From 36ea4e85530c75e0d115b999438fcbbb4095556d Mon Sep 17 00:00:00 2001 From: Jonathan Kim Date: Tue, 6 Sep 2011 15:26:08 -0500 Subject: [svn-r21368] Purpose: HDFFV-7712 - h5diff: segfault over combinations of complex container types (compound, array, vlen) Description: - Fixed segfault over dataset with container types (array,lven) with multiple nested compound types. (ex: compound->array->compound, compound->vlen->compound) - Merged from HDF5 trunk r21358. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam) --- MANIFEST | 3 + release_docs/RELEASE.txt | 4 + tools/h5diff/CMakeLists.txt | 14 + tools/h5diff/h5diffgentest.c | 565 +++++++++++++++++++++++- tools/h5diff/testfiles/compounds_array_vlen1.h5 | Bin 0 -> 26912 bytes tools/h5diff/testfiles/compounds_array_vlen2.h5 | Bin 0 -> 26912 bytes tools/h5diff/testfiles/h5diff_540.txt | 86 ++++ tools/h5diff/testh5diff.sh | 10 +- tools/lib/h5diff_array.c | 70 +-- windows/tools/h5diff/testh5diff.bat | 11 + 10 files changed, 728 insertions(+), 35 deletions(-) create mode 100644 tools/h5diff/testfiles/compounds_array_vlen1.h5 create mode 100644 tools/h5diff/testfiles/compounds_array_vlen2.h5 create mode 100644 tools/h5diff/testfiles/h5diff_540.txt diff --git a/MANIFEST b/MANIFEST index 3445190..fabc971 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1708,6 +1708,7 @@ ./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 @@ -1745,6 +1746,8 @@ ./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 diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 465abff..5d45d82 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -148,6 +148,10 @@ Bug Fixes since HDF5-1.8.7 Tools ----- + - h5diff: fixed segfault over dataset with container types + (array,lven) along with multiple nested compound types. + (ex: compound->array->compound, compound->vlen->compound) + HDFFV-7712 JKM (09/01/2011) - Fixed h5jam not to allow specifying an HDF5 formatted file as input file for -u (user block file) option, because the original HDF5 file will not be accessible if allows. HDFFV-5941 (JKM 08/19/2011) diff --git a/tools/h5diff/CMakeLists.txt b/tools/h5diff/CMakeLists.txt index 95a599d..91af561 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}) @@ -475,6 +478,9 @@ 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) @@ -701,6 +707,8 @@ 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 @@ -1301,6 +1309,12 @@ 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= 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= 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 Binary files /dev/null and b/tools/h5diff/testfiles/compounds_array_vlen1.h5 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 Binary files /dev/null and b/tools/h5diff/testfiles/compounds_array_vlen2.h5 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: > and > +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: and +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: and +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: and +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: and +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 ecfc238..e6a9d05 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 6de2261..b25cbde 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 @@ -925,6 +929,13 @@ 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 ####################################################################### -- cgit v0.12