ginfo; /* Group information */
unsigned bin; /* "bin" the number of objects falls in */
herr_t ret_value = SUCCEED; /* Return value */
/* Gather statistics about this type of object */
iter->uniq_groups++;
@ -414,8 +415,8 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
iter->group_ohdr_info.free_size += oi->hdr.space.free;
/* Get group information */
ret = H5Gget_info_by_name(iter->fid, name, &ginfo, H5P_DEFAULT);
HDassert(ret >= 0);
if((ret_value = H5Gget_info_by_name(iter->fid, name, &ginfo, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_info_by_name() failed");
/* Update link stats */
/* Collect statistics for small groups */
@ -429,10 +430,10 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
bin = ceil_log10((unsigned long)ginfo.nlinks);
if((bin + 1) > iter->group_nbins) {
/* Allocate more storage for info about dataset's datatype */
iter->group_bins = (unsigned long *)HDrealloc(iter->group_bins, (bin + 1) * sizeof(unsigned long));
HDassert(iter->group_bins);
if((iter->group_bins = (unsigned long *)HDrealloc(iter->group_bins, (bin + 1) * sizeof(unsigned long))) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Drealloc() failed");
/* Initialize counts for intermediate bins */
/* Initialize counts for intermediate bins */
while(iter->group_nbins < bin)
iter->group_bins[iter->group_nbins++] = 0;
iter->group_nbins++;
@ -448,10 +449,11 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
iter->groups_heap_storage_size += oi->meta_size.obj.heap_size;
/* Update attribute metadata info */
ret = attribute_stats(iter, oi);
HDassert(ret >= 0);
if((ret_value = attribute_stats(iter, oi)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "attribute_stats failed");
return 0;
done:
return ret_value;
} /* end group_stats() */
@ -461,7 +463,6 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
* Purpose: Gather statistics about the dataset
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Quincey Koziol
@ -472,22 +473,22 @@ group_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
static herr_t
dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
{
unsigned bin; /* "bin" the number of objects falls in */
hid_t did; /* Dataset ID */
hid_t sid; /* Dataspace ID */
hid_t tid; /* Datatype ID */
hid_t dcpl; /* Dataset creation property list ID */
hsize_t dims[H5S_MAX_RANK];/* Dimensions of dataset */
H5D_layout_t lout; /* Layout of dataset */
unsigned type_found; /* Whether the dataset's datatype was */
/* already found */
int ndims; /* Number of dimensions of dataset */
hsize_t storage; /* Size of dataset storage */
unsigned u; /* Local index variable */
int num_ext; /* Number of external files for a dataset */
int nfltr; /* Number of filters for a dataset */
H5Z_filter_t fltr; /* Filter identifier */
herr_t ret;
unsigned bin; /* "bin" the number of objects falls in */
hid_t did; /* Dataset ID */
hid_t sid; /* Dataspace ID */
hid_t tid; /* Datatype ID */
hid_t dcpl; /* Dataset creation property list ID */
hsize_t dims[H5S_MAX_RANK]; /* Dimensions of dataset */
H5D_layout_t lout; /* Layout of dataset */
unsigned type_found; /* Whether the dataset's datatype was */
/* already found */
int ndims; /* Number of dimensions of dataset */
hsize_t storage; /* Size of dataset storage */
unsigned u; /* Local index variable */
int num_ext; /* Number of external files for a dataset */
int nfltr; /* Number of filters for a dataset */
H5Z_filter_t fltr; /* Filter identifier */
herr_t ret_value = SUCCEED; /* Return value */
/* Gather statistics about this type of object */
iter->uniq_dsets++;
@ -496,26 +497,27 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
iter->dset_ohdr_info.total_size += oi->hdr.space.total;
iter->dset_ohdr_info.free_size += oi->hdr.space.free;
did = H5Dopen2(iter->fid, name, H5P_DEFAULT);
HDassert(did > 0);
if((did = H5Dopen2(iter->fid, name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen() failed");
/* Update dataset metadata info */
iter->datasets_index_storage_size += oi->meta_size.obj.index_size;
iter->datasets_heap_storage_size += oi->meta_size.obj.heap_size;
/* Update attribute metadata info */
ret = attribute_stats(iter, oi);
HDassert(ret >= 0);
if((ret_value = attribute_stats(iter, oi)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "attribute_stats() failed");
/* Get storage info */
storage = H5Dget_storage_size(did);
if((storage = H5Dget_storage_size(did)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_storage_size() failed");
/* Gather layout statistics */
dcpl = H5Dget_create_plist(did);
HDassert(dcpl > 0);
if((dcpl = H5Dget_create_plist(did)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist() failed");
lout = H5Pget_layout(dcpl);
HDassert(lout >= 0);
if((lout = H5Pget_layout(dcpl)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout() failed");
/* Object header's total size for H5D_COMPACT layout includes raw data size */
/* "storage" also includes H5D_COMPACT raw data size */
@ -526,8 +528,8 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
(iter->dset_layouts[lout])++;
/* Get the number of external files for the dataset */
num_ext = H5Pget_external_count(dcpl);
assert (num_ext >= 0);
if((num_ext = H5Pget_external_count(dcpl)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_external_count() failed");
/* Accumulate raw data size accordingly */
if(num_ext) {
@ -537,11 +539,11 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
iter->dset_storage_size += storage;
/* Gather dataspace statistics */
sid = H5Dget_space(did);
HDassert(sid > 0);
if((sid = H5Dget_space(did)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_space() failed");
ndims = H5Sget_simple_extent_dims(sid, dims, NULL);
HDassert(ndims >= 0);
if((ndims = H5Sget_simple_extent_dims(sid, dims, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims() failed");
/* Check for larger rank of dataset */
if((unsigned)ndims > iter->max_dset_rank)
@ -552,38 +554,38 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
/* Only gather dim size statistics on 1-D datasets */
if(ndims == 1) {
/* Determine maximum dimension size */
if(dims[0] > iter->max_dset_dims)
iter->max_dset_dims = dims[0];
/* Collect statistics for small datasets */
if(dims[0] < (hsize_t)sdsets_threshold)
(iter->small_dset_dims[(size_t)dims[0]])++;
/* Determine maximum dimension size */
if(dims[0] > iter->max_dset_dims)
iter->max_dset_dims = dims[0];
/* Collect statistics for small datasets */
if(dims[0] < (hsize_t)sdsets_threshold)
(iter->small_dset_dims[(size_t)dims[0]])++;
/* Add dim count to proper bin */
bin = ceil_log10((unsigned long)dims[0]);
if((bin + 1) > iter->dset_dim_nbins) {
/* Allocate more storage for info about dataset's datatype */
iter->dset_dim_bins = (unsigned long *)HDrealloc(iter->dset_dim_bins, (bin + 1) * sizeof(unsigned long));
HDassert(iter->dset_dim_bins);
/* Add dim count to proper bin */
bin = ceil_log10((unsigned long)dims[0]);
if((bin + 1) > iter->dset_dim_nbins) {
/* Allocate more storage for info about dataset's datatype */
if((iter->dset_dim_bins = (unsigned long *)HDrealloc(iter->dset_dim_bins, (bin + 1) * sizeof(unsigned long))) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Drealloc() failed");
/* Initialize counts for intermediate bins */
while(iter->dset_dim_nbins < bin)
iter->dset_dim_bins[iter->dset_dim_nbins++] = 0;
iter->dset_dim_nbins++;
/* Initialize counts for intermediate bins */
while(iter->dset_dim_nbins < bin)
iter->dset_dim_bins[iter->dset_dim_nbins++] = 0;
iter->dset_dim_nbins++;
/* Initialize count for this bin */
iter->dset_dim_bins[bin] = 1;
/* Initialize count for this bin */
iter->dset_dim_bins[bin] = 1;
} /* end if */
else
(iter->dset_dim_bins[bin])++;
} /* end if */
ret = H5Sclose(sid);
HDassert(ret >= 0);
if(H5Sclose(sid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose() failed");
/* Gather datatype statistics */
tid = H5Dget_type(did);
HDassert(tid > 0);
if((tid = H5Dget_type(did)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type() failed");
type_found = FALSE;
for(u = 0; u < iter->dset_ntypes; u++)
@ -591,6 +593,7 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
type_found = TRUE;
break;
} /* end for */
if(type_found)
(iter->dset_type_info[u].count)++;
else {
@ -600,12 +603,12 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
iter->dset_ntypes++;
/* Allocate more storage for info about dataset's datatype */
iter->dset_type_info = (dtype_info_t *)HDrealloc(iter->dset_type_info, iter->dset_ntypes * sizeof(dtype_info_t));
HDassert(iter->dset_type_info);
if((iter->dset_type_info = (dtype_info_t *)HDrealloc(iter->dset_type_info, iter->dset_ntypes * sizeof(dtype_info_t))) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Drealloc() failed");
/* Initialize information about datatype */
iter->dset_type_info[curr_ntype].tid = H5Tcopy(tid);
HDassert(iter->dset_type_info[curr_ntype].tid > 0);
if((iter->dset_type_info[curr_ntype].tid = H5Tcopy(tid)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcopy() failed");
iter->dset_type_info[curr_ntype].count = 1;
iter->dset_type_info[curr_ntype].named = 0;
@ -617,8 +620,8 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
if(H5Tcommitted(tid) > 0)
(iter->dset_type_info[u].named)++;
ret = H5Tclose(tid);
HDassert(ret >= 0);
if(H5Tclose(tid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose() failed");
/* Track different filters */
if((nfltr = H5Pget_nfilters(dcpl)) >= 0) {
@ -635,13 +638,14 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
} /* end for */
} /* endif nfltr */
ret = H5Pclose(dcpl);
HDassert(ret >= 0);
if(H5Pclose(dcpl) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose() failed");
ret = H5Dclose(did);
HDassert(ret >= 0);
if(H5Dclose(did) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose() failed");
return 0;
done:
return ret_value;
} /* end dataset_stats() */
@ -660,7 +664,7 @@ dataset_stats(iter_t *iter, const char *name, const H5O_info_t *oi)
static herr_t
datatype_stats(iter_t *iter, const H5O_info_t *oi)
{
herr_t ret;
herr_t ret_value = SUCCEED;
/* Gather statistics about this type of object */
iter->uniq_dtypes++;
@ -670,10 +674,10 @@ datatype_stats(iter_t *iter, const H5O_info_t *oi)
iter->dtype_ohdr_info.free_size += oi->hdr.space.free;
/* Update attribute metadata info */
ret = attribute_stats(iter, oi);
HDassert(ret >= 0);
return 0;
if((ret_value = attribute_stats(iter, oi)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "attribute_stats() failed");
done:
return ret_value;
} /* end datatype_stats() */
@ -695,6 +699,7 @@ obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited,
void *_iter)
{
iter_t *iter = (iter_t *)_iter;
herr_t ret_value = SUCCEED;
/* If the object has already been seen then just return */
if(NULL == already_visited) {
@ -704,15 +709,18 @@ obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited,
switch(oi->type) {
case H5O_TYPE_GROUP:
group_stats(iter, path, oi);
if(group_stats(iter, path, oi) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "group_stats failed");
break;
case H5O_TYPE_DATASET:
dataset_stats(iter, path, oi);
if(dataset_stats(iter, path, oi) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "dataset_stats failed");
break;
case H5O_TYPE_NAMED_DATATYPE:
datatype_stats(iter, oi);
if(datatype_stats(iter, oi) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "datatype_stats failed");
break;
case H5O_TYPE_UNKNOWN:
@ -724,7 +732,8 @@ obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited,
} /* end switch */
} /* end if */
return 0;
done:
return ret_value;
} /* end obj_stats() */
@ -733,9 +742,8 @@ obj_stats(const char *path, const H5O_info_t *oi, const char *already_visited,
*
* Purpose: Gather statistics about a link
*
* Return: Success: 0
*
* Failure: -1
* Return: Success: 0
* Failure: -1
*
* Programmer: Quincey Koziol
* Tuesday, November 6, 2007
@ -892,6 +900,10 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
goto done;
break;
case 'E':
enable_error_stack = 1;
break;
case 'F':
display_all = FALSE;
display_file_metadata = TRUE;
@ -913,14 +925,14 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
break;
case 'l':
if(opt_arg) {
sgroups_threshold = HDatoi(opt_arg);
if(sgroups_threshold < 1) {
error_msg("Invalid threshold for small groups\n");
goto error;
}
} else
error_msg("Missing threshold for small groups\n");
if(opt_arg) {
sgroups_threshold = HDatoi(opt_arg);
if(sgroups_threshold < 1) {
error_msg("Invalid threshold for small groups\n");
goto error;
}
} else
error_msg("Missing threshold for small groups\n");
break;
@ -935,14 +947,14 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
break;
case 'm':
if(opt_arg) {
sdsets_threshold = HDatoi(opt_arg);
if(sdsets_threshold < 1) {
error_msg("Invalid threshold for small datasets\n");
goto error;
}
} else
error_msg("Missing threshold for small datasets\n");
if(opt_arg) {
sdsets_threshold = HDatoi(opt_arg);
if(sdsets_threshold < 1) {
error_msg("Invalid threshold for small datasets\n");
goto error;
}
} else
error_msg("Missing threshold for small datasets\n");
break;
@ -957,13 +969,13 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
break;
case 'a':
if(opt_arg) {
sattrs_threshold = HDatoi(opt_arg);
if(sattrs_threshold < 1) {
error_msg("Invalid threshold for small # of attributes\n");
goto error;
}
} else
if(opt_arg) {
sattrs_threshold = HDatoi(opt_arg);
if(sattrs_threshold < 1) {
error_msg("Invalid threshold for small # of attributes\n");
goto error;
}
} else
error_msg("Missing threshold for small # of attributes\n");
break;
@ -1249,9 +1261,8 @@ print_group_info(const iter_t *iter)
*
* Purpose: Prints file space information for groups' metadata
*
* Return: Success: 0
*
* Failure: Never fails
* Return: Success: 0
* Failure: Never fails
*
* Programmer: Vailin Choi; October 2009
*
@ -1277,9 +1288,8 @@ print_group_metadata(const iter_t *iter)
*
* Purpose: Prints information about datasets in the file
*
* Return: Success: 0
*
* Failure: Never fails
* Return: Success: 0
* Failure: Never fails
*
* Programmer: Elena Pourmal
* Saturday, August 12, 2006
@ -1340,7 +1350,7 @@ print_dataset_info(const iter_t *iter)
printf("Dataset layout information:\n");
for(u = 0; u < H5D_NLAYOUTS; u++)
printf("\tDataset layout counts[%s]: %lu\n", (u == H5D_COMPACT ? "COMPACT" :
printf("\tDataset layout counts[%s]: %lu\n", (u == H5D_COMPACT ? "COMPACT" :
(u == H5D_CONTIGUOUS ? "CONTIG" : (u == H5D_CHUNKED ? "CHUNKED" : "VIRTUAL"))), iter->dset_layouts[u]);
printf("\tNumber of external files : %lu\n", iter->nexternal);
@ -1704,16 +1714,25 @@ main(int argc, const char *argv[])
iter_t iter;
const char *fname = NULL;
hid_t fid = -1;
H5E_auto2_t func;
H5E_auto2_t tools_func;
void *edata;
void *tools_edata;
struct handler_t *hand = NULL;
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();
/* Disable tools error reporting */
H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata);
H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL);
HDmemset(&iter, 0, sizeof(iter));
@ -1722,6 +1741,11 @@ main(int argc, const char *argv[])
fname = argv[opt_ind];
if(enable_error_stack > 0) {
H5Eset_auto2(H5E_DEFAULT, func, edata);
H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
}
/* Check for filename given */
if(fname) {
hid_t fcpl;
@ -1788,16 +1812,18 @@ main(int argc, const char *argv[])
unsigned u;
for(u = 0; u < hand->obj_count; u++) {
if(h5trav_visit(fid, hand->obj[u], TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < 0)
warn_msg("Unable to traverse object \"%s\"\n", hand->obj[u]);
else
if(h5trav_visit(fid, hand->obj[u], TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < 0) {
error_msg("unable to traverse object \"%s\"\n", hand->obj[u]);
h5tools_setstatus(EXIT_FAILURE);
} else
print_statistics(hand->obj[u], &iter);
} /* end for */
} /* end if */
else {
if(h5trav_visit(fid, "/", TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < 0)
warn_msg("Unable to traverse objects/links in file \"%s\"\n", fname);
else
if(h5trav_visit(fid, "/", TRUE, TRUE, obj_stats, lnk_stats, &iter, H5O_INFO_ALL) < 0) {
error_msg("unable to traverse objects/links in file \"%s\"\n", fname);
h5tools_setstatus(EXIT_FAILURE);
} else
print_statistics("/", &iter);
} /* end else */
} /* end if */
@ -1813,6 +1839,8 @@ done:
h5tools_setstatus(EXIT_FAILURE);
} /* end if */
H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(h5tools_getstatus());
} /* end main() */

86
tools/test/h5dump/h5dumpgentest.c
View File

@ -113,6 +113,7 @@
#define FILE83 "tvlenstr_array.h5"
#define FILE84 "tudfilter.h5"
#define FILE85 "tgrpnullspace.h5"
#define FILE86 "err_attr_dspace.h5"
/*-------------------------------------------------------------------------
* prototypes
@ -10476,6 +10477,89 @@ static void gent_null_space_group(void)
H5Fclose(fid);
}
/*-------------------------------------------------------------------------
* Function: gent_err_attr_dspace
*
* Purpose: Generate a file with shared dataspace message.
* Then write an illegal version to the shared dataspace message
* to trigger the error.
* This is to verify HDFFV-10333 that h5dump will exit
* gracefully when encountered error similar to
* H5O_attr_decode in the jira issue.
*
*-------------------------------------------------------------------------
*/
static void
gent_err_attr_dspace()
{
hid_t fid = -1; /* File identifier */
hid_t fcpl = -1; /* File access property list */
hid_t sid; /* Dataspace identifier */
hid_t aid; /* Attribute identifier */
hsize_t dims = 2; /* Dimensino size */
int wdata[2] = {7, 42}; /* The buffer to write */
int fd = -1; /* The file descriptor */
char val = 6; /* An invalid version */
/* Create an fcpl */
if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
goto error;
/* Set up the dataspace message to be shared */
if(H5Pset_shared_mesg_nindexes(fcpl, 1) < 0)
goto error;
if(H5Pset_shared_mesg_index(fcpl, 0, H5O_SHMESG_SDSPACE_FLAG, 1) < 0)
goto error;
/* Create the file with the shared message setting */
if((fid = H5Fcreate(FILE86, H5F_ACC_TRUNC, fcpl, H5P_DEFAULT)) < 0)
goto error;
/* Create the dataspace */
if((sid = H5Screate_simple(1, &dims, &dims)) < 0)
goto error;
/* Create an attribute with shared dataspace */
if((aid = H5Acreate2(fid, "attribute", H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(H5Awrite(aid, H5T_NATIVE_INT, wdata) < 0)
goto error;
/* Closing */
if(H5Aclose(aid) < 0)
goto error;
if(H5Sclose(sid) < 0)
goto error;
if(H5Pclose(fcpl) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
/* This section of code will write an illegal version to the "version" field
of the shared dataspace message */
if((fd = HDopen(FILE86, O_RDWR, 0633)) < 0)
goto error;
/* Offset of the "version" field to modify is as follows: */
/* 1916: offset of the object header containing the attribute message */
/* 32: offset of the attribute message in the object header */
/* 30: offset in the attribute message containing the version of the shared dataspace message */
if(HDlseek(fd, 1916+32+30, SEEK_SET) < 0)
goto error;
if(HDwrite(fd, &val, 1) < 0)
goto error;
if(HDclose(fd) < 0)
goto error;
error:
H5E_BEGIN_TRY {
H5Pclose(fcpl);
H5Aclose(aid);
H5Sclose(sid);
H5Fclose(fid);
} H5E_END_TRY;
} /* gen_err_attr_dspace() */
int main(void)
{
gent_group();
@ -10569,6 +10653,8 @@ int main(void)
gent_udfilter();
gent_err_attr_dspace();
return 0;
}

5
tools/test/h5dump/testh5dump.sh.in
View File

@ -175,6 +175,7 @@ $SRC_H5DUMP_TESTFILES/tvldtypes5.h5
$SRC_H5DUMP_TESTFILES/tvlenstr_array.h5
$SRC_H5DUMP_TESTFILES/tvlstr.h5
$SRC_H5DUMP_TESTFILES/tvms.h5
$SRC_H5DUMP_TESTFILES/err_attr_dspace.h5
"
LIST_OTHER_TEST_FILES="
@ -360,6 +361,7 @@ $SRC_H5DUMP_TESTFILES/twithddlfile.exp
$SRC_H5DUMP_TESTFILES/h5dump-help.txt
$SRC_H5DUMP_TESTFILES/out3.h5import
$SRC_H5DUMP_TESTFILES/tbinregR.exp
$SRC_H5DUMP_TESTFILES/err_attr_dspace.ddl
"
LIST_ERROR_TEST_FILES="
@ -1322,6 +1324,9 @@ TOOLTEST tattrreg.ddl --enable-error-stack tattrreg.h5
TOOLTEST4 tattrregR.ddl --enable-error-stack -R tattrreg.h5
TOOLTEST2 tbinregR.exp --enable-error-stack -d /Dataset1 -s 0 -R -y -o tbinregR.txt tdatareg.h5
# test to verify HDFFV-10333: error similar to H5O_attr_decode in the jira issue
TOOLTEST err_attr_dspace.ddl err_attr_dspace.h5
# Clean up text output files
if test -z "$HDF5_NOCLEANUP"; then
rm -f tbinregR.txt

142
tools/test/h5stat/h5stat_gentest.c
View File

@ -21,6 +21,7 @@
* of the expected output and update the corresponding *.ddl files.
*/
#include "hdf5.h"
#include "H5private.h"
/* For gen_newgrat_file() */
#define NEWGRAT_FILE "h5stat_newgrat.h5"
@ -43,6 +44,9 @@
#define THRES_NUM 10
#define THRES_NUM_25 25
/* For gen_err_refcount() */
#define ERR_REFCOUNT_FILE "h5stat_err_refcount.h5"
/*
* Generate HDF5 file with latest format with
* NUM_GRPS groups and NUM_ATTRS attributes for the dataset
@ -434,6 +438,141 @@ error:
} /* gen_idx_file() */
/*
* Function: gen_err_refcount_file
*
* Purpose: Create a file with a refcount message ID.
* Then a refcount message ID is written to a
* message in a version 1 object header.
* This will trigger the error as a version 1
* object header does not support a refcount message.
* This is to verify HDFFV-10333 that h5stat will exit
* gracefully when encountered error similar to
* H5O_refcount_decode in the jira issue.
*
*/
static void
gen_err_refcount(const char *fname)
{
hid_t fid = -1; /* File identifier */
hid_t fapl = -1; /* File access property list */
hid_t sid = -1; /* Dataspace message */
hid_t did = -1; /* Dataset identifier */
hid_t gid = -1; /* Group identifier */
hid_t aid1 = -1, aid2 = -1; /* Attribute identifier */
hid_t tid = -1; /* Datatype identifier */
int i, n; /* Local index variables */
int buf[10]; /* Data buffer */
hsize_t dims[1]; /* Dimension size */
int fd = -1; /* File descriptor */
unsigned short val = 22; /* The refcount message ID */
/* Initialize data buffer */
n = 0;
for(i = 0; i < 10; i++)
buf[i] = n++;
/* Create the file */
if((fid = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Create a group */
if((gid = H5Gcreate2(fid, "group", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Create a committed datatype in the group */
if((tid = H5Tcopy(H5T_NATIVE_INT)) < 0)
goto error;
if(H5Tcommit2(gid, "dtype", tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
/* Create the dataspace */
dims[0] = 10;
if((sid = H5Screate_simple(1, dims, NULL)) < 0)
goto error;
/* Create a dataset with the committed datatype in the file */
if((did = H5Dcreate2(fid, "dset", tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Write to the dataset */
if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/* Attach an attribute with the committed datatype to the group */
if((aid1 = H5Acreate2(gid, "attr", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Attach an attribute with the committed datatype to the dataset */
if((aid2 = H5Acreate2(did, "attr", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Closing */
if(H5Aclose(aid1) < 0)
goto error;
if(H5Aclose(aid2) < 0)
goto error;
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did) < 0)
goto error;
if(H5Gclose(gid) < 0)
goto error;
if(H5Tclose(tid) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
/* This section of code will write a refcount message ID to a message in the
version 1 object header which does not support a refcount message */
/* Offset of the message ID to modify is as follows: */
/* 4520: the offset of the object header containing the attribute message
with the committed datatype */
/* 24: the offset in the object header containing the version of the
attribute message */
if((fd = HDopen(fname, O_RDWR, 0633)) < 0)
goto error;
if(HDlseek(fd, 4520+24, SEEK_SET) < 0)
goto error;
if(HDwrite(fd, &val, 2) < 0)
goto error;
if(HDclose(fd) < 0)
goto error;
error:
H5E_BEGIN_TRY {
H5Gclose(gid);
H5Dclose(did);
H5Tclose(tid);
H5Sclose(sid);
H5Aclose(aid1);
H5Aclose(aid2);
H5Fclose(fid);
} H5E_END_TRY;
} /* gen_err_refcount() */
/*
* The following two test files are generated with older versions
* of the library for HDFFV-10333. They are used for testing in
* testh5stat.sh.in.
*
* (1) h5stat_err_old_layout.h5
* This file is generated with the 1.6 library so that a file
* with a version 2 layout message is created.
* Then a "0" is written to the "dimension" field in the layout
* message to trigger the error.
* This is to verify HDFFV-10333 that h5stat will exit gracefully
* when encountered error similar to H5O__layout_decode in the
* jira issue.
*
* (2) h5stat_err_old_fill.h5
* This file is generated with the 1.4 library so that a file
* with an old fill value message is created.
* Then an illegal size is written to the "size" fild in the
* fill value message to trigger the error.
* This is to verify HDFFV-10333 that h5stat will exit gracefully
* when encountered error similar to H5O_fill_old_decode in the
* jira issue.
*/
int main(void)
{
gen_newgrat_file(NEWGRAT_FILE);
@ -442,6 +581,9 @@ int main(void)
/* Generate an HDF file to test for datasets with Fixed Array indexing */
gen_idx_file(IDX_FILE);
/* Generate a file with a refcount message ID */
gen_err_refcount(ERR_REFCOUNT_FILE);
return 0;
}

2
tools/test/h5stat/testfiles/h5stat_err_old_fill.ddl Normal file
View File

@ -0,0 +1,2 @@
Filename: h5stat_err_old_fill.h5
h5stat error: unable to traverse objects/links in file "h5stat_err_old_fill.h5"

BIN
tools/test/h5stat/testfiles/h5stat_err_old_fill.h5 Normal file
View File

Binary file not shown.

2
tools/test/h5stat/testfiles/h5stat_err_old_layout.ddl Normal file
View File

@ -0,0 +1,2 @@
Filename: h5stat_err_old_layout.h5
h5stat error: unable to traverse objects/links in file "h5stat_err_old_layout.h5"

BIN
tools/test/h5stat/testfiles/h5stat_err_old_layout.h5 Normal file
View File

Binary file not shown.

2
tools/test/h5stat/testfiles/h5stat_err_refcount.ddl Normal file
View File

@ -0,0 +1,2 @@
Filename: h5stat_err_refcount.h5
h5stat error: unable to traverse objects/links in file "h5stat_err_refcount.h5"

BIN
tools/test/h5stat/testfiles/h5stat_err_refcount.h5 Normal file
View File

Binary file not shown.

1
tools/test/h5stat/testfiles/h5stat_help1.ddl
View File

@ -22,3 +22,4 @@ Usage: h5stat [OPTIONS] file
than 0. The default threshold is 10.
-s, --freespace Print free space information
-S, --summary Print summary of file space information
--enable-error-stack Prints messages from the HDF5 error stack as they occur

1
tools/test/h5stat/testfiles/h5stat_help2.ddl
View File

@ -22,3 +22,4 @@ Usage: h5stat [OPTIONS] file
than 0. The default threshold is 10.
-s, --freespace Print free space information
-S, --summary Print summary of file space information
--enable-error-stack Prints messages from the HDF5 error stack as they occur

1
tools/test/h5stat/testfiles/h5stat_nofile.ddl
View File

@ -22,4 +22,5 @@ Usage: h5stat [OPTIONS] file
than 0. The default threshold is 10.
-s, --freespace Print free space information
-S, --summary Print summary of file space information
--enable-error-stack Prints messages from the HDF5 error stack as they occur
h5stat error: missing file name

15
tools/test/h5stat/testh5stat.sh.in
View File

@ -74,6 +74,9 @@ $SRC_H5STAT_TESTFILES/h5stat_tsohm.h5
$SRC_H5STAT_TESTFILES/h5stat_newgrat.h5
$SRC_H5STAT_TESTFILES/h5stat_idx.h5
$SRC_H5STAT_TESTFILES/h5stat_threshold.h5
$SRC_H5STAT_TESTFILES/h5stat_err_refcount.h5
$SRC_H5STAT_TESTFILES/h5stat_err_old_layout.h5
$SRC_H5STAT_TESTFILES/h5stat_err_old_fill.h5
"
LIST_OTHER_TEST_FILES="
@ -109,6 +112,9 @@ $SRC_H5STAT_TESTFILES/h5stat_numattrs1.ddl
$SRC_H5STAT_TESTFILES/h5stat_numattrs2.ddl
$SRC_H5STAT_TESTFILES/h5stat_numattrs3.ddl
$SRC_H5STAT_TESTFILES/h5stat_numattrs4.ddl
$SRC_H5STAT_TESTFILES/h5stat_err_refcount.ddl
$SRC_H5STAT_TESTFILES/h5stat_err_old_layout.ddl
$SRC_H5STAT_TESTFILES/h5stat_err_old_fill.ddl
"
#
@ -243,6 +249,7 @@ TOOLTEST h5stat_help2.ddl --help
TOOLTEST h5stat_notexist.ddl notexist.h5
TOOLTEST h5stat_nofile.ddl ''
# Test file with groups, compressed datasets, user-applied fileters, etc.
# h5stat_filters.h5 is a copy of ../../testfiles/tfilters.h5 as of release 1.8.0-alpha4
TOOLTEST h5stat_filters.ddl h5stat_filters.h5
@ -304,7 +311,13 @@ TOOLTEST h5stat_numattrs3.ddl -A --numattrs=25 h5stat_threshold.h5
# -A -a 100
TOOLTEST h5stat_numattrs4.ddl -A -a 100 h5stat_newgrat.h5
#
#
# Tests to verify HDFFV-10333
TOOLTEST h5stat_err_refcount.ddl h5stat_err_refcount.h5
TOOLTEST h5stat_err_old_layout.ddl h5stat_err_old_layout.h5
TOOLTEST h5stat_err_old_fill.ddl h5stat_err_old_fill.h5
#
#
# Clean up temporary files/directories
CLEAN_TESTFILES_AND_TESTDIR

5
tools/testfiles/err_attr_dspace.ddl Normal file
View File

@ -0,0 +1,5 @@
HDF5 "err_attr_dspace.h5" {
GROUP "/" {
}
}
h5dump error: error getting attribute information

BIN
tools/testfiles/err_attr_dspace.h5 Normal file
View File

Binary file not shown.