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Merge pull request #2486 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:tools_vol_update to develop

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* commit '110cafb9c7b5b9f9170340432062295d630f3ee6':
  Updated tools dump output when dataset offset is undefined.
  Added checks for native optional call support in some of the tools.
  Misc changes for h5dump VOL changes.
This commit is contained in:
Dana Robinson 2020-04-06 13:53:22 -05:00
commit 4830a17964
9 changed files with 137 additions and 81 deletions
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2
src/H5Dint.c
View File

@ -2563,7 +2563,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5D__get_offset
*
* Purpose: Private function for H5D__get_offset. Returns the address
* Purpose: Private function for H5Dget_offset(). Returns the address
* of dataset in file.
*
* Return: Success: The address of dataset

2
src/H5VL.c
View File

@ -663,7 +663,7 @@ done:
/*---------------------------------------------------------------------------
* Function: H5VLobject
*
* Purpose: Retrieve the object pointer associated with an hid_t for a.
* Purpose: Retrieve the object pointer associated with an hid_t for a
* VOL object.
*
* Note: This routine is mainly targeted toward unwrapping objects for

102
tools/lib/h5tools_dump.c
View File

@ -2099,11 +2099,11 @@ h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_
if(obj) {
if(!obj->recorded) {
char *obj_addr_str = NULL;
char *obj_tok_str = NULL;
H5Otoken_to_str(type, &oinfo.token, &obj_addr_str);
h5tools_str_append(buffer,"\"/#%s\"", obj_addr_str);
H5free_memory(obj_addr_str);
H5Otoken_to_str(type, &oinfo.token, &obj_tok_str);
h5tools_str_append(buffer,"\"/#%s\"", obj_tok_str);
H5free_memory(obj_tok_str);
}
else
h5tools_str_append(buffer, "\"%s\"", obj->objname);
@ -3110,7 +3110,7 @@ h5tools_print_fill_value(h5tools_str_t *buffer/*in,out*/, const h5tool_format_t
*/
void
h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, hid_t dcpl_id, hid_t type_id, hid_t obj_id)
h5tools_context_t *ctx, hid_t dcpl_id, hid_t type_id, hid_t dset_id)
{
int nfilters; /* number of filters */
int rank; /* rank */
@ -3141,7 +3141,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
if (info->line_ncols > 0)
ncols = info->line_ncols;
storage_size = H5Dget_storage_size(obj_id);
storage_size = H5Dget_storage_size(dset_id);
nfilters = H5Pget_nfilters(dcpl_id);
HDstrcpy(f_name,"\0");
@ -3182,8 +3182,8 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
double ratio = 0;
int ok = 0;
hid_t tid = H5Dget_type(obj_id);
hid_t sid = H5Dget_space(obj_id);
hid_t tid = H5Dget_type(dset_id);
hid_t sid = H5Dget_space(dset_id);
size_t datum_size = H5Tget_size(tid);
int ndims = H5Sget_simple_extent_dims(sid, dims, NULL);
@ -3241,16 +3241,15 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
break;
case H5D_CONTIGUOUS:
{
int next;
int n_external;
next = H5Pget_external_count(dcpl_id);
n_external = H5Pget_external_count(dcpl_id);
/*-------------------------------------------------------------------------
* EXTERNAL_FILE
*-------------------------------------------------------------------------
*/
ctx->indent_level++;
if (next) {
if (n_external) {
/* EXTERNAL FILE */
ctx->need_prefix = TRUE;
h5tools_str_reset(&buffer);
@ -3264,7 +3263,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0);
ctx->indent_level++;
for (j = 0; j < (unsigned) next; j++) {
for (j = 0; j < (unsigned) n_external; j++) {
H5Pget_external(dcpl_id, j, sizeof(name), name, &offset, &size);
ctx->need_prefix = TRUE;
@ -3284,6 +3283,11 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
}
else {
haddr_t ioffset;
void *obj = NULL;
hid_t connector_id = H5I_INVALID_HID;
hbool_t supported = FALSE;
/* NORMAL FILE */
ctx->need_prefix = TRUE;
@ -3297,12 +3301,26 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
h5tools_str_append(&buffer,"SIZE " HSIZE_T_FORMAT, storage_size);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0);
ctx->need_prefix = TRUE;
/* Only dump the offset if the VOL connector implements
* the functionality.
*/
obj = H5VLobject(dset_id);
connector_id = H5VLget_connector_id(dset_id);
H5VLintrospect_opt_query(obj, connector_id, H5VL_SUBCLS_DATASET, H5VL_NATIVE_DATASET_GET_OFFSET, &supported);
H5VLclose(connector_id);
h5tools_str_reset(&buffer);
ioffset = H5Dget_offset(obj_id);
h5tools_str_append(&buffer, "OFFSET "H5_PRINTF_HADDR_FMT, ioffset);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0);
if (supported) {
ctx->need_prefix = TRUE;
h5tools_str_reset(&buffer);
ioffset = H5Dget_offset(dset_id);
if (HADDR_UNDEF == ioffset)
h5tools_str_append(&buffer, "OFFSET HADDR_UNDEF");
else
h5tools_str_append(&buffer, "OFFSET "H5_PRINTF_HADDR_FMT, ioffset);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0);
}
}
ctx->indent_level--;
}
@ -3311,23 +3329,23 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
case H5D_VIRTUAL:
{
char dsetname[256]; /* virtual datset name */
size_t vmaps;
size_t n_vmaps;
H5Pget_virtual_count(dcpl_id, &vmaps);
H5Pget_virtual_count(dcpl_id, &n_vmaps);
if (vmaps) {
size_t next;
if (n_vmaps) {
size_t curr_vmap;
ssize_t H5_ATTR_NDEBUG_UNUSED ssize_out;
ctx->indent_level++;
for (next = 0; next < (unsigned) vmaps; next++) {
hid_t virtual_vspace = H5Pget_virtual_vspace(dcpl_id, next);
hid_t virtual_srcspace = H5Pget_virtual_srcspace(dcpl_id, next);
for (curr_vmap = 0; curr_vmap < n_vmaps; curr_vmap++) {
hid_t virtual_vspace = H5Pget_virtual_vspace(dcpl_id, curr_vmap);
hid_t virtual_srcspace = H5Pget_virtual_srcspace(dcpl_id, curr_vmap);
ctx->need_prefix = TRUE;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %ld %s ", VDS_MAPPING, next, BEGIN);
h5tools_str_append(&buffer, "%s %ld %s ", VDS_MAPPING, curr_vmap, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0);
ctx->indent_level++;
@ -3358,14 +3376,14 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
ctx->indent_level++;
ssize_out = H5Pget_virtual_filename(dcpl_id, next, NULL, 0);
ssize_out = H5Pget_virtual_filename(dcpl_id, curr_vmap, NULL, 0);
HDassert(ssize_out > 0);
HDassert((size_t)ssize_out < sizeof(name));
H5Pget_virtual_filename(dcpl_id, next, name, sizeof(name));
ssize_out = H5Pget_virtual_dsetname(dcpl_id, next, NULL, 0);
H5Pget_virtual_filename(dcpl_id, curr_vmap, name, sizeof(name));
ssize_out = H5Pget_virtual_dsetname(dcpl_id, curr_vmap, NULL, 0);
HDassert(ssize_out > 0);
HDassert((size_t)ssize_out < sizeof(name));
H5Pget_virtual_dsetname(dcpl_id, next, dsetname, sizeof(dsetname));
H5Pget_virtual_dsetname(dcpl_id, curr_vmap, dsetname, sizeof(dsetname));
ctx->need_prefix = TRUE;
@ -3629,7 +3647,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info,
break;
case H5D_FILL_VALUE_USER_DEFINED:
ctx->indent_level--;
h5tools_print_fill_value(&buffer, info, ctx, dcpl_id, type_id, obj_id);
h5tools_print_fill_value(&buffer, info, ctx, dcpl_id, type_id, dset_id);
ctx->indent_level++;
break;
case H5D_FILL_VALUE_ERROR:
@ -3714,6 +3732,17 @@ h5tools_dump_comment(FILE *stream, const h5tool_format_t *info, h5tools_context_
* instead of the current stripmine position i; this is necessary
* to print the array indices
*/
void *obj = NULL;
hid_t connector_id = H5I_INVALID_HID;
hbool_t supported = FALSE;
/* Check if comments are supported and return if not */
obj = H5VLobject(obj_id);
connector_id = H5VLget_connector_id(obj_id);
H5VLintrospect_opt_query(obj, connector_id, H5VL_SUBCLS_OBJECT, H5VL_NATIVE_OBJECT_GET_COMMENT, &supported);
H5VLclose(connector_id);
if (!supported)
return;
/* setup */
HDmemset(&buffer, 0, sizeof(h5tools_str_t));
@ -3723,8 +3752,7 @@ h5tools_dump_comment(FILE *stream, const h5tool_format_t *info, h5tools_context_
cmt_bufsize = H5Oget_comment(obj_id, comment, buf_size);
/* call H5Oget_comment again with the correct value.
* If the call to H5Oget_comment returned an error, skip this block */
/* call H5Oget_comment again with the correct value */
if (cmt_bufsize > 0) {
comment = (char *)HDmalloc((size_t)(cmt_bufsize+1)); /* new_size including null terminator */
if(comment) {
@ -3739,7 +3767,7 @@ h5tools_dump_comment(FILE *stream, const h5tool_format_t *info, h5tools_context_
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
h5tools_str_close(&buffer);
} /* end if */
}
HDfree(comment);
}
}

14
tools/lib/h5tools_str.c
View File

@ -1101,12 +1101,12 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
{
/* Object references -- show the type and OID of the referenced object. */
H5O_info2_t oi;
char *obj_addr_str = NULL;
char *obj_tok_str = NULL;
H5TOOLS_DEBUG("ref_type is H5R_OBJECT1");
if((obj = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
H5Oget_info3(obj, &oi, H5O_INFO_BASIC);
H5Otoken_to_str(obj, &oi.token, &obj_addr_str);
H5Otoken_to_str(obj, &oi.token, &obj_tok_str);
}
else
H5TOOLS_ERROR(NULL, "H5Ropen_object H5R_OBJECT1 failed");
@ -1137,13 +1137,13 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
/* Print OID */
if(info->obj_hidefileno)
h5tools_str_append(str, info->obj_format, obj_addr_str);
h5tools_str_append(str, info->obj_format, obj_tok_str);
else
h5tools_str_append(str, info->obj_format, oi.fileno, obj_addr_str);
h5tools_str_append(str, info->obj_format, oi.fileno, obj_tok_str);
if(obj_addr_str) {
H5free_memory(obj_addr_str);
obj_addr_str = NULL;
if(obj_tok_str) {
H5free_memory(obj_tok_str);
obj_tok_str = NULL;
}
if(obj >= 0)

8
tools/lib/h5tools_utils.c
View File

@ -648,17 +648,17 @@ static void
dump_table(hid_t fid, char* tablename, table_t *table)
{
unsigned u;
char *obj_addr_str = NULL;
char *obj_tok_str = NULL;
PRINTSTREAM(rawoutstream,"%s: # of entries = %d\n", tablename,table->nobjs);
for (u = 0; u < table->nobjs; u++) {
H5VLconnector_token_to_str(fid, table->objs[u].obj_token, &obj_addr_str);
H5VLconnector_token_to_str(fid, table->objs[u].obj_token, &obj_tok_str);
PRINTSTREAM(rawoutstream,"%s %s %d %d\n", obj_addr_str,
PRINTSTREAM(rawoutstream,"%s %s %d %d\n", obj_tok_str,
table->objs[u].objname,
table->objs[u].displayed, table->objs[u].recorded);
H5VLfree_token_str(fid, obj_addr_str);
H5VLfree_token_str(fid, obj_tok_str);
}
}

16
tools/src/h5dump/h5dump_ddl.c
View File

@ -1136,6 +1136,22 @@ dump_fcpl(hid_t fid)
unsigned sym_ik; /* symbol table B-tree internal 'K' value */
unsigned istore_ik; /* indexed storage B-tree internal 'K' value */
void *obj = NULL;
hid_t connector_id = H5I_INVALID_HID;
hbool_t supported = FALSE;
/* Dumping the information here only makes sense for the native
* VOL connector. The only VOL call here is H5Fget_info(), so we'll
* use that as a proxy for "native-ness". If that isn't supported, we'll
* just return.
*/
obj = H5VLobject(fid);
connector_id = H5VLget_connector_id(fid);
H5VLintrospect_opt_query(obj, connector_id, H5VL_SUBCLS_FILE, H5VL_NATIVE_FILE_GET_INFO, &supported);
H5VLclose(connector_id);
if (!supported)
return;
fcpl=H5Fget_create_plist(fid);
H5Fget_info2(fid, &finfo);
H5Pget_userblock(fcpl,&userblock);

68
tools/src/h5ls/h5ls.c
View File

@ -2334,13 +2334,13 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
} /* end if */
else {
hid_t obj = H5I_INVALID_HID; /* ID of object opened */
hid_t obj_id = H5I_INVALID_HID; /* ID of object opened */
/* Open the object. Not all objects can be opened. If this is the case
* then return right away.
*/
H5TOOLS_DEBUG("Open object name=%s", name);
if (obj_type >= 0 && (obj = H5Oopen(iter->fid, name, H5P_DEFAULT)) < 0) {
if (obj_type >= 0 && (obj_id = H5Oopen(iter->fid, name, H5P_DEFAULT)) < 0) {
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " *ERROR*\n");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
@ -2350,7 +2350,7 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
/* List the first line of information for the object. */
H5TOOLS_DEBUG("Object type:%d", obj_type);
if (obj_type >= 0 && dispatch_g[obj_type].list1)
(dispatch_g[obj_type].list1)(obj);
(dispatch_g[obj_type].list1)(obj_id);
if (!iter->symlink_target || (verbose_g > 0)) {
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "\n");
@ -2362,23 +2362,26 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
if (verbose_g > 0) {
size_t buf_size = 0;
char* comment = NULL;
char* obj_addr_str = NULL;
char* obj_tok_str = NULL;
ssize_t cmt_bufsize = -1;
void *obj = NULL;
hid_t connector_id = H5I_INVALID_HID;
hbool_t supported = FALSE;
/* Display attributes */
H5TOOLS_DEBUG("Display attributes");
if (obj_type >= 0)
H5Aiterate2(obj, H5_INDEX_NAME, H5_ITER_INC, NULL, list_attr, NULL);
H5Aiterate2(obj_id, H5_INDEX_NAME, H5_ITER_INC, NULL, list_attr, NULL);
/* Object location & reference count */
H5Otoken_to_str(obj, &oinfo->token, &obj_addr_str);
H5Otoken_to_str(obj_id, &oinfo->token, &obj_tok_str);
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " %-10s %lu:%s\n", "Location:", oinfo->fileno, obj_addr_str);
h5tools_str_append(&buffer, " %-10s %lu:%s\n", "Location:", oinfo->fileno, obj_tok_str);
h5tools_str_append(&buffer, " %-10s %u\n", "Links:", (unsigned)oinfo->rc);
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
H5free_memory(obj_addr_str);
H5free_memory(obj_tok_str);
/* Modification time */
if (oinfo->mtime > 0) {
@ -2397,36 +2400,45 @@ list_obj(const char *name, const H5O_info2_t *oinfo, const char *first_seen, voi
} /* end if */
} /* end if */
/* Object comment */
cmt_bufsize = H5Oget_comment(obj, comment, buf_size);
/* Only emit comments if the VOL connector supports that */
obj = H5VLobject(obj_id);
connector_id = H5VLget_connector_id(obj_id);
H5VLintrospect_opt_query(obj, connector_id, H5VL_SUBCLS_OBJECT, H5VL_NATIVE_OBJECT_GET_COMMENT, &supported);
H5VLclose(connector_id);
/* if the actual length of the comment is longer than cmt_bufsize, then call
* H5Oget_comment again with the correct value.
* If the call to H5Oget_comment returned an error, skip this block */
if (cmt_bufsize > 0) {
comment = (char *)HDmalloc((size_t)cmt_bufsize + 1); /* new_size including null terminator */
if (comment) {
cmt_bufsize = H5Oget_comment(obj, comment, (size_t)cmt_bufsize);
if (cmt_bufsize > 0) {
comment[cmt_bufsize] = 0;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " %-10s \"", "Comment:");
print_string(&buffer, comment, FALSE);
h5tools_str_append(&buffer, "\"\n");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
} /* end if */
HDfree(comment);
if (supported) {
/* Object comment */
cmt_bufsize = H5Oget_comment(obj_id, comment, buf_size);
/* if the actual length of the comment is longer than cmt_bufsize, then call
* H5Oget_comment again with the correct value.
*/
if (cmt_bufsize > 0) {
comment = (char *)HDmalloc((size_t)cmt_bufsize + 1); /* new_size including null terminator */
if (comment) {
cmt_bufsize = H5Oget_comment(obj_id, comment, (size_t)cmt_bufsize);
if (cmt_bufsize > 0) {
comment[cmt_bufsize] = 0;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " %-10s \"", "Comment:");
print_string(&buffer, comment, FALSE);
h5tools_str_append(&buffer, "\"\n");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
} /* end if */
HDfree(comment);
}
}
}
} /* end if */
/* Detailed list for object */
if (obj_type >= 0 && dispatch_g[obj_type].list2)
(dispatch_g[obj_type].list2)(obj, name);
(dispatch_g[obj_type].list2)(obj_id, name);
/* Close the object. */
if (obj_type >= 0)
H5Oclose(obj);
H5Oclose(obj_id);
} /* end else */
done:

4
tools/src/h5repack/h5repack.c
View File

@ -259,7 +259,7 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
/* Update the address and id */
/* Update the token/address and id */
HDmemcpy(&dt->obj_token, &travt->objs[i].obj_token, sizeof(H5O_token_t));
dt->id_out = H5I_INVALID_HID;
@ -282,7 +282,7 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t
dt_ret->next = *named_dt_head_p;
*named_dt_head_p = dt_ret;
/* Update the address and id */
/* Update the token/address and id */
HDmemcpy(&dt_ret->obj_token, &oinfo.token, sizeof(H5O_token_t));
dt_ret->id_out = H5I_INVALID_HID;
} /* end if requested datatype not found */

2
tools/testfiles/tgrpnullspace.ddl
View File

@ -13,7 +13,7 @@ GROUP "/" {
STORAGE_LAYOUT {
CONTIGUOUS
SIZE 0
OFFSET 18446744073709551615
OFFSET HADDR_UNDEF
}
FILTERS {
NONE