summaryrefslogtreecommitdiffstats
diff options
context:
space:
mode:
Diffstat
-rw-r--r--MANIFEST3
-rw-r--r--release_docs/RELEASE.txt4
-rw-r--r--tools/h5diff/CMakeLists.txt14
-rw-r--r--tools/h5diff/h5diffgentest.c565
-rw-r--r--tools/h5diff/testfiles/compounds_array_vlen1.h5bin0 -> 26912 bytes
-rw-r--r--tools/h5diff/testfiles/compounds_array_vlen2.h5bin0 -> 26912 bytes
-rw-r--r--tools/h5diff/testfiles/h5diff_540.txt86
-rwxr-xr-xtools/h5diff/testh5diff.sh10
-rw-r--r--tools/lib/h5diff_array.c70
-rw-r--r--windows/tools/h5diff/testh5diff.bat11
10 files changed, 728 insertions, 35 deletions
diff --git a/MANIFEST b/MANIFEST
index 50a40a4..caacb8c 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1856,6 +1856,7 @@
./tools/h5diff/testfiles/h5diff_517.txt
./tools/h5diff/testfiles/h5diff_518.txt
./tools/h5diff/testfiles/h5diff_530.txt
+./tools/h5diff/testfiles/h5diff_540.txt
./tools/h5diff/testfiles/h5diff_attr1.h5
./tools/h5diff/testfiles/h5diff_attr2.h5
@@ -1893,6 +1894,8 @@
./tools/h5diff/testfiles/h5diff_dset_zero_dim_size1.h5
./tools/h5diff/testfiles/h5diff_dset_zero_dim_size2.h5
./tools/h5diff/testfiles/h5diff_enum_invalid_values.h5
+./tools/h5diff/testfiles/compounds_array_vlen1.h5
+./tools/h5diff/testfiles/compounds_array_vlen2.h5
#test files for h5repack
./tools/h5repack/testfiles/h5repack_fill.h5
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 2efea2d..31f6d4b 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -571,6 +571,10 @@ Bug Fixes since HDF5-1.8.0 release
Tools
-----
+ - h5diff: fixed segfault over dataset with container types
+ (array,lven) with multiple nested compound types.
+ (ex: compound->array->compound, compound->vlen->compound)
+ HDFFV-7712 JKM (09/01/2011)
- h5repack: added macro to handle failure in H5Dread/write when memory
allocation failed inside the library. (PC -- 2011/08/19)
- Fixed h5jam not to allow specifying an HDF5 formatted file as input
diff --git a/tools/h5diff/CMakeLists.txt b/tools/h5diff/CMakeLists.txt
index 52a58eb..12dc388 100644
--- a/tools/h5diff/CMakeLists.txt
+++ b/tools/h5diff/CMakeLists.txt
@@ -158,6 +158,7 @@ IF (BUILD_TESTING)
h5diff_517.txt
h5diff_518.txt
h5diff_530.txt
+ h5diff_540.txt
h5diff_600.txt
h5diff_601.txt
h5diff_603.txt
@@ -245,6 +246,8 @@ IF (BUILD_TESTING)
h5diff_comp_vl_strs.h5
h5diff_attr_v_level1.h5
h5diff_attr_v_level2.h5
+ compounds_array_vlen1.h5
+ compounds_array_vlen2.h5
)
FOREACH (txt_file ${HDF5_REFERENCE_FILES})
@@ -477,6 +480,9 @@ IF (BUILD_TESTING)
SET (EXCLUDE_FILE2_2 h5diff_exclude2-2.h5)
# compound type with multiple vlen string types
SET (COMP_VL_STRS_FILE h5diff_comp_vl_strs.h5)
+ # container types (array,vlen) with multiple nested compound types
+ SET (COMPS_ARRAY_VLEN_FILE1 compounds_array_vlen1.h5)
+ SET (COMPS_ARRAY_VLEN_FILE2 compounds_array_vlen2.h5)
# attrs with verbose option level
SET (ATTR_VERBOSE_LEVEL_FILE1 h5diff_attr_v_level1.h5)
SET (ATTR_VERBOSE_LEVEL_FILE2 h5diff_attr_v_level2.h5)
@@ -703,6 +709,8 @@ IF (BUILD_TESTING)
h5diff_518.out.err
h5diff_530.out
h5diff_530.out.err
+ h5diff_540.out
+ h5diff_540.out.err
h5diff_600.out
h5diff_600.out.err
h5diff_601.out
@@ -1303,6 +1311,12 @@ ADD_H5_TEST (h5diff_484 0 -v --exclude-path "/dset3" ${EXCLUDE_FILE1_1} ${EXCLUD
ADD_H5_TEST (h5diff_530 0 -v ${COMP_VL_STRS_FILE} ${COMP_VL_STRS_FILE} /group /group_copy)
# ##############################################################################
+# # Test container types (array,vlen) with multiple nested compound types
+# # Complex compound types in dataset and attribute
+# ##############################################################################
+ADD_H5_TEST (h5diff_540 1 -v ${COMPS_ARRAY_VLEN_FILE1} ${COMPS_ARRAY_VLEN_FILE2})
+
+# ##############################################################################
# # Test mutually exclusive options
# ##############################################################################
#
diff --git a/tools/h5diff/h5diffgentest.c b/tools/h5diff/h5diffgentest.c
index 719707f..562c579 100644
--- a/tools/h5diff/h5diffgentest.c
+++ b/tools/h5diff/h5diffgentest.c
@@ -77,6 +77,9 @@
#define ATTR_VERBOSE_LEVEL_FILE2 "h5diff_attr_v_level2.h5"
/* file containing valid/invalid enum value mix */
#define ENUM_INVALID_VALUES "h5diff_enum_invalid_values.h5"
+/* file with container types (array,vlen) with multiple compounds */
+#define COMPS_COMPLEX1 "compounds_array_vlen1.h5"
+#define COMPS_COMPLEX2 "compounds_array_vlen2.h5"
#define UIMAX 4294967295u /*Maximum value for a variable of type unsigned int */
#define STR_SIZE 3
@@ -134,6 +137,10 @@ static int test_exclude_obj2(const char *fname1, const char *fname2);
static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int is_file_new);
static int test_attributes_verbose_level(const char *fname1, const char *fname2);
static int test_enums(const char *fname);
+static void test_comps_array (const char *fname, const char *dset, const char *attr,int diff, int is_file_new);
+static void test_comps_vlen (const char *fname, const char *dset,const char *attr, int diff, int is_file_new);
+static void test_comps_array_vlen (const char *fname, const char *dset, const char *attr, int diff, int is_file_new);
+static void test_comps_vlen_arry (const char *fname, const char *dset,const char *attr, int diff, int is_file_new);
/* called by test_attributes() and test_datasets() */
static void write_attr_in(hid_t loc_id,const char* dset_name,hid_t fid,int make_diffs);
@@ -207,6 +214,21 @@ int main(void)
*/
test_enums(ENUM_INVALID_VALUES);
+ /* -------------------------------------------------
+ * Create test files with dataset and attribute with container types
+ * (array, vlen) with multiple nested compound types.
+ */
+ /* file1 */
+ test_comps_array(COMPS_COMPLEX1,"dset1", "attr1", 0, 1);
+ test_comps_vlen(COMPS_COMPLEX1,"dset2", "attr2", 0, 0);
+ test_comps_array_vlen(COMPS_COMPLEX1,"dset3", "attr3", 0, 0);
+ test_comps_vlen_arry(COMPS_COMPLEX1,"dset4", "attr4", 0, 0);
+ /* file2 */
+ test_comps_array(COMPS_COMPLEX2,"dset1", "attr1", 5, 1);
+ test_comps_vlen(COMPS_COMPLEX2,"dset2", "attr2",5, 0);
+ test_comps_array_vlen(COMPS_COMPLEX2,"dset3", "attr3", 5, 0);
+ test_comps_vlen_arry(COMPS_COMPLEX2,"dset4", "attr4", 5, 0);
+
return 0;
}
@@ -940,7 +962,6 @@ int test_attributes(const char *file,
*/
static int test_attributes_verbose_level(const char *fname1, const char *fname2)
{
- int i;
herr_t status = SUCCEED;
hid_t fid1, fid2;
hid_t f1_gid, f2_gid;
@@ -2713,18 +2734,15 @@ static int test_group_recurse2(void)
hid_t grp1=0, grp2;
hid_t grp3=0;
hid_t grp4=0;
- hid_t tid;
hid_t dset1, dset2;
hid_t datatype, dataspace; /* handles */
hid_t fileid2;
hid_t fileid3;
hid_t fileid4;
- hid_t fileid4_1;
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status=0;
int data1[4][2] = {{0,0},{1,1},{2,2},{3,3}};
int data2[4][2] = {{0,0},{0,1},{0,2},{3,3}};
- int i, j;
/*-----------------------------------------------------------------------
* FILE 1
@@ -4110,6 +4128,545 @@ out:
return status;
}
+/*-------------------------------------------------------------------------
+*
+* Purpose:
+* Create test files with dataset and attribute with container types
+* (array, vlen) with multiple nested compound types.
+*
+* Function: test_comps_array()
+* - type: compound->array->compound
+*
+* Function: test_comps_vlen()
+* - type: compound->vlen->compound
+*
+* Function: test_comps_array_vlen()
+* - type: compound->array->compound->vlen->compound
+*
+* Function: test_comps_vlen_arry()
+* - type: compound->vlen->compound->array->compound
+*
+* Programmer: Jonathan Kim (Sep, 1, 2011)
+*
+*-------------------------------------------------------------------------*/
+#define SDIM_DSET 2
+#define SDIM_CMPD_ARRAY 2
+
+static void test_comps_array (const char *fname, const char *dset, const char *attr,int diff, int is_file_new)
+{
+ /* sub compound 2 */
+ typedef struct {
+ int i2;
+ float f2;
+ } cmpd2_t;
+
+ /* top compound 1 */
+ typedef struct {
+ int i1;
+ cmpd2_t cmpd2[SDIM_CMPD_ARRAY];
+ } cmpd1_t;
+
+ cmpd1_t wdata[SDIM_DSET]; /* dataset with compound1 */
+
+ hid_t fid; /* HDF5 File IDs */
+ hid_t did_dset; /* Dataset ID */
+ hid_t sid_dset; /* Dataset space ID */
+ hid_t tid_cmpd1; /* Compound1 type ID */
+ hid_t tid_arry1; /* Array type ID in compound1 */
+ hid_t tid_cmpd2; /* Compound2 type ID */
+ hid_t tid_attr;
+ hsize_t sdims_dset[] = {SDIM_DSET};
+ hsize_t sdims_cmpd_arry[] = {SDIM_CMPD_ARRAY};
+ int i,j;
+ herr_t ret; /* Generic return value */
+
+ /* Initialize array data to write */
+ for(i=0; i < SDIM_DSET; i++)
+ {
+ wdata[i].i1 = i;
+ for(j=0; j < SDIM_CMPD_ARRAY; j++)
+ {
+ wdata[i].cmpd2[j].i2 = i*10 + diff;
+ wdata[i].cmpd2[j].f2 = (float)(i*10.5) + diff;
+ } /* end for */
+ }
+
+ /*-----------------------------------------------------------------------
+ * Create file(s)
+ *------------------------------------------------------------------------*/
+ if (is_file_new == 1)
+ fid = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ else
+ fid = H5Fopen (fname, H5F_ACC_RDWR, H5P_DEFAULT);
+
+
+ /* -------------------------------
+ * Create a sub compound2 datatype */
+ tid_cmpd2 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd2_t));
+
+ /* Insert integer field */
+ ret = H5Tinsert(tid_cmpd2, "int2", HOFFSET(cmpd2_t, i2), H5T_NATIVE_INT);
+ assert(ret >= 0);
+
+ /* Insert float field */
+ ret = H5Tinsert(tid_cmpd2, "float2", HOFFSET(cmpd2_t, f2), H5T_NATIVE_FLOAT);
+ assert(ret >= 0);
+
+ /*-----------------------------------
+ * Create a top compound1.
+ */
+ tid_cmpd1 = H5Tcreate (H5T_COMPOUND, sizeof(cmpd1_t));
+
+ ret = H5Tinsert(tid_cmpd1, "int1", HOFFSET(cmpd1_t, i1), H5T_NATIVE_INT);
+ assert(ret >= 0);
+
+ /* Create an array datatype */
+ tid_arry1 = H5Tarray_create2(tid_cmpd2, 1, sdims_cmpd_arry);
+ /* insert the array */
+ ret = H5Tinsert(tid_cmpd1, "array_cmpd1", HOFFSET(cmpd1_t, cmpd2), tid_arry1);
+ assert(ret >= 0);
+
+
+ /* -------------------
+ * Create a dataset
+ */
+ /* Create dataspace for datasets */
+ sid_dset = H5Screate_simple(1, sdims_dset, NULL);
+
+ did_dset = H5Dcreate2(fid, dset, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ /* Write dataset to disk */
+ ret = H5Dwrite(did_dset, tid_cmpd1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
+ assert(ret >= 0);
+
+ /*-----------------------------------
+ * Create an attribute in root group
+ */
+ tid_attr = H5Acreate2(fid, attr, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT);
+ ret = H5Awrite(tid_attr, tid_cmpd1, wdata);
+ assert(ret >= 0);
+
+ /* ----------------
+ * Close Dataset */
+ ret = H5Aclose(tid_attr);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_arry1);
+ assert(ret >= 0);
+ ret = H5Dclose(did_dset);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd1);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd2);
+ assert(ret >= 0);
+ ret = H5Sclose(sid_dset);
+ assert(ret >= 0);
+ ret = H5Fclose(fid);
+ assert(ret >= 0);
+}
+
+
+
+static void test_comps_vlen (const char * fname, const char *dset, const char *attr, int diff, int is_file_new)
+{
+ /* sub compound 2 */
+ typedef struct {
+ int i2;
+ float f2;
+ } cmpd2_t;
+
+ /* top compound 1 */
+ typedef struct {
+ int i1;
+ hvl_t vl; /* VL information for compound2 */
+ } cmpd1_t;
+
+ cmpd1_t wdata[SDIM_DSET]; /* Dataset for compound1 */
+
+ hid_t fid; /* HDF5 File ID */
+ hid_t did_dset; /* dataset ID */
+ hid_t sid_dset; /* dataset space ID */
+ hid_t tid_cmpd2; /* compound2 type ID */
+ hid_t tid_cmpd1; /* compound1 type ID */
+ hid_t tid_cmpd1_vlen;
+ hsize_t sdims_dset[] = {SDIM_DSET};
+
+ unsigned i,j; /* counting variables */
+ herr_t ret; /* Generic return value */
+
+ /* Allocate and initialize VL data to write */
+ for(i=0; i<SDIM_DSET; i++)
+ {
+ wdata[i].i1 = i;
+ wdata[i].vl.p = malloc((i+1)*sizeof(cmpd2_t));
+ wdata[i].vl.len = i+1;
+ for(j=0; j<(i+1); j++)
+ {
+ ((cmpd2_t *)wdata[i].vl.p)[j].i2 = i*10 + diff;
+ ((cmpd2_t *)wdata[i].vl.p)[j].f2 = (float)(i*10.5) + diff;
+ } /* end for */
+ } /* end for */
+
+ /*-----------------------------------------------------------------------
+ * Create file(s)
+ *------------------------------------------------------------------------*/
+ if (is_file_new == 1)
+ fid = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ else
+ fid = H5Fopen (fname, H5F_ACC_RDWR, H5P_DEFAULT);
+
+ /* -----------------------------
+ * Create sub compound2 type */
+ tid_cmpd2 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd2_t));
+
+ /* Insert fields */
+ ret = H5Tinsert(tid_cmpd2, "int2", HOFFSET(cmpd2_t, i2), H5T_NATIVE_INT);
+ assert(ret >= 0);
+ ret = H5Tinsert(tid_cmpd2, "float2", HOFFSET(cmpd2_t, f2), H5T_NATIVE_FLOAT);
+ assert(ret >= 0);
+
+ /* ---------------------------
+ * Create top compound1 type */
+ tid_cmpd1 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd1_t));
+ /* Insert fields */
+ ret = H5Tinsert(tid_cmpd1, "int1", HOFFSET(cmpd1_t, i1), H5T_NATIVE_INT);
+ assert(ret >= 0);
+ /* Create a VL datatype */
+ tid_cmpd1_vlen = H5Tvlen_create(tid_cmpd2);
+
+ ret = H5Tinsert(tid_cmpd1, "vlen_cmpd1", HOFFSET(cmpd1_t, vl), tid_cmpd1_vlen);
+ assert(ret >= 0);
+
+ /* -------------------------------
+ * Create dataset with compound1
+ */
+ /* Create dataspace for dataset */
+ sid_dset = H5Screate_simple(1, sdims_dset, NULL);
+
+ /* Create a dataset */
+ did_dset = H5Dcreate2(fid, dset, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ /* Write dataset to disk */
+ ret = H5Dwrite(did_dset, tid_cmpd1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
+ assert(ret >= 0);
+
+ /* Reclaim the write VL data */
+ ret = H5Dvlen_reclaim(tid_cmpd1, sid_dset, H5P_DEFAULT, wdata);
+ assert(ret >= 0);
+
+ /*-----------------------------------
+ * Create an attribute in root group
+ */
+ /* TODO: creating vlen with compound type doesn't work for attribute now.
+ * so add this later when it's fixed
+ tid_attr = H5Acreate2(fid, attr, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT);
+ ret = H5Awrite(tid_attr, tid_cmpd1, wdata);
+ assert(ret >= 0);
+ */
+
+ /* ----------------
+ * Close IDs */
+ ret = H5Dclose(did_dset);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd2);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd1);
+ assert(ret >= 0);
+ ret = H5Sclose(sid_dset);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd1_vlen);
+ assert(ret >= 0);
+ ret = H5Fclose(fid);
+ assert(ret >= 0);
+}
+
+
+static void test_comps_array_vlen (const char * fname, const char *dset,const char *attr, int diff, int is_file_new)
+{
+ typedef struct {
+ int i3;
+ float f3;
+ } cmpd3_t;
+
+ typedef struct { /* Typedef for compound datatype */
+ int i2;
+ hvl_t vl; /* VL information to write */
+ } cmpd2_t;
+
+ typedef struct {
+ int i1;
+ cmpd2_t cmpd2[SDIM_CMPD_ARRAY];
+ } cmpd1_t;
+
+ cmpd1_t wdata[SDIM_DSET]; /* Information to write */
+ hid_t fid; /* HDF5 File IDs */
+ hid_t did_dset; /* Dataset ID */
+ hid_t sid_dset; /* Dataspace ID */
+ hid_t tid_cmpd1; /* Compound1 Datatype ID */
+ hid_t tid_arry1; /* Array Datatype ID */
+ hid_t tid_cmpd2; /* Compound2 Datatype ID */
+ hid_t tid_cmpd2_vlen;
+ hid_t tid_cmpd3; /* Compound3 Datatype ID */
+ hsize_t sdims_dset[] = {SDIM_DSET};
+ hsize_t sdims_arry[] = {SDIM_CMPD_ARRAY};
+ int i,j,k; /* counting variables */
+ herr_t ret; /* Generic return value */
+
+
+
+ /* Initialize array data to write in compound1 */
+ for(i=0; i < SDIM_DSET; i++)
+ {
+ wdata[i].i1 = i;
+ /* Allocate and initialize VL data to write in compound2 */
+ for(j=0; j < SDIM_CMPD_ARRAY; j++)
+ {
+ wdata[i].cmpd2[j].i2 = j*10;
+ wdata[i].cmpd2[j].vl.p = malloc((j+1)*sizeof(cmpd3_t));
+ wdata[i].cmpd2[j].vl.len = j+1;
+ for(k=0; k<(j+1); k++)
+ {
+ /* Initialize data of compound3 */
+ ((cmpd3_t *)wdata[i].cmpd2[j].vl.p)[k].i3 = j*10 + diff;
+ ((cmpd3_t *)wdata[i].cmpd2[j].vl.p)[k].f3 = (float)(j*10.5) + diff;
+ } /* end for */
+ } /* end for */
+ }
+
+ /*-----------------------------------------------------------------------
+ * Create file(s)
+ *------------------------------------------------------------------------*/
+ if (is_file_new == 1)
+ fid = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ else
+ fid = H5Fopen (fname, H5F_ACC_RDWR, H5P_DEFAULT);
+
+ /* Create dataspace for datasets */
+ sid_dset = H5Screate_simple(1, sdims_dset, NULL);
+
+ /*-------------------------------------
+ * Create a sub compound3 datatype */
+ tid_cmpd3 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd3_t));
+
+ /* Insert integer field */
+ ret = H5Tinsert(tid_cmpd3, "int", HOFFSET(cmpd3_t, i3), H5T_NATIVE_INT);
+ assert(ret >= 0);
+
+ /* Insert float field */
+ ret = H5Tinsert(tid_cmpd3, "float", HOFFSET(cmpd3_t, f3), H5T_NATIVE_FLOAT);
+ assert(ret >= 0);
+
+
+ /*-------------------------------------
+ * Create a sub compound2 datatype */
+ tid_cmpd2 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd2_t));
+
+ /* Insert integer field */
+ ret = H5Tinsert(tid_cmpd2, "int", HOFFSET(cmpd2_t, i2), H5T_NATIVE_INT);
+ assert(ret >= 0);
+ /* Create a VL datatype */
+ tid_cmpd2_vlen = H5Tvlen_create(tid_cmpd3);
+ ret = H5Tinsert(tid_cmpd2, "vlen", HOFFSET(cmpd2_t, vl), tid_cmpd2_vlen);
+ assert(ret >= 0);
+
+
+ /*-----------------------------------
+ * Create a top compound1 datatype for dataset.
+ */
+ tid_cmpd1 = H5Tcreate (H5T_COMPOUND, sizeof(cmpd1_t));
+
+ /* Create an array datatype */
+ tid_arry1 = H5Tarray_create2(tid_cmpd2, 1, sdims_arry);
+ /* insert the array */
+ H5Tinsert(tid_cmpd1, "array_comp", HOFFSET(cmpd1_t, cmpd2), tid_arry1);
+
+
+ /* ----------------------
+ * Create a dataset */
+ did_dset = H5Dcreate2(fid, dset, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ /* Write dataset to disk */
+ ret = H5Dwrite(did_dset, tid_cmpd1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
+ assert(ret >= 0);
+
+ /* Reclaim the write VL data */
+ ret = H5Dvlen_reclaim(tid_cmpd1, sid_dset, H5P_DEFAULT, wdata);
+ assert(ret >= 0);
+
+ /*-----------------------------------
+ * Create an attribute in root group
+ */
+ /* TODO: creating vlen with compound type doesn't work for attribute now.
+ * so add this later when it's fixed
+ tid_attr = H5Acreate2(fid, attr, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT);
+ ret = H5Awrite(tid_attr, tid_cmpd1, wdata);
+ assert(ret >= 0);
+ */
+
+ /*-------------------
+ * Close IDs */
+ ret = H5Tclose(tid_arry1);
+ assert(ret >= 0);
+ ret = H5Dclose(did_dset);
+ assert(ret >= 0);
+ ret = H5Sclose(sid_dset);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd3);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd2);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd2_vlen);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd1);
+ assert(ret >= 0);
+ ret = H5Fclose(fid);
+ assert(ret >= 0);
+}
+
+
+static void test_comps_vlen_arry (const char * fname, const char *dset, const char *attr, int diff, int is_file_new)
+{
+ /* sub compound 3 */
+ typedef struct {
+ int i3;
+ float f3;
+ } cmpd3_t;
+
+ /* sub compound 2 */
+ typedef struct {
+ int i2;
+ cmpd3_t cmpd3[SDIM_CMPD_ARRAY];
+ } cmpd2_t;
+
+ /* top compound 1 */
+ typedef struct {
+ int i1;
+ hvl_t vl; /* VL information for compound2 */
+ } cmpd1_t;
+
+ cmpd1_t wdata[SDIM_DSET]; /* Dataset for compound1 */
+
+ hid_t fid; /* HDF5 File ID */
+ hid_t did_dset; /* dataset ID */
+ hid_t sid_dset; /* dataset space ID */
+ hid_t tid_cmpd3; /* compound3 type ID */
+ hid_t tid_cmpd2; /* compound2 type ID */
+ hid_t tid_cmpd2_arry;
+ hid_t tid_cmpd1; /* compound1 type ID */
+ hid_t tid_cmpd1_vlen;
+ hsize_t sdims_dset[] = {SDIM_DSET};
+ hsize_t sdims_cmpd_arry[] = {SDIM_CMPD_ARRAY};
+
+ unsigned i,j,k; /* counting variables */
+ herr_t ret; /* Generic return value */
+
+ /* Allocate and initialize VL data to write */
+ for(i=0; i<SDIM_DSET; i++)
+ {
+ /* compound 1 data */
+ wdata[i].i1 = i;
+ wdata[i].vl.p = malloc((i+1)*sizeof(cmpd2_t));
+ wdata[i].vl.len = i+1;
+ for(j=0; j<(i+1); j++)
+ {
+ /* compound2 data */
+ ((cmpd2_t *)wdata[i].vl.p)[j].i2 = i*10 + diff;
+ for (k=0; k < SDIM_CMPD_ARRAY; k++)
+ {
+ /* compound 3 data */
+ ((cmpd2_t *)(wdata[i].vl.p))[j].cmpd3[k].i3 = k*10.5 + diff;
+ ((cmpd2_t *)(wdata[i].vl.p))[j].cmpd3[k].f3 = (float)(k*10.5) + diff;
+ }
+ } /* end for */
+ } /* end for */
+
+ /*-----------------------------------------------------------------------
+ * Create file(s)
+ *------------------------------------------------------------------------*/
+ if (is_file_new == 1)
+ fid = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ else
+ fid = H5Fopen (fname, H5F_ACC_RDWR, H5P_DEFAULT);
+
+ /* -----------------------------
+ * Create sub compound3 type */
+ tid_cmpd3 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd3_t));
+
+ /* Insert fields */
+ ret = H5Tinsert(tid_cmpd3, "int3", HOFFSET(cmpd3_t, i3), H5T_NATIVE_INT);
+ assert(ret >= 0);
+ ret = H5Tinsert(tid_cmpd3, "float3", HOFFSET(cmpd3_t, f3), H5T_NATIVE_FLOAT);
+ assert(ret >= 0);
+
+ /* -----------------------------
+ * Create sub compound2 type */
+ tid_cmpd2 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd2_t));
+
+ ret = H5Tinsert(tid_cmpd2, "int2", HOFFSET(cmpd2_t, i2), H5T_NATIVE_INT);
+ assert(ret >= 0);
+
+ tid_cmpd2_arry = H5Tarray_create2(tid_cmpd3, 1, sdims_cmpd_arry);
+ ret = H5Tinsert(tid_cmpd2, "array_cmpd2", HOFFSET(cmpd2_t, cmpd3), tid_cmpd2_arry);
+ assert(ret >= 0);
+
+ /* ---------------------------
+ * Create top compound1 type
+ */
+ /* Create a VL datatype */
+ tid_cmpd1 = H5Tcreate(H5T_COMPOUND, sizeof(cmpd1_t));
+ /* Insert fields */
+ ret = H5Tinsert(tid_cmpd1, "int1", HOFFSET(cmpd1_t, i1), H5T_NATIVE_INT);
+ assert(ret >= 0);
+ tid_cmpd1_vlen = H5Tvlen_create(tid_cmpd2);
+ ret = H5Tinsert(tid_cmpd1, "vlen_cmpd1", HOFFSET(cmpd1_t, vl), tid_cmpd1_vlen);
+ assert(ret >= 0);
+
+ /* -------------------------------
+ * Create dataset with compound1
+ */
+ /* Create dataspace for dataset */
+ sid_dset = H5Screate_simple(1, sdims_dset, NULL);
+
+ /* Create a dataset */
+ did_dset = H5Dcreate2(fid, dset, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ /* Write dataset to disk */
+ ret = H5Dwrite(did_dset, tid_cmpd1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
+ assert(ret >= 0);
+
+ /* Reclaim the write VL data */
+ ret = H5Dvlen_reclaim(tid_cmpd1, sid_dset, H5P_DEFAULT, wdata);
+ assert(ret >= 0);
+
+ /*-----------------------------------
+ * Create an attribute in root group
+ */
+ /* TODO: creating vlen with compound type doesn't work for attribute now.
+ * so add this later when it's fixed
+ tid_attr = H5Acreate2(fid, attr, tid_cmpd1, sid_dset, H5P_DEFAULT, H5P_DEFAULT);
+ ret = H5Awrite(tid_attr, tid_cmpd1, wdata);
+ assert(ret >= 0);
+ */
+
+ /* ----------------
+ * Close IDs */
+ ret = H5Dclose(did_dset);
+ assert(ret >= 0);
+ ret = H5Sclose(sid_dset);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd3);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd2_arry);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd2);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd1_vlen);
+ assert(ret >= 0);
+ ret = H5Tclose(tid_cmpd1);
+ assert(ret >= 0);
+ ret = H5Fclose(fid);
+ assert(ret >= 0);
+}
+
/*-------------------------------------------------------------------------
* Function: write_attr_in
diff --git a/tools/h5diff/testfiles/compounds_array_vlen1.h5 b/tools/h5diff/testfiles/compounds_array_vlen1.h5
new file mode 100644
index 0000000..398026c
--- /dev/null
+++ b/tools/h5diff/testfiles/compounds_array_vlen1.h5
Binary files differ
diff --git a/tools/h5diff/testfiles/compounds_array_vlen2.h5 b/tools/h5diff/testfiles/compounds_array_vlen2.h5
new file mode 100644
index 0000000..f6f0868
--- /dev/null
+++ b/tools/h5diff/testfiles/compounds_array_vlen2.h5
Binary files differ
diff --git a/tools/h5diff/testfiles/h5diff_540.txt b/tools/h5diff/testfiles/h5diff_540.txt
new file mode 100644
index 0000000..a6903c8
--- /dev/null
+++ b/tools/h5diff/testfiles/h5diff_540.txt
@@ -0,0 +1,86 @@
+
+file1 file2
+---------------------------------------
+ x x /
+ x x /dset1
+ x x /dset2
+ x x /dset3
+ x x /dset4
+
+group : </> and </>
+0 differences found
+attribute: <attr1 of </>> and <attr1 of </>>
+size: [2] [2]
+position attr1 of </> attr1 of </> difference
+------------------------------------------------------------
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+8 differences found
+dataset: </dset1> and </dset1>
+size: [2] [2]
+position dset1 dset1 difference
+------------------------------------------------------------
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+8 differences found
+dataset: </dset2> and </dset2>
+size: [2] [2]
+position dset2 dset2 difference
+------------------------------------------------------------
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+6 differences found
+dataset: </dset3> and </dset3>
+size: [2] [2]
+position dset3 dset3 difference
+------------------------------------------------------------
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 0 ] 10 15 5
+[ 0 ] 10.5 15.5 5
+[ 0 ] 10 15 5
+[ 0 ] 10.5 15.5 5
+[ 1 ] 0 5 5
+[ 1 ] 0 5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+12 differences found
+dataset: </dset4> and </dset4>
+size: [2] [2]
+position dset4 dset4 difference
+------------------------------------------------------------
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 0 ] 0 5 5
+[ 0 ] 10 15 5
+[ 0 ] 10.5 15.5 5
+[ 1 ] 10 15 5
+[ 1 ] 0 5 5
+[ 1 ] 0 5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+[ 1 ] 10 15 5
+[ 1 ] 0 5 5
+[ 1 ] 0 5 5
+[ 1 ] 10 15 5
+[ 1 ] 10.5 15.5 5
+15 differences found
+EXIT CODE: 1
diff --git a/tools/h5diff/testh5diff.sh b/tools/h5diff/testh5diff.sh
index 8d38171..e318a15 100755
--- a/tools/h5diff/testh5diff.sh
+++ b/tools/h5diff/testh5diff.sh
@@ -112,6 +112,8 @@ $SRC_H5DIFF_TESTFILES/h5diff_exclude1-2.h5
$SRC_H5DIFF_TESTFILES/h5diff_exclude2-1.h5
$SRC_H5DIFF_TESTFILES/h5diff_exclude2-2.h5
$SRC_H5DIFF_TESTFILES/h5diff_comp_vl_strs.h5
+$SRC_H5DIFF_TESTFILES/compounds_array_vlen1.h5
+$SRC_H5DIFF_TESTFILES/compounds_array_vlen2.h5
$SRC_H5DIFF_TESTFILES/h5diff_attr_v_level1.h5
$SRC_H5DIFF_TESTFILES/h5diff_attr_v_level2.h5
$SRC_H5DIFF_TESTFILES/h5diff_enum_invalid_values.h5
@@ -227,6 +229,7 @@ $SRC_H5DIFF_TESTFILES/h5diff_516.txt
$SRC_H5DIFF_TESTFILES/h5diff_517.txt
$SRC_H5DIFF_TESTFILES/h5diff_518.txt
$SRC_H5DIFF_TESTFILES/h5diff_530.txt
+$SRC_H5DIFF_TESTFILES/h5diff_540.txt
$SRC_H5DIFF_TESTFILES/h5diff_600.txt
$SRC_H5DIFF_TESTFILES/h5diff_601.txt
$SRC_H5DIFF_TESTFILES/h5diff_603.txt
@@ -989,9 +992,14 @@ TOOLTEST h5diff_484.txt -v --exclude-path "/dset3" h5diff_exclude1-1.h5 h5diff_e
TOOLTEST h5diff_530.txt -v h5diff_comp_vl_strs.h5 h5diff_comp_vl_strs.h5 /group /group_copy
# ##############################################################################
+# # Test container types (array,vlen) with multiple nested compound types
+# # Complex compound types in dataset and attribute
+# ##############################################################################
+TOOLTEST h5diff_540.txt -v compounds_array_vlen1.h5 compounds_array_vlen2.h5
+
+# ##############################################################################
# # Test mutually exclusive options
# ##############################################################################
-#
# Test with -d , -p and --use-system-epsilon.
TOOLTEST h5diff_640.txt -v -d 5 -p 0.05 --use-system-epsilon h5diff_basic1.h5 h5diff_basic2.h5 /g1/dset3 /g1/dset4
TOOLTEST h5diff_641.txt -v -d 5 -p 0.05 h5diff_basic1.h5 h5diff_basic2.h5 /g1/dset3 /g1/dset4
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index 3e3db02..91b94b8 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -186,8 +186,8 @@ static int my_isnan(dtype_t type, void *val);
* XCAO, 11/10/2010
* added to improve performance for compound datasets
*/
-static void set_comp_members(hid_t tid, mcomp_t *members);
-static void free_comp_members(mcomp_t *members);
+static void get_member_types(hid_t tid, mcomp_t *members);
+static void close_member_types(mcomp_t *members);
@@ -318,7 +318,7 @@ hsize_t diff_array( void *_mem1,
case H5T_VLEN:
case H5T_REFERENCE:
HDmemset(&members, 0, sizeof (mcomp_t));
- set_comp_members(m_type, &members);
+ get_member_types(m_type, &members);
for ( i = 0; i < nelmts; i++)
{
nfound+=diff_datum(
@@ -338,11 +338,11 @@ hsize_t diff_array( void *_mem1,
&ph, &members);
if (options->n && nfound>=options->count)
{
- free_comp_members(&members);
+ close_member_types(&members);
return nfound;
}
} /* i */
- free_comp_members(&members);
+ close_member_types(&members);
} /* switch */
return nfound;
@@ -726,7 +726,7 @@ hsize_t diff_datum(void *_mem1,
obj2,
container1_id,
container2_id,
- ph, NULL);
+ ph, members);
}
H5Tclose(memb_type);
}
@@ -873,7 +873,7 @@ hsize_t diff_datum(void *_mem1,
obj2,
container1_id,
container2_id,
- ph, NULL);
+ ph, members);
H5Tclose(memb_type);
@@ -6117,36 +6117,46 @@ static void h5diff_print_char(char ch)
* added to improve performance for compound datasets
* set up compound datatype structures.
*/
-static void set_comp_members(hid_t tid, mcomp_t *members)
+static void get_member_types(hid_t tid, mcomp_t *members)
{
int i;
+ int tclass;
if (tid <=0 || !members)
return;
- if (H5Tget_class(tid) != H5T_COMPOUND)
- return;
-
- members->n = H5Tget_nmembers( tid );
- if (members->n <=0)
- return;
+ tclass = H5Tget_class(tid);
+ if (tclass == H5T_ARRAY || tclass == H5T_VLEN)
+ {
+ hid_t base_tid = H5Tget_super(tid);
+ get_member_types(base_tid, members);
+ H5Tclose(base_tid);
+ }
+ else if (tclass == H5T_COMPOUND)
+ {
+ members->n = H5Tget_nmembers( tid );
+ if (members->n <=0)
+ return;
- members->ids = HDcalloc(members->n, sizeof(hid_t));
- members->flags = HDcalloc(members->n, sizeof(unsigned char));
- members->offsets = HDcalloc(members->n, sizeof(size_t));
- members->m = HDcalloc(members->n, sizeof(mcomp_t *));
+ members->ids = HDcalloc(members->n, sizeof(hid_t));
+ members->flags = HDcalloc(members->n, sizeof(unsigned char));
+ members->offsets = HDcalloc(members->n, sizeof(size_t));
+ members->m = HDcalloc(members->n, sizeof(mcomp_t *));
- for (i=0; i< members->n; i++)
- {
- members->ids[i] = H5Tget_member_type( tid, i );
- members->flags[i] = H5Tis_variable_str( members->ids[i] );
- members->offsets[i] = H5Tget_member_offset( tid, i );
- if (H5Tget_class( members->ids[i])==H5T_COMPOUND)
- {
- members->m[i] = (mcomp_t *)HDmalloc(sizeof(mcomp_t));
- set_comp_members(members->ids[i], members->m[i]);
- }
+ for (i=0; i< members->n; i++)
+ {
+ members->ids[i] = H5Tget_member_type( tid, i );
+ members->flags[i] = H5Tis_variable_str( members->ids[i] );
+ members->offsets[i] = H5Tget_member_offset( tid, i );
+ members->m[i] = (mcomp_t *)HDmalloc(sizeof(mcomp_t));
+ HDmemset(members->m[i], 0, sizeof(mcomp_t));
+ get_member_types(members->ids[i], members->m[i]);
+ }
}
+
+ return;
+
+
}
/*-------------------------------------------------------------------------
@@ -6154,7 +6164,7 @@ static void set_comp_members(hid_t tid, mcomp_t *members)
* added to improve performance for compound datasets
* clean and close compound members.
*/
-static void free_comp_members(mcomp_t *members)
+static void close_member_types(mcomp_t *members)
{
int i;
@@ -6165,7 +6175,7 @@ static void free_comp_members(mcomp_t *members)
{
if (members->m[i])
{
- free_comp_members(members->m[i]);
+ close_member_types(members->m[i]);
HDfree(members->m[i]);
}
H5Tclose(members->ids[i]);
diff --git a/windows/tools/h5diff/testh5diff.bat b/windows/tools/h5diff/testh5diff.bat
index 0235c44..491332f 100644
--- a/windows/tools/h5diff/testh5diff.bat
+++ b/windows/tools/h5diff/testh5diff.bat
@@ -59,6 +59,8 @@ set srcexclude1_2=h5diff_exclude1-2.h5
set srcexclude2_1=h5diff_exclude2-1.h5
set srcexclude2_2=h5diff_exclude2-2.h5
set src_comp_vl_strs=h5diff_comp_vl_strs.h5
+set src_COMPS_ARRAY_VLEN1=compounds_array_vlen1.h5
+set src_COMPS_ARRAY_VLEN2=compounds_array_vlen2.h5
set src_ATTR_VERBOSE_LEVEL_FILE1=h5diff_attr_v_level1.h5
set src_ATTR_VERBOSE_LEVEL_FILE2=h5diff_attr_v_level2.h5
@@ -93,6 +95,8 @@ set exclude1_2=%indir%\h5diff_exclude1-2.h5
set exclude2_1=%indir%\h5diff_exclude2-1.h5
set exclude2_2=%indir%\h5diff_exclude2-2.h5
set comp_vl_strs=%indir%\h5diff_comp_vl_strs.h5
+set COMPS_ARRAY_VLEN1=%indir%\compounds_array_vlen1.h5
+set COMPS_ARRAY_VLEN2=%indir%\compounds_array_vlen2.h5
set ATTR_VERBOSE_LEVEL_FILE1=%indir%\h5diff_attr_v_level1.h5
set ATTR_VERBOSE_LEVEL_FILE2=%indir%\h5diff_attr_v_level2.h5
@@ -929,6 +933,13 @@ rem ############################################################################
call :testing %h5diff% -v %src_comp_vl_strs% %src_comp_vl_strs% /group /group_copy
call :tooltest h5diff_530.txt -v %comp_vl_strs% %comp_vl_strs% /group /group_copy
+ rem # #####################################################################
+ rem # # Test container types (array,vlen) with multiple nested compound types
+ rem # # Complex compound types in dataset and attribute
+ rem # #####################################################################
+ call :testing %h5diff% -v %src_COMPS_ARRAY_VLEN1% %src_COMPS_ARRAY_VLEN2%
+ call :tooltest h5diff_540.txt -v %COMPS_ARRAY_VLEN1% %COMPS_ARRAY_VLEN2%
+
rem #######################################################################
rem # Test mutually exclusive options
rem #######################################################################
generated by cgit v0.12 at 2024-07-08 11:22:28 (GMT)