diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 4 | ||||
| -rw-r--r-- | tools/lib/h5diff.h | 15 | ||||
| -rw-r--r-- | tools/lib/h5diff_array.c | 153 |
3 files changed, 136 insertions, 36 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 6cc1b46..35854bf 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -474,6 +474,10 @@ Bug Fixes since HDF5-1.8.0 release Tools ----- + - Improve h5diff performance. 1) use HDmemcmp() before comparing each + elements. 2) replace expensive H5Tequals() calls 3) retrieve datatype + information at dataset level not each element level for compound + datasets - Fixed h5ls to display nested compound type with curly bracket when -S (--simple) option is used with -l (--label), so it shows which member (in curly bracket) belong to which nested compound type diff --git a/tools/lib/h5diff.h b/tools/lib/h5diff.h index c89b9d3..7e4e016 100644 --- a/tools/lib/h5diff.h +++ b/tools/lib/h5diff.h @@ -172,6 +172,18 @@ int print_objname(diff_opt_t *options, hsize_t nfound); void do_print_objname (const char *OBJ, const char *path1, const char *path2); +/*------------------------------------------------------------------------- + * XCAO, 11/10/2010 + * added to improve performance for compound datasets + */ +typedef struct mcomp_t +{ + int n; /* number of members */ + hid_t *ids; /* member type id */ + unsigned char *flags; + size_t *offsets; + struct mcomp_t **m; /* members */ +}mcomp_t; hsize_t diff_datum(void *_mem1, void *_mem2, @@ -186,7 +198,8 @@ hsize_t diff_datum(void *_mem1, const char *obj2, hid_t container1_id, hid_t container2_id, /*where the reference came from*/ - int *ph); /*print header */ + int *ph, /*print header */ + mcomp_t *members); /*compound members */ diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c index 6005ed8..e137db2 100644 --- a/tools/lib/h5diff_array.c +++ b/tools/lib/h5diff_array.c @@ -182,6 +182,13 @@ typedef enum dtype_t 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); + /*------------------------------------------------------------------------- @@ -220,10 +227,15 @@ hsize_t diff_array( void *_mem1, int ph=1; /* print header */ hsize_t i; int j; - + mcomp_t members; + H5T_class_t type_class; /* get the size. */ size = H5Tget_size( m_type ); + type_class = H5Tget_class(m_type); + + if (type_class != H5T_REFERENCE && HDmemcmp(mem1, mem2, size*nelmts)==0) + return 0; if ( rank > 0 ) { @@ -255,7 +267,7 @@ hsize_t diff_array( void *_mem1, name2, container1_id, container2_id, - &ph); + &ph, NULL); if (options->n && nfound>=options->count) return nfound; } /* i */ @@ -263,7 +275,7 @@ hsize_t diff_array( void *_mem1, else { - switch (H5Tget_class(m_type)) + switch (type_class) { default: assert(0); @@ -324,7 +336,8 @@ hsize_t diff_array( void *_mem1, case H5T_ARRAY: case H5T_VLEN: case H5T_REFERENCE: - + HDmemset(&members, 0, sizeof (mcomp_t)); + set_comp_members(m_type, &members); for ( i = 0; i < nelmts; i++) { nfound+=diff_datum( @@ -341,10 +354,14 @@ hsize_t diff_array( void *_mem1, name2, container1_id, container2_id, - &ph); + &ph, &members); if (options->n && nfound>=options->count) + { + free_comp_members(&members); return nfound; + } } /* i */ + free_comp_members(&members); } /* switch */ } /* else */ @@ -388,7 +405,6 @@ hsize_t diff_array( void *_mem1, * Dereference the object and compare the type (basic object type). *------------------------------------------------------------------------- */ - hsize_t diff_datum(void *_mem1, void *_mem2, hid_t m_type, @@ -402,13 +418,16 @@ hsize_t diff_datum(void *_mem1, const char *obj2, hid_t container1_id, hid_t container2_id, /*where the reference came from*/ - int *ph) /*print header */ + int *ph, /*print header */ + mcomp_t *members) /*compound members */ { unsigned char *mem1 = (unsigned char*)_mem1; unsigned char *mem2 = (unsigned char*)_mem2; unsigned u; hid_t memb_type; size_t type_size; + H5T_sign_t type_sign; + H5T_class_t type_class; size_t offset; int nmembs; int j; @@ -425,6 +444,10 @@ hsize_t diff_datum(void *_mem1, int both_zero; type_size = H5Tget_size( m_type ); + type_class = H5Tget_class(m_type); + + if (type_class!=H5T_REFERENCE && HDmemcmp(mem1, mem2, type_size)==0) + return 0; switch (H5Tget_class(m_type)) { @@ -441,14 +464,14 @@ hsize_t diff_datum(void *_mem1, */ case H5T_COMPOUND: - nmembs = H5Tget_nmembers(m_type); + nmembs = members->n; for (j = 0; j < nmembs; j++) { - offset = H5Tget_member_offset(m_type, (unsigned)j); - memb_type = H5Tget_member_type(m_type, (unsigned)j); + offset = members->offsets[j]; + memb_type = members->ids[j]; /* if member type is vlen string */ - if(H5Tis_variable_str(memb_type)) + if(members->flags[j]) { nfound+=diff_datum( ((unsigned char**)mem1)[j], @@ -464,7 +487,7 @@ hsize_t diff_datum(void *_mem1, obj2, container1_id, container2_id, - ph); + ph, NULL); } else { @@ -482,9 +505,8 @@ hsize_t diff_datum(void *_mem1, obj2, container1_id, container2_id, - ph); + ph, members->m[j]); } - H5Tclose(memb_type); } break; @@ -504,8 +526,11 @@ hsize_t diff_datum(void *_mem1, /* check for NULL pointer for string */ if(s!=NULL) { - if(H5Tis_variable_str(m_type)) + if(H5Tis_variable_str(m_type)) { size = HDstrlen(s); + if (HDmemcmp(mem1, mem2, size)==0) + break; + } else size = H5Tget_size(m_type); @@ -671,7 +696,7 @@ hsize_t diff_datum(void *_mem1, obj2, container1_id, container2_id, - ph); + ph, NULL); } else { @@ -689,7 +714,7 @@ hsize_t diff_datum(void *_mem1, obj2, container1_id, container2_id, - ph); + ph, NULL); } } H5Tclose(memb_type); @@ -719,8 +744,7 @@ hsize_t diff_datum(void *_mem1, * Dataset region reference *------------------------------------------------------------------------- */ - - if (H5Tequal(m_type, H5T_STD_REF_DSETREG)) + if (type_size==H5R_DSET_REG_REF_BUF_SIZE) { hid_t region1_id; hid_t region2_id; @@ -754,7 +778,7 @@ hsize_t diff_datum(void *_mem1, * Object references. get the type and OID of the referenced object *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_STD_REF_OBJ)) + else if (type_size == H5R_OBJ_REF_BUF_SIZE) { H5O_type_t obj1_type; H5O_type_t obj2_type; @@ -838,7 +862,7 @@ hsize_t diff_datum(void *_mem1, obj2, container1_id, container2_id, - ph); + ph, NULL); H5Tclose(memb_type); @@ -852,13 +876,13 @@ hsize_t diff_datum(void *_mem1, */ case H5T_INTEGER: - + type_sign = H5Tget_sign(m_type); /*------------------------------------------------------------------------- * H5T_NATIVE_SCHAR *------------------------------------------------------------------------- */ - if (H5Tequal(m_type, H5T_NATIVE_SCHAR)) + if (type_size==1 && type_sign!=H5T_SGN_NONE) { char temp1_char; char temp2_char; @@ -954,7 +978,7 @@ hsize_t diff_datum(void *_mem1, * H5T_NATIVE_UCHAR *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_UCHAR)) + else if (type_size==1 && type_sign==H5T_SGN_NONE) { unsigned char temp1_uchar; unsigned char temp2_uchar; @@ -1053,7 +1077,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_SHORT)) + else if (type_size==2 && type_sign!=H5T_SGN_NONE) { short temp1_short; short temp2_short; @@ -1152,7 +1176,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_USHORT)) + else if (type_size==2 && type_sign==H5T_SGN_NONE) { unsigned short temp1_ushort; unsigned short temp2_ushort; @@ -1252,7 +1276,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_INT)) + else if (type_size==4 && type_sign!=H5T_SGN_NONE) { int temp1_int; int temp2_int; @@ -1350,7 +1374,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_UINT)) + else if (type_size==4 && type_sign==H5T_SGN_NONE) { unsigned int temp1_uint; unsigned int temp2_uint; @@ -1448,7 +1472,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_LONG)) + else if (type_size==8 && type_sign!=H5T_SGN_NONE) { long temp1_long; long temp2_long; @@ -1548,7 +1572,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_ULONG)) + else if (type_size==8 && type_sign==H5T_SGN_NONE) { unsigned long temp1_ulong; unsigned long temp2_ulong; @@ -1647,7 +1671,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_LLONG)) + else if (type_size==8 && type_sign!=H5T_SGN_NONE) { long long temp1_llong; long long temp2_llong; @@ -1745,7 +1769,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_ULLONG)) + else if (type_size==8 && type_sign==H5T_SGN_NONE) { unsigned long long temp1_ullong; unsigned long long temp2_ullong; @@ -1862,7 +1886,7 @@ hsize_t diff_datum(void *_mem1, * H5T_NATIVE_FLOAT *------------------------------------------------------------------------- */ - if (H5Tequal(m_type, H5T_NATIVE_FLOAT)) + if (type_size==4) { float temp1_float; float temp2_float; @@ -2075,7 +2099,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_DOUBLE)) + else if (type_size==8) { double temp1_double; double temp2_double; @@ -2291,7 +2315,7 @@ hsize_t diff_datum(void *_mem1, *------------------------------------------------------------------------- */ - else if (H5Tequal(m_type, H5T_NATIVE_LDOUBLE)) + else if (type_size==8) { long double temp1_double; long double temp2_double; @@ -6046,3 +6070,62 @@ static void h5diff_print_char(char ch) break; } } + + +/*------------------------------------------------------------------------- + * XCAO, 11/10/2010 + * added to improve performance for compound datasets + * set up compound datatype structures. + */ +static void set_comp_members(hid_t tid, mcomp_t *members) +{ + if (tid <=0 || !members) + return; + + if (H5Tget_class(tid) != H5T_COMPOUND) + return; + + 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 *)); + + for (int 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]); + } + } +} + +/*------------------------------------------------------------------------- + * XCAO, 11/10/2010 + * added to improve performance for compound datasets + * clean and close compound members. + */ +static void free_comp_members(mcomp_t *members) +{ + if (!members || members->n<=0 || !members->ids) + return; + + for (int i=0; i<members->n; i++) { + if (members->m[i]) { + free_comp_members(members->m[i]); + HDfree(members->m[i]); + } + H5Tclose(members->ids[i]); + } + + HDfree (members->m); + HDfree (members->ids); + HDfree (members->flags); + HDfree (members->offsets); +} + |