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-rw-r--r--MANIFEST2
-rwxr-xr-xtools/h5repack/h5repack.sh.in4
-rw-r--r--tools/h5repack/h5repack_refs.c16
-rw-r--r--tools/h5repack/h5repacktst.c323
-rw-r--r--tools/h5repack/testfiles/h5repack_refs.h5bin0 -> 9280 bytes
-rw-r--r--tools/lib/h5diff_array.c3
6 files changed, 342 insertions, 6 deletions
diff --git a/MANIFEST b/MANIFEST
index d13e1ea..9ab9509 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1609,7 +1609,7 @@
./tools/h5repack/testfiles/h5repack_ext.h5
./tools/h5repack/testfiles/ublock.bin
./tools/h5repack/testfiles/h5repack_named_dtypes.h5
-
+./tools/h5repack/testfiles/h5repack_refs.h5
# jam utility and tests
./tools/h5jam/h5jam.c
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 32622a0..35fc5fd 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -59,6 +59,7 @@ FILE14=h5repack_layouto.h5 # A file with an older version of the layout mes
# (copy of test/tlayouto.h5)
FILE15=h5repack_named_dtypes.h5
FILE16=tfamily%05d.h5 # located in common testfiles folder
+FILE_REF=h5repack_refs.h5
nerrors=0
@@ -531,6 +532,9 @@ TOOLTEST $FILE15
# tests family driver (file is located in common testfiles folder, uses TOOLTEST1
TOOLTEST1 $FILE16
+# test various references (bug 1814)
+TOOLTEST $FILE_REF
+
if test $nerrors -eq 0 ; then
echo "All $TESTNAME tests passed."
exit $EXIT_SUCCESS
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index fddcf0e..9945f49 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -690,23 +690,31 @@ static const char* MapIdToName(hid_t refobj_id,
trav_table_t *travt)
{
unsigned int i;
+ const char* ret = NULL;
+ H5O_info_t ref_oinfo; /* Stat for the refobj id */
/* linear search */
for(i = 0; i < travt->nobjs; i++)
{
- if(travt->objs[i].type == H5O_TYPE_DATASET)
+ if(travt->objs[i].type == H5O_TYPE_DATASET ||
+ travt->objs[i].type == H5O_TYPE_GROUP ||
+ travt->objs[i].type == H5O_TYPE_NAMED_DATATYPE)
{
H5O_info_t ref_oinfo; /* Stat for the refobj id */
/* obtain information to identify the referenced object uniquely */
if(H5Oget_info(refobj_id, &ref_oinfo) < 0)
- return NULL;
+ goto out;
if(ref_oinfo.addr == travt->objs[i].objno)
- return(travt->objs[i].name);
+ {
+ ret = travt->objs[i].name;
+ goto out;
+ }
} /* end if */
} /* i */
- return NULL;
+out:
+ return ret;
}
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 17ece99..d4cd347 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -78,6 +78,8 @@
#define FNAME_UB "ublock.bin"
+/* obj and region references */
+#define FNAME_REF "h5repack_refs.h5"
const char *H5REPACK_FILENAMES[] = {
"h5repack_big_out",
@@ -100,6 +102,13 @@ int d_status = EXIT_SUCCESS;
/* Size of userblock (for userblock test) */
#define USERBLOCK_SIZE 2048
+/* obj and region references */
+#define NAME_OBJ_DS "Dset1"
+#define NAME_OBJ_GRP "Group"
+#define NAME_OBJ_NDTYPE "NamedDatatype"
+#define REG_REF_DS1 "Dset_REGREF"
+#define REG_REF_DS2 "Dset2"
+
/*-------------------------------------------------------------------------
* prototypes
*-------------------------------------------------------------------------
@@ -132,6 +141,7 @@ static int make_userblock(void);
static int verify_userblock( const char* filename);
static int make_userblock_file(void);
static int make_named_dtype(hid_t loc_id);
+static int make_references(hid_t loc_id);
/*-------------------------------------------------------------------------
@@ -1763,6 +1773,16 @@ int make_testfiles(void)
if(H5Fclose(fid) < 0)
return -1;
+ /*-------------------------------------------------------------------------
+ * create a file with obj and region references
+ *-------------------------------------------------------------------------*/
+ if((fid = H5Fcreate(FNAME_REF,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT)) < 0)
+ return -1;
+ if (make_references(fid) < 0)
+ goto out;
+ if(H5Fclose(fid) < 0)
+ return -1;
+
return 0;
out:
@@ -5583,3 +5603,306 @@ out:
return -1;
} /* end make_named_dtype() */
+/*-------------------------------------------------------------------------
+ * Function: gen_obj_ref
+ *
+ * Purpose:
+ * Generate object references to objects (dataset,group and named datatype)
+ *
+ * Note:
+ * copied from h5copygentest.c and upate to create named datatype
+ *
+ * Programmer: Jonathan Kim (March 18, 2010)
+ *------------------------------------------------------------------------*/
+static herr_t gen_obj_ref(hid_t loc_id)
+{
+ hid_t sid=0, oid=0, tid=0;
+ hsize_t dims1[1]={3};
+ hsize_t dims2[1]={3};
+ int data[3] = {10,20,30};
+ int status;
+ herr_t ret = SUCCEED;
+
+ /*--------------
+ * add dataset */
+ sid = H5Screate_simple(1, dims1, NULL);
+ if (sid < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ oid = H5Dcreate2 (loc_id, NAME_OBJ_DS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if (oid < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ status = H5Dwrite(oid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ H5Dclose(oid);
+ H5Sclose(sid);
+
+ /*--------------
+ * add group */
+ oid = H5Gcreate2 (loc_id, NAME_OBJ_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if (oid < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+ H5Gclose(oid);
+
+ /*----------------------
+ * add named datatype
+ */
+ tid = H5Tcopy(H5T_NATIVE_INT);
+ status = H5Tcommit2(loc_id, NAME_OBJ_NDTYPE, tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Tcommit2 failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /*---------------------------------------------------------
+ * create obj references to the previously created objects.
+ * Passing -1 as reference is an object.*/
+ hobj_ref_t objref_buf[3]; /* write buffer for */
+
+ /* obj ref to dataset */
+ status = H5Rcreate (&objref_buf[0], loc_id, NAME_OBJ_DS, H5R_OBJECT, -1);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* obj ref to group */
+ status = H5Rcreate (&objref_buf[1], loc_id, NAME_OBJ_GRP, H5R_OBJECT, -1);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* obj ref to named-datatype */
+ status = H5Rcreate (&objref_buf[2], loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT, -1);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /*---------------------------------------------------------
+ * create dataset contain references
+ */
+ sid = H5Screate_simple (1, dims2, NULL);
+ if (sid < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ oid = H5Dcreate2 (loc_id, "Dset_OBJREF", H5T_STD_REF_OBJ, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
+ if (oid < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ status = H5Dwrite(oid, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, objref_buf);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+out:
+ if(oid > 0)
+ H5Dclose(oid);
+ if(tid > 0)
+ H5Tclose(tid);
+ if(sid > 0)
+ H5Sclose(sid);
+
+ return ret;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: gen_region_ref
+ *
+ * Purpose: Generate dataset region references
+ *
+ * Note:
+ * copied from h5copygentest.c
+ *
+ * Programmer: Jonathan Kim (March 18, 2010)
+ *------------------------------------------------------------------------*/
+static herr_t gen_region_ref(hid_t loc_id)
+{
+ hid_t sid=0, oid1=0, oid2=0;
+ int status;
+ herr_t ret = SUCCEED;
+ char data[3][16] = {"The quick brown", "fox jumps over ", "the 5 lazy dogs"};
+ hsize_t dims2[2] = {3,16};
+ hsize_t coords[4][2] = { {0,1}, {2,11}, {1,0}, {2,4} };
+
+ hdset_reg_ref_t rr_data[2];
+ hsize_t start[2] = {0,0};
+ hsize_t stride[2] = {2,11};
+ hsize_t count[2] = {2,2};
+ hsize_t block[2] = {1,3};
+ hsize_t dims1[1] = {2};
+
+ sid = H5Screate_simple (2, dims2, NULL);
+ if (sid < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* create normal dataset which is refered */
+ oid2 = H5Dcreate2 (loc_id, REG_REF_DS2, H5T_STD_I8LE, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
+ if (oid2 < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* write values to dataset */
+ status = H5Dwrite (oid2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* select elements space for reference */
+ status = H5Sselect_elements (sid, H5S_SELECT_SET, 4, coords[0]);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* create region reference from elements space */
+ status = H5Rcreate (&rr_data[0], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* select hyperslab space for reference */
+ status = H5Sselect_hyperslab (sid, H5S_SELECT_SET, start, stride, count, block);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Sselect_hyperslab failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* create region reference from hyperslab space */
+ status = H5Rcreate (&rr_data[1], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ H5Sclose (sid);
+
+ /* Create dataspace. */
+ sid = H5Screate_simple (1, dims1, NULL);
+ if (sid < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* create region reference dataset */
+ oid1 = H5Dcreate2 (loc_id, REG_REF_DS1, H5T_STD_REF_DSETREG, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
+ if (oid1 < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+ /* write data as region references */
+ status = H5Dwrite (oid1, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, rr_data);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+ ret = FAIL;
+ goto out;
+ }
+
+out:
+ if (oid1 > 0)
+ H5Dclose (oid1);
+ if (oid2 > 0)
+ H5Dclose (oid2);
+ if (sid > 0)
+ H5Sclose (sid);
+
+ return ret;
+}
+
+/*-------------------------------------------------------------------------
+* Function: make_references
+*
+* Purpose: create a file with obj and region references
+*
+* Programmer: Jonathan Kim (March 18, 2010)
+*-------------------------------------------------------------------------
+*/
+static herr_t make_references(hid_t loc_id)
+{
+ herr_t ret = SUCCEED;
+ herr_t status;
+
+ /* add object reference */
+ status = gen_obj_ref(loc_id);
+ if (status == FAIL)
+ {
+ fprintf(stderr, "Failed to generate object reference.\n");
+ ret = FAIL;
+ }
+
+ /* add region reference */
+ status = gen_region_ref(loc_id);
+ if (status == FAIL)
+ {
+ fprintf(stderr, "Failed to generate region reference.\n");
+ ret = FAIL;
+ }
+
+ return ret;
+}
+
diff --git a/tools/h5repack/testfiles/h5repack_refs.h5 b/tools/h5repack/testfiles/h5repack_refs.h5
new file mode 100644
index 0000000..23d53e6
--- /dev/null
+++ b/tools/h5repack/testfiles/h5repack_refs.h5
Binary files differ
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index 6572594..48e08a5 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -747,7 +747,8 @@ hsize_t diff_datum(void *_mem1,
NULL,
options);
else {
- parallel_print("Warning: Comparison not possible of object types referenced: <%s> and <%s>",
+ if(options->m_verbose)
+ parallel_print("Warning: Comparison not possible of object types referenced: <%s> and <%s>\n",
obj1, obj2);
options->not_cmp = 1;
}