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-rw-r--r--tools/h5dump/h5dump.c25
-rw-r--r--tools/h5ls/h5ls.c12
-rw-r--r--tools/lib/h5tools.c56
-rw-r--r--tools/lib/h5tools.h1
4 files changed, 90 insertions, 4 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index bebc892..cf02a47 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -2545,11 +2545,18 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index)
char string_prefix[64];
h5tool_format_t string_dataformat;
+ /* VL data special information */
+ unsigned int vl_data = 0; /* contains VL datatypes */
+
type = H5Aget_type(obj_id);
p_type = h5tools_get_native_type(type);
ndims = H5Sget_simple_extent_dims(space, size, NULL);
+ /* Check if we have VL data in the dataset's datatype */
+ if (H5Tdetect_vlen_str(p_type) == TRUE)
+ vl_data = TRUE;
+
for (i = 0; i < ndims; i++)
nelmts *= size[i];
@@ -2590,6 +2597,10 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index)
status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type,
space, buf, depth);
+ /* Reclaim any VL memory, if necessary */
+ if (vl_data)
+ H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf);
+
free(buf);
H5Tclose(p_type);
H5Tclose(type);
@@ -5502,10 +5513,16 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t UNUSED * sset, int UNU
H5Tclose(type);
} else if (H5Tget_class(type) == H5T_STRING) {
status = xml_print_strs(obj_id, ATTRIBUTE_DATA);
- } else {
- /* all other data */
+ } else { /* all other data */
+ /* VL data special information */
+ unsigned int vl_data = 0; /* contains VL datatypes */
+
p_type = h5tools_get_native_type(type);
+ /* Check if we have VL data in the dataset's datatype */
+ if (H5Tdetect_vlen_str(p_type) == TRUE)
+ vl_data = TRUE;
+
H5Tclose(type);
space = H5Aget_space(obj_id);
@@ -5522,6 +5539,10 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t UNUSED * sset, int UNU
status = h5tools_dump_mem(stdout, outputformat, obj_id,
p_type, space, buf, depth);
+ /* Reclaim any VL memory, if necessary */
+ if (vl_data)
+ H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf);
+
free(buf);
H5Tclose(p_type);
H5Sclose(space);
diff --git a/tools/h5ls/h5ls.c b/tools/h5ls/h5ls.c
index 420ff3f..d2233ce 100644
--- a/tools/h5ls/h5ls.c
+++ b/tools/h5ls/h5ls.c
@@ -1449,6 +1449,13 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t UNUSED *ainfo,
p_type = h5tools_get_native_type(type);
if(p_type >= 0) {
+ /* VL data special information */
+ unsigned int vl_data = 0; /* contains VL datatypes */
+
+ /* Check if we have VL data in the dataset's datatype */
+ if (H5Tdetect_vlen_str(p_type) == TRUE)
+ vl_data = TRUE;
+
temp_need= nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type));
assert(temp_need == (hsize_t)((size_t)temp_need));
need = (size_t)temp_need;
@@ -1456,6 +1463,11 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t UNUSED *ainfo,
assert(buf);
if(H5Aread(attr, p_type, buf) >= 0)
h5tools_dump_mem(stdout, &info, attr, p_type, space, buf, -1);
+
+ /* Reclaim any VL memory, if necessary */
+ if (vl_data)
+ H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf);
+
free(buf);
H5Tclose(p_type);
} /* end if */
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 00040ad..0286bea 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -622,6 +622,47 @@ h5tools_ncols(const char *s)
}
/*-------------------------------------------------------------------------
+ * Function: H5Tdetect_vlen_str
+ *
+ * Purpose: Recursive check for variable length string of a datatype.
+ *
+ * Return: TRUE if type conatains a variable string type, else FALSE
+ *
+ *-------------------------------------------------------------------------
+ */
+htri_t
+H5Tdetect_vlen_str(hid_t tid)
+{
+ int n = 0;
+ htri_t has_vlen_str = FALSE;
+ H5T_class_t tclass = -1;
+
+ if (H5Tis_variable_str(tid) == TRUE)
+ return TRUE;
+
+ tclass = H5Tget_class(tid);
+ if (tclass == H5T_ARRAY) {
+ hid_t btid = H5Tget_super(tid);
+ has_vlen_str = H5Tdetect_vlen_str(btid);
+ H5Tclose(btid);
+ return has_vlen_str;
+ }
+ else if (tclass == H5T_COMPOUND) {
+ n = H5Tget_nmembers(tid);
+ for (int i = 0; i < n; i++) {
+ hid_t mtid = H5Tget_member_type(tid, i);
+ has_vlen_str = H5Tdetect_vlen_str(mtid);
+ if (has_vlen_str == TRUE) {
+ H5Tclose(mtid);
+ return TRUE;
+ }
+ H5Tclose(mtid);
+ }
+ }
+ return FALSE;
+}
+
+/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Emit a simple prefix to STREAM.
@@ -1976,6 +2017,9 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
hsize_t size_row_block; /* size for blocks along rows */
hsize_t row_counter = 0;
+ /* VL data special information */
+ unsigned int vl_data = 0; /* contains VL datatypes */
+
if ((size_t) ctx->ndims > NELMTS(sm_size))
H5E_THROW(FAIL, H5E_tools_min_id_g, "ndims and sm_size comparision failed");
@@ -1984,6 +2028,10 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
size_row_block = sset->block.data[row_dim];
+ /* Check if we have VL data in the dataset's datatype */
+ if (H5Tdetect_vlen_str(p_type) == TRUE)
+ vl_data = TRUE;
+
/* display loop */
for (; hyperslab_count > 0; temp_start[row_dim] += temp_stride[row_dim], hyperslab_count--) {
/* jump rows if size of block exceeded
@@ -2067,6 +2115,10 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c
h5tools_dump_simple_data(stream, info, dset, ctx, flags, sm_nelmts, p_type, sm_buf);
+ /* Reclaim any VL memory, if necessary */
+ if (vl_data)
+ H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);
+
if(H5Sclose(sm_space) < 0)
H5E_THROW(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
if(sm_buf)
@@ -2415,9 +2467,9 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info,
}
/* Check if we have VL data in the dataset's datatype */
- if (H5Tdetect_class(p_type, H5T_VLEN) == TRUE)
+ if (H5Tdetect_vlen_str(p_type) == TRUE)
vl_data = TRUE;
-
+
/*
* Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h
index b3e3dd2..9c100ea 100644
--- a/tools/lib/h5tools.h
+++ b/tools/lib/h5tools.h
@@ -553,6 +553,7 @@ H5TOOLS_DLL hid_t h5tools_get_native_type(hid_t type);
H5TOOLS_DLL hid_t h5tools_get_little_endian_type(hid_t type);
H5TOOLS_DLL hid_t h5tools_get_big_endian_type(hid_t type);
+H5TOOLS_DLL htri_t H5Tdetect_vlen_str(hid_t tid);
H5TOOLS_DLL void h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t container,
h5tools_context_t *ctx/*in,out*/, unsigned flags,