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| author | Binh-Minh Ribler <bmribler@hdfgroup.org> | 2019-03-20 19:07:40 (GMT) |
|---|---|---|
| committer | Binh-Minh Ribler <bmribler@hdfgroup.org> | 2019-03-20 19:07:40 (GMT) |
| commit | 222346f3732ba3bfb007da410e1b808be129aaaf (patch) | |
| tree | 061d33723552465bbb3b672bfff10e4fe6bc2b96 /src | |
| parent | 7add52ff4f2443357648d53d52add274d1b18b5f (diff) | |
| parent | 604b67df19a164824b74fba0aa5e489b5a64d1ae (diff) | |
| download | hdf5-222346f3732ba3bfb007da410e1b808be129aaaf.zip hdf5-222346f3732ba3bfb007da410e1b808be129aaaf.tar.gz hdf5-222346f3732ba3bfb007da410e1b808be129aaaf.tar.bz2 | |
Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
Diffstat (limited to 'src')
162 files changed, 5424 insertions, 5284 deletions
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index ff7402b..5f7bd48 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -944,6 +944,12 @@ if (BUILD_SHARED_LIBS) endif () if (LOCAL_BATCH_TEST) + if (LOCAL_BATCH_SCRIPT_COMMAND STREQUAL "raybsub") + configure_file ( + ${HDF5_SOURCE_DIR}/bin/batch/${LOCAL_BATCH_SCRIPT_COMMAND} + ${HDF5_BINARY_DIR}/${LOCAL_BATCH_SCRIPT_COMMAND} ESCAPE_QUOTES @ONLY + ) + endif () if (LOCAL_BATCH_SCRIPT_NAME) configure_file ( ${HDF5_SOURCE_DIR}/bin/batch/${LOCAL_BATCH_SCRIPT_NAME}.in.cmake @@ -1112,6 +1118,11 @@ target_link_libraries (${HDF5_LIB_TARGET} PRIVATE ${LINK_LIBS} ${LINK_COMP_LIBS} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>" PUBLIC $<$<NOT:$<PLATFORM_ID:Windows>>:${CMAKE_DL_LIBS}> ) +if (NOT WIN32) + target_link_libraries (${HDF5_LIB_TARGET} + PRIVATE $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads> + ) +endif () set_global_variable (HDF5_LIBRARIES_TO_EXPORT ${HDF5_LIB_TARGET}) H5_SET_LIB_OPTIONS (${HDF5_LIB_TARGET} ${HDF5_LIB_NAME} STATIC 0) set_target_properties (${HDF5_LIB_TARGET} PROPERTIES FOLDER libraries) @@ -1141,8 +1152,8 @@ if (BUILD_SHARED_LIBS) ) TARGET_C_PROPERTIES (${HDF5_LIBSH_TARGET} SHARED) target_link_libraries (${HDF5_LIBSH_TARGET} - PRIVATE ${LINK_LIBS} ${LINK_COMP_LIBS} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>" - PUBLIC $<$<NOT:$<PLATFORM_ID:Windows>>:${CMAKE_DL_LIBS}> $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads> + PRIVATE ${LINK_LIBS} ${LINK_COMP_LIBS} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>" $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:Threads::Threads> + PUBLIC $<$<NOT:$<PLATFORM_ID:Windows>>:${CMAKE_DL_LIBS}> ) set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_LIBSH_TARGET}") H5_SET_LIB_OPTIONS (${HDF5_LIBSH_TARGET} ${HDF5_LIB_NAME} SHARED "LIB") @@ -349,7 +349,7 @@ H5AC_create(const H5F_t *f, H5AC_cache_config_t *config_ptr, H5AC_cache_image_co aux_ptr->sync_point_done = NULL; aux_ptr->p0_image_len = 0; - sprintf(prefix, "%d:", mpi_rank); + HDsprintf(prefix, "%d:", mpi_rank); if(mpi_rank == 0) { if(NULL == (aux_ptr->d_slist_ptr = H5SL_create(H5SL_TYPE_HADDR, NULL))) @@ -1612,7 +1612,7 @@ H5AC_unprotect(H5F_t *f, const H5AC_class_t *type, haddr_t addr, void *thing, done: /* If currently logging, generate a message */ if(f->shared->cache->log_info->logging) - if(H5C_log_write_unprotect_entry_msg(f->shared->cache, (H5AC_info_t *)thing, type->id, flags, ret_value) < 0) + if(H5C_log_write_unprotect_entry_msg(f->shared->cache, addr, type->id, flags, ret_value) < 0) HDONE_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "unable to emit log message") FUNC_LEAVE_NOAPI(ret_value) @@ -2403,8 +2403,18 @@ H5AC_cork(H5F_t *f, haddr_t obj_addr, unsigned action, hbool_t *corked) HDassert(H5F_addr_defined(obj_addr)); HDassert(action == H5AC__SET_CORK || action == H5AC__UNCORK || action == H5AC__GET_CORKED); - if(action == H5AC__GET_CORKED) - HDassert(corked); + /* Skip the search on "tag_list" when there are no "corked" objects. + * This is done to mitigate the slow down when closing objects. + * Re-visit this optimization when we optimize tag info management + * in the future. + */ + if(action == H5AC__GET_CORKED) { + HDassert(corked); + if(H5C_get_num_objs_corked(f->shared->cache) == 0) { + *corked = FALSE; + HGOTO_DONE(SUCCEED) + } + } if(H5C_cork(f->shared->cache, obj_addr, action, corked) < 0) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Cannot perform the cork action") diff --git a/src/H5Abtree2.c b/src/H5Abtree2.c index 07da8e2..3377aa2 100644 --- a/src/H5Abtree2.c +++ b/src/H5Abtree2.c @@ -35,6 +35,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5Apkg.h" /* Attributes */ #include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ #include "H5SMprivate.h" /* Shared object header messages */ @@ -318,7 +319,7 @@ H5A__dense_btree2_name_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR_U FUNC_ENTER_STATIC_NOERR /* Encode the record's fields */ - HDmemcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN); + H5MM_memcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN); raw += H5O_FHEAP_ID_LEN; *raw++ = nrecord->flags; UINT32ENCODE(raw, nrecord->corder) @@ -349,7 +350,7 @@ H5A__dense_btree2_name_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR_U FUNC_ENTER_STATIC_NOERR /* Decode the record's fields */ - HDmemcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN); + H5MM_memcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN); raw += H5O_FHEAP_ID_LEN; nrecord->flags = *raw++; UINT32DECODE(raw, nrecord->corder) @@ -477,7 +478,7 @@ H5A__dense_btree2_corder_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR FUNC_ENTER_STATIC_NOERR /* Encode the record's fields */ - HDmemcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN); + H5MM_memcpy(raw, nrecord->id.id, (size_t)H5O_FHEAP_ID_LEN); raw += H5O_FHEAP_ID_LEN; *raw++ = nrecord->flags; UINT32ENCODE(raw, nrecord->corder) @@ -507,7 +508,7 @@ H5A__dense_btree2_corder_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR FUNC_ENTER_STATIC_NOERR /* Decode the record's fields */ - HDmemcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN); + H5MM_memcpy(nrecord->id.id, raw, (size_t)H5O_FHEAP_ID_LEN); raw += H5O_FHEAP_ID_LEN; nrecord->flags = *raw++; UINT32DECODE(raw, nrecord->corder) diff --git a/src/H5Aint.c b/src/H5Aint.c index 6502fa4..88a4780 100644 --- a/src/H5Aint.c +++ b/src/H5Aint.c @@ -646,21 +646,21 @@ H5A__read(const H5A_t *attr, const H5T_t *mem_type, void *buf) HGOTO_ERROR(H5E_ATTR, H5E_NOSPACE, FAIL, "memory allocation failed") /* Copy the attribute data into the buffer for conversion */ - HDmemcpy(tconv_buf, attr->shared->data, (src_type_size * nelmts)); + H5MM_memcpy(tconv_buf, attr->shared->data, (src_type_size * nelmts)); /* Perform datatype conversion. */ if(H5T_convert(tpath, src_id, dst_id, nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf) < 0) HGOTO_ERROR(H5E_ATTR, H5E_CANTENCODE, FAIL, "datatype conversion failed") /* Copy the converted data into the user's buffer */ - HDmemcpy(buf, tconv_buf, (dst_type_size * nelmts)); + H5MM_memcpy(buf, tconv_buf, (dst_type_size * nelmts)); } /* end if */ /* No type conversion necessary */ else { HDassert(dst_type_size == src_type_size); /* Copy the attribute data into the user's buffer */ - HDmemcpy(buf, attr->shared->data, (dst_type_size * nelmts)); + H5MM_memcpy(buf, attr->shared->data, (dst_type_size * nelmts)); } /* end else */ } /* end else */ } /* end if */ @@ -747,7 +747,7 @@ H5A__write(H5A_t *attr, const H5T_t *mem_type, const void *buf) HGOTO_ERROR(H5E_ATTR, H5E_CANTALLOC, FAIL, "memory allocation failed") /* Copy the user's data into the buffer for conversion */ - HDmemcpy(tconv_buf, buf, (src_type_size * nelmts)); + H5MM_memcpy(tconv_buf, buf, (src_type_size * nelmts)); /* Perform datatype conversion */ if(H5T_convert(tpath, src_id, dst_id, nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf) < 0) @@ -771,7 +771,7 @@ H5A__write(H5A_t *attr, const H5T_t *mem_type, const void *buf) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") /* Copy the attribute data into the user's buffer */ - HDmemcpy(attr->shared->data, buf, (dst_type_size * nelmts)); + H5MM_memcpy(attr->shared->data, buf, (dst_type_size * nelmts)); } /* end else */ /* Modify the attribute in the object header */ @@ -827,7 +827,7 @@ H5A__get_name(H5A_t *attr, size_t buf_size, char *buf) /* Copy all/some of the name */ if(buf && copy_len > 0) { - HDmemcpy(buf, attr->shared->name, copy_len); + H5MM_memcpy(buf, attr->shared->name, copy_len); /* Terminate the string */ buf[copy_len]='\0'; @@ -2240,7 +2240,7 @@ H5A__attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_s if(NULL == (buf = H5FL_BLK_MALLOC(attr_buf, buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation NULLed for raw data chunk") - HDmemcpy(buf, attr_src->shared->data, attr_src->shared->data_size); + H5MM_memcpy(buf, attr_src->shared->data, attr_src->shared->data_size); /* Allocate background memory */ if(H5T_path_bkg(tpath_src_mem) || H5T_path_bkg(tpath_mem_dst)) @@ -2251,7 +2251,7 @@ H5A__attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_s if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, bkg_buf) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") - HDmemcpy(reclaim_buf, buf, buf_size); + H5MM_memcpy(reclaim_buf, buf, buf_size); /* Set background buffer to all zeros */ if(bkg_buf) @@ -2261,14 +2261,14 @@ H5A__attr_copy_file(const H5A_t *attr_src, H5F_t *file_dst, hbool_t *recompute_s if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg_buf) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "datatype conversion NULLed") - HDmemcpy(attr_dst->shared->data, buf, attr_dst->shared->data_size); + H5MM_memcpy(attr_dst->shared->data, buf, attr_dst->shared->data_size); if(H5D_vlen_reclaim(tid_mem, buf_space, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, NULL, "unable to reclaim variable-length data") } /* end if */ else { HDassert(attr_dst->shared->data_size == attr_src->shared->data_size); - HDmemcpy(attr_dst->shared->data, attr_src->shared->data, attr_src->shared->data_size); + H5MM_memcpy(attr_dst->shared->data, attr_src->shared->data, attr_src->shared->data_size); } /* end else */ } /* end if(attr_src->shared->data) */ @@ -107,6 +107,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5Iprivate.h" /* IDs */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Pprivate.h" /* Property lists */ @@ -436,8 +437,8 @@ H5B__split(H5F_t *f, H5B_ins_ud_t *bt_ud, unsigned idx, side = "LEFT"; else side = "MIDDLE"; - fprintf(H5DEBUG(B), "H5B__split: %3u {%5.3f,%5.3f,%5.3f} %6s", - shared->two_k, split_ratios[0], split_ratios[1], split_ratios[2], side); + HDfprintf(H5DEBUG(B), "H5B__split: %3u {%5.3f,%5.3f,%5.3f} %6s", + shared->two_k, split_ratios[0], split_ratios[1], split_ratios[2], side); } #endif @@ -464,7 +465,7 @@ H5B__split(H5F_t *f, H5B_ins_ud_t *bt_ud, unsigned idx, nright = shared->two_k - nleft; #ifdef H5B_DEBUG if(H5DEBUG(B)) - fprintf(H5DEBUG(B), " split %3d/%-3d\n", nleft, nright); + HDfprintf(H5DEBUG(B), " split %3d/%-3d\n", nleft, nright); #endif /* @@ -484,10 +485,10 @@ H5B__split(H5F_t *f, H5B_ins_ud_t *bt_ud, unsigned idx, */ split_bt_ud->cache_flags = H5AC__DIRTIED_FLAG; - HDmemcpy(split_bt_ud->bt->native, + H5MM_memcpy(split_bt_ud->bt->native, bt_ud->bt->native + nleft * shared->type->sizeof_nkey, (nright + 1) * shared->type->sizeof_nkey); - HDmemcpy(split_bt_ud->bt->child, + H5MM_memcpy(split_bt_ud->bt->child, &bt_ud->bt->child[nleft], nright * sizeof(haddr_t)); @@ -612,9 +613,9 @@ H5B_insert(H5F_t *f, const H5B_class_t *type, haddr_t addr, void *udata) /* update left and right keys */ if(!lt_key_changed) - HDmemcpy(lt_key, H5B_NKEY(bt_ud.bt,shared,0), type->sizeof_nkey); + H5MM_memcpy(lt_key, H5B_NKEY(bt_ud.bt,shared,0), type->sizeof_nkey); if(!rt_key_changed) - HDmemcpy(rt_key, H5B_NKEY(split_bt_ud.bt,shared,split_bt_ud.bt->nchildren), type->sizeof_nkey); + H5MM_memcpy(rt_key, H5B_NKEY(split_bt_ud.bt,shared,split_bt_ud.bt->nchildren), type->sizeof_nkey); /* * Copy the old root node to some other file location and make the new root @@ -657,11 +658,11 @@ H5B_insert(H5F_t *f, const H5B_class_t *type, haddr_t addr, void *udata) new_root_bt->nchildren = 2; new_root_bt->child[0] = bt_ud.addr; - HDmemcpy(H5B_NKEY(new_root_bt, shared, 0), lt_key, shared->type->sizeof_nkey); + H5MM_memcpy(H5B_NKEY(new_root_bt, shared, 0), lt_key, shared->type->sizeof_nkey); new_root_bt->child[1] = split_bt_ud.addr; - HDmemcpy(H5B_NKEY(new_root_bt, shared, 1), md_key, shared->type->sizeof_nkey); - HDmemcpy(H5B_NKEY(new_root_bt, shared, 2), rt_key, shared->type->sizeof_nkey); + H5MM_memcpy(H5B_NKEY(new_root_bt, shared, 1), md_key, shared->type->sizeof_nkey); + H5MM_memcpy(H5B_NKEY(new_root_bt, shared, 2), rt_key, shared->type->sizeof_nkey); /* Insert the modified copy of the old root into the file again */ if(H5AC_insert_entry(f, H5AC_BT, addr, new_root_bt, H5AC__NO_FLAGS_SET) < 0) @@ -726,9 +727,9 @@ H5B__insert_child(H5B_t *bt, unsigned *bt_flags, unsigned idx, base = H5B_NKEY(bt, shared, (idx + 1)); if((idx + 1) == bt->nchildren) { /* Make room for the new key */ - HDmemcpy(base + shared->type->sizeof_nkey, base, + H5MM_memcpy(base + shared->type->sizeof_nkey, base, shared->type->sizeof_nkey); /* No overlap possible - memcpy() OK */ - HDmemcpy(base, md_key, shared->type->sizeof_nkey); + H5MM_memcpy(base, md_key, shared->type->sizeof_nkey); /* The MD_KEY is the left key of the new node */ if(H5B_INS_RIGHT == anchor) @@ -741,7 +742,7 @@ H5B__insert_child(H5B_t *bt, unsigned *bt_flags, unsigned idx, /* Make room for the new key */ HDmemmove(base + shared->type->sizeof_nkey, base, (bt->nchildren - idx) * shared->type->sizeof_nkey); - HDmemcpy(base, md_key, shared->type->sizeof_nkey); + H5MM_memcpy(base, md_key, shared->type->sizeof_nkey); /* The MD_KEY is the left key of the new node */ if(H5B_INS_RIGHT == anchor) @@ -915,7 +916,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type, * node. This node is not empty (handled above). */ my_ins = H5B_INS_LEFT; - HDmemcpy(md_key, H5B_NKEY(bt,shared,idx), type->sizeof_nkey); + H5MM_memcpy(md_key, H5B_NKEY(bt,shared,idx), type->sizeof_nkey); if((type->new_node)(f, H5B_INS_LEFT, H5B_NKEY(bt, shared, idx), udata, md_key, &new_child_bt_ud.addr/*out*/) < 0) HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR, "can't insert minimum leaf node") @@ -963,7 +964,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type, */ idx = bt->nchildren - 1; my_ins = H5B_INS_RIGHT; - HDmemcpy(md_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey); + H5MM_memcpy(md_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey); if((type->new_node)(f, H5B_INS_RIGHT, md_key, udata, H5B_NKEY(bt, shared, idx + 1), &new_child_bt_ud.addr/*out*/) < 0) HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR, "can't insert maximum leaf node") @@ -1021,7 +1022,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type, *lt_key_changed = FALSE; } /* end if */ else - HDmemcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey); + H5MM_memcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey); } /* end if */ if(*rt_key_changed) { bt_ud->cache_flags |= H5AC__DIRTIED_FLAG; @@ -1031,7 +1032,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type, *rt_key_changed = FALSE; } /* end if */ else - HDmemcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey); + H5MM_memcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey); } /* end if */ /* @@ -1080,7 +1081,7 @@ H5B__insert_helper(H5F_t *f, H5B_ins_ud_t *bt_ud, const H5B_class_t *type, * by the left and right node). */ if(split_bt_ud->bt) { - HDmemcpy(md_key, H5B_NKEY(split_bt_ud->bt, shared, 0), type->sizeof_nkey); + H5MM_memcpy(md_key, H5B_NKEY(split_bt_ud->bt, shared, 0), type->sizeof_nkey); ret_value = H5B_INS_RIGHT; #ifdef H5B_DEBUG /* @@ -1339,7 +1340,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, /* Don't propagate change out of this B-tree node */ *lt_key_changed = FALSE; else - HDmemcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey); + H5MM_memcpy(lt_key, H5B_NKEY(bt, shared, idx), type->sizeof_nkey); } /* end if */ if(*rt_key_changed) { HDassert(type->critical_key == H5B_RIGHT); @@ -1348,7 +1349,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, /* Don't propagate change out of this B-tree node */ *rt_key_changed = FALSE; else - HDmemcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey); + H5MM_memcpy(rt_key, H5B_NKEY(bt, shared, idx + 1), type->sizeof_nkey); } /* end if */ /* @@ -1383,7 +1384,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, * in its left neighbor, but only if it is not the critical * key for the right-most child of the left neighbor */ if(type->critical_key == H5B_LEFT) - HDmemcpy(H5B_NKEY(sibling, shared, sibling->nchildren), + H5MM_memcpy(H5B_NKEY(sibling, shared, sibling->nchildren), H5B_NKEY(bt, shared, 1), type->sizeof_nkey); sibling->right = bt->right; @@ -1400,7 +1401,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, * its right neighbor, but only if it is not the critical * key for the left-most child of the right neighbor */ if(type->critical_key == H5B_RIGHT) - HDmemcpy(H5B_NKEY(sibling, shared, 0), + H5MM_memcpy(H5B_NKEY(sibling, shared, 0), H5B_NKEY(bt, shared, 0), type->sizeof_nkey); sibling->left = bt->left; @@ -1442,7 +1443,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, /* Slide all keys down 1, update lt_key */ HDmemmove(H5B_NKEY(bt, shared, 0), H5B_NKEY(bt, shared, 1), bt->nchildren * type->sizeof_nkey); - HDmemcpy(lt_key, H5B_NKEY(bt, shared, 0), type->sizeof_nkey); + H5MM_memcpy(lt_key, H5B_NKEY(bt, shared, 0), type->sizeof_nkey); *lt_key_changed = TRUE; } else /* Slide all but the leftmost 2 keys down, leaving the leftmost @@ -1471,7 +1472,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, H5B_NKEY(bt, shared, bt->nchildren), type->sizeof_nkey); else { /* Just update rt_key */ - HDmemcpy(rt_key, H5B_NKEY(bt, shared, bt->nchildren - 1), + H5MM_memcpy(rt_key, H5B_NKEY(bt, shared, bt->nchildren - 1), type->sizeof_nkey); *rt_key_changed = TRUE; } /* end else */ @@ -1516,7 +1517,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, if(NULL == (sibling = (H5B_t *)H5AC_protect(f, H5AC_BT, bt->left, &cache_udata, H5AC__NO_FLAGS_SET))) HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, H5B_INS_ERROR, "unable to protect node") - HDmemcpy(H5B_NKEY(sibling, shared, sibling->nchildren), + H5MM_memcpy(H5B_NKEY(sibling, shared, sibling->nchildren), H5B_NKEY(bt, shared, 0), type->sizeof_nkey); if(H5AC_unprotect(f, H5AC_BT, bt->left, sibling, H5AC__DIRTIED_FLAG) < 0) @@ -1531,7 +1532,7 @@ H5B__remove_helper(H5F_t *f, haddr_t addr, const H5B_class_t *type, int level, if(NULL == (sibling = (H5B_t *)H5AC_protect(f, H5AC_BT, bt->right, &cache_udata, H5AC__NO_FLAGS_SET))) HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, H5B_INS_ERROR, "unable to protect node") - HDmemcpy(H5B_NKEY(sibling, shared, 0), + H5MM_memcpy(H5B_NKEY(sibling, shared, 0), H5B_NKEY(bt, shared, bt->nchildren), type->sizeof_nkey); if(H5AC_unprotect(f, H5AC_BT, bt->right, sibling, H5AC__DIRTIED_FLAG) < 0) @@ -1811,7 +1812,7 @@ H5B__copy(const H5B_t *old_bt) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree root node") /* Copy the main structure */ - HDmemcpy(new_node, old_bt, sizeof(H5B_t)); + H5MM_memcpy(new_node, old_bt, sizeof(H5B_t)); /* Reset cache info */ HDmemset(&new_node->cache_info, 0, sizeof(H5AC_info_t)); @@ -1821,8 +1822,8 @@ H5B__copy(const H5B_t *old_bt) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree root node") /* Copy the other structures */ - HDmemcpy(new_node->native, old_bt->native, shared->sizeof_keys); - HDmemcpy(new_node->child, old_bt->child, (sizeof(haddr_t) * shared->two_k)); + H5MM_memcpy(new_node->native, old_bt->native, shared->sizeof_keys); + H5MM_memcpy(new_node->child, old_bt->child, (sizeof(haddr_t) * shared->two_k)); /* Increment the ref-count on the raw page */ H5UC_INC(new_node->rc_shared); @@ -662,7 +662,7 @@ H5B2_find(H5B2_t *bt2, void *udata, H5B2_found_t op, void *op_data) if(hdr->min_native_rec == NULL) if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info") - HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ if(idx == (unsigned)(leaf->nrec - 1)) { @@ -670,7 +670,7 @@ H5B2_find(H5B2_t *bt2, void *udata, H5B2_found_t op, void *op_data) if(hdr->max_native_rec == NULL) if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info") - HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ } /* end if */ @@ -1343,7 +1343,7 @@ H5B2_modify(H5B2_t *bt2, void *udata, H5B2_modify_t op, void *op_data) if(hdr->min_native_rec == NULL) if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info") - HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ if(idx == (unsigned)(leaf->nrec - 1)) { @@ -1351,7 +1351,7 @@ H5B2_modify(H5B2_t *bt2, void *udata, H5B2_modify_t op, void *op_data) if(hdr->max_native_rec == NULL) if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info") - HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ } /* end if */ diff --git a/src/H5B2cache.c b/src/H5B2cache.c index 2e1d37b..2a77bd5 100644 --- a/src/H5B2cache.c +++ b/src/H5B2cache.c @@ -391,7 +391,7 @@ H5B2__cache_hdr_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le HDassert(hdr); /* Magic number */ - HDmemcpy(image, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -811,7 +811,7 @@ H5B2__cache_int_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le HDassert(internal->hdr); /* Magic number */ - HDmemcpy(image, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -1212,7 +1212,7 @@ H5B2__cache_leaf_serialize(const H5F_t H5_ATTR_UNUSED *f, void *_image, size_t H HDassert(leaf->hdr); /* magic number */ - HDmemcpy(image, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* version # */ diff --git a/src/H5B2int.c b/src/H5B2int.c index b3f855f..9940cd7 100644 --- a/src/H5B2int.c +++ b/src/H5B2int.c @@ -35,6 +35,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5B2pkg.h" /* v2 B-trees */ #include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vectors and arrays */ @@ -241,17 +242,17 @@ H5B2__split1(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr, mid_record = old_node_nrec / 2; /* Copy "upper half" of records to new child */ - HDmemcpy(H5B2_NAT_NREC(right_native, hdr, 0), + H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(left_native, hdr, mid_record + (unsigned)1), hdr->cls->nrec_size * (old_node_nrec - (mid_record + (unsigned)1))); /* Copy "upper half" of node pointers, if the node is an internal node */ if(depth > 1) - HDmemcpy(&(right_node_ptrs[0]), &(left_node_ptrs[mid_record + (unsigned)1]), + H5MM_memcpy(&(right_node_ptrs[0]), &(left_node_ptrs[mid_record + (unsigned)1]), sizeof(H5B2_node_ptr_t) * (size_t)(old_node_nrec - mid_record)); /* Copy "middle" record to internal node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, mid_record), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, mid_record), hdr->cls->nrec_size); /* Mark nodes as dirty */ left_child_flags |= H5AC__DIRTIED_FLAG; @@ -510,14 +511,14 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, uint16_t move_nrec = (uint16_t)(*right_nrec - new_right_nrec); /* Number of records to move from right node to left */ /* Copy record from parent node down into left child */ - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); /* See if we need to move records from right node */ if(move_nrec > 1) - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, (*left_nrec + 1)), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (size_t)(move_nrec - 1)); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, (*left_nrec + 1)), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (size_t)(move_nrec - 1)); /* Move record from right node into parent node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), hdr->cls->nrec_size); /* Slide records in right node down */ HDmemmove(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(right_native, hdr, move_nrec), hdr->cls->nrec_size * new_right_nrec); @@ -534,7 +535,7 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, right_moved_nrec -= (hssize_t)moved_nrec; /* Copy node pointers from right node to left */ - HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * move_nrec); + H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * move_nrec); /* Slide node pointers in right node down */ HDmemmove(&(right_node_ptrs[0]), &(right_node_ptrs[move_nrec]), sizeof(H5B2_node_ptr_t) * (new_right_nrec + (unsigned)1)); @@ -569,14 +570,14 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, hdr->cls->nrec_size * (*right_nrec)); /* Copy record from parent node down into right child */ - HDmemcpy(H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, (move_nrec - 1)), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); /* See if we need to move records from left node */ if(move_nrec > 1) - HDmemcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(left_native, hdr, ((*left_nrec - move_nrec) + 1)), hdr->cls->nrec_size * (size_t)(move_nrec - 1)); + H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(left_native, hdr, ((*left_nrec - move_nrec) + 1)), hdr->cls->nrec_size * (size_t)(move_nrec - 1)); /* Move record from left node into parent node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, (*left_nrec - move_nrec)), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(left_native, hdr, (*left_nrec - move_nrec)), hdr->cls->nrec_size); /* Handle node pointers, if we have an internal node */ if(depth > 1) { @@ -587,7 +588,7 @@ H5B2__redistribute2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, HDmemmove(&(right_node_ptrs[move_nrec]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1)); /* Copy node pointers from left node to right */ - HDmemcpy(&(right_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * move_nrec); + H5MM_memcpy(&(right_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * move_nrec); /* Count the number of records being moved */ for(u = 0; u < move_nrec; u++) @@ -775,16 +776,16 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, uint16_t moved_middle_nrec = 0; /* Number of records moved into left node */ /* Move left parent record down to left node */ - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size); /* Move records from middle node into left node */ if((new_left_nrec - 1) > *left_nrec) { moved_middle_nrec = (uint16_t)(new_left_nrec - (*left_nrec + 1)); - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * moved_middle_nrec); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * moved_middle_nrec); } /* end if */ /* Move record from middle node up to parent node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, moved_middle_nrec), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, moved_middle_nrec), hdr->cls->nrec_size); moved_middle_nrec++; /* Slide records in middle node down */ @@ -798,7 +799,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, /* Move middle node pointers into left node */ move_nptrs = (unsigned)(new_left_nrec - *left_nrec); - HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t)*move_nptrs); + H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t)*move_nptrs); /* Count the number of records being moved into the left node */ for(u = 0, moved_nrec = 0; u < move_nptrs; u++) @@ -832,14 +833,14 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, HDmemmove(H5B2_NAT_NREC(right_native, hdr, right_nrec_move), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec)); /* Move right parent record down to right node */ - HDmemcpy(H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); /* Move records from middle node into right node */ if(right_nrec_move > 1) - HDmemcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(middle_native, hdr, ((curr_middle_nrec - right_nrec_move) + 1)), hdr->cls->nrec_size * (right_nrec_move - 1)); + H5MM_memcpy(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(middle_native, hdr, ((curr_middle_nrec - right_nrec_move) + 1)), hdr->cls->nrec_size * (right_nrec_move - 1)); /* Move record from middle node up to parent node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(middle_native, hdr, (curr_middle_nrec - right_nrec_move)), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(middle_native, hdr, (curr_middle_nrec - right_nrec_move)), hdr->cls->nrec_size); /* Move node pointers also if this is an internal node */ if(depth > 1) { @@ -850,7 +851,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, HDmemmove(&(right_node_ptrs[right_nrec_move]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1)); /* Move middle node pointers into right node */ - HDmemcpy(&(right_node_ptrs[0]), &(middle_node_ptrs[(curr_middle_nrec - right_nrec_move) + 1]), sizeof(H5B2_node_ptr_t) * right_nrec_move); + H5MM_memcpy(&(right_node_ptrs[0]), &(middle_node_ptrs[(curr_middle_nrec - right_nrec_move) + 1]), sizeof(H5B2_node_ptr_t) * right_nrec_move); /* Count the number of records being moved into the right node */ for(u = 0, moved_nrec = 0; u < right_nrec_move; u++) @@ -881,14 +882,14 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, HDmemmove(H5B2_NAT_NREC(middle_native, hdr, left_nrec_move), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * curr_middle_nrec); /* Move left parent record down to middle node */ - HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, left_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, left_nrec_move - 1), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size); /* Move left records to middle node */ if(left_nrec_move > 1) HDmemmove(H5B2_NAT_NREC(middle_native, hdr, 0), H5B2_NAT_NREC(left_native, hdr, new_left_nrec + 1), hdr->cls->nrec_size * (left_nrec_move - 1)); /* Move left parent record up from left node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(left_native, hdr, new_left_nrec), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(left_native, hdr, new_left_nrec), hdr->cls->nrec_size); /* Move node pointers also if this is an internal node */ if(depth > 1) { @@ -899,7 +900,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, HDmemmove(&(middle_node_ptrs[left_nrec_move]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(curr_middle_nrec + 1)); /* Move left node pointers into middle node */ - HDmemcpy(&(middle_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * left_nrec_move); + H5MM_memcpy(&(middle_node_ptrs[0]), &(left_node_ptrs[new_left_nrec + 1]), sizeof(H5B2_node_ptr_t) * left_nrec_move); /* Count the number of records being moved into the left node */ for(u = 0, moved_nrec = 0; u < left_nrec_move; u++) @@ -927,13 +928,13 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, unsigned right_nrec_move = (unsigned)(*right_nrec - new_right_nrec); /* Number of records to move out of right node */ /* Move right parent record down to middle node */ - HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, curr_middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, curr_middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); /* Move right records to middle node */ HDmemmove(H5B2_NAT_NREC(middle_native, hdr, (curr_middle_nrec + 1)), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (right_nrec_move - 1)); /* Move right parent record up from right node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx), H5B2_NAT_NREC(right_native, hdr, right_nrec_move - 1), hdr->cls->nrec_size); /* Slide right records down */ HDmemmove(H5B2_NAT_NREC(right_native, hdr, 0), H5B2_NAT_NREC(right_native, hdr, right_nrec_move), hdr->cls->nrec_size * new_right_nrec); @@ -944,7 +945,7 @@ H5B2__redistribute3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, unsigned u; /* Local index variable */ /* Move right node pointers into middle node */ - HDmemcpy(&(middle_node_ptrs[curr_middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * right_nrec_move); + H5MM_memcpy(&(middle_node_ptrs[curr_middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * right_nrec_move); /* Count the number of records being moved into the right node */ for(u = 0, moved_nrec = 0; u < right_nrec_move; u++) @@ -1113,14 +1114,14 @@ H5B2__merge2(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr, /* Redistribute records into left node */ { /* Copy record from parent node to proper location */ - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); /* Copy records from right node to left node */ - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec)); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec)); /* Copy node pointers from right node into left node */ if(depth > 1) - HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1)); + H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1)); /* Update flush dependencies for grandchildren, if using SWMR */ if(hdr->swmr_write && depth > 1) @@ -1304,13 +1305,13 @@ H5B2__merge3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr, middle_moved_nrec = middle_nrec_move; /* Copy record from parent node to proper location in left node */ - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec), H5B2_INT_NREC(internal, hdr, idx - 1), hdr->cls->nrec_size); /* Copy records from middle node to left node */ - HDmemcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * (middle_nrec_move - 1)); + H5MM_memcpy(H5B2_NAT_NREC(left_native, hdr, *left_nrec + 1), H5B2_NAT_NREC(middle_native, hdr, 0), hdr->cls->nrec_size * (middle_nrec_move - 1)); /* Copy record from middle node to proper location in parent node */ - HDmemcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, (middle_nrec_move - 1)), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_INT_NREC(internal, hdr, idx - 1), H5B2_NAT_NREC(middle_native, hdr, (middle_nrec_move - 1)), hdr->cls->nrec_size); /* Slide records in middle node down */ HDmemmove(H5B2_NAT_NREC(middle_native, hdr, 0), H5B2_NAT_NREC(middle_native, hdr, middle_nrec_move), hdr->cls->nrec_size * (*middle_nrec - middle_nrec_move)); @@ -1320,7 +1321,7 @@ H5B2__merge3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr, unsigned u; /* Local index variable */ /* Copy node pointers from middle node into left node */ - HDmemcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * middle_nrec_move); + H5MM_memcpy(&(left_node_ptrs[*left_nrec + 1]), &(middle_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * middle_nrec_move); /* Count the number of records being moved into the left node */ for(u = 0; u < middle_nrec_move; u++) @@ -1348,15 +1349,15 @@ H5B2__merge3(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node_ptr, /* Redistribute records into middle node */ { /* Copy record from parent node to proper location in middle node */ - HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec), H5B2_INT_NREC(internal, hdr, idx), hdr->cls->nrec_size); /* Copy records from right node to middle node */ - HDmemcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec)); + H5MM_memcpy(H5B2_NAT_NREC(middle_native, hdr, *middle_nrec + 1), H5B2_NAT_NREC(right_native, hdr, 0), hdr->cls->nrec_size * (*right_nrec)); /* Move node pointers also if this is an internal node */ if(depth > 1) /* Copy node pointers from right node into middle node */ - HDmemcpy(&(middle_node_ptrs[*middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1)); + H5MM_memcpy(&(middle_node_ptrs[*middle_nrec + 1]), &(right_node_ptrs[0]), sizeof(H5B2_node_ptr_t) * (size_t)(*right_nrec + 1)); /* Update flush dependencies for grandchildren, if using SWMR */ if(hdr->swmr_write && depth > 1) @@ -1539,7 +1540,7 @@ H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree internal node pointers") /* Copy the node pointers */ - HDmemcpy(node_ptrs, internal->node_ptrs, (sizeof(H5B2_node_ptr_t) * (size_t)(curr_node->node_nrec + 1))); + H5MM_memcpy(node_ptrs, internal->node_ptrs, (sizeof(H5B2_node_ptr_t) * (size_t)(curr_node->node_nrec + 1))); } /* end if */ else { H5B2_leaf_t *leaf; /* Pointer to leaf node */ @@ -1559,7 +1560,7 @@ H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree internal native keys") /* Copy the native keys */ - HDmemcpy(native, node_native, (hdr->cls->nrec_size * curr_node->node_nrec)); + H5MM_memcpy(native, node_native, (hdr->cls->nrec_size * curr_node->node_nrec)); /* Unlock the node */ if(H5AC_unprotect(hdr->f, curr_node_class, curr_node->addr, node, (unsigned)(hdr->swmr_write ? H5AC__PIN_ENTRY_FLAG : H5AC__NO_FLAGS_SET)) < 0) diff --git a/src/H5B2leaf.c b/src/H5B2leaf.c index 54d40ea..beca40c 100644 --- a/src/H5B2leaf.c +++ b/src/H5B2leaf.c @@ -412,7 +412,7 @@ H5B2__insert_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr, if(hdr->min_native_rec == NULL) if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info") - HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ if(idx == (unsigned)(leaf->nrec - 1)) { @@ -420,7 +420,7 @@ H5B2__insert_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr, if(hdr->max_native_rec == NULL) if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info") - HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ } /* end if */ @@ -561,7 +561,7 @@ H5B2__update_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr, if(hdr->min_native_rec == NULL) if(NULL == (hdr->min_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree min record info") - HDmemcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->min_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ if(idx == (unsigned)(leaf->nrec - 1)) { @@ -569,7 +569,7 @@ H5B2__update_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr, if(hdr->max_native_rec == NULL) if(NULL == (hdr->max_native_rec = H5MM_malloc(hdr->cls->nrec_size))) HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, FAIL, "memory allocation failed for v2 B-tree max record info") - HDmemcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); + H5MM_memcpy(hdr->max_native_rec, H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size); } /* end if */ } /* end if */ } /* end if */ @@ -664,9 +664,9 @@ H5B2__swap_leaf(H5B2_hdr_t *hdr, uint16_t depth, H5B2_internal_t *internal, } /* end else */ /* Swap records (use disk page as temporary buffer) */ - HDmemcpy(hdr->page, H5B2_NAT_NREC(child_native, hdr, 0), hdr->cls->nrec_size); - HDmemcpy(H5B2_NAT_NREC(child_native, hdr, 0), swap_loc, hdr->cls->nrec_size); - HDmemcpy(swap_loc, hdr->page, hdr->cls->nrec_size); + H5MM_memcpy(hdr->page, H5B2_NAT_NREC(child_native, hdr, 0), hdr->cls->nrec_size); + H5MM_memcpy(H5B2_NAT_NREC(child_native, hdr, 0), swap_loc, hdr->cls->nrec_size); + H5MM_memcpy(swap_loc, hdr->page, hdr->cls->nrec_size); /* Mark parent as dirty */ *internal_flags_ptr |= H5AC__DIRTIED_FLAG; diff --git a/src/H5Bcache.c b/src/H5Bcache.c index a0a75c8..c2c7a80 100644 --- a/src/H5Bcache.c +++ b/src/H5Bcache.c @@ -35,6 +35,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5Bpkg.h" /* B-link trees */ #include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -304,7 +305,7 @@ H5B__cache_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED len, HDassert(shared->type->encode); /* magic number */ - HDmemcpy(image, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += 4; /* node type and level */ diff --git a/src/H5Bdbg.c b/src/H5Bdbg.c index c491783..665e826 100644 --- a/src/H5Bdbg.c +++ b/src/H5Bdbg.c @@ -193,13 +193,13 @@ H5B__assert(H5F_t *f, haddr_t addr, const H5B_class_t *type, void *udata) FUNC_ENTER_PACKAGE if(0 == ncalls++) { - if(H5DEBUG(B)) - fprintf(H5DEBUG(B), "H5B: debugging B-trees (expensive)\n"); + if(H5DEBUG(B)) + HDfprintf(H5DEBUG(B), "H5B: debugging B-trees (expensive)\n"); } /* end if */ /* Get shared info for B-tree */ if(NULL == (rc_shared = (type->get_shared)(f, udata))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "can't retrieve B-tree's shared ref. count object") + HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "can't retrieve B-tree's shared ref. count object") shared = (H5B_shared_t *)H5UC_GET_OBJ(rc_shared); HDassert(shared); @@ -327,6 +327,7 @@ H5C_create(size_t max_cache_size, /* Tagging Field Initializations */ cache_ptr->ignore_tags = FALSE; + cache_ptr->num_objs_corked = 0; cache_ptr->slist_changed = FALSE; cache_ptr->slist_len = 0; @@ -1482,31 +1483,17 @@ H5C_insert_entry(H5F_t * f, H5C__UPDATE_STATS_FOR_INSERTION(cache_ptr, entry_ptr) #ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) { - coll_access = (H5P_USER_TRUE == f->coll_md_read ? TRUE : FALSE); - - /* If not explicitly disabled, get the cmdr setting from the API context */ - if(!coll_access && H5P_FORCE_FALSE != f->coll_md_read) - coll_access = H5CX_get_coll_metadata_read(); - } /* end if */ + if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) + coll_access = H5CX_get_coll_metadata_read(); entry_ptr->coll_access = coll_access; if(coll_access) { H5C__INSERT_IN_COLL_LIST(cache_ptr, entry_ptr, FAIL) /* Make sure the size of the collective entries in the cache remain in check */ - if(H5P_USER_TRUE == f->coll_md_read) { - if(cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) { - if(H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") - } /* end if */ - } /* end if */ - else { - if(cache_ptr->max_cache_size * 40 < cache_ptr->coll_list_size * 100) { - if(H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") - } /* end if */ - } /* end else */ + if(cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) + if(H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") } /* end if */ #endif @@ -2242,13 +2229,8 @@ H5C_protect(H5F_t * f, ring = H5CX_get_ring(); #ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) { - coll_access = (H5P_USER_TRUE == f->coll_md_read ? TRUE : FALSE); - - /* If not explicitly disabled, get the cmdr setting from the API context */ - if(!coll_access && H5P_FORCE_FALSE != f->coll_md_read) - coll_access = H5CX_get_coll_metadata_read(); - } /* end if */ + if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) + coll_access = H5CX_get_coll_metadata_read(); #endif /* H5_HAVE_PARALLEL */ /* first check to see if the target is in cache */ @@ -2285,7 +2267,7 @@ H5C_protect(H5F_t * f, the entry in their cache still have to participate in the bcast. */ #ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI) && coll_access) { + if(coll_access) { if(!(entry_ptr->is_dirty) && !(entry_ptr->coll_access)) { MPI_Comm comm; /* File MPI Communicator */ int mpi_code; /* MPI error code */ @@ -2303,7 +2285,7 @@ H5C_protect(H5F_t * f, if(NULL == (entry_ptr->image_ptr = H5MM_malloc(entry_ptr->size + H5C_IMAGE_EXTRA_SPACE))) HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "memory allocation failed for on disk image buffer") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ if(0 == mpi_rank) if(H5C__generate_image(f, cache_ptr, entry_ptr) < 0) @@ -2600,21 +2582,11 @@ H5C_protect(H5F_t * f, } /* end if */ #ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) { - /* Make sure the size of the collective entries in the cache remain in check */ - if(coll_access) { - if(H5P_USER_TRUE == f->coll_md_read) { - if(cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) - if(H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") - } /* end if */ - else { - if(cache_ptr->max_cache_size * 40 < cache_ptr->coll_list_size * 100) - if(H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") - } /* end else */ - } /* end if */ - } /* end if */ + /* Make sure the size of the collective entries in the cache remain in check */ + if(coll_access) + if(cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) + if(H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") #endif /* H5_HAVE_PARALLEL */ done: @@ -6070,7 +6042,7 @@ H5C__flush_single_entry(H5F_t *f, H5C_cache_entry_t *entry_ptr, unsigned flags) if(NULL == (entry_ptr->image_ptr = H5MM_malloc(entry_ptr->size + H5C_IMAGE_EXTRA_SPACE))) HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + entry_ptr->size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ } /* end if */ @@ -6570,7 +6542,7 @@ H5C_load_entry(H5F_t * f, if(NULL == (image = (uint8_t *)H5MM_malloc(len + H5C_IMAGE_EXTRA_SPACE))) HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "memory allocation failed for on disk image buffer") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ #ifdef H5_HAVE_PARALLEL @@ -6608,7 +6580,7 @@ H5C_load_entry(H5F_t * f, HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "image null after H5MM_realloc()") image = (uint8_t *)new_image; #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ } /* end if */ @@ -6652,7 +6624,7 @@ H5C_load_entry(H5F_t * f, HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "image null after H5MM_realloc()") image = (uint8_t *)new_image; #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(image + actual_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(image + actual_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ if(actual_len > len) { @@ -7729,6 +7701,8 @@ H5C_cork(H5C_t *cache_ptr, haddr_t obj_addr, unsigned action, hbool_t *corked) /* Set the corked status for the entire object */ tag_info->corked = TRUE; + cache_ptr->num_objs_corked++; + } /* end if */ else { /* Sanity check */ @@ -7740,6 +7714,7 @@ H5C_cork(H5C_t *cache_ptr, haddr_t obj_addr, unsigned action, hbool_t *corked) /* Set the corked status for the entire object */ tag_info->corked = FALSE; + cache_ptr->num_objs_corked--; /* Remove the tag info from the tag list, if there's no more entries with this tag */ if(0 == tag_info->entry_cnt) { @@ -8481,7 +8456,7 @@ H5C__serialize_single_entry(H5F_t *f, H5C_t *cache_ptr, H5C_cache_entry_t *entry if(NULL == (entry_ptr->image_ptr = H5MM_malloc(entry_ptr->size + H5C_IMAGE_EXTRA_SPACE)) ) HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + image_size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + image_size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ } /* end if */ @@ -8598,7 +8573,7 @@ H5C__generate_image(H5F_t *f, H5C_t *cache_ptr, H5C_cache_entry_t *entry_ptr) if(NULL == (entry_ptr->image_ptr = H5MM_realloc(entry_ptr->image_ptr, new_len + H5C_IMAGE_EXTRA_SPACE))) HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)entry_ptr->image_ptr) + new_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(((uint8_t *)entry_ptr->image_ptr) + new_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ /* Update statistics for resizing the entry */ @@ -53,7 +53,7 @@ * each thread individually. The association of contexts to threads will * be handled by the pthread library. * - * In order for this macro to work, H5E__get_my_stack() must be preceeded + * In order for this macro to work, H5CX_get_my_context() must be preceeded * by "H5CX_node_t *ctx =". */ #define H5CX_get_my_context() H5CX__get_context() @@ -64,17 +64,22 @@ #define H5CX_get_my_context() (&H5CX_head_g) #endif /* H5_HAVE_THREADSAFE */ +/* Common macro for the retrieving the pointer to a property list */ +#define H5CX_RETRIEVE_PLIST(PL, FAILVAL) \ + /* Check if the property list is already available */ \ + if(NULL == (*head)->ctx.PL) \ + /* Get the property list pointer */ \ + if(NULL == ((*head)->ctx.PL = (H5P_genplist_t *)H5I_object((*head)->ctx.H5_GLUE(PL,_id)))) \ + HGOTO_ERROR(H5E_CONTEXT, H5E_BADTYPE, (FAILVAL), "can't get property list") + /* Common macro for the duplicated code to retrieve properties from a property list */ #define H5CX_RETRIEVE_PROP_COMMON(PL, DEF_PL, PROP_NAME, PROP_FIELD) \ /* Check for default property list */ \ if((*head)->ctx.H5_GLUE(PL,_id) == (DEF_PL)) \ - HDmemcpy(&(*head)->ctx.PROP_FIELD, &H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD, sizeof(H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD)); \ + H5MM_memcpy(&(*head)->ctx.PROP_FIELD, &H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD, sizeof(H5_GLUE3(H5CX_def_,PL,_cache).PROP_FIELD)); \ else { \ - /* Check if the property list is already available */ \ - if(NULL == (*head)->ctx.PL) \ - /* Get the dataset transfer property list pointer */ \ - if(NULL == ((*head)->ctx.PL = (H5P_genplist_t *)H5I_object((*head)->ctx.H5_GLUE(PL,_id)))) \ - HGOTO_ERROR(H5E_CONTEXT, H5E_BADTYPE, FAIL, "can't get default dataset transfer property list") \ + /* Retrieve the property list */ \ + H5CX_RETRIEVE_PLIST(PL, FAIL) \ \ /* Get the property */ \ if(H5P_get((*head)->ctx.PL, (PROP_NAME), &(*head)->ctx.PROP_FIELD) < 0) \ @@ -108,11 +113,8 @@ \ /* Check if property exists in DXPL */ \ if(!(*head)->ctx.H5_GLUE(PROP_FIELD,_set)) { \ - /* Check if the property list is already available */ \ - if(NULL == (*head)->ctx.dxpl) \ - /* Get the dataset transfer property list pointer */ \ - if(NULL == ((*head)->ctx.dxpl = (H5P_genplist_t *)H5I_object((*head)->ctx.dxpl_id))) \ - HGOTO_ERROR(H5E_CONTEXT, H5E_BADTYPE, FAIL, "can't get default dataset transfer property list") \ + /* Retrieve the dataset transfer property list */ \ + H5CX_RETRIEVE_PLIST(dxpl, FAIL) \ \ if((check_prop = H5P_exist_plist((*head)->ctx.dxpl, PROP_NAME)) < 0) \ HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "error checking for property") \ @@ -129,15 +131,12 @@ /* Macro for the duplicated code to test and set properties for a property list */ #define H5CX_SET_PROP(PROP_NAME, PROP_FIELD) \ if((*head)->ctx.H5_GLUE(PROP_FIELD,_set)) { \ - /* Check if the property list is already available */ \ - if(NULL == (*head)->ctx.dxpl) \ - /* Get the dataset transfer property list pointer */ \ - if(NULL == ((*head)->ctx.dxpl = (H5P_genplist_t *)H5I_object((*head)->ctx.dxpl_id))) \ - HGOTO_ERROR(H5E_CONTEXT, H5E_BADTYPE, NULL, "can't get default dataset transfer property list") \ + /* Retrieve the dataset transfer property list */ \ + H5CX_RETRIEVE_PLIST(dxpl, NULL) \ \ - /* Set the chunk filter mask property */ \ + /* Set the property */ \ if(H5P_set((*head)->ctx.dxpl, PROP_NAME, &(*head)->ctx.PROP_FIELD) < 0) \ - HGOTO_ERROR(H5E_CONTEXT, H5E_CANTSET, NULL, "error setting filter mask xfer property") \ + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTSET, NULL, "error setting data xfer property") \ } /* end if */ #endif /* H5_HAVE_PARALLEL */ @@ -175,7 +174,7 @@ * corresponding property in the property list to be set when the API * context is popped, when returning from the API routine. Note that the * naming of these fields, <foo> and <foo>_set, is important for the -* H5CX_TEST_SET_PROP and H5CX_SET_PROP macros to work properly. + * H5CX_TEST_SET_PROP and H5CX_SET_PROP macros to work properly. */ typedef struct H5CX_t { /* DXPL */ @@ -186,6 +185,10 @@ typedef struct H5CX_t { hid_t lapl_id; /* LAPL ID for API operation */ H5P_genplist_t *lapl; /* Link Access Property List */ + /* DCPL */ + hid_t dcpl_id; /* DCPL ID for API operation */ + H5P_genplist_t *dcpl; /* Dataset Creation Property List */ + /* Internal: Object tagging info */ haddr_t tag; /* Current object's tag (ohdr chunk #0 address) */ @@ -271,6 +274,10 @@ typedef struct H5CX_t { size_t nlinks; /* Number of soft / UD links to traverse (H5L_ACS_NLINKS_NAME) */ hbool_t nlinks_valid; /* Whether number of soft / UD links to traverse is valid */ + /* Cached DCPL properties */ + hbool_t do_min_dset_ohdr; /* Whether to minimize dataset object header */ + hbool_t do_min_dset_ohdr_valid; /* Whether minimize dataset object header flag is valid */ + /* Cached VOL settings */ H5VL_connector_prop_t vol_connector_prop; /* Property for VOL connector ID & info */ hbool_t vol_connector_prop_valid; /* Whether property for VOL connector ID & info is valid */ @@ -325,6 +332,12 @@ typedef struct H5CX_lapl_cache_t { size_t nlinks; /* Number of soft / UD links to traverse (H5L_ACS_NLINKS_NAME) */ } H5CX_lapl_cache_t; +/* Typedef for cached default dataset creation property list information */ +/* (Same as the cached DXPL struct, above, except for the default DCPL) */ +typedef struct H5CX_dcpl_cache_t { + hbool_t do_min_dset_ohdr; /* Whether to minimize dataset object header */ +} H5CX_dcpl_cache_t; + /********************/ /* Local Prototypes */ @@ -358,9 +371,15 @@ static H5CX_dxpl_cache_t H5CX_def_dxpl_cache; /* Define a "default" link access property list cache structure to use for default LAPLs */ static H5CX_lapl_cache_t H5CX_def_lapl_cache; +/* Define a "default" dataset creation property list cache structure to use for default DCPLs */ +static H5CX_dcpl_cache_t H5CX_def_dcpl_cache; + /* Declare a static free list to manage H5CX_node_t structs */ H5FL_DEFINE_STATIC(H5CX_node_t); +/* Declare a static free list to manage H5CX_state_t structs */ +H5FL_DEFINE_STATIC(H5CX_state_t); + /*-------------------------------------------------------------------------- @@ -378,6 +397,7 @@ H5CX__init_package(void) { H5P_genplist_t *dx_plist; /* Data transfer property list */ H5P_genplist_t *la_plist; /* Link access property list */ + H5P_genplist_t *dc_plist; /* Dataset creation property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -477,6 +497,20 @@ H5CX__init_package(void) if(H5P_get(la_plist, H5L_ACS_NLINKS_NAME, &H5CX_def_lapl_cache.nlinks) < 0) HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve number of soft / UD links to traverse") + + /* Reset the "default DCPL cache" information */ + HDmemset(&H5CX_def_dcpl_cache, 0, sizeof(H5CX_dcpl_cache_t)); + + /* Get the default DCPL cache information */ + + /* Get the default dataset creation property list */ + if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(H5P_DATASET_CREATE_DEFAULT))) + HGOTO_ERROR(H5E_CONTEXT, H5E_BADTYPE, FAIL, "not a dataset create property list") + + /* Get flag to indicate whether to minimize dataset object header */ + if(H5P_get(dc_plist, H5D_CRT_MIN_DSET_HDR_SIZE_NAME, &H5CX_def_dcpl_cache.do_min_dset_ohdr) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve dataset minimize flag") + done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5CX__init_package() */ @@ -677,6 +711,226 @@ H5CX_push_special(void) /*------------------------------------------------------------------------- + * Function: H5CX_retrieve_state + * + * Purpose: Retrieve the state of an API context, for later resumption. + * + * Note: This routine _only_ tracks the state of API context information + * set before the VOL callback is invoked, not values that are + * set internal to the library. It's main purpose is to provide + * API context state to VOL connectors. + * + * Return: Non-negative on success / Negative on failure + * + * Programmer: Quincey Koziol + * January 8, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5CX_retrieve_state(H5CX_state_t **api_state) +{ + H5CX_node_t **head = H5CX_get_my_context(); /* Get the pointer to the head of the API context, for this thread */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Sanity check */ + HDassert(head && *head); + HDassert(api_state); + + /* Allocate & clear API context state */ + if(NULL == (*api_state = H5FL_CALLOC(H5CX_state_t))) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTALLOC, FAIL, "unable to allocate new API context state") + + /* Check for non-default DXPL */ + if(H5P_DATASET_XFER_DEFAULT != (*head)->ctx.dxpl_id) { + /* Retrieve the DXPL property list */ + H5CX_RETRIEVE_PLIST(dxpl, FAIL) + + /* Copy the DXPL ID */ + if(((*api_state)->dxpl_id = H5P_copy_plist((H5P_genplist_t *)(*head)->ctx.dxpl, FALSE)) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTCOPY, FAIL, "can't copy property list") + } /* end if */ + else + (*api_state)->dxpl_id = H5P_DATASET_XFER_DEFAULT; + + /* Check for non-default LAPL */ + if(H5P_LINK_ACCESS_DEFAULT != (*head)->ctx.lapl_id) { + /* Retrieve the LAPL property list */ + H5CX_RETRIEVE_PLIST(lapl, FAIL) + + /* Copy the LAPL ID */ + if(((*api_state)->lapl_id = H5P_copy_plist((H5P_genplist_t *)(*head)->ctx.lapl, FALSE)) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTCOPY, FAIL, "can't copy property list") + } /* end if */ + else + (*api_state)->lapl_id = H5P_LINK_ACCESS_DEFAULT; + + /* Keep a reference to the current VOL wrapping context */ + (*api_state)->vol_wrap_ctx = (*head)->ctx.vol_wrap_ctx; + if(NULL != (*api_state)->vol_wrap_ctx) + if(H5VL_inc_vol_wrapper((*api_state)->vol_wrap_ctx) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTINC, FAIL, "can't increment refcount on VOL wrapping context") + + /* Keep a copy of the VOL connector property, if there is one */ + if((*head)->ctx.vol_connector_prop_valid && (*head)->ctx.vol_connector_prop.connector_id > 0) { + /* Get the connector property */ + H5MM_memcpy(&(*api_state)->vol_connector_prop, &(*head)->ctx.vol_connector_prop, sizeof(H5VL_connector_prop_t)); + + /* Check for actual VOL connector property */ + if((*api_state)->vol_connector_prop.connector_id) { + /* Copy connector info, if it exists */ + if((*api_state)->vol_connector_prop.connector_info) { + H5VL_class_t *connector; /* Pointer to connector */ + void *new_connector_info = NULL; /* Copy of connector info */ + + /* Retrieve the connector for the ID */ + if(NULL == (connector = (H5VL_class_t *)H5I_object((*api_state)->vol_connector_prop.connector_id))) + HGOTO_ERROR(H5E_CONTEXT, H5E_BADTYPE, FAIL, "not a VOL connector ID") + + /* Allocate and copy connector info */ + if(H5VL_copy_connector_info(connector, &new_connector_info, (*api_state)->vol_connector_prop.connector_info) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTCOPY, FAIL, "connector info copy failed") + (*api_state)->vol_connector_prop.connector_info = new_connector_info; + } /* end if */ + + /* Increment the refcount on the connector ID */ + if(H5I_inc_ref((*api_state)->vol_connector_prop.connector_id, FALSE) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTINC, FAIL, "incrementing VOL connector ID failed") + } /* end if */ + } /* end if */ + +#ifdef H5_HAVE_PARALLEL + /* Save parallel I/O settings */ + (*api_state)->coll_metadata_read = (*head)->ctx.coll_metadata_read; +#endif /* H5_HAVE_PARALLEL */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5CX_retrieve_state() */ + + +/*------------------------------------------------------------------------- + * Function: H5CX_restore_state + * + * Purpose: Restore an API context, from a previously retrieved state. + * + * Note: This routine _only_ resets the state of API context information + * set before the VOL callback is invoked, not values that are + * set internal to the library. It's main purpose is to restore + * API context state from VOL connectors. + * + * Return: Non-negative on success / Negative on failure + * + * Programmer: Quincey Koziol + * January 9, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5CX_restore_state(const H5CX_state_t *api_state) +{ + H5CX_node_t **head = H5CX_get_my_context(); /* Get the pointer to the head of the API context, for this thread */ + + FUNC_ENTER_NOAPI_NOINIT_NOERR + + /* Sanity check */ + HDassert(head && *head); + HDassert(api_state); + + /* Restore the DXPL info */ + (*head)->ctx.dxpl_id = api_state->dxpl_id; + (*head)->ctx.dxpl = NULL; + + /* Restore the LAPL info */ + (*head)->ctx.lapl_id = api_state->lapl_id; + (*head)->ctx.lapl = NULL; + + /* Restore the VOL wrapper context */ + (*head)->ctx.vol_wrap_ctx = api_state->vol_wrap_ctx; + + /* Restore the VOL connector info */ + if(api_state->vol_connector_prop.connector_id) { + H5MM_memcpy(&(*head)->ctx.vol_connector_prop, &api_state->vol_connector_prop, sizeof(H5VL_connector_prop_t)); + (*head)->ctx.vol_connector_prop_valid = TRUE; + } /* end if */ + +#ifdef H5_HAVE_PARALLEL + /* Restore parallel I/O settings */ + (*head)->ctx.coll_metadata_read = api_state->coll_metadata_read; +#endif /* H5_HAVE_PARALLEL */ + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5CX_restore_state() */ + + +/*------------------------------------------------------------------------- + * Function: H5CX_free_state + * + * Purpose: Free a previously retrievedAPI context state + * + * Return: Non-negative on success / Negative on failure + * + * Programmer: Quincey Koziol + * January 9, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5CX_free_state(H5CX_state_t *api_state) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Sanity check */ + HDassert(api_state); + + /* Release the DXPL */ + if(api_state->dxpl_id != H5P_DATASET_XFER_DEFAULT) + if(H5I_dec_ref(api_state->dxpl_id) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTDEC, FAIL, "can't decrement refcount on DXPL") + + /* Release the LAPL */ + if(api_state->lapl_id != H5P_LINK_ACCESS_DEFAULT) + if(H5I_dec_ref(api_state->lapl_id) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTDEC, FAIL, "can't decrement refcount on LAPL") + + /* Release the VOL wrapper context */ + if(api_state->vol_wrap_ctx) + if(H5VL_dec_vol_wrapper(api_state->vol_wrap_ctx) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTDEC, FAIL, "can't decrement refcount on VOL wrapping context") + + /* Release the VOL connector property, if it was set */ + if(api_state->vol_connector_prop.connector_id) { + /* Clean up any VOL connector info */ + if(api_state->vol_connector_prop.connector_info) { + H5VL_class_t *connector; /* Pointer to connector */ + + /* Retrieve the connector for the ID */ + if(NULL == (connector = (H5VL_class_t *)H5I_object(api_state->vol_connector_prop.connector_id))) + HGOTO_ERROR(H5E_CONTEXT, H5E_BADTYPE, FAIL, "not a VOL connector ID") + + /* Free the connector info */ + if(H5VL_free_connector_info(connector, api_state->vol_connector_prop.connector_info) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTRELEASE, FAIL, "unable to release VOL connector info object") + } /* end if */ + + /* Decrement connector ID */ + if(H5I_dec_ref(api_state->vol_connector_prop.connector_id) < 0) + HDONE_ERROR(H5E_CONTEXT, H5E_CANTDEC, FAIL, "can't close VOL connector ID") + } /* end if */ + + /* Free the state */ + api_state = H5FL_FREE(H5CX_state_t, api_state); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5CX_free_state() */ + + +/*------------------------------------------------------------------------- * Function: H5CX_is_def_dxpl * * Purpose: Checks if the API context is using the library's default DXPL @@ -732,6 +986,35 @@ H5CX_set_dxpl(hid_t dxpl_id) /*------------------------------------------------------------------------- + * Function: H5CX_set_dcpl + * + * Purpose: Sets the DCPL for the current API call context. + * + * Return: <none> + * + * Programmer: Quincey Koziol + * March 6, 2019 + * + *------------------------------------------------------------------------- + */ +void +H5CX_set_dcpl(hid_t dcpl_id) +{ + H5CX_node_t **head = H5CX_get_my_context(); /* Get the pointer to the head of the API context, for this thread */ + + FUNC_ENTER_NOAPI_NOINIT_NOERR + + /* Sanity check */ + HDassert(*head); + + /* Set the API context's DCPL to a new value */ + (*head)->ctx.dcpl_id = dcpl_id; + + FUNC_LEAVE_NOAPI_VOID +} /* end H5CX_set_dcpl() */ + + +/*------------------------------------------------------------------------- * Function: H5CX_set_lapl * * Purpose: Sets the LAPL for the current API call context. @@ -815,8 +1098,8 @@ H5CX_set_apl(hid_t *acspl_id, const H5P_libclass_t *libclass, #ifdef H5_HAVE_PARALLEL /* If this routine is not guaranteed to be collective (i.e. it doesn't - * modify the structural metadata in a file), check if we should use - * a collective metadata read. + * modify the structural metadata in a file), check if the application + * specified a collective metadata read for just this operation. */ if(!is_collective) { H5P_genplist_t *plist; /* Property list pointer */ @@ -890,6 +1173,7 @@ H5CX_set_loc(hid_t #endif /* H5_HAVE_PARALLEL */ loc_id) { +#ifdef H5_HAVE_PARALLEL H5CX_node_t **head = H5CX_get_my_context(); /* Get the pointer to the head of the API context, for this thread */ herr_t ret_value = SUCCEED; /* Return value */ @@ -898,7 +1182,6 @@ H5CX_set_loc(hid_t /* Sanity check */ HDassert(head && *head); -#ifdef H5_HAVE_PARALLEL /* Set collective metadata read flag */ (*head)->ctx.coll_metadata_read = TRUE; @@ -919,10 +1202,14 @@ H5CX_set_loc(hid_t if(mpi_comm != MPI_COMM_NULL) MPI_Barrier(mpi_comm); } /* end if */ -#endif /* H5_HAVE_PARALLEL */ done: FUNC_LEAVE_NOAPI(ret_value) +#else /* H5_HAVE_PARALLEL */ + FUNC_ENTER_NOAPI_NOINIT_NOERR + + FUNC_LEAVE_NOAPI(SUCCEED) +#endif /* H5_HAVE_PARALLEL */ } /* end H5CX_set_loc() */ @@ -984,7 +1271,7 @@ H5CX_set_vol_connector_prop(const H5VL_connector_prop_t *vol_connector_prop) HDassert(head && *head); /* Set the API context value */ - HDmemcpy(&(*head)->ctx.vol_connector_prop, vol_connector_prop, sizeof(H5VL_connector_prop_t)); + H5MM_memcpy(&(*head)->ctx.vol_connector_prop, vol_connector_prop, sizeof(H5VL_connector_prop_t)); /* Mark the value as valid */ (*head)->ctx.vol_connector_prop_valid = TRUE; @@ -1109,7 +1396,7 @@ H5CX_get_vol_connector_prop(H5VL_connector_prop_t *vol_connector_prop) /* Check for value that was set */ if((*head)->ctx.vol_connector_prop_valid) /* Get the value */ - HDmemcpy(vol_connector_prop, &(*head)->ctx.vol_connector_prop, sizeof(H5VL_connector_prop_t)); + H5MM_memcpy(vol_connector_prop, &(*head)->ctx.vol_connector_prop, sizeof(H5VL_connector_prop_t)); else HDmemset(vol_connector_prop, 0, sizeof(H5VL_connector_prop_t)); @@ -1314,7 +1601,7 @@ H5CX_get_btree_split_ratios(double split_ratio[3]) H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_BTREE_SPLIT_RATIO_NAME, btree_split_ratio) /* Get the B-tree split ratio values */ - HDmemcpy(split_ratio, &(*head)->ctx.btree_split_ratio, sizeof((*head)->ctx.btree_split_ratio)); + H5MM_memcpy(split_ratio, &(*head)->ctx.btree_split_ratio, sizeof((*head)->ctx.btree_split_ratio)); done: FUNC_LEAVE_NOAPI(ret_value) @@ -2001,6 +2288,42 @@ done: /*------------------------------------------------------------------------- + * Function: H5CX_get_dset_min_ohdr_flag + * + * Purpose: Retrieves the flag that indicates whether the dataset object + * header should be minimized + * + * Return: Non-negative on success / Negative on failure + * + * Programmer: Quincey Koziol + * March 6, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5CX_get_dset_min_ohdr_flag(hbool_t *dset_min_ohdr_flag) +{ + H5CX_node_t **head = H5CX_get_my_context(); /* Get the pointer to the head of the API context, for this thread */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Sanity check */ + HDassert(dset_min_ohdr_flag); + HDassert(head && *head); + HDassert(H5P_DEFAULT != (*head)->ctx.dcpl_id); + + H5CX_RETRIEVE_PROP_VALID(dcpl, H5P_DATASET_CREATE_DEFAULT, H5D_CRT_MIN_DSET_HDR_SIZE_NAME, do_min_dset_ohdr) + + /* Get the value */ + *dset_min_ohdr_flag = (*head)->ctx.do_min_dset_ohdr; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5CX_get_dset_min_ohdr_flag() */ + + +/*------------------------------------------------------------------------- * Function: H5CX_set_tag * * Purpose: Sets the object tag for the current API call context. diff --git a/src/H5CXprivate.h b/src/H5CXprivate.h index 46d25d0..80f1ac4 100644 --- a/src/H5CXprivate.h +++ b/src/H5CXprivate.h @@ -39,6 +39,19 @@ /* Library Private Typedefs */ /****************************/ +/* API context state */ +typedef struct H5CX_state_t { + hid_t dxpl_id; /* DXPL for operation */ + hid_t lapl_id; /* LAPL for operation */ + void *vol_wrap_ctx; /* VOL connector's "wrap context" for creating IDs */ + H5VL_connector_prop_t vol_connector_prop; /* VOL connector property */ + +#ifdef H5_HAVE_PARALLEL + /* Internal: Parallel I/O settings */ + hbool_t coll_metadata_read; /* Whether to use collective I/O for metadata read */ +#endif /* H5_HAVE_PARALLEL */ +} H5CX_state_t; + /*****************************/ /* Library-private Variables */ @@ -57,9 +70,15 @@ H5_DLL herr_t H5CX_pop(void); H5_DLL void H5CX_push_special(void); H5_DLL hbool_t H5CX_is_def_dxpl(void); +/* API context state routines */ +H5_DLL herr_t H5CX_retrieve_state(H5CX_state_t **api_state); +H5_DLL herr_t H5CX_restore_state(const H5CX_state_t *api_state); +H5_DLL herr_t H5CX_free_state(H5CX_state_t *api_state); + /* "Setter" routines for API context info */ H5_DLL void H5CX_set_dxpl(hid_t dxpl_id); H5_DLL void H5CX_set_lapl(hid_t lapl_id); +H5_DLL void H5CX_set_dcpl(hid_t dcpl_id); H5_DLL herr_t H5CX_set_apl(hid_t *acspl_id, const H5P_libclass_t *libclass, hid_t loc_id, hbool_t is_collective); H5_DLL herr_t H5CX_set_loc(hid_t loc_id); @@ -105,6 +124,9 @@ H5_DLL herr_t H5CX_get_dt_conv_cb(H5T_conv_cb_t *cb_struct); /* "Getter" routines for LAPL properties cached in API context */ H5_DLL herr_t H5CX_get_nlinks(size_t *nlinks); +/* "Getter" routines for DCPL properties cached in API context */ +H5_DLL herr_t H5CX_get_dset_min_ohdr_flag(hbool_t *dset_min_ohdr_flag); + /* "Setter" routines for API context info */ H5_DLL void H5CX_set_tag(haddr_t tag); H5_DLL void H5CX_set_ring(H5AC_ring_t ring); diff --git a/src/H5Cimage.c b/src/H5Cimage.c index bdab1a3..db44c7a 100644 --- a/src/H5Cimage.c +++ b/src/H5Cimage.c @@ -1065,9 +1065,9 @@ H5C__read_cache_image(H5F_t *f, H5C_t *cache_ptr) H5C__UPDATE_STATS_FOR_CACHE_IMAGE_READ(cache_ptr) #ifdef H5_HAVE_PARALLEL - if ( aux_ptr ) { + if ( aux_ptr ) { - /* Broadcast cache image */ + /* Broadcast cache image */ if ( MPI_SUCCESS != (mpi_result = MPI_Bcast(cache_ptr->image_buffer, (int)cache_ptr->image_len, MPI_BYTE, @@ -2020,11 +2020,11 @@ H5C__decode_cache_image_entry(const H5F_t *f, const H5C_t *cache_ptr, HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for on disk image buffer") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(((uint8_t *)image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ /* Copy the entry image from the cache image block */ - HDmemcpy(image_ptr, p, size); + H5MM_memcpy(image_ptr, p, size); p += size; /* Copy data into target */ @@ -2219,7 +2219,7 @@ H5C__encode_cache_image_header(const H5F_t *f, const H5C_t *cache_ptr, p = *buf; /* write signature */ - HDmemcpy(p, H5C__MDCI_BLOCK_SIGNATURE, (size_t)H5C__MDCI_BLOCK_SIGNATURE_LEN); + H5MM_memcpy(p, H5C__MDCI_BLOCK_SIGNATURE, (size_t)H5C__MDCI_BLOCK_SIGNATURE_LEN); p += H5C__MDCI_BLOCK_SIGNATURE_LEN; /* write version */ @@ -2355,7 +2355,7 @@ H5C__encode_cache_image_entry(H5F_t *f, H5C_t *cache_ptr, uint8_t **buf, H5F_addr_encode(f, &p, ie_ptr->fd_parent_addrs[u]); /* Copy entry image */ - HDmemcpy(p, ie_ptr->image_ptr, ie_ptr->size); + H5MM_memcpy(p, ie_ptr->image_ptr, ie_ptr->size); p += ie_ptr->size; /* Update buffer pointer */ @@ -3422,11 +3422,11 @@ H5C__reconstruct_cache_entry(const H5F_t *f, H5C_t *cache_ptr, if(NULL == (pf_entry_ptr->image_ptr = H5MM_malloc(pf_entry_ptr->size + H5C_IMAGE_EXTRA_SPACE))) HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "memory allocation failed for on disk image buffer") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)pf_entry_ptr->image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + H5MM_memcpy(((uint8_t *)pf_entry_ptr->image_ptr) + size, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ /* Copy the entry image from the cache image block */ - HDmemcpy(pf_entry_ptr->image_ptr, p, pf_entry_ptr->size); + H5MM_memcpy(pf_entry_ptr->image_ptr, p, pf_entry_ptr->size); p += pf_entry_ptr->size; /* Initialize the rest of the fields in the prefetched entry */ diff --git a/src/H5Clog.c b/src/H5Clog.c index 0ae7f13..cf9b7e8 100644 --- a/src/H5Clog.c +++ b/src/H5Clog.c @@ -887,7 +887,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, +H5C_log_write_unprotect_entry_msg(H5C_t *cache, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value) { herr_t ret_value = SUCCEED; @@ -898,9 +898,8 @@ H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, HDassert(cache); /* Write a log message */ - HDassert(entry); if(cache->log_info->cls->write_unprotect_entry_log_msg) - if(cache->log_info->cls->write_unprotect_entry_log_msg(cache->log_info->udata, entry, type_id, flags, fxn_ret_value) < 0) + if(cache->log_info->cls->write_unprotect_entry_log_msg(cache->log_info->udata, address, type_id, flags, fxn_ret_value) < 0) HGOTO_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "log-specific unprotect entry call failed") done: diff --git a/src/H5Clog.h b/src/H5Clog.h index 9ba6786..0235c4a 100644 --- a/src/H5Clog.h +++ b/src/H5Clog.h @@ -59,7 +59,7 @@ typedef struct H5C_log_class_t { herr_t (*write_resize_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); herr_t (*write_unpin_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); herr_t (*write_destroy_fd_log_msg)(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); - herr_t (*write_unprotect_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); + herr_t (*write_unprotect_entry_log_msg)(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); herr_t (*write_set_cache_config_log_msg)(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value); herr_t (*write_remove_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); @@ -102,7 +102,7 @@ H5_DLL herr_t H5C_log_write_protect_entry_msg(H5C_t *cache, const H5C_cache_entr H5_DLL herr_t H5C_log_write_resize_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_unpin_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_destroy_fd_msg(H5C_t *cache, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); -H5_DLL herr_t H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); +H5_DLL herr_t H5C_log_write_unprotect_entry_msg(H5C_t *cache, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_set_cache_config_msg(H5C_t *cache, const H5AC_cache_config_t *config, herr_t fxn_ret_value); H5_DLL herr_t H5C_log_write_remove_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); diff --git a/src/H5Clog_json.c b/src/H5Clog_json.c index ccfa222..dd9e9b2 100644 --- a/src/H5Clog_json.c +++ b/src/H5Clog_json.c @@ -41,7 +41,7 @@ /****************/ /* Max log message size */ -#define H5C_MAX_JSON_LOG_MSG_SIZE 128 +#define H5C_MAX_JSON_LOG_MSG_SIZE 1024 /******************/ @@ -87,7 +87,7 @@ static herr_t H5C__json_write_protect_entry_log_msg(void *udata, const H5C_cache static herr_t H5C__json_write_resize_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); static herr_t H5C__json_write_unpin_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); static herr_t H5C__json_write_destroy_fd_log_msg(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); -static herr_t H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); +static herr_t H5C__json_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); static herr_t H5C__json_write_set_cache_config_log_msg(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value); static herr_t H5C__json_write_remove_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); @@ -1232,7 +1232,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, +H5C__json_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value) { H5C_log_json_udata_t *json_udata = (H5C_log_json_udata_t *)(udata); @@ -1243,7 +1243,6 @@ H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *en /* Sanity checks */ HDassert(json_udata); HDassert(json_udata->message); - HDassert(entry); /* Create the log message string */ HDsnprintf(json_udata->message, H5C_MAX_JSON_LOG_MSG_SIZE, @@ -1257,7 +1256,7 @@ H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *en \"returned\":%d\ },\n\ " - , (long long)HDtime(NULL), (unsigned long)entry->addr, + , (long long)HDtime(NULL), (unsigned long)address, type_id, flags, (int)fxn_ret_value); /* Write the log message to the file */ diff --git a/src/H5Clog_trace.c b/src/H5Clog_trace.c index f7d6889..7c1305c 100644 --- a/src/H5Clog_trace.c +++ b/src/H5Clog_trace.c @@ -82,7 +82,7 @@ static herr_t H5C__trace_write_protect_entry_log_msg(void *udata, const H5C_cach static herr_t H5C__trace_write_resize_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value); static herr_t H5C__trace_write_unpin_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); static herr_t H5C__trace_write_destroy_fd_log_msg(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value); -static herr_t H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value); +static herr_t H5C__trace_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value); static herr_t H5C__trace_write_set_cache_config_log_msg(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value); static herr_t H5C__trace_write_remove_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value); @@ -872,7 +872,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, +H5C__trace_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value) { H5C_log_trace_udata_t *trace_udata = (H5C_log_trace_udata_t *)(udata); @@ -883,11 +883,10 @@ H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *e /* Sanity checks */ HDassert(trace_udata); HDassert(trace_udata->message); - HDassert(entry); /* Create the log message string */ HDsnprintf(trace_udata->message, H5C_MAX_TRACE_LOG_MSG_SIZE, "H5AC_unprotect 0x%lx %d 0x%x %d\n", - (unsigned long)(entry->addr), type_id, flags, (int)fxn_ret_value); + (unsigned long)(address), type_id, flags, (int)fxn_ret_value); /* Write the log message to the file */ if(H5C__trace_write_log_message(trace_udata) < 0) diff --git a/src/H5Cmpio.c b/src/H5Cmpio.c index ecaed62..84ec16c 100644 --- a/src/H5Cmpio.c +++ b/src/H5Cmpio.c @@ -214,10 +214,10 @@ H5C_apply_candidate_list(H5F_t * f, HDmemset(tbl_buf, 0, sizeof(tbl_buf)); - sprintf(&(tbl_buf[0]), "candidate list = "); + HDsprintf(&(tbl_buf[0]), "candidate list = "); for(u = 0; u < num_candidates; u++) - sprintf(&(tbl_buf[HDstrlen(tbl_buf)]), " 0x%llx", (long long)(*(candidates_list_ptr + u))); - sprintf(&(tbl_buf[HDstrlen(tbl_buf)]), "\n"); + HDsprintf(&(tbl_buf[HDstrlen(tbl_buf)]), " 0x%llx", (long long)(*(candidates_list_ptr + u))); + HDsprintf(&(tbl_buf[HDstrlen(tbl_buf)]), "\n"); HDfprintf(stdout, "%s", tbl_buf); #endif /* H5C_APPLY_CANDIDATE_LIST__DEBUG */ @@ -280,10 +280,10 @@ H5C_apply_candidate_list(H5F_t * f, #if H5C_APPLY_CANDIDATE_LIST__DEBUG for ( i = 0; i < 1024; i++ ) tbl_buf[i] = '\0'; - sprintf(&(tbl_buf[0]), "candidate assignment table = "); + HDsprintf(&(tbl_buf[0]), "candidate assignment table = "); for(i = 0; i <= mpi_size; i++) - sprintf(&(tbl_buf[HDstrlen(tbl_buf)]), " %d", candidate_assignment_table[i]); - sprintf(&(tbl_buf[HDstrlen(tbl_buf)]), "\n"); + HDsprintf(&(tbl_buf[HDstrlen(tbl_buf)]), " %d", candidate_assignment_table[i]); + HDsprintf(&(tbl_buf[HDstrlen(tbl_buf)]), "\n"); HDfprintf(stdout, "%s", tbl_buf); HDfprintf(stdout, "%s:%d: flush entries [%u, %u].\n", diff --git a/src/H5Cpkg.h b/src/H5Cpkg.h index 9201afb..9156c0d 100644 --- a/src/H5Cpkg.h +++ b/src/H5Cpkg.h @@ -3823,6 +3823,13 @@ typedef struct H5C_tag_info_t { * * ignore_tags: Boolean flag to disable tag validation during entry insertion. * + * num_objs_corked: Unsigned integer field containing the number of objects + * that are "corked". The "corked" status of an object is + * found by searching the "tag_list". This field is added + * for optimization so that the skip list search on "tag_list" + * can be skipped if this field is zero, i.e. no "corked" + * objects. + * * When a cache entry is protected, it must be removed from the LRU * list(s) as it cannot be either flushed or evicted until it is unprotected. * The following fields are used to implement the protected list (pl). @@ -4693,6 +4700,7 @@ struct H5C_t { /* Fields for maintaining list of tagged entries */ H5SL_t * tag_list; hbool_t ignore_tags; + uint32_t num_objs_corked; /* Fields for tracking protected entries */ uint32_t pl_len; diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h index c39c1df..d4ed6fc 100644 --- a/src/H5Cprivate.h +++ b/src/H5Cprivate.h @@ -2301,6 +2301,7 @@ H5_DLL herr_t H5C_validate_resize_config(H5C_auto_size_ctl_t *config_ptr, unsigned int tests); H5_DLL herr_t H5C_ignore_tags(H5C_t *cache_ptr); H5_DLL hbool_t H5C_get_ignore_tags(const H5C_t *cache_ptr); +H5_DLL uint32_t H5C_get_num_objs_corked(const H5C_t *cache_ptr); H5_DLL herr_t H5C_retag_entries(H5C_t * cache_ptr, haddr_t src_tag, haddr_t dest_tag); H5_DLL herr_t H5C_cork(H5C_t *cache_ptr, haddr_t obj_addr, unsigned action, hbool_t *corked); H5_DLL herr_t H5C_get_entry_ring(const H5F_t *f, haddr_t addr, H5C_ring_t *ring); diff --git a/src/H5Ctag.c b/src/H5Ctag.c index 0f08ede..807e68d 100644 --- a/src/H5Ctag.c +++ b/src/H5Ctag.c @@ -175,6 +175,32 @@ H5C_get_ignore_tags(const H5C_t *cache_ptr) /*------------------------------------------------------------------------- * + * Function: H5C_get_num_objs_corked + * + * Purpose: Retrieve the 'num_objs_corked' field for the cache + * + * Return: 'num_objs_corked' value (can't fail) + * + * Programmer: Vailin Choi; Feb 2019 + * + *------------------------------------------------------------------------- + */ +uint32_t +H5C_get_num_objs_corked(const H5C_t *cache_ptr) +{ + FUNC_ENTER_NOAPI_NOERR + + /* Sanity checks */ + HDassert(cache_ptr); + HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC); + + /* Return value for num_objs_corked */ + FUNC_LEAVE_NOAPI(cache_ptr->num_objs_corked) +} /* H5C_get_num_objs_corked */ + + +/*------------------------------------------------------------------------- + * * Function: H5C__tag_entry * * Purpose: Tags an entry with the provided tag (contained in the API context). diff --git a/src/H5Dbtree.c b/src/H5Dbtree.c index b61aed4..c13c36a 100644 --- a/src/H5Dbtree.c +++ b/src/H5Dbtree.c @@ -39,6 +39,7 @@ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MFprivate.h" /* File space management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Sprivate.h" /* Dataspaces */ #include "H5VMprivate.h" /* Vector and array functions */ @@ -847,7 +848,7 @@ H5D__btree_shared_create(const H5F_t *f, H5O_storage_chunk_t *store, /* Set up the "local" information for this dataset's chunks */ if(NULL == (my_layout = H5FL_MALLOC(H5O_layout_chunk_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk layout") - HDmemcpy(my_layout, layout, sizeof(H5O_layout_chunk_t)); + H5MM_memcpy(my_layout, layout, sizeof(H5O_layout_chunk_t)); shared->udata = my_layout; /* Make shared B-tree info reference counted */ @@ -1087,7 +1088,7 @@ H5D__btree_idx_iterate_cb(H5F_t H5_ATTR_UNUSED *f, const void *_lt_key, HDcompile_assert(sizeof(chunk_rec.filter_mask) == sizeof(lt_key->filter_mask)); /* Compose generic chunk record for callback */ - HDmemcpy(&chunk_rec, lt_key, sizeof(*lt_key)); + H5MM_memcpy(&chunk_rec, lt_key, sizeof(*lt_key)); chunk_rec.chunk_addr = addr; /* Make "generic chunk" callback */ diff --git a/src/H5Dbtree2.c b/src/H5Dbtree2.c index b32f395..d25e0f0 100644 --- a/src/H5Dbtree2.c +++ b/src/H5Dbtree2.c @@ -32,6 +32,7 @@ #include "H5Dpkg.h" /* Datasets */ #include "H5FLprivate.h" /* Free Lists */ #include "H5MFprivate.h" /* File space management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vector and array functions */ @@ -248,7 +249,7 @@ H5D__bt2_crt_context(void *_udata) /* Set up the "local" information for this dataset's chunk dimension sizes */ if(NULL == (my_dim = (uint32_t *)H5FL_BLK_MALLOC(chunk_dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate chunk dims") - HDmemcpy(my_dim, udata->dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t)); + H5MM_memcpy(my_dim, udata->dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t)); ctx->dim = my_dim; /* diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index e165569..93b4427 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -313,6 +313,7 @@ const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{ H5D__chunk_construct, H5D__chunk_init, H5D__chunk_is_space_alloc, + H5D__chunk_is_data_cached, H5D__chunk_io_init, H5D__chunk_read, H5D__chunk_write, @@ -340,6 +341,7 @@ const H5D_layout_ops_t H5D_LOPS_NONEXISTENT[1] = {{ NULL, NULL, NULL, + NULL, #ifdef H5_HAVE_PARALLEL NULL, NULL, @@ -394,10 +396,13 @@ H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters, hsize_t *offset, FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) + /* Sanity checks */ + HDassert(layout->type == H5D_CHUNKED); + io_info.dset = dset; /* Allocate dataspace and initialize it if it hasn't been. */ - if(!(*layout->ops->is_space_alloc)(&layout->storage)) + if(!H5D__chunk_is_space_alloc(&layout->storage)) /* Allocate storage */ if(H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, FALSE, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") @@ -435,13 +440,17 @@ H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters, hsize_t *offset, if(0 == idx_info.pline->nused && H5F_addr_defined(old_chunk.offset)) /* If there are no filters and we are overwriting the chunk we can just set values */ need_insert = FALSE; - else + else { /* Otherwise, create the chunk it if it doesn't exist, or reallocate the chunk * if its size has changed. */ if(H5D__chunk_file_alloc(&idx_info, &old_chunk, &udata.chunk_block, &need_insert, scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") + /* Cache the new chunk information */ + H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata); + } /* end else */ + /* Make sure the address of the chunk is returned. */ if(!H5F_addr_defined(udata.chunk_block.offset)) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk address isn't defined") @@ -506,7 +515,8 @@ H5D__chunk_direct_read(const H5D_t *dset, hsize_t *offset, uint32_t* filters, *filters = 0; /* Allocate dataspace and initialize it if it hasn't been. */ - if(!(*layout->ops->is_space_alloc)(&layout->storage)) + if(!H5D__chunk_is_space_alloc(&layout->storage) + && !H5D__chunk_is_data_cached(dset->shared)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "storage is not initialized") /* Calculate the index of this chunk */ @@ -1019,6 +1029,30 @@ H5D__chunk_is_space_alloc(const H5O_storage_t *storage) /*------------------------------------------------------------------------- + * Function: H5D__chunk_is_data_cached + * + * Purpose: Query if raw data is cached for dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * Wednessday, March 6, 2016 + * + *------------------------------------------------------------------------- + */ +hbool_t +H5D__chunk_is_data_cached(const H5D_shared_t *shared_dset) +{ + FUNC_ENTER_PACKAGE_NOERR + + /* Sanity checks */ + HDassert(shared_dset); + + FUNC_LEAVE_NOAPI(shared_dset->cache.chunk.nused > 0) +} /* end H5D__chunk_is_data_cached() */ + + +/*------------------------------------------------------------------------- * Function: H5D__chunk_io_init * * Purpose: Performs initialization before any sort of I/O on the raw data @@ -1073,21 +1107,19 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf if((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to normalize selection") - /* Decide the number of chunks in each dimension*/ - for(u = 0; u < f_ndims; u++) { + /* Decide the number of chunks in each dimension */ + for(u = 0; u < f_ndims; u++) /* Keep the size of the chunk dimensions as hsize_t for various routines */ fm->chunk_dim[u] = fm->layout->u.chunk.dim[u]; - } /* end for */ #ifdef H5_HAVE_PARALLEL /* Calculate total chunk in file map*/ fm->select_chunk = NULL; if(io_info->using_mpi_vfd) { H5_CHECK_OVERFLOW(fm->layout->u.chunk.nchunks, hsize_t, size_t); - if(fm->layout->u.chunk.nchunks) { + if(fm->layout->u.chunk.nchunks) if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->layout->u.chunk.nchunks * sizeof(H5D_chunk_info_t *)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") - } } /* end if */ #endif /* H5_HAVE_PARALLEL */ @@ -1129,10 +1161,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf HDassert(fm->single_space); /* Allocate the single chunk information */ - if(NULL == dataset->shared->cache.chunk.single_chunk_info) { + if(NULL == dataset->shared->cache.chunk.single_chunk_info) if(NULL == (dataset->shared->cache.chunk.single_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") - } /* end if */ fm->single_chunk_info = dataset->shared->cache.chunk.single_chunk_info; HDassert(fm->single_chunk_info); @@ -1147,10 +1178,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf hbool_t sel_hyper_flag; /* Whether file selection is a hyperslab */ /* Initialize skip list for chunk selections */ - if(NULL == dataset->shared->cache.chunk.sel_chunks) { + if(NULL == dataset->shared->cache.chunk.sel_chunks) if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, NULL))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections") - } /* end if */ fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks; HDassert(fm->sel_chunks); @@ -1245,10 +1275,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf fm->mchunk_tmpl = tmp_mspace; /* Create temporary datatypes for selection iteration */ - if(!file_type) { + if(!file_type) if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype") - } /* end if */ /* Create selection iterator for memory selection */ if(0 == (elmt_size = H5T_get_size(mem_type))) @@ -1540,7 +1569,7 @@ done: /*------------------------------------------------------------------------- * Function: H5D__create_chunk_file_map_hyper * - * Purpose: Create all chunk selections in file. + * Purpose: Create all chunk selections in file, for a hyperslab selection. * * Return: Non-negative on success/Negative on failure * @@ -1556,8 +1585,8 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t #endif /* H5_HAVE_PARALLEL */ *io_info) { - hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ + hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ + hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ hsize_t sel_points; /* Number of elements in file selection */ hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */ hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ @@ -1572,7 +1601,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t FUNC_ENTER_STATIC /* Sanity check */ - HDassert(fm->f_ndims>0); + HDassert(fm->f_ndims > 0); /* Get number of elements selected in file */ sel_points = fm->nelmts; @@ -1596,7 +1625,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Iterate through each chunk in the dataset */ while(sel_points) { - /* Check for intersection of temporary chunk and file selection */ + /* Check for intersection of current chunk and file selection */ /* (Casting away const OK - QAK) */ if(TRUE == H5S_hyper_intersect_block((H5S_t *)fm->file_space, coords, end)) { H5S_t *tmp_fchunk; /* Temporary file dataspace */ @@ -1634,7 +1663,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Add temporary chunk to the list of chunks */ /* Allocate the file & memory chunk information */ - if (NULL==(new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) { + if(NULL == (new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") } /* end if */ @@ -1642,7 +1671,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Initialize the chunk information */ /* Set the chunk index */ - new_chunk_info->index=chunk_index; + new_chunk_info->index = chunk_index; #ifdef H5_HAVE_PARALLEL /* Store chunk selection information, for multi-chunk I/O */ @@ -1655,16 +1684,13 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t new_chunk_info->fspace_shared = FALSE; /* Set the memory chunk dataspace */ - new_chunk_info->mspace=NULL; + new_chunk_info->mspace = NULL; new_chunk_info->mspace_shared = FALSE; /* Copy the chunk's scaled coordinates */ - HDmemcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); + H5MM_memcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); new_chunk_info->scaled[fm->f_ndims] = 0; - /* Copy the chunk's scaled coordinates */ - HDmemcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); - /* Insert the new chunk into the skip list */ if(H5SL_insert(fm->sel_chunks, new_chunk_info, &new_chunk_info->index) < 0) { H5D__free_chunk_info(new_chunk_info, NULL, NULL); @@ -1688,12 +1714,11 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t chunk_index++; /* Set current increment dimension */ - curr_dim=(int)fm->f_ndims-1; + curr_dim = (int)fm->f_ndims - 1; /* Increment chunk location in fastest changing dimension */ - H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t); - coords[curr_dim]+=fm->chunk_dim[curr_dim]; - end[curr_dim]+=fm->chunk_dim[curr_dim]; + coords[curr_dim] += fm->chunk_dim[curr_dim]; + end[curr_dim] += fm->chunk_dim[curr_dim]; scaled[curr_dim]++; /* Bring chunk location back into bounds, if necessary */ @@ -1707,11 +1732,14 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Decrement current dimension */ curr_dim--; - /* Increment chunk location in current dimension */ - scaled[curr_dim]++; - coords[curr_dim] += fm->chunk_dim[curr_dim]; - end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1; - } while(coords[curr_dim] > sel_end[curr_dim]); + /* Check for valid current dim */ + if(curr_dim >= 0) { + /* Increment chunk location in current dimension */ + scaled[curr_dim]++; + coords[curr_dim] += fm->chunk_dim[curr_dim]; + end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1; + } /* end if */ + } while(curr_dim >= 0 && (coords[curr_dim] > sel_end[curr_dim])); /* Re-calculate the index of this chunk */ chunk_index = H5VM_array_offset_pre(fm->f_ndims, fm->layout->u.chunk.down_chunks, scaled); @@ -1743,12 +1771,12 @@ static herr_t H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) { H5SL_node_t *curr_node; /* Current node in skip list */ - hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */ - hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */ + hsize_t file_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ + hsize_t file_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ + hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ + hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ + hssize_t adjust[H5S_MAX_RANK]; /* Adjustment to make to all file chunks */ + hssize_t chunk_adjust[H5S_MAX_RANK]; /* Adjustment to make to a particular chunk */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ @@ -1762,7 +1790,7 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ /* Get the node */ - curr_node=H5SL_first(fm->sel_chunks); + curr_node = H5SL_first(fm->sel_chunks); /* Get pointer to chunk's information */ chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); @@ -1785,15 +1813,15 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") /* Calculate the adjustment for memory selection from file selection */ - HDassert(fm->m_ndims==fm->f_ndims); - for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(file_sel_start[u],hsize_t,hssize_t); - H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t); - adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u]; + HDassert(fm->m_ndims == fm->f_ndims); + for(u = 0; u < fm->f_ndims; u++) { + H5_CHECK_OVERFLOW(file_sel_start[u], hsize_t, hssize_t); + H5_CHECK_OVERFLOW(mem_sel_start[u], hsize_t, hssize_t); + adjust[u] = (hssize_t)file_sel_start[u] - (hssize_t)mem_sel_start[u]; } /* end for */ /* Iterate over each chunk in the chunk list */ - curr_node=H5SL_first(fm->sel_chunks); + curr_node = H5SL_first(fm->sel_chunks); while(curr_node) { H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ @@ -1832,7 +1860,7 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to adjust selection") /* Get the next chunk node in the skip list */ - curr_node=H5SL_next(curr_node); + curr_node = H5SL_next(curr_node); } /* end while */ } /* end else */ @@ -1920,9 +1948,9 @@ H5D__chunk_file_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, chunk_info->chunk_points = 0; /* Set the chunk's scaled coordinates */ - HDmemcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); + H5MM_memcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); chunk_info->scaled[fm->f_ndims] = 0; - HDmemcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); + H5MM_memcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); /* Insert the new chunk into the skip list */ if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) { @@ -1976,7 +2004,7 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u { H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */ H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ - hsize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ + hsize_t coords_in_mem[H5S_MAX_RANK]; /* Coordinates of element in memory */ hsize_t chunk_index; /* Chunk index */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2001,11 +2029,10 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, H5_ITER_ERROR, "can't locate chunk in skip list") /* Check if the chunk already has a memory space */ - if(NULL == chunk_info->mspace) { + if(NULL == chunk_info->mspace) /* Copy the template memory chunk dataspace */ if(NULL == (chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, H5_ITER_ERROR, "unable to copy file space") - } /* end else */ /* Update the "last chunk seen" information */ fm->last_index = chunk_index; @@ -2164,11 +2191,11 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, HDassert(fm); /* Set up "nonexistent" I/O info object */ - HDmemcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info)); + H5MM_memcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info)); nonexistent_io_info.layout_ops = *H5D_LOPS_NONEXISTENT; /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); + H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; @@ -2176,7 +2203,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t); /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); + H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); cpt_io_info.store = &cpt_store; cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; @@ -2314,7 +2341,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, HDassert(fm); /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); + H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; @@ -2322,7 +2349,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t); /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); + H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); cpt_io_info.store = &cpt_store; cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; @@ -2677,7 +2704,7 @@ H5D__chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *ud HDassert(udata->common.scaled); /* Stored the information to cache */ - HDmemcpy(last->scaled, udata->common.scaled, sizeof(hsize_t) * udata->common.layout->ndims); + H5MM_memcpy(last->scaled, udata->common.scaled, sizeof(hsize_t) * udata->common.layout->ndims); last->addr = udata->chunk_block.offset; H5_CHECKED_ASSIGN(last->nbytes, uint32_t, udata->chunk_block.length, hsize_t); last->chunk_idx = udata->chunk_idx; @@ -2914,9 +2941,6 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, /* Check for cached information */ if(!H5D__chunk_cinfo_cache_found(&dset->shared->cache.chunk.last, udata)) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ -#ifdef H5_HAVE_PARALLEL - H5P_coll_md_read_flag_t temp_cmr; /* Temp value to hold the coll metadata read setting */ -#endif /* H5_HAVE_PARALLEL */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; @@ -2925,25 +2949,18 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, idx_info.storage = &dset->shared->layout.storage.u.chunk; #ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) { - /* disable collective metadata read for chunk indexes - as it is highly unlikely that users would read the - same chunks from all processes. MSC - might turn on - for root node? */ - temp_cmr = H5F_COLL_MD_READ(idx_info.f); - H5F_set_coll_md_read(idx_info.f, H5P_FORCE_FALSE); - } /* end if */ + /* Disable collective metadata read for chunk indexes as it is + * highly unlikely that users would read the same chunks from all + * processes. + */ + if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) + H5CX_set_coll_metadata_read(FALSE); #endif /* H5_HAVE_PARALLEL */ /* Go get the chunk information */ if((dset->shared->layout.storage.u.chunk.ops->get_addr)(&idx_info, udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address") -#ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) - H5F_set_coll_md_read(idx_info.f, temp_cmr); -#endif /* H5_HAVE_PARALLEL */ - /* * Cache the information retrieved. * @@ -3056,7 +3073,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset) */ if(NULL == (buf = H5MM_malloc(alloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline") - HDmemcpy(buf, ent->chunk, alloc); + H5MM_memcpy(buf, ent->chunk, alloc); } /* end if */ else { /* @@ -3469,7 +3486,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, */ if(NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") - HDmemcpy(chunk, ent->chunk, chunk_size); + H5MM_memcpy(chunk, ent->chunk, chunk_size); ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline); ent->chunk = (uint8_t *)chunk; chunk = NULL; @@ -3495,7 +3512,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, */ if(NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") - HDmemcpy(chunk, ent->chunk, chunk_size); + H5MM_memcpy(chunk, ent->chunk, chunk_size); ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline); ent->chunk = (uint8_t *)chunk; @@ -3624,7 +3641,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, (void)H5D__chunk_mem_xfree(tmp_chunk, old_pline); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") } /* end if */ - HDmemcpy(chunk, tmp_chunk, chunk_size); + H5MM_memcpy(chunk, tmp_chunk, chunk_size); (void)H5D__chunk_mem_xfree(tmp_chunk, old_pline); } /* end if */ } /* end if */ @@ -3705,7 +3722,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, ent->chunk_block.offset = chunk_addr; ent->chunk_block.length = chunk_alloc; ent->chunk_idx = udata->chunk_idx; - HDmemcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); + H5MM_memcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); H5_CHECKED_ASSIGN(ent->rd_count, uint32_t, chunk_size, size_t); H5_CHECKED_ASSIGN(ent->wr_count, uint32_t, chunk_size, size_t); ent->chunk = (uint8_t *)chunk; @@ -3833,7 +3850,7 @@ H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, fake_ent.edge_chunk_state = H5D_RDCC_DISABLE_FILTERS; if(udata->new_unfilt_chunk) fake_ent.edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS; - HDmemcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); + H5MM_memcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); HDassert(layout->u.chunk.size > 0); fake_ent.chunk_idx = udata->chunk_idx; fake_ent.chunk_block.offset = udata->chunk_block.offset; @@ -4120,7 +4137,7 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_ if(has_unfilt_edge_chunks) { if(NULL == (unfilt_fill_buf = H5D__chunk_mem_alloc(orig_chunk_size, &def_pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") - HDmemcpy(unfilt_fill_buf, fb_info.fill_buf, orig_chunk_size); + H5MM_memcpy(unfilt_fill_buf, fb_info.fill_buf, orig_chunk_size); } /* end if */ /* Retrieve filter settings from API context */ @@ -5654,7 +5671,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) if(udata->chunk_in_cache && udata->chunk) { HDassert(!H5F_addr_defined(chunk_rec->chunk_addr)); - HDmemcpy(buf, udata->chunk, nbytes); + H5MM_memcpy(buf, udata->chunk, nbytes); udata->chunk = NULL; } else { @@ -5688,7 +5705,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) HDassert(H5F_addr_defined(ent->chunk_block.offset)); H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t); - HDmemcpy(buf, ent->chunk, nbytes); + H5MM_memcpy(buf, ent->chunk, nbytes); } else { /* read chunk data from the source file */ @@ -5722,7 +5739,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ - HDmemcpy(reclaim_buf, buf, reclaim_buf_size); + H5MM_memcpy(reclaim_buf, buf, reclaim_buf_size); /* Set background buffer to all zeros */ HDmemset(bkg, 0, buf_size); @@ -5753,7 +5770,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) } /* end if */ /* After fix ref, copy the new reference elements to the buffer to write out */ - HDmemcpy(buf, bkg, buf_size); + H5MM_memcpy(buf, bkg, buf_size); } /* end if */ /* Set up destination chunk callback information for insertion */ @@ -6053,7 +6070,7 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src, for(ent = shared_fo->cache.chunk.head; ent; ent = next) { if(!H5F_addr_defined(ent->chunk_block.offset)) { - HDmemcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled)); + H5MM_memcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled)); udata.chunk = ent->chunk; udata.chunk_in_cache = TRUE; if(H5D__chunk_copy_cb(&chunk_rec, &udata) < 0) @@ -6303,15 +6320,16 @@ H5D__chunk_stats(const H5D_t *dset, hbool_t headers) HGOTO_DONE(SUCCEED) if (headers) { - fprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n"); - fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n", + HDfprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n"); + HDfprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n", "Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes"); - fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n", + HDfprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n", "-----", "----", "------", "--------", "-----", "-------"); } #ifdef H5AC_DEBUG - if (H5DEBUG(AC)) headers = TRUE; + if (H5DEBUG(AC)) + headers = TRUE; #endif if (headers) { @@ -6322,12 +6340,12 @@ H5D__chunk_stats(const H5D_t *dset, hbool_t headers) miss_rate = 0.0; } if (miss_rate > 100) { - sprintf(ascii, "%7d%%", (int) (miss_rate + 0.5)); + HDsprintf(ascii, "%7d%%", (int) (miss_rate + 0.5)); } else { - sprintf(ascii, "%7.2f%%", miss_rate); + HDsprintf(ascii, "%7.2f%%", miss_rate); } - fprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", + HDfprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", "raw data chunks", rdcc->stats.nhits, rdcc->stats.nmisses, ascii, rdcc->stats.ninits, (long)(rdcc->stats.nflushes)-(long)(rdcc->stats.ninits)); } diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index c0c2a80..df61856 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -80,6 +80,7 @@ const H5D_layout_ops_t H5D_LOPS_COMPACT[1] = {{ H5D__compact_construct, NULL, H5D__compact_is_space_alloc, + NULL, H5D__compact_io_init, H5D__contig_read, H5D__contig_write, @@ -528,7 +529,7 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds if(NULL == (buf = H5FL_BLK_MALLOC(type_conv, buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - HDmemcpy(buf, storage_src->buf, storage_src->size); + H5MM_memcpy(buf, storage_src->buf, storage_src->size); /* allocate temporary bkg buff for data conversion */ if(NULL == (bkg = H5FL_BLK_MALLOC(type_conv, buf_size))) @@ -539,7 +540,7 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ - HDmemcpy(reclaim_buf, buf, buf_size); + H5MM_memcpy(reclaim_buf, buf, buf_size); /* Set background buffer to all zeros */ HDmemset(bkg, 0, buf_size); @@ -548,7 +549,7 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") - HDmemcpy(storage_dst->buf, buf, storage_dst->size); + H5MM_memcpy(storage_dst->buf, buf, storage_dst->size); if(H5D_vlen_reclaim(tid_mem, buf_space, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data") @@ -573,11 +574,11 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *_storage_src, H5F_t *f_ds } /* end if */ else /* Type conversion not necessary */ - HDmemcpy(storage_dst->buf, storage_src->buf, storage_src->size); + H5MM_memcpy(storage_dst->buf, storage_src->buf, storage_src->size); } /* end if */ else /* Type conversion not necessary */ - HDmemcpy(storage_dst->buf, storage_src->buf, storage_src->size); + H5MM_memcpy(storage_dst->buf, storage_src->buf, storage_src->size); /* Mark destination buffer as dirty */ storage_dst->dirty = TRUE; diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index ad12ba0..ed12a6a 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -40,6 +40,7 @@ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5FOprivate.h" /* File objects */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ @@ -118,6 +119,7 @@ const H5D_layout_ops_t H5D_LOPS_CONTIG[1] = {{ H5D__contig_construct, H5D__contig_init, H5D__contig_is_space_alloc, + H5D__contig_is_data_cached, H5D__contig_io_init, H5D__contig_read, H5D__contig_write, @@ -538,6 +540,30 @@ H5D__contig_is_space_alloc(const H5O_storage_t *storage) /*------------------------------------------------------------------------- + * Function: H5D__contig_is_data_cached + * + * Purpose: Query if raw data is cached for dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * Wednessday, March 6, 2016 + * + *------------------------------------------------------------------------- + */ +hbool_t +H5D__contig_is_data_cached(const H5D_shared_t *shared_dset) +{ + FUNC_ENTER_PACKAGE_NOERR + + /* Sanity checks */ + HDassert(shared_dset); + + FUNC_LEAVE_NOAPI(shared_dset->cache.contig.sieve_size > 0) +} /* end H5D__contig_is_data_cached() */ + + +/*------------------------------------------------------------------------- * Function: H5D__contig_io_init * * Purpose: Performs initialization before any sort of I/O on the raw data @@ -751,7 +777,7 @@ H5D__contig_readvv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(buf, dset_contig->sieve_buf, len); + H5MM_memcpy(buf, dset_contig->sieve_buf, len); /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; @@ -771,7 +797,7 @@ H5D__contig_readvv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, unsigned char *base_sieve_buf = dset_contig->sieve_buf + (addr - sieve_start); /* Grab the data out of the buffer */ - HDmemcpy(buf, base_sieve_buf, len); + H5MM_memcpy(buf, base_sieve_buf, len); } /* end if */ /* Entire request is not within this data sieve buffer */ else { @@ -835,7 +861,7 @@ H5D__contig_readvv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(buf, dset_contig->sieve_buf, len); + H5MM_memcpy(buf, dset_contig->sieve_buf, len); /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; @@ -1033,7 +1059,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, } /* end if */ /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(dset_contig->sieve_buf, buf, len); + H5MM_memcpy(dset_contig->sieve_buf, buf, len); /* Set sieve buffer dirty flag */ dset_contig->sieve_dirty = TRUE; @@ -1053,7 +1079,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, unsigned char *base_sieve_buf = dset_contig->sieve_buf + (addr - sieve_start); /* Put the data into the sieve buffer */ - HDmemcpy(base_sieve_buf, buf, len); + H5MM_memcpy(base_sieve_buf, buf, len); /* Set sieve buffer dirty flag */ dset_contig->sieve_dirty = TRUE; @@ -1096,7 +1122,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, HDmemmove(dset_contig->sieve_buf + len, dset_contig->sieve_buf, dset_contig->sieve_size); /* Copy in new information (must be first in sieve buffer) */ - HDmemcpy(dset_contig->sieve_buf, buf, len); + H5MM_memcpy(dset_contig->sieve_buf, buf, len); /* Adjust sieve location */ dset_contig->sieve_loc = addr; @@ -1105,7 +1131,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, /* Append to existing sieve buffer */ else { /* Copy in new information */ - HDmemcpy(dset_contig->sieve_buf + sieve_size, buf, len); + H5MM_memcpy(dset_contig->sieve_buf + sieve_size, buf, len); } /* end else */ /* Adjust sieve size */ @@ -1159,7 +1185,7 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, } /* end if */ /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(dset_contig->sieve_buf, buf, len); + H5MM_memcpy(dset_contig->sieve_buf, buf, len); /* Set sieve buffer dirty flag */ dset_contig->sieve_dirty = TRUE; @@ -1514,7 +1540,7 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, if(try_sieve && (addr_src >= sieve_start) && ((addr_src + src_nbytes -1) < sieve_end)) { unsigned char *base_sieve_buf = shared_fo->cache.contig.sieve_buf + (addr_src - sieve_start); - HDmemcpy(buf, base_sieve_buf, src_nbytes); + H5MM_memcpy(buf, base_sieve_buf, src_nbytes); } else /* Read raw data from source file */ if(H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, src_nbytes, buf) < 0) @@ -1527,7 +1553,7 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ - HDmemcpy(reclaim_buf, buf, mem_nbytes); + H5MM_memcpy(reclaim_buf, buf, mem_nbytes); /* Set background buffer to all zeros */ HDmemset(bkg, 0, buf_size); @@ -1553,7 +1579,7 @@ H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute") /* After fix ref, copy the new reference elements to the buffer to write out */ - HDmemcpy(buf, bkg, buf_size); + H5MM_memcpy(buf, bkg, buf_size); } /* end if */ else /* Reset value to zero */ diff --git a/src/H5Dearray.c b/src/H5Dearray.c index a20145a..b23ac46 100644 --- a/src/H5Dearray.c +++ b/src/H5Dearray.c @@ -37,6 +37,7 @@ #include "H5EAprivate.h" /* Extensible arrays */ #include "H5FLprivate.h" /* Free Lists */ #include "H5MFprivate.h" /* File space management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vector functions */ @@ -437,7 +438,7 @@ H5D__earray_debug(FILE *stream, int indent, int fwidth, hsize_t idx, HDassert(elmt); /* Print element */ - sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, temp_str, *(const haddr_t *)elmt); @@ -596,7 +597,7 @@ H5D__earray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx, HDassert(elmt); /* Print element */ - sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s {%a, %u, %0x}\n", indent, "", fwidth, temp_str, elmt->addr, elmt->nbytes, elmt->filter_mask); @@ -1197,11 +1198,11 @@ H5D__earray_idx_resize(H5O_layout_chunk_t *layout) hsize_t swizzled_max_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of max # of chunks in each dimension */ /* Get the swizzled chunk dimensions */ - HDmemcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0])); + H5MM_memcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0])); H5VM_swizzle_coords(uint32_t, layout->u.earray.swizzled_dim, layout->u.earray.unlim_dim); /* Get the swizzled number of chunks in each dimension */ - HDmemcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0])); + H5MM_memcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0])); H5VM_swizzle_coords(hsize_t, swizzled_chunks, layout->u.earray.unlim_dim); /* Get the swizzled "down" sizes for each dimension */ @@ -1209,7 +1210,7 @@ H5D__earray_idx_resize(H5O_layout_chunk_t *layout) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute swizzled 'down' chunk size value") /* Get the swizzled max number of chunks in each dimension */ - HDmemcpy(swizzled_max_chunks, layout->max_chunks, (layout->ndims - 1) * sizeof(swizzled_max_chunks[0])); + H5MM_memcpy(swizzled_max_chunks, layout->max_chunks, (layout->ndims - 1) * sizeof(swizzled_max_chunks[0])); H5VM_swizzle_coords(hsize_t, swizzled_max_chunks, layout->u.earray.unlim_dim); /* Get the swizzled max "down" sizes for each dimension */ diff --git a/src/H5Defl.c b/src/H5Defl.c index b2f9b29..19f3a00 100644 --- a/src/H5Defl.c +++ b/src/H5Defl.c @@ -91,6 +91,7 @@ const H5D_layout_ops_t H5D_LOPS_EFL[1] = {{ H5D__efl_construct, NULL, H5D__efl_is_space_alloc, + NULL, H5D__efl_io_init, H5D__contig_read, H5D__contig_write, @@ -226,7 +227,7 @@ H5D__efl_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR_UNU { FUNC_ENTER_STATIC_NOERR - HDmemcpy(&io_info->store->efl, &(io_info->dset->shared->dcpl_cache.efl), sizeof(H5O_efl_t)); + H5MM_memcpy(&io_info->store->efl, &(io_info->dset->shared->dcpl_cache.efl), sizeof(H5O_efl_t)); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D__efl_io_init() */ diff --git a/src/H5Dfarray.c b/src/H5Dfarray.c index 372ae26..2d85e3b 100644 --- a/src/H5Dfarray.c +++ b/src/H5Dfarray.c @@ -434,7 +434,7 @@ H5D__farray_debug(FILE *stream, int indent, int fwidth, hsize_t idx, HDassert(elmt); /* Print element */ - sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, temp_str, *(const haddr_t *)elmt); @@ -699,7 +699,7 @@ H5D__farray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx, HDassert(elmt); /* Print element */ - sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s {%a, %u, %0x}\n", indent, "", fwidth, temp_str, elmt->addr, elmt->nbytes, elmt->filter_mask); diff --git a/src/H5Dfill.c b/src/H5Dfill.c index 619f699..69f4ff8 100644 --- a/src/H5Dfill.c +++ b/src/H5Dfill.c @@ -38,6 +38,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vector and array functions */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -300,7 +301,7 @@ H5D__fill(const void *fill, const H5T_t *fill_type, void *buf, HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't get actual buffer") /* Copy the user's data into the buffer for conversion */ - HDmemcpy(elem_ptr, fill, src_type_size); + H5MM_memcpy(elem_ptr, fill, src_type_size); /* If there's no VL type of data, do conversion first then fill the data into * the memory buffer. */ @@ -577,7 +578,7 @@ H5D__fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts) HDassert(fb_info->fill_buf); /* Make a copy of the (disk-based) fill value into the buffer */ - HDmemcpy(fb_info->fill_buf, fb_info->fill->buf, fb_info->file_elmt_size); + H5MM_memcpy(fb_info->fill_buf, fb_info->fill->buf, fb_info->file_elmt_size); /* Reset first element of background buffer, if necessary */ if(H5T_path_bkg(fb_info->fill_to_mem_tpath)) @@ -603,7 +604,7 @@ H5D__fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts) if(!buf) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed for temporary fill buffer") - HDmemcpy(buf, fb_info->fill_buf, fb_info->fill_buf_size); + H5MM_memcpy(buf, fb_info->fill_buf, fb_info->fill_buf_size); /* Type convert the dataset buffer, to copy any VL components */ if(H5T_convert(fb_info->mem_to_dset_tpath, fb_info->mem_tid, fb_info->file_tid, nelmts, (size_t)0, (size_t)0, fb_info->fill_buf, fb_info->bkg_buf) < 0) diff --git a/src/H5Dint.c b/src/H5Dint.c index 7eb1aaf..6fc02de 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -470,7 +470,7 @@ H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the default dataset information */ - HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t)); + H5MM_memcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t)); /* If we are using the default dataset creation property list, during creation * don't bother to copy it, just increment the reference count @@ -488,6 +488,9 @@ H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) new_dset->dcpl_id = H5P_copy_plist(plist, FALSE); } /* end else */ + /* Set the DCPL for the API context */ + H5CX_set_dcpl(new_dset->dcpl_id); + /* Set return value */ ret_value = new_dset; @@ -678,7 +681,6 @@ done: static herr_t H5D__use_minimized_dset_headers(H5F_t *file, H5D_t *dset, hbool_t *minimize) { - H5P_genplist_t *plist = NULL; herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT; @@ -687,11 +689,9 @@ H5D__use_minimized_dset_headers(H5F_t *file, H5D_t *dset, hbool_t *minimize) HDassert(dset); HDassert(minimize); - plist = H5P_object_verify(dset->shared->dcpl_id, H5P_DATASET_CREATE); - if(NULL == plist) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "problem getting dcpl") - if(H5P_get(plist, H5D_CRT_MIN_DSET_HDR_SIZE_NAME, minimize) == FAIL) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get minimize value from dcpl") + /* Get the dataset object header minimize flag for this call */ + if(H5CX_get_dset_min_ohdr_flag(minimize) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset object header minimize flag from API context") if(FALSE == *minimize) *minimize = H5F_get_min_dset_ohdr(file); @@ -774,7 +774,7 @@ H5D__calculate_minimum_header_size(H5F_t *file, H5D_t *dset, H5O_t *ohdr) /* Shallow copy the fill value property */ /* guards against shared component modification */ - HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); + H5MM_memcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); if (H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't reset the copied fill property") @@ -1000,7 +1000,7 @@ H5D__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id) /* Shallow copy the fill value property */ /* (we only want to make certain that the shared component isn't modified) */ - HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); + H5MM_memcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); /* Reset shared component info */ H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop); @@ -1642,7 +1642,7 @@ H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id) dset->shared->append_flush.ndims = info.ndims; dset->shared->append_flush.func = info.func; dset->shared->append_flush.udata = info.udata; - HDmemcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary)); + H5MM_memcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary)); } /* end if */ } /* end if */ } /* end if */ @@ -2778,7 +2778,7 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size) /* Keep the current dataspace dimensions for later */ HDcompile_assert(sizeof(curr_dims) == sizeof(dset->shared->curr_dims)); - HDmemcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0])); + H5MM_memcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0])); /* Modify the size of the dataspace */ if((changed = H5S_set_extent(dset->shared->space, size)) < 0) @@ -2898,7 +2898,8 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size) *------------------------------------------------------------------------- */ if(H5D_CHUNKED == dset->shared->layout.type) { - if(shrink && (*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) + if(shrink && ((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage) + || (dset->shared->layout.ops->is_data_cached && (*dset->shared->layout.ops->is_data_cached)(dset->shared)))) /* Remove excess chunks */ if(H5D__chunk_prune_by_extent(dset, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks") @@ -3062,7 +3063,7 @@ H5D__format_convert(H5D_t *dataset) idx_info.storage = &dataset->shared->layout.storage.u.chunk; /* Copy the current layout info to the new layout */ - HDmemcpy(newlayout, &dataset->shared->layout, sizeof(H5O_layout_t)); + H5MM_memcpy(newlayout, &dataset->shared->layout, sizeof(H5O_layout_t)); /* Set up info for version 1 B-tree in the new layout */ newlayout->version = H5O_LAYOUT_VERSION_3; @@ -3113,7 +3114,7 @@ H5D__format_convert(H5D_t *dataset) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") /* Copy the new layout to the dataset's layout */ - HDmemcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t)); + H5MM_memcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t)); break; diff --git a/src/H5Dio.c b/src/H5Dio.c index 607bfcf..9343b80 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -518,7 +518,8 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, * has been overwritten. So just proceed in reading. */ if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 && - !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage)) { + !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) && + !(dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared))) { H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ /* Retrieve dataset's fill-value properties */ @@ -550,6 +551,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* Sanity check that space is allocated, if there are elements */ if(nelmts > 0) HDassert((*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) + || (dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared)) || dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT); @@ -1031,16 +1033,13 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, if(type_info->request_nelmts == 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small") - /* - * Get a temporary buffer for type conversion unless the app has already + /* Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a - * buffer which is the exact size, we allocate the target size. The - * malloc() is usually less resource-intensive if we allocate/free the - * same size over and over. + * buffer which is the exact size, we allocate the target size. */ if(NULL == (type_info->tconv_buf = (uint8_t *)tconv_buf)) { /* Allocate temporary buffer */ - if(NULL == (type_info->tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size))) + if(NULL == (type_info->tconv_buf = H5FL_BLK_CALLOC(type_conv, target_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion") type_info->tconv_buf_allocated = TRUE; } /* end if */ diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index f5da33d..d23cb63 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -800,6 +800,10 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf HDassert(type_info); HDassert(fm); + /* Disable collective metadata reads for chunked dataset I/O operations + * in order to prevent potential hangs */ + H5CX_set_coll_metadata_read(FALSE); + /* Check the optional property list for the collective chunk IO optimization option */ if(H5CX_get_mpio_chunk_opt_mode(&chunk_opt_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get chunk optimization option") @@ -1423,7 +1427,7 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in for (i = 0, offset = 0; i < (size_t) mpi_rank; i++) offset += num_chunks_selected_array[i]; - HDmemcpy(chunk_list, &collective_chunk_list[offset], num_chunks_selected_array[mpi_rank] * sizeof(H5D_filtered_collective_io_info_t)); + H5MM_memcpy(chunk_list, &collective_chunk_list[offset], num_chunks_selected_array[mpi_rank] * sizeof(H5D_filtered_collective_io_info_t)); /* Create single MPI type encompassing each selection in the dataspace */ if (H5D__mpio_filtered_collective_write_type(chunk_list, chunk_list_num_entries, @@ -1549,7 +1553,7 @@ if(H5DEBUG(D)) HGOTO_ERROR(H5E_DATASET, H5E_CANTRECV, FAIL, "unable to obtain MPIO mode") /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); + H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; @@ -1557,7 +1561,7 @@ if(H5DEBUG(D)) ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size; /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); + H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); cpt_io_info.store = &cpt_store; cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; @@ -1784,7 +1788,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list") /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); + H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; @@ -1889,7 +1893,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i /* Collect the new chunk info back to the local copy, since only the record in the * collective array gets updated by the chunk re-allocation */ - HDmemcpy(&chunk_list[i].chunk_states.new_chunk, &collective_chunk_list[offset].chunk_states.new_chunk, sizeof(chunk_list[i].chunk_states.new_chunk)); + H5MM_memcpy(&chunk_list[i].chunk_states.new_chunk, &collective_chunk_list[offset].chunk_states.new_chunk, sizeof(chunk_list[i].chunk_states.new_chunk)); H5_CHECKED_ASSIGN(mpi_type_count, int, chunk_list[i].chunk_states.new_chunk.length, hsize_t); @@ -2313,7 +2317,7 @@ if(H5DEBUG(D)) /* Broadcasting the MPI_IO option info. and chunk address info. */ if(MPI_SUCCESS != (mpi_code = MPI_Bcast(total_chunk_addr_array, (int)(sizeof(haddr_t) * fm->layout->u.chunk.nchunks), MPI_BYTE, (int)0, io_info->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code) + HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code) } /* end if */ /* Start at first node in chunk skip list */ @@ -2513,8 +2517,8 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, /* merge buffer io_mode info and chunk addr into one */ - HDmemcpy(mergebuf, assign_io_mode, total_chunks); - HDmemcpy(tempbuf, chunk_addr, sizeof(haddr_t) * total_chunks); + H5MM_memcpy(mergebuf, assign_io_mode, total_chunks); + H5MM_memcpy(tempbuf, chunk_addr, sizeof(haddr_t) * total_chunks); H5MM_free(nproc_per_chunk); } /* end if */ @@ -2523,8 +2527,8 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, if(MPI_SUCCESS != (mpi_code = MPI_Bcast(mergebuf, ((sizeof(haddr_t) + 1) * total_chunks), MPI_BYTE, root, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code) - HDmemcpy(assign_io_mode, mergebuf, total_chunks); - HDmemcpy(chunk_addr, tempbuf, sizeof(haddr_t) * total_chunks); + H5MM_memcpy(assign_io_mode, mergebuf, total_chunks); + H5MM_memcpy(chunk_addr, tempbuf, sizeof(haddr_t) * total_chunks); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY { @@ -2626,7 +2630,7 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ local_info_array[i].async_info.receive_buffer_array = NULL; local_info_array[i].async_info.receive_requests_array = NULL; - HDmemcpy(local_info_array[i].scaled, chunk_info->scaled, sizeof(chunk_info->scaled)); + H5MM_memcpy(local_info_array[i].scaled, chunk_info->scaled, sizeof(chunk_info->scaled)); if ((select_npoints = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") @@ -2837,45 +2841,45 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty size_t mod_data_size; /* Look up the chunk and get its file and memory dataspaces */ - if (NULL == (chunk_info = (H5D_chunk_info_t *) H5SL_search(fm->sel_chunks, &chunk_entry->index))) + if(NULL == (chunk_info = (H5D_chunk_info_t *) H5SL_search(fm->sel_chunks, &chunk_entry->index))) HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list") /* Determine size of serialized chunk file dataspace, plus the size of * the data being written */ - if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) + if(H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to get encoded dataspace size") - if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) + if((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") mod_data_size += (size_t) iter_nelmts * type_info->src_type_size; - if (NULL == (mod_data[num_send_requests] = (unsigned char *) H5MM_malloc(mod_data_size))) + if(NULL == (mod_data[num_send_requests] = (unsigned char *) H5MM_malloc(mod_data_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk modification send buffer") /* Serialize the chunk's file dataspace into the buffer */ mod_data_p = mod_data[num_send_requests]; - if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) + if(H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to encode dataspace") /* Initialize iterator for memory selection */ - if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size) < 0) + if(H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") mem_iter_init = TRUE; /* Collect the modification data into the buffer */ - if(!H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t)iter_nelmts, mod_data_p)) + if(0 == H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t)iter_nelmts, mod_data_p)) HGOTO_ERROR(H5E_IO, H5E_CANTGATHER, FAIL, "couldn't gather from write buffer") /* Send modification data to new owner */ H5_CHECK_OVERFLOW(mod_data_size, size_t, int) H5_CHECK_OVERFLOW(chunk_entry->index, hsize_t, int) - if (MPI_SUCCESS != (mpi_code = MPI_Isend(mod_data[num_send_requests], (int) mod_data_size, MPI_BYTE, + if(MPI_SUCCESS != (mpi_code = MPI_Isend(mod_data[num_send_requests], (int) mod_data_size, MPI_BYTE, chunk_entry->owners.new_owner, (int) chunk_entry->index, io_info->comm, &send_requests[num_send_requests]))) HMPI_GOTO_ERROR(FAIL, "MPI_Isend failed", mpi_code) - if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if(mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release memory selection iterator") mem_iter_init = FALSE; @@ -3044,11 +3048,11 @@ H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chun } /* end if */ done: - if (write_buf_array) + if(write_buf_array) H5MM_free(write_buf_array); - if (file_offset_array) + if(file_offset_array) H5MM_free(file_offset_array); - if (length_array) + if(length_array) H5MM_free(length_array); FUNC_LEAVE_NOAPI(ret_value) @@ -3166,7 +3170,7 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk if (NULL == (mem_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate memory iterator") - if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size) < 0) + if(H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") mem_iter_init = TRUE; @@ -3176,53 +3180,53 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk * from the current process, then apply any modifications from other processes. Finally, * filter the newly-updated chunk. */ - switch (io_info->op_type) { + switch(io_info->op_type) { case H5D_IO_OP_READ: - if (NULL == (file_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t)))) + if(NULL == (file_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file iterator") - if (H5S_select_iter_init(file_iter, chunk_info->fspace, type_info->src_type_size) < 0) + if(H5S_select_iter_init(file_iter, chunk_info->fspace, type_info->src_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") file_iter_init = TRUE; - if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace)) < 0) + if((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") - if (NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size))) + if(NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") - if (!H5D__gather_mem(chunk_entry->buf, chunk_info->fspace, file_iter, (size_t) iter_nelmts, tmp_gath_buf)) + if(!H5D__gather_mem(chunk_entry->buf, chunk_info->fspace, file_iter, (size_t) iter_nelmts, tmp_gath_buf)) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't gather from chunk buffer") - if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) + if((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") - if (H5D__scatter_mem(tmp_gath_buf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, io_info->u.rbuf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer") + if(H5D__scatter_mem(tmp_gath_buf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, io_info->u.rbuf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer") break; case H5D_IO_OP_WRITE: - if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) + if((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") - if (NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size))) + if(NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") /* Gather modification data from the application write buffer into a temporary buffer */ - if(!H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, tmp_gath_buf)) + if(0 == H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, tmp_gath_buf)) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't gather from write buffer") - if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if(H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") mem_iter_init = FALSE; /* Initialize iterator for file selection */ - if (H5S_select_iter_init(mem_iter, chunk_info->fspace, type_info->dst_type_size) < 0) + if(H5S_select_iter_init(mem_iter, chunk_info->fspace, type_info->dst_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information") mem_iter_init = TRUE; - if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace)) < 0) + if((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") /* Scatter the owner's modification data into the chunk data buffer according to @@ -3231,44 +3235,44 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk if(H5D__scatter_mem(tmp_gath_buf, chunk_info->fspace, mem_iter, (size_t) iter_nelmts, chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to chunk data buffer") - if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if(H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") mem_iter_init = FALSE; - if (MPI_SUCCESS != (mpi_code = MPI_Waitall(chunk_entry->async_info.num_receive_requests, + if(MPI_SUCCESS != (mpi_code = MPI_Waitall(chunk_entry->async_info.num_receive_requests, chunk_entry->async_info.receive_requests_array, MPI_STATUSES_IGNORE))) HMPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code) /* For each asynchronous receive call previously posted, receive the chunk modification * buffer from another rank and update the chunk data */ - for (i = 0; i < (size_t) chunk_entry->async_info.num_receive_requests; i++) { + for(i = 0; i < (size_t) chunk_entry->async_info.num_receive_requests; i++) { const unsigned char *mod_data_p; /* Decode the process' chunk file dataspace */ mod_data_p = chunk_entry->async_info.receive_buffer_array[i]; - if (NULL == (dataspace = H5S_decode(&mod_data_p))) + if(NULL == (dataspace = H5S_decode(&mod_data_p))) HGOTO_ERROR(H5E_DATASET, H5E_CANTDECODE, FAIL, "unable to decode dataspace") - if (H5S_select_iter_init(mem_iter, dataspace, type_info->dst_type_size) < 0) + if(H5S_select_iter_init(mem_iter, dataspace, type_info->dst_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") mem_iter_init = TRUE; - if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(dataspace)) < 0) + if((iter_nelmts = H5S_GET_SELECT_NPOINTS(dataspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") /* Update the chunk data with the received modification data */ if(H5D__scatter_mem(mod_data_p, dataspace, mem_iter, (size_t) iter_nelmts, chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't scatter to write buffer") - if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if(H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") mem_iter_init = FALSE; - if (dataspace) { - if (H5S_close(dataspace) < 0) + if(dataspace) { + if(H5S_close(dataspace) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace") dataspace = NULL; - } + } /* end if */ H5MM_free(chunk_entry->async_info.receive_buffer_array[i]); } /* end for */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 2767aa1..e7c623b 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -113,12 +113,14 @@ typedef struct H5D_type_info_t { /* Forward declaration of structs used below */ struct H5D_io_info_t; struct H5D_chunk_map_t; +typedef struct H5D_shared_t H5D_shared_t; /* Function pointers for I/O on particular types of dataset layouts */ typedef herr_t (*H5D_layout_construct_func_t)(H5F_t *f, H5D_t *dset); typedef herr_t (*H5D_layout_init_func_t)(H5F_t *f, const H5D_t *dset, hid_t dapl_id); typedef hbool_t (*H5D_layout_is_space_alloc_func_t)(const H5O_storage_t *storage); +typedef hbool_t (*H5D_layout_is_data_cached_func_t)(const H5D_shared_t *shared_dset); typedef herr_t (*H5D_layout_io_init_func_t)(const struct H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, @@ -144,6 +146,7 @@ typedef struct H5D_layout_ops_t { H5D_layout_construct_func_t construct; /* Layout constructor for new datasets */ H5D_layout_init_func_t init; /* Layout initializer for dataset */ H5D_layout_is_space_alloc_func_t is_space_alloc; /* Query routine to determine if storage is allocated */ + H5D_layout_is_data_cached_func_t is_data_cached; /* Query routine to determine if any raw data is cached. If routine is not present then the layout type never caches raw data. */ H5D_layout_io_init_func_t io_init; /* I/O initialization routine */ H5D_layout_read_func_t ser_read; /* High-level I/O routine for reading data in serial */ H5D_layout_write_func_t ser_write; /* High-level I/O routine for writing data in serial */ @@ -429,7 +432,7 @@ typedef struct H5D_rdcdc_t { * created once for a given dataset. Thus, if a dataset is opened twice, * there will be two IDs and two H5D_t structs, both sharing one H5D_shared_t. */ -typedef struct H5D_shared_t { +struct H5D_shared_t { size_t fo_count; /* Reference count */ hbool_t closing; /* Flag to indicate dataset is closing */ hid_t type_id; /* ID for dataset's datatype */ @@ -459,7 +462,7 @@ typedef struct H5D_shared_t { H5D_append_flush_t append_flush; /* Append flush property information */ char *extfile_prefix; /* expanded external file prefix */ char *vds_prefix; /* expanded vds prefix */ -} H5D_shared_t; +}; struct H5D_t { H5O_loc_t oloc; /* Object header location */ @@ -618,6 +621,7 @@ H5_DLL herr_t H5D__layout_oh_write(const H5D_t *dataset, H5O_t *oh, unsigned upd /* Functions that operate on contiguous storage */ H5_DLL herr_t H5D__contig_alloc(H5F_t *f, H5O_storage_contig_t *storage); H5_DLL hbool_t H5D__contig_is_space_alloc(const H5O_storage_t *storage); +H5_DLL hbool_t H5D__contig_is_data_cached(const H5D_shared_t *shared_dset); H5_DLL herr_t H5D__contig_fill(const H5D_io_info_t *io_info); H5_DLL herr_t H5D__contig_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, @@ -636,6 +640,7 @@ H5_DLL htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, H5_DLL herr_t H5D__chunk_create(const H5D_t *dset /*in,out*/); H5_DLL herr_t H5D__chunk_set_info(const H5D_t *dset); H5_DLL hbool_t H5D__chunk_is_space_alloc(const H5O_storage_t *storage); +H5_DLL hbool_t H5D__chunk_is_data_cached(const H5D_shared_t *shared_dset); H5_DLL herr_t H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udata); H5_DLL herr_t H5D__chunk_allocated(const H5D_t *dset, hsize_t *nbytes); diff --git a/src/H5Dscatgath.c b/src/H5Dscatgath.c index 266f5f5..0e0edf7 100644 --- a/src/H5Dscatgath.c +++ b/src/H5Dscatgath.c @@ -27,6 +27,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -117,7 +118,7 @@ H5D__scatter_file(const H5D_io_info_t *_io_info, HDassert(_buf); /* Set up temporary I/O info object */ - HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info)); + H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info)); tmp_io_info.op_type = H5D_IO_OP_WRITE; tmp_io_info.u.wbuf = _buf; @@ -220,7 +221,7 @@ H5D__gather_file(const H5D_io_info_t *_io_info, HDassert(_buf); /* Set up temporary I/O info object */ - HDmemcpy(&tmp_io_info, _io_info, sizeof(*_io_info)); + H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info)); tmp_io_info.op_type = H5D_IO_OP_READ; tmp_io_info.u.rbuf = _buf; @@ -337,7 +338,7 @@ H5D__scatter_mem (const void *_tscat_buf, const H5S_t *space, /* Get the number of bytes in sequence */ curr_len = len[curr_seq]; - HDmemcpy(buf + off[curr_seq], tscat_buf, curr_len); + H5MM_memcpy(buf + off[curr_seq], tscat_buf, curr_len); /* Advance offset in destination buffer */ tscat_buf += curr_len; @@ -425,7 +426,7 @@ H5D__gather_mem(const void *_buf, const H5S_t *space, /* Get the number of bytes in sequence */ curr_len = len[curr_seq]; - HDmemcpy(tgath_buf, buf + off[curr_seq], curr_len); + H5MM_memcpy(tgath_buf, buf + off[curr_seq], curr_len); /* Advance offset in gather buffer */ tgath_buf += curr_len; diff --git a/src/H5Dvirtual.c b/src/H5Dvirtual.c index c0d49d8..6c0cfba 100644 --- a/src/H5Dvirtual.c +++ b/src/H5Dvirtual.c @@ -78,6 +78,7 @@ /********************/ /* Layout operation callbacks */ +static hbool_t H5D__virtual_is_data_cached(const H5D_shared_t *shared_dset); static herr_t H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm); @@ -121,6 +122,7 @@ const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1] = {{ NULL, H5D__virtual_init, H5D__virtual_is_space_alloc, + H5D__virtual_is_data_cached, NULL, H5D__virtual_read, H5D__virtual_write, @@ -491,11 +493,11 @@ H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout) /* Encode each entry */ for(i = 0; i < layout->storage.u.virt.list_nused; i++) { /* Source file name */ - HDmemcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_file_name, str_size[2 * i]); + H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_file_name, str_size[2 * i]); heap_block_p += str_size[2 * i]; /* Source dataset name */ - HDmemcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_dset_name, str_size[(2 * i) + 1]); + H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_dset_name, str_size[(2 * i) + 1]); heap_block_p += str_size[(2 * i) + 1]; /* Source selection */ @@ -1107,7 +1109,7 @@ H5D__virtual_str_append(const char *src, size_t src_len, char **p, char **buf, /* Copy string to *p. Note that since src in not NULL terminated, we must * use memcpy */ - (void)HDmemcpy(*p, src, src_len); + (void)H5MM_memcpy(*p, src, src_len); /* Advance *p */ *p += src_len; @@ -2207,6 +2209,54 @@ H5D__virtual_is_space_alloc(const H5O_storage_t H5_ATTR_UNUSED *storage) /*------------------------------------------------------------------------- + * Function: H5D__virtual_is_data_cached + * + * Purpose: Query if raw data is cached for dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * Wednessday, March 6, 2016 + * + *------------------------------------------------------------------------- + */ +static hbool_t +H5D__virtual_is_data_cached(const H5D_shared_t *shared_dset) +{ + const H5O_storage_virtual_t *storage; /* Convenience pointer */ + size_t i, j; /* Local index variables */ + hbool_t ret_value = FALSE; /* Return value */ + + FUNC_ENTER_PACKAGE_NOERR + + /* Sanity checks */ + HDassert(shared_dset); + storage = &shared_dset->layout.storage.u.virt; + + /* Iterate over mappings */ + for(i = 0; i < storage->list_nused; i++) + /* Check for "printf" source dataset resolution */ + if(storage->list[i].psfn_nsubs || storage->list[i].psdn_nsubs) { + /* Iterate over sub-source dsets */ + for(j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++) + /* Check for cahced data in source dset */ + if(storage->list[i].sub_dset[j].dset + && storage->list[i].sub_dset[j].dset->shared->layout.ops->is_data_cached + && storage->list[i].sub_dset[j].dset->shared->layout.ops->is_data_cached(storage->list[i].sub_dset[j].dset->shared)) + HGOTO_DONE(TRUE); + } /* end if */ + else + if(storage->list[i].source_dset.dset + && storage->list[i].source_dset.dset->shared->layout.ops->is_data_cached + && storage->list[i].source_dset.dset->shared->layout.ops->is_data_cached(storage->list[i].source_dset.dset->shared)) + HGOTO_DONE(TRUE); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__virtual_is_data_cached() */ + + +/*------------------------------------------------------------------------- * Function: H5D__virtual_pre_io * * Purpose: Project all virtual mappings onto mem_space, with the @@ -1386,7 +1386,7 @@ H5Epush2(hid_t err_stack, const char *file, const char *func, unsigned line, */ /* Format the description */ - va_start(ap, fmt); + HDva_start(ap, fmt); va_started = TRUE; #ifdef H5_HAVE_VASPRINTF @@ -1402,8 +1402,8 @@ H5Epush2(hid_t err_stack, const char *file, const char *func, unsigned line, /* If the description doesn't fit into the initial buffer size, allocate more space and try again */ while((desc_len = HDvsnprintf(tmp, (size_t)tmp_len, fmt, ap)) > (tmp_len - 1)) { /* shutdown & restart the va_list */ - va_end(ap); - va_start(ap, fmt); + HDva_end(ap); + HDva_start(ap, fmt); /* Release the previous description, it's too small */ H5MM_xfree(tmp); @@ -1421,7 +1421,7 @@ H5Epush2(hid_t err_stack, const char *file, const char *func, unsigned line, done: if(va_started) - va_end(ap); + HDva_end(ap); #ifdef H5_HAVE_VASPRINTF /* Memory was allocated with HDvasprintf so it needs to be freed * with HDfree @@ -46,6 +46,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5EApkg.h" /* Extensible Arrays */ #include "H5FLprivate.h" /* Free Lists */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vector functions */ @@ -693,7 +694,7 @@ H5EA_set(const H5EA_t *ea, hsize_t idx, const void *elmt)) HDassert(thing_unprot_func); /* Set element in thing's element buffer */ - HDmemcpy(thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size); + H5MM_memcpy(thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size); thing_cache_flags |= H5AC__DIRTIED_FLAG; /* Update max. element set in array, if appropriate */ @@ -765,7 +766,7 @@ H5EA_get(const H5EA_t *ea, hsize_t idx, void *elmt)) } /* end if */ else /* Get element from thing's element buffer */ - HDmemcpy(elmt, thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), hdr->cparam.cls->nat_elmt_size); + H5MM_memcpy(elmt, thing_elmt_buf + (hdr->cparam.cls->nat_elmt_size * thing_elmt_idx), hdr->cparam.cls->nat_elmt_size); } /* end else */ CATCH diff --git a/src/H5EAcache.c b/src/H5EAcache.c index 8138991..da67e6b 100644 --- a/src/H5EAcache.c +++ b/src/H5EAcache.c @@ -41,6 +41,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5EApkg.h" /* Extensible Arrays */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vectors and arrays */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -479,7 +480,7 @@ H5EA__cache_hdr_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le HDassert(hdr); /* Magic number */ - HDmemcpy(image, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -867,7 +868,7 @@ H5EA__cache_iblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED /* Get temporary pointer to serialized info */ /* Magic number */ - HDmemcpy(image, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -1179,7 +1180,7 @@ H5EA__cache_sblock_deserialize(const void *_image, size_t len, size_t tot_page_init_size = sblock->ndblks * sblock->dblk_page_init_size; /* Compute total size of 'page init' buffer */ /* Retrieve the 'page init' bitmasks */ - HDmemcpy(sblock->page_init, image, tot_page_init_size); + H5MM_memcpy(sblock->page_init, image, tot_page_init_size); image += tot_page_init_size; } /* end if */ @@ -1276,7 +1277,7 @@ H5EA__cache_sblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED HDassert(sblock->hdr); /* Magic number */ - HDmemcpy(image, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -1298,7 +1299,7 @@ H5EA__cache_sblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED size_t tot_page_init_size = sblock->ndblks * sblock->dblk_page_init_size; /* Compute total size of 'page init' buffer */ /* Store the 'page init' bitmasks */ - HDmemcpy(image, sblock->page_init, tot_page_init_size); + H5MM_memcpy(image, sblock->page_init, tot_page_init_size); image += tot_page_init_size; } /* end if */ @@ -1690,7 +1691,7 @@ H5EA__cache_dblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED HDassert(dblock->hdr); /* Magic number */ - HDmemcpy(image, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ diff --git a/src/H5EAdbg.c b/src/H5EAdbg.c index 1a2b973..3d6c2ed 100644 --- a/src/H5EAdbg.c +++ b/src/H5EAdbg.c @@ -264,7 +264,7 @@ H5EA__iblock_debug(H5F_t *f, haddr_t H5_ATTR_UNUSED addr, FILE *stream, int inde HDfprintf(stream, "%*sData Block Addresses in Index Block:\n", indent, ""); for(u = 0; u < iblock->ndblk_addrs; u++) { /* Print address */ - sprintf(temp_str, "Address #%u:", u); + HDsprintf(temp_str, "Address #%u:", u); HDfprintf(stream, "%*s%-*s %a\n", (indent + 3), "", MAX(0, (fwidth - 3)), temp_str, iblock->dblk_addrs[u]); @@ -280,7 +280,7 @@ H5EA__iblock_debug(H5F_t *f, haddr_t H5_ATTR_UNUSED addr, FILE *stream, int inde HDfprintf(stream, "%*sSuper Block Addresses in Index Block:\n", indent, ""); for(u = 0; u < iblock->nsblk_addrs; u++) { /* Print address */ - sprintf(temp_str, "Address #%u:", u); + HDsprintf(temp_str, "Address #%u:", u); HDfprintf(stream, "%*s%-*s %a\n", (indent + 3), "", MAX(0, (fwidth - 3)), temp_str, iblock->sblk_addrs[u]); @@ -371,7 +371,7 @@ H5EA__sblock_debug(H5F_t *f, haddr_t addr, FILE *stream, int indent, HDfprintf(stream, "%*sData Block Addresses in Super Block:\n", indent, ""); for(u = 0; u < sblock->ndblks; u++) { /* Print address */ - sprintf(temp_str, "Address #%u:", u); + HDsprintf(temp_str, "Address #%u:", u); HDfprintf(stream, "%*s%-*s %a\n", (indent + 3), "", MAX(0, (fwidth - 3)), temp_str, sblock->dblk_addrs[u]); diff --git a/src/H5EAhdr.c b/src/H5EAhdr.c index 62a23b8..18d642f 100644 --- a/src/H5EAhdr.c +++ b/src/H5EAhdr.c @@ -41,6 +41,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5EApkg.h" /* Extensible Arrays */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vectors and arrays */ @@ -407,7 +408,7 @@ H5EA__hdr_create(H5F_t *f, const H5EA_create_t *cparam, void *ctx_udata)) hdr->idx_blk_addr = HADDR_UNDEF; /* Set the creation parameters for the array */ - HDmemcpy(&hdr->cparam, cparam, sizeof(hdr->cparam)); + H5MM_memcpy(&hdr->cparam, cparam, sizeof(hdr->cparam)); /* Finish initializing extensible array header */ if(H5EA__hdr_init(hdr, ctx_udata) < 0) diff --git a/src/H5EAstat.c b/src/H5EAstat.c index 72c4d14..509d3f8 100644 --- a/src/H5EAstat.c +++ b/src/H5EAstat.c @@ -40,6 +40,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5EApkg.h" /* Extensible Arrays */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -108,7 +109,7 @@ HDfprintf(stderr, "%s: Called\n", FUNC); HDassert(stats); /* Copy extensible array statistics */ - HDmemcpy(stats, &ea->hdr->stats, sizeof(ea->hdr->stats)); + H5MM_memcpy(stats, &ea->hdr->stats, sizeof(ea->hdr->stats)); END_FUNC(PRIV) /* end H5EA_get_stats() */ diff --git a/src/H5EAtest.c b/src/H5EAtest.c index 7c02e16..814e64f 100644 --- a/src/H5EAtest.c +++ b/src/H5EAtest.c @@ -336,7 +336,7 @@ H5EA__test_debug(FILE *stream, int indent, int fwidth, hsize_t idx, HDassert(elmt); /* Print element */ - sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s %llu\n", indent, "", fwidth, temp_str, (unsigned long long)*(const uint64_t *)elmt); diff --git a/src/H5Eint.c b/src/H5Eint.c index 66653ca..7818879 100644 --- a/src/H5Eint.c +++ b/src/H5Eint.c @@ -704,7 +704,7 @@ H5E_printf_stack(H5E_t *estack, const char *file, const char *func, unsigned lin */ /* Start the variable-argument parsing */ - va_start(ap, fmt); + HDva_start(ap, fmt); va_started = TRUE; #ifdef H5_HAVE_VASPRINTF @@ -720,8 +720,8 @@ H5E_printf_stack(H5E_t *estack, const char *file, const char *func, unsigned lin /* If the description doesn't fit into the initial buffer size, allocate more space and try again */ while((desc_len = HDvsnprintf(tmp, (size_t)tmp_len, fmt, ap)) > (tmp_len - 1)) { /* shutdown & restart the va_list */ - va_end(ap); - va_start(ap, fmt); + HDva_end(ap); + HDva_start(ap, fmt); /* Release the previous description, it's too small */ H5MM_xfree(tmp); @@ -739,7 +739,7 @@ H5E_printf_stack(H5E_t *estack, const char *file, const char *func, unsigned lin done: if(va_started) - va_end(ap); + HDva_end(ap); #ifdef H5_HAVE_VASPRINTF /* Memory was allocated with HDvasprintf so it needs to be freed * with HDfree @@ -41,6 +41,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FApkg.h" /* Fixed Arrays */ #include "H5FLprivate.h" /* Free Lists */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vector functions */ @@ -371,7 +372,7 @@ H5FA_set(const H5FA_t *fa, hsize_t idx, const void *elmt)) /* Check for paging data block */ if(!dblock->npages) { /* Set element in data block */ - HDmemcpy(((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), elmt, hdr->cparam.cls->nat_elmt_size); + H5MM_memcpy(((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), elmt, hdr->cparam.cls->nat_elmt_size); dblock_cache_flags |= H5AC__DIRTIED_FLAG; } /* end if */ else { /* paging */ @@ -410,7 +411,7 @@ H5FA_set(const H5FA_t *fa, hsize_t idx, const void *elmt)) H5E_THROW(H5E_CANTPROTECT, "unable to protect fixed array data block page, address = %llu", (unsigned long long)dblk_page_addr) /* Set the element in the data block page */ - HDmemcpy(((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size); + H5MM_memcpy(((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), elmt, hdr->cparam.cls->nat_elmt_size); dblk_page_cache_flags |= H5AC__DIRTIED_FLAG; } /* end else */ @@ -474,7 +475,7 @@ H5FA_get(const H5FA_t *fa, hsize_t idx, void *elmt)) /* Check for paged data block */ if(!dblock->npages) /* Retrieve element from data block */ - HDmemcpy(elmt, ((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), hdr->cparam.cls->nat_elmt_size); + H5MM_memcpy(elmt, ((uint8_t *)dblock->elmts) + (hdr->cparam.cls->nat_elmt_size * idx), hdr->cparam.cls->nat_elmt_size); else { /* paging */ size_t page_idx; /* Index of page within data block */ @@ -512,7 +513,7 @@ H5FA_get(const H5FA_t *fa, hsize_t idx, void *elmt)) H5E_THROW(H5E_CANTPROTECT, "unable to protect fixed array data block page, address = %llu", (unsigned long long)dblk_page_addr) /* Retrieve element from data block */ - HDmemcpy(elmt, ((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), hdr->cparam.cls->nat_elmt_size); + H5MM_memcpy(elmt, ((uint8_t *)dblk_page->elmts) + (hdr->cparam.cls->nat_elmt_size * elmt_idx), hdr->cparam.cls->nat_elmt_size); } /* end else */ } /* end else */ } /* end else */ diff --git a/src/H5FAcache.c b/src/H5FAcache.c index 1f199e9..f440efe 100644 --- a/src/H5FAcache.c +++ b/src/H5FAcache.c @@ -41,6 +41,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FApkg.h" /* Fixed Arrays */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vectors and arrays */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -409,7 +410,7 @@ H5FA__cache_hdr_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le HDassert(hdr); /* Magic number */ - HDmemcpy(image, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -693,7 +694,7 @@ H5FA__cache_dblock_deserialize(const void *_image, size_t len, /* Page initialization flags */ if(dblock->npages > 0) { - HDmemcpy(dblock->dblk_page_init, image, dblock->dblk_page_init_size); + H5MM_memcpy(dblock->dblk_page_init, image, dblock->dblk_page_init_size); image += dblock->dblk_page_init_size; } /* end if */ @@ -797,7 +798,7 @@ H5FA__cache_dblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED HDassert(dblock->hdr); /* Magic number */ - HDmemcpy(image, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -812,7 +813,7 @@ H5FA__cache_dblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED /* Page init flags */ if(dblock->npages > 0) { /* Store the 'page init' bitmasks */ - HDmemcpy(image, dblock->dblk_page_init, dblock->dblk_page_init_size); + H5MM_memcpy(image, dblock->dblk_page_init, dblock->dblk_page_init_size); image += dblock->dblk_page_init_size; } /* end if */ diff --git a/src/H5FAhdr.c b/src/H5FAhdr.c index 2e3db0b..8f29b83 100644 --- a/src/H5FAhdr.c +++ b/src/H5FAhdr.c @@ -39,6 +39,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FApkg.h" /* Fixed Arrays */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -207,7 +208,7 @@ H5FA__hdr_create(H5F_t *f, const H5FA_create_t *cparam, void *ctx_udata)) hdr->dblk_addr = HADDR_UNDEF; /* Set the creation parameters for the array */ - HDmemcpy(&hdr->cparam, cparam, sizeof(hdr->cparam)); + H5MM_memcpy(&hdr->cparam, cparam, sizeof(hdr->cparam)); /* Finish initializing fixed array header */ if(H5FA__hdr_init(hdr, ctx_udata) < 0) diff --git a/src/H5FAstat.c b/src/H5FAstat.c index 3c06855..49a56a9 100644 --- a/src/H5FAstat.c +++ b/src/H5FAstat.c @@ -38,6 +38,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5FApkg.h" /* Fixed Arrays */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -105,7 +106,7 @@ HDfprintf(stderr, "%s: Called\n", FUNC); HDassert(stats); /* Copy fixed array statistics */ - HDmemcpy(stats, &fa->hdr->stats, sizeof(fa->hdr->stats)); + H5MM_memcpy(stats, &fa->hdr->stats, sizeof(fa->hdr->stats)); END_FUNC(PRIV) /* end H5FA_get_stats() */ diff --git a/src/H5FAtest.c b/src/H5FAtest.c index 27cd8b7..e55d408 100644 --- a/src/H5FAtest.c +++ b/src/H5FAtest.c @@ -315,7 +315,7 @@ H5FA__test_debug(FILE *stream, int indent, int fwidth, hsize_t idx, HDassert(elmt); /* Print element */ - sprintf(temp_str, "Element #%llu:", (unsigned long long)idx); + HDsprintf(temp_str, "Element #%llu:", (unsigned long long)idx); HDfprintf(stream, "%*s%-*s %llu\n", indent, "", fwidth, temp_str, (unsigned long long)*(const uint64_t *)elmt); @@ -293,7 +293,7 @@ H5FD_register(const void *_cls, size_t size, hbool_t app_ref) /* Copy the class structure so the caller can reuse or free it */ if(NULL == (saved = (H5FD_class_t *)H5MM_malloc(size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5I_INVALID_HID, "memory allocation failed for file driver class struct") - HDmemcpy(saved, cls, size); + H5MM_memcpy(saved, cls, size); /* Create the new class ID */ if((ret_value = H5I_register(H5I_VFL, saved, app_ref)) < 0) @@ -1367,7 +1367,7 @@ H5FD_get_fs_type_map(const H5FD_t *file, H5FD_mem_t *type_map) } /* end if */ else /* Copy class's default free space type mapping */ - HDmemcpy(type_map, file->cls->fl_map, sizeof(file->cls->fl_map)); + H5MM_memcpy(type_map, file->cls->fl_map, sizeof(file->cls->fl_map)); done: FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5FDcore.c b/src/H5FDcore.c index ed05e95..6db8af6 100644 --- a/src/H5FDcore.c +++ b/src/H5FDcore.c @@ -348,14 +348,17 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size) HDassert(file); - /* Write to backing store */ - if((off_t)addr != HDlseek(file->fd, (off_t)addr, SEEK_SET)) +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pwrite) */ + if((HDoff_t)addr != HDlseek(file->fd, (off_t)addr, SEEK_SET)) HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "error seeking in backing store") +#endif /* H5_HAVE_PREADWRITE */ while (size > 0) { h5_posix_io_t bytes_in = 0; /* # of bytes to write */ h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */ + HDoff_t offset = (HDoff_t)addr; /* Trying to write more bytes than the return type can handle is * undefined behavior in POSIX. @@ -366,15 +369,21 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size) bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_wrote = HDpwrite(file->fd, ptr, bytes_in, offset); + offset += bytes_wrote; +#else bytes_wrote = HDwrite(file->fd, ptr, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_wrote && EINTR == errno); if(-1 == bytes_wrote) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to backing store failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', ptr = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), ptr, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to backing store failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', ptr = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), ptr, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset); } /* end if */ HDassert(bytes_wrote > 0); @@ -839,7 +848,7 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr HGOTO_ERROR(H5E_FILE, H5E_CANTCOPY, NULL, "image_memcpy callback failed") } /* end if */ else - HDmemcpy(file->mem, file_image_info.buffer, size); + H5MM_memcpy(file->mem, file_image_info.buffer, size); } /* end if */ /* Read in existing data from the file if there is no image */ else { @@ -852,6 +861,7 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr while(size > 0) { h5_posix_io_t bytes_in = 0; /* # of bytes to read */ h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + HDoff_t offset = (HDoff_t)0; /* Trying to read more bytes than the return type can handle is * undefined behavior in POSIX. @@ -862,15 +872,21 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_read = HDpread(file->fd, mem, bytes_in, offset); + offset += bytes_read; +#else bytes_read = HDread(file->fd, mem, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_read && EINTR == errno); if(-1 == bytes_read) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', file->mem = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), file->mem, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', file->mem = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), file->mem, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset); } /* end if */ HDassert(bytes_read >= 0); @@ -1284,7 +1300,7 @@ H5FD__core_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU nbytes = MIN(size,(size_t)(file->eof-addr)); #endif /* NDEBUG */ - HDmemcpy(buf, file->mem + addr, nbytes); + H5MM_memcpy(buf, file->mem + addr, nbytes); size -= nbytes; addr += nbytes; buf = (char *)buf + nbytes; @@ -1370,7 +1386,7 @@ H5FD__core_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN } /* Write from BUF to memory */ - HDmemcpy(file->mem + addr, buf, size); + H5MM_memcpy(file->mem + addr, buf, size); /* Mark memory buffer as modified */ file->dirty = TRUE; diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c index 10c368a..33a0ef4 100644 --- a/src/H5FDdirect.c +++ b/src/H5FDdirect.c @@ -422,7 +422,7 @@ H5FD_direct_fapl_copy(const void *_old_fa) HDassert(new_fa); /* Copy the general information */ - HDmemcpy(new_fa, old_fa, sizeof(H5FD_direct_fapl_t)); + H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_direct_fapl_t)); FUNC_LEAVE_NOAPI(new_fa) } /* end H5FD_direct_fapl_copy() */ @@ -976,12 +976,12 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN * next section of data. */ p2 = (unsigned char*)copy_buf + copy_offset; if((copy_size + copy_offset) <= alloc_size) { - HDmemcpy(buf, p2, copy_size); + H5MM_memcpy(buf, p2, copy_size); buf = (unsigned char *)buf + copy_size; copy_size = 0; } /* end if */ else { - HDmemcpy(buf, p2, alloc_size - copy_offset); + H5MM_memcpy(buf, p2, alloc_size - copy_offset); buf = (unsigned char*)buf + alloc_size - copy_offset; copy_size -= alloc_size - copy_offset; copy_offset = 0; @@ -1189,11 +1189,11 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_U */ p1 = (unsigned char *)copy_buf + copy_offset; if((copy_size + copy_offset) <= alloc_size) { - HDmemcpy(p1, p3, copy_size); + H5MM_memcpy(p1, p3, copy_size); copy_size = 0; } /* end if */ else { - HDmemcpy(p1, p3, alloc_size - copy_offset); + H5MM_memcpy(p1, p3, alloc_size - copy_offset); p3 = (const unsigned char *)p3 + (alloc_size - copy_offset); copy_size -= alloc_size - copy_offset; copy_offset = 0; diff --git a/src/H5FDfamily.c b/src/H5FDfamily.c index 4d40cf3..047fb25 100644 --- a/src/H5FDfamily.c +++ b/src/H5FDfamily.c @@ -411,7 +411,7 @@ H5FD_family_fapl_copy(const void *_old_fa) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the fields of the structure */ - HDmemcpy(new_fa, old_fa, sizeof(H5FD_family_fapl_t)); + H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_family_fapl_t)); /* Deep copy the property list objects in the structure */ if(old_fa->memb_fapl_id==H5P_FILE_ACCESS_DEFAULT) { diff --git a/src/H5FDlog.c b/src/H5FDlog.c index 97d1b41..06a0e61 100644 --- a/src/H5FDlog.c +++ b/src/H5FDlog.c @@ -405,7 +405,7 @@ H5FD_log_fapl_copy(const void *_old_fa) HGOTO_ERROR(H5E_FILE, H5E_CANTALLOC, NULL, "unable to allocate log file FAPL") /* Copy the general information */ - HDmemcpy(new_fa, old_fa, sizeof(H5FD_log_fapl_t)); + H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_log_fapl_t)); /* Deep copy the log file name */ if(old_fa->logfile != NULL) @@ -1191,7 +1191,8 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd } /* end if */ } /* end if */ - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pread) */ if(addr != file->pos || OP_READ != file->op) { #ifdef H5_HAVE_GETTIMEOFDAY if(file->fa.flags & H5FD_LOG_TIME_SEEK) @@ -1234,6 +1235,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd #endif /* H5_HAVE_GETTIMEOFDAY */ } /* end if */ } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* * Read data, being careful of interrupted system calls, partial results, @@ -1247,6 +1249,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd h5_posix_io_t bytes_in = 0; /* # of bytes to read */ h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + HDoff_t offset = (HDoff_t)addr; /* Trying to read more bytes than the return type can handle is * undefined behavior in POSIX. @@ -1257,18 +1260,24 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_read = HDpread(file->fd, buf, bytes_in, offset); + offset += bytes_read; +#else bytes_read = HDread(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_read && EINTR == errno); if(-1 == bytes_read) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); if(file->fa.flags & H5FD_LOG_LOC_READ) HDfprintf(file->logfp, "Error! Reading: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size); - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset); + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset); } /* end if */ if(0 == bytes_read) { @@ -1398,7 +1407,8 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had file->nwrite[tmp_addr++]++; } /* end if */ - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pwrite) */ if(addr != file->pos || OP_WRITE != file->op) { #ifdef H5_HAVE_GETTIMEOFDAY if(file->fa.flags & H5FD_LOG_TIME_SEEK) @@ -1441,6 +1451,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had #endif /* H5_HAVE_GETTIMEOFDAY */ } /* end if */ } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* * Write the data, being careful of interrupted system calls and partial @@ -1454,6 +1465,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had h5_posix_io_t bytes_in = 0; /* # of bytes to write */ h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */ + HDoff_t offset = (HDoff_t)addr; /* Trying to write more bytes than the return type can handle is * undefined behavior in POSIX. @@ -1464,18 +1476,24 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset); + offset += bytes_wrote; +#else bytes_wrote = HDwrite(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_wrote && EINTR == errno); if(-1 == bytes_wrote) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); if(file->fa.flags & H5FD_LOG_LOC_WRITE) HDfprintf(file->logfp, "Error! Writing: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size); - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset); + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset); } /* end if */ HDassert(bytes_wrote > 0); diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index 3ab90aa..d5aa170 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -745,7 +745,7 @@ if(H5FD_mpio_Debug[(int)'t']) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the general information */ - HDmemcpy(new_fa, old_fa, sizeof(H5FD_mpio_fapl_t)); + H5MM_memcpy(new_fa, old_fa, sizeof(H5FD_mpio_fapl_t)); /* Duplicate communicator and Info object. */ if(H5FD_mpi_comm_info_dup(old_fa->comm, old_fa->info, &new_fa->comm, &new_fa->info) < 0) diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c index c507387..0054a86 100644 --- a/src/H5FDsec2.c +++ b/src/H5FDsec2.c @@ -682,11 +682,13 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS if(REGION_OVERFLOW(addr, size)) HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu", (unsigned long long)addr) - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pread) */ if(addr != file->pos || OP_READ != file->op) { if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0) HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* Read data, being careful of interrupted system calls, partial results, * and the end of the file. @@ -694,7 +696,8 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS while(size > 0) { h5_posix_io_t bytes_in = 0; /* # of bytes to read */ - h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */ + HDoff_t offset = (HDoff_t)addr; /* Trying to read more bytes than the return type can handle is * undefined behavior in POSIX. @@ -705,15 +708,21 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_read = HDpread(file->fd, buf, bytes_in, offset); + offset += bytes_read; +#else bytes_read = HDread(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_read && EINTR == errno); if(-1 == bytes_read) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset); } /* end if */ if(0 == bytes_read) { @@ -777,11 +786,13 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU if(REGION_OVERFLOW(addr, size)) HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu, size = %llu", (unsigned long long)addr, (unsigned long long)size) - /* Seek to the correct location */ +#ifndef H5_HAVE_PREADWRITE + /* Seek to the correct location (if we don't have pwrite) */ if(addr != file->pos || OP_WRITE != file->op) { if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0) HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") } /* end if */ +#endif /* H5_HAVE_PREADWRITE */ /* Write the data, being careful of interrupted system calls and partial * results @@ -790,6 +801,7 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU h5_posix_io_t bytes_in = 0; /* # of bytes to write */ h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */ + HDoff_t offset = (HDoff_t)addr; /* Trying to write more bytes than the return type can handle is * undefined behavior in POSIX. @@ -800,15 +812,21 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU bytes_in = (h5_posix_io_t)size; do { +#ifdef H5_HAVE_PREADWRITE + bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset); + offset += bytes_wrote; +#else bytes_wrote = HDwrite(file->fd, buf, bytes_in); +#endif /* H5_HAVE_PREADWRITE */ } while(-1 == bytes_wrote && EINTR == errno); if(-1 == bytes_wrote) { /* error */ int myerrno = errno; time_t mytime = HDtime(NULL); - HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset); + offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR); + + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset); } /* end if */ HDassert(bytes_wrote > 0); @@ -642,7 +642,7 @@ H5FL__reg_term(void) tmp = H5FL_reg_gc_head.first->next; #ifdef H5FL_DEBUG -printf("%s: head->name = %s, head->allocated = %d\n", FUNC, H5FL_reg_gc_head.first->list->name, (int)H5FL_reg_gc_head.first->list->allocated); +HDprintf("%s: head->name = %s, head->allocated = %d\n", FUNC, H5FL_reg_gc_head.first->list->name, (int)H5FL_reg_gc_head.first->list->allocated); #endif /* H5FL_DEBUG */ /* Check if the list has allocations outstanding */ if(H5FL_reg_gc_head.first->list->allocated > 0) { @@ -1142,7 +1142,7 @@ H5FL_blk_realloc(H5FL_blk_head_t *head, void *block, size_t new_size H5FL_TRACK_ if((ret_value=H5FL_blk_malloc(head,new_size H5FL_TRACK_INFO_INT))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for block") blk_size=MIN(new_size,temp->size); - HDmemcpy(ret_value,block,blk_size); + H5MM_memcpy(ret_value,block,blk_size); H5FL_blk_free(head,block); } /* end if */ else { @@ -1312,7 +1312,7 @@ H5FL__blk_term(void) tmp = H5FL_blk_gc_head.first->next; #ifdef H5FL_DEBUG -printf("%s: head->name = %s, head->allocated = %d\n", FUNC, H5FL_blk_gc_head.first->pq->name, (int)H5FL_blk_gc_head.first->pq->allocated); +HDprintf("%s: head->name = %s, head->allocated = %d\n", FUNC, H5FL_blk_gc_head.first->pq->name, (int)H5FL_blk_gc_head.first->pq->allocated); #endif /* H5FL_DEBUG */ /* Check if the list has allocations outstanding */ @@ -1630,7 +1630,7 @@ H5FL_arr_realloc(H5FL_arr_head_t *head, void * obj, size_t new_elem) /* Copy the appropriate amount of elements */ blk_size = head->list_arr[MIN(temp->nelem, new_elem)].size; - HDmemcpy(ret_value, obj, blk_size); + H5MM_memcpy(ret_value, obj, blk_size); /* Free the old block */ H5FL_arr_free(head, obj); @@ -1780,7 +1780,7 @@ H5FL__arr_term(void) /* Check if the list has allocations outstanding */ #ifdef H5FL_DEBUG -printf("%s: head->name = %s, head->allocated = %d\n", FUNC, H5FL_arr_gc_head.first->list->name, (int)H5FL_arr_gc_head.first->list->allocated); +HDprintf("%s: head->name = %s, head->allocated = %d\n", FUNC, H5FL_arr_gc_head.first->list->name, (int)H5FL_arr_gc_head.first->list->allocated); #endif /* H5FL_DEBUG */ if(H5FL_arr_gc_head.first->list->allocated > 0) { /* Add free list to the list of nodes with allocations open still */ @@ -2408,7 +2408,7 @@ H5FL__fac_term_all(void) tmp = H5FL_fac_gc_head.first->next; #ifdef H5FL_DEBUG -printf("%s: head->size = %d, head->allocated = %d\n", FUNC, (int)H5FL_fac_gc_head.first->list->size, (int)H5FL_fac_gc_head.first->list->allocated); +HDprintf("%s: head->size = %d, head->allocated = %d\n", FUNC, (int)H5FL_fac_gc_head.first->list->size, (int)H5FL_fac_gc_head.first->list->allocated); #endif /* H5FL_DEBUG */ /* The list cannot have any allocations outstanding */ @@ -36,6 +36,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FSpkg.h" /* File free space */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -615,7 +616,7 @@ H5FS__new(const H5F_t *f, uint16_t nclasses, const H5FS_section_class_t *classes HDassert(u == classes[u]->type); /* Copy the class information into the free space manager */ - HDmemcpy(&fspace->sect_cls[u], classes[u], sizeof(H5FS_section_class_t)); + H5MM_memcpy(&fspace->sect_cls[u], classes[u], sizeof(H5FS_section_class_t)); /* Call the class initialization routine, if there is one */ if(fspace->sect_cls[u].init_cls) diff --git a/src/H5FScache.c b/src/H5FScache.c index ac0874e..7525a9a 100644 --- a/src/H5FScache.c +++ b/src/H5FScache.c @@ -38,6 +38,7 @@ #include "H5Fprivate.h" /* File */ #include "H5FSpkg.h" /* File free space */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vectors and arrays */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -707,7 +708,7 @@ H5FS__cache_hdr_serialize(const H5F_t *f, void *_image, size_t len, (fspace->alloc_sect_size == (size_t)fspace->sect_size))); /* Magic number */ - HDmemcpy(image, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -1265,7 +1266,7 @@ H5FS__cache_sinfo_serialize(const H5F_t *f, void *_image, size_t len, HDassert(fspace->sect_cls); /* Magic number */ - HDmemcpy(image, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ diff --git a/src/H5Faccum.c b/src/H5Faccum.c index 0b33f8e..8d7852b 100644 --- a/src/H5Faccum.c +++ b/src/H5Faccum.c @@ -38,6 +38,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5Fpkg.h" /* File access */ #include "H5FDprivate.h" /* File drivers */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vectors and arrays */ @@ -198,7 +199,7 @@ H5F__accum_read(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, } /* end if */ /* Copy the data out of the buffer */ - HDmemcpy(buf, accum->buf + (addr - new_addr), size); + H5MM_memcpy(buf, accum->buf + (addr - new_addr), size); /* Adjust the accumulator address & size */ accum->loc = new_addr; @@ -250,7 +251,7 @@ H5F__accum_read(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, } /* end else */ /* Copy the dirty region to buffer */ - HDmemcpy((unsigned char *)buf + buf_off, (unsigned char *)accum->buf + accum->dirty_off + dirty_off, overlap_size); + H5MM_memcpy((unsigned char *)buf + buf_off, (unsigned char *)accum->buf + accum->dirty_off + dirty_off, overlap_size); } /* end if */ } /* end else */ } /* end if */ @@ -457,7 +458,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, HDmemmove(accum->buf + size, accum->buf, accum->size); /* Copy the new metadata at the front */ - HDmemcpy(accum->buf, buf, size); + H5MM_memcpy(accum->buf, buf, size); /* Set the new size & location of the metadata accumulator */ accum->loc = addr; @@ -479,7 +480,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, HGOTO_ERROR(H5E_IO, H5E_CANTRESIZE, FAIL, "can't adjust metadata accumulator") /* Copy the new metadata to the end */ - HDmemcpy(accum->buf + accum->size, buf, size); + H5MM_memcpy(accum->buf + accum->size, buf, size); /* Adjust the dirty region and mark accumulator dirty */ if(accum->dirty) @@ -502,7 +503,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, size_t dirty_off = (size_t)(addr - accum->loc); /* Copy the new metadata to the proper location within the accumulator */ - HDmemcpy(accum->buf + dirty_off, buf, size); + H5MM_memcpy(accum->buf + dirty_off, buf, size); /* Adjust the dirty region and mark accumulator dirty */ if(accum->dirty) { @@ -545,7 +546,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, HDmemmove(accum->buf + size, accum->buf + old_offset, (accum->size - old_offset)); /* Copy the new metadata at the front */ - HDmemcpy(accum->buf, buf, size); + H5MM_memcpy(accum->buf, buf, size); /* Set the new size & location of the metadata accumulator */ accum->loc = addr; @@ -582,7 +583,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, dirty_off = (size_t)(addr - accum->loc); /* Copy the new metadata to the end */ - HDmemcpy(accum->buf + dirty_off, buf, size); + H5MM_memcpy(accum->buf + dirty_off, buf, size); /* Set the new size of the metadata accumulator */ accum->size += add_size; @@ -625,7 +626,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, } /* end if */ /* Copy the new metadata to the buffer */ - HDmemcpy(accum->buf, buf, size); + H5MM_memcpy(accum->buf, buf, size); /* Set the new size & location of the metadata accumulator */ accum->loc = addr; @@ -688,7 +689,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, accum->size = size; /* Store the piece of metadata in the accumulator */ - HDmemcpy(accum->buf, buf, size); + H5MM_memcpy(accum->buf, buf, size); /* Adjust the dirty region and mark accumulator dirty */ accum->dirty_off = 0; @@ -721,7 +722,7 @@ H5F__accum_write(H5F_t *f, H5FD_mem_t map_type, haddr_t addr, accum->size = size; /* Store the piece of metadata in the accumulator */ - HDmemcpy(accum->buf, buf, size); + H5MM_memcpy(accum->buf, buf, size); /* Adjust the dirty region and mark accumulator dirty */ accum->dirty_off = 0; diff --git a/src/H5Fint.c b/src/H5Fint.c index 8a7019d..5775275 100644 --- a/src/H5Fint.c +++ b/src/H5Fint.c @@ -3254,7 +3254,7 @@ H5F_get_metadata_read_retry_info(H5F_t *file, H5F_retry_info_t *info) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") /* Copy the information */ - HDmemcpy(info->retries[j], file->shared->retries[i], tot_size); + H5MM_memcpy(info->retries[j], file->shared->retries[i], tot_size); } /* Increment location in info->retries[] array */ diff --git a/src/H5Fmpi.c b/src/H5Fmpi.c index 6ddbfbb..5bbd717 100644 --- a/src/H5Fmpi.c +++ b/src/H5Fmpi.c @@ -94,7 +94,7 @@ H5F_get_mpi_handle(const H5F_t *f, MPI_File **f_handle) FUNC_ENTER_NOAPI(FAIL) - assert(f && f->shared); + HDassert(f && f->shared); /* Dispatch to driver */ if ((ret_value = H5FD_get_vfd_handle(f->shared->lf, fapl, (void **)f_handle)) < 0) diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 5f7a1b2..e3860a0 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -28,6 +28,7 @@ typedef struct H5F_t H5F_t; #include "H5FDpublic.h" /* File drivers */ /* Private headers needed by this file */ +#include "H5MMprivate.h" /* Memory management */ #ifdef H5_HAVE_PARALLEL #include "H5Pprivate.h" /* Property lists */ #endif /* H5_HAVE_PARALLEL */ @@ -134,7 +135,7 @@ typedef struct H5F_t H5F_t; \ HDcompile_assert(sizeof(double) == 8); \ HDcompile_assert(sizeof(double) == sizeof(uint64_t)); \ - HDmemcpy(&_n, &n, sizeof(double)); \ + H5MM_memcpy(&_n, &n, sizeof(double)); \ for(_u = 0; _u < sizeof(uint64_t); _u++, _n >>= 8) \ *_p++ = (uint8_t)(_n & 0xff); \ (p) = (uint8_t *)(p) + 8; \ @@ -240,7 +241,7 @@ typedef struct H5F_t H5F_t; (p) += 8; \ for(_u = 0; _u < sizeof(uint64_t); _u++) \ _n = (_n << 8) | *(--p); \ - HDmemcpy(&(n), &_n, sizeof(double)); \ + H5MM_memcpy(&(n), &_n, sizeof(double)); \ (p) += 8; \ } diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c index 489cc21..3c225a2 100644 --- a/src/H5Fsuper.c +++ b/src/H5Fsuper.c @@ -555,7 +555,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) /* Set the B-tree internal node values, etc */ if(H5P_set(c_plist, H5F_CRT_BTREE_RANK_NAME, udata.btree_k) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "unable to set rank for btree internal nodes") - HDmemcpy(sblock->btree_k, udata.btree_k, sizeof(unsigned) * (size_t)H5B_NUM_BTREE_ID); + H5MM_memcpy(sblock->btree_k, udata.btree_k, sizeof(unsigned) * (size_t)H5B_NUM_BTREE_ID); } /* end if */ else { /* Get the (default) B-tree internal node values, etc */ diff --git a/src/H5Fsuper_cache.c b/src/H5Fsuper_cache.c index 361f8a1..125d6cf 100644 --- a/src/H5Fsuper_cache.c +++ b/src/H5Fsuper_cache.c @@ -269,7 +269,7 @@ H5F__drvrinfo_prefix_decode(H5O_drvinfo_t *drvrinfo, char *drv_name, /* Driver name and/or version */ if(drv_name) { - HDmemcpy(drv_name, (const char *)image, (size_t)8); + H5MM_memcpy(drv_name, (const char *)image, (size_t)8); drv_name[8] = '\0'; image += 8; /* advance past name/version */ } /* end if */ @@ -682,7 +682,7 @@ H5F__cache_superblock_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNU HDassert(sblock->cache_info.flush_me_last); /* Encode the common portion of the file superblock for all versions */ - HDmemcpy(image, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN); + H5MM_memcpy(image, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN); image += H5F_SIGNATURE_LEN; *image++ = (uint8_t)sblock->super_vers; diff --git a/src/H5Gbtree2.c b/src/H5Gbtree2.c index 721d591..71e0b2d 100644 --- a/src/H5Gbtree2.c +++ b/src/H5Gbtree2.c @@ -35,6 +35,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5Gpkg.h" /* Groups */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -206,7 +207,7 @@ H5G_dense_btree2_name_store(void *_nrecord, const void *_udata) /* Copy user information info native record */ nrecord->hash = udata->common.name_hash; - HDmemcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); + H5MM_memcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); FUNC_LEAVE_NOAPI(SUCCEED) } /* H5G_dense_btree2_name_store() */ @@ -305,7 +306,7 @@ H5G_dense_btree2_name_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR_UN /* Encode the record's fields */ UINT32ENCODE(raw, nrecord->hash) - HDmemcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); + H5MM_memcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); FUNC_LEAVE_NOAPI(SUCCEED) } /* H5G_dense_btree2_name_encode() */ @@ -333,7 +334,7 @@ H5G_dense_btree2_name_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR_UN /* Decode the record's fields */ UINT32DECODE(raw, nrecord->hash) - HDmemcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN); + H5MM_memcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN); FUNC_LEAVE_NOAPI(SUCCEED) } /* H5G_dense_btree2_name_decode() */ @@ -393,7 +394,7 @@ H5G_dense_btree2_corder_store(void *_nrecord, const void *_udata) /* Copy user information info native record */ nrecord->corder = udata->common.corder; - HDmemcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); + H5MM_memcpy(nrecord->id, udata->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); FUNC_LEAVE_NOAPI(SUCCEED) } /* H5G_dense_btree2_corder_store() */ @@ -469,7 +470,7 @@ H5G_dense_btree2_corder_encode(uint8_t *raw, const void *_nrecord, void H5_ATTR_ /* Encode the record's fields */ INT64ENCODE(raw, nrecord->corder) - HDmemcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); + H5MM_memcpy(raw, nrecord->id, (size_t)H5G_DENSE_FHEAP_ID_LEN); FUNC_LEAVE_NOAPI(SUCCEED) } /* H5G_dense_btree2_corder_encode() */ @@ -497,7 +498,7 @@ H5G_dense_btree2_corder_decode(const uint8_t *raw, void *_nrecord, void H5_ATTR_ /* Decode the record's fields */ INT64DECODE(raw, nrecord->corder) - HDmemcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN); + H5MM_memcpy(nrecord->id, raw, (size_t)H5G_DENSE_FHEAP_ID_LEN); FUNC_LEAVE_NOAPI(SUCCEED) } /* H5G_dense_btree2_corder_decode() */ diff --git a/src/H5Gcache.c b/src/H5Gcache.c index b447cad..0ffdc53 100644 --- a/src/H5Gcache.c +++ b/src/H5Gcache.c @@ -36,6 +36,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5Gpkg.h" /* Groups */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -287,7 +288,7 @@ H5G__cache_node_serialize(const H5F_t *f, void *_image, size_t len, HDassert(len == sym->node_size); /* magic number */ - HDmemcpy(image, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* version number */ diff --git a/src/H5Gent.c b/src/H5Gent.c index baee35c..19aef10 100644 --- a/src/H5Gent.c +++ b/src/H5Gent.c @@ -32,6 +32,7 @@ #include "H5FLprivate.h" /* Free Lists */ #include "H5Gpkg.h" /* Groups */ #include "H5HLprivate.h" /* Local Heaps */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -331,7 +332,7 @@ H5G__ent_copy(H5G_entry_t *dst, const H5G_entry_t *src, H5_copy_depth_t depth) HDassert(depth == H5_COPY_SHALLOW || depth == H5_COPY_DEEP); /* Copy the top level information */ - HDmemcpy(dst, src, sizeof(H5G_entry_t)); + H5MM_memcpy(dst, src, sizeof(H5G_entry_t)); /* Deep copy the names */ if(depth == H5_COPY_DEEP) { diff --git a/src/H5Gname.c b/src/H5Gname.c index 2aece2b..fa0a925 100644 --- a/src/H5Gname.c +++ b/src/H5Gname.c @@ -522,7 +522,7 @@ H5G_name_copy(H5G_name_t *dst, const H5G_name_t *src, H5_copy_depth_t depth) HDassert(depth == H5_COPY_SHALLOW || depth == H5_COPY_DEEP); /* Copy the top level information */ - HDmemcpy(dst, src, sizeof(H5G_name_t)); + H5MM_memcpy(dst, src, sizeof(H5G_name_t)); /* Deep copy the names */ if(depth == H5_COPY_DEEP) { diff --git a/src/H5Gnode.c b/src/H5Gnode.c index 72b3633..b79b7d2 100644 --- a/src/H5Gnode.c +++ b/src/H5Gnode.c @@ -672,7 +672,7 @@ H5G__node_insert(H5F_t *f, haddr_t addr, void H5_ATTR_UNUSED *_lt_key, if(NULL == (snrt = (H5G_node_t *)H5AC_protect(f, H5AC_SNODE, *new_node_p, f, H5AC__NO_FLAGS_SET))) HGOTO_ERROR(H5E_SYM, H5E_CANTLOAD, H5B_INS_ERROR, "unable to split symbol table node") - HDmemcpy(snrt->entry, sn->entry + H5F_SYM_LEAF_K(f), + H5MM_memcpy(snrt->entry, sn->entry + H5F_SYM_LEAF_K(f), H5F_SYM_LEAF_K(f) * sizeof(H5G_entry_t)); snrt->nsyms = H5F_SYM_LEAF_K(f); snrt_flags |= H5AC__DIRTIED_FLAG; @@ -1262,7 +1262,7 @@ H5G__node_copy(H5F_t *f, const void H5_ATTR_UNUSED *_lt_key, haddr_t addr, char *link_name; /* Pointer to value of soft link */ /* Make a temporary copy, so that it will not change the info in the cache */ - HDmemcpy(&tmp_src_ent, src_ent, sizeof(H5G_entry_t)); + H5MM_memcpy(&tmp_src_ent, src_ent, sizeof(H5G_entry_t)); /* Set up group location for soft link to start in */ H5G_name_reset(&grp_path); diff --git a/src/H5Gtraverse.c b/src/H5Gtraverse.c index d029bea..492b5b9 100644 --- a/src/H5Gtraverse.c +++ b/src/H5Gtraverse.c @@ -555,7 +555,7 @@ H5G__traverse_real(const H5G_loc_t *_loc, const char *name, unsigned target, * Copy the component name into a null-terminated buffer so * we can pass it down to the other symbol table functions. */ - HDmemcpy(comp, name, nchars); + H5MM_memcpy(comp, name, nchars); comp[nchars] = '\0'; /* @@ -670,7 +670,7 @@ H5G__traverse_real(const H5G_loc_t *_loc, const char *name, unsigned target, /* Only keep the creation order information from the parent * group's link info */ - HDmemcpy(&tmp_linfo, &def_linfo, sizeof(H5O_linfo_t)); + H5MM_memcpy(&tmp_linfo, &def_linfo, sizeof(H5O_linfo_t)); tmp_linfo.track_corder = par_linfo.track_corder; tmp_linfo.index_corder = par_linfo.index_corder; linfo = &tmp_linfo; @@ -42,6 +42,8 @@ #include "H5FOprivate.h" /* File objects */ #include "H5HFpkg.h" /* Fractal heaps */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ + /****************/ /* Local Macros */ @@ -104,7 +106,7 @@ H5HF_op_read(const void *obj, size_t obj_len, void *op_data) FUNC_ENTER_NOAPI_NOINIT_NOERR /* Perform "read", using memcpy() */ - HDmemcpy(op_data, obj, obj_len); + H5MM_memcpy(op_data, obj, obj_len); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5HF_op_read() */ @@ -129,7 +131,7 @@ H5HF_op_write(const void *obj, size_t obj_len, void *op_data) FUNC_ENTER_NOAPI_NOINIT_NOERR /* Perform "write", using memcpy() */ - HDmemcpy((void *)obj, op_data, obj_len); /* Casting away const OK -QAK */ + H5MM_memcpy((void *)obj, op_data, obj_len); /* Casting away const OK -QAK */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5HF_op_write() */ diff --git a/src/H5HFcache.c b/src/H5HFcache.c index 0c5d3aa..2d1c1f2 100644 --- a/src/H5HFcache.c +++ b/src/H5HFcache.c @@ -772,7 +772,7 @@ H5HF__cache_hdr_serialize(const H5F_t *f, void *_image, size_t len, hdr->f = f; /* Magic number */ - HDmemcpy(image, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -1362,7 +1362,7 @@ H5HF__cache_iblock_serialize(const H5F_t *f, void *_image, size_t len, hdr->f = f; /* Magic number */ - HDmemcpy(image, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -1677,7 +1677,7 @@ H5HF__cache_dblock_verify_chksum(const void *_image, size_t len, void *_udata) /* Set up parameters for filter pipeline */ nbytes = len; filter_mask = udata->filter_mask; - HDmemcpy(read_buf, image, len); + H5MM_memcpy(read_buf, image, len); /* Push direct block data through I/O filter pipeline */ if(H5Z_pipeline(&(hdr->pline), H5Z_FLAG_REVERSE, &filter_mask, H5Z_ENABLE_EDC, filter_cb, &nbytes, &len, &read_buf) < 0) @@ -1724,7 +1724,7 @@ H5HF__cache_dblock_verify_chksum(const void *_image, size_t len, void *_udata) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") /* Copy un-filtered data into block's buffer */ - HDmemcpy(udata->dblk, read_buf, len); + H5MM_memcpy(udata->dblk, read_buf, len); } /* end if */ done: @@ -1829,7 +1829,7 @@ H5HF__cache_dblock_deserialize(const void *_image, size_t len, void *_udata, HGOTO_ERROR(H5E_HEAP, H5E_NOSPACE, NULL, "memory allocation failed for pipeline buffer") /* Copy compressed image into buffer */ - HDmemcpy(read_buf, image, len); + H5MM_memcpy(read_buf, image, len); /* Push direct block data through I/O filter pipeline */ nbytes = len; @@ -1841,7 +1841,7 @@ H5HF__cache_dblock_deserialize(const void *_image, size_t len, void *_udata, HDassert(nbytes == dblock->size); /* Copy un-filtered data into block's buffer */ - HDmemcpy(dblock->blk, read_buf, dblock->size); + H5MM_memcpy(dblock->blk, read_buf, dblock->size); } /* end if */ } /* end if */ else { @@ -1856,7 +1856,7 @@ H5HF__cache_dblock_deserialize(const void *_image, size_t len, void *_udata, /* Copy image to dblock->blk */ HDassert(dblock->size == len); - HDmemcpy(dblock->blk, image, dblock->size); + H5MM_memcpy(dblock->blk, image, dblock->size); } /* end else */ /* Start decoding direct block */ @@ -2146,7 +2146,7 @@ H5HF__cache_dblock_pre_serialize(H5F_t *f, void *_thing, image = dblock->blk; /* Magic number */ - HDmemcpy(image, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Version # */ @@ -2201,7 +2201,7 @@ H5HF__cache_dblock_pre_serialize(H5F_t *f, void *_thing, HGOTO_ERROR(H5E_HEAP, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline buffer") /* Copy the direct block's image into the buffer to compress */ - HDmemcpy(write_buf, dblock->blk, write_size); + H5MM_memcpy(write_buf, dblock->blk, write_size); /* Push direct block data through I/O filter pipeline */ nbytes = write_size; @@ -2460,7 +2460,7 @@ H5HF__cache_dblock_serialize(const H5F_t *f, void *image, size_t len, HDassert(dblock->write_size == len); /* Copy the image from *(dblock->write_buf) to *image */ - HDmemcpy(image, dblock->write_buf, dblock->write_size); + H5MM_memcpy(image, dblock->write_buf, dblock->write_size); /* Free *(dblock->write_buf) if it was allocated by the * pre-serialize function diff --git a/src/H5HFdbg.c b/src/H5HFdbg.c index fc437dc..22de0c4 100644 --- a/src/H5HFdbg.c +++ b/src/H5HFdbg.c @@ -483,7 +483,7 @@ H5HF_dblock_debug_cb(H5FS_section_info_t *_sect, void *_udata) /* Flag overlaps */ if (overlap) - fprintf(udata->stream, "***THAT FREE BLOCK OVERLAPPED A PREVIOUS ONE!\n"); + HDfprintf(udata->stream, "***THAT FREE BLOCK OVERLAPPED A PREVIOUS ONE!\n"); else udata->amount_free += len; } /* end if */ diff --git a/src/H5HFhdr.c b/src/H5HFhdr.c index b014017..5750a03 100644 --- a/src/H5HFhdr.c +++ b/src/H5HFhdr.c @@ -36,6 +36,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5HFpkg.h" /* Fractal heaps */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5VMprivate.h" /* Vectors and arrays */ /****************/ @@ -387,7 +388,7 @@ H5HF_hdr_create(H5F_t *f, const H5HF_create_t *cparam) /* Set the creation parameters for the heap */ hdr->max_man_size = cparam->max_man_size; hdr->checksum_dblocks = cparam->checksum_dblocks; - HDmemcpy(&(hdr->man_dtable.cparam), &(cparam->managed), sizeof(H5HF_dtable_cparam_t)); + H5MM_memcpy(&(hdr->man_dtable.cparam), &(cparam->managed), sizeof(H5HF_dtable_cparam_t)); /* Set root table address to indicate that the heap is empty currently */ hdr->man_dtable.table_addr = HADDR_UNDEF; diff --git a/src/H5HFhuge.c b/src/H5HFhuge.c index 6e475ad..d496d62 100644 --- a/src/H5HFhuge.c +++ b/src/H5HFhuge.c @@ -355,7 +355,7 @@ HDfprintf(stderr, "%s: obj_size = %Zu\n", FUNC, obj_size); write_size = obj_size; if(NULL == (write_buf = H5MM_malloc(write_size))) HGOTO_ERROR(H5E_HEAP, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline buffer") - HDmemcpy(write_buf, obj, write_size); + H5MM_memcpy(write_buf, obj, write_size); /* Push direct block data through I/O filter pipeline */ nbytes = write_size; @@ -794,7 +794,7 @@ H5HF__huge_op_real(H5HF_hdr_t *hdr, const uint8_t *id, hbool_t is_read, /* Copy object to user's buffer if there's filters on heap data */ /* (if there's no filters, the object was read directly into the user's buffer) */ if(hdr->filter_len > 0) - HDmemcpy(op_data, read_buf, (size_t)obj_size); + H5MM_memcpy(op_data, read_buf, (size_t)obj_size); } /* end if */ else { /* Call the user's 'op' callback */ diff --git a/src/H5HFman.c b/src/H5HFman.c index 7f90f49..e5b5cb8 100644 --- a/src/H5HFman.c +++ b/src/H5HFman.c @@ -183,7 +183,7 @@ H5HF__man_insert(H5HF_hdr_t *hdr, size_t obj_size, const void *obj, void *_id) p = dblock->blk + blk_off; /* Copy the object's data into the heap */ - HDmemcpy(p, obj, obj_size); + H5MM_memcpy(p, obj, obj_size); p += obj_size; /* Sanity check */ diff --git a/src/H5HFsection.c b/src/H5HFsection.c index 36e966e..f5ac8e5 100644 --- a/src/H5HFsection.c +++ b/src/H5HFsection.c @@ -3082,7 +3082,7 @@ H5HF__sect_indirect_reduce_row(H5HF_hdr_t *hdr, H5HF_free_section_t *row_sect, HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, FAIL, "allocation failed for row section pointer array") /* Transfer row sections between current & peer sections */ - HDmemcpy(&peer_sect->u.indirect.dir_rows[0], + H5MM_memcpy(&peer_sect->u.indirect.dir_rows[0], §->u.indirect.dir_rows[0], (sizeof(H5HF_free_section_t *) * peer_dir_nrows)); HDmemmove(§->u.indirect.dir_rows[0], @@ -3321,7 +3321,7 @@ H5HF__sect_indirect_reduce(H5HF_hdr_t *hdr, H5HF_free_section_t *sect, HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, FAIL, "allocation failed for indirect section pointer array") /* Transfer child indirect sections between current & peer sections */ - HDmemcpy(&peer_sect->u.indirect.indir_ents[0], + H5MM_memcpy(&peer_sect->u.indirect.indir_ents[0], §->u.indirect.indir_ents[sect->u.indirect.indir_nents - peer_nentries], (sizeof(H5HF_free_section_t *) * peer_nentries)); sect->u.indirect.indir_nents -= (peer_nentries + 1); /* Transferred blocks, plus child entry */ @@ -3636,7 +3636,7 @@ H5HF__sect_indirect_merge_row(H5HF_hdr_t *hdr, H5HF_free_section_t *row_sect1, sect1->u.indirect.dir_rows = new_dir_rows; /* Transfer the second section's rows to first section */ - HDmemcpy(§1->u.indirect.dir_rows[sect1->u.indirect.dir_nrows], + H5MM_memcpy(§1->u.indirect.dir_rows[sect1->u.indirect.dir_nrows], §2->u.indirect.dir_rows[src_row2], (sizeof(H5HF_free_section_t *) * nrows_moved2)); @@ -3682,7 +3682,7 @@ H5HF__sect_indirect_merge_row(H5HF_hdr_t *hdr, H5HF_free_section_t *row_sect1, sect1->u.indirect.indir_ents = new_indir_ents; /* Transfer the second section's entries to first section */ - HDmemcpy(§1->u.indirect.indir_ents[sect1->u.indirect.indir_nents], + H5MM_memcpy(§1->u.indirect.indir_ents[sect1->u.indirect.indir_nents], §2->u.indirect.indir_ents[0], (sizeof(H5HF_free_section_t *) * sect2->u.indirect.indir_nents)); } /* end else */ diff --git a/src/H5HFtest.c b/src/H5HFtest.c index 1b1f688..6f174bb 100644 --- a/src/H5HFtest.c +++ b/src/H5HFtest.c @@ -32,6 +32,8 @@ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5HFpkg.h" /* Fractal heaps */ +#include "H5MMprivate.h" /* Memory management */ + /****************/ /* Local Macros */ @@ -100,7 +102,7 @@ H5HF_get_cparam_test(const H5HF_t *fh, H5HF_create_t *cparam) else H5_CHECKED_ASSIGN(cparam->id_len, uint16_t, fh->hdr->id_len, unsigned); cparam->max_man_size = fh->hdr->max_man_size; - HDmemcpy(&(cparam->managed), &(fh->hdr->man_dtable.cparam), sizeof(H5HF_dtable_cparam_t)); + H5MM_memcpy(&(cparam->managed), &(fh->hdr->man_dtable.cparam), sizeof(H5HF_dtable_cparam_t)); H5O_msg_copy(H5O_PLINE_ID, &(fh->hdr->pline), &(cparam->pline)); FUNC_LEAVE_NOAPI(SUCCEED) diff --git a/src/H5HFtiny.c b/src/H5HFtiny.c index 5cf1c08..0c27180 100644 --- a/src/H5HFtiny.c +++ b/src/H5HFtiny.c @@ -35,6 +35,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5HFpkg.h" /* Fractal heaps */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -176,7 +177,7 @@ HDfprintf(stderr, "%s: obj_size = %Zu\n", FUNC, obj_size); *id++ = enc_obj_size & H5HF_TINY_MASK_EXT_2; } /* end else */ - HDmemcpy(id, obj, obj_size); + H5MM_memcpy(id, obj, obj_size); HDmemset(id + obj_size, 0, (hdr->id_len - ((size_t)1 + (size_t)hdr->tiny_len_extended + obj_size))); /* Update statistics about heap */ @@ -168,7 +168,7 @@ H5HG__create(H5F_t *f, size_t size) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed") /* Initialize the header */ - HDmemcpy(heap->chunk, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(heap->chunk, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC); p = heap->chunk + H5_SIZEOF_MAGIC; *p++ = H5HG_VERSION; *p++ = 0; /*reserved*/ @@ -553,7 +553,7 @@ H5HG_insert(H5F_t *f, size_t size, void *obj, H5HG_t *hobj/*out*/) /* Copy data into the heap */ if(size > 0) { - HDmemcpy(heap->obj[idx].begin + H5HG_SIZEOF_OBJHDR(f), obj, size); + H5MM_memcpy(heap->obj[idx].begin + H5HG_SIZEOF_OBJHDR(f), obj, size); #ifdef OLD_WAY /* Don't bother zeroing out the rest of the info in the heap -QAK */ HDmemset(heap->obj[idx].begin + H5HG_SIZEOF_OBJHDR(f) + size, 0, @@ -618,7 +618,7 @@ H5HG_read(H5F_t *f, H5HG_t *hobj, void *object/*out*/, size_t *buf_size) /* Allocate a buffer for the object read in, if the user didn't give one */ if(!object && NULL == (object = H5MM_malloc(size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(object, p, size); + H5MM_memcpy(object, p, size); /* * Advance the heap in the CWFS list. We might have done this already diff --git a/src/H5HGcache.c b/src/H5HGcache.c index beaea7b..29e88df 100644 --- a/src/H5HGcache.c +++ b/src/H5HGcache.c @@ -271,7 +271,7 @@ H5HG__cache_heap_deserialize(const void *_image, size_t len, void *_udata, HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the image buffer into the newly allocate chunk */ - HDmemcpy(heap->chunk, _image, len); + H5MM_memcpy(heap->chunk, _image, len); /* Deserialize the heap's header */ if(H5HG__hdr_deserialize(heap, (const uint8_t *)heap->chunk, f) < 0) @@ -448,7 +448,7 @@ H5HG__cache_heap_serialize(const H5F_t *f, void *image, size_t len, HDassert(heap->chunk); /* copy the image into the buffer */ - HDmemcpy(image, heap->chunk, len); + H5MM_memcpy(image, heap->chunk, len); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5HG__cache_heap_serialize() */ @@ -725,7 +725,7 @@ H5HL_insert(H5F_t *f, H5HL_t *heap, size_t buf_size, const void *buf)) } /* end if */ /* Copy the data into the heap */ - HDmemcpy(heap->dblk_image + offset, buf, buf_size); + H5MM_memcpy(heap->dblk_image + offset, buf, buf_size); /* Set return value */ ret_value = offset; diff --git a/src/H5HLcache.c b/src/H5HLcache.c index 926f787..8b04b47 100644 --- a/src/H5HLcache.c +++ b/src/H5HLcache.c @@ -36,6 +36,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5HLpkg.h" /* Local Heaps */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -464,7 +465,7 @@ H5HL__cache_prefix_deserialize(const void *_image, size_t len, void *_udata, image = ((const uint8_t *)_image) + heap->prfx_size; /* Copy the heap data from the speculative read buffer */ - HDmemcpy(heap->dblk_image, image, heap->dblk_size); + H5MM_memcpy(heap->dblk_image, image, heap->dblk_size); /* Build free list */ if(H5HL__fl_deserialize(heap) < 0) @@ -587,7 +588,7 @@ H5HL__cache_prefix_serialize(const H5F_t *f, void *_image, size_t len, heap->free_block = heap->freelist ? heap->freelist->offset : H5HL_FREE_NULL; /* Serialize the heap prefix */ - HDmemcpy(image, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; *image++ = H5HL_VERSION; *image++ = 0; /*reserved*/ @@ -615,7 +616,7 @@ H5HL__cache_prefix_serialize(const H5F_t *f, void *_image, size_t len, H5HL__fl_serialize(heap); /* Copy the heap data block into the cache image */ - HDmemcpy(image, heap->dblk_image, heap->dblk_size); + H5MM_memcpy(image, heap->dblk_image, heap->dblk_size); /* Sanity check */ HDassert((size_t)(image - (uint8_t *)_image) + heap->dblk_size == len); @@ -756,7 +757,7 @@ H5HL__cache_datablock_deserialize(const void *image, size_t len, void *_udata, HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, NULL, "can't allocate data block image buffer"); /* copy the datablock from the read buffer */ - HDmemcpy(heap->dblk_image, image, len); + H5MM_memcpy(heap->dblk_image, image, len); /* Build free list */ if(FAIL == H5HL__fl_deserialize(heap)) @@ -851,7 +852,7 @@ H5HL__cache_datablock_serialize(const H5F_t *f, void *image, size_t len, H5HL__fl_serialize(heap); /* Copy the heap's data block into the cache's image */ - HDmemcpy(image, heap->dblk_image, heap->dblk_size); + H5MM_memcpy(image, heap->dblk_image, heap->dblk_size); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5HL__cache_datablock_serialize() */ @@ -1676,7 +1676,7 @@ H5L_register(const H5L_class_t *cls) } /* end if */ /* Copy link class info into table */ - HDmemcpy(H5L_table_g + i, cls, sizeof(H5L_class_t)); + H5MM_memcpy(H5L_table_g + i, cls, sizeof(H5L_class_t)); done: FUNC_LEAVE_NOAPI(ret_value) @@ -2217,7 +2217,7 @@ H5L__create_ud(const H5G_loc_t *link_loc, const char *link_name, /* Fill in UD link-specific information in the link struct*/ if(ud_data_size > 0) { lnk.u.ud.udata = H5MM_malloc((size_t)ud_data_size); - HDmemcpy(lnk.u.ud.udata, ud_data, (size_t) ud_data_size); + H5MM_memcpy(lnk.u.ud.udata, ud_data, (size_t) ud_data_size); } /* end if */ else lnk.u.ud.udata = NULL; diff --git a/src/H5Lexternal.c b/src/H5Lexternal.c index 0f3296f..d838d77 100644 --- a/src/H5Lexternal.c +++ b/src/H5Lexternal.c @@ -306,7 +306,7 @@ H5L__extern_query(const char H5_ATTR_UNUSED * link_name, const void *_udata, siz buf_size = udata_size; /* Copy the udata verbatim up to buf_size */ - HDmemcpy(buf, udata, buf_size); + H5MM_memcpy(buf, udata, buf_size); } /* end if */ /* Set return value */ @@ -274,7 +274,7 @@ H5MM_malloc(size_t size) #if defined H5_MEMORY_ALLOC_SANITY_CHECK /* Initialize block list head singleton */ if(!H5MM_init_s) { - HDmemcpy(H5MM_block_head_s.sig, H5MM_block_signature_s, H5MM_SIG_SIZE); + H5MM_memcpy(H5MM_block_head_s.sig, H5MM_block_signature_s, H5MM_SIG_SIZE); H5MM_block_head_s.next = &H5MM_block_head_s; H5MM_block_head_s.prev = &H5MM_block_head_s; H5MM_block_head_s.u.info.size = SIZET_MAX; @@ -291,15 +291,15 @@ H5MM_malloc(size_t size) if(NULL != (block = (H5MM_block_t *)HDmalloc(alloc_size))) { /* Set up block */ - HDmemcpy(block->sig, H5MM_block_signature_s, H5MM_SIG_SIZE); + H5MM_memcpy(block->sig, H5MM_block_signature_s, H5MM_SIG_SIZE); block->next = H5MM_block_head_s.next; H5MM_block_head_s.next = block; block->next->prev = block; block->prev = &H5MM_block_head_s; block->u.info.size = size; block->u.info.in_use = TRUE; - HDmemcpy(block->b, H5MM_block_head_guard_s, H5MM_HEAD_GUARD_SIZE); - HDmemcpy(block->b + H5MM_HEAD_GUARD_SIZE + size, H5MM_block_tail_guard_s, H5MM_TAIL_GUARD_SIZE); + H5MM_memcpy(block->b, H5MM_block_head_guard_s, H5MM_HEAD_GUARD_SIZE); + H5MM_memcpy(block->b + H5MM_HEAD_GUARD_SIZE + size, H5MM_block_tail_guard_s, H5MM_TAIL_GUARD_SIZE); /* Update statistics */ H5MM_total_alloc_bytes_s += size; @@ -417,7 +417,7 @@ H5MM_realloc(void *mem, size_t size) H5MM__sanity_check(mem); ret_value = H5MM_malloc(size); - HDmemcpy(ret_value, mem, MIN(size, old_size)); + H5MM_memcpy(ret_value, mem, MIN(size, old_size)); H5MM_xfree(mem); } /* end if */ else @@ -564,3 +564,41 @@ H5MM_xfree(void *mem) FUNC_LEAVE_NOAPI(NULL) } /* end H5MM_xfree() */ + +/*------------------------------------------------------------------------- + * Function: H5MM_memcpy + * + * Purpose: Like memcpy(3) but with sanity checks on the parameters, + * particularly buffer overlap. + * + * Return: Success: pointer to dest + * Failure: NULL + * + * Programmer: Dana Robinson + * Spring 2019 + * + *------------------------------------------------------------------------- + */ +void * +H5MM_memcpy(void *dest, const void *src, size_t n) +{ + void *ret = NULL; + + /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ + FUNC_ENTER_NOAPI_NOINIT_NOERR + + HDassert(dest); + HDassert(src); +#if 0 + /* Commented out while we investigate overlapping buffers in the + * parallel filter code (HDFFV-10735). + */ + HDassert((char *)dest >= (const char *)src + n || (const char *)src >= (char *)dest + n); +#endif + + ret = HDmemcpy(dest, src, n); + + FUNC_LEAVE_NOAPI(ret) + +} /* end H5MM_memcpy() */ + diff --git a/src/H5MMprivate.h b/src/H5MMprivate.h index 0524601..2053215 100644 --- a/src/H5MMprivate.h +++ b/src/H5MMprivate.h @@ -45,6 +45,7 @@ H5_DLL void *H5MM_realloc(void *mem, size_t size); H5_DLL char *H5MM_xstrdup(const char *s); H5_DLL char *H5MM_strdup(const char *s); H5_DLL void *H5MM_xfree(void *mem); +H5_DLL void *H5MM_memcpy(void *dest, const void *src, size_t n); #if defined H5_MEMORY_ALLOC_SANITY_CHECK H5_DLL void H5MM_sanity_check_all(void); H5_DLL void H5MM_final_sanity_check(void); diff --git a/src/H5Oalloc.c b/src/H5Oalloc.c index 23dd928..c1f90cb 100644 --- a/src/H5Oalloc.c +++ b/src/H5Oalloc.c @@ -36,6 +36,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free lists */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Opkg.h" /* Object headers */ /****************/ @@ -949,7 +950,7 @@ H5O__alloc_chunk(H5F_t *f, H5O_t *oh, size_t size, size_t found_null, * # at the beginning of the chunk image. */ if(oh->version > H5O_VERSION_1) { - HDmemcpy(p, H5O_CHK_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(p, H5O_CHK_MAGIC, (size_t)H5_SIZEOF_MAGIC); p += H5_SIZEOF_MAGIC; } /* end if */ @@ -988,7 +989,7 @@ H5O__alloc_chunk(H5F_t *f, H5O_t *oh, size_t size, size_t found_null, HDassert(curr_msg->type->id != H5O_CONT_ID); /* Copy the raw data */ - HDmemcpy(p, curr_msg->raw - (size_t)H5O_SIZEOF_MSGHDR_OH(oh), + H5MM_memcpy(p, curr_msg->raw - (size_t)H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh)); /* Update the message info */ @@ -1044,7 +1045,7 @@ H5O__alloc_chunk(H5F_t *f, H5O_t *oh, size_t size, size_t found_null, null_msg->chunkno = oh->mesg[found_msg->msgno].chunkno; /* Copy the message to move (& its prefix) to its new location */ - HDmemcpy(p, oh->mesg[found_msg->msgno].raw - H5O_SIZEOF_MSGHDR_OH(oh), + H5MM_memcpy(p, oh->mesg[found_msg->msgno].raw - H5O_SIZEOF_MSGHDR_OH(oh), oh->mesg[found_msg->msgno].raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh)); /* Switch moved message to point to new location */ @@ -1519,7 +1520,7 @@ H5O__move_cont(H5F_t *f, H5O_t *oh, unsigned cont_u) move_size = curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh); /* Move message out of deleted chunk */ - HDmemcpy(move_start, curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), move_size); + H5MM_memcpy(move_start, curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), move_size); curr_msg->raw = move_start + H5O_SIZEOF_MSGHDR_OH(oh); curr_msg->chunkno = cont_chunkno; chk_dirtied = TRUE; @@ -1791,7 +1792,7 @@ H5O__move_msgs_forward(H5F_t *f, H5O_t *oh) } /* end if */ /* Copy raw data for non-null message to new chunk */ - HDmemcpy(null_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh)); + H5MM_memcpy(null_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), curr_msg->raw_size + (size_t)H5O_SIZEOF_MSGHDR_OH(oh)); /* Point non-null message at null message's space */ curr_msg->chunkno = null_msg->chunkno; diff --git a/src/H5Oattr.c b/src/H5Oattr.c index c420046..0a7c4bf 100644 --- a/src/H5Oattr.c +++ b/src/H5Oattr.c @@ -208,7 +208,7 @@ H5O_attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, HGOTO_ERROR(H5E_ATTR, H5E_CANTDECODE, NULL, "can't decode attribute dataspace") /* Copy the extent information to the dataspace */ - HDmemcpy(&(attr->shared->ds->extent), extent, sizeof(H5S_extent_t)); + H5MM_memcpy(&(attr->shared->ds->extent), extent, sizeof(H5S_extent_t)); /* Release temporary extent information */ extent = H5FL_FREE(H5S_extent_t, extent); @@ -240,7 +240,7 @@ H5O_attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, if(attr->shared->data_size) { if(NULL == (attr->shared->data = H5FL_BLK_MALLOC(attr_buf, attr->shared->data_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(attr->shared->data, p, attr->shared->data_size); + H5MM_memcpy(attr->shared->data, p, attr->shared->data_size); } /* end if */ /* Increment the reference count for this object header message in cache(compact @@ -336,7 +336,7 @@ H5O_attr_encode(H5F_t *f, uint8_t *p, const void *mesg) *p++ = attr->shared->encoding; /* Write the name including null terminator */ - HDmemcpy(p, attr->shared->name, name_len); + H5MM_memcpy(p, attr->shared->name, name_len); if(attr->shared->version < H5O_ATTR_VERSION_2) { /* Pad to the correct number of bytes */ HDmemset(p + name_len, 0, H5O_ALIGN_OLD(name_len) - name_len); @@ -369,7 +369,7 @@ H5O_attr_encode(H5F_t *f, uint8_t *p, const void *mesg) /* Store attribute data. If there's no data, store 0 as fill value. */ if(attr->shared->data) - HDmemcpy(p, attr->shared->data, attr->shared->data_size); + H5MM_memcpy(p, attr->shared->data, attr->shared->data_size); else HDmemset(p, 0, attr->shared->data_size); diff --git a/src/H5Oattribute.c b/src/H5Oattribute.c index 6e135c5..57ec9b8 100644 --- a/src/H5Oattribute.c +++ b/src/H5Oattribute.c @@ -862,7 +862,7 @@ H5O__attr_write_cb(H5O_t *oh, H5O_mesg_t *mesg/*in,out*/, /* (Needs to occur before updating the shared message, or the hash * value on the old & new messages will be the same) */ - HDmemcpy(((H5A_t *)mesg->native)->shared->data, udata->attr->shared->data, udata->attr->shared->data_size); + H5MM_memcpy(((H5A_t *)mesg->native)->shared->data, udata->attr->shared->data, udata->attr->shared->data_size); } /* end if */ /* Mark the message as modified */ diff --git a/src/H5Ocache.c b/src/H5Ocache.c index 578cff0..683d155 100644 --- a/src/H5Ocache.c +++ b/src/H5Ocache.c @@ -36,6 +36,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free lists */ #include "H5MFprivate.h" /* File memory management */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Opkg.h" /* Object headers */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -542,7 +543,7 @@ H5O__cache_serialize(const H5F_t *f, void *image, size_t len, void *_thing) * Can we rework things so that the object header and the cache * share a buffer? */ - HDmemcpy(image, oh->chunk[0].image, len); + H5MM_memcpy(image, oh->chunk[0].image, len); done: FUNC_LEAVE_NOAPI(ret_value) @@ -900,7 +901,7 @@ H5O__cache_chk_serialize(const H5F_t *f, void *image, size_t len, void *_thing) /* copy the chunk into the image -- this is potentially expensive. * Can we rework things so that the chunk and the cache share a buffer? */ - HDmemcpy(image, chk_proxy->oh->chunk[chk_proxy->chunkno].image, len); + H5MM_memcpy(image, chk_proxy->oh->chunk[chk_proxy->chunkno].image, len); done: FUNC_LEAVE_NOAPI(ret_value) @@ -1352,7 +1353,7 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image oh->chunk[chunkno].chunk_proxy = NULL; /* Copy disk image into chunk's image */ - HDmemcpy(oh->chunk[chunkno].image, image, oh->chunk[chunkno].size); + H5MM_memcpy(oh->chunk[chunkno].image, image, oh->chunk[chunkno].size); /* Point into chunk image to decode */ chunk_image = oh->chunk[chunkno].image; diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c index a3d4884..9578f95 100644 --- a/src/H5Ocopy.c +++ b/src/H5Ocopy.c @@ -732,7 +732,7 @@ H5O__copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out*/, * header. This will be written when the header is flushed to disk. */ if(oh_dst->version > H5O_VERSION_1) - HDmemcpy(current_pos, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(current_pos, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); current_pos += H5O_SIZEOF_HDR(oh_dst) - H5O_SIZEOF_CHKSUM_OH(oh_dst); /* Loop through destination messages, updating their "raw" info */ @@ -755,7 +755,7 @@ H5O__copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out*/, /* Copy each message that wasn't dirtied above */ if(!mesg_dst->dirty) /* Copy the message header plus the message's raw data. */ - HDmemcpy(current_pos, mesg_src->raw - msghdr_size, msghdr_size + mesg_src->raw_size); + H5MM_memcpy(current_pos, mesg_src->raw - msghdr_size, msghdr_size + mesg_src->raw_size); /* Set message's raw pointer to destination chunk's new "image" */ mesg_dst->raw = current_pos + msghdr_size; diff --git a/src/H5Odrvinfo.c b/src/H5Odrvinfo.c index 159c950..eb678e4 100644 --- a/src/H5Odrvinfo.c +++ b/src/H5Odrvinfo.c @@ -101,7 +101,7 @@ H5O_drvinfo_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for driver info message") /* Retrieve driver name */ - HDmemcpy(mesg->name, p, 8); + H5MM_memcpy(mesg->name, p, 8); mesg->name[8] = '\0'; p += 8; @@ -116,7 +116,7 @@ H5O_drvinfo_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, } /* end if */ /* Copy encoded driver info into buffer */ - HDmemcpy(mesg->buf, p, mesg->len); + H5MM_memcpy(mesg->buf, p, mesg->len); /* Set return value */ ret_value = (void *)mesg; @@ -152,11 +152,11 @@ H5O_drvinfo_encode(H5F_t H5_ATTR_UNUSED *f, hbool_t H5_ATTR_UNUSED disable_share /* Store version, driver name, buffer length, & encoded buffer */ *p++ = H5O_DRVINFO_VERSION; - HDmemcpy(p, mesg->name, 8); + H5MM_memcpy(p, mesg->name, 8); p += 8; HDassert(mesg->len <= 65535); UINT16ENCODE(p, mesg->len); - HDmemcpy(p, mesg->buf, mesg->len); + H5MM_memcpy(p, mesg->buf, mesg->len); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5O_drvinfo_encode() */ @@ -200,7 +200,7 @@ H5O_drvinfo_copy(const void *_mesg, void *_dest) dest = (H5O_drvinfo_t *)H5MM_xfree(dest); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") } /* end if */ - HDmemcpy(dest->buf, mesg->buf, mesg->len); + H5MM_memcpy(dest->buf, mesg->buf, mesg->len); /* Set return value */ ret_value = dest; diff --git a/src/H5Odtype.c b/src/H5Odtype.c index 28970d1..39d8bac 100644 --- a/src/H5Odtype.c +++ b/src/H5Odtype.c @@ -250,7 +250,7 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned *ioflags/*in,out*/, const uint8_t **p HDassert(0 == (z & 0x7)); /*must be aligned*/ if(NULL == (dt->shared->u.opaque.tag = (char *)H5MM_malloc(z + 1))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - HDmemcpy(dt->shared->u.opaque.tag, *pp, z); + H5MM_memcpy(dt->shared->u.opaque.tag, *pp, z); dt->shared->u.opaque.tag[z] = '\0'; *pp += z; break; @@ -483,7 +483,7 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned *ioflags/*in,out*/, const uint8_t **p } /* end for */ /* Values */ - HDmemcpy(dt->shared->u.enumer.value, *pp, + H5MM_memcpy(dt->shared->u.enumer.value, *pp, dt->shared->u.enumer.nmembs * dt->shared->parent->shared->size); *pp += dt->shared->u.enumer.nmembs * dt->shared->parent->shared->size; break; @@ -882,7 +882,7 @@ H5O_dtype_encode_helper(const H5F_t *f, uint8_t **pp, const H5T_t *dt) z = HDstrlen(dt->shared->u.opaque.tag); aligned = (z + 7) & (H5T_OPAQUE_TAG_MAX - 8); flags = (unsigned)(flags | aligned); - HDmemcpy(*pp, dt->shared->u.opaque.tag, MIN(z,aligned)); + H5MM_memcpy(*pp, dt->shared->u.opaque.tag, MIN(z,aligned)); for(n = MIN(z, aligned); n < aligned; n++) (*pp)[n] = 0; *pp += aligned; @@ -997,7 +997,7 @@ H5O_dtype_encode_helper(const H5F_t *f, uint8_t **pp, const H5T_t *dt) } /* end for */ /* Values */ - HDmemcpy(*pp, dt->shared->u.enumer.value, dt->shared->u.enumer.nmembs * dt->shared->parent->shared->size); + H5MM_memcpy(*pp, dt->shared->u.enumer.value, dt->shared->u.enumer.nmembs * dt->shared->parent->shared->size); *pp += dt->shared->u.enumer.nmembs * dt->shared->parent->shared->size; break; diff --git a/src/H5Oefl.c b/src/H5Oefl.c index 6a81a46..b18d819 100644 --- a/src/H5Oefl.c +++ b/src/H5Oefl.c @@ -461,7 +461,7 @@ H5O__efl_copy_file(H5F_t H5_ATTR_UNUSED *file_src, void *mesg_src, H5F_t *file_d HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the "top level" information */ - HDmemcpy(efl_dst, efl_src, sizeof(H5O_efl_t)); + H5MM_memcpy(efl_dst, efl_src, sizeof(H5O_efl_t)); /* Determine size needed for destination heap */ heap_size = H5HL_ALIGN(1); /* "empty" name */ @@ -488,7 +488,7 @@ H5O__efl_copy_file(H5F_t H5_ATTR_UNUSED *file_src, void *mesg_src, H5F_t *file_d HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* copy content from the source. Need to update later */ - HDmemcpy(efl_dst->slot, efl_src->slot, size); + H5MM_memcpy(efl_dst->slot, efl_src->slot, size); } /* end if */ /* copy the name from the source */ diff --git a/src/H5Ofill.c b/src/H5Ofill.c index 125da36..ebd885c 100644 --- a/src/H5Ofill.c +++ b/src/H5Ofill.c @@ -232,7 +232,7 @@ H5O_fill_new_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "destination buffer too small") if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value") - HDmemcpy(fill->buf, p, (size_t)fill->size); + H5MM_memcpy(fill->buf, p, (size_t)fill->size); } /* end if */ } /* end if */ else @@ -270,7 +270,7 @@ H5O_fill_new_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh, H5_CHECK_OVERFLOW(fill->size, ssize_t, size_t); if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value") - HDmemcpy(fill->buf, p, (size_t)fill->size); + H5MM_memcpy(fill->buf, p, (size_t)fill->size); /* Set the "defined" flag */ fill->fill_defined = TRUE; @@ -353,7 +353,7 @@ H5O_fill_old_decode(H5F_t *f, H5O_t *open_oh, if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value") - HDmemcpy(fill->buf, p, (size_t)fill->size); + H5MM_memcpy(fill->buf, p, (size_t)fill->size); fill->fill_defined = TRUE; } /* end if */ else @@ -420,7 +420,7 @@ H5O_fill_new_encode(H5F_t H5_ATTR_UNUSED *f, uint8_t *p, const void *_fill) if(fill->size > 0) if(fill->buf) { H5_CHECK_OVERFLOW(fill->size, ssize_t, size_t); - HDmemcpy(p, fill->buf, (size_t)fill->size); + H5MM_memcpy(p, fill->buf, (size_t)fill->size); } /* end if */ } /* end if */ } /* end if */ @@ -459,7 +459,7 @@ H5O_fill_new_encode(H5F_t H5_ATTR_UNUSED *f, uint8_t *p, const void *_fill) /* Encode the fill value */ HDassert(fill->buf); H5_CHECK_OVERFLOW(fill->size, ssize_t, size_t); - HDmemcpy(p, fill->buf, (size_t)fill->size); + H5MM_memcpy(p, fill->buf, (size_t)fill->size); } /* end if */ else { /* Flags */ @@ -499,7 +499,7 @@ H5O_fill_old_encode(H5F_t H5_ATTR_UNUSED *f, uint8_t *p, const void *_fill) UINT32ENCODE(p, fill->size); if(fill->buf) - HDmemcpy(p, fill->buf, (size_t)fill->size); + H5MM_memcpy(p, fill->buf, (size_t)fill->size); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5O_fill_old_encode() */ @@ -551,7 +551,7 @@ H5O_fill_copy(const void *_src, void *_dst) H5_CHECK_OVERFLOW(src->size, ssize_t, size_t); if(NULL == (dst->buf = H5MM_malloc((size_t)src->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value") - HDmemcpy(dst->buf, src->buf, (size_t)src->size); + H5MM_memcpy(dst->buf, src->buf, (size_t)src->size); /* Check for needing to convert/copy fill value */ if(src->type) { @@ -890,40 +890,40 @@ H5O__fill_debug(H5F_t H5_ATTR_UNUSED *f, const void *_fill, FILE *stream, HDfprintf(stream, "%*s%-*s ", indent, "", fwidth, "Space Allocation Time:"); switch(fill->alloc_time) { case H5D_ALLOC_TIME_EARLY: - fprintf(stream,"Early\n"); + HDfprintf(stream,"Early\n"); break; case H5D_ALLOC_TIME_LATE: - fprintf(stream,"Late\n"); + HDfprintf(stream,"Late\n"); break; case H5D_ALLOC_TIME_INCR: - fprintf(stream,"Incremental\n"); + HDfprintf(stream,"Incremental\n"); break; case H5D_ALLOC_TIME_DEFAULT: case H5D_ALLOC_TIME_ERROR: default: - fprintf(stream,"Unknown!\n"); + HDfprintf(stream,"Unknown!\n"); break; } /* end switch */ HDfprintf(stream, "%*s%-*s ", indent, "", fwidth, "Fill Time:"); switch(fill->fill_time) { case H5D_FILL_TIME_ALLOC: - fprintf(stream,"On Allocation\n"); + HDfprintf(stream,"On Allocation\n"); break; case H5D_FILL_TIME_NEVER: - fprintf(stream,"Never\n"); + HDfprintf(stream,"Never\n"); break; case H5D_FILL_TIME_IFSET: - fprintf(stream,"If Set\n"); + HDfprintf(stream,"If Set\n"); break; case H5D_FILL_TIME_ERROR: default: - fprintf(stream,"Unknown!\n"); + HDfprintf(stream,"Unknown!\n"); break; } /* end switch */ @@ -931,20 +931,20 @@ H5O__fill_debug(H5F_t H5_ATTR_UNUSED *f, const void *_fill, FILE *stream, H5P_is_fill_value_defined((const H5O_fill_t *)fill, &fill_status); switch(fill_status) { case H5D_FILL_VALUE_UNDEFINED: - fprintf(stream,"Undefined\n"); + HDfprintf(stream,"Undefined\n"); break; case H5D_FILL_VALUE_DEFAULT: - fprintf(stream,"Default\n"); + HDfprintf(stream,"Default\n"); break; case H5D_FILL_VALUE_USER_DEFINED: - fprintf(stream,"User Defined\n"); + HDfprintf(stream,"User Defined\n"); break; case H5D_FILL_VALUE_ERROR: default: - fprintf(stream,"Unknown!\n"); + HDfprintf(stream,"Unknown!\n"); break; } /* end switch */ @@ -1025,7 +1025,7 @@ H5O_fill_convert(H5O_fill_t *fill, H5T_t *dset_type, hbool_t *fill_changed) else { if(NULL == (buf = H5MM_malloc(H5T_get_size(dset_type)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion") - HDmemcpy(buf, fill->buf, H5T_get_size(fill->type)); + H5MM_memcpy(buf, fill->buf, H5T_get_size(fill->type)); } /* end else */ /* Use CALLOC here to clear the buffer in case later the library thinks there's diff --git a/src/H5Oint.c b/src/H5Oint.c index d3a409c..570f94e 100644 --- a/src/H5Oint.c +++ b/src/H5Oint.c @@ -38,9 +38,7 @@ #include "H5Iprivate.h" /* IDs */ #include "H5Lprivate.h" /* Links */ #include "H5MFprivate.h" /* File memory management */ -#ifdef H5O_ENABLE_BOGUS #include "H5MMprivate.h" /* Memory management */ -#endif /* H5O_ENABLE_BOGUS */ #include "H5Opkg.h" /* Object headers */ #include "H5VLprivate.h" /* Virtual Object Layer */ @@ -496,7 +494,7 @@ H5O__apply_ohdr(H5F_t *f, H5O_t *oh, hid_t ocpl_id, size_t size_hint, size_t ini /* Put magic # for object header in first chunk */ if(H5O_VERSION_1 < oh->version) - HDmemcpy(oh->chunk[0].image, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(oh->chunk[0].image, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC); /* Create the message list */ oh->nmesgs = 1; @@ -1921,7 +1919,7 @@ H5O_loc_copy(H5O_loc_t *dst, H5O_loc_t *src, H5_copy_depth_t depth) HDassert(depth == H5_COPY_SHALLOW || depth == H5_COPY_DEEP); /* Copy the top level information */ - HDmemcpy(dst, src, sizeof(H5O_loc_t)); + H5MM_memcpy(dst, src, sizeof(H5O_loc_t)); /* Deep copy the names */ if(depth == H5_COPY_DEEP) { diff --git a/src/H5Olayout.c b/src/H5Olayout.c index 2b65e0c..138f219 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -189,7 +189,7 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, if(mesg->storage.u.compact.size > 0) { if(NULL == (mesg->storage.u.compact.buf = H5MM_malloc(mesg->storage.u.compact.size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for compact data buffer") - HDmemcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); + H5MM_memcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); p += mesg->storage.u.compact.size; } /* end if */ } /* end if */ @@ -210,7 +210,7 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, HGOTO_ERROR(H5E_OHDR, H5E_CANTALLOC, NULL, "memory allocation failed for compact data buffer") /* Compact data */ - HDmemcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); + H5MM_memcpy(mesg->storage.u.compact.buf, p, mesg->storage.u.compact.size); p += mesg->storage.u.compact.size; } /* end if */ @@ -425,14 +425,14 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, tmp_size = HDstrlen((const char *)heap_block_p) + 1; if(NULL == (mesg->storage.u.virt.list[i].source_file_name = (char *)H5MM_malloc(tmp_size))) HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, NULL, "unable to allocate memory for source file name") - (void)HDmemcpy(mesg->storage.u.virt.list[i].source_file_name, heap_block_p, tmp_size); + (void)H5MM_memcpy(mesg->storage.u.virt.list[i].source_file_name, heap_block_p, tmp_size); heap_block_p += tmp_size; /* Source dataset name */ tmp_size = HDstrlen((const char *)heap_block_p) + 1; if(NULL == (mesg->storage.u.virt.list[i].source_dset_name = (char *)H5MM_malloc(tmp_size))) HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, NULL, "unable to allocate memory for source dataset name") - (void)HDmemcpy(mesg->storage.u.virt.list[i].source_dset_name, heap_block_p, tmp_size); + (void)H5MM_memcpy(mesg->storage.u.virt.list[i].source_dset_name, heap_block_p, tmp_size); heap_block_p += tmp_size; /* Source selection */ @@ -581,7 +581,7 @@ H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, /* Raw data */ if(mesg->storage.u.compact.size > 0) { if(mesg->storage.u.compact.buf) - HDmemcpy(p, mesg->storage.u.compact.buf, mesg->storage.u.compact.size); + H5MM_memcpy(p, mesg->storage.u.compact.buf, mesg->storage.u.compact.size); else HDmemset(p, 0, mesg->storage.u.compact.size); p += mesg->storage.u.compact.size; @@ -742,7 +742,7 @@ H5O__layout_copy(const void *_mesg, void *_dest) HGOTO_ERROR(H5E_OHDR, H5E_NOSPACE, NULL, "unable to allocate memory for compact dataset") /* Copy over the raw data */ - HDmemcpy(dest->storage.u.compact.buf, mesg->storage.u.compact.buf, dest->storage.u.compact.size); + H5MM_memcpy(dest->storage.u.compact.buf, mesg->storage.u.compact.buf, dest->storage.u.compact.size); } /* end if */ else HDassert(dest->storage.u.compact.buf == NULL); @@ -1039,7 +1039,8 @@ H5O__layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, layout_dst->storage.u.contig.size = H5S_extent_nelem(udata->src_space_extent) * H5T_get_size(udata->src_dtype); - if(H5D__contig_is_space_alloc(&layout_src->storage)) { + if(H5D__contig_is_space_alloc(&layout_src->storage) + || (cpy_info->shared_fo && H5D__contig_is_data_cached((const H5D_shared_t *)cpy_info->shared_fo))) { /* copy contiguous raw data */ if(H5D__contig_copy(file_src, &layout_src->storage.u.contig, file_dst, &layout_dst->storage.u.contig, udata->src_dtype, cpy_info) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy contiguous storage") @@ -1048,7 +1049,8 @@ H5O__layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, break; case H5D_CHUNKED: - if(H5D__chunk_is_space_alloc(&layout_src->storage)) { + if(H5D__chunk_is_space_alloc(&layout_src->storage) + || (cpy_info->shared_fo && H5D__chunk_is_data_cached((const H5D_shared_t *)cpy_info->shared_fo))) { /* Create chunked layout */ if(H5D__chunk_copy(file_src, &layout_src->storage.u.chunk, &layout_src->u.chunk, file_dst, &layout_dst->storage.u.chunk, udata->src_space_extent, udata->src_dtype, udata->common.src_pline, cpy_info) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy chunked storage") diff --git a/src/H5Olink.c b/src/H5Olink.c index 55e1aee..4bd952b 100644 --- a/src/H5Olink.c +++ b/src/H5Olink.c @@ -202,7 +202,7 @@ H5O__link_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, /* Get the link's name */ if(NULL == (lnk->name = (char *)H5MM_malloc(len + 1))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(lnk->name, p, len); + H5MM_memcpy(lnk->name, p, len); lnk->name[len] = '\0'; p += len; @@ -220,7 +220,7 @@ H5O__link_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid link length") if(NULL == (lnk->u.soft.name = (char *)H5MM_malloc((size_t)len + 1))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(lnk->u.soft.name, p, len); + H5MM_memcpy(lnk->u.soft.name, p, len); lnk->u.soft.name[len] = '\0'; p += len; break; @@ -240,7 +240,7 @@ H5O__link_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, { if(NULL == (lnk->u.ud.udata = H5MM_malloc((size_t)len))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(lnk->u.ud.udata, p, len); + H5MM_memcpy(lnk->u.ud.udata, p, len); p += len; } else @@ -349,7 +349,7 @@ H5O_link_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, con } /* end switch */ /* Store the link's name */ - HDmemcpy(p, lnk->name, (size_t)len); + H5MM_memcpy(p, lnk->name, (size_t)len); p += len; /* Store the appropriate information for each type of link */ @@ -364,7 +364,7 @@ H5O_link_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, con len = (uint16_t)HDstrlen(lnk->u.soft.name); HDassert(len > 0); UINT16ENCODE(p, len) - HDmemcpy(p, lnk->u.soft.name, (size_t)len); + H5MM_memcpy(p, lnk->u.soft.name, (size_t)len); p += len; break; @@ -380,7 +380,7 @@ H5O_link_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p, con UINT16ENCODE(p, len) if(len > 0) { - HDmemcpy(p, lnk->u.ud.udata, (size_t)len); + H5MM_memcpy(p, lnk->u.ud.udata, (size_t)len); p+=len; } break; @@ -437,7 +437,7 @@ H5O_link_copy(const void *_mesg, void *_dest) if(lnk->u.ud.size > 0) { if(NULL == (dest->u.ud.udata = H5MM_malloc(lnk->u.ud.size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(dest->u.ud.udata, lnk->u.ud.udata, lnk->u.ud.size); + H5MM_memcpy(dest->u.ud.udata, lnk->u.ud.udata, lnk->u.ud.size); } /* end if */ } /* end if */ diff --git a/src/H5Omtime.c b/src/H5Omtime.c index 172f9ab..fbf7613 100644 --- a/src/H5Omtime.c +++ b/src/H5Omtime.c @@ -289,7 +289,7 @@ H5O_mtime_encode(H5F_t H5_ATTR_UNUSED *f, hbool_t H5_ATTR_UNUSED disable_shared, /* encode */ tm = HDgmtime(mesg); - sprintf((char*)p, "%04d%02d%02d%02d%02d%02d", + HDsprintf((char*)p, "%04d%02d%02d%02d%02d%02d", 1900+tm->tm_year, 1+tm->tm_mon, tm->tm_mday, tm->tm_hour, tm->tm_min, tm->tm_sec); diff --git a/src/H5Oname.c b/src/H5Oname.c index a710944..1f20f10 100644 --- a/src/H5Oname.c +++ b/src/H5Oname.c @@ -297,7 +297,7 @@ H5O__name_debug(H5F_t H5_ATTR_UNUSED *f, const void *_mesg, FILE *stream, HDassert(indent >= 0); HDassert(fwidth >= 0); - fprintf(stream, "%*s%-*s `%s'\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s `%s'\n", indent, "", fwidth, "Name:", mesg->s); diff --git a/src/H5Opline.c b/src/H5Opline.c index 1fae1b8..85a95b7 100644 --- a/src/H5Opline.c +++ b/src/H5Opline.c @@ -318,7 +318,7 @@ H5O_pline_encode(H5F_t H5_ATTR_UNUSED *f, uint8_t *p/*out*/, const void *mesg) /* Encode name, if there is one to encode */ if(name_length > 0) { /* Store name, with null terminator */ - HDmemcpy(p, name, name_length); + H5MM_memcpy(p, name, name_length); p += name_length; /* Pad out name to alignment, in older versions */ @@ -409,7 +409,7 @@ H5O_pline_copy(const void *_src, void *_dst/*out*/) if(NULL == (dst->filter[i].cd_values = (unsigned *)H5MM_malloc(src->filter[i].cd_nelmts* sizeof(unsigned)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(dst->filter[i].cd_values, src->filter[i].cd_values, + H5MM_memcpy(dst->filter[i].cd_values, src->filter[i].cd_values, src->filter[i].cd_nelmts * sizeof(unsigned)); } /* end if */ else diff --git a/src/H5Osdspace.c b/src/H5Osdspace.c index 74fa72e..b7f70d1 100644 --- a/src/H5Osdspace.c +++ b/src/H5Osdspace.c @@ -189,7 +189,7 @@ H5O__sdspace_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, done: if(!ret_value && sdim) { - H5S_extent_release(sdim); + H5S__extent_release(sdim); sdim = H5FL_FREE(H5S_extent_t, sdim); } /* end if */ @@ -310,7 +310,7 @@ H5O_sdspace_copy(const void *_mesg, void *_dest) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy extent information */ - if(H5S_extent_copy_real(dest, mesg, TRUE) < 0) + if(H5S__extent_copy_real(dest, mesg, TRUE) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, NULL, "can't copy extent") /* Set return value */ @@ -391,7 +391,7 @@ H5O__sdspace_reset(void *_mesg) FUNC_ENTER_STATIC_NOERR - H5S_extent_release(mesg); + H5S__extent_release(mesg); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5O__sdspace_reset() */ @@ -470,7 +470,7 @@ H5O_sdspace_pre_copy_file(H5F_t H5_ATTR_UNUSED *file_src, const void *mesg_src, HGOTO_ERROR(H5E_DATASPACE, H5E_NOSPACE, FAIL, "dataspace extent allocation failed") /* Create a copy of the dataspace extent */ - if(H5S_extent_copy_real(udata->src_space_extent, src_space_extent, TRUE) < 0) + if(H5S__extent_copy_real(udata->src_space_extent, src_space_extent, TRUE) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't copy extent") } /* end if */ diff --git a/src/H5Oshared.c b/src/H5Oshared.c index 4fc0488..67ca76f 100644 --- a/src/H5Oshared.c +++ b/src/H5Oshared.c @@ -39,6 +39,7 @@ #include "H5Fprivate.h" /* File access */ #include "H5Gprivate.h" /* Groups */ #include "H5HFprivate.h" /* Fractal heap */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Opkg.h" /* Object headers */ #include "H5SMprivate.h" /* Shared object header messages */ #include "H5WBprivate.h" /* Wrapped Buffers */ @@ -358,7 +359,7 @@ H5O__shared_decode(H5F_t *f, H5O_t *open_oh, unsigned *ioflags, const uint8_t *b */ if(sh_mesg.type == H5O_SHARE_TYPE_SOHM) { HDassert(version >= H5O_SHARED_VERSION_3); - HDmemcpy(&sh_mesg.u.heap_id, buf, sizeof(sh_mesg.u.heap_id)); + H5MM_memcpy(&sh_mesg.u.heap_id, buf, sizeof(sh_mesg.u.heap_id)); } /* end if */ else { /* The H5O_COMMITTED_FLAG should be set if this message @@ -426,7 +427,7 @@ H5O__shared_encode(const H5F_t *f, uint8_t *buf/*out*/, const H5O_shared_t *sh_m * object header that holds it. */ if(sh_mesg->type == H5O_SHARE_TYPE_SOHM) - HDmemcpy(buf, &(sh_mesg->u.heap_id), sizeof(sh_mesg->u.heap_id)); + H5MM_memcpy(buf, &(sh_mesg->u.heap_id), sizeof(sh_mesg->u.heap_id)); else H5F_addr_encode(f, &buf, sh_mesg->u.loc.oh_addr); @@ -36,6 +36,7 @@ #include "H5Fpkg.h" /* Files */ #include "H5FDprivate.h" /* File drivers */ #include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ #include "H5PBpkg.h" /* File access */ #include "H5SLprivate.h" /* Skip List */ @@ -252,7 +253,7 @@ H5PB_print_stats(const H5PB_t *page_buf) HDassert(page_buf); - printf("PAGE BUFFER STATISTICS:\n"); + HDprintf("PAGE BUFFER STATISTICS:\n"); HDprintf("******* METADATA\n"); HDprintf("\t Total Accesses: %u\n", page_buf->accesses[0]); @@ -609,7 +610,7 @@ H5PB_update_entry(H5PB_t *page_buf, haddr_t addr, size_t size, const void *buf) HDassert(addr + size <= page_addr + page_buf->page_size); offset = addr - page_addr; - HDmemcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, size); + H5MM_memcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, size); /* move to top of LRU list */ H5PB__MOVE_TO_TOP_LRU(page_buf, page_entry) @@ -818,7 +819,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/ offset = addr - first_page_addr; HDassert(page_buf->page_size > offset); - HDmemcpy(buf, (uint8_t *)page_entry->page_buf_ptr + offset, + H5MM_memcpy(buf, (uint8_t *)page_entry->page_buf_ptr + offset, page_buf->page_size - (size_t)offset); /* move to top of LRU list */ @@ -829,7 +830,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/ offset = (num_touched_pages-2)*page_buf->page_size + (page_buf->page_size - (addr - first_page_addr)); - HDmemcpy((uint8_t *)buf + offset, page_entry->page_buf_ptr, + H5MM_memcpy((uint8_t *)buf + offset, page_entry->page_buf_ptr, (size_t)((addr + size) - last_page_addr)); /* move to top of LRU list */ @@ -839,7 +840,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/ else { offset = i*page_buf->page_size; - HDmemcpy((uint8_t *)buf+(i*page_buf->page_size) , page_entry->page_buf_ptr, + H5MM_memcpy((uint8_t *)buf+(i*page_buf->page_size) , page_entry->page_buf_ptr, page_buf->page_size); } /* end else */ } /* end if */ @@ -872,7 +873,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/ buf_offset = (0 == i ? 0 : size - access_size); /* copy the requested data from the page into the input buffer */ - HDmemcpy((uint8_t *)buf + buf_offset, (uint8_t *)page_entry->page_buf_ptr + offset, access_size); + H5MM_memcpy((uint8_t *)buf + buf_offset, (uint8_t *)page_entry->page_buf_ptr + offset, access_size); /* Update LRU */ H5PB__MOVE_TO_TOP_LRU(page_buf, page_entry) @@ -937,7 +938,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/ /* Copy the requested data from the page into the input buffer */ offset = (0 == i ? addr - search_addr : 0); buf_offset = (0 == i ? 0 : size - access_size); - HDmemcpy((uint8_t *)buf + buf_offset, (uint8_t *)new_page_buf + offset, access_size); + H5MM_memcpy((uint8_t *)buf + buf_offset, (uint8_t *)new_page_buf + offset, access_size); /* Create the new PB entry */ if(NULL == (page_entry = H5FL_CALLOC(H5PB_entry_t))) @@ -1102,7 +1103,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, HDassert(page_buf->page_size > offset); /* Update page's data */ - HDmemcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, page_buf->page_size - (size_t)offset); + H5MM_memcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, page_buf->page_size - (size_t)offset); /* Mark page dirty and push to top of LRU */ page_entry->is_dirty = TRUE; @@ -1121,7 +1122,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, (page_buf->page_size - (addr - first_page_addr)); /* Update page's data */ - HDmemcpy(page_entry->page_buf_ptr, (const uint8_t *)buf + offset, + H5MM_memcpy(page_entry->page_buf_ptr, (const uint8_t *)buf + offset, (size_t)((addr + size) - last_page_addr)); /* Mark page dirty and push to top of LRU */ @@ -1173,7 +1174,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, buf_offset = (0 == i ? 0 : size - access_size); /* Copy the requested data from the input buffer into the page */ - HDmemcpy((uint8_t *)page_entry->page_buf_ptr + offset, (const uint8_t *)buf + buf_offset, access_size); + H5MM_memcpy((uint8_t *)page_entry->page_buf_ptr + offset, (const uint8_t *)buf + buf_offset, access_size); /* Mark page dirty and push to top of LRU */ page_entry->is_dirty = TRUE; @@ -1289,7 +1290,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, } /* end else */ /* Copy the requested data from the page into the input buffer */ - HDmemcpy((uint8_t *)new_page_buf + offset, (const uint8_t *)buf+buf_offset, access_size); + H5MM_memcpy((uint8_t *)new_page_buf + offset, (const uint8_t *)buf+buf_offset, access_size); /* Page is dirty now */ page_entry->is_dirty = TRUE; diff --git a/src/H5Pdapl.c b/src/H5Pdapl.c index 00e598f..5ce12b4 100644 --- a/src/H5Pdapl.c +++ b/src/H5Pdapl.c @@ -37,8 +37,8 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5Fprivate.h" /* Files */ #include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Ppkg.h" /* Property lists */ -#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -341,7 +341,7 @@ H5P__dapl_vds_file_pref_enc(const void *value, void **_pp, size_t *size) /* encode the prefix */ if(NULL != vds_file_pref) { - HDmemcpy(*(char **)pp, vds_file_pref, len); + H5MM_memcpy(*(char **)pp, vds_file_pref, len); *pp += len; } /* end if */ } /* end if */ @@ -589,7 +589,7 @@ H5P__dapl_efile_pref_enc(const void *value, void **_pp, size_t *size) /* encode the prefix */ if(NULL != efile_pref) { - HDmemcpy(*(char **)pp, efile_pref, len); + H5MM_memcpy(*(char **)pp, efile_pref, len); *pp += len; } /* end if */ } /* end if */ diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c index b85f105..41d7c78 100644 --- a/src/H5Pdcpl.c +++ b/src/H5Pdcpl.c @@ -439,13 +439,13 @@ H5P__dcrt_layout_enc(const void *value, void **_pp, size_t *size) for(u = 0; u < layout->storage.u.virt.list_nused; u++) { /* Source file name */ tmp_size = HDstrlen(layout->storage.u.virt.list[u].source_file_name) + (size_t)1; - (void)HDmemcpy(*pp, layout->storage.u.virt.list[u].source_file_name, tmp_size); + (void)H5MM_memcpy(*pp, layout->storage.u.virt.list[u].source_file_name, tmp_size); *pp += tmp_size; *size += tmp_size; /* Source dataset name */ tmp_size = HDstrlen(layout->storage.u.virt.list[u].source_dset_name) + (size_t)1; - (void)HDmemcpy(*pp, layout->storage.u.virt.list[u].source_dset_name, tmp_size); + (void)H5MM_memcpy(*pp, layout->storage.u.virt.list[u].source_dset_name, tmp_size); *pp += tmp_size; *size += tmp_size; @@ -615,14 +615,14 @@ H5P__dcrt_layout_dec(const void **_pp, void *value) tmp_size = HDstrlen((const char *)*pp) + 1; if(NULL == (tmp_layout.storage.u.virt.list[u].source_file_name = (char *)H5MM_malloc(tmp_size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "unable to allocate memory for source file name") - (void)HDmemcpy(tmp_layout.storage.u.virt.list[u].source_file_name, *pp, tmp_size); + (void)H5MM_memcpy(tmp_layout.storage.u.virt.list[u].source_file_name, *pp, tmp_size); *pp += tmp_size; /* Source dataset name */ tmp_size = HDstrlen((const char *)*pp) + 1; if(NULL == (tmp_layout.storage.u.virt.list[u].source_dset_name = (char *)H5MM_malloc(tmp_size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "unable to allocate memory for source dataset name") - (void)HDmemcpy(tmp_layout.storage.u.virt.list[u].source_dset_name, *pp, tmp_size); + (void)H5MM_memcpy(tmp_layout.storage.u.virt.list[u].source_dset_name, *pp, tmp_size); *pp += tmp_size; /* Source selection */ @@ -687,7 +687,7 @@ H5P__dcrt_layout_dec(const void **_pp, void *value) } /* end switch */ /* Set the value */ - HDmemcpy(value, layout, sizeof(H5O_layout_t)); + H5MM_memcpy(value, layout, sizeof(H5O_layout_t)); done: FUNC_LEAVE_NOAPI(ret_value) @@ -1036,7 +1036,7 @@ H5P__dcrt_fill_value_enc(const void *value, void **_pp, size_t *size) /* Encode the fill value & datatype */ if(fill->size > 0) { /* Encode the fill value itself */ - HDmemcpy(*pp, (uint8_t *)fill->buf, (size_t)fill->size); + H5MM_memcpy(*pp, (uint8_t *)fill->buf, (size_t)fill->size); *pp += fill->size; /* Encode fill value datatype */ @@ -1133,7 +1133,7 @@ H5P__dcrt_fill_value_dec(const void **_pp, void *_value) /* Allocate fill buffer and copy the contents in it */ if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for fill value buffer") - HDmemcpy((uint8_t *)fill->buf, *pp, (size_t)fill->size); + H5MM_memcpy((uint8_t *)fill->buf, *pp, (size_t)fill->size); *pp += fill->size; enc_size = *(*pp)++; @@ -1448,7 +1448,7 @@ H5P__dcrt_ext_file_list_enc(const void *value, void **_pp, size_t *size) UINT64ENCODE_VAR(*pp, enc_value, enc_size); /* Encode name */ - HDmemcpy(*pp, (uint8_t *)(efl->slot[u].name), len); + H5MM_memcpy(*pp, (uint8_t *)(efl->slot[u].name), len); *pp += len; /* Encode offset */ @@ -2035,7 +2035,7 @@ H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]) #endif /* H5_HAVE_C99_DESIGNATED_INITIALIZER */ /* Verify & initialize property's chunk dims */ - HDmemcpy(&chunk_layout, &H5D_def_layout_chunk_g, sizeof(H5D_def_layout_chunk_g)); + H5MM_memcpy(&chunk_layout, &H5D_def_layout_chunk_g, sizeof(H5D_def_layout_chunk_g)); HDmemset(&chunk_layout.u.chunk.dim, 0, sizeof(chunk_layout.u.chunk.dim)); chunk_nelmts = 1; for(u = 0; u < (unsigned)ndims; u++) { @@ -2204,7 +2204,7 @@ H5Pset_virtual(hid_t dcpl_id, hid_t vspace_id, const char *src_file_name, HGOTO_ERROR(H5E_PLIST, H5E_CANTRESET, FAIL, "can't release layout message") /* Copy the default virtual layout */ - HDmemcpy(&virtual_layout, &H5D_def_layout_virtual_g, sizeof(H5D_def_layout_virtual_g)); + H5MM_memcpy(&virtual_layout, &H5D_def_layout_virtual_g, sizeof(H5D_def_layout_virtual_g)); /* Sanity check */ HDassert(virtual_layout.storage.u.virt.list_nalloc == 0); @@ -3243,7 +3243,7 @@ H5Pset_fill_value(hid_t plist_id, hid_t type_id, const void *value) fill.size = (ssize_t)H5T_get_size(type); if(NULL == (fill.buf = H5MM_malloc((size_t)fill.size))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "memory allocation failed for fill value") - HDmemcpy(fill.buf, value, (size_t)fill.size); + H5MM_memcpy(fill.buf, value, (size_t)fill.size); /* Set up type conversion function */ if(NULL == (tpath = H5T_path_find(type, type))) @@ -3351,7 +3351,7 @@ H5P_get_fill_value(H5P_genplist_t *plist, const H5T_t *type, void *value/*out*/) if(H5T_path_bkg(tpath) && NULL == (bkg = H5MM_malloc(H5T_get_size(fill.type)))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for type conversion") } /* end else */ - HDmemcpy(buf, fill.buf, H5T_get_size(fill.type)); + H5MM_memcpy(buf, fill.buf, H5T_get_size(fill.type)); /* Do the conversion */ if((dst_id = H5I_register(H5I_DATATYPE, H5T_copy(type, H5T_COPY_TRANSIENT), FALSE)) < 0) @@ -3359,7 +3359,7 @@ H5P_get_fill_value(H5P_genplist_t *plist, const H5T_t *type, void *value/*out*/) if(H5T_convert(tpath, src_id, dst_id, (size_t)1, (size_t)0, (size_t)0, buf, bkg) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "datatype conversion failed") if(buf != value) - HDmemcpy(value, buf, H5T_get_size(type)); + H5MM_memcpy(value, buf, H5T_get_size(type)); done: if(buf != value) diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c index 8338d84..df9cf4e 100644 --- a/src/H5Pdxpl.c +++ b/src/H5Pdxpl.c @@ -695,7 +695,7 @@ H5P__dxfr_xform_enc(const void *value, void **_pp, size_t *size) HDassert(pexp); /* Copy the expression into the buffer */ - HDmemcpy(*pp, (const uint8_t *)pexp, len); + H5MM_memcpy(*pp, (const uint8_t *)pexp, len); *pp += len; *pp[0] = '\0'; } /* end if */ diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c index 452ea3f..57b20d7 100644 --- a/src/H5Pfapl.c +++ b/src/H5Pfapl.c @@ -1064,7 +1064,7 @@ H5P__file_driver_copy(void *value) else if(driver->fapl_size > 0) { if(NULL == (new_pl = H5MM_malloc(driver->fapl_size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "driver info allocation failed") - HDmemcpy(new_pl, info->driver_info, driver->fapl_size); + H5MM_memcpy(new_pl, info->driver_info, driver->fapl_size); } /* end else-if */ else HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "no way to copy driver info") @@ -2597,7 +2597,7 @@ H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTCOPY, FAIL, "image_memcpy callback failed") } /* end if */ else - HDmemcpy(image_info.buffer, buf_ptr, buf_len); + H5MM_memcpy(image_info.buffer, buf_ptr, buf_len); } /* end if */ else image_info.buffer = NULL; @@ -2691,7 +2691,7 @@ H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTCOPY, FAIL, "image_memcpy callback failed") } /* end if */ else - HDmemcpy(copy_ptr, image_info.buffer, image_info.size); + H5MM_memcpy(copy_ptr, image_info.buffer, image_info.size); } /* end if */ *buf_ptr_ptr = copy_ptr; @@ -2894,7 +2894,7 @@ H5P__file_image_info_copy(void *value) HGOTO_ERROR(H5E_PLIST, H5E_CANTCOPY, FAIL, "image_memcpy callback failed") } /* end if */ else - HDmemcpy(info->buffer, old_buffer, info->size); + H5MM_memcpy(info->buffer, old_buffer, info->size); } /* end if */ /* Copy udata if it exists */ @@ -3089,7 +3089,7 @@ H5P__facc_cache_image_config_dec(const void **_pp, void *_value) HDcompile_assert(sizeof(size_t) <= sizeof(uint64_t)); /* Set property to default value */ - HDmemcpy(config, &H5F_def_mdc_initCacheImageCfg_g, sizeof(H5AC_cache_image_config_t)); + H5MM_memcpy(config, &H5F_def_mdc_initCacheImageCfg_g, sizeof(H5AC_cache_image_config_t)); /* Decode type sizes */ enc_size = *(*pp)++; @@ -3480,7 +3480,7 @@ H5P__facc_cache_config_enc(const void *value, void **_pp, size_t *size) H5_ENCODE_UNSIGNED(*pp, config->close_trace_file); - HDmemcpy(*pp, (const uint8_t *)(config->trace_file_name), (size_t)(H5AC__MAX_TRACE_FILE_NAME_LEN + 1)); + H5MM_memcpy(*pp, (const uint8_t *)(config->trace_file_name), (size_t)(H5AC__MAX_TRACE_FILE_NAME_LEN + 1)); *pp += H5AC__MAX_TRACE_FILE_NAME_LEN + 1; H5_ENCODE_UNSIGNED(*pp, config->evictions_enabled); @@ -3615,7 +3615,7 @@ H5P__facc_cache_config_dec(const void **_pp, void *_value) HDcompile_assert(sizeof(size_t) <= sizeof(uint64_t)); /* Set property to default value */ - HDmemcpy(config, &H5F_def_mdc_initCacheCfg_g, sizeof(H5AC_cache_config_t)); + H5MM_memcpy(config, &H5F_def_mdc_initCacheCfg_g, sizeof(H5AC_cache_config_t)); /* Decode type sizes */ enc_size = *(*pp)++; @@ -4195,7 +4195,7 @@ H5Pget_mdc_log_options(hid_t plist_id, hbool_t *is_enabled, char *location, /* Copy log location to output buffer */ if(location_ptr && location) - HDmemcpy(location, location_ptr, *location_size); + H5MM_memcpy(location, location_ptr, *location_size); /* Get location size, including terminating NULL */ if(location_size) { @@ -4250,7 +4250,7 @@ H5P_facc_mdc_log_location_enc(const void *value, void **_pp, size_t *size) /* encode the prefix */ if(NULL != log_location) { - HDmemcpy(*(char **)pp, log_location, len); + H5MM_memcpy(*(char **)pp, log_location, len); *pp += len; } /* end if */ } /* end if */ @@ -4536,7 +4536,7 @@ H5P__encode_coll_md_read_flag_t(const void *value, void **_pp, size_t *size) if(NULL != *pp) { /* Encode the value */ - HDmemcpy(*pp, coll_md_read_flag, sizeof(H5P_coll_md_read_flag_t)); + H5MM_memcpy(*pp, coll_md_read_flag, sizeof(H5P_coll_md_read_flag_t)); *pp += sizeof(H5P_coll_md_read_flag_t); } /* end if */ @@ -5231,7 +5231,7 @@ H5P__facc_vol_cmp(const void *_info1, const void *_info2, size_t H5_ATTR_UNUSED /* Use one of the classes (cls1) info comparison routines to compare the * info objects */ - HDassert(cls1->info_cmp == cls2->info_cmp); + HDassert(cls1->info_cls.cmp == cls2->info_cls.cmp); status = H5VL_cmp_connector_info(cls1, &cmp_value, info1->connector_info, info2->connector_info); HDassert(status >= 0); diff --git a/src/H5Pint.c b/src/H5Pint.c index e2ae792..e1b20a5 100644 --- a/src/H5Pint.c +++ b/src/H5Pint.c @@ -631,7 +631,7 @@ H5P__do_prop_cb1(H5SL_t *slist, H5P_genprop_t *prop, H5P_prp_cb1_t cb) /* Allocate space for a temporary copy of the property value */ if(NULL == (tmp_value = H5MM_malloc(prop->size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for temporary property value") - HDmemcpy(tmp_value, prop->value, prop->size); + H5MM_memcpy(tmp_value, prop->value, prop->size); /* Call "type 1" callback ('create', 'copy' or 'close') */ if(cb(prop->name, prop->size, tmp_value) < 0) @@ -642,7 +642,7 @@ H5P__do_prop_cb1(H5SL_t *slist, H5P_genprop_t *prop, H5P_prp_cb1_t cb) HGOTO_ERROR(H5E_PLIST, H5E_CANTCOPY, FAIL, "Can't copy property") /* Copy the changed value into the new property */ - HDmemcpy(pcopy->value, tmp_value, prop->size); + H5MM_memcpy(pcopy->value, tmp_value, prop->size); /* Insert the changed property into the property list */ if(H5P__add_prop(slist, pcopy) < 0) @@ -990,7 +990,7 @@ H5P__dup_prop(H5P_genprop_t *oprop, H5P_prop_within_t type) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy basic property information */ - HDmemcpy(prop, oprop, sizeof(H5P_genprop_t)); + H5MM_memcpy(prop, oprop, sizeof(H5P_genprop_t)); /* Check if we should duplicate the name or share it */ @@ -1030,7 +1030,7 @@ H5P__dup_prop(H5P_genprop_t *oprop, H5P_prop_within_t type) HDassert(prop->size > 0); if(NULL == (prop->value = H5MM_malloc(prop->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(prop->value, oprop->value, prop->size); + H5MM_memcpy(prop->value, oprop->value, prop->size); } /* end if */ /* Set return value */ @@ -1117,7 +1117,7 @@ H5P__create_prop(const char *name, size_t size, H5P_prop_within_t type, if(value != NULL) { if(NULL == (prop->value = H5MM_malloc (prop->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(prop->value, value, prop->size); + H5MM_memcpy(prop->value, value, prop->size); } /* end if */ else prop->value = NULL; @@ -2727,7 +2727,7 @@ H5P__poke_plist_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "property has zero size") /* Overwrite value in property */ - HDmemcpy(prop->value, udata->value, prop->size); + H5MM_memcpy(prop->value, udata->value, prop->size); done: FUNC_LEAVE_NOAPI(ret_value) @@ -2779,7 +2779,7 @@ H5P__poke_pclass_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop if(NULL == (pcopy = H5P__dup_prop(prop, H5P_PROP_WITHIN_LIST))) HGOTO_ERROR(H5E_PLIST, H5E_CANTCOPY, FAIL, "Can't copy property") - HDmemcpy(pcopy->value, udata->value, pcopy->size); + H5MM_memcpy(pcopy->value, udata->value, pcopy->size); /* Insert the changed property into the property list */ if(H5P__add_prop(plist->props, pcopy) < 0) @@ -2888,7 +2888,7 @@ H5P__set_plist_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, /* Make a copy of the current value, in case the callback fails */ if(NULL == (tmp_value = H5MM_malloc(prop->size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed temporary property value") - HDmemcpy(tmp_value, udata->value, prop->size); + H5MM_memcpy(tmp_value, udata->value, prop->size); /* Call user's callback */ if((*(prop->set))(plist->plist_id, name, prop->size, tmp_value) < 0) @@ -2909,7 +2909,7 @@ H5P__set_plist_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, } /* end if */ /* Copy new [possibly unchanged] value into property value */ - HDmemcpy(prop->value, prp_value, prop->size); + H5MM_memcpy(prop->value, prp_value, prop->size); done: /* Free the temporary value buffer */ @@ -2968,7 +2968,7 @@ H5P__set_pclass_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, /* Make a copy of the current value, in case the callback fails */ if(NULL == (tmp_value = H5MM_malloc(prop->size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed temporary property value") - HDmemcpy(tmp_value, udata->value, prop->size); + H5MM_memcpy(tmp_value, udata->value, prop->size); /* Call user's callback */ if((*(prop->set))(plist->plist_id, name, prop->size, tmp_value) < 0) @@ -2985,7 +2985,7 @@ H5P__set_pclass_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, if(NULL == (pcopy = H5P__dup_prop(prop, H5P_PROP_WITHIN_LIST))) HGOTO_ERROR(H5E_PLIST, H5E_CANTCOPY, FAIL, "Can't copy property") - HDmemcpy(pcopy->value, prp_value, pcopy->size); + H5MM_memcpy(pcopy->value, prp_value, pcopy->size); /* Insert the changed property into the property list */ if(H5P__add_prop(plist->props, pcopy) < 0) @@ -4234,7 +4234,7 @@ H5P__peek_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "property has zero size") /* Make a (shallow) copy of the value */ - HDmemcpy(udata->value, prop->value, prop->size); + H5MM_memcpy(udata->value, prop->value, prop->size); done: FUNC_LEAVE_NOAPI(ret_value) @@ -4334,18 +4334,18 @@ H5P__get_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, /* Make a copy of the current value, in case the callback fails */ if(NULL == (tmp_value = H5MM_malloc(prop->size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed temporary property value") - HDmemcpy(tmp_value, prop->value, prop->size); + H5MM_memcpy(tmp_value, prop->value, prop->size); /* Call user's callback */ if((*(prop->get))(plist->plist_id, name, prop->size, tmp_value) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't set property value") /* Copy new [possibly unchanged] value into return value */ - HDmemcpy(udata->value, tmp_value, prop->size); + H5MM_memcpy(udata->value, tmp_value, prop->size); } /* end if */ /* No 'get' callback, just copy value */ else - HDmemcpy(udata->value, prop->value, prop->size); + H5MM_memcpy(udata->value, prop->value, prop->size); done: /* Free the temporary value buffer */ @@ -4518,7 +4518,7 @@ H5P__del_pclass_cb(H5P_genplist_t *plist, const char *name, H5P_genprop_t *prop, /* Allocate space for a temporary copy of the property value */ if(NULL == (tmp_value = H5MM_malloc(prop->size))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for temporary property value") - HDmemcpy(tmp_value, prop->value, prop->size); + H5MM_memcpy(tmp_value, prop->value, prop->size); /* Call user's callback */ if((*(prop->del))(plist->plist_id, name, prop->size, tmp_value) < 0) @@ -4967,7 +4967,7 @@ H5P_close(void *_plist) /* Allocate space for a temporary copy of the property value */ if(NULL==(tmp_value=H5MM_malloc(tmp->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for temporary property value") - HDmemcpy(tmp_value,tmp->value,tmp->size); + H5MM_memcpy(tmp_value,tmp->value,tmp->size); /* Call the 'close' callback */ (tmp->close)(tmp->name,tmp->size,tmp_value); diff --git a/src/H5Plapl.c b/src/H5Plapl.c index bedeed9..7a7cc23 100644 --- a/src/H5Plapl.c +++ b/src/H5Plapl.c @@ -715,7 +715,7 @@ H5P__lacc_elink_pref_enc(const void *value, void **_pp, size_t *size) /* encode the prefix */ if(NULL != elink_pref) { - HDmemcpy(*(char **)pp, elink_pref, len); + H5MM_memcpy(*(char **)pp, elink_pref, len); *pp += len; } /* end if */ } /* end if */ diff --git a/src/H5Pocpl.c b/src/H5Pocpl.c index c2bf6cb..a60c593 100644 --- a/src/H5Pocpl.c +++ b/src/H5Pocpl.c @@ -1501,7 +1501,7 @@ H5P__ocrt_pipeline_enc(const void *value, void **_pp, size_t *size) *(*pp)++ = (uint8_t)TRUE; /* encode filter name */ - HDmemcpy(*pp, (uint8_t *)(pline->filter[u].name), H5Z_COMMON_NAME_LEN); + H5MM_memcpy(*pp, (uint8_t *)(pline->filter[u].name), H5Z_COMMON_NAME_LEN); *pp += H5Z_COMMON_NAME_LEN; } /* end if */ else diff --git a/src/H5Pocpypl.c b/src/H5Pocpypl.c index 666a945..2dc92f9 100644 --- a/src/H5Pocpypl.c +++ b/src/H5Pocpypl.c @@ -384,7 +384,7 @@ H5P__ocpy_merge_comm_dt_list_enc(const void *value, void **_pp, size_t *size) /* Encode merge committed dtype list */ if(*pp) { - HDmemcpy(*(char **)pp, dt_list->path, len); + H5MM_memcpy(*(char **)pp, dt_list->path, len); *pp += len; } /* end if */ @@ -26,6 +26,7 @@ #include "H5Fprivate.h" /* Files */ #include "H5FLprivate.h" /* Free lists */ #include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Spkg.h" /* Dataspaces */ @@ -46,7 +47,12 @@ /********************/ /* Local Prototypes */ /********************/ -static htri_t H5S_is_simple(const H5S_t *sdim); +static htri_t H5S__is_simple(const H5S_t *sdim); + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ /*********************/ @@ -63,15 +69,6 @@ const unsigned H5O_sdspace_ver_bounds[] = { H5O_SDSPACE_VERSION_LATEST /* H5F_LIBVER_LATEST */ }; -/*****************************/ -/* Library Private Variables */ -/*****************************/ - - -/*******************/ -/* Local Variables */ -/*******************/ - /* Declare a free list to manage the H5S_extent_t struct */ H5FL_DEFINE(H5S_extent_t); @@ -81,6 +78,11 @@ H5FL_DEFINE(H5S_t); /* Declare a free list to manage the array's of hsize_t's */ H5FL_ARR_DEFINE(hsize_t, H5S_MAX_RANK); + +/*******************/ +/* Local Variables */ +/*******************/ + /* Dataspace ID class */ static const H5I_class_t H5I_DATASPACE_CLS[1] = {{ H5I_DATASPACE, /* ID class value */ @@ -112,9 +114,9 @@ H5S__init_package(void) FUNC_ENTER_PACKAGE - /* Initialize the atom group for the file IDs */ + /* Initialize the atom group for the dataspace IDs */ if(H5I_register_type(H5I_DATASPACE_CLS) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize interface") + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize dataspace ID class") /* Mark "top" of interface as initialized, too */ H5S_top_package_initialize_s = TRUE; @@ -329,10 +331,9 @@ H5S_create(H5S_class_t type) ret_value = new_ds; done: - if(ret_value == NULL) { + if(ret_value == NULL) if(new_ds && H5S_close(new_ds) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, NULL, "unable to release dataspace") - } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5S_create() */ @@ -359,7 +360,7 @@ done: hid_t H5Screate(H5S_class_t type) { - H5S_t *new_ds=NULL; /* New dataspace structure */ + H5S_t *new_ds = NULL; /* New dataspace structure */ hid_t ret_value; /* Return value */ FUNC_ENTER_API(FAIL) @@ -373,21 +374,20 @@ H5Screate(H5S_class_t type) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace") /* Atomize */ - if((ret_value = H5I_register (H5I_DATASPACE, new_ds, TRUE)) < 0) + if((ret_value = H5I_register(H5I_DATASPACE, new_ds, TRUE)) < 0) HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace atom") done: - if(ret_value < 0) { + if(ret_value < 0) if(new_ds && H5S_close(new_ds) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") - } /* end if */ FUNC_LEAVE_API(ret_value) } /* end H5Screate() */ /*------------------------------------------------------------------------- - * Function: H5S_extent_release + * Function: H5S__extent_release * * Purpose: Releases all memory associated with a dataspace extent. * @@ -396,16 +396,12 @@ done: * Programmer: Quincey Koziol * Thursday, July 23, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ herr_t -H5S_extent_release(H5S_extent_t *extent) +H5S__extent_release(H5S_extent_t *extent) { - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_PACKAGE_NOERR HDassert(extent); @@ -417,9 +413,8 @@ H5S_extent_release(H5S_extent_t *extent) extent->max = H5FL_ARR_FREE(hsize_t, extent->max); } /* end if */ -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_extent_release() */ + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5S__extent_release() */ /*------------------------------------------------------------------------- @@ -445,11 +440,11 @@ H5S_close(H5S_t *ds) /* Release selection (this should come before the extent release) */ if(H5S_SELECT_RELEASE(ds) < 0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace selection") + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace selection") /* Release extent */ - if(H5S_extent_release(&ds->extent) < 0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace extent") + if(H5S__extent_release(&ds->extent) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace extent") /* Release the main structure */ ds = H5FL_FREE(H5S_t, ds); @@ -466,13 +461,9 @@ done: * * Return: Non-negative on success/Negative on failure * - * Errors: - * * Programmer: Robb Matzke * Tuesday, December 9, 1997 * - * Modifications: - * *------------------------------------------------------------------------- */ herr_t @@ -484,7 +475,7 @@ H5Sclose(hid_t space_id) H5TRACE1("e", "i", space_id); /* Check args */ - if (NULL == H5I_object_verify(space_id,H5I_DATASPACE)) + if(NULL == H5I_object_verify(space_id, H5I_DATASPACE)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") /* When the reference count reaches zero the resources are freed */ @@ -502,14 +493,11 @@ done: * Purpose: Copies a dataspace. * * Return: Success: ID of the new dataspace - * * Failure: Negative * * Programmer: Robb Matzke * Friday, January 30, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ hid_t @@ -535,10 +523,9 @@ H5Scopy(hid_t space_id) HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace atom") done: - if(ret_value < 0) { + if(ret_value < 0) if(dst && H5S_close(dst) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") - } /* end if */ FUNC_LEAVE_API(ret_value) } /* end H5Scopy() */ @@ -554,8 +541,6 @@ done: * Programmer: Quincey Koziol * Thursday, July 23, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ herr_t @@ -593,8 +578,6 @@ done: * Programmer: Neil Fortner * Monday, February 23, 2015 * - * Modifications: - * *------------------------------------------------------------------------- */ herr_t @@ -608,7 +591,7 @@ H5S_extent_copy(H5S_t *dst, const H5S_t *src) HDassert(src); /* Copy extent */ - if(H5S_extent_copy_real(&(dst->extent), &(src->extent), TRUE) < 0) + if(H5S__extent_copy_real(&(dst->extent), &(src->extent), TRUE) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't copy extent") /* If the selection is 'all', update the number of elements selected in the @@ -623,7 +606,7 @@ done: /*------------------------------------------------------------------------- - * Function: H5S_extent_copy_real + * Function: H5S__extent_copy_real * * Purpose: Copies a dataspace extent * @@ -632,20 +615,18 @@ done: * Programmer: Quincey Koziol * Wednesday, June 3, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ herr_t -H5S_extent_copy_real(H5S_extent_t *dst, const H5S_extent_t *src, hbool_t copy_max) +H5S__extent_copy_real(H5S_extent_t *dst, const H5S_extent_t *src, hbool_t copy_max) { unsigned u; herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_PACKAGE /* Release destination extent before we copy over it */ - if(H5S_extent_release(dst) < 0) + if(H5S__extent_release(dst) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace extent") /* Copy the regular fields */ @@ -690,7 +671,7 @@ H5S_extent_copy_real(H5S_extent_t *dst, const H5S_extent_t *src, hbool_t copy_ma done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_extent_copy_real() */ +} /* end H5S__extent_copy_real() */ /*------------------------------------------------------------------------- @@ -704,14 +685,11 @@ done: * selection) * * Return: Success: A pointer to a new copy of SRC - * * Failure: NULL * * Programmer: Robb Matzke * Thursday, December 4, 1997 * - * Modifications: - * *------------------------------------------------------------------------- */ H5S_t * @@ -726,7 +704,7 @@ H5S_copy(const H5S_t *src, hbool_t share_selection, hbool_t copy_max) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy the source dataspace's extent */ - if(H5S_extent_copy_real(&(dst->extent), &(src->extent), copy_max) < 0) + if(H5S__extent_copy_real(&(dst->extent), &(src->extent), copy_max) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, NULL, "can't copy extent") /* Copy the source dataspace's selection */ @@ -751,7 +729,6 @@ done: * Purpose: Determines how many data points a dataset extent has. * * Return: Success: Number of data points in the dataset extent. - * * Failure: negative * * Programmer: Robb Matzke @@ -761,9 +738,6 @@ done: * pattern, don't call it directly, use the appropriate macro * defined in H5Sprivate.h. * - * Modifications: - * Changed Name - QAK 7/7/98 - * *------------------------------------------------------------------------- */ hssize_t @@ -790,15 +764,11 @@ done: * Purpose: Determines how many data points a dataset extent has. * * Return: Success: Number of data points in the dataset. - * * Failure: negative * * Programmer: Robb Matzke * Tuesday, December 9, 1997 * - * Modifications: - * Changed Name - QAK 7/7/98 - * *------------------------------------------------------------------------- */ hssize_t @@ -832,14 +802,11 @@ done: * * Return: Success: Maximum number of data points the dataspace * may have. - * * Failure: 0 * * Programmer: Robb Matzke * Tuesday, December 9, 1997 * - * Modifications: - * *------------------------------------------------------------------------- */ hsize_t @@ -853,7 +820,7 @@ H5S_get_npoints_max(const H5S_t *ds) /* check args */ HDassert(ds); - switch (H5S_GET_EXTENT_TYPE(ds)) { + switch(H5S_GET_EXTENT_TYPE(ds)) { case H5S_NULL: ret_value = 0; break; @@ -863,31 +830,30 @@ H5S_get_npoints_max(const H5S_t *ds) break; case H5S_SIMPLE: - if (ds->extent.max) { - for (ret_value=1, u=0; u<ds->extent.rank; u++) { - if (H5S_UNLIMITED==ds->extent.max[u]) { + if(ds->extent.max) { + for(ret_value = 1, u = 0; u < ds->extent.rank; u++) { + if(H5S_UNLIMITED == ds->extent.max[u]) { ret_value = HSIZET_MAX; break; - } + } /* end if */ else ret_value *= ds->extent.max[u]; - } - } - else { - for (ret_value=1, u=0; u<ds->extent.rank; u++) + } /* end for */ + } /* end if */ + else + for(ret_value = 1, u = 0; u < ds->extent.rank; u++) ret_value *= ds->extent.size[u]; - } break; case H5S_NO_CLASS: default: HDassert("unknown dataspace class" && 0); HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, 0, "internal error (unknown dataspace class)") - } + } /* end switch */ done: FUNC_LEAVE_NOAPI(ret_value) -} +} /* end H5S_get_npoints_max() */ /*------------------------------------------------------------------------- @@ -896,21 +862,18 @@ done: * Purpose: Determines the dimensionality of a dataspace. * * Return: Success: The number of dimensions in a dataspace. - * * Failure: Negative * * Programmer: Robb Matzke * Thursday, December 11, 1997 * - * Modifications: - * *------------------------------------------------------------------------- */ int H5Sget_simple_extent_ndims(hid_t space_id) { - H5S_t *ds; - int ret_value; + H5S_t *ds; + int ret_value; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE1("Is", "i", space_id); @@ -933,7 +896,6 @@ done: * * Return: Success: Non-negative number of dimensions. Zero * implies a scalar. - * * Failure: Negative * * Programmer: Robb Matzke @@ -943,8 +905,6 @@ done: * pattern, don't call it directly, use the appropriate macro * defined in H5Sprivate.h. * - * Modifications: - * *------------------------------------------------------------------------- */ int @@ -979,43 +939,36 @@ done: * Function: H5Sget_simple_extent_dims * * Purpose: Returns the size and maximum sizes in each dimension of - * a dataspace DS through the DIMS and MAXDIMS arguments. + * a dataspace DS through the DIMS and MAXDIMS arguments. * * Return: Success: Number of dimensions, the same value as * returned by H5Sget_simple_extent_ndims(). - * * Failure: Negative * * Programmer: Robb Matzke * Thursday, December 11, 1997 * - * Modifications: - * June 18, 1998 Albert Cheng - * Added maxdims argument. Removed dims argument check - * since it can still return ndims even if both dims and - * maxdims are NULLs. - * *------------------------------------------------------------------------- */ int H5Sget_simple_extent_dims(hid_t space_id, hsize_t dims[]/*out*/, - hsize_t maxdims[]/*out*/) + hsize_t maxdims[]/*out*/) { - H5S_t *ds; - int ret_value; + H5S_t *ds; + int ret_value; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE3("Is", "ixx", space_id, dims, maxdims); /* Check args */ - if (NULL == (ds = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) + if(NULL == (ds = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") ret_value = H5S_get_simple_extent_dims(ds, dims, maxdims); done: FUNC_LEAVE_API(ret_value) -} +} /* end H5Sget_simple_extent_dims() */ /*------------------------------------------------------------------------- @@ -1081,14 +1034,11 @@ done: * function may not be meaningful for all types of dataspaces. * * Return: Success: Number of dimensions. Zero implies scalar. - * * Failure: Negative * * Programmer: Robb Matzke * Thursday, December 11, 1997 * - * Modifications: - * *------------------------------------------------------------------------- */ int @@ -1155,13 +1105,6 @@ done: * Programmer: Quincey Koziol * Tuesday, December 31, 2002 * - * Modifications: - * - * John Mainzer, 6/6/05 - * Updated function to use the new dirtied parameter of - * H5AC_unprotect() instead of manipulating the is_dirty - * field of the cache info. - * *------------------------------------------------------------------------- */ herr_t @@ -1191,7 +1134,6 @@ done: * Purpose: Reads the dataspace from an object header. * * Return: Success: Pointer to a new dataspace. - * * Failure: NULL * * Programmer: Robb Matzke @@ -1224,10 +1166,9 @@ H5S_read(const H5O_loc_t *loc) ret_value = ds; done: - if(ret_value == NULL) { + if(ret_value == NULL) if(ds != NULL) ds = H5FL_FREE(H5S_t, ds); - } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5S_read() */ @@ -1235,11 +1176,11 @@ done: /*-------------------------------------------------------------------------- NAME - H5S_is_simple + H5S__is_simple PURPOSE Check if a dataspace is simple (internal) USAGE - htri_t H5S_is_simple(sdim) + htri_t H5S__is_simple(sdim) H5S_t *sdim; IN: Pointer to dataspace object to query RETURNS TRUE/FALSE/FAIL @@ -1248,21 +1189,21 @@ done: has orthogonal, evenly spaced dimensions. --------------------------------------------------------------------------*/ static htri_t -H5S_is_simple(const H5S_t *sdim) +H5S__is_simple(const H5S_t *sdim) { htri_t ret_value = FAIL; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args and all the boring stuff. */ HDassert(sdim); /* H5S_NULL shouldn't be simple dataspace */ ret_value = (H5S_GET_EXTENT_TYPE(sdim) == H5S_SIMPLE || - H5S_GET_EXTENT_TYPE(sdim) == H5S_SCALAR) ? TRUE : FALSE; + H5S_GET_EXTENT_TYPE(sdim) == H5S_SCALAR) ? TRUE : FALSE; FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_is_simple() */ +} /* end H5S__is_simple() */ /*-------------------------------------------------------------------------- @@ -1282,21 +1223,21 @@ H5S_is_simple(const H5S_t *sdim) htri_t H5Sis_simple(hid_t space_id) { - H5S_t *space; /* dataspace to modify */ - htri_t ret_value; + H5S_t *space; /* Dataspace to check */ + htri_t ret_value; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE1("t", "i", space_id); /* Check args and all the boring stuff. */ - if ((space = (H5S_t *)H5I_object_verify(space_id,H5I_DATASPACE)) == NULL) + if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "not a dataspace") - ret_value = H5S_is_simple(space); + ret_value = H5S__is_simple(space); - done: +done: FUNC_LEAVE_API(ret_value) -} +} /* end H5Sis_simple() */ /*-------------------------------------------------------------------------- @@ -1324,56 +1265,44 @@ H5Sis_simple(hid_t space_id) Currently, only the first dimension in the array (the slowest) may be unlimited in size. - MODIFICATION - A null dataspace cannot be created from simple space with this function. - - Christian Chilan 01/17/2007 - Verifies that each element of DIMS is not equal to H5S_UNLIMITED. - - Raymond Lu 03/30/2011 - We allow 0 dimension size for non-unlimited dimension starting from 1.8.7 - release. --------------------------------------------------------------------------*/ herr_t H5Sset_extent_simple(hid_t space_id, int rank, const hsize_t dims[/*rank*/], - const hsize_t max[/*rank*/]) + const hsize_t max[/*rank*/]) { - H5S_t *space; /* dataspace to modify */ - int u; /* local counting variable */ - herr_t ret_value=SUCCEED; /* Return value */ + H5S_t *space; /* Dataspace to modify */ + int u; /* Local counting variable */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE4("e", "iIs*[a1]h*[a1]h", space_id, rank, dims, max); /* Check args */ - if ((space = (H5S_t *)H5I_object_verify(space_id,H5I_DATASPACE)) == NULL) + if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "not a dataspace") - if (rank > 0 && dims == NULL) + if(rank > 0 && dims == NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no dimensions specified") - if (rank<0 || rank>H5S_MAX_RANK) + if(rank < 0 || rank > H5S_MAX_RANK) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid rank") - if (dims) { - for (u=0; u<rank; u++) { - if (H5S_UNLIMITED==dims[u]) + if(dims) + for(u = 0; u < rank; u++) + if(H5S_UNLIMITED == dims[u]) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "current dimension must have a specific size, not H5S_UNLIMITED") - } - } - if (max!=NULL) { - if(dims==NULL) + if(max != NULL) { + if(dims == NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "maximum dimension specified, but no current dimensions specified") - for (u=0; u<rank; u++) { - if (max[u]!=H5S_UNLIMITED && max[u]<dims[u]) + for(u = 0; u < rank; u++) + if(max[u] != H5S_UNLIMITED && max[u] < dims[u]) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid maximum dimension size") - } - } + } /* end if */ /* Do it */ - if (H5S_set_extent_simple(space, (unsigned)rank, dims, max)<0) + if(H5S_set_extent_simple(space, (unsigned)rank, dims, max) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to set simple extent") done: FUNC_LEAVE_API(ret_value) -} +} /* end H5Sset_extent_simple() */ /*------------------------------------------------------------------------- @@ -1384,19 +1313,17 @@ done: * * Return: Non-negative on success/Negative on failure * - * Programmer: Robb Matzke (copied from H5Sset_extent_simple) + * Programmer: Robb Matzke * Wednesday, July 8, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ herr_t H5S_set_extent_simple(H5S_t *space, unsigned rank, const hsize_t *dims, - const hsize_t *max) + const hsize_t *max) { unsigned u; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -1405,7 +1332,7 @@ H5S_set_extent_simple(H5S_t *space, unsigned rank, const hsize_t *dims, HDassert(0 == rank || dims); /* shift out of the previous state to a "simple" dataspace. */ - if(H5S_extent_release(&space->extent) < 0) + if(H5S__extent_release(&space->extent) < 0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTFREE, FAIL, "failed to release previous dataspace extent") if(rank == 0) { /* scalar variable */ @@ -1432,12 +1359,11 @@ H5S_set_extent_simple(H5S_t *space, unsigned rank, const hsize_t *dims, /* Copy the maximum dimensions if specified. Otherwise, the maximal dimensions are the * same as the dimension */ space->extent.max = (hsize_t *)H5FL_ARR_MALLOC(hsize_t, (size_t)rank); - if(max != NULL) { - HDmemcpy(space->extent.max, max, sizeof(hsize_t) * rank); - } else { + if(max != NULL) + H5MM_memcpy(space->extent.max, max, sizeof(hsize_t) * rank); + else for(u = 0; u < space->extent.rank; u++) space->extent.max[u] = dims[u]; - } } /* end else */ /* Selection related cleanup */ @@ -1453,7 +1379,7 @@ H5S_set_extent_simple(H5S_t *space, unsigned rank, const hsize_t *dims, done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_set_extent_simple() */ +} /* end H5S_set_extent_simple() */ /*------------------------------------------------------------------------- @@ -1469,26 +1395,20 @@ done: * than the corresponding element of DIMS. * * Return: Success: The ID for the new simple dataspace object. - * * Failure: Negative * * Programmer: Quincey Koziol * Tuesday, January 27, 1998 * - * Modification: - * Raymond Lu 03/30/2011 - * We allow 0-dimension for non-unlimited dimension starting - * from 1.8.7 release. - * *------------------------------------------------------------------------- */ hid_t H5Screate_simple(int rank, const hsize_t dims[/*rank*/], - const hsize_t maxdims[/*rank*/]) + const hsize_t maxdims[/*rank*/]) { H5S_t *space = NULL; int i; - hid_t ret_value; + hid_t ret_value; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE3("i", "Is*[a0]h*[a0]h", rank, dims, maxdims); @@ -1514,7 +1434,7 @@ H5Screate_simple(int rank, const hsize_t dims[/*rank*/], } /* end for */ /* Create the space and set the extent */ - if(NULL == (space = H5S_create_simple((unsigned)rank,dims,maxdims))) + if(NULL == (space = H5S_create_simple((unsigned)rank, dims, maxdims))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* Atomize */ @@ -1522,10 +1442,9 @@ H5Screate_simple(int rank, const hsize_t dims[/*rank*/], HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID") done: - if(ret_value < 0) { + if(ret_value < 0) if(space && H5S_close(space) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") - } /* end if */ FUNC_LEAVE_API(ret_value) } /* end H5Screate_simple() */ @@ -1539,32 +1458,26 @@ done: * Return: Success: The ID for the new simple dataspace object. * Failure: Negative * - * Errors: - * * Programmer: Quincey Koziol * Thursday, April 3, 2003 * - * Modifications: - * Extracted from H5Screate_simple - * Quincey Koziol, Thursday, April 3, 2003 - * *------------------------------------------------------------------------- */ H5S_t * H5S_create_simple(unsigned rank, const hsize_t dims[/*rank*/], - const hsize_t maxdims[/*rank*/]) + const hsize_t maxdims[/*rank*/]) { H5S_t *ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI(NULL) /* Check arguments */ - HDassert(rank <=H5S_MAX_RANK); + HDassert(rank <= H5S_MAX_RANK); /* Create the space and set the extent */ - if(NULL==(ret_value=H5S_create(H5S_SIMPLE))) + if(NULL == (ret_value = H5S_create(H5S_SIMPLE))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, NULL, "can't create simple dataspace") - if(H5S_set_extent_simple(ret_value,rank,dims,maxdims)<0) + if(H5S_set_extent_simple(ret_value, rank, dims, maxdims) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, NULL, "can't set dimensions") done: @@ -1579,15 +1492,12 @@ done: * (including selection) into binary in a buffer. * * Return: Success: non-negative - * * Failure: negative * * Programmer: Raymond Lu * slu@ncsa.uiuc.edu * July 14, 2004 * - * Modifications: - * *------------------------------------------------------------------------- */ herr_t @@ -1600,15 +1510,15 @@ H5Sencode(hid_t obj_id, void *buf, size_t *nalloc) H5TRACE3("e", "i*x*z", obj_id, buf, nalloc); /* Check argument and retrieve object */ - if (NULL == (dspace = (H5S_t *)H5I_object_verify(obj_id, H5I_DATASPACE))) + if(NULL == (dspace = (H5S_t *)H5I_object_verify(obj_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if(H5S_encode(dspace, (unsigned char **)&buf, nalloc)<0) + if(H5S_encode(dspace, (unsigned char **)&buf, nalloc) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTENCODE, FAIL, "can't encode dataspace") done: FUNC_LEAVE_API(ret_value) -} +} /* end H5Sencode() */ /*------------------------------------------------------------------------- @@ -1697,7 +1607,6 @@ done: * return a new object handle. * * Return: Success: dataspace ID(non-negative) - * * Failure: negative * * Programmer: Raymond Lu @@ -1737,7 +1646,6 @@ done: * description of dataspace and returns a new object handle. * * Return: Success: dataspace ID(non-negative) - * * Failure: negative * * Programmer: Raymond Lu @@ -1784,11 +1692,11 @@ H5S_decode(const unsigned char **p) pp += extent_size; /* Copy the extent into dataspace structure */ - if((ds = H5FL_CALLOC(H5S_t))==NULL) + if(NULL == (ds = H5FL_CALLOC(H5S_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for dataspace conversion path table") - if(H5O_msg_copy(H5O_SDSPACE_ID, extent, &(ds->extent)) == NULL) + if(NULL == H5O_msg_copy(H5O_SDSPACE_ID, extent, &(ds->extent))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, NULL, "can't copy object") - if(H5S_extent_release(extent) < 0) + if(H5S__extent_release(extent) < 0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTDELETE, NULL, "can't release previous dataspace") extent = H5FL_FREE(H5S_extent_t, extent); @@ -1819,11 +1727,8 @@ done: * Purpose: Internal function for retrieving the type of extent for a dataspace object * * Return: Success: The class of the dataspace object - * * Failure: N5S_NO_CLASS * - * Errors: - * * Programmer: Quincey Koziol * Thursday, September 28, 2000 * @@ -1831,8 +1736,6 @@ done: * pattern, don't call it directly, use the appropriate macro * defined in H5Sprivate.h. * - * Modifications: - * *------------------------------------------------------------------------- */ H5S_class_t @@ -1844,11 +1747,11 @@ H5S_get_simple_extent_type(const H5S_t *space) HDassert(space); - ret_value=H5S_GET_EXTENT_TYPE(space); + ret_value = H5S_GET_EXTENT_TYPE(space); done: FUNC_LEAVE_NOAPI(ret_value) -} +} /* end H5S_get_simple_extent_type() */ /*------------------------------------------------------------------------- @@ -1857,36 +1760,31 @@ done: * Purpose: Retrieves the type of extent for a dataspace object * * Return: Success: The class of the dataspace object - * * Failure: N5S_NO_CLASS * - * Errors: - * * Programmer: Quincey Koziol * Thursday, July 23, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ H5S_class_t H5Sget_simple_extent_type(hid_t sid) { H5S_t *space; - H5S_class_t ret_value; + H5S_class_t ret_value; /* Return value */ FUNC_ENTER_API(H5S_NO_CLASS) H5TRACE1("Sc", "i", sid); /* Check arguments */ - if (NULL == (space = (H5S_t *)H5I_object_verify(sid, H5I_DATASPACE))) + if(NULL == (space = (H5S_t *)H5I_object_verify(sid, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5S_NO_CLASS, "not a dataspace") - ret_value=H5S_GET_EXTENT_TYPE(space); + ret_value = H5S_GET_EXTENT_TYPE(space); done: FUNC_LEAVE_API(ret_value) -} +} /* end H5Sget_simple_extent_type() */ /*-------------------------------------------------------------------------- @@ -1906,68 +1804,25 @@ done: herr_t H5Sset_extent_none(hid_t space_id) { - H5S_t *space; /* dataspace to modify */ - herr_t ret_value=SUCCEED; /* Return value */ + H5S_t *space; /* Dataspace to modify */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE1("e", "i", space_id); /* Check args */ - if (NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) + if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "not a dataspace") /* Clear the previous extent from the dataspace */ - if(H5S_extent_release(&space->extent)<0) + if(H5S__extent_release(&space->extent) < 0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTDELETE, FAIL, "can't release previous dataspace") - space->extent.type=H5S_NO_CLASS; - -done: - FUNC_LEAVE_API(ret_value) -} /* end H5Sset_extent_none() */ - - -/*-------------------------------------------------------------------------- - NAME - H5Soffset_simple - PURPOSE - Changes the offset of a selection within a simple dataspace extent - USAGE - herr_t H5Soffset_simple(space_id, offset) - hid_t space_id; IN: Dataspace object to reset - const hssize_t *offset; IN: Offset to position the selection at - RETURNS - Non-negative on success/Negative on failure - DESCRIPTION - This function creates an offset for the selection within an extent, allowing - the same shaped selection to be moved to different locations within a - dataspace without requiring it to be re-defined. ---------------------------------------------------------------------------*/ -herr_t -H5Soffset_simple(hid_t space_id, const hssize_t *offset) -{ - H5S_t *space; /* dataspace to modify */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_API(FAIL) - H5TRACE2("e", "i*Hs", space_id, offset); - - /* Check args */ - if (NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "not a dataspace") - if (space->extent.rank==0 || (H5S_GET_EXTENT_TYPE(space)==H5S_SCALAR - || H5S_GET_EXTENT_TYPE(space)==H5S_NULL)) - HGOTO_ERROR(H5E_ATOM, H5E_UNSUPPORTED, FAIL, "can't set offset on scalar or null dataspace") - if (offset == NULL) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no offset specified") - - /* Set the selection offset */ - if(H5S_select_offset(space,offset)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "can't set offset") + space->extent.type = H5S_NO_CLASS; done: FUNC_LEAVE_API(ret_value) -} /* end H5Soffset_simple() */ +} /* end H5Sset_extent_none() */ /*------------------------------------------------------------------------- @@ -1996,7 +1851,7 @@ H5S_set_extent(H5S_t *space, const hsize_t *size) HDassert(size); /* Verify that the dimensions being changed are allowed to change */ - for(u = 0; u < space->extent.rank; u++) { + for(u = 0; u < space->extent.rank; u++) if(space->extent.size[u] != size[u]) { /* Check for invalid dimension size modification */ if(space->extent.max && H5S_UNLIMITED != space->extent.max[u] && @@ -2006,7 +1861,6 @@ H5S_set_extent(H5S_t *space, const hsize_t *size) /* Indicate that dimension size can be modified */ ret_value = TRUE; } /* end if */ - } /* end for */ /* Update dimension size(s) */ if(ret_value) @@ -2033,7 +1887,7 @@ done: * *------------------------------------------------------------------------- */ -hbool_t +H5_ATTR_PURE hbool_t H5S_has_extent(const H5S_t *ds) { hbool_t ret_value = FALSE; /* Return value */ @@ -2104,7 +1958,6 @@ done: * Purpose: Determines if two dataspace extents are equal. * * Return: Success: TRUE if equal, FALSE if unequal - * * Failure: Negative * * Programmer: Quincey Koziol @@ -2116,7 +1969,7 @@ htri_t H5Sextent_equal(hid_t space1_id, hid_t space2_id) { const H5S_t *ds1, *ds2; /* Dataspaces to compare */ - htri_t ret_value; + htri_t ret_value; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE2("t", "ii", space1_id, space2_id); @@ -2148,7 +2001,7 @@ done: DESCRIPTION Compare two dataspaces if their extents are identical. --------------------------------------------------------------------------*/ -htri_t +H5_ATTR_PURE htri_t H5S_extent_equal(const H5S_t *ds1, const H5S_t *ds2) { unsigned u; /* Local index variable */ @@ -2209,7 +2062,7 @@ done: * *------------------------------------------------------------------------- */ -hsize_t +H5_ATTR_PURE hsize_t H5S_extent_nelem(const H5S_extent_t *ext) { FUNC_ENTER_NOAPI_NOINIT_NOERR @@ -2257,6 +2110,5 @@ H5S_set_version(H5F_t *f, H5S_t *ds) done: FUNC_LEAVE_NOAPI(ret_value) - } /* end H5S_set_version() */ @@ -240,7 +240,7 @@ /* Allocate space for new forward pointers */ \ if(NULL == (_tmp = (H5SL_node_t **)H5FL_FAC_MALLOC(H5SL_fac_g[X->log_nalloc]))) \ HGOTO_ERROR(H5E_SLIST, H5E_CANTALLOC, ERR, "memory allocation failed") \ - HDmemcpy((void *)_tmp, (const void *)X->forward, (LVL + 1) * sizeof(H5SL_node_t *)); \ + H5MM_memcpy((void *)_tmp, (const void *)X->forward, (LVL + 1) * sizeof(H5SL_node_t *)); \ X->forward = (H5SL_node_t **)H5FL_FAC_FREE(H5SL_fac_g[X->log_nalloc-1], (void *)X->forward); \ X->forward = _tmp; \ } /* end if */ \ @@ -262,7 +262,7 @@ /* Allocate space for new forward pointers */ \ if(NULL == (_tmp = (H5SL_node_t **)H5FL_FAC_MALLOC(H5SL_fac_g[X->log_nalloc]))) \ HGOTO_ERROR(H5E_SLIST, H5E_NOSPACE, NULL, "memory allocation failed") \ - HDmemcpy((void *)_tmp, (const void *)X->forward, (LVL) * sizeof(H5SL_node_t *)); \ + H5MM_memcpy((void *)_tmp, (const void *)X->forward, (LVL) * sizeof(H5SL_node_t *)); \ X->forward = (H5SL_node_t **)H5FL_FAC_FREE(H5SL_fac_g[X->log_nalloc+1], (void *)X->forward); \ X->forward = _tmp; \ } /* end if */ \ @@ -2318,7 +2318,7 @@ H5SM__read_iter_op(H5O_t *oh, H5O_mesg_t *mesg/*in,out*/, unsigned sequence, HGOTO_ERROR(H5E_SOHM, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed") /* Copy the encoded message into the buffer to return */ - HDmemcpy(udata->encoding_buf, mesg->raw, udata->buf_size); + H5MM_memcpy(udata->encoding_buf, mesg->raw, udata->buf_size); /* Found the message we were looking for */ ret_value = H5_ITER_STOP; @@ -2356,7 +2356,7 @@ H5SM__read_mesg_fh_cb(const void *obj, size_t obj_len, void *_udata) HGOTO_ERROR(H5E_SOHM, H5E_NOSPACE, FAIL, "memory allocation failed") /* Copy the message from the heap */ - HDmemcpy(udata->encoding_buf, obj, obj_len); + H5MM_memcpy(udata->encoding_buf, obj, obj_len); udata->buf_size = obj_len; done: diff --git a/src/H5SMbtree2.c b/src/H5SMbtree2.c index f0c4963..7f6c804 100644 --- a/src/H5SMbtree2.c +++ b/src/H5SMbtree2.c @@ -24,6 +24,7 @@ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Opkg.h" /* Object Headers */ #include "H5SMpkg.h" /* Shared object header messages */ @@ -248,7 +249,7 @@ H5SM_bt2_convert_to_list_op(const void * record, void *op_data) /* Insert this message at the end of the list */ HDassert(list->messages[mesg_idx].location == H5SM_NO_LOC); HDassert(message->location != H5SM_NO_LOC); - HDmemcpy(&(list->messages[mesg_idx]), message, sizeof(H5SM_sohm_t)); + H5MM_memcpy(&(list->messages[mesg_idx]), message, sizeof(H5SM_sohm_t)); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5SM_bt2_convert_to_list_op() */ diff --git a/src/H5SMcache.c b/src/H5SMcache.c index f0b469a..49ce2b4 100644 --- a/src/H5SMcache.c +++ b/src/H5SMcache.c @@ -388,7 +388,7 @@ H5SM__cache_table_serialize(const H5F_t *f, void *_image, size_t len, HDassert(H5F_SOHM_VERS(f) == HDF5_SHAREDHEADER_VERSION); /* Encode magic number */ - HDmemcpy(image, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* Encode each index header */ @@ -710,7 +710,7 @@ H5SM__cache_list_serialize(const H5F_t *f, void *_image, size_t len, HDassert(list->header->list_size == len); /* Encode magic number */ - HDmemcpy(image, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC); + H5MM_memcpy(image, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC); image += H5_SIZEOF_MAGIC; /* serialize messages from the messages array */ diff --git a/src/H5SMmessage.c b/src/H5SMmessage.c index ad84b24..0cca6bb 100644 --- a/src/H5SMmessage.c +++ b/src/H5SMmessage.c @@ -24,6 +24,7 @@ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Opkg.h" /* Object Headers */ #include "H5SMpkg.h" /* Shared object header messages */ @@ -302,7 +303,7 @@ H5SM__message_encode(uint8_t *raw, const void *_nrecord, void *_ctx) if(message->location == H5SM_IN_HEAP) { UINT32ENCODE(raw, message->u.heap_loc.ref_count); - HDmemcpy(raw, message->u.heap_loc.fheap_id.id, (size_t)H5O_FHEAP_ID_LEN); + H5MM_memcpy(raw, message->u.heap_loc.fheap_id.id, (size_t)H5O_FHEAP_ID_LEN); } /* end if */ else { HDassert(message->location == H5SM_IN_OH); @@ -343,7 +344,7 @@ H5SM__message_decode(const uint8_t *raw, void *_nrecord, void *_ctx) if(message->location == H5SM_IN_HEAP) { UINT32DECODE(raw, message->u.heap_loc.ref_count); - HDmemcpy(message->u.heap_loc.fheap_id.id, raw, (size_t)H5O_FHEAP_ID_LEN); + H5MM_memcpy(message->u.heap_loc.fheap_id.id, raw, (size_t)H5O_FHEAP_ID_LEN); } /* end if */ else { HDassert(message->location == H5SM_IN_OH); @@ -743,19 +743,19 @@ H5ST__dump_internal(H5ST_ptr_t p) FUNC_ENTER_STATIC_NOERR if(p) { - printf("p=%p\n", (void *)p); - printf("\tp->up=%p\n", (void *)p->up); - printf("\tp->parent=%p\n", (void *)p->parent); - printf("\tp->lokid=%p\n", (void *)p->lokid); - printf("\tp->hikid=%p\n", (void *)p->hikid); - printf("\tp->eqkid=%p\n", (void *)p->eqkid); - printf("\tp->splitchar=%c\n", p->splitchar); + HDprintf("p=%p\n", (void *)p); + HDprintf("\tp->up=%p\n", (void *)p->up); + HDprintf("\tp->parent=%p\n", (void *)p->parent); + HDprintf("\tp->lokid=%p\n", (void *)p->lokid); + HDprintf("\tp->hikid=%p\n", (void *)p->hikid); + HDprintf("\tp->eqkid=%p\n", (void *)p->eqkid); + HDprintf("\tp->splitchar=%c\n", p->splitchar); H5ST__dump_internal(p->lokid); if(p->splitchar) H5ST__dump_internal(p->eqkid); else - printf("%s\n", (char *)p->eqkid); + HDprintf("%s\n", (char *)p->eqkid); H5ST__dump_internal(p->hikid); } /* end if */ diff --git a/src/H5Sall.c b/src/H5Sall.c index 3b77b98..0aa2f05 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -18,16 +18,36 @@ * Purpose: "All" selection dataspace I/O functions. */ +/****************/ +/* Module Setup */ +/****************/ + #include "H5Smodule.h" /* This source code file is part of the H5S module */ +/***********/ +/* Headers */ +/***********/ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5Iprivate.h" /* ID Functions */ #include "H5Spkg.h" /* Dataspace functions */ -#include "H5VMprivate.h" /* Vector functions */ +#include "H5VMprivate.h" /* Vector functions */ + + +/****************/ +/* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ + -/* Static function prototypes */ +/********************/ +/* Local Prototypes */ +/********************/ /* Selection callbacks */ static herr_t H5S__all_copy(H5S_t *dst, const H5S_t *src, hbool_t share_selection); @@ -60,6 +80,16 @@ static herr_t H5S__all_iter_next(H5S_sel_iter_t *sel_iter, size_t nelem); static herr_t H5S__all_iter_next_block(H5S_sel_iter_t *sel_iter); static herr_t H5S__all_iter_release(H5S_sel_iter_t *sel_iter); + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*********************/ +/* Package Variables */ +/*********************/ + /* Selection properties for "all" selections */ const H5S_select_class_t H5S_sel_all[1] = {{ H5S_SEL_ALL, @@ -85,6 +115,11 @@ const H5S_select_class_t H5S_sel_all[1] = {{ H5S__all_iter_init, }}; + +/*******************/ +/* Local Variables */ +/*******************/ + /* Iteration properties for "all" selections */ static const H5S_sel_iter_class_t H5S_sel_iter_all[1] = {{ H5S_SEL_ALL, @@ -99,13 +134,14 @@ static const H5S_sel_iter_class_t H5S_sel_iter_all[1] = {{ H5S__all_iter_release, }}; + /*------------------------------------------------------------------------- * Function: H5S__all_iter_init * * Purpose: Initializes iteration information for "all" selection. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Tuesday, June 16, 1998 @@ -132,7 +168,7 @@ H5S__all_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) iter->type = H5S_sel_iter_all; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_iter_init() */ +} /* end H5S__all_iter_init() */ /*------------------------------------------------------------------------- @@ -141,7 +177,7 @@ H5S__all_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) * Purpose: Retrieve the current coordinates of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, April 22, 2003 @@ -165,7 +201,7 @@ H5S__all_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S__all_iter_coords() */ +} /* end H5S__all_iter_coords() */ /*------------------------------------------------------------------------- @@ -174,7 +210,7 @@ done: * Purpose: Retrieve the current block of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Monday, June 2, 2003 @@ -204,7 +240,7 @@ H5S__all_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) } /* end for */ FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_iter_block() */ +} /* end H5S__all_iter_block() */ /*------------------------------------------------------------------------- @@ -212,7 +248,7 @@ H5S__all_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) * * Purpose: Return number of elements left to process in iterator * - * Return: non-negative number of elements on success, zero on failure + * Return: Non-negative number of elements on success, zero on failure * * Programmer: Quincey Koziol * Tuesday, June 16, 1998 @@ -228,7 +264,7 @@ H5S__all_iter_nelmts(const H5S_sel_iter_t *iter) HDassert(iter); FUNC_LEAVE_NOAPI(iter->elmt_left) -} /* H5S__all_iter_nelmts() */ +} /* end H5S__all_iter_nelmts() */ /*-------------------------------------------------------------------------- @@ -257,7 +293,7 @@ H5S__all_iter_has_next_block(const H5S_sel_iter_t H5_ATTR_UNUSED *iter) HDassert(iter); FUNC_LEAVE_NOAPI(FALSE) -} /* H5S__all_iter_has_next_block() */ +} /* end H5S__all_iter_has_next_block() */ /*-------------------------------------------------------------------------- @@ -292,7 +328,7 @@ H5S__all_iter_next(H5S_sel_iter_t *iter, size_t nelem) iter->u.all.byte_offset += (nelem * iter->elmt_size); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_iter_next() */ +} /* end H5S__all_iter_next() */ /*-------------------------------------------------------------------------- @@ -321,7 +357,81 @@ H5S__all_iter_next_block(H5S_sel_iter_t H5_ATTR_UNUSED *iter) HDassert(iter); FUNC_LEAVE_NOAPI(FAIL) -} /* H5S__all_iter_next_block() */ +} /* end H5S__all_iter_next_block() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S__all_get_seq_list + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S__all_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + unsigned flags; IN: Flags for extra information about operation + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxelem; IN: Maximum number of elements to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nelem; OUT: Actual number of elements in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S__all_get_seq_list(const H5S_t H5_ATTR_UNUSED *space, unsigned H5_ATTR_UNUSED flags, H5S_sel_iter_t *iter, + size_t H5_ATTR_UNUSED maxseq, size_t maxelem, size_t *nseq, size_t *nelem, + hsize_t *off, size_t *len) +{ + size_t elem_used; /* The number of elements used */ + + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(space); + HDassert(iter); + HDassert(maxseq > 0); + HDassert(maxelem > 0); + HDassert(nseq); + HDassert(nelem); + HDassert(off); + HDassert(len); + + /* Determine the actual number of elements to use */ + H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); + elem_used = MIN(maxelem, (size_t)iter->elmt_left); + HDassert(elem_used > 0); + + /* Compute the offset in the dataset */ + off[0] = iter->u.all.byte_offset; + len[0] = elem_used * iter->elmt_size; + + /* Should only need one sequence for 'all' selections */ + *nseq = 1; + + /* Set the number of elements used */ + *nelem = elem_used; + + /* Update the iterator */ + iter->elmt_left -= elem_used; + iter->u.all.elmt_offset += elem_used; + iter->u.all.byte_offset += len[0]; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5S__all_get_seq_list() */ /*-------------------------------------------------------------------------- @@ -350,7 +460,7 @@ H5S__all_iter_release(H5S_sel_iter_t H5_ATTR_UNUSED * iter) HDassert(iter); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_iter_release() */ +} /* end H5S__all_iter_release() */ /*-------------------------------------------------------------------------- @@ -382,7 +492,7 @@ H5S__all_release(H5S_t *space) space->select.num_elem = 0; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_release() */ +} /* end H5S__all_release() */ /*-------------------------------------------------------------------------- @@ -391,9 +501,10 @@ H5S__all_release(H5S_t *space) PURPOSE Copy a selection from one dataspace to another USAGE - herr_t H5S__all_copy(dst, src) + herr_t H5S__all_copy(dst, src, share_selection) H5S_t *dst; OUT: Pointer to the destination dataspace H5S_t *src; IN: Pointer to the source dataspace + hbool_t; IN: Whether to share the selection between the dataspaces RETURNS Non-negative on success/Negative on failure DESCRIPTION @@ -527,7 +638,7 @@ H5S__all_serialize(const H5S_t *space, uint8_t **p) *p = pp; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_serialize() */ +} /* end H5S__all_serialize() */ /*-------------------------------------------------------------------------- @@ -572,7 +683,7 @@ H5S__all_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t H5_A done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S__all_deserialize() */ +} /* end H5S__all_deserialize() */ /*-------------------------------------------------------------------------- @@ -622,7 +733,7 @@ H5S__all_bounds(const H5S_t *space, hsize_t *start, hsize_t *end) } /* end for */ FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_bounds() */ +} /* end H5S__all_bounds() */ /*-------------------------------------------------------------------------- @@ -657,7 +768,7 @@ H5S__all_offset(const H5S_t H5_ATTR_UNUSED *space, hsize_t *offset) *offset = 0; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_offset() */ +} /* end H5S__all_offset() */ /*-------------------------------------------------------------------------- @@ -716,7 +827,7 @@ H5S__all_is_contiguous(const H5S_t H5_ATTR_UNUSED *space) HDassert(space); FUNC_LEAVE_NOAPI(TRUE) -} /* H5S__all_is_contiguous() */ +} /* end H5S__all_is_contiguous() */ /*-------------------------------------------------------------------------- @@ -745,7 +856,7 @@ H5S__all_is_single(const H5S_t H5_ATTR_UNUSED *space) HDassert(space); FUNC_LEAVE_NOAPI(TRUE) -} /* H5S__all_is_single() */ +} /* end H5S__all_is_single() */ /*-------------------------------------------------------------------------- @@ -776,7 +887,7 @@ H5S__all_is_regular(const H5S_t H5_ATTR_UNUSED *space) HDassert(space); FUNC_LEAVE_NOAPI(TRUE) -} /* H5S__all_is_regular() */ +} /* end H5S__all_is_regular() */ /*-------------------------------------------------------------------------- @@ -807,7 +918,7 @@ H5S__all_adjust_u(H5S_t H5_ATTR_UNUSED *space, const hsize_t H5_ATTR_UNUSED *off HDassert(offset); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_adjust_u() */ +} /* end H5S__all_adjust_u() */ /*------------------------------------------------------------------------- @@ -816,7 +927,7 @@ H5S__all_adjust_u(H5S_t H5_ATTR_UNUSED *space, const hsize_t H5_ATTR_UNUSED *off * Purpose: Projects a single element 'all' selection into a scalar * dataspace * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -836,7 +947,7 @@ H5S__all_project_scalar(const H5S_t H5_ATTR_UNUSED *space, hsize_t *offset) *offset = 0; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S__all_project_scalar() */ +} /* end H5S__all_project_scalar() */ /*------------------------------------------------------------------------- @@ -845,7 +956,7 @@ H5S__all_project_scalar(const H5S_t H5_ATTR_UNUSED *space, hsize_t *offset) * Purpose: Projects an 'all' selection onto/into a simple dataspace * of a different rank * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -853,7 +964,8 @@ H5S__all_project_scalar(const H5S_t H5_ATTR_UNUSED *space, hsize_t *offset) *------------------------------------------------------------------------- */ static herr_t -H5S__all_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *offset) +H5S__all_project_simple(const H5S_t H5_ATTR_UNUSED *base_space, + H5S_t *new_space, hsize_t H5_ATTR_UNUSED *offset) { herr_t ret_value = SUCCEED; /* Return value */ @@ -870,7 +982,7 @@ H5S__all_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *offs done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S__all_project_simple() */ +} /* end H5S__all_project_simple() */ /*-------------------------------------------------------------------------- @@ -914,7 +1026,7 @@ H5S_select_all(H5S_t *space, hbool_t rel_prev) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_all() */ +} /* end H5S_select_all() */ /*-------------------------------------------------------------------------- @@ -953,79 +1065,5 @@ H5Sselect_all(hid_t spaceid) done: FUNC_LEAVE_API(ret_value) -} /* H5Sselect_all() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S__all_get_seq_list - PURPOSE - Create a list of offsets & lengths for a selection - USAGE - herr_t H5S__all_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) - H5S_t *space; IN: Dataspace containing selection to use. - unsigned flags; IN: Flags for extra information about operation - H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last - position of interest in selection. - size_t maxseq; IN: Maximum number of sequences to generate - size_t maxelem; IN: Maximum number of elements to include in the - generated sequences - size_t *nseq; OUT: Actual number of sequences generated - size_t *nelem; OUT: Actual number of elements in sequences generated - hsize_t *off; OUT: Array of offsets - size_t *len; OUT: Array of lengths - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to generate a list of byte offsets and - lengths for the region(s) selected. Start/Restart from the position in the - ITER parameter. The number of sequences generated is limited by the MAXSEQ - parameter and the number of sequences actually generated is stored in the - NSEQ parameter. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S__all_get_seq_list(const H5S_t H5_ATTR_UNUSED *space, unsigned H5_ATTR_UNUSED flags, H5S_sel_iter_t *iter, - size_t H5_ATTR_UNUSED maxseq, size_t maxelem, size_t *nseq, size_t *nelem, - hsize_t *off, size_t *len) -{ - size_t elem_used; /* The number of elements used */ - - FUNC_ENTER_STATIC_NOERR - - /* Check args */ - HDassert(space); - HDassert(iter); - HDassert(maxseq > 0); - HDassert(maxelem > 0); - HDassert(nseq); - HDassert(nelem); - HDassert(off); - HDassert(len); - - /* Determine the actual number of elements to use */ - H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); - elem_used = MIN(maxelem, (size_t)iter->elmt_left); - HDassert(elem_used > 0); - - /* Compute the offset in the dataset */ - off[0] = iter->u.all.byte_offset; - len[0] = elem_used * iter->elmt_size; - - /* Should only need one sequence for 'all' selections */ - *nseq = 1; - - /* Set the number of elements used */ - *nelem = elem_used; - - /* Update the iterator */ - iter->elmt_left -= elem_used; - iter->u.all.elmt_offset += elem_used; - iter->u.all.byte_offset += len[0]; - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5S__all_get_seq_list() */ +} /* end H5Sselect_all() */ diff --git a/src/H5Sdbg.c b/src/H5Sdbg.c index ebd05ce..8171191 100644 --- a/src/H5Sdbg.c +++ b/src/H5Sdbg.c @@ -57,16 +57,16 @@ /********************/ -/*********************/ -/* Package Variables */ -/*********************/ - - /*****************************/ /* Library Private Variables */ /*****************************/ +/*********************/ +/* Package Variables */ +/*********************/ + + /*******************/ /* Local Variables */ /*******************/ @@ -94,24 +94,24 @@ H5S_debug(H5F_t *f, const void *_mesg, FILE *stream, int indent, int fwidth) switch(H5S_GET_EXTENT_TYPE(mesg)) { case H5S_NULL: - fprintf(stream, "%*s%-*s H5S_NULL\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s H5S_NULL\n", indent, "", fwidth, "Space class:"); break; case H5S_SCALAR: - fprintf(stream, "%*s%-*s H5S_SCALAR\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s H5S_SCALAR\n", indent, "", fwidth, "Space class:"); break; case H5S_SIMPLE: - fprintf(stream, "%*s%-*s H5S_SIMPLE\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s H5S_SIMPLE\n", indent, "", fwidth, "Space class:"); H5O_debug_id(H5O_SDSPACE_ID, f, &(mesg->extent), stream, indent + 3, MAX(0, fwidth - 3)); break; case H5S_NO_CLASS: default: - fprintf(stream, "%*s%-*s **UNKNOWN-%ld**\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s **UNKNOWN-%ld**\n", indent, "", fwidth, "Space class:", (long)(H5S_GET_EXTENT_TYPE(mesg))); break; } /* end switch */ diff --git a/src/H5Shyper.c b/src/H5Shyper.c index 88c570d..4cb5e28 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -18,21 +18,38 @@ * Purpose: Hyperslab selection dataspace I/O functions. */ +/****************/ +/* Module Setup */ +/****************/ + #include "H5Smodule.h" /* This source code file is part of the H5S module */ +/***********/ +/* Headers */ +/***********/ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* ID Functions */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Spkg.h" /* Dataspace functions */ -#include "H5VMprivate.h" /* Vector functions */ +#include "H5VMprivate.h" /* Vector functions */ + +/****************/ /* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ -/* Local datatypes */ -/* Static function prototypes */ +/********************/ +/* Local Prototypes */ +/********************/ static H5S_hyper_span_t *H5S__hyper_new_span(hsize_t low, hsize_t high, H5S_hyper_span_info_t *down, H5S_hyper_span_t *next); static herr_t H5S__hyper_span_precompute(H5S_hyper_span_info_t *spans, size_t elmt_size); @@ -64,10 +81,6 @@ static herr_t H5S__hyper_generate_spans(H5S_t *space); static herr_t H5S__generate_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], const hsize_t stride[], const hsize_t count[], const hsize_t block[]); -/* Needed for use in hyperslab code (H5Shyper.c) */ -#ifdef NEW_HYPERSLAB_API -static herr_t H5S_select_select (H5S_t *space1, H5S_seloper_t op, H5S_t *space2); -#endif /*NEW_HYPERSLAB_API*/ static void H5S__hyper_get_clip_diminfo(hsize_t start, hsize_t stride, hsize_t *count, hsize_t *block, hsize_t clip_size); static hsize_t H5S__hyper_get_clip_extent_real(const H5S_t *clip_space, @@ -111,6 +124,15 @@ static hbool_t H5S__hyper_rebuild_helper(const H5S_hyper_span_t *span, H5S_hyper_dim_t span_slab_info[], unsigned rank); static hbool_t H5S__hyper_rebuild(H5S_t *space); +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*********************/ +/* Package Variables */ +/*********************/ + /* Selection properties for hyperslab selections */ const H5S_select_class_t H5S_sel_hyper[1] = {{ H5S_SEL_HYPERSLABS, @@ -136,6 +158,11 @@ const H5S_select_class_t H5S_sel_hyper[1] = {{ H5S__hyper_iter_init, }}; + +/*******************/ +/* Local Variables */ +/*******************/ + /* Iteration properties for hyperslab selections */ static const H5S_sel_iter_class_t H5S_sel_iter_hyper[1] = {{ H5S_SEL_HYPERSLABS, @@ -153,16 +180,16 @@ static const H5S_sel_iter_class_t H5S_sel_iter_hyper[1] = {{ /* Static variables */ /* Arrays for default stride, block, etc. */ -static const hsize_t H5S_hyper_zeros_g[H5O_LAYOUT_NDIMS] = { +static const hsize_t H5S_hyper_zeros_g[H5S_MAX_RANK] = { 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, - 0,0,0,0, 0,0,0,0,0}; -static const hsize_t H5S_hyper_ones_g[H5O_LAYOUT_NDIMS] = { + 0,0,0,0, 0,0,0,0}; +static const hsize_t H5S_hyper_ones_g[H5S_MAX_RANK] = { 1,1,1,1, 1,1,1,1, 1,1,1,1, 1,1,1,1, 1,1,1,1, 1,1,1,1, - 1,1,1,1, 1,1,1,1,1}; + 1,1,1,1, 1,1,1,1}; /* Declare a free list to manage the H5S_hyper_sel_t struct */ H5FL_DEFINE_STATIC(H5S_hyper_sel_t); @@ -261,9 +288,9 @@ H5S__hyper_print_diminfo(FILE *f, const H5S_t *space) /*------------------------------------------------------------------------- * Function: H5S__hyper_iter_init * - * Purpose: Initializes iteration information for hyperslab span tree selection. + * Purpose: Initializes iteration information for hyperslab selection. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Saturday, February 24, 2001 @@ -334,7 +361,7 @@ H5S__hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) /* Check if the regular selection can be "flattened" */ if(cont_dim > 0) { hsize_t acc; /* Accumulator for "flattened" dimension's sizes */ - unsigned last_dim_flattened = 1; /* Flag to indicate that the last dimension was flattened */ + hbool_t last_dim_flattened = TRUE; /* Flag to indicate that the last dimension was flattened */ unsigned flat_rank = rank-cont_dim; /* Number of dimensions after flattening */ unsigned curr_dim; /* Current dimension */ int i; /* Index variable */ @@ -351,7 +378,7 @@ H5S__hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) acc *= mem_size[i]; /* Indicate that the dimension was flattened */ - last_dim_flattened = 1; + last_dim_flattened = TRUE; } /* end if */ else { if(last_dim_flattened) { @@ -369,7 +396,7 @@ H5S__hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) iter->u.hyp.sel_off[curr_dim] = space->select.offset[i] * (hssize_t)acc; /* Reset the "last dim flattened" flag to avoid flattened any further dimensions */ - last_dim_flattened = 0; + last_dim_flattened = FALSE; /* Reset the "accumulator" for possible further dimension flattening */ acc = 1; @@ -414,10 +441,9 @@ H5S__hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) /* Initialize irregular region information also (for release) */ iter->u.hyp.spans = NULL; } /* end if */ - else { + else { /* Initialize the information needed for non-regular hyperslab I/O */ H5S_hyper_span_info_t *spans; /* Pointer to hyperslab span info node */ -/* Initialize the information needed for non-regular hyperslab I/O */ HDassert(space->select.sel_info.hslab->span_lst); /* Make a copy of the span tree to iterate over */ iter->u.hyp.spans = H5S__hyper_copy_span(space->select.sel_info.hslab->span_lst); @@ -459,7 +485,7 @@ H5S__hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) * Purpose: Retrieve the current coordinates of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, April 22, 2003 @@ -529,10 +555,10 @@ H5S__hyper_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords) HDassert(v < 0); } /* end if */ else - HDmemcpy(coords, iter->u.hyp.off, sizeof(hsize_t) * iter->rank); + H5MM_memcpy(coords, iter->u.hyp.off, sizeof(hsize_t) * iter->rank); } /* end if */ else - HDmemcpy(coords, iter->u.hyp.off, sizeof(hsize_t) * iter->rank); + H5MM_memcpy(coords, iter->u.hyp.off, sizeof(hsize_t) * iter->rank); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5S__hyper_iter_coords() */ @@ -544,7 +570,7 @@ H5S__hyper_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords) * Purpose: Retrieve the current block of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Monday, June 2, 2003 @@ -570,7 +596,7 @@ H5S__hyper_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) /* Check for a single "regular" hyperslab */ if(iter->u.hyp.diminfo_valid) { - /* Compute the end of the block */ + /* Copy the start and compute the end of the block */ for(u = 0; u < iter->rank; u++) { start[u] = iter->u.hyp.off[u]; end[u] = (start[u] + iter->u.hyp.diminfo[u].block) - 1; @@ -595,7 +621,7 @@ H5S__hyper_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) * * Purpose: Return number of elements left to process in iterator * - * Return: non-negative number of elements on success, zero on failure + * Return: Non-negative number of elements on success, zero on failure * * Programmer: Quincey Koziol * Tuesday, June 16, 1998 @@ -631,7 +657,7 @@ H5S__hyper_iter_nelmts(const H5S_sel_iter_t *iter) EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -static htri_t +static H5_ATTR_PURE htri_t H5S__hyper_iter_has_next_block(const H5S_sel_iter_t *iter) { unsigned u; /* Local index variable */ @@ -689,7 +715,7 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem) { unsigned ndims; /* Number of dimensions of dataset */ int fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - unsigned i; /* Counters */ + unsigned u; /* Counters */ FUNC_ENTER_STATIC_NOERR @@ -697,19 +723,17 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem) /* (i.e. a regular hyperslab selection */ if(iter->u.hyp.diminfo_valid) { const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ - hsize_t iter_offset[H5O_LAYOUT_NDIMS]; - hsize_t iter_count[H5O_LAYOUT_NDIMS]; + hsize_t iter_offset[H5S_MAX_RANK]; + hsize_t iter_count[H5S_MAX_RANK]; int temp_dim; /* Temporary rank holder */ /* Check if this is a "flattened" regular hyperslab selection */ - if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < iter->rank) { + if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < iter->rank) /* Set the aliases for the dimension rank */ ndims = iter->u.hyp.iter_rank; - } /* end if */ - else { + else /* Set the aliases for the dimension rank */ ndims = iter->rank; - } /* end else */ /* Set the fastest dimension rank */ fast_dim = (int)ndims - 1; @@ -718,14 +742,14 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem) tdiminfo = iter->u.hyp.diminfo; /* Calculate the offset and block count for each dimension */ - for(i = 0; i < ndims; i++) { - if(tdiminfo[i].count == 1) { - iter_offset[i] = iter->u.hyp.off[i] - tdiminfo[i].start; - iter_count[i] = 0; + for(u = 0; u < ndims; u++) { + if(tdiminfo[u].count == 1) { + iter_offset[u] = iter->u.hyp.off[u] - tdiminfo[u].start; + iter_count[u] = 0; } /* end if */ else { - iter_offset[i] = (iter->u.hyp.off[i] - tdiminfo[i].start) % tdiminfo[i].stride; - iter_count[i] = (iter->u.hyp.off[i] - tdiminfo[i].start) / tdiminfo[i].stride; + iter_offset[u] = (iter->u.hyp.off[u] - tdiminfo[u].start) % tdiminfo[u].stride; + iter_count[u] = (iter->u.hyp.off[u] - tdiminfo[u].start) / tdiminfo[u].stride; } /* end else */ } /* end for */ @@ -750,10 +774,9 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem) /* Decrement the number of elements advanced */ nelem -= actual_elem; } /* end if */ - else { + else /* Move to the next row in the current dimension */ iter_offset[temp_dim]++; - } /* end else */ /* If this block is still in the range of blocks to output for the dimension, break out of loop */ if(iter_offset[temp_dim] < tdiminfo[temp_dim].block) @@ -776,8 +799,8 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem) } /* end while */ /* Translate current iter_offset and iter_count into iterator position */ - for(i = 0; i < ndims; i++) - iter->u.hyp.off[i] = tdiminfo[i].start + (tdiminfo[i].stride * iter_count[i]) + iter_offset[i]; + for(u = 0; u < ndims; u++) + iter->u.hyp.off[u] = tdiminfo[u].start + (tdiminfo[u].stride * iter_count[u]) + iter_offset[u]; } /* end if */ /* Must be an irregular hyperslab selection */ else { @@ -821,15 +844,13 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem) /* Decrement the number of elements advanced */ nelem -= actual_elem; } /* end if */ - else { + else /* Move to the next row in the current dimension */ abs_arr[curr_dim]++; - } /* end else */ /* Check if we are still within the span */ - if(abs_arr[curr_dim] <= curr_span->high) { + if(abs_arr[curr_dim] <= curr_span->high) break; - } /* end if */ /* If we walked off that span, advance to the next span */ else { /* Advance span in this dimension */ @@ -845,10 +866,9 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem) break; } /* end if */ - else { + else /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ curr_dim--; - } /* end else */ } /* end else */ } /* end while */ @@ -907,22 +927,20 @@ H5S__hyper_iter_next_block(H5S_sel_iter_t *iter) FUNC_ENTER_STATIC_NOERR /* Check for the special case of just one H5Sselect_hyperslab call made */ - /* (i.e. a regular hyperslab selection */ + /* (i.e. a regular hyperslab selection) */ if(iter->u.hyp.diminfo_valid) { const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ - hsize_t iter_offset[H5O_LAYOUT_NDIMS]; - hsize_t iter_count[H5O_LAYOUT_NDIMS]; + hsize_t iter_offset[H5S_MAX_RANK]; + hsize_t iter_count[H5S_MAX_RANK]; int temp_dim; /* Temporary rank holder */ /* Check if this is a "flattened" regular hyperslab selection */ - if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < iter->rank) { + if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < iter->rank) /* Set the aliases for the dimension rank */ ndims = iter->u.hyp.iter_rank; - } /* end if */ - else { + else /* Set the aliases for the dimension rank */ ndims = iter->rank; - } /* end else */ /* Set the fastest dimension rank */ fast_dim = (int)ndims - 1; @@ -945,14 +963,12 @@ H5S__hyper_iter_next_block(H5S_sel_iter_t *iter) /* Advance one block */ temp_dim = fast_dim; /* Start with the fastest changing dimension */ while(temp_dim >= 0) { - if(temp_dim == fast_dim) { + if(temp_dim == fast_dim) /* Move iterator over current block */ iter_offset[temp_dim] += tdiminfo[temp_dim].block; - } /* end if */ - else { + else /* Move to the next row in the current dimension */ iter_offset[temp_dim]++; - } /* end else */ /* If this block is still in the range of blocks to output for the dimension, break out of loop */ if(iter_offset[temp_dim] < tdiminfo[temp_dim].block) @@ -1001,19 +1017,16 @@ H5S__hyper_iter_next_block(H5S_sel_iter_t *iter) curr_span = ispan[curr_dim]; /* Increment absolute position */ - if(curr_dim == fast_dim) { + if(curr_dim == fast_dim) /* Move the iterator over rest of element in span */ abs_arr[curr_dim] = curr_span->high + 1; - } /* end if */ - else { + else /* Move to the next row in the current dimension */ abs_arr[curr_dim]++; - } /* end else */ /* Check if we are still within the span */ - if(abs_arr[curr_dim] <= curr_span->high) { + if(abs_arr[curr_dim] <= curr_span->high) break; - } /* end if */ /* If we walked off that span, advance to the next span */ else { /* Advance span in this dimension */ @@ -1029,10 +1042,9 @@ H5S__hyper_iter_next_block(H5S_sel_iter_t *iter) break; } /* end if */ - else { + else /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ curr_dim--; - } /* end else */ } /* end else */ } /* end while */ @@ -1063,7 +1075,1333 @@ H5S__hyper_iter_next_block(H5S_sel_iter_t *iter) } /* end else */ FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5S__hyper_iter_next() */ +} /* end H5S__hyper_iter_next_block() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S__hyper_get_seq_list_gen + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S_select_hyper_get_file_list_gen(space,iter,maxseq,maxelem,nseq,nelem,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxelem; IN: Maximum number of elements to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nelem; OUT: Actual number of elements in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S__hyper_get_seq_list_gen(const H5S_t *space, H5S_sel_iter_t *iter, + size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, + hsize_t *off, size_t *len) +{ + H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ + H5S_hyper_span_t **ispan; /* Iterator's hyperslab span nodes */ + hsize_t slab[H5S_MAX_RANK]; /* Cumulative size of each dimension in bytes */ + hsize_t acc; /* Accumulator for computing cumulative sizes */ + hsize_t loc_off; /* Element offset in the dataspace */ + hsize_t last_span_end = 0; /* The offset of the end of the last span */ + hsize_t *abs_arr; /* Absolute hyperslab span position */ + const hssize_t *off_arr; /* Offset within the dataspace extent */ + size_t span_size = 0; /* Number of bytes in current span to actually process */ + size_t io_left; /* Number of elements left to process */ + size_t io_bytes_left; /* Number of bytes left to process */ + size_t io_used; /* Number of elements processed */ + size_t curr_seq = 0; /* Number of sequence/offsets stored in the arrays */ + size_t elem_size; /* Size of each element iterating over */ + unsigned ndims; /* Number of dimensions of dataset */ + unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ + int curr_dim; /* Current dimension being operated on */ + unsigned u; /* Index variable */ + int i; /* Index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(space); + HDassert(iter); + HDassert(maxseq > 0); + HDassert(maxelem > 0); + HDassert(nseq); + HDassert(nelem); + HDassert(off); + HDassert(len); + + /* Set the rank of the fastest changing dimension */ + ndims = space->extent.rank; + fast_dim = (ndims - 1); + + /* Get the pointers to the current span info and span nodes */ + curr_span = iter->u.hyp.span[fast_dim]; + abs_arr = iter->u.hyp.off; + off_arr = space->select.offset; + ispan = iter->u.hyp.span; + elem_size = iter->elmt_size; + + /* Set the amount of elements to perform I/O on, etc. */ + H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); + io_left = MIN(maxelem, (size_t)iter->elmt_left); + io_bytes_left = io_left * elem_size; + + /* Compute the cumulative size of dataspace dimensions */ + for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { + slab[i] = acc; + acc *= space->extent.size[i]; + } /* end for */ + + /* Set the offset of the first element iterated on */ + for(u = 0, loc_off = 0; u < ndims; u++) + /* Compute the sequential element offset */ + loc_off += ((hsize_t)((hssize_t)abs_arr[u] + off_arr[u])) * slab[u]; + + /* Range check against number of elements left in selection */ + HDassert(io_bytes_left <= (iter->elmt_left * elem_size)); + + /* Take care of any partial spans leftover from previous I/Os */ + if(abs_arr[fast_dim] != curr_span->low) { + /* Finish the span in the fastest changing dimension */ + + /* Compute the number of bytes to attempt in this span */ + H5_CHECKED_ASSIGN(span_size, size_t, ((curr_span->high - abs_arr[fast_dim])+1)*elem_size, hsize_t); + + /* Check number of bytes against upper bounds allowed */ + if(span_size > io_bytes_left) + span_size = io_bytes_left; + + /* Add the partial span to the list of sequences */ + off[curr_seq] = loc_off; + len[curr_seq] = span_size; + + /* Increment sequence count */ + curr_seq++; + + /* Set the location of the last span's end */ + last_span_end = loc_off + span_size; + + /* Decrement I/O left to perform */ + io_bytes_left -= span_size; + + /* Check if we are done */ + if(io_bytes_left > 0) { + /* Move to next span in fastest changing dimension */ + curr_span = curr_span->next; + + if(NULL != curr_span) { + /* Move location offset of destination */ + loc_off += (curr_span->low - abs_arr[fast_dim]) * elem_size; + + /* Move iterator for fastest changing dimension */ + abs_arr[fast_dim] = curr_span->low; + } /* end if */ + } /* end if */ + else { + /* Advance the hyperslab iterator */ + abs_arr[fast_dim] += span_size / elem_size; + + /* Check if we are still within the span */ + if(abs_arr[fast_dim] <= curr_span->high) { + iter->u.hyp.span[fast_dim] = curr_span; + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span = curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(NULL != curr_span) { + /* Reset absolute position */ + abs_arr[fast_dim] = curr_span->low; + iter->u.hyp.span[fast_dim] = curr_span; + } /* end if */ + } /* end else */ + } /* end else */ + + /* Adjust iterator pointers */ + + if(NULL == curr_span) { +/* Same as code in main loop */ + /* Start at the next fastest dim */ + curr_dim = (int)(fast_dim - 1); + + /* Work back up through the dimensions */ + while(curr_dim >= 0) { + /* Reset the current span */ + curr_span = iter->u.hyp.span[curr_dim]; + + /* Increment absolute position */ + abs_arr[curr_dim]++; + + /* Check if we are still within the span */ + if(abs_arr[curr_dim] <= curr_span->high) { + break; + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span = curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(NULL != curr_span) { + /* Reset the span in the current dimension */ + ispan[curr_dim] = curr_span; + + /* Reset absolute position */ + abs_arr[curr_dim] = curr_span->low; + + break; + } /* end if */ + else + /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ + curr_dim--; + } /* end else */ + } /* end while */ + + /* Check if we have more spans in the tree */ + if(curr_dim >= 0) { + /* Walk back down the iterator positions, resetting them */ + while((unsigned)curr_dim < fast_dim) { + HDassert(curr_span); + HDassert(curr_span->down); + HDassert(curr_span->down->head); + + /* Increment current dimension */ + curr_dim++; + + /* Set the new span_info & span for this dimension */ + iter->u.hyp.span[curr_dim] = curr_span->down->head; + + /* Advance span down the tree */ + curr_span = curr_span->down->head; + + /* Reset the absolute offset for the dim */ + abs_arr[curr_dim] = curr_span->low; + } /* end while */ + + /* Verify that the curr_span points to the fastest dim */ + HDassert(curr_span == iter->u.hyp.span[fast_dim]); + + /* Reset the buffer offset */ + for(u = 0, loc_off = 0; u < ndims; u++) + loc_off += ((hsize_t)((hssize_t)abs_arr[u] + off_arr[u])) * slab[u]; + } /* end else */ + else + /* We had better be done with I/O or bad things are going to happen... */ + HDassert(io_bytes_left == 0); + } /* end if */ + } /* end if */ + + /* Perform the I/O on the elements, based on the position of the iterator */ + while(io_bytes_left > 0 && curr_seq < maxseq) { + /* Sanity check */ + HDassert(curr_span); + + /* Adjust location offset of destination to compensate for initial increment below */ + loc_off -= curr_span->pstride; + + /* Loop over all the spans in the fastest changing dimension */ + while(curr_span != NULL) { + /* Move location offset of destination */ + loc_off += curr_span->pstride; + + /* Compute the number of elements to attempt in this span */ + H5_CHECKED_ASSIGN(span_size, size_t, curr_span->nelem, hsize_t); + + /* Check number of elements against upper bounds allowed */ + if(span_size >= io_bytes_left) { + /* Trim the number of bytes to output */ + span_size = io_bytes_left; + io_bytes_left = 0; + +/* COMMON */ + /* Store the I/O information for the span */ + + /* Check if this is appending onto previous sequence */ + if(curr_seq > 0 && last_span_end == loc_off) + len[curr_seq - 1] += span_size; + else { + off[curr_seq] = loc_off; + len[curr_seq] = span_size; + + /* Increment the number of sequences in arrays */ + curr_seq++; + } /* end else */ + + /* Set the location of the last span's end */ + last_span_end = loc_off + span_size; +/* end COMMON */ + + /* Break out now, we are finished with I/O */ + break; + } /* end if */ + else { + /* Decrement I/O left to perform */ + io_bytes_left -= span_size; + +/* COMMON */ + /* Store the I/O information for the span */ + + /* Check if this is appending onto previous sequence */ + if(curr_seq > 0 && last_span_end == loc_off) + len[curr_seq - 1] += span_size; + else { + off[curr_seq] = loc_off; + len[curr_seq] = span_size; + + /* Increment the number of sequences in arrays */ + curr_seq++; + } /* end else */ + + /* Set the location of the last span's end */ + last_span_end = loc_off + span_size; +/* end COMMON */ + + /* If the sequence & offset arrays are full, do what? */ + if(curr_seq >= maxseq) + /* Break out now, we are finished with sequences */ + break; + } /* end else */ + + /* Move to next span in fastest changing dimension */ + curr_span = curr_span->next; + } /* end while */ + + /* Check if we are done */ + if(io_bytes_left == 0 || curr_seq >= maxseq) { + HDassert(curr_span); + abs_arr[fast_dim] = curr_span->low + (span_size / elem_size); + + /* Check if we are still within the span */ + if(abs_arr[fast_dim] <= curr_span->high) { + iter->u.hyp.span[fast_dim]=curr_span; + break; + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span = curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(curr_span != NULL) { + /* Reset absolute position */ + abs_arr[fast_dim] = curr_span->low; + iter->u.hyp.span[fast_dim] = curr_span; + break; + } /* end if */ + } /* end else */ + } /* end if */ + + /* Adjust iterator pointers */ + + /* Start at the next fastest dim */ + curr_dim = (int)(fast_dim - 1); + + /* Work back up through the dimensions */ + while(curr_dim >= 0) { + /* Reset the current span */ + curr_span=iter->u.hyp.span[curr_dim]; + + /* Increment absolute position */ + abs_arr[curr_dim]++; + + /* Check if we are still within the span */ + if(abs_arr[curr_dim]<=curr_span->high) { + break; + } /* end if */ + /* If we walked off that span, advance to the next span */ + else { + /* Advance span in this dimension */ + curr_span = curr_span->next; + + /* Check if we have a valid span in this dimension still */ + if(curr_span != NULL) { + /* Reset the span in the current dimension */ + ispan[curr_dim] = curr_span; + + /* Reset absolute position */ + abs_arr[curr_dim] = curr_span->low; + + break; + } /* end if */ + else + /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ + curr_dim--; + } /* end else */ + } /* end while */ + + /* Check if we are finished with the spans in the tree */ + if(curr_dim < 0) { + /* We had better be done with I/O or bad things are going to happen... */ + HDassert(io_bytes_left == 0); + break; + } /* end if */ + else { + /* Walk back down the iterator positions, resetting them */ + while((unsigned)curr_dim < fast_dim) { + HDassert(curr_span); + HDassert(curr_span->down); + HDassert(curr_span->down->head); + + /* Increment current dimension to the next dimension down */ + curr_dim++; + + /* Set the new span for the next dimension down */ + iter->u.hyp.span[curr_dim] = curr_span->down->head; + + /* Advance span down the tree */ + curr_span = curr_span->down->head; + + /* Reset the absolute offset for the dim */ + abs_arr[curr_dim] = curr_span->low; + } /* end while */ + + /* Verify that the curr_span points to the fastest dim */ + HDassert(curr_span == iter->u.hyp.span[fast_dim]); + } /* end else */ + + /* Reset the buffer offset */ + for(u = 0, loc_off = 0; u < ndims; u++) + loc_off += ((hsize_t)((hssize_t)abs_arr[u] + off_arr[u])) * slab[u]; + } /* end while */ + + /* Decrement number of elements left in iterator */ + io_used = (io_left - (io_bytes_left / elem_size)); + iter->elmt_left -= io_used; + + /* Set the number of sequences generated */ + *nseq = curr_seq; + + /* Set the number of elements used */ + *nelem = io_used; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5S__hyper_get_seq_list_gen() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S__hyper_get_seq_list_opt + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S_select_hyper_get_file_list_opt(space,iter,maxseq,maxelem,nseq,nelem,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxelem; IN: Maximum number of elements to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nelem; OUT: Actual number of elements in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S__hyper_get_seq_list_opt(const H5S_t *space, H5S_sel_iter_t *iter, + size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, + hsize_t *off, size_t *len) +{ + hsize_t *mem_size; /* Size of the source buffer */ + hsize_t slab[H5S_MAX_RANK]; /* Hyperslab size */ + const hssize_t *sel_off; /* Selection offset in dataspace */ + hsize_t offset[H5S_MAX_RANK]; /* Coordinate offset in dataspace */ + hsize_t tmp_count[H5S_MAX_RANK]; /* Temporary block count */ + hsize_t tmp_block[H5S_MAX_RANK]; /* Temporary block offset */ + hsize_t wrap[H5S_MAX_RANK]; /* Bytes to wrap around at the end of a row */ + hsize_t skip[H5S_MAX_RANK]; /* Bytes to skip between blocks */ + const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ + hsize_t fast_dim_start, /* Local copies of fastest changing dimension info */ + fast_dim_stride, + fast_dim_block, + fast_dim_offset; + size_t fast_dim_buf_off; /* Local copy of amount to move fastest dimension buffer offset */ + size_t fast_dim_count; /* Number of blocks left in fastest changing dimension */ + size_t tot_blk_count; /* Total number of blocks left to output */ + size_t act_blk_count; /* Actual number of blocks to output */ + size_t total_rows; /* Total number of entire rows to output */ + size_t curr_rows; /* Current number of entire rows to output */ + unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ + unsigned ndims; /* Number of dimensions of dataset */ + int temp_dim; /* Temporary rank holder */ + hsize_t acc; /* Accumulator */ + hsize_t loc; /* Coordinate offset */ + size_t curr_seq = 0; /* Current sequence being operated on */ + size_t actual_elem; /* The actual number of elements to count */ + size_t actual_bytes;/* The actual number of bytes to copy */ + size_t io_left; /* The number of elements left in I/O operation */ + size_t start_io_left; /* The initial number of elements left in I/O operation */ + size_t elem_size; /* Size of each element iterating over */ + unsigned u; /* Local index variable */ + int i; /* Local index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(space); + HDassert(iter); + HDassert(maxseq > 0); + HDassert(maxelem > 0); + HDassert(nseq); + HDassert(nelem); + HDassert(off); + HDassert(len); + + /* Set the local copy of the diminfo pointer */ + tdiminfo = iter->u.hyp.diminfo; + + /* Check if this is a "flattened" regular hyperslab selection */ + if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < space->extent.rank) { + /* Set the aliases for a few important dimension ranks */ + ndims = iter->u.hyp.iter_rank; + fast_dim = ndims - 1; + + /* Set the local copy of the selection offset */ + sel_off = iter->u.hyp.sel_off; + + /* Set up the pointer to the size of the memory space */ + mem_size = iter->u.hyp.size; + } /* end if */ + else { + /* Set the aliases for a few important dimension ranks */ + ndims = space->extent.rank; + fast_dim = ndims - 1; + + /* Set the local copy of the selection offset */ + sel_off = space->select.offset; + + /* Set up the pointer to the size of the memory space */ + mem_size = space->extent.size; + } /* end else */ + + /* initialize row sizes for each dimension */ + elem_size = iter->elmt_size; + for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { + slab[i] = acc; + acc *= mem_size[i]; + } /* end for */ + + /* Calculate the number of elements to sequence through */ + H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); + io_left = MIN((size_t)iter->elmt_left, maxelem); + + /* Sanity check that there aren't any "remainder" sequences in process */ + HDassert(!((iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start) % tdiminfo[fast_dim].stride != 0 || + ((iter->u.hyp.off[fast_dim] != tdiminfo[fast_dim].start) && tdiminfo[fast_dim].count == 1))); + + /* We've cleared the "remainder" of the previous fastest dimension + * sequence before calling this routine, so we must be at the beginning of + * a sequence. Use the fancy algorithm to compute the offsets and run + * through as many as possible, until the buffer fills up. + */ + + /* Keep the number of elements we started with */ + start_io_left = io_left; + + /* Compute the arrays to perform I/O on */ + + /* Copy the location of the point to get */ + /* (Add in the selection offset) */ + for(u = 0; u < ndims; u++) + offset[u] = (hsize_t)((hssize_t)iter->u.hyp.off[u] + sel_off[u]); + + /* Compute the current "counts" for this location */ + for(u = 0; u < ndims; u++) { + if(tdiminfo[u].count == 1) { + tmp_count[u] = 0; + tmp_block[u] = iter->u.hyp.off[u] - tdiminfo[u].start; + } /* end if */ + else { + tmp_count[u] = (iter->u.hyp.off[u] - tdiminfo[u].start) / tdiminfo[u].stride; + tmp_block[u] = (iter->u.hyp.off[u] - tdiminfo[u].start) % tdiminfo[u].stride; + } /* end else */ + } /* end for */ + + /* Compute the initial buffer offset */ + for(u = 0, loc = 0; u < ndims; u++) + loc += offset[u] * slab[u]; + + /* Set the number of elements to write each time */ + H5_CHECKED_ASSIGN(actual_elem, size_t, tdiminfo[fast_dim].block, hsize_t); + + /* Set the number of actual bytes */ + actual_bytes = actual_elem * elem_size; + + /* Set local copies of information for the fastest changing dimension */ + fast_dim_start = tdiminfo[fast_dim].start; + fast_dim_stride = tdiminfo[fast_dim].stride; + fast_dim_block = tdiminfo[fast_dim].block; + H5_CHECKED_ASSIGN(fast_dim_buf_off, size_t, slab[fast_dim] * fast_dim_stride, hsize_t); + fast_dim_offset = (hsize_t)((hssize_t)fast_dim_start + sel_off[fast_dim]); + + /* Compute the number of blocks which would fit into the buffer */ + H5_CHECK_OVERFLOW(io_left / fast_dim_block, hsize_t, size_t); + tot_blk_count = (size_t)(io_left / fast_dim_block); + + /* Don't go over the maximum number of sequences allowed */ + tot_blk_count = MIN(tot_blk_count, (maxseq - curr_seq)); + + /* Compute the amount to wrap at the end of each row */ + for(u = 0; u < ndims; u++) + wrap[u] = (mem_size[u] - (tdiminfo[u].stride * tdiminfo[u].count)) * slab[u]; + + /* Compute the amount to skip between blocks */ + for(u = 0; u < ndims; u++) + skip[u] = (tdiminfo[u].stride - tdiminfo[u].block) * slab[u]; + + /* Check if there is a partial row left (with full blocks) */ + if(tmp_count[fast_dim] > 0) { + /* Get number of blocks in fastest dimension */ + H5_CHECKED_ASSIGN(fast_dim_count, size_t, tdiminfo[fast_dim].count - tmp_count[fast_dim], hsize_t); + + /* Make certain this entire row will fit into buffer */ + fast_dim_count = MIN(fast_dim_count, tot_blk_count); + + /* Number of blocks to sequence over */ + act_blk_count = fast_dim_count; + + /* Loop over all the blocks in the fastest changing dimension */ + while(fast_dim_count > 0) { + /* Store the sequence information */ + off[curr_seq] = loc; + len[curr_seq] = actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc += fast_dim_buf_off; + + /* Decrement number of blocks */ + fast_dim_count--; + } /* end while */ + + /* Decrement number of elements left */ + io_left -= actual_elem * act_blk_count; + + /* Decrement number of blocks left */ + tot_blk_count -= act_blk_count; + + /* Increment information to reflect block just processed */ + tmp_count[fast_dim] += act_blk_count; + + /* Check if we finished the entire row of blocks */ + if(tmp_count[fast_dim] >= tdiminfo[fast_dim].count) { + /* Increment offset in destination buffer */ + loc += wrap[fast_dim]; + + /* Increment information to reflect block just processed */ + offset[fast_dim] = fast_dim_offset; /* reset the offset in the fastest dimension */ + tmp_count[fast_dim] = 0; + + /* Increment the offset and count for the other dimensions */ + temp_dim = (int)fast_dim - 1; + while(temp_dim >= 0) { + /* Move to the next row in the curent dimension */ + offset[temp_dim]++; + tmp_block[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_block[temp_dim] < tdiminfo[temp_dim].block) + break; + else { + /* Move to the next block in the current dimension */ + offset[temp_dim] += (tdiminfo[temp_dim].stride - tdiminfo[temp_dim].block); + loc += skip[temp_dim]; + tmp_block[temp_dim] = 0; + tmp_count[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_count[temp_dim] < tdiminfo[temp_dim].count) + break; + else { + offset[temp_dim] = (hsize_t)((hssize_t)tdiminfo[temp_dim].start + sel_off[temp_dim]); + loc += wrap[temp_dim]; + tmp_count[temp_dim] = 0; /* reset back to the beginning of the line */ + tmp_block[temp_dim] = 0; + } /* end else */ + } /* end else */ + + /* Decrement dimension count */ + temp_dim--; + } /* end while */ + } /* end if */ + else { + /* Update the offset in the fastest dimension */ + offset[fast_dim] += (fast_dim_stride * act_blk_count); + } /* end else */ + } /* end if */ + + /* Compute the number of entire rows to read in */ + H5_CHECK_OVERFLOW(tot_blk_count / tdiminfo[fast_dim].count, hsize_t, size_t); + curr_rows = total_rows = (size_t)(tot_blk_count / tdiminfo[fast_dim].count); + + /* Reset copy of number of blocks in fastest dimension */ + H5_CHECKED_ASSIGN(fast_dim_count, size_t, tdiminfo[fast_dim].count, hsize_t); + + /* Read in data until an entire sequence can't be written out any longer */ + while(curr_rows > 0) { + +#define DUFF_GUTS \ +/* Store the sequence information */ \ +off[curr_seq] = loc; \ +len[curr_seq] = actual_bytes; \ + \ +/* Increment sequence count */ \ +curr_seq++; \ + \ +/* Increment information to reflect block just processed */ \ +loc += fast_dim_buf_off; + +#ifdef NO_DUFFS_DEVICE + /* Loop over all the blocks in the fastest changing dimension */ + while(fast_dim_count > 0) { + DUFF_GUTS + + /* Decrement number of blocks */ + fast_dim_count--; + } /* end while */ +#else /* NO_DUFFS_DEVICE */ + { + size_t duffs_index; /* Counting index for Duff's device */ + + duffs_index = (fast_dim_count + 7) / 8; + switch (fast_dim_count % 8) { + default: + HDassert(0 && "This Should never be executed!"); + break; + case 0: + do + { + DUFF_GUTS + case 7: + DUFF_GUTS + case 6: + DUFF_GUTS + case 5: + DUFF_GUTS + case 4: + DUFF_GUTS + case 3: + DUFF_GUTS + case 2: + DUFF_GUTS + case 1: + DUFF_GUTS + } while (--duffs_index > 0); + } /* end switch */ + } +#endif /* NO_DUFFS_DEVICE */ +#undef DUFF_GUTS + + /* Increment offset in destination buffer */ + loc += wrap[fast_dim]; + + /* Increment the offset and count for the other dimensions */ + temp_dim = (int)fast_dim - 1; + while(temp_dim >= 0) { + /* Move to the next row in the curent dimension */ + offset[temp_dim]++; + tmp_block[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_block[temp_dim] < tdiminfo[temp_dim].block) + break; + else { + /* Move to the next block in the current dimension */ + offset[temp_dim] += (tdiminfo[temp_dim].stride - tdiminfo[temp_dim].block); + loc += skip[temp_dim]; + tmp_block[temp_dim] = 0; + tmp_count[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_count[temp_dim] < tdiminfo[temp_dim].count) + break; + else { + offset[temp_dim] = (hsize_t)((hssize_t)tdiminfo[temp_dim].start + sel_off[temp_dim]); + loc += wrap[temp_dim]; + tmp_count[temp_dim] = 0; /* reset back to the beginning of the line */ + tmp_block[temp_dim] = 0; + } /* end else */ + } /* end else */ + + /* Decrement dimension count */ + temp_dim--; + } /* end while */ + + /* Decrement the number of rows left */ + curr_rows--; + } /* end while */ + + /* Adjust the number of blocks & elements left to transfer */ + + /* Decrement number of elements left */ + H5_CHECK_OVERFLOW(actual_elem * (total_rows * tdiminfo[fast_dim].count), hsize_t, size_t); + io_left -= (size_t)(actual_elem * (total_rows * tdiminfo[fast_dim].count)); + + /* Decrement number of blocks left */ + H5_CHECK_OVERFLOW((total_rows * tdiminfo[fast_dim].count), hsize_t, size_t); + tot_blk_count -= (size_t)(total_rows * tdiminfo[fast_dim].count); + + /* Read in partial row of blocks */ + if(io_left > 0 && curr_seq < maxseq) { + /* Get remaining number of blocks left to output */ + fast_dim_count = tot_blk_count; + + /* Loop over all the blocks in the fastest changing dimension */ + while(fast_dim_count > 0) { + /* Store the sequence information */ + off[curr_seq] = loc; + len[curr_seq] = actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Increment information to reflect block just processed */ + loc += fast_dim_buf_off; + + /* Decrement number of blocks */ + fast_dim_count--; + } /* end while */ + + /* Decrement number of elements left */ + io_left -= actual_elem * tot_blk_count; + + /* Increment information to reflect block just processed */ + offset[fast_dim] += (fast_dim_stride * tot_blk_count); /* move the offset in the fastest dimension */ + + /* Handle any leftover, partial blocks in this row */ + if(io_left > 0 && curr_seq < maxseq) { + actual_elem = io_left; + actual_bytes = actual_elem * elem_size; + + /* Store the sequence information */ + off[curr_seq] = loc; + len[curr_seq] = actual_bytes; + + /* Increment sequence count */ + curr_seq++; + + /* Decrement the number of elements left */ + io_left -= actual_elem; + + /* Increment buffer correctly */ + offset[fast_dim] += actual_elem; + } /* end if */ + + /* don't bother checking slower dimensions */ + HDassert(io_left == 0 || curr_seq == maxseq); + } /* end if */ + + /* Update the iterator */ + + /* Update the iterator with the location we stopped */ + /* (Subtract out the selection offset) */ + for(u = 0; u < ndims; u++) + iter->u.hyp.off[u] = (hsize_t)((hssize_t)offset[u] - sel_off[u]); + + /* Decrement the number of elements left in selection */ + iter->elmt_left -= (start_io_left - io_left); + + /* Increment the number of sequences generated */ + *nseq += curr_seq; + + /* Increment the number of elements used */ + *nelem += start_io_left - io_left; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5S__hyper_get_seq_list_opt() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S__hyper_get_seq_list_single + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S__hyper_get_seq_list_single(space, flags, iter, maxseq, maxelem, nseq, nelem, off, len) + H5S_t *space; IN: Dataspace containing selection to use. + unsigned flags; IN: Flags for extra information about operation + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxelem; IN: Maximum number of elements to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nelem; OUT: Actual number of elements in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S__hyper_get_seq_list_single(const H5S_t *space, H5S_sel_iter_t *iter, + size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, + hsize_t *off, size_t *len) +{ + const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ + const hssize_t *sel_off; /* Selection offset in dataspace */ + hsize_t *mem_size; /* Size of the source buffer */ + hsize_t base_offset[H5S_MAX_RANK]; /* Base coordinate offset in dataspace */ + hsize_t offset[H5S_MAX_RANK]; /* Coordinate offset in dataspace */ + hsize_t slab[H5S_MAX_RANK]; /* Hyperslab size */ + hsize_t fast_dim_block; /* Local copies of fastest changing dimension info */ + hsize_t acc; /* Accumulator */ + hsize_t loc; /* Coordinate offset */ + size_t tot_blk_count; /* Total number of blocks left to output */ + size_t elem_size; /* Size of each element iterating over */ + size_t io_left; /* The number of elements left in I/O operation */ + size_t actual_elem; /* The actual number of elements to count */ + unsigned ndims; /* Number of dimensions of dataset */ + unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ + unsigned skip_dim; /* Rank of the dimension to skip along */ + unsigned u; /* Local index variable */ + int i; /* Local index variable */ + + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(space); + HDassert(iter); + HDassert(maxseq > 0); + HDassert(maxelem > 0); + HDassert(nseq); + HDassert(nelem); + HDassert(off); + HDassert(len); + + /* Set a local copy of the diminfo pointer */ + tdiminfo = iter->u.hyp.diminfo; + + /* Check if this is a "flattened" regular hyperslab selection */ + if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < space->extent.rank) { + /* Set the aliases for a few important dimension ranks */ + ndims = iter->u.hyp.iter_rank; + + /* Set the local copy of the selection offset */ + sel_off = iter->u.hyp.sel_off; + + /* Set up the pointer to the size of the memory space */ + mem_size = iter->u.hyp.size; + } /* end if */ + else { + /* Set the aliases for a few important dimension ranks */ + ndims = space->extent.rank; + + /* Set the local copy of the selection offset */ + sel_off = space->select.offset; + + /* Set up the pointer to the size of the memory space */ + mem_size = space->extent.size; + } /* end else */ + fast_dim = ndims - 1; + + /* initialize row sizes for each dimension */ + elem_size = iter->elmt_size; + for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { + slab[i] = acc; + acc *= mem_size[i]; + } /* end for */ + + /* Copy the base location of the block */ + /* (Add in the selection offset) */ + for(u = 0; u < ndims; u++) + base_offset[u] = (hsize_t)((hssize_t)tdiminfo[u].start + sel_off[u]); + + /* Copy the location of the point to get */ + /* (Add in the selection offset) */ + for(u = 0; u < ndims; u++) + offset[u] = (hsize_t)((hssize_t)iter->u.hyp.off[u] + sel_off[u]); + + /* Compute the initial buffer offset */ + for(u = 0, loc = 0; u < ndims; u++) + loc += offset[u] * slab[u]; + + /* Set local copies of information for the fastest changing dimension */ + fast_dim_block = tdiminfo[fast_dim].block; + + /* Calculate the number of elements to sequence through */ + H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); + io_left = MIN((size_t)iter->elmt_left, maxelem); + + /* Compute the number of blocks which would fit into the buffer */ + H5_CHECK_OVERFLOW(io_left / fast_dim_block, hsize_t, size_t); + tot_blk_count = (size_t)(io_left / fast_dim_block); + + /* Don't go over the maximum number of sequences allowed */ + tot_blk_count = MIN(tot_blk_count, maxseq); + + /* Set the number of elements to write each time */ + H5_CHECKED_ASSIGN(actual_elem, size_t, fast_dim_block, hsize_t); + + /* Check for blocks to operate on */ + if(tot_blk_count > 0) { + size_t actual_bytes; /* The actual number of bytes to copy */ + + /* Set the number of actual bytes */ + actual_bytes = actual_elem * elem_size; + + /* Check for 1-dim selection */ + if(0 == fast_dim) { + /* Sanity checks */ + HDassert(1 == tot_blk_count); + HDassert(io_left == actual_elem); + + /* Store the sequence information */ + *off++ = loc; + *len++ = actual_bytes; + } /* end if */ + else { + hsize_t skip_slab; /* Temporary copy of slab[fast_dim - 1] */ + size_t blk_count; /* Total number of blocks left to output */ + + /* Find first dimension w/block >1 */ + skip_dim = fast_dim; + for(i = (int)(fast_dim - 1); i >= 0; i--) + if(tdiminfo[i].block > 1) { + skip_dim = (unsigned)i; + break; + } /* end if */ + skip_slab = slab[skip_dim]; + + /* Check for being able to use fast algorithm for 1-D */ + if(0 == skip_dim) { + /* Create sequences until an entire row can't be used */ + blk_count = tot_blk_count; + while(blk_count > 0) { + /* Store the sequence information */ + *off++ = loc; + *len++ = actual_bytes; + + /* Increment offset in destination buffer */ + loc += skip_slab; + + /* Decrement block count */ + blk_count--; + } /* end while */ + + /* Move to the next location */ + offset[skip_dim] += tot_blk_count; + } /* end if */ + else { + hsize_t tmp_block[H5S_MAX_RANK]; /* Temporary block offset */ + hsize_t skip[H5S_MAX_RANK]; /* Bytes to skip between blocks */ + int temp_dim; /* Temporary rank holder */ + + /* Set the starting block location */ + for(u = 0; u < ndims; u++) + tmp_block[u] = iter->u.hyp.off[u] - tdiminfo[u].start; + + /* Compute the amount to skip between sequences */ + for(u = 0; u < ndims; u++) + skip[u] = (mem_size[u] - tdiminfo[u].block) * slab[u]; + + /* Create sequences until an entire row can't be used */ + blk_count = tot_blk_count; + while(blk_count > 0) { + /* Store the sequence information */ + *off++ = loc; + *len++ = actual_bytes; + + /* Set temporary dimension for advancing offsets */ + temp_dim = (int)skip_dim; + + /* Increment offset in destination buffer */ + loc += skip_slab; + + /* Increment the offset and count for the other dimensions */ + while(temp_dim >= 0) { + /* Move to the next row in the curent dimension */ + offset[temp_dim]++; + tmp_block[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_block[temp_dim] < tdiminfo[temp_dim].block) + break; + else { + offset[temp_dim] = base_offset[temp_dim]; + loc += skip[temp_dim]; + tmp_block[temp_dim] = 0; + } /* end else */ + + /* Decrement dimension count */ + temp_dim--; + } /* end while */ + + /* Decrement block count */ + blk_count--; + } /* end while */ + } /* end else */ + } /* end else */ + + /* Update the iterator, if there were any blocks used */ + + /* Decrement the number of elements left in selection */ + iter->elmt_left -= tot_blk_count * actual_elem; + + /* Check if there are elements left in iterator */ + if(iter->elmt_left > 0) { + /* Update the iterator with the location we stopped */ + /* (Subtract out the selection offset) */ + for(u = 0; u < ndims; u++) + iter->u.hyp.off[u] = (hsize_t)((hssize_t)offset[u] - sel_off[u]); + } /* end if */ + + /* Increment the number of sequences generated */ + *nseq += tot_blk_count; + + /* Increment the number of elements used */ + *nelem += tot_blk_count * actual_elem; + } /* end if */ + + /* Check for partial block, with room for another sequence */ + if(io_left > (tot_blk_count * actual_elem) && tot_blk_count < maxseq) { + size_t elmt_remainder; /* Elements remaining */ + + /* Compute elements left */ + elmt_remainder = io_left - (tot_blk_count * actual_elem); + HDassert(elmt_remainder < fast_dim_block); + HDassert(elmt_remainder > 0); + + /* Store the sequence information */ + *off++ = loc; + *len++ = elmt_remainder * elem_size; + + /* Update the iterator with the location we stopped */ + iter->u.hyp.off[fast_dim] += (hsize_t)elmt_remainder; + + /* Decrement the number of elements left in selection */ + iter->elmt_left -= elmt_remainder; + + /* Increment the number of sequences generated */ + (*nseq)++; + + /* Increment the number of elements used */ + *nelem += elmt_remainder; + } /* end if */ + + /* Sanity check */ + HDassert(*nseq > 0); + HDassert(*nelem > 0); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5S__hyper_get_seq_list_single() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S__hyper_get_seq_list + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S__hyper_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + unsigned flags; IN: Flags for extra information about operation + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxelem; IN: Maximum number of elements to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nelem; OUT: Actual number of elements in sequences generated + hsize_t *off; OUT: Array of offsets (in bytes) + size_t *len; OUT: Array of lengths (in bytes) + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S__hyper_get_seq_list(const H5S_t *space, unsigned H5_ATTR_UNUSED flags, H5S_sel_iter_t *iter, + size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, + hsize_t *off, size_t *len) +{ + herr_t ret_value = FAIL; /* return value */ + + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(space); + HDassert(iter); + HDassert(iter->elmt_left > 0); + HDassert(maxseq > 0); + HDassert(maxelem > 0); + HDassert(nseq); + HDassert(nelem); + HDassert(off); + HDassert(len); + HDassert(space->select.sel_info.hslab->unlim_dim < 0); + + /* Check for the special case of just one H5Sselect_hyperslab call made */ + if(space->select.sel_info.hslab->diminfo_valid) { + const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ + const hssize_t *sel_off; /* Selection offset in dataspace */ + hsize_t *mem_size; /* Size of the source buffer */ + unsigned ndims; /* Number of dimensions of dataset */ + unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ + hbool_t single_block; /* Whether the selection is a single block */ + unsigned u; /* Local index variable */ + + /* Set a local copy of the diminfo pointer */ + tdiminfo = iter->u.hyp.diminfo; + + /* Check if this is a "flattened" regular hyperslab selection */ + if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < space->extent.rank) { + /* Set the aliases for a few important dimension ranks */ + ndims = iter->u.hyp.iter_rank; + + /* Set the local copy of the selection offset */ + sel_off = iter->u.hyp.sel_off; + + /* Set up the pointer to the size of the memory space */ + mem_size = iter->u.hyp.size; + } /* end if */ + else { + /* Set the aliases for a few important dimension ranks */ + ndims = space->extent.rank; + + /* Set the local copy of the selection offset */ + sel_off = space->select.offset; + + /* Set up the pointer to the size of the memory space */ + mem_size = space->extent.size; + } /* end else */ + fast_dim = ndims - 1; + + /* Check if we stopped in the middle of a sequence of elements */ + if((iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start) % tdiminfo[fast_dim].stride != 0 || + ((iter->u.hyp.off[fast_dim] != tdiminfo[fast_dim].start) && tdiminfo[fast_dim].count == 1)) { + hsize_t slab[H5S_MAX_RANK]; /* Hyperslab size */ + hsize_t loc; /* Coordinate offset */ + hsize_t acc; /* Accumulator */ + size_t leftover; /* The number of elements left over from the last sequence */ + size_t actual_elem; /* The actual number of elements to count */ + size_t elem_size; /* Size of each element iterating over */ + int i; /* Local index variable */ + + + /* Calculate the number of elements left in the sequence */ + if(tdiminfo[fast_dim].count == 1) { + H5_CHECKED_ASSIGN(leftover, size_t, tdiminfo[fast_dim].block - (iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start), hsize_t); + } /* end if */ + else { + H5_CHECKED_ASSIGN(leftover, size_t, tdiminfo[fast_dim].block - ((iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start) % tdiminfo[fast_dim].stride), hsize_t); + } /* end else */ + + /* Make certain that we don't write too many */ + actual_elem = MIN3(leftover, (size_t)iter->elmt_left, maxelem); + + /* Initialize row sizes for each dimension */ + elem_size = iter->elmt_size; + for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { + slab[i] = acc; + acc *= mem_size[i]; + } /* end for */ + + /* Compute the initial buffer offset */ + for(u = 0, loc = 0; u < ndims; u++) + loc += ((hsize_t)((hssize_t)iter->u.hyp.off[u] + sel_off[u])) * slab[u]; + + /* Add a new sequence */ + off[0] = loc; + H5_CHECKED_ASSIGN(len[0], size_t, actual_elem * elem_size, hsize_t); + + /* Increment sequence array locations */ + off++; + len++; + + /* Advance the hyperslab iterator */ + H5S__hyper_iter_next(iter, actual_elem); + + /* Decrement the number of elements left in selection */ + iter->elmt_left -= actual_elem; + + /* Decrement element/sequence limits */ + maxelem -= actual_elem; + maxseq--; + + /* Set the number of sequences generated and elements used */ + *nseq = 1; + *nelem = actual_elem; + + /* Check for using up all the sequences/elements */ + if(0 == iter->elmt_left || 0 == maxelem || 0 == maxseq) + return(SUCCEED); + } /* end if */ + else { + /* Reset the number of sequences generated and elements used */ + *nseq = 0; + *nelem = 0; + } /* end else */ + + /* Check for a single block selected */ + single_block = TRUE; + for(u = 0; u < ndims; u++) + if(1 != tdiminfo[u].count) { + single_block = FALSE; + break; + } /* end if */ + + /* Check for single block selection */ + if(single_block) + /* Use single-block optimized call to generate sequence list */ + ret_value = H5S__hyper_get_seq_list_single(space, iter, maxseq, maxelem, nseq, nelem, off, len); + else + /* Use optimized call to generate sequence list */ + ret_value = H5S__hyper_get_seq_list_opt(space, iter, maxseq, maxelem, nseq, nelem, off, len); + } /* end if */ + else + /* Call the general sequence generator routine */ + ret_value = H5S__hyper_get_seq_list_gen(space, iter, maxseq, maxelem, nseq, nelem, off, len); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5S__hyper_get_seq_list() */ /*-------------------------------------------------------------------------- @@ -1091,8 +2429,7 @@ H5S__hyper_iter_release(H5S_sel_iter_t *iter) /* Check args */ HDassert(iter); -/* Release the information needed for non-regular hyperslab I/O */ - /* Free the copy of the selections span tree */ + /* Free the copy of the hyperslab selection span tree */ if(iter->u.hyp.spans != NULL) H5S__hyper_free_span_info(iter->u.hyp.spans); @@ -1111,7 +2448,7 @@ H5S__hyper_iter_release(H5S_sel_iter_t *iter) H5S_hyper_span_info_t *down; IN: Down span tree for new node H5S_hyper_span_t *next; IN: Next span for new node RETURNS - Pointer to next span node on success, NULL on failure + Pointer to new span node on success, NULL on failure DESCRIPTION Allocate and initialize a new hyperslab span node, filling in the low & high bounds, the down span and next span pointers also. Increment the @@ -1122,7 +2459,8 @@ H5S__hyper_iter_release(H5S_sel_iter_t *iter) REVISION LOG --------------------------------------------------------------------------*/ static H5S_hyper_span_t * -H5S__hyper_new_span(hsize_t low, hsize_t high, H5S_hyper_span_info_t *down, H5S_hyper_span_t *next) +H5S__hyper_new_span(hsize_t low, hsize_t high, H5S_hyper_span_info_t *down, + H5S_hyper_span_t *next) { H5S_hyper_span_t *ret_value = NULL; /* Return value */ @@ -1404,6 +2742,7 @@ H5S__hyper_copy_span(H5S_hyper_span_info_t *spans) FUNC_ENTER_STATIC + /* Sanity check */ HDassert(spans); /* Copy the hyperslab span tree */ @@ -1422,23 +2761,24 @@ done: NAME H5S__hyper_cmp_spans PURPOSE - Check if two hyperslab slabs are the same + Check if two hyperslab span trees are the same USAGE hbool_t H5S__hyper_cmp_spans(span1, span2) - H5S_hyper_span_t *span1; IN: First span tree to compare - H5S_hyper_span_t *span2; IN: Second span tree to compare + H5S_hyper_span_info_t *span_info1; IN: First span tree to compare + H5S_hyper_span_info_t *span_info2; IN: Second span tree to compare RETURNS TRUE (1) or FALSE (0) on success, can't fail DESCRIPTION - Compare two hyperslab slabs to determine if they refer to the same - selection. If span1 & span2 are both NULL, that counts as equal + Compare two hyperslab span trees to determine if they refer to the same + selection. If span1 & span2 are both NULL, that counts as equal. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -static hbool_t -H5S__hyper_cmp_spans(const H5S_hyper_span_info_t *span_info1, const H5S_hyper_span_info_t *span_info2) +static H5_ATTR_PURE hbool_t +H5S__hyper_cmp_spans(const H5S_hyper_span_info_t *span_info1, + const H5S_hyper_span_info_t *span_info2) { hbool_t ret_value = FALSE; /* Return value */ @@ -1610,9 +2950,10 @@ done: PURPOSE Copy a selection from one dataspace to another USAGE - herr_t H5S__hyper_copy(dst, src) + herr_t H5S__hyper_copy(dst, src, share_selection) H5S_t *dst; OUT: Pointer to the destination dataspace H5S_t *src; IN: Pointer to the source dataspace + hbool_t; IN: Whether to share the selection between the dataspaces RETURNS Non-negative on success/Negative on failure DESCRIPTION @@ -2045,7 +3386,7 @@ H5S__hyper_serialize_helper(const H5S_hyper_span_info_t *spans, HDassert(spans); HDassert(start); HDassert(end); - HDassert(rank < H5O_LAYOUT_NDIMS); + HDassert(rank < H5S_MAX_RANK); HDassert(p && pp); /* Walk through the list of spans, recursing or outputting them */ @@ -2088,7 +3429,7 @@ H5S__hyper_serialize_helper(const H5S_hyper_span_info_t *spans, *p = pp; FUNC_LEAVE_NOAPI_VOID -} /* H5S__hyper_serialize_helper() */ +} /* end H5S__hyper_serialize_helper() */ /*-------------------------------------------------------------------------- @@ -2170,8 +3511,8 @@ H5S__hyper_serialize(const H5S_t *space, uint8_t **p) /* Check for a "regular" hyperslab selection */ else if(space->select.sel_info.hslab->diminfo_valid) { const H5S_hyper_dim_t *diminfo; /* Alias for dataspace's diminfo information */ - hsize_t offset[H5O_LAYOUT_NDIMS]; /* Offset of element in dataspace */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary hyperslab counts */ + hsize_t offset[H5S_MAX_RANK]; /* Offset of element in dataspace */ + hsize_t tmp_count[H5S_MAX_RANK]; /* Temporary hyperslab counts */ unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ unsigned ndims; /* Rank of the dataspace */ unsigned u; /* Local counting variable */ @@ -2261,8 +3602,8 @@ H5S__hyper_serialize(const H5S_t *space, uint8_t **p) } /* end while */ } /* end if */ else { - hsize_t start[H5O_LAYOUT_NDIMS]; /* Location of start of hyperslab */ - hsize_t end[H5O_LAYOUT_NDIMS]; /* Location of end of hyperslab */ + hsize_t start[H5S_MAX_RANK]; /* Location of start of hyperslab */ + hsize_t end[H5S_MAX_RANK]; /* Location of end of hyperslab */ /* Encode number of hyperslabs */ block_count = H5S__hyper_span_nblocks(space->select.sel_info.hslab->span_lst); @@ -2318,8 +3659,8 @@ H5S__hyper_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t fl { unsigned rank; /* Rank of points */ const uint8_t *pp; /* Local pointer for decoding */ - hsize_t start[H5O_LAYOUT_NDIMS]; /* Hyperslab start information */ - hsize_t block[H5O_LAYOUT_NDIMS]; /* Hyperslab block information */ + hsize_t start[H5S_MAX_RANK]; /* Hyperslab start information */ + hsize_t block[H5S_MAX_RANK]; /* Hyperslab block information */ unsigned u; /* Local counting variable */ herr_t ret_value = FAIL; /* Return value */ @@ -2337,8 +3678,8 @@ H5S__hyper_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t fl /* If there is an unlimited dimension, only encode opt_unlim_diminfo */ if(flags & H5S_SELECT_FLAG_UNLIM) { - hsize_t stride[H5O_LAYOUT_NDIMS]; /* Hyperslab stride information */ - hsize_t count[H5O_LAYOUT_NDIMS]; /* Hyperslab count information */ + hsize_t stride[H5S_MAX_RANK]; /* Hyperslab stride information */ + hsize_t count[H5S_MAX_RANK]; /* Hyperslab count information */ /* Sanity checks */ HDassert(H5S_UNLIMITED == HSIZE_UNDEF); @@ -2360,7 +3701,7 @@ H5S__hyper_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t fl else { const hsize_t *stride; /* Hyperslab stride information */ const hsize_t *count; /* Hyperslab count information */ - hsize_t end[H5O_LAYOUT_NDIMS]; /* Hyperslab end information */ + hsize_t end[H5S_MAX_RANK]; /* Hyperslab end information */ hsize_t *tstart; /* Temporary hyperslab pointers */ hsize_t *tend; /* Temporary hyperslab pointers */ hsize_t *tblock; /* Temporary hyperslab pointers */ @@ -2447,7 +3788,7 @@ H5S__hyper_span_blocklist(const H5S_hyper_span_info_t *spans, hsize_t start[], /* Sanity checks */ HDassert(spans); - HDassert(rank < H5O_LAYOUT_NDIMS); + HDassert(rank < H5S_MAX_RANK); HDassert(start); HDassert(end); HDassert(startblock); @@ -2479,18 +3820,18 @@ H5S__hyper_span_blocklist(const H5S_hyper_span_info_t *spans, hsize_t start[], /* Copy previous starting points */ for(u = 0; u < rank; u++, (*buf)++) - HDmemcpy(*buf, &start[u], sizeof(hsize_t)); + H5MM_memcpy(*buf, &start[u], sizeof(hsize_t)); /* Copy starting point for this span */ - HDmemcpy(*buf, &curr->low, sizeof(hsize_t)); + H5MM_memcpy(*buf, &curr->low, sizeof(hsize_t)); (*buf)++; /* Copy previous ending points */ for(u = 0; u < rank; u++, (*buf)++) - HDmemcpy(*buf, &end[u], sizeof(hsize_t)); + H5MM_memcpy(*buf, &end[u], sizeof(hsize_t)); /* Copy starting point for this span */ - HDmemcpy(*buf, &curr->high, sizeof(hsize_t)); + H5MM_memcpy(*buf, &curr->high, sizeof(hsize_t)); (*buf)++; /* Decrement the number of blocks processed */ @@ -2551,8 +3892,8 @@ H5S__get_select_hyper_blocklist(H5S_t *space, hbool_t internal, hsize_t startblo /* Check for a "regular" hyperslab selection */ if(space->select.sel_info.hslab->diminfo_valid) { const H5S_hyper_dim_t *diminfo; /* Alias for dataspace's diminfo information */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary hyperslab counts */ - hsize_t offset[H5O_LAYOUT_NDIMS]; /* Offset of element in dataspace */ + hsize_t tmp_count[H5S_MAX_RANK]; /* Temporary hyperslab counts */ + hsize_t offset[H5S_MAX_RANK]; /* Offset of element in dataspace */ unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ unsigned ndims; /* Rank of the dataspace */ hbool_t done; /* Whether we are done with the iteration */ @@ -2603,11 +3944,11 @@ H5S__get_select_hyper_blocklist(H5S_t *space, hbool_t internal, hsize_t startblo /* Check if we should copy this block information */ if(startblock == 0) { /* Copy the starting location */ - HDmemcpy(buf, offset, sizeof(hsize_t) * ndims); + H5MM_memcpy(buf, offset, sizeof(hsize_t) * ndims); buf += ndims; /* Compute the ending location */ - HDmemcpy(buf, offset, sizeof(hsize_t) * ndims); + H5MM_memcpy(buf, offset, sizeof(hsize_t) * ndims); for(u = 0; u < ndims; u++) buf[u] += (diminfo[u].block - 1); buf += ndims; @@ -2662,8 +4003,8 @@ H5S__get_select_hyper_blocklist(H5S_t *space, hbool_t internal, hsize_t startblo } /* end while */ } /* end if */ else { - hsize_t start[H5O_LAYOUT_NDIMS]; /* Location of start of hyperslab */ - hsize_t end[H5O_LAYOUT_NDIMS]; /* Location of end of hyperslab */ + hsize_t start[H5S_MAX_RANK]; /* Location of start of hyperslab */ + hsize_t end[H5S_MAX_RANK]; /* Location of end of hyperslab */ ret_value = H5S__hyper_span_blocklist(space->select.sel_info.hslab->span_lst, start, end, (hsize_t)0, &startblock, &numblocks, &buf); } /* end else */ @@ -2771,7 +4112,7 @@ H5S_hyper_bounds_helper(const H5S_hyper_span_info_t *spans, const hssize_t *offs HDassert(spans); HDassert(offset); - HDassert(rank < H5O_LAYOUT_NDIMS); + HDassert(rank < H5S_MAX_RANK); HDassert(start); HDassert(end); @@ -3075,7 +4416,7 @@ done: EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -static htri_t +static H5_ATTR_PURE htri_t H5S__hyper_is_contiguous(const H5S_t *space) { hbool_t small_contiguous, /* Flag for small contiguous block */ @@ -3145,10 +4486,10 @@ H5S__hyper_is_contiguous(const H5S_t *space) /* * For a hyperslab to be contiguous, it must have only one block and - * (either it's size must be the same as the dataspace extent's in all - * but the slowest changing dimension - * OR - * block size must be 1 in all but the fastest changing dimension). + * either it's size must be the same as the dataspace extent's in all + * but the slowest changing dimension + * OR + * block size must be 1 in all but the fastest changing dimension. */ /* Initialize flags */ large_contiguous = TRUE; /* assume true and reset if the dimensions don't match */ @@ -3260,7 +4601,7 @@ H5S__hyper_is_contiguous(const H5S_t *space) EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -static htri_t +static H5_ATTR_PURE htri_t H5S__hyper_is_single(const H5S_t *space) { htri_t ret_value = TRUE; /* return value */ @@ -3888,125 +5229,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5S_hyper_convert() */ -#ifdef LATER - -/*-------------------------------------------------------------------------- - NAME - H5S_hyper_intersect_helper - PURPOSE - Helper routine to detect intersections in span trees - USAGE - htri_t H5S_hyper_intersect_helper(spans1, spans2) - H5S_hyper_span_info_t *spans1; IN: First span tree to operate with - H5S_hyper_span_info_t *spans2; IN: Second span tree to operate with - RETURNS - Non-negative on success, negative on failure - DESCRIPTION - Quickly detect intersections between two span trees - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static htri_t -H5S_hyper_intersect_helper (H5S_hyper_span_info_t *spans1, H5S_hyper_span_info_t *spans2) -{ - H5S_hyper_span_t *curr1; /* Pointer to current span in 1st span tree */ - H5S_hyper_span_t *curr2; /* Pointer to current span in 2nd span tree */ - htri_t status; /* Status from recursive call */ - htri_t ret_value=FALSE; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - /* Sanity check */ - HDassert((spans1 && spans2) || (spans1 == NULL && spans2 == NULL)); - - /* "NULL" span trees compare as overlapping */ - if(spans1==NULL && spans2==NULL) - HGOTO_DONE(TRUE); - - /* Get the span lists for each span in this tree */ - curr1=spans1->head; - curr2=spans2->head; - - /* Iterate over the spans in each tree */ - while(curr1!=NULL && curr2!=NULL) { - /* Check for 1st span entirely before 2nd span */ - if(curr1->high<curr2->low) - curr1=curr1->next; - /* Check for 2nd span entirely before 1st span */ - else if(curr2->high<curr1->low) - curr2=curr2->next; - /* Spans must overlap */ - else { - /* Recursively check spans in next dimension down */ - if((status=H5S_hyper_intersect_helper(curr1->down,curr2->down))<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab intersection check") - - /* If there is a span intersection in the down dimensions, the span trees overlap */ - if(status==TRUE) - HGOTO_DONE(TRUE); - - /* No intersection in down dimensions, advance to next span */ - if(curr1->high<curr2->high) - curr1=curr1->next; - else - curr2=curr2->next; - } /* end else */ - } /* end while */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_hyper_intersect_helper() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_hyper_intersect - PURPOSE - Detect intersections in span trees - USAGE - htri_t H5S_hyper_intersect(space1, space2) - H5S_t *space1; IN: First dataspace to operate on span tree - H5S_t *space2; IN: Second dataspace to operate on span tree - RETURNS - Non-negative on success, negative on failure - DESCRIPTION - Quickly detect intersections between two span trees - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -htri_t -H5S_hyper_intersect (H5S_t *space1, H5S_t *space2) -{ - htri_t ret_value=FAIL; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - /* Sanity check */ - HDassert(space1); - HDassert(space2); - - /* Check that the space selections both have span trees */ - if(space1->select.sel_info.hslab->span_lst==NULL || - space2->select.sel_info.hslab->span_lst==NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNINITIALIZED, FAIL, "dataspace does not have span tree") - - /* Check that the dataspaces are both the same rank */ - if(space1->extent.rank!=space2->extent.rank) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "dataspace ranks don't match") - - /* Perform the span-by-span intersection check */ - if((ret_value=H5S_hyper_intersect_helper(space1->select.sel_info.hslab->span_lst,space2->select.sel_info.hslab->span_lst))<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab intersection check") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_hyper_intersect() */ -#endif /* LATER */ - /*-------------------------------------------------------------------------- NAME @@ -4242,7 +5464,7 @@ H5S__hyper_adjust_u(H5S_t *space, const hsize_t *offset) * Purpose: Projects a single element hyperslab selection into a scalar * dataspace * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -4305,7 +5527,7 @@ H5S__hyper_project_scalar(const H5S_t *space, hsize_t *offset) * Purpose: Projects a hyperslab selection onto/into a simple dataspace * of a lower rank * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -4352,7 +5574,7 @@ H5S__hyper_project_simple_lower(const H5S_t *base_space, H5S_t *new_space) * Purpose: Projects a hyperslab selection onto/into a simple dataspace * of a higher rank * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -4442,7 +5664,7 @@ done: * Purpose: Projects a hyperslab selection onto/into a simple dataspace * of a different rank * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -4450,7 +5672,8 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5S__hyper_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *offset) +H5S__hyper_project_simple(const H5S_t *base_space, H5S_t *new_space, + hsize_t *offset) { herr_t ret_value = SUCCEED; /* Return value */ @@ -4807,7 +6030,7 @@ H5S_hyper_denormalize_offset(H5S_t *space, const hssize_t *old_offset) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "can't adjust selection") /* Copy the selection offset over */ - HDmemcpy(space->select.offset, old_offset, sizeof(hssize_t) * space->extent.rank); + H5MM_memcpy(space->select.offset, old_offset, sizeof(hssize_t) * space->extent.rank); done: FUNC_LEAVE_NOAPI(ret_value) @@ -4939,9 +6162,10 @@ done: DESCRIPTION Clip one span tree ('a') against another span tree ('b'). Creates span trees for the area defined by the 'a' span tree which does not overlap the - 'b' span tree, the area defined by the overlap of the 'a' hyperslab span - tree and the 'b' span tree, and the area defined by the 'b' hyperslab span - tree which does not overlap the 'a' span tree. + 'b' span tree ("a not b"), the area defined by the overlap of the 'a' + hyperslab span tree and the 'b' span tree ("a and b"), and the area defined + by the 'b' hyperslab span tree which does not overlap the 'a' span + tree ("b not a"). GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES @@ -5850,12 +7074,12 @@ H5S__hyper_spans_nelem(const H5S_hyper_span_info_t *spans) Create a span tree USAGE H5S_hyper_span_t *H5S__hyper_make_spans(rank, start, stride, count, block) - unsigned rank; IN: # of dimensions of the space - const hsize_t *start; IN: Starting location of the hyperslabs - const hsize_t *stride; IN: Stride from the beginning of one block to + unsigned rank; IN: # of dimensions of the space + const hsize_t *start; IN: Starting location of the hyperslabs + const hsize_t *stride; IN: Stride from the beginning of one block to the next - const hsize_t *count; IN: Number of blocks - const hsize_t *block; IN: Size of hyperslab block + const hsize_t *count; IN: Number of blocks + const hsize_t *block; IN: Size of hyperslab block RETURNS Pointer to new span tree on success, NULL on failure DESCRIPTION @@ -6032,7 +7256,7 @@ H5S__hyper_rebuild_helper(const H5S_hyper_span_t *span, H5S_hyper_dim_t span_sla if(!H5S__hyper_rebuild_helper(span->down->head, span_slab_info, rank - 1)) HGOTO_DONE(FALSE) - HDmemcpy(canon_down_span_slab_info, span_slab_info, sizeof(H5S_hyper_dim_t) * rank); + H5MM_memcpy(canon_down_span_slab_info, span_slab_info, sizeof(H5S_hyper_dim_t) * rank); } /* end if */ /* Assign the initial starting point & block size */ @@ -6139,7 +7363,7 @@ done: static hbool_t H5S__hyper_rebuild(H5S_t *space) { - H5S_hyper_dim_t top_span_slab_info[H5O_LAYOUT_NDIMS]; + H5S_hyper_dim_t top_span_slab_info[H5S_MAX_RANK]; unsigned rank, curr_dim; hbool_t ret_value = TRUE; /* Return value */ @@ -6201,12 +7425,12 @@ done: static herr_t H5S__hyper_generate_spans(H5S_t *space) { - hsize_t tmp_start[H5O_LAYOUT_NDIMS]; /* Temporary start information */ - hsize_t tmp_stride[H5O_LAYOUT_NDIMS]; /* Temporary stride information */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary count information */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block information */ - unsigned u; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ + hsize_t tmp_start[H5S_MAX_RANK]; /* Temporary start information */ + hsize_t tmp_stride[H5S_MAX_RANK]; /* Temporary stride information */ + hsize_t tmp_count[H5S_MAX_RANK]; /* Temporary count information */ + hsize_t tmp_block[H5S_MAX_RANK]; /* Temporary block information */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -6238,7 +7462,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5S__hyper_generate_spans() */ -#ifndef NEW_HYPERSLAB_API /*------------------------------------------------------------------------- * Function: H5S__generate_hyperlab @@ -6247,19 +7470,14 @@ done: * * Return: Non-negative on success/Negative on failure * - * Programmer: Quincey Koziol (split from HS_select_hyperslab()). + * Programmer: Quincey Koziol * Tuesday, September 12, 2000 * - * Modifications: - * *------------------------------------------------------------------------- */ static herr_t -H5S__generate_hyperslab (H5S_t *space, H5S_seloper_t op, - const hsize_t start[], - const hsize_t stride[], - const hsize_t count[], - const hsize_t block[]) +H5S__generate_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], + const hsize_t stride[], const hsize_t count[], const hsize_t block[]) { H5S_hyper_span_info_t *new_spans=NULL; /* Span tree for new hyperslab */ H5S_hyper_span_info_t *a_not_b = NULL; /* Span tree for hyperslab spans in old span tree and not in new span tree */ @@ -6291,7 +7509,7 @@ H5S__generate_hyperslab (H5S_t *space, H5S_seloper_t op, space->select.num_elem = H5S__hyper_spans_nelem(new_spans); /* Indicate that the new_spans are owned */ - new_spans=NULL; + new_spans = NULL; } /* end if */ else { hbool_t updated_spans = FALSE; /* Whether the spans in the selection were modified */ @@ -6500,9 +7718,9 @@ herr_t H5S_select_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], const hsize_t *stride, const hsize_t count[], const hsize_t *block) { - hsize_t int_stride[H5O_LAYOUT_NDIMS]; /* Internal storage for stride information */ - hsize_t int_count[H5O_LAYOUT_NDIMS]; /* Internal storage for count information */ - hsize_t int_block[H5O_LAYOUT_NDIMS]; /* Internal storage for block information */ + hsize_t int_stride[H5S_MAX_RANK]; /* Internal storage for stride information */ + hsize_t int_count[H5S_MAX_RANK]; /* Internal storage for count information */ + hsize_t int_block[H5S_MAX_RANK]; /* Internal storage for block information */ const hsize_t *opt_stride; /* Optimized stride information */ const hsize_t *opt_count; /* Optimized count information */ const hsize_t *opt_block; /* Optimized block information */ @@ -6526,9 +7744,7 @@ H5S_select_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], if(block == NULL) block = H5S_hyper_ones_g; - /* - * Check new selection. - */ + /* Check new selection */ for(u = 0; u < space->extent.rank; u++) { /* Check for overlapping hyperslab blocks in new selection. */ if(count[u] > 1 && stride[u] < block[u]) @@ -6564,7 +7780,7 @@ H5S_select_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], if(unlim_dim >= 0) HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "cannot have more than one unlimited dimension in selection") else { - if(count[u] == block[u] /* == H5S_UNLIMITED */) + if(count[u] == block[u]) /* Both are H5S_UNLIMITED */ HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "count and block cannot both be unlimited") unlim_dim = (int)u; } /* end else */ @@ -6793,7 +8009,8 @@ H5S_select_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get selection bounds") /* Patch count and block to remove unlimited and include the - * existing selection */ + * existing selection. + */ H5S__hyper_get_clip_diminfo(start[unlim_dim], opt_stride[unlim_dim], &tmp_count, &tmp_block, bounds_end[unlim_dim] + (hsize_t)1); HDassert((tmp_count == 1) || (opt_count != H5S_hyper_ones_g)); HDassert((tmp_block == 1) || (opt_block != H5S_hyper_ones_g)); @@ -6893,2342 +8110,6 @@ H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[], done: FUNC_LEAVE_API(ret_value) } /* end H5Sselect_hyperslab() */ -#else /* NEW_HYPERSLAB_API */ /* Works */ - -/*------------------------------------------------------------------------- - * Function: H5S_operate_hyperslab - * - * Purpose: Combines two hyperslabs with an operation, putting the - * result into a third hyperslab selection - * - * Return: non-negative on success/NULL on failure - * - * Programmer: Quincey Koziol - * Tuesday, October 30, 2001 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S_operate_hyperslab (H5S_t *result, H5S_hyper_span_info_t *spans1, H5S_seloper_t op, H5S_hyper_span_info_t *spans2, - hbool_t can_own_span2, hbool_t *span2_owned) -{ - H5S_hyper_span_info_t *a_not_b=NULL; /* Span tree for hyperslab spans in old span tree and not in new span tree */ - H5S_hyper_span_info_t *a_and_b=NULL; /* Span tree for hyperslab spans in both old and new span trees */ - H5S_hyper_span_info_t *b_not_a=NULL; /* Span tree for hyperslab spans in new span tree and not in old span tree */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - /* Check args */ - HDassert(result); - HDassert(spans2); - HDassert(op > H5S_SELECT_NOOP && op < H5S_SELECT_INVALID); - - /* Just copy the selection from spans2 if we are setting the selection */ - /* ('space1' to 'result' aliasing happens at the next layer up) */ - if(op==H5S_SELECT_SET) { - if(H5S__hyper_merge_spans(result,spans2,can_own_span2)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem = H5S__hyper_spans_nelem(spans2); - - /* Indicate that we took ownership of span2, if allowed */ - if(can_own_span2) - *span2_owned=TRUE; - } /* end if */ - else { - hbool_t updated_spans = FALSE; /* Whether the spans in the selection were modified */ - - HDassert(spans1); - - /* Generate lists of spans which overlap and don't overlap */ - if(H5S__hyper_clip_spans(spans1,spans2,&a_not_b,&a_and_b,&b_not_a)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLIP, FAIL, "can't clip hyperslab information") - - /* Switch on the operation */ - switch(op) { - case H5S_SELECT_OR: - /* Copy spans from spans1 to current selection */ - if(spans1!=NULL) { - if(H5S__hyper_merge_spans(result,spans1,FALSE)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem = H5S__hyper_spans_nelem(spans1); - } /* end if */ - - /* Add any new spans from spans2 to current selection */ - if(b_not_a!=NULL) { - if(H5S__hyper_merge_spans(result,b_not_a,FALSE)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem += H5S__hyper_spans_nelem(b_not_a); - - /* Indicate that the spans were updated */ - updated_spans = TRUE; - } /* end if */ - break; - - case H5S_SELECT_AND: - /* Check if there are any overlapped selections */ - if(a_and_b!=NULL) { - if(H5S__hyper_merge_spans(result,a_and_b,TRUE)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem = H5S__hyper_spans_nelem(a_and_b); - - /* Indicate that the result owns the a_and_b spans */ - a_and_b=NULL; - - /* Indicate that the spans were updated */ - updated_spans = TRUE; - } /* end if */ - break; - - case H5S_SELECT_XOR: - /* Check if there are any non-overlapped selections */ - if(a_not_b!=NULL) { - if(H5S__hyper_merge_spans(result,a_not_b,FALSE)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem = H5S__hyper_spans_nelem(a_not_b); - - /* Indicate that the spans were updated */ - updated_spans = TRUE; - } /* end if */ - if(b_not_a!=NULL) { - if(H5S__hyper_merge_spans(result,b_not_a,FALSE)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem += H5S__hyper_spans_nelem(b_not_a); - - /* Indicate that the spans were updated */ - updated_spans = TRUE; - } /* end if */ - break; - - case H5S_SELECT_NOTB: - /* Check if there are any non-overlapped selections */ - if(a_not_b!=NULL) { - if(H5S__hyper_merge_spans(result,a_not_b,TRUE)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem = H5S__hyper_spans_nelem(a_not_b); - - /* Indicate that the result owns the a_not_b spans */ - a_not_b=NULL; - - /* Indicate that the spans were updated */ - updated_spans = TRUE; - } /* end if */ - break; - - case H5S_SELECT_NOTA: - /* Check if there are any non-overlapped selections */ - if(b_not_a!=NULL) { - if(H5S__hyper_merge_spans(result,b_not_a,TRUE)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert hyperslabs") - - /* Update the number of elements in current selection */ - result->select.num_elem = H5S__hyper_spans_nelem(b_not_a); - - /* Indicate that the result owns the b_not_a spans */ - b_not_a=NULL; - - /* Indicate that the spans were updated */ - updated_spans = TRUE; - } /* end if */ - break; - - default: - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - } /* end switch */ - - /* Free the hyperslab trees generated from the clipping algorithm */ - if(a_not_b) - H5S__hyper_free_span_info(a_not_b); - if(a_and_b) - H5S__hyper_free_span_info(a_and_b); - if(b_not_a) - H5S__hyper_free_span_info(b_not_a); - - /* Check if the resulting hyperslab span tree is empty */ - if(result->select.sel_info.hslab->span_lst==NULL) { - H5S_hyper_span_info_t *spans; /* Empty hyperslab span tree */ - - /* Sanity check */ - HDassert(result->select.num_elem == 0); - - /* Allocate a span info node */ - if((spans = H5FL_MALLOC(H5S_hyper_span_info_t))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "can't allocate hyperslab span") - - /* Set the reference count */ - spans->count=1; - - /* Reset the scratch pad space */ - spans->scratch=0; - - /* Set to empty tree */ - spans->head=NULL; - - /* Set pointer to empty span tree */ - result->select.sel_info.hslab->span_lst=spans; - } /* end if */ - else { - /* Check if we updated the spans */ - if(updated_spans) { - /* Attempt to rebuild "optimized" start/stride/count/block information. - * from resulting hyperslab span tree - */ - H5S__hyper_rebuild(result); - } /* end if */ - } /* end else */ - } /* end else */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_operate_hyperslab() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_generate_hyperlab - * - * Purpose: Generate hyperslab information from H5S_select_hyperslab() - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol (split from HS_select_hyperslab()). - * Tuesday, September 12, 2000 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S__generate_hyperslab(H5S_t *space, H5S_seloper_t op, const hsize_t start[], - const hsize_t stride[], const hsize_t count[], const hsize_t block[]) -{ - H5S_hyper_span_info_t *new_spans=NULL; /* Span tree for new hyperslab */ - H5S_hyper_span_info_t *tmp_spans=NULL; /* Temporary copy of selection */ - hbool_t span2_owned=FALSE; /* Flag to indicate that span2 was used in H5S_operate_hyperslab() */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - /* Check args */ - HDassert(space); - HDassert(op > H5S_SELECT_NOOP && op < H5S_SELECT_INVALID); - HDassert(start); - HDassert(stride); - HDassert(count); - HDassert(block); - - /* Generate span tree for new hyperslab information */ - if(NULL == (new_spans = H5S__hyper_make_spans(space->extent.rank, start, stride, count, block))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't create hyperslab information") - - /* Copy the original dataspace */ - if(space->select.sel_info.hslab->span_lst!=NULL) { - /* Take ownership of the dataspace's hyperslab spans */ - /* (These are freed later) */ - tmp_spans=space->select.sel_info.hslab->span_lst; - space->select.sel_info.hslab->span_lst=NULL; - - /* Reset the other dataspace selection information */ - if(H5S_SELECT_RELEASE(space)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't release selection") - - /* Allocate space for the hyperslab selection information */ - if((space->select.sel_info.hslab=H5FL_MALLOC(H5S_hyper_sel_t))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate hyperslab info") - - /* Set unlim_dim */ - space->select.sel_info.hslab->unlim_dim = -1; - } /* end if */ - - /* Combine tmp_space (really space) & new_space, with the result in space */ - if(H5S_operate_hyperslab(space,tmp_spans,op,new_spans,TRUE,&span2_owned)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLIP, FAIL, "can't clip hyperslab information") - -done: - /* Free temporary data structures */ - if(tmp_spans!=NULL) - if(H5S__hyper_free_span_info(tmp_spans)<0) - HDONE_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "failed to release temporary hyperslab spans") - if(new_spans!=NULL && span2_owned==FALSE) - if(H5S__hyper_free_span_info(new_spans)<0) - HDONE_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "failed to release temporary hyperslab spans") - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S__generate_hyperslab() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_select_hyperslab - * - * Purpose: Internal version of H5Sselect_hyperslab(). - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Wednesday, January 10, 2001 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5S_select_hyperslab (H5S_t *space, H5S_seloper_t op, - const hsize_t start[], - const hsize_t *stride, - const hsize_t count[], - const hsize_t *block) -{ - hsize_t int_stride[H5O_LAYOUT_NDIMS]; /* Internal storage for stride information */ - hsize_t int_count[H5O_LAYOUT_NDIMS]; /* Internal storage for count information */ - hsize_t int_block[H5O_LAYOUT_NDIMS]; /* Internal storage for block information */ - const hsize_t *opt_stride; /* Optimized stride information */ - const hsize_t *opt_count; /* Optimized count information */ - const hsize_t *opt_block; /* Optimized block information */ - unsigned u; /* Counters */ - int unlim_dim = -1; /* Unlimited dimension in selection, of -1 if none */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(FAIL) - - /* Check args */ - HDassert(space); - HDassert(start); - HDassert(count); - HDassert(op > H5S_SELECT_NOOP && op < H5S_SELECT_INVALID); - - /* Point to the correct stride values */ - if(stride==NULL) - stride = H5S_hyper_ones_g; - - /* Point to the correct block values */ - if(block==NULL) - block = H5S_hyper_ones_g; - - /* Check for unlimited dimension */ - for(u = 0; u<space->extent.rank; u++) - if((count[u] == H5S_UNLIMITED) || (block[u] == H5S_UNLIMITED)) { - if(unlim_dim >= 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "cannot have more than one unlimited dimension in selection") - else { - if(count[u] == block[u] /* == H5S_UNLIMITED */) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "count and block cannot both be unlimited") - unlim_dim = (int)u; - } /* end else */ - } /* end if */ - - /* - * Check new selection. - */ - for(u=0; u<space->extent.rank; u++) { - /* Check for overlapping hyperslab blocks in new selection. */ - if(count[u]>1 && stride[u]<block[u]) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "hyperslab blocks overlap") - - /* Detect zero-sized hyperslabs in new selection */ - if(count[u] == 0 || block[u] == 0) { - switch(op) { - case H5S_SELECT_SET: /* Select "set" operation */ - case H5S_SELECT_AND: /* Binary "and" operation for hyperslabs */ - case H5S_SELECT_NOTA: /* Binary "B not A" operation for hyperslabs */ - /* Convert to "none" selection */ - if(H5S_select_none(space)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't convert selection") - HGOTO_DONE(SUCCEED); - - case H5S_SELECT_OR: /* Binary "or" operation for hyperslabs */ - case H5S_SELECT_XOR: /* Binary "xor" operation for hyperslabs */ - case H5S_SELECT_NOTB: /* Binary "A not B" operation for hyperslabs */ - HGOTO_DONE(SUCCEED); /* Selection stays same */ - - default: - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - } /* end switch */ - } /* end if */ - } /* end for */ - - /* Optimize hyperslab parameters to merge contiguous blocks, etc. */ - if(stride == H5S_hyper_ones_g && block == H5S_hyper_ones_g) { - /* Point to existing arrays */ - opt_stride = H5S_hyper_ones_g; - opt_count = H5S_hyper_ones_g; - opt_block = count; - } /* end if */ - else { - /* Point to local arrays */ - opt_stride = int_stride; - opt_count = int_count; - opt_block = int_block; - for(u=0; u<space->extent.rank; u++) { - /* contiguous hyperslabs have the block size equal to the stride */ - if((stride[u] == block[u]) && (count[u] != H5S_UNLIMITED)) { - int_count[u]=1; - int_stride[u]=1; - if(block[u]==1) - int_block[u]=count[u]; - else - int_block[u]=block[u]*count[u]; - } /* end if */ - else { - if(count[u]==1) - int_stride[u]=1; - else { - HDassert((stride[u] > block[u]) || ((stride[u] == block[u]) - && (count[u] == H5S_UNLIMITED))); - int_stride[u]=stride[u]; - } /* end else */ - int_count[u]=count[u]; - int_block[u]=block[u]; - } /* end else */ - } /* end for */ - } /* end else */ - - /* Check for operating on unlimited selection */ - if((H5S_GET_SELECT_TYPE(space) == H5S_SEL_HYPERSLABS) - && (space->select.sel_info.hslab->unlim_dim >= 0) - && (op != H5S_SELECT_SET)) - { - /* Check for invalid operation */ - if(unlim_dim >= 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "cannot modify unlimited selection with another unlimited selection") - if(!((op == H5S_SELECT_AND) || (op == H5S_SELECT_NOTA))) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "unsupported operation on unlimited selection") - HDassert(space->select.sel_info.hslab->diminfo_valid); - - /* Clip unlimited selection to include new selection */ - if(H5S_hyper_clip_unlim(space, - start[space->select.sel_info.hslab->unlim_dim] - + ((opt_count[space->select.sel_info.hslab->unlim_dim] - - (hsize_t)1) - * opt_stride[space->select.sel_info.hslab->unlim_dim]) - + opt_block[space->select.sel_info.hslab->unlim_dim]) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLIP, FAIL, "failed to clip unlimited selection") - - /* If an empty space was returned it must be "none" */ - HDassert((space->select.num_elem > (hsize_t)0) - || (space->select.type->type == H5S_SEL_NONE)); - } /* end if */ - - /* Fixup operation for non-hyperslab selections */ - switch(H5S_GET_SELECT_TYPE(space)) { - case H5S_SEL_NONE: /* No elements selected in dataspace */ - switch(op) { - case H5S_SELECT_SET: /* Select "set" operation */ - /* Change "none" selection to hyperslab selection */ - break; - - case H5S_SELECT_OR: /* Binary "or" operation for hyperslabs */ - case H5S_SELECT_XOR: /* Binary "xor" operation for hyperslabs */ - case H5S_SELECT_NOTA: /* Binary "B not A" operation for hyperslabs */ - op=H5S_SELECT_SET; /* Maps to "set" operation when applied to "none" selection */ - break; - - case H5S_SELECT_AND: /* Binary "and" operation for hyperslabs */ - case H5S_SELECT_NOTB: /* Binary "A not B" operation for hyperslabs */ - HGOTO_DONE(SUCCEED); /* Selection stays "none" */ - - default: - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - } /* end switch */ - break; - - case H5S_SEL_ALL: /* All elements selected in dataspace */ - switch(op) { - case H5S_SELECT_SET: /* Select "set" operation */ - /* Change "all" selection to hyperslab selection */ - break; - - case H5S_SELECT_OR: /* Binary "or" operation for hyperslabs */ - HGOTO_DONE(SUCCEED); /* Selection stays "all" */ - - case H5S_SELECT_AND: /* Binary "and" operation for hyperslabs */ - op=H5S_SELECT_SET; /* Maps to "set" operation when applied to "none" selection */ - break; - - case H5S_SELECT_XOR: /* Binary "xor" operation for hyperslabs */ - case H5S_SELECT_NOTB: /* Binary "A not B" operation for hyperslabs */ - /* Convert current "all" selection to "real" hyperslab selection */ - /* Then allow operation to proceed */ - { - hsize_t tmp_start[H5O_LAYOUT_NDIMS]; /* Temporary start information */ - hsize_t tmp_stride[H5O_LAYOUT_NDIMS]; /* Temporary stride information */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary count information */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block information */ - - /* Fill in temporary information for the dimensions */ - for(u=0; u<space->extent.rank; u++) { - tmp_start[u]=0; - tmp_stride[u]=1; - tmp_count[u]=1; - tmp_block[u]=space->extent.size[u]; - } /* end for */ - - /* Convert to hyperslab selection */ - if(H5S_select_hyperslab(space,H5S_SELECT_SET,tmp_start,tmp_stride,tmp_count,tmp_block)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't convert selection") - } /* end case */ - break; - - case H5S_SELECT_NOTA: /* Binary "B not A" operation for hyperslabs */ - /* Convert to "none" selection */ - if(H5S_select_none(space)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't convert selection") - HGOTO_DONE(SUCCEED); - - default: - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - } /* end switch */ - break; - - case H5S_SEL_HYPERSLABS: - /* Hyperslab operation on hyperslab selection, OK */ - break; - - case H5S_SEL_POINTS: /* Can't combine hyperslab operations and point selections currently */ - if(op==H5S_SELECT_SET) /* Allow only "set" operation to proceed */ - break; - /* Else fall through to error */ - - default: - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - } /* end switch */ - - - if(op==H5S_SELECT_SET) { - /* If we are setting a new selection, remove current selection first */ - if(H5S_SELECT_RELEASE(space)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't release hyperslab") - - /* Allocate space for the hyperslab selection information */ - if(NULL == (space->select.sel_info.hslab = H5FL_MALLOC(H5S_hyper_sel_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate hyperslab info") - - /* Save the diminfo */ - space->select.num_elem=1; - for(u=0; u<space->extent.rank; u++) { - space->select.sel_info.hslab->app_diminfo[u].start = start[u]; - space->select.sel_info.hslab->app_diminfo[u].stride = stride[u]; - space->select.sel_info.hslab->app_diminfo[u].count = count[u]; - space->select.sel_info.hslab->app_diminfo[u].block = block[u]; - - space->select.sel_info.hslab->opt_diminfo[u].start = start[u]; - space->select.sel_info.hslab->opt_diminfo[u].stride = opt_stride[u]; - space->select.sel_info.hslab->opt_diminfo[u].count = opt_count[u]; - space->select.sel_info.hslab->opt_diminfo[u].block = opt_block[u]; - - space->select.num_elem*=(opt_count[u]*opt_block[u]); - } /* end for */ - - /* Save unlim_dim */ - space->select.sel_info.hslab->unlim_dim = unlim_dim; - - /* Indicate that the dimension information is valid */ - space->select.sel_info.hslab->diminfo_valid = TRUE; - - /* Indicate that there's no slab information */ - space->select.sel_info.hslab->span_lst = NULL; - - /* Handle unlimited selections */ - if(unlim_dim >= 0) { - /* Calculate num_elem_non_unlim */ - space->select.sel_info.hslab->num_elem_non_unlim = (hsize_t)1; - for(u = 0; u < space->extent.rank; u++) - if((int)u != unlim_dim) - space->select.sel_info.hslab->num_elem_non_unlim *= (opt_count[u] * opt_block[u]); - - /* Set num_elem */ - if(space->select.num_elem != (hsize_t)0) - space->select.num_elem = H5S_UNLIMITED; - } /* end if */ - } /* end if */ - else if(op>=H5S_SELECT_OR && op<=H5S_SELECT_NOTA) { - /* Sanity check */ - HDassert(H5S_GET_SELECT_TYPE(space) == H5S_SEL_HYPERSLABS); - - /* Handle unlimited selections */ - if(unlim_dim >= 0) { - hsize_t bounds_start[H5S_MAX_RANK]; - hsize_t bounds_end[H5S_MAX_RANK]; - hsize_t tmp_count = opt_count[unlim_dim]; - hsize_t tmp_block = opt_block[unlim_dim]; - - /* Check for invalid operation */ - if(space->select.sel_info.hslab->unlim_dim >= 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "cannot modify unlimited selection with another unlimited selection") - if(!((op == H5S_SELECT_AND) || (op == H5S_SELECT_NOTB))) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "unsupported operation with unlimited selection") - - /* Get bounds of existing selection */ - if(H5S_hyper_bounds(space, bounds_start, bounds_end) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get selection bounds") - - /* Patch count and block to remove unlimited and include the - * existing selection */ - H5S__hyper_get_clip_diminfo(start[unlim_dim], opt_stride[unlim_dim], &tmp_count, &tmp_block, bounds_end[unlim_dim] + (hsize_t)1); - HDassert((tmp_count == 1) || (opt_count != H5S_hyper_ones_g)); - HDassert((tmp_block == 1) || (opt_block != H5S_hyper_ones_g)); - if(opt_count != H5S_hyper_ones_g) { - HDassert(opt_count == int_count); - int_count[unlim_dim] = tmp_count; - } /* end if */ - if(opt_block != H5S_hyper_ones_g) { - HDassert(opt_block == int_block); - int_block[unlim_dim] = tmp_block; - } /* end if */ - } /* end if */ - - /* Check if there's no hyperslab span information currently */ - if(NULL == space->select.sel_info.hslab->span_lst) - if(H5S__hyper_generate_spans(space) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNINITIALIZED, FAIL, "dataspace does not have span tree") - - /* Indicate that the regular dimensions are no longer valid */ - space->select.sel_info.hslab->diminfo_valid = FALSE; - - /* Add in the new hyperslab information */ - if(H5S__generate_hyperslab (space, op, start, opt_stride, opt_count, opt_block)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't generate hyperslabs") - } /* end if */ - else - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - - /* Set selection type */ - space->select.type = H5S_sel_hyper; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_select_hyperslab() */ - - -/*-------------------------------------------------------------------------- - NAME - H5Sselect_hyperslab - PURPOSE - Specify a hyperslab to combine with the current hyperslab selection - USAGE - herr_t H5Sselect_hyperslab(dsid, op, start, stride, count, block) - hid_t dsid; IN: Dataspace ID of selection to modify - H5S_seloper_t op; IN: Operation to perform on current selection - const hsize_t *start; IN: Offset of start of hyperslab - const hsize_t *stride; IN: Hyperslab stride - const hsize_t *count; IN: Number of blocks included in hyperslab - const hsize_t *block; IN: Size of block in hyperslab - RETURNS - Non-negative on success/Negative on failure - DESCRIPTION - Combines a hyperslab selection with the current selection for a dataspace. - If the current selection is not a hyperslab, it is freed and the hyperslab - parameters passed in are combined with the H5S_SEL_ALL hyperslab (ie. a - selection composing the entire current extent). If STRIDE or BLOCK is - NULL, they are assumed to be set to all '1'. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -herr_t -H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[], - const hsize_t stride[], const hsize_t count[], const hsize_t block[]) -{ - H5S_t *space = NULL; /* Dataspace to modify selection of */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_API(FAIL) - H5TRACE6("e", "iSs*h*h*h*h", space_id, op, start, stride, count, block); - - /* Check args */ - if (NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if (H5S_SCALAR==H5S_GET_EXTENT_TYPE(space)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "hyperslab doesn't support H5S_SCALAR space") - if (H5S_NULL==H5S_GET_EXTENT_TYPE(space)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "hyperslab doesn't support H5S_NULL space") - if(start==NULL || count==NULL) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "hyperslab not specified") - if(!(op>H5S_SELECT_NOOP && op<H5S_SELECT_INVALID)) - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - if(stride!=NULL) { - unsigned u; /* Local index variable */ - - /* Check for 0-sized strides */ - for(u=0; u<space->extent.rank; u++) { - if(stride[u]==0) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid stride==0 value") - } /* end for */ - } /* end if */ - - if (H5S_select_hyperslab(space, op, start, stride, count, block)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to set hyperslab selection") - -done: - FUNC_LEAVE_API(ret_value) -} /* end H5Sselect_hyperslab() */ - - -/*-------------------------------------------------------------------------- - NAME - H5Scombine_hyperslab - PURPOSE - Specify a hyperslab to combine with the current hyperslab selection and - return a new dataspace with the combined selection as the selection in the - new dataspace. - USAGE - hid_t H5Srefine_hyperslab(dsid, op, start, stride, count, block) - hid_t dsid; IN: Dataspace ID of selection to use - H5S_seloper_t op; IN: Operation to perform on current selection - const hsize_t *start; IN: Offset of start of hyperslab - const hsize_t *stride; IN: Hyperslab stride - const hsize_t *count; IN: Number of blocks included in hyperslab - const hsize_t *block; IN: Size of block in hyperslab - RETURNS - Dataspace ID on success/Negative on failure - DESCRIPTION - Combines a hyperslab selection with the current selection for a dataspace, - creating a new dataspace to return the generated selection. - If the current selection is not a hyperslab, it is freed and the hyperslab - parameters passed in are combined with the H5S_SEL_ALL hyperslab (ie. a - selection composing the entire current extent). If STRIDE or BLOCK is - NULL, they are assumed to be set to all '1'. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -hid_t -H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[], - const hsize_t stride[], const hsize_t count[], const hsize_t block[]) -{ - H5S_t *space; /* Dataspace to modify selection of */ - H5S_t *new_space = NULL; /* New dataspace created */ - hid_t ret_value; /* Return value */ - - FUNC_ENTER_API(FAIL) - H5TRACE6("i", "iSs*h*h*h*h", space_id, op, start, stride, count, block); - - /* Check args */ - if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if(start == NULL || count == NULL) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "hyperslab not specified") - if(!(op >= H5S_SELECT_SET && op <= H5S_SELECT_NOTA)) - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - - /* Copy the first dataspace */ - if (NULL == (new_space = H5S_copy (space, TRUE, TRUE))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, NULL, "unable to copy dataspace") - - /* Go modify the selection in the new dataspace */ - if (H5S_select_hyperslab(new_space, op, start, stride, count, block)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to set hyperslab selection") - - /* Atomize */ - if((ret_value = H5I_register(H5I_DATASPACE, new_space, TRUE)) < 0) - HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace atom") - -done: - if(ret_value < 0 && new_space) - H5S_close(new_space); - - FUNC_LEAVE_API(ret_value) -} /* end H5Scombine_hyperslab() */ - - -/*------------------------------------------------------------------------- - * Function: H5S__combine_select - * - * Purpose: Internal version of H5Scombine_select(). - * - * Return: New dataspace on success/NULL on failure - * - * Programmer: Quincey Koziol - * Tuesday, October 30, 2001 - * - * Chao Mei - * Wednesday, June 29, 2011 - * - *------------------------------------------------------------------------- - */ -static H5S_t * -H5S__combine_select(H5S_t *space1, H5S_seloper_t op, H5S_t *space2) -{ - H5S_t *new_space = NULL; /* New dataspace generated */ - hbool_t span2_owned=FALSE; /* Flag to indicate that span2 was used in H5S_operate_hyperslab() */ - H5S_t *ret_value; /* return value */ - - FUNC_ENTER_STATIC - - /* Check args */ - HDassert(space1); - HDassert(space2); - HDassert(op >= H5S_SELECT_OR && op <= H5S_SELECT_NOTA); - - /* Check that the space selections both have span trees */ - if(space1->select.sel_info.hslab->span_lst==NULL) - if(H5S__hyper_generate_spans(space1)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNINITIALIZED, NULL, "dataspace does not have span tree") - if(space2->select.sel_info.hslab->span_lst==NULL) - if(H5S__hyper_generate_spans(space2)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNINITIALIZED, NULL, "dataspace does not have span tree") - - /* Copy the first dataspace */ - if (NULL == (new_space = H5S_copy (space1, TRUE, TRUE))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, NULL, "unable to copy dataspace") - - /* Free the current selection for the new dataspace */ - if(H5S_SELECT_RELEASE(new_space)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, NULL, "can't release selection") - - /* Allocate space for the hyperslab selection information */ - if((new_space->select.sel_info.hslab=H5FL_CALLOC(H5S_hyper_sel_t))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "can't allocate hyperslab info") - - /* Set unlim_dim */ - new_space->select.sel_info.hslab->unlim_dim = -1; - - /* Combine space1 & space2, with the result in new_space */ - if(H5S_operate_hyperslab(new_space,space1->select.sel_info.hslab->span_lst,op,space2->select.sel_info.hslab->span_lst,FALSE,&span2_owned)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLIP, NULL, "can't clip hyperslab information") - - /* Set return value */ - ret_value = new_space; - -done: - if(ret_value == NULL && new_space) - H5S_close(new_space); - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S__combine_select() */ - - -/*-------------------------------------------------------------------------- - NAME - H5Scombine_select - PURPOSE - Combine two hyperslab selections with an operation, returning a dataspace - with the resulting selection. - USAGE - hid_t H5Scombine_select(space1, op, space2) - hid_t space1; IN: First Dataspace ID - H5S_seloper_t op; IN: Selection operation - hid_t space2; IN: Second Dataspace ID - RETURNS - Dataspace ID on success/Negative on failure - DESCRIPTION - Combine two existing hyperslab selections with an operation, returning - a new dataspace with the resulting selection. The dataspace extent from - space1 is copied for the dataspace extent of the newly created dataspace. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -hid_t -H5Scombine_select(hid_t space1_id, H5S_seloper_t op, hid_t space2_id) -{ - H5S_t *space1; /* First Dataspace */ - H5S_t *space2; /* Second Dataspace */ - H5S_t *new_space = NULL; /* New Dataspace */ - hid_t ret_value; /* Return value */ - - FUNC_ENTER_API(FAIL) - H5TRACE3("i", "iSsi", space1_id, op, space2_id); - - /* Check args */ - if(NULL == (space1 = (H5S_t *)H5I_object_verify(space1_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if(NULL == (space2 = (H5S_t *)H5I_object_verify(space2_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if(!(op >= H5S_SELECT_OR && op <= H5S_SELECT_NOTA)) - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - - /* Check that both dataspaces have the same rank */ - if(space1->extent.rank != space2->extent.rank) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspaces not same rank") - - /* Check that both dataspaces have hyperslab selections */ - if(H5S_GET_SELECT_TYPE(space1) != H5S_SEL_HYPERSLABS || H5S_GET_SELECT_TYPE(space2) != H5S_SEL_HYPERSLABS) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspaces don't have hyperslab selections") - - /* Go combine the dataspaces */ - if(NULL == (new_space = H5S__combine_select(space1, op, space2))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to create hyperslab selection") - - /* Atomize */ - if((ret_value = H5I_register(H5I_DATASPACE, new_space, TRUE)) < 0) - HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace atom") - -done: - if(ret_value < 0 && new_space) - H5S_close(new_space); - - FUNC_LEAVE_API(ret_value) -} /* end H5Scombine_select() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_select_select - * - * Purpose: Internal version of H5Sselect_select(). - * - * Return: New dataspace on success/NULL on failure - * - * Programmer: Quincey Koziol - * Tuesday, October 30, 2001 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S_select_select (H5S_t *space1, H5S_seloper_t op, H5S_t *space2) -{ - H5S_hyper_span_info_t *tmp_spans=NULL; /* Temporary copy of selection */ - hbool_t span2_owned=FALSE; /* Flag to indicate that span2 was used in H5S_operate_hyperslab() */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - /* Check args */ - HDassert(space1); - HDassert(space2); - HDassert(op > H5S_SELECT_NOOP && op < H5S_SELECT_INVALID); - - /* Check that the space selections both have span trees */ - if(space1->select.sel_info.hslab->span_lst==NULL) - if(H5S__hyper_generate_spans(space1)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNINITIALIZED, FAIL, "dataspace does not have span tree") - if(space2->select.sel_info.hslab->span_lst==NULL) - if(H5S__hyper_generate_spans(space2)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_UNINITIALIZED, FAIL, "dataspace does not have span tree") - - /* Take ownership of the dataspace's hyperslab spans */ - /* (These are freed later) */ - tmp_spans=space1->select.sel_info.hslab->span_lst; - space1->select.sel_info.hslab->span_lst=NULL; - - /* Reset the other dataspace selection information */ - if(H5S_SELECT_RELEASE(space1)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't release selection") - - /* Allocate space for the hyperslab selection information */ - if((space1->select.sel_info.hslab=H5FL_CALLOC(H5S_hyper_sel_t))==NULL) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate hyperslab info") - - /* Set unlim_dim */ - space1->select.sel_info.hslab->unlim_dim = -1; - - /* Combine tmp_spans (from space1) & spans from space2, with the result in space1 */ - if(H5S_operate_hyperslab(space1,tmp_spans,op,space2->select.sel_info.hslab->span_lst,FALSE,&span2_owned)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLIP, FAIL, "can't clip hyperslab information") - -done: - if(tmp_spans!=NULL) - H5S__hyper_free_span_info(tmp_spans); - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_select_select() */ - - -/*-------------------------------------------------------------------------- - NAME - H5Sselect_select - PURPOSE - Refine a hyperslab selection with an operation using a second hyperslab - to modify it. - USAGE - herr_t H5Sselect_select(space1, op, space2) - hid_t space1; IN/OUT: First Dataspace ID - H5S_seloper_t op; IN: Selection operation - hid_t space2; IN: Second Dataspace ID - RETURNS - Non-negative on success/Negative on failure - DESCRIPTION - Refine an existing hyperslab selection with an operation, using a second - hyperslab. The first selection is modified to contain the result of - space1 operated on by space2. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -herr_t -H5Sselect_select(hid_t space1_id, H5S_seloper_t op, hid_t space2_id) -{ - H5S_t *space1; /* First Dataspace */ - H5S_t *space2; /* Second Dataspace */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_API(FAIL) - H5TRACE3("e", "iSsi", space1_id, op, space2_id); - - /* Check args */ - if(NULL == (space1 = (H5S_t *)H5I_object_verify(space1_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if(NULL == (space2 = (H5S_t *)H5I_object_verify(space2_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if(!(op >= H5S_SELECT_OR && op <= H5S_SELECT_NOTA)) - HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation") - - /* Check that both dataspaces have the same rank */ - if(space1->extent.rank != space2->extent.rank) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspaces not same rank") - - /* Check that both dataspaces have hyperslab selections */ - if(H5S_GET_SELECT_TYPE(space1) != H5S_SEL_HYPERSLABS || H5S_GET_SELECT_TYPE(space2) != H5S_SEL_HYPERSLABS) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspaces don't have hyperslab selections") - - /* Go refine the first selection */ - if (H5S_select_select(space1, op, space2)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to modify hyperslab selection") - -done: - FUNC_LEAVE_API(ret_value) -} /* end H5Sselect_select() */ -#endif /* NEW_HYPERSLAB_API */ /* Works */ - - -/*-------------------------------------------------------------------------- - NAME - H5S__hyper_get_seq_list_gen - PURPOSE - Create a list of offsets & lengths for a selection - USAGE - herr_t H5S_select_hyper_get_file_list_gen(space,iter,maxseq,maxelem,nseq,nelem,off,len) - H5S_t *space; IN: Dataspace containing selection to use. - H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last - position of interest in selection. - size_t maxseq; IN: Maximum number of sequences to generate - size_t maxelem; IN: Maximum number of elements to include in the - generated sequences - size_t *nseq; OUT: Actual number of sequences generated - size_t *nelem; OUT: Actual number of elements in sequences generated - hsize_t *off; OUT: Array of offsets - size_t *len; OUT: Array of lengths - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to generate a list of byte offsets and - lengths for the region(s) selected. Start/Restart from the position in the - ITER parameter. The number of sequences generated is limited by the MAXSEQ - parameter and the number of sequences actually generated is stored in the - NSEQ parameter. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S__hyper_get_seq_list_gen(const H5S_t *space, H5S_sel_iter_t *iter, - size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, - hsize_t *off, size_t *len) -{ - H5S_hyper_span_t *curr_span; /* Current hyperslab span node */ - H5S_hyper_span_t **ispan; /* Iterator's hyperslab span nodes */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Cumulative size of each dimension in bytes */ - hsize_t acc; /* Accumulator for computing cumulative sizes */ - hsize_t loc_off; /* Element offset in the dataspace */ - hsize_t last_span_end = 0; /* The offset of the end of the last span */ - hsize_t *abs_arr; /* Absolute hyperslab span position */ - const hssize_t *off_arr; /* Offset within the dataspace extent */ - size_t span_size = 0; /* Number of bytes in current span to actually process */ - size_t io_left; /* Number of elements left to process */ - size_t io_bytes_left; /* Number of bytes left to process */ - size_t io_used; /* Number of elements processed */ - size_t curr_seq = 0; /* Number of sequence/offsets stored in the arrays */ - size_t elem_size; /* Size of each element iterating over */ - unsigned ndims; /* Number of dimensions of dataset */ - unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - int curr_dim; /* Current dimension being operated on */ - unsigned u; /* Index variable */ - int i; /* Index variable */ - - FUNC_ENTER_STATIC_NOERR - - /* Check args */ - HDassert(space); - HDassert(iter); - HDassert(maxseq > 0); - HDassert(maxelem > 0); - HDassert(nseq); - HDassert(nelem); - HDassert(off); - HDassert(len); - - /* Set the rank of the fastest changing dimension */ - ndims = space->extent.rank; - fast_dim = (ndims - 1); - - /* Get the pointers to the current span info and span nodes */ - curr_span = iter->u.hyp.span[fast_dim]; - abs_arr = iter->u.hyp.off; - off_arr = space->select.offset; - ispan = iter->u.hyp.span; - elem_size = iter->elmt_size; - - /* Set the amount of elements to perform I/O on, etc. */ - H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); - io_left = MIN(maxelem, (size_t)iter->elmt_left); - io_bytes_left = io_left * elem_size; - - /* Compute the cumulative size of dataspace dimensions */ - for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { - slab[i] = acc; - acc *= space->extent.size[i]; - } /* end for */ - - /* Set the offset of the first element iterated on */ - for(u = 0, loc_off = 0; u < ndims; u++) - /* Compute the sequential element offset */ - loc_off += ((hsize_t)((hssize_t)abs_arr[u] + off_arr[u])) * slab[u]; - - /* Range check against number of elements left in selection */ - HDassert(io_bytes_left <= (iter->elmt_left * elem_size)); - - /* Take care of any partial spans leftover from previous I/Os */ - if(abs_arr[fast_dim]!=curr_span->low) { - - /* Finish the span in the fastest changing dimension */ - - /* Compute the number of bytes to attempt in this span */ - H5_CHECKED_ASSIGN(span_size, size_t, ((curr_span->high-abs_arr[fast_dim])+1)*elem_size, hsize_t); - - /* Check number of bytes against upper bounds allowed */ - if(span_size>io_bytes_left) - span_size=io_bytes_left; - - /* Add the partial span to the list of sequences */ - off[curr_seq]=loc_off; - len[curr_seq]=span_size; - - /* Increment sequence count */ - curr_seq++; - - /* Set the location of the last span's end */ - last_span_end=loc_off+span_size; - - /* Decrement I/O left to perform */ - io_bytes_left-=span_size; - - /* Advance the hyperslab iterator */ - /* Check if we are done */ - if(io_bytes_left > 0) { - /* Move to next span in fastest changing dimension */ - curr_span = curr_span->next; - - if(NULL != curr_span) { - /* Move location offset of destination */ - loc_off += (curr_span->low - abs_arr[fast_dim]) * elem_size; - - /* Move iterator for fastest changing dimension */ - abs_arr[fast_dim] = curr_span->low; - } /* end if */ - } /* end if */ - else { - abs_arr[fast_dim] += span_size / elem_size; - - /* Check if we are still within the span */ - if(abs_arr[fast_dim] <= curr_span->high) { - iter->u.hyp.span[fast_dim] = curr_span; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span = curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(NULL != curr_span) { - /* Reset absolute position */ - abs_arr[fast_dim] = curr_span->low; - iter->u.hyp.span[fast_dim] = curr_span; - } /* end if */ - } /* end else */ - } /* end else */ - - /* Adjust iterator pointers */ - - if(NULL == curr_span) { -/* Same as code in main loop */ - /* Start at the next fastest dim */ - curr_dim = (int)(fast_dim - 1); - - /* Work back up through the dimensions */ - while(curr_dim >= 0) { - /* Reset the current span */ - curr_span = iter->u.hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim] <= curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span = curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(NULL != curr_span) { - /* Reset the span in the current dimension */ - ispan[curr_dim] = curr_span; - - /* Reset absolute position */ - abs_arr[curr_dim] = curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we have more spans in the tree */ - if(curr_dim >= 0) { - /* Walk back down the iterator positions, resetting them */ - while((unsigned)curr_dim < fast_dim) { - HDassert(curr_span); - HDassert(curr_span->down); - HDassert(curr_span->down->head); - - /* Increment current dimension */ - curr_dim++; - - /* Set the new span_info & span for this dimension */ - iter->u.hyp.span[curr_dim] = curr_span->down->head; - - /* Advance span down the tree */ - curr_span = curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim] = curr_span->low; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - HDassert(curr_span == iter->u.hyp.span[fast_dim]); - - /* Reset the buffer offset */ - for(u = 0, loc_off = 0; u < ndims; u++) - loc_off += ((hsize_t)((hssize_t)abs_arr[u] + off_arr[u])) * slab[u]; - } /* end else */ - else - /* We had better be done with I/O or bad things are going to happen... */ - HDassert(io_bytes_left == 0); - } /* end if */ - } /* end if */ - - /* Perform the I/O on the elements, based on the position of the iterator */ - while(io_bytes_left > 0 && curr_seq < maxseq) { - /* Sanity check */ - HDassert(curr_span); - - /* Adjust location offset of destination to compensate for initial increment below */ - loc_off -= curr_span->pstride; - - /* Loop over all the spans in the fastest changing dimension */ - while(curr_span != NULL) { - /* Move location offset of destination */ - loc_off += curr_span->pstride; - - /* Compute the number of elements to attempt in this span */ - H5_CHECKED_ASSIGN(span_size, size_t, curr_span->nelem, hsize_t); - - /* Check number of elements against upper bounds allowed */ - if(span_size >= io_bytes_left) { - /* Trim the number of bytes to output */ - span_size = io_bytes_left; - io_bytes_left = 0; - -/* COMMON */ - /* Store the I/O information for the span */ - - /* Check if this is appending onto previous sequence */ - if(curr_seq > 0 && last_span_end == loc_off) - len[curr_seq - 1] += span_size; - else { - off[curr_seq] = loc_off; - len[curr_seq] = span_size; - - /* Increment the number of sequences in arrays */ - curr_seq++; - } /* end else */ - - /* Set the location of the last span's end */ - last_span_end = loc_off + span_size; -/* end COMMON */ - - /* Break out now, we are finished with I/O */ - break; - } /* end if */ - else { - /* Decrement I/O left to perform */ - io_bytes_left -= span_size; - -/* COMMON */ - /* Store the I/O information for the span */ - - /* Check if this is appending onto previous sequence */ - if(curr_seq > 0 && last_span_end == loc_off) - len[curr_seq-1]+=span_size; - else { - off[curr_seq] = loc_off; - len[curr_seq] = span_size; - - /* Increment the number of sequences in arrays */ - curr_seq++; - } /* end else */ - - /* Set the location of the last span's end */ - last_span_end = loc_off + span_size; -/* end COMMON */ - - /* If the sequence & offset arrays are full, do what? */ - if(curr_seq >= maxseq) { - /* Break out now, we are finished with sequences */ - break; - } /* end else */ - } /* end else */ - - /* Move to next span in fastest changing dimension */ - curr_span=curr_span->next; - } /* end while */ - - /* Check if we are done */ - if(io_bytes_left==0 || curr_seq>=maxseq) { - HDassert(curr_span); - abs_arr[fast_dim]=curr_span->low+(span_size/elem_size); - - /* Check if we are still within the span */ - if(abs_arr[fast_dim]<=curr_span->high) { - iter->u.hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset absolute position */ - abs_arr[fast_dim]=curr_span->low; - iter->u.hyp.span[fast_dim]=curr_span; - break; - } /* end if */ - } /* end else */ - } /* end if */ - - /* Adjust iterator pointers */ - - /* Start at the next fastest dim */ - curr_dim = (int)(fast_dim - 1); - - /* Work back up through the dimensions */ - while(curr_dim >= 0) { - /* Reset the current span */ - curr_span=iter->u.hyp.span[curr_dim]; - - /* Increment absolute position */ - abs_arr[curr_dim]++; - - /* Check if we are still within the span */ - if(abs_arr[curr_dim]<=curr_span->high) { - break; - } /* end if */ - /* If we walked off that span, advance to the next span */ - else { - /* Advance span in this dimension */ - curr_span=curr_span->next; - - /* Check if we have a valid span in this dimension still */ - if(curr_span!=NULL) { - /* Reset the span in the current dimension */ - ispan[curr_dim]=curr_span; - - /* Reset absolute position */ - abs_arr[curr_dim]=curr_span->low; - - break; - } /* end if */ - else { - /* If we finished the span list in this dimension, decrement the dimension worked on and loop again */ - curr_dim--; - } /* end else */ - } /* end else */ - } /* end while */ - - /* Check if we are finished with the spans in the tree */ - if(curr_dim < 0) { - /* We had better be done with I/O or bad things are going to happen... */ - HDassert(io_bytes_left == 0); - break; - } /* end if */ - else { - /* Walk back down the iterator positions, resetting them */ - while((unsigned)curr_dim < fast_dim) { - HDassert(curr_span); - HDassert(curr_span->down); - HDassert(curr_span->down->head); - - /* Increment current dimension to the next dimension down */ - curr_dim++; - - /* Set the new span for the next dimension down */ - iter->u.hyp.span[curr_dim] = curr_span->down->head; - - /* Advance span down the tree */ - curr_span = curr_span->down->head; - - /* Reset the absolute offset for the dim */ - abs_arr[curr_dim] = curr_span->low; - } /* end while */ - - /* Verify that the curr_span points to the fastest dim */ - HDassert(curr_span == iter->u.hyp.span[fast_dim]); - } /* end else */ - - /* Reset the buffer offset */ - for(u = 0, loc_off = 0; u < ndims; u++) - loc_off += ((hsize_t)((hssize_t)abs_arr[u] + off_arr[u])) * slab[u]; - } /* end while */ - - /* Decrement number of elements left in iterator */ - io_used = (io_left - (io_bytes_left / elem_size)); - iter->elmt_left -= io_used; - - /* Set the number of sequences generated */ - *nseq = curr_seq; - - /* Set the number of elements used */ - *nelem = io_used; - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5S__hyper_get_seq_list_gen() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S__hyper_get_seq_list_opt - PURPOSE - Create a list of offsets & lengths for a selection - USAGE - herr_t H5S_select_hyper_get_file_list_opt(space,iter,maxseq,maxelem,nseq,nelem,off,len) - H5S_t *space; IN: Dataspace containing selection to use. - H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last - position of interest in selection. - size_t maxseq; IN: Maximum number of sequences to generate - size_t maxelem; IN: Maximum number of elements to include in the - generated sequences - size_t *nseq; OUT: Actual number of sequences generated - size_t *nelem; OUT: Actual number of elements in sequences generated - hsize_t *off; OUT: Array of offsets - size_t *len; OUT: Array of lengths - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to generate a list of byte offsets and - lengths for the region(s) selected. Start/Restart from the position in the - ITER parameter. The number of sequences generated is limited by the MAXSEQ - parameter and the number of sequences actually generated is stored in the - NSEQ parameter. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S__hyper_get_seq_list_opt(const H5S_t *space, H5S_sel_iter_t *iter, - size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, - hsize_t *off, size_t *len) -{ - hsize_t *mem_size; /* Size of the source buffer */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - const hssize_t *sel_off; /* Selection offset in dataspace */ - hsize_t offset[H5O_LAYOUT_NDIMS]; /* Coordinate offset in dataspace */ - hsize_t tmp_count[H5O_LAYOUT_NDIMS];/* Temporary block count */ - hsize_t tmp_block[H5O_LAYOUT_NDIMS];/* Temporary block offset */ - hsize_t wrap[H5O_LAYOUT_NDIMS]; /* Bytes to wrap around at the end of a row */ - hsize_t skip[H5O_LAYOUT_NDIMS]; /* Bytes to skip between blocks */ - const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ - hsize_t fast_dim_start, /* Local copies of fastest changing dimension info */ - fast_dim_stride, - fast_dim_block, - fast_dim_offset; - size_t fast_dim_buf_off; /* Local copy of amount to move fastest dimension buffer offset */ - size_t fast_dim_count; /* Number of blocks left in fastest changing dimension */ - size_t tot_blk_count; /* Total number of blocks left to output */ - size_t act_blk_count; /* Actual number of blocks to output */ - size_t total_rows; /* Total number of entire rows to output */ - size_t curr_rows; /* Current number of entire rows to output */ - unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - unsigned ndims; /* Number of dimensions of dataset */ - int temp_dim; /* Temporary rank holder */ - hsize_t acc; /* Accumulator */ - hsize_t loc; /* Coordinate offset */ - size_t curr_seq = 0; /* Current sequence being operated on */ - size_t actual_elem; /* The actual number of elements to count */ - size_t actual_bytes;/* The actual number of bytes to copy */ - size_t io_left; /* The number of elements left in I/O operation */ - size_t start_io_left; /* The initial number of elements left in I/O operation */ - size_t elem_size; /* Size of each element iterating over */ - unsigned u; /* Local index variable */ - int i; /* Local index variable */ - - FUNC_ENTER_STATIC_NOERR - - /* Check args */ - HDassert(space); - HDassert(iter); - HDassert(maxseq > 0); - HDassert(maxelem > 0); - HDassert(nseq); - HDassert(nelem); - HDassert(off); - HDassert(len); - - /* Set the local copy of the diminfo pointer */ - tdiminfo = iter->u.hyp.diminfo; - - /* Check if this is a "flattened" regular hyperslab selection */ - if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < space->extent.rank) { - /* Set the aliases for a few important dimension ranks */ - ndims = iter->u.hyp.iter_rank; - fast_dim = ndims - 1; - - /* Set the local copy of the selection offset */ - sel_off = iter->u.hyp.sel_off; - - /* Set up the pointer to the size of the memory space */ - mem_size = iter->u.hyp.size; - } /* end if */ - else { - /* Set the aliases for a few important dimension ranks */ - ndims = space->extent.rank; - fast_dim = ndims - 1; - - /* Set the local copy of the selection offset */ - sel_off = space->select.offset; - - /* Set up the pointer to the size of the memory space */ - mem_size = space->extent.size; - } /* end else */ - - /* initialize row sizes for each dimension */ - elem_size = iter->elmt_size; - for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { - slab[i] = acc; - acc *= mem_size[i]; - } /* end for */ - - /* Calculate the number of elements to sequence through */ - H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); - io_left = MIN((size_t)iter->elmt_left, maxelem); - - /* Sanity check that there aren't any "remainder" sequences in process */ - HDassert(!((iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start) % tdiminfo[fast_dim].stride != 0 || - ((iter->u.hyp.off[fast_dim] != tdiminfo[fast_dim].start) && tdiminfo[fast_dim].count == 1))); - - /* We've cleared the "remainder" of the previous fastest dimension - * sequence before calling this routine, so we must be at the beginning of - * a sequence. Use the fancy algorithm to compute the offsets and run - * through as many as possible, until the buffer fills up. - */ - - /* Keep the number of elements we started with */ - start_io_left = io_left; - - /* Compute the arrays to perform I/O on */ - - /* Copy the location of the point to get */ - /* (Add in the selection offset) */ - for(u = 0; u < ndims; u++) - offset[u] = (hsize_t)((hssize_t)iter->u.hyp.off[u] + sel_off[u]); - - /* Compute the current "counts" for this location */ - for(u = 0; u < ndims; u++) { - if(tdiminfo[u].count == 1) { - tmp_count[u] = 0; - tmp_block[u] = iter->u.hyp.off[u] - tdiminfo[u].start; - } /* end if */ - else { - tmp_count[u] = (iter->u.hyp.off[u] - tdiminfo[u].start) / tdiminfo[u].stride; - tmp_block[u] = (iter->u.hyp.off[u] - tdiminfo[u].start) % tdiminfo[u].stride; - } /* end else */ - } /* end for */ - - /* Compute the initial buffer offset */ - for(u = 0, loc = 0; u < ndims; u++) - loc += offset[u] * slab[u]; - - /* Set the number of elements to write each time */ - H5_CHECKED_ASSIGN(actual_elem, size_t, tdiminfo[fast_dim].block, hsize_t); - - /* Set the number of actual bytes */ - actual_bytes = actual_elem * elem_size; - - /* Set local copies of information for the fastest changing dimension */ - fast_dim_start = tdiminfo[fast_dim].start; - fast_dim_stride = tdiminfo[fast_dim].stride; - fast_dim_block = tdiminfo[fast_dim].block; - H5_CHECKED_ASSIGN(fast_dim_buf_off, size_t, slab[fast_dim] * fast_dim_stride, hsize_t); - fast_dim_offset = (hsize_t)((hssize_t)fast_dim_start + sel_off[fast_dim]); - - /* Compute the number of blocks which would fit into the buffer */ - H5_CHECK_OVERFLOW(io_left / fast_dim_block, hsize_t, size_t); - tot_blk_count = (size_t)(io_left / fast_dim_block); - - /* Don't go over the maximum number of sequences allowed */ - tot_blk_count = MIN(tot_blk_count, (maxseq - curr_seq)); - - /* Compute the amount to wrap at the end of each row */ - for(u = 0; u < ndims; u++) - wrap[u] = (mem_size[u] - (tdiminfo[u].stride * tdiminfo[u].count)) * slab[u]; - - /* Compute the amount to skip between blocks */ - for(u = 0; u < ndims; u++) - skip[u] = (tdiminfo[u].stride - tdiminfo[u].block) * slab[u]; - - /* Check if there is a partial row left (with full blocks) */ - if(tmp_count[fast_dim] > 0) { - /* Get number of blocks in fastest dimension */ - H5_CHECKED_ASSIGN(fast_dim_count, size_t, tdiminfo[fast_dim].count - tmp_count[fast_dim], hsize_t); - - /* Make certain this entire row will fit into buffer */ - fast_dim_count = MIN(fast_dim_count, tot_blk_count); - - /* Number of blocks to sequence over */ - act_blk_count = fast_dim_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count > 0) { - /* Store the sequence information */ - off[curr_seq] = loc; - len[curr_seq] = actual_bytes; - - /* Increment sequence count */ - curr_seq++; - - /* Increment information to reflect block just processed */ - loc += fast_dim_buf_off; - - /* Decrement number of blocks */ - fast_dim_count--; - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_elem * act_blk_count; - - /* Decrement number of blocks left */ - tot_blk_count -= act_blk_count; - - /* Increment information to reflect block just processed */ - tmp_count[fast_dim] += act_blk_count; - - /* Check if we finished the entire row of blocks */ - if(tmp_count[fast_dim] >= tdiminfo[fast_dim].count) { - /* Increment offset in destination buffer */ - loc += wrap[fast_dim]; - - /* Increment information to reflect block just processed */ - offset[fast_dim] = fast_dim_offset; /* reset the offset in the fastest dimension */ - tmp_count[fast_dim] = 0; - - /* Increment the offset and count for the other dimensions */ - temp_dim = (int)fast_dim - 1; - while(temp_dim >= 0) { - /* Move to the next row in the curent dimension */ - offset[temp_dim]++; - tmp_block[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_block[temp_dim] < tdiminfo[temp_dim].block) - break; - else { - /* Move to the next block in the current dimension */ - offset[temp_dim] += (tdiminfo[temp_dim].stride - tdiminfo[temp_dim].block); - loc += skip[temp_dim]; - tmp_block[temp_dim] = 0; - tmp_count[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_count[temp_dim] < tdiminfo[temp_dim].count) - break; - else { - offset[temp_dim] = (hsize_t)((hssize_t)tdiminfo[temp_dim].start + sel_off[temp_dim]); - loc += wrap[temp_dim]; - tmp_count[temp_dim] = 0; /* reset back to the beginning of the line */ - tmp_block[temp_dim] = 0; - } /* end else */ - } /* end else */ - - /* Decrement dimension count */ - temp_dim--; - } /* end while */ - } /* end if */ - else { - /* Update the offset in the fastest dimension */ - offset[fast_dim] += (fast_dim_stride * act_blk_count); - } /* end else */ - } /* end if */ - - /* Compute the number of entire rows to read in */ - H5_CHECK_OVERFLOW(tot_blk_count / tdiminfo[fast_dim].count, hsize_t, size_t); - curr_rows = total_rows = (size_t)(tot_blk_count / tdiminfo[fast_dim].count); - - /* Reset copy of number of blocks in fastest dimension */ - H5_CHECKED_ASSIGN(fast_dim_count, size_t, tdiminfo[fast_dim].count, hsize_t); - - /* Read in data until an entire sequence can't be written out any longer */ - while(curr_rows > 0) { - -#define DUFF_GUTS \ -/* Store the sequence information */ \ -off[curr_seq] = loc; \ -len[curr_seq] = actual_bytes; \ - \ -/* Increment sequence count */ \ -curr_seq++; \ - \ -/* Increment information to reflect block just processed */ \ -loc += fast_dim_buf_off; - -#ifdef NO_DUFFS_DEVICE - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count > 0) { - DUFF_GUTS - - /* Decrement number of blocks */ - fast_dim_count--; - } /* end while */ -#else /* NO_DUFFS_DEVICE */ - { - size_t duffs_index; /* Counting index for Duff's device */ - - duffs_index = (fast_dim_count + 7) / 8; - switch (fast_dim_count % 8) { - default: - HDassert(0 && "This Should never be executed!"); - break; - case 0: - do - { - DUFF_GUTS - case 7: - DUFF_GUTS - case 6: - DUFF_GUTS - case 5: - DUFF_GUTS - case 4: - DUFF_GUTS - case 3: - DUFF_GUTS - case 2: - DUFF_GUTS - case 1: - DUFF_GUTS - } while (--duffs_index > 0); - } /* end switch */ - } -#endif /* NO_DUFFS_DEVICE */ -#undef DUFF_GUTS - - /* Increment offset in destination buffer */ - loc += wrap[fast_dim]; - - /* Increment the offset and count for the other dimensions */ - temp_dim = (int)fast_dim - 1; - while(temp_dim >= 0) { - /* Move to the next row in the curent dimension */ - offset[temp_dim]++; - tmp_block[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_block[temp_dim] < tdiminfo[temp_dim].block) - break; - else { - /* Move to the next block in the current dimension */ - offset[temp_dim] += (tdiminfo[temp_dim].stride - tdiminfo[temp_dim].block); - loc += skip[temp_dim]; - tmp_block[temp_dim] = 0; - tmp_count[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_count[temp_dim] < tdiminfo[temp_dim].count) - break; - else { - offset[temp_dim] = (hsize_t)((hssize_t)tdiminfo[temp_dim].start + sel_off[temp_dim]); - loc += wrap[temp_dim]; - tmp_count[temp_dim] = 0; /* reset back to the beginning of the line */ - tmp_block[temp_dim] = 0; - } /* end else */ - } /* end else */ - - /* Decrement dimension count */ - temp_dim--; - } /* end while */ - - /* Decrement the number of rows left */ - curr_rows--; - } /* end while */ - - /* Adjust the number of blocks & elements left to transfer */ - - /* Decrement number of elements left */ - H5_CHECK_OVERFLOW(actual_elem * (total_rows * tdiminfo[fast_dim].count), hsize_t, size_t); - io_left -= (size_t)(actual_elem * (total_rows * tdiminfo[fast_dim].count)); - - /* Decrement number of blocks left */ - H5_CHECK_OVERFLOW((total_rows * tdiminfo[fast_dim].count), hsize_t, size_t); - tot_blk_count -= (size_t)(total_rows * tdiminfo[fast_dim].count); - - /* Read in partial row of blocks */ - if(io_left > 0 && curr_seq < maxseq) { - /* Get remaining number of blocks left to output */ - fast_dim_count = tot_blk_count; - - /* Loop over all the blocks in the fastest changing dimension */ - while(fast_dim_count > 0) { - /* Store the sequence information */ - off[curr_seq] = loc; - len[curr_seq] = actual_bytes; - - /* Increment sequence count */ - curr_seq++; - - /* Increment information to reflect block just processed */ - loc += fast_dim_buf_off; - - /* Decrement number of blocks */ - fast_dim_count--; - } /* end while */ - - /* Decrement number of elements left */ - io_left -= actual_elem * tot_blk_count; - - /* Increment information to reflect block just processed */ - offset[fast_dim] += (fast_dim_stride * tot_blk_count); /* move the offset in the fastest dimension */ - - /* Handle any leftover, partial blocks in this row */ - if(io_left > 0 && curr_seq < maxseq) { - actual_elem = io_left; - actual_bytes = actual_elem * elem_size; - - /* Store the sequence information */ - off[curr_seq] = loc; - len[curr_seq] = actual_bytes; - - /* Increment sequence count */ - curr_seq++; - - /* Decrement the number of elements left */ - io_left -= actual_elem; - - /* Increment buffer correctly */ - offset[fast_dim] += actual_elem; - } /* end if */ - - /* don't bother checking slower dimensions */ - HDassert(io_left == 0 || curr_seq == maxseq); - } /* end if */ - - /* Update the iterator */ - - /* Update the iterator with the location we stopped */ - /* (Subtract out the selection offset) */ - for(u = 0; u < ndims; u++) - iter->u.hyp.off[u] = (hsize_t)((hssize_t)offset[u] - sel_off[u]); - - /* Decrement the number of elements left in selection */ - iter->elmt_left -= (start_io_left - io_left); - - /* Increment the number of sequences generated */ - *nseq += curr_seq; - - /* Increment the number of elements used */ - *nelem += start_io_left - io_left; - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5S__hyper_get_seq_list_opt() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S__hyper_get_seq_list_single - PURPOSE - Create a list of offsets & lengths for a selection - USAGE - herr_t H5S__hyper_get_seq_list_single(space, flags, iter, maxseq, maxelem, nseq, nelem, off, len) - H5S_t *space; IN: Dataspace containing selection to use. - unsigned flags; IN: Flags for extra information about operation - H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last - position of interest in selection. - size_t maxseq; IN: Maximum number of sequences to generate - size_t maxelem; IN: Maximum number of elements to include in the - generated sequences - size_t *nseq; OUT: Actual number of sequences generated - size_t *nelem; OUT: Actual number of elements in sequences generated - hsize_t *off; OUT: Array of offsets - size_t *len; OUT: Array of lengths - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to generate a list of byte offsets and - lengths for the region(s) selected. Start/Restart from the position in the - ITER parameter. The number of sequences generated is limited by the MAXSEQ - parameter and the number of sequences actually generated is stored in the - NSEQ parameter. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S__hyper_get_seq_list_single(const H5S_t *space, H5S_sel_iter_t *iter, - size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, - hsize_t *off, size_t *len) -{ - const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ - const hssize_t *sel_off; /* Selection offset in dataspace */ - hsize_t *mem_size; /* Size of the source buffer */ - hsize_t base_offset[H5O_LAYOUT_NDIMS]; /* Base coordinate offset in dataspace */ - hsize_t offset[H5O_LAYOUT_NDIMS]; /* Coordinate offset in dataspace */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hsize_t fast_dim_block; /* Local copies of fastest changing dimension info */ - hsize_t acc; /* Accumulator */ - hsize_t loc; /* Coordinate offset */ - size_t tot_blk_count; /* Total number of blocks left to output */ - size_t elem_size; /* Size of each element iterating over */ - size_t io_left; /* The number of elements left in I/O operation */ - size_t actual_elem; /* The actual number of elements to count */ - unsigned ndims; /* Number of dimensions of dataset */ - unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - unsigned skip_dim; /* Rank of the dimension to skip along */ - unsigned u; /* Local index variable */ - int i; /* Local index variable */ - - FUNC_ENTER_STATIC_NOERR - - /* Check args */ - HDassert(space); - HDassert(iter); - HDassert(maxseq > 0); - HDassert(maxelem > 0); - HDassert(nseq); - HDassert(nelem); - HDassert(off); - HDassert(len); - - /* Set a local copy of the diminfo pointer */ - tdiminfo = iter->u.hyp.diminfo; - - /* Check if this is a "flattened" regular hyperslab selection */ - if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < space->extent.rank) { - /* Set the aliases for a few important dimension ranks */ - ndims = iter->u.hyp.iter_rank; - - /* Set the local copy of the selection offset */ - sel_off = iter->u.hyp.sel_off; - - /* Set up the pointer to the size of the memory space */ - mem_size = iter->u.hyp.size; - } /* end if */ - else { - /* Set the aliases for a few important dimension ranks */ - ndims = space->extent.rank; - - /* Set the local copy of the selection offset */ - sel_off = space->select.offset; - - /* Set up the pointer to the size of the memory space */ - mem_size = space->extent.size; - } /* end else */ - fast_dim = ndims - 1; - - /* initialize row sizes for each dimension */ - elem_size = iter->elmt_size; - for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { - slab[i] = acc; - acc *= mem_size[i]; - } /* end for */ - - /* Copy the base location of the block */ - /* (Add in the selection offset) */ - for(u = 0; u < ndims; u++) - base_offset[u] = (hsize_t)((hssize_t)tdiminfo[u].start + sel_off[u]); - - /* Copy the location of the point to get */ - /* (Add in the selection offset) */ - for(u = 0; u < ndims; u++) - offset[u] = (hsize_t)((hssize_t)iter->u.hyp.off[u] + sel_off[u]); - - /* Compute the initial buffer offset */ - for(u = 0, loc = 0; u < ndims; u++) - loc += offset[u] * slab[u]; - - /* Set local copies of information for the fastest changing dimension */ - fast_dim_block = tdiminfo[fast_dim].block; - - /* Calculate the number of elements to sequence through */ - H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); - io_left = MIN((size_t)iter->elmt_left, maxelem); - - /* Compute the number of blocks which would fit into the buffer */ - H5_CHECK_OVERFLOW(io_left / fast_dim_block, hsize_t, size_t); - tot_blk_count = (size_t)(io_left / fast_dim_block); - - /* Don't go over the maximum number of sequences allowed */ - tot_blk_count = MIN(tot_blk_count, maxseq); - - /* Set the number of elements to write each time */ - H5_CHECKED_ASSIGN(actual_elem, size_t, fast_dim_block, hsize_t); - - /* Check for blocks to operate on */ - if(tot_blk_count > 0) { - size_t actual_bytes; /* The actual number of bytes to copy */ - - /* Set the number of actual bytes */ - actual_bytes = actual_elem * elem_size; - - /* Check for 1-dim selection */ - if(0 == fast_dim) { - /* Sanity checks */ - HDassert(1 == tot_blk_count); - HDassert(io_left == actual_elem); - - /* Store the sequence information */ - *off++ = loc; - *len++ = actual_bytes; - } /* end if */ - else { - hsize_t skip_slab; /* Temporary copy of slab[fast_dim - 1] */ - size_t blk_count; /* Total number of blocks left to output */ - - /* Find first dimension w/block >1 */ - skip_dim = fast_dim; - for(i = (int)(fast_dim - 1); i >= 0; i--) - if(tdiminfo[i].block > 1) { - skip_dim = (unsigned)i; - break; - } /* end if */ - skip_slab = slab[skip_dim]; - - /* Check for being able to use fast algorithm for 1-D */ - if(0 == skip_dim) { - /* Create sequences until an entire row can't be used */ - blk_count = tot_blk_count; - while(blk_count > 0) { - /* Store the sequence information */ - *off++ = loc; - *len++ = actual_bytes; - - /* Increment offset in destination buffer */ - loc += skip_slab; - - /* Decrement block count */ - blk_count--; - } /* end while */ - - /* Move to the next location */ - offset[skip_dim] += tot_blk_count; - } /* end if */ - else { - hsize_t tmp_block[H5O_LAYOUT_NDIMS];/* Temporary block offset */ - hsize_t skip[H5O_LAYOUT_NDIMS]; /* Bytes to skip between blocks */ - int temp_dim; /* Temporary rank holder */ - - /* Set the starting block location */ - for(u = 0; u < ndims; u++) - tmp_block[u] = iter->u.hyp.off[u] - tdiminfo[u].start; - - /* Compute the amount to skip between sequences */ - for(u = 0; u < ndims; u++) - skip[u] = (mem_size[u] - tdiminfo[u].block) * slab[u]; - - /* Create sequences until an entire row can't be used */ - blk_count = tot_blk_count; - while(blk_count > 0) { - /* Store the sequence information */ - *off++ = loc; - *len++ = actual_bytes; - - /* Set temporary dimension for advancing offsets */ - temp_dim = (int)skip_dim; - - /* Increment offset in destination buffer */ - loc += skip_slab; - - /* Increment the offset and count for the other dimensions */ - while(temp_dim >= 0) { - /* Move to the next row in the curent dimension */ - offset[temp_dim]++; - tmp_block[temp_dim]++; - - /* If this block is still in the range of blocks to output for the dimension, break out of loop */ - if(tmp_block[temp_dim] < tdiminfo[temp_dim].block) - break; - else { - offset[temp_dim] = base_offset[temp_dim]; - loc += skip[temp_dim]; - tmp_block[temp_dim] = 0; - } /* end else */ - - /* Decrement dimension count */ - temp_dim--; - } /* end while */ - - /* Decrement block count */ - blk_count--; - } /* end while */ - } /* end else */ - } /* end else */ - - /* Update the iterator, if there were any blocks used */ - - /* Decrement the number of elements left in selection */ - iter->elmt_left -= tot_blk_count * actual_elem; - - /* Check if there are elements left in iterator */ - if(iter->elmt_left > 0) { - /* Update the iterator with the location we stopped */ - /* (Subtract out the selection offset) */ - for(u = 0; u < ndims; u++) - iter->u.hyp.off[u] = (hsize_t)((hssize_t)offset[u] - sel_off[u]); - } /* end if */ - - /* Increment the number of sequences generated */ - *nseq += tot_blk_count; - - /* Increment the number of elements used */ - *nelem += tot_blk_count * actual_elem; - } /* end if */ - - /* Check for partial block, with room for another sequence */ - if(io_left > (tot_blk_count * actual_elem) && tot_blk_count < maxseq) { - size_t elmt_remainder; /* Elements remaining */ - - /* Compute elements left */ - elmt_remainder = io_left - (tot_blk_count * actual_elem); - HDassert(elmt_remainder < fast_dim_block); - HDassert(elmt_remainder > 0); - - /* Store the sequence information */ - *off++ = loc; - *len++ = elmt_remainder * elem_size; - - /* Update the iterator with the location we stopped */ - iter->u.hyp.off[fast_dim] += (hsize_t)elmt_remainder; - - /* Decrement the number of elements left in selection */ - iter->elmt_left -= elmt_remainder; - - /* Increment the number of sequences generated */ - (*nseq)++; - - /* Increment the number of elements used */ - *nelem += elmt_remainder; - } /* end if */ - - /* Sanity check */ - HDassert(*nseq > 0); - HDassert(*nelem > 0); - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5S__hyper_get_seq_list_single() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S__hyper_get_seq_list - PURPOSE - Create a list of offsets & lengths for a selection - USAGE - herr_t H5S__hyper_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) - H5S_t *space; IN: Dataspace containing selection to use. - unsigned flags; IN: Flags for extra information about operation - H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last - position of interest in selection. - size_t maxseq; IN: Maximum number of sequences to generate - size_t maxelem; IN: Maximum number of elements to include in the - generated sequences - size_t *nseq; OUT: Actual number of sequences generated - size_t *nelem; OUT: Actual number of elements in sequences generated - hsize_t *off; OUT: Array of offsets - size_t *len; OUT: Array of lengths - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to generate a list of byte offsets and - lengths for the region(s) selected. Start/Restart from the position in the - ITER parameter. The number of sequences generated is limited by the MAXSEQ - parameter and the number of sequences actually generated is stored in the - NSEQ parameter. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S__hyper_get_seq_list(const H5S_t *space, unsigned H5_ATTR_UNUSED flags, H5S_sel_iter_t *iter, - size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, - hsize_t *off, size_t *len) -{ - herr_t ret_value = FAIL; /* return value */ - - FUNC_ENTER_STATIC_NOERR - - /* Check args */ - HDassert(space); - HDassert(iter); - HDassert(iter->elmt_left > 0); - HDassert(maxseq > 0); - HDassert(maxelem > 0); - HDassert(nseq); - HDassert(nelem); - HDassert(off); - HDassert(len); - HDassert(space->select.sel_info.hslab->unlim_dim < 0); - - /* Check for the special case of just one H5Sselect_hyperslab call made */ - if(space->select.sel_info.hslab->diminfo_valid) { - const H5S_hyper_dim_t *tdiminfo; /* Temporary pointer to diminfo information */ - const hssize_t *sel_off; /* Selection offset in dataspace */ - hsize_t *mem_size; /* Size of the source buffer */ - unsigned ndims; /* Number of dimensions of dataset */ - unsigned fast_dim; /* Rank of the fastest changing dimension for the dataspace */ - hbool_t single_block; /* Whether the selection is a single block */ - unsigned u; /* Local index variable */ - - /* Set a local copy of the diminfo pointer */ - tdiminfo = iter->u.hyp.diminfo; - - /* Check if this is a "flattened" regular hyperslab selection */ - if(iter->u.hyp.iter_rank != 0 && iter->u.hyp.iter_rank < space->extent.rank) { - /* Set the aliases for a few important dimension ranks */ - ndims = iter->u.hyp.iter_rank; - - /* Set the local copy of the selection offset */ - sel_off = iter->u.hyp.sel_off; - - /* Set up the pointer to the size of the memory space */ - mem_size = iter->u.hyp.size; - } /* end if */ - else { - /* Set the aliases for a few important dimension ranks */ - ndims = space->extent.rank; - - /* Set the local copy of the selection offset */ - sel_off = space->select.offset; - - /* Set up the pointer to the size of the memory space */ - mem_size = space->extent.size; - } /* end else */ - fast_dim = ndims - 1; - - /* Check if we stopped in the middle of a sequence of elements */ - if((iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start) % tdiminfo[fast_dim].stride != 0 || - ((iter->u.hyp.off[fast_dim] != tdiminfo[fast_dim].start) && tdiminfo[fast_dim].count == 1)) { - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hsize_t loc; /* Coordinate offset */ - hsize_t acc; /* Accumulator */ - size_t leftover; /* The number of elements left over from the last sequence */ - size_t actual_elem; /* The actual number of elements to count */ - size_t elem_size; /* Size of each element iterating over */ - int i; /* Local index variable */ - - - /* Calculate the number of elements left in the sequence */ - if(tdiminfo[fast_dim].count == 1) { - H5_CHECKED_ASSIGN(leftover, size_t, tdiminfo[fast_dim].block - (iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start), hsize_t); - } /* end if */ - else { - H5_CHECKED_ASSIGN(leftover, size_t, tdiminfo[fast_dim].block - ((iter->u.hyp.off[fast_dim] - tdiminfo[fast_dim].start) % tdiminfo[fast_dim].stride), hsize_t); - } /* end else */ - - /* Make certain that we don't write too many */ - actual_elem = MIN3(leftover, (size_t)iter->elmt_left, maxelem); - - /* Initialize row sizes for each dimension */ - elem_size = iter->elmt_size; - for(i = (int)fast_dim, acc = elem_size; i >= 0; i--) { - slab[i] = acc; - acc *= mem_size[i]; - } /* end for */ - - /* Compute the initial buffer offset */ - for(u = 0, loc = 0; u < ndims; u++) - loc += ((hsize_t)((hssize_t)iter->u.hyp.off[u] + sel_off[u])) * slab[u]; - - /* Add a new sequence */ - off[0] = loc; - H5_CHECKED_ASSIGN(len[0], size_t, actual_elem * elem_size, hsize_t); - - /* Increment sequence array locations */ - off++; - len++; - - /* Advance the hyperslab iterator */ - H5S__hyper_iter_next(iter, actual_elem); - - /* Decrement the number of elements left in selection */ - iter->elmt_left -= actual_elem; - - /* Decrement element/sequence limits */ - maxelem -= actual_elem; - maxseq--; - - /* Set the number of sequences generated and elements used */ - *nseq = 1; - *nelem = actual_elem; - - /* Check for using up all the sequences/elements */ - if(0 == iter->elmt_left || 0 == maxelem || 0 == maxseq) - return(SUCCEED); - } /* end if */ - else { - /* Reset the number of sequences generated and elements used */ - *nseq = 0; - *nelem = 0; - } /* end else */ - - /* Check for a single block selected */ - single_block = TRUE; - for(u = 0; u < ndims; u++) - if(1 != tdiminfo[u].count) { - single_block = FALSE; - break; - } /* end if */ - - /* Check for single block selection */ - if(single_block) - /* Use single-block optimized call to generate sequence list */ - ret_value = H5S__hyper_get_seq_list_single(space, iter, maxseq, maxelem, nseq, nelem, off, len); - else - /* Use optimized call to generate sequence list */ - ret_value = H5S__hyper_get_seq_list_opt(space, iter, maxseq, maxelem, nseq, nelem, off, len); - } /* end if */ - else - /* Call the general sequence generator routine */ - ret_value = H5S__hyper_get_seq_list_gen(space, iter, maxseq, maxelem, nseq, nelem, off, len); - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S__hyper_get_seq_list() */ /*-------------------------------------------------------------------------- @@ -9249,11 +8130,10 @@ H5S__hyper_get_seq_list(const H5S_t *space, unsigned H5_ATTR_UNUSED flags, H5S_s DESCRIPTION Projects the intersection of of the selections of src_space and src_intersect_space within the selection of src_space as a selection - within the selection of dst_space. The result is placed in the - selection of proj_space. Note src_space, dst_space, and - src_intersect_space do not need to use hyperslab selections, but they - cannot use point selections. The result is always a hyperslab - selection. + within the selection of dst_space. The result is placed in the selection + of proj_space. Note src_space, dst_space, and src_intersect_space do not + need to use hyperslab selections, but they cannot use point selections. + The result is always a hyperslab selection. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES @@ -9312,7 +8192,7 @@ H5S__hyper_project_intersection(const H5S_t *src_space, const H5S_t *dst_space, HDassert(dst_space); HDassert(src_intersect_space); HDassert(proj_space); - + /* Assert that src_space and src_intersect_space have same extent and there * are no point selections */ HDassert(H5S_GET_EXTENT_NDIMS(src_space) == H5S_GET_EXTENT_NDIMS(src_intersect_space)); @@ -9475,7 +8355,7 @@ H5S__hyper_project_intersection(const H5S_t *src_space, const H5S_t *dst_space, * selection and advance any sequences we complete */ if(ss_off[ss_i] >= sis_off[sis_i]) int_sel_off = ss_sel_off; - else + else int_sel_off = sis_off[sis_i] - ss_off[ss_i] + ss_sel_off; if((ss_off[ss_i] + (hsize_t)ss_len[ss_i]) <= (sis_off[sis_i] + (hsize_t)sis_len[sis_i])) { @@ -9599,8 +8479,9 @@ loop_end: /* Set the number of elements in current selection */ proj_space->select.num_elem = H5S__hyper_spans_nelem(proj_space->select.sel_info.hslab->span_lst); - /* Attempt to rebuild "optimized" start/stride/count/block information. - * from resulting hyperslab span tree */ + /* Attempt to build "optimized" start/stride/count/block information + * from resulting hyperslab span tree. + */ H5S__hyper_rebuild(proj_space); } /* end if */ else @@ -9841,7 +8722,7 @@ H5S_hyper_clip_unlim(H5S_t *space, hsize_t clip_size) hsize_t orig_count; /* Original count in unlimited dimension */ int orig_unlim_dim; /* Original unliminted dimension */ H5S_hyper_dim_t *diminfo; /* Convenience pointer to opt_diminfo in unlimited dimension */ - herr_t ret_value = SUCCEED; + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -10225,7 +9106,7 @@ H5S_hyper_get_unlim_block(const H5S_t *space, hsize_t block_index) /* Create output space, copy extent */ if(NULL == (space_out = H5S_create(H5S_SIMPLE))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, NULL, "unable to create output dataspace") - if(H5S_extent_copy_real(&space_out->extent, &space->extent, TRUE) < 0) + if(H5S__extent_copy_real(&space_out->extent, &space->extent, TRUE) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, NULL, "unable to copy destination space extent") /* Select block as defined by start/stride/count/block computed above */ @@ -10352,7 +9233,7 @@ H5Sis_regular_hyperslab(hid_t spaceid) done: FUNC_LEAVE_API(ret_value) -} /* H5Sis_regular_hyperslab() */ +} /* end H5Sis_regular_hyperslab() */ /*-------------------------------------------------------------------------- @@ -10416,5 +9297,5 @@ H5Sget_regular_hyperslab(hid_t spaceid, hsize_t start[], hsize_t stride[], done: FUNC_LEAVE_API(ret_value) -} /* H5Sget_regular_hyperslab() */ +} /* end H5Sget_regular_hyperslab() */ diff --git a/src/H5Smpio.c b/src/H5Smpio.c index 935d279..01ec3e1 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -14,60 +14,86 @@ /* * Programmer: rky 980813 * - * Purpose: Functions to read/write directly between app buffer and file. + * Purpose: Create MPI data types for HDF5 selections. * - * Beware of the ifdef'ed print statements. - * I didn't make them portable. */ +/****************/ +/* Module Setup */ +/****************/ + #include "H5Smodule.h" /* This source code file is part of the H5S module */ +/***********/ +/* Headers */ +/***********/ #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ -#include "H5Fprivate.h" /* File access */ -#include "H5FDprivate.h" /* File drivers */ -#include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ -#include "H5Oprivate.h" /* Object headers */ -#include "H5Pprivate.h" /* Property lists */ #include "H5Spkg.h" /* Dataspaces */ #include "H5VMprivate.h" /* Vector and array functions */ #ifdef H5_HAVE_PARALLEL -static herr_t H5S_mpio_all_type(const H5S_t *space, size_t elmt_size, +/****************/ +/* Local Macros */ +/****************/ +#define H5S_MPIO_INITIAL_ALLOC_COUNT 256 +#define TWO_GIG_LIMIT 2147483648 +#ifndef H5S_MAX_MPI_COUNT +#define H5S_MAX_MPI_COUNT 536870911 /* (2^29)-1 */ +#endif + + +/******************/ +/* Local Typedefs */ +/******************/ + + +/********************/ +/* Local Prototypes */ +/********************/ +static herr_t H5S__mpio_all_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); -static herr_t H5S_mpio_none_type(MPI_Datatype *new_type, int *count, +static herr_t H5S__mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); -static herr_t H5S_mpio_create_point_datatype(size_t elmt_size, hsize_t num_points, +static herr_t H5S__mpio_create_point_datatype(size_t elmt_size, hsize_t num_points, MPI_Aint *disp, MPI_Datatype *new_type); -static herr_t H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, +static herr_t H5S__mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute_map, hbool_t *is_permuted); -static herr_t H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, +static herr_t H5S__mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute_map, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); -static herr_t H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, +static herr_t H5S__mpio_reg_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); -static herr_t H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, +static herr_t H5S__mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); -static herr_t H5S_obtain_datatype(const hsize_t down[], H5S_hyper_span_t* span, +static herr_t H5S__obtain_datatype(const hsize_t down[], H5S_hyper_span_t* span, const MPI_Datatype *elmt_type, MPI_Datatype *span_type, size_t elmt_size); -static herr_t H5S_mpio_create_large_type (hsize_t, MPI_Aint, MPI_Datatype , MPI_Datatype *); +static herr_t H5S__mpio_create_large_type(hsize_t, MPI_Aint, MPI_Datatype , MPI_Datatype *); -#define H5S_MPIO_INITIAL_ALLOC_COUNT 256 +/*****************************/ +/* Library Private Variables */ +/*****************************/ -#define TWO_GIG_LIMIT 2147483648 -#ifndef H5S_MAX_MPI_COUNT -#define H5S_MAX_MPI_COUNT 536870911 /* (2^29)-1 */ -#endif +/*********************/ +/* Package Variables */ +/*********************/ + +/*******************/ +/* Local Variables */ +/*******************/ static hsize_t bigio_count = H5S_MAX_MPI_COUNT; + + + /*------------------------------------------------------------------------- * Function: H5S_mpio_set_bigio_count * @@ -75,7 +101,7 @@ static hsize_t bigio_count = H5S_MAX_MPI_COUNT; * when we utilize derived datatypes. This is of * particular interest for allowing nightly testing * - * Return: the current/previous value of bigio_count. + * Return: The current/previous value of bigio_count. * * Programmer: Richard Warren, March 10, 2017 * @@ -85,19 +111,20 @@ hsize_t H5S_mpio_set_bigio_count(hsize_t new_count) { hsize_t orig_count = bigio_count; - if ((new_count > 0) && (new_count < TWO_GIG_LIMIT)) { + + if((new_count > 0) && (new_count < TWO_GIG_LIMIT)) bigio_count = new_count; - } + return orig_count; -} +} /* end H5S_mpio_set_bigio_count() */ /*------------------------------------------------------------------------- - * Function: H5S_mpio_all_type + * Function: H5S__mpio_all_type * * Purpose: Translate an HDF5 "all" selection into an MPI type. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection @@ -105,16 +132,11 @@ H5S_mpio_set_bigio_count(hsize_t new_count) * *is_derived_type 0 if MPI primitive type, 1 if derived * * Programmer: rky 980813 - * Modifications: - * Mohamad Chaarawi - * Adding support for large datatypes (beyond the limit of a - * 32 bit integer. - * * *------------------------------------------------------------------------- */ static herr_t -H5S_mpio_all_type(const H5S_t *space, size_t elmt_size, +H5S__mpio_all_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { hsize_t total_bytes; @@ -122,7 +144,7 @@ H5S_mpio_all_type(const H5S_t *space, size_t elmt_size, hsize_t nelmts; /* Total number of elmts */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(space); @@ -133,34 +155,33 @@ H5S_mpio_all_type(const H5S_t *space, size_t elmt_size, H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t); total_bytes = (hsize_t)elmt_size * nelmts; + /* Verify that the size can be expressed as a 32 bit integer */ if(bigio_count >= total_bytes) { - /* fill in the return values */ - *new_type = MPI_BYTE; - H5_CHECKED_ASSIGN(*count, int, total_bytes, hsize_t); - *is_derived_type = FALSE; - } + /* fill in the return values */ + *new_type = MPI_BYTE; + H5_CHECKED_ASSIGN(*count, int, total_bytes, hsize_t); + *is_derived_type = FALSE; + } /* end if */ else { - /* Create a LARGE derived datatype for this transfer */ - if (H5S_mpio_create_large_type (total_bytes, 0, MPI_BYTE, new_type) < 0) { - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, - "couldn't create a large datatype from the all selection") - } - *count = 1; - *is_derived_type = TRUE; - } + /* Create a LARGE derived datatype for this transfer */ + if(H5S__mpio_create_large_type(total_bytes, 0, MPI_BYTE, new_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large datatype from the all selection") + *count = 1; + *is_derived_type = TRUE; + } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_mpio_all_type() */ +} /* H5S__mpio_all_type() */ /*------------------------------------------------------------------------- - * Function: H5S_mpio_none_type + * Function: H5S__mpio_none_type * * Purpose: Translate an HDF5 "none" selection into an MPI type. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection @@ -172,9 +193,9 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) +H5S__mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* fill in the return values */ *new_type = MPI_BYTE; @@ -182,15 +203,15 @@ H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) *is_derived_type = FALSE; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_mpio_none_type() */ +} /* H5S__mpio_none_type() */ /*------------------------------------------------------------------------- - * Function: H5S_mpio_create_point_datatype + * Function: H5S__mpio_create_point_datatype * * Purpose: Create a derived datatype for point selections. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * @@ -198,18 +219,23 @@ H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) * *------------------------------------------------------------------------- */ -static herr_t -H5S_mpio_create_point_datatype (size_t elmt_size, hsize_t num_points, - MPI_Aint *disp, MPI_Datatype *new_type) +static herr_t +H5S__mpio_create_point_datatype(size_t elmt_size, hsize_t num_points, + MPI_Aint *disp, MPI_Datatype *new_type) { MPI_Datatype elmt_type; /* MPI datatype for individual element */ hbool_t elmt_type_created = FALSE; /* Whether the element MPI datatype was created */ - int mpi_code; /* MPI error code */ + int *inner_blocks = NULL; /* Arrays for MPI datatypes when "large" datatype needed */ + MPI_Aint *inner_disps = NULL; + MPI_Datatype *inner_types = NULL; +#if MPI_VERSION < 3 int *blocks = NULL; /* Array of block sizes for MPI hindexed create call */ hsize_t u; /* Local index variable */ +#endif + int mpi_code; /* MPI error code */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Create an MPI datatype for an element */ if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type))) @@ -219,146 +245,127 @@ H5S_mpio_create_point_datatype (size_t elmt_size, hsize_t num_points, /* Check whether standard or BIGIO processing will be employeed */ if(bigio_count >= num_points) { #if MPI_VERSION >= 3 - /* Create an MPI datatype for the whole point selection */ - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block((int)num_points, 1, disp, elmt_type, new_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_indexed_block failed", mpi_code) + /* Create an MPI datatype for the whole point selection */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block((int)num_points, 1, disp, elmt_type, new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_indexed_block failed", mpi_code) #else - /* Allocate block sizes for MPI datatype call */ - if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * num_points))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") + /* Allocate block sizes for MPI datatype call */ + if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") - for(u = 0; u < num_points; u++) - blocks[u] = 1; + for(u = 0; u < num_points; u++) + blocks[u] = 1; - /* Create an MPI datatype for the whole point selection */ - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_points, blocks, disp, elmt_type, new_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) + /* Create an MPI datatype for the whole point selection */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_points, blocks, disp, elmt_type, new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) #endif - /* Commit MPI datatype for later use */ - if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) - } - else { - /* use LARGE_DATATYPE:: - * We'll create an hindexed_block type for every 2G point count and then combine - * those and any remaining points into a single large datatype. - */ - int total_types, i; - int remaining_points; - int num_big_types; - hsize_t leftover; - - int *inner_blocks; - MPI_Aint *inner_disps; - MPI_Datatype *inner_types = NULL; + /* Commit MPI datatype for later use */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + } /* end if */ + else { + /* use LARGE_DATATYPE:: + * We'll create an hindexed_block type for every 2G point count and then combine + * those and any remaining points into a single large datatype. + */ + int total_types, i; + int remaining_points; + int num_big_types; + hsize_t leftover; - /* Calculate how many Big MPI datatypes are needed to represent the buffer */ - num_big_types = (int)(num_points/bigio_count); + /* Calculate how many Big MPI datatypes are needed to represent the buffer */ + num_big_types = (int)(num_points / bigio_count); - leftover = (hsize_t)num_points - (hsize_t)num_big_types * (hsize_t)bigio_count; - H5_CHECKED_ASSIGN(remaining_points, int, leftover, hsize_t); + leftover = (hsize_t)num_points - (hsize_t)num_big_types * (hsize_t)bigio_count; + H5_CHECKED_ASSIGN(remaining_points, int, leftover, hsize_t); - total_types = (int)(remaining_points) ? (num_big_types + 1) : num_big_types; + total_types = (int)(remaining_points) ? (num_big_types + 1) : num_big_types; - /* Allocate array if MPI derived types needed */ - if(NULL == (inner_types = (MPI_Datatype *)H5MM_malloc((sizeof(MPI_Datatype) * (size_t)total_types)))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") + /* Allocate array if MPI derived types needed */ + if(NULL == (inner_types = (MPI_Datatype *)H5MM_malloc((sizeof(MPI_Datatype) * (size_t)total_types)))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") - if(NULL == (inner_blocks = (int *)H5MM_malloc(sizeof(int) * (size_t)total_types))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") + if(NULL == (inner_blocks = (int *)H5MM_malloc(sizeof(int) * (size_t)total_types))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") - if(NULL == (inner_disps = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * (size_t)total_types))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") + if(NULL == (inner_disps = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * (size_t)total_types))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") #if MPI_VERSION < 3 - /* Allocate block sizes for MPI datatype call */ - if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * bigio_count))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") + /* Allocate block sizes for MPI datatype call */ + if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * bigio_count))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") - for(u = 0; u < bigio_count; u++) - blocks[u] = 1; + for(u = 0; u < bigio_count; u++) + blocks[u] = 1; #endif - for(i=0 ; i<num_big_types ; i++) { + for(i = 0; i < num_big_types; i++) { #if MPI_VERSION >= 3 - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block(bigio_count, - 1, - &disp[i*bigio_count], - elmt_type, - &inner_types[i]))) { - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code); - } + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block(bigio_count, + 1, &disp[i*bigio_count], elmt_type, &inner_types[i]))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code) #else - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)bigio_count, - blocks, - &disp[i*bigio_count], - elmt_type, - &inner_types[i]))) { - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) - } + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)bigio_count, + blocks, &disp[i*bigio_count], elmt_type, &inner_types[i]))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) #endif - inner_blocks[i] = 1; - inner_disps[i] = 0; - } + inner_blocks[i] = 1; + inner_disps[i] = 0; + } /* end for*/ - if(remaining_points) { + if(remaining_points) { #if MPI_VERSION >= 3 - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block(remaining_points, - 1, - &disp[num_big_types*bigio_count], - elmt_type, - &inner_types[num_big_types]))) { - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code); - } + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block(remaining_points, + 1, &disp[num_big_types*bigio_count], elmt_type, &inner_types[num_big_types]))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code) #else - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)remaining_points, - blocks, - &disp[num_big_types*bigio_count], - elmt_type, - &inner_types[num_big_types]))) { - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) - } + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)remaining_points, + blocks, &disp[num_big_types*bigio_count], elmt_type, &inner_types[num_big_types]))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) #endif - inner_blocks[num_big_types] = 1; - inner_disps[num_big_types] = 0; - } - - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(total_types, - inner_blocks, - inner_disps, - inner_types, - new_type))) { - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct", mpi_code); - } - for(i=0 ; i<total_types ; i++) - MPI_Type_free(&inner_types[i]); - - H5MM_free(inner_types); - H5MM_free(inner_blocks); - H5MM_free(inner_disps); - - /* Commit MPI datatype for later use */ - if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) - } + inner_blocks[num_big_types] = 1; + inner_disps[num_big_types] = 0; + } /* end if */ + + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(total_types, + inner_blocks, inner_disps, inner_types, new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct", mpi_code) + for(i = 0; i < total_types; i++) + MPI_Type_free(&inner_types[i]); + + /* Commit MPI datatype for later use */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + } /* end else */ + done: if(elmt_type_created) MPI_Type_free(&elmt_type); +#if MPI_VERSION < 3 if(blocks) H5MM_free(blocks); +#endif + if(inner_types) + H5MM_free(inner_types); + if(inner_blocks) + H5MM_free(inner_blocks); + if(inner_disps) + H5MM_free(inner_disps); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_mpio_create_point_datatype() */ +} /* H5S__mpio_create_point_datatype() */ /*------------------------------------------------------------------------- - * Function: H5S_mpio_point_type + * Function: H5S__mpio_point_type * * Purpose: Translate an HDF5 "point" selection into an MPI type. * Create a permutation array to handle out-of-order point selections. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection @@ -373,7 +380,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, +H5S__mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute, hbool_t *is_permuted) { @@ -384,7 +391,7 @@ H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type hsize_t u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(space); @@ -406,23 +413,23 @@ H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type /* Iterate through list of elements */ curr = space->select.sel_info.pnt_lst->head; for(u = 0 ; u < num_points ; u++) { - /* calculate the displacement of the current point */ + /* Calculate the displacement of the current point */ disp[u] = H5VM_array_offset(space->extent.rank, space->extent.size, curr->pnt); disp[u] *= elmt_size; - /* This is a File Space used to set the file view, so adjust the displacements + /* This is a File Space used to set the file view, so adjust the displacements * to have them monotonically non-decreasing. - * Generate the permutation array by indicating at each point being selected, - * the position it will shifted in the new displacement. Example: - * Suppose 4 points with corresponding are selected - * Pt 1: disp=6 ; Pt 2: disp=3 ; Pt 3: disp=0 ; Pt 4: disp=4 + * Generate the permutation array by indicating at each point being selected, + * the position it will shifted in the new displacement. Example: + * Suppose 4 points with corresponding are selected + * Pt 1: disp=6 ; Pt 2: disp=3 ; Pt 3: disp=0 ; Pt 4: disp=4 * The permute map to sort the displacements in order will be: * point 1: map[0] = L, indicating that this point is not moved (1st point selected) - * point 2: map[1] = 0, indicating that this point is moved to the first position, + * point 2: map[1] = 0, indicating that this point is moved to the first position, * since disp_pt1(6) > disp_pt2(3) - * point 3: map[2] = 0, move to position 0, bec it has the lowest disp between + * point 3: map[2] = 0, move to position 0, bec it has the lowest disp between * the points selected so far. - * point 4: map[3] = 2, move the 2nd position since point 1 has a higher disp, + * point 4: map[3] = 2, move the 2nd position since point 1 has a higher disp, * but points 2 and 3 have lower displacements. */ if(do_permute) { @@ -447,7 +454,7 @@ H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type HDmemmove(disp + m + 1, disp + m, (u - m) * sizeof(MPI_Aint)); disp[m] = temp; } /* end if */ - (*permute)[u] = m; + (*permute)[u] = m; } /* end if */ else (*permute)[u] = num_points; @@ -455,7 +462,7 @@ H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type /* this is a memory space, and no permutation is necessary to create the derived datatype */ else { - ;/* do nothing */ + ; /* do nothing */ } /* end else */ /* get the next point */ @@ -463,7 +470,7 @@ H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type } /* end for */ /* Create the MPI datatype for the set of element displacements */ - if(H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) + if(H5S__mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") /* Set values about MPI datatype created */ @@ -481,11 +488,11 @@ done: } /* end if */ FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_mpio_point_type() */ +} /* H5S__mpio_point_type() */ /*------------------------------------------------------------------------- - * Function: H5S_mpio_permute_type + * Function: H5S__mpio_permute_type * * Purpose: Translate an HDF5 "all/hyper/point" selection into an MPI type, * while applying the permutation map. This function is called if @@ -496,7 +503,7 @@ done: * Note: This routine is called from H5S_mpio_space_type(), which is * called first for the file dataspace and creates * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection @@ -508,7 +515,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, +H5S__mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { MPI_Aint *disp = NULL; /* Datatype displacement for each point*/ @@ -520,7 +527,7 @@ H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, hsize_t u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(space); @@ -571,12 +578,12 @@ H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, /* Set the displacement of the current point */ disp[u] = curr_off; - /* This is a memory displacement, so for each point selected, + /* This is a memory displacement, so for each point selected, * apply the map that was generated by the file selection */ if((*permute)[u] != num_points) { MPI_Aint temp = disp[u]; - HDmemmove(disp + (*permute)[u] + 1, disp + (*permute)[u], + HDmemmove(disp + (*permute)[u] + 1, disp + (*permute)[u], (u - (*permute)[u]) * sizeof(MPI_Aint)); disp[(*permute)[u]] = temp; } /* end if */ @@ -597,7 +604,7 @@ H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, } /* end while */ /* Create the MPI datatype for the set of element displacements */ - if(H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) + if(H5S__mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") /* Set values about MPI datatype created */ @@ -619,15 +626,15 @@ done: } /* end if */ FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_mpio_permute_type() */ +} /* H5S__mpio_permute_type() */ /*------------------------------------------------------------------------- - * Function: H5S_mpio_hyper_type + * Function: H5S__mpio_reg_hyper_type * - * Purpose: Translate an HDF5 hyperslab selection into an MPI type. + * Purpose: Translate a regular HDF5 hyperslab selection into an MPI type. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection @@ -635,14 +642,11 @@ done: * *is_derived_type 0 if MPI primitive type, 1 if derived * * Programmer: rky 980813 - * Modifications: - * Mohamad Chaarawi - * Adding support for large datatypes (beyond the limit of a - * 32 bit integer. + * *------------------------------------------------------------------------- */ static herr_t -H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, +H5S__mpio_reg_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { H5S_sel_iter_t sel_iter; /* Selection iteration info */ @@ -668,7 +672,7 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, int mpi_code; /* MPI return code */ herr_t ret_value = SUCCEED; - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(space); @@ -683,16 +687,15 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, diminfo = sel_iter.u.hyp.diminfo; HDassert(diminfo); - /* make a local copy of the dimension info so we can operate with them */ + /* Make a local copy of the dimension info so we can operate with them */ /* Check if this is a "flattened" regular hyperslab selection */ if(sel_iter.u.hyp.iter_rank != 0 && sel_iter.u.hyp.iter_rank < space->extent.rank) { /* Flattened selection */ rank = sel_iter.u.hyp.iter_rank; - HDassert(rank <= H5S_MAX_RANK); /* within array bounds */ #ifdef H5S_DEBUG - if(H5DEBUG(S)) - HDfprintf(H5DEBUG(S), "%s: Flattened selection\n",FUNC); +if(H5DEBUG(S)) + HDfprintf(H5DEBUG(S), "%s: Flattened selection\n",FUNC); #endif for(u = 0; u < rank; ++u) { H5_CHECK_OVERFLOW(diminfo[u].start, hsize_t, hssize_t) @@ -701,33 +704,30 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, d[u].block = diminfo[u].block; d[u].count = diminfo[u].count; d[u].xtent = sel_iter.u.hyp.size[u]; + #ifdef H5S_DEBUG - if(H5DEBUG(S)){ - HDfprintf(H5DEBUG(S), "%s: start=%Hd stride=%Hu count=%Hu block=%Hu xtent=%Hu", - FUNC, d[u].start, d[u].strid, d[u].count, d[u].block, d[u].xtent ); - if (u==0) - HDfprintf(H5DEBUG(S), " rank=%u\n", rank ); - else - HDfprintf(H5DEBUG(S), "\n" ); - } +if(H5DEBUG(S)) { + HDfprintf(H5DEBUG(S), "%s: start=%Hd stride=%Hu count=%Hu block=%Hu xtent=%Hu", + FUNC, d[u].start, d[u].strid, d[u].count, d[u].block, d[u].xtent); + if(u == 0) + HDfprintf(H5DEBUG(S), " rank=%u\n", rank); + else + HDfprintf(H5DEBUG(S), "\n"); +} #endif - if(0 == d[u].block) - goto empty; - if(0 == d[u].count) - goto empty; - if(0 == d[u].xtent) - goto empty; + + /* Sanity check */ + HDassert(d[u].block > 0); + HDassert(d[u].count > 0); + HDassert(d[u].xtent > 0); } /* end for */ } /* end if */ else { /* Non-flattened selection */ rank = space->extent.rank; - HDassert(rank <= H5S_MAX_RANK); /* within array bounds */ - if(0 == rank) - goto empty; #ifdef H5S_DEBUG - if(H5DEBUG(S)) - HDfprintf(H5DEBUG(S),"%s: Non-flattened selection\n",FUNC); +if(H5DEBUG(S)) + HDfprintf(H5DEBUG(S),"%s: Non-flattened selection\n",FUNC); #endif for(u = 0; u < rank; ++u) { H5_CHECK_OVERFLOW(diminfo[u].start, hsize_t, hssize_t) @@ -736,22 +736,22 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, d[u].block = diminfo[u].block; d[u].count = diminfo[u].count; d[u].xtent = space->extent.size[u]; + #ifdef H5S_DEBUG - if(H5DEBUG(S)){ +if(H5DEBUG(S)) { HDfprintf(H5DEBUG(S), "%s: start=%Hd stride=%Hu count=%Hu block=%Hu xtent=%Hu", - FUNC, d[u].start, d[u].strid, d[u].count, d[u].block, d[u].xtent ); - if (u==0) - HDfprintf(H5DEBUG(S), " rank=%u\n", rank ); + FUNC, d[u].start, d[u].strid, d[u].count, d[u].block, d[u].xtent); + if(u == 0) + HDfprintf(H5DEBUG(S), " rank=%u\n", rank); else - HDfprintf(H5DEBUG(S), "\n" ); - } + HDfprintf(H5DEBUG(S), "\n"); +} #endif - if(0 == d[u].block) - goto empty; - if(0 == d[u].count) - goto empty; - if(0 == d[u].xtent) - goto empty; + + /* Sanity check */ + HDassert(d[u].block > 0); + HDassert(d[u].count > 0); + HDassert(d[u].xtent > 0); } /* end for */ } /* end else */ @@ -762,56 +762,52 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, offset[rank - 1] = 1; max_xtent[rank - 1] = d[rank - 1].xtent; #ifdef H5S_DEBUG - if(H5DEBUG(S)) { - i = ((int)rank) - 1; - HDfprintf(H5DEBUG(S), " offset[%2d]=%Hu; max_xtent[%2d]=%Hu\n", - i, offset[i], i, max_xtent[i]); - } +if(H5DEBUG(S)) { + i = ((int)rank) - 1; + HDfprintf(H5DEBUG(S), " offset[%2d]=%Hu; max_xtent[%2d]=%Hu\n", i, offset[i], i, max_xtent[i]); +} #endif for(i = ((int)rank) - 2; i >= 0; --i) { offset[i] = offset[i + 1] * d[i + 1].xtent; max_xtent[i] = max_xtent[i + 1] * d[i].xtent; #ifdef H5S_DEBUG - if(H5DEBUG(S)) - HDfprintf(H5DEBUG(S), " offset[%2d]=%Hu; max_xtent[%2d]=%Hu\n", - i, offset[i], i, max_xtent[i]); +if(H5DEBUG(S)) + HDfprintf(H5DEBUG(S), " offset[%2d]=%Hu; max_xtent[%2d]=%Hu\n", i, offset[i], i, max_xtent[i]); #endif } /* end for */ /* Create a type covering the selected hyperslab. * Multidimensional dataspaces are stored in row-major order. * The type is built from the inside out, going from the - * fastest-changing (i.e., inner) dimension * to the slowest (outer). */ + * fastest-changing (i.e., inner) dimension * to the slowest (outer). + */ /******************************************************* * Construct contig type for inner contig dims: *******************************************************/ #ifdef H5S_DEBUG - if(H5DEBUG(S)) { +if(H5DEBUG(S)) { HDfprintf(H5DEBUG(S), "%s: Making contig type %Zu MPI_BYTEs\n", FUNC, elmt_size); for(i = ((int)rank) - 1; i >= 0; --i) HDfprintf(H5DEBUG(S), "d[%d].xtent=%Hu \n", i, d[i].xtent); - } +} #endif /* LARGE_DATATYPE:: - * Check if the number of elements to form the inner type fits into a 32 bit integer. + * Check if the number of elements to form the inner type fits into a 32 bit integer. * If yes then just create the innertype with MPI_Type_contiguous. * Otherwise create a compound datatype by iterating as many times as needed * for the innertype to be created. */ if(bigio_count >= elmt_size) { - /* Use a single MPI datatype that has a 32 bit size */ - if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &inner_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - } - else { - /* Create the compound datatype for this operation (> 2GB) */ - if (H5S_mpio_create_large_type (elmt_size, 0, MPI_BYTE, &inner_type) < 0) { - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, - "couldn't ccreate a large inner datatype in hyper selection") - } - } + /* Use a single MPI datatype that has a 32 bit size */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &inner_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) + } /* end if */ + else + /* Create the compound datatype for this operation (> 2GB) */ + if(H5S__mpio_create_large_type(elmt_size, 0, MPI_BYTE, &inner_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large inner datatype in hyper selection") /******************************************************* * Construct the type by walking the hyperslab dims @@ -819,65 +815,57 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, *******************************************************/ for(i = ((int)rank) - 1; i >= 0; --i) { #ifdef H5S_DEBUG - if(H5DEBUG(S)) - HDfprintf(H5DEBUG(S), "%s: Dimension i=%d \n" - "start=%Hd count=%Hu block=%Hu stride=%Hu, xtent=%Hu max_xtent=%d\n", - FUNC, i, d[i].start, d[i].count, d[i].block, d[i].strid, d[i].xtent, max_xtent[i]); +if(H5DEBUG(S)) + HDfprintf(H5DEBUG(S), "%s: Dimension i=%d \n" + "start=%Hd count=%Hu block=%Hu stride=%Hu, xtent=%Hu max_xtent=%d\n", + FUNC, i, d[i].start, d[i].count, d[i].block, d[i].strid, d[i].xtent, max_xtent[i]); #endif #ifdef H5S_DEBUG - if(H5DEBUG(S)) - HDfprintf(H5DEBUG(S), "%s: i=%d Making vector-type \n", FUNC,i); +if(H5DEBUG(S)) + HDfprintf(H5DEBUG(S), "%s: i=%d Making vector-type \n", FUNC,i); #endif /**************************************** - * Build vector type of the selection. - ****************************************/ - if (bigio_count >= d[i].count && - bigio_count >= d[i].block && - bigio_count >= d[i].strid) { - - /* All the parameters fit into 32 bit integers so create the vector type normally */ - mpi_code = MPI_Type_vector((int)(d[i].count), /* count */ - (int)(d[i].block), /* blocklength */ - (int)(d[i].strid), /* stride */ - inner_type, /* old type */ - &outer_type); /* new type */ - - MPI_Type_free(&inner_type); - if(mpi_code != MPI_SUCCESS) - HMPI_GOTO_ERROR(FAIL, "couldn't create MPI vector type", mpi_code) - } + * Build vector type of the selection. + ****************************************/ + if(bigio_count >= d[i].count && + bigio_count >= d[i].block && bigio_count >= d[i].strid) { + /* All the parameters fit into 32 bit integers so create the vector type normally */ + mpi_code = MPI_Type_vector((int)(d[i].count), /* count */ + (int)(d[i].block), /* blocklength */ + (int)(d[i].strid), /* stride */ + inner_type, /* old type */ + &outer_type); /* new type */ + + MPI_Type_free(&inner_type); + if(mpi_code != MPI_SUCCESS) + HMPI_GOTO_ERROR(FAIL, "couldn't create MPI vector type", mpi_code) + } /* end if */ else { - /* Things get a bit more complicated and require LARGE_DATATYPE processing - * There are two MPI datatypes that need to be created: - * 1) an internal contiguous block; and - * 2) a collection of elements where an element is a contiguous block(1). - * Remember that the input arguments to the MPI-IO functions use integer - * values to represent element counts. We ARE allowed however, in the - * more recent MPI implementations to use constructed datatypes whereby - * the total number of bytes in a transfer could be : - * (2GB-1)number_of_blocks * the_datatype_extent. - */ + /* Things get a bit more complicated and require LARGE_DATATYPE processing + * There are two MPI datatypes that need to be created: + * 1) an internal contiguous block; and + * 2) a collection of elements where an element is a contiguous block(1). + * Remember that the input arguments to the MPI-IO functions use integer + * values to represent element counts. We ARE allowed however, in the + * more recent MPI implementations to use constructed datatypes whereby + * the total number of bytes in a transfer could be : + * (2GB-1)number_of_blocks * the_datatype_extent. + */ MPI_Aint stride_in_bytes, inner_extent; MPI_Datatype block_type; - /* create a contiguous datatype inner_type x number of BLOCKS. - * Again we need to check that the number of BLOCKS can fit into + /* Create a contiguous datatype inner_type x number of BLOCKS. + * Again we need to check that the number of BLOCKS can fit into * a 32 bit integer */ - if (bigio_count < d[i].block) { - if (H5S_mpio_create_large_type(d[i].block, 0, inner_type, - &block_type) < 0) { - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, - "couldn't ccreate a large block datatype in hyper selection") - } - } - else { - if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)d[i].block, - inner_type, - &block_type))) + if(bigio_count < d[i].block) { + if(H5S__mpio_create_large_type(d[i].block, 0, inner_type, &block_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large block datatype in hyper selection") + } /* end if */ + else + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)d[i].block, inner_type, &block_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - } /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default, * so we're using the MPI-2 version even though we don't need the lb @@ -892,40 +880,38 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, /* If the element count is larger than what a 32 bit integer can hold, * we call the large type creation function to handle that */ - if (bigio_count < d[i].count) { - if (H5S_mpio_create_large_type (d[i].count, stride_in_bytes, block_type, - &outer_type) < 0) { - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, - "couldn't create a large outer datatype in hyper selection") - } - } + if(bigio_count < d[i].count) { + if(H5S__mpio_create_large_type(d[i].count, stride_in_bytes, block_type, &outer_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large outer datatype in hyper selection") + } /* end if */ /* otherwise a regular create_hvector will do */ - else { - mpi_code = MPI_Type_create_hvector((int)d[i].count, /* count */ - 1, /* blocklength */ - stride_in_bytes, /* stride in bytes*/ - block_type, /* old type */ - &outer_type); /* new type */ - if(MPI_SUCCESS != mpi_code) + else + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector((int)d[i].count, /* count */ + 1, /* blocklength */ + stride_in_bytes, /* stride in bytes*/ + block_type, /* old type */ + &outer_type))) /* new type */ HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) - } + MPI_Type_free(&block_type); MPI_Type_free(&inner_type); - } - /**************************************** - * Then build the dimension type as (start, vector type, xtent). - ****************************************/ - /* calculate start and extent values of this dimension */ + } /* end else */ + + /**************************************** + * Then build the dimension type as (start, vector type, xtent). + ****************************************/ + + /* Calculate start and extent values of this dimension */ start_disp = d[i].start * offset[i] * elmt_size; new_extent = (MPI_Aint)elmt_size * max_xtent[i]; if(MPI_SUCCESS != (mpi_code = MPI_Type_get_extent(outer_type, &lb, &extent_len))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_get_extent failed", mpi_code) /************************************************* - * Restructure this datatype ("outer_type") - * so that it still starts at 0, but its extent - * is the full extent in this dimension. - *************************************************/ + * Restructure this datatype ("outer_type") + * so that it still starts at 0, but its extent + * is the full extent in this dimension. + *************************************************/ if(start_disp > 0 || extent_len < new_extent) { MPI_Datatype interm_type; int block_len = 1; @@ -957,13 +943,6 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, /* fill in the remaining return values */ *count = 1; /* only have to move one of these suckers! */ *is_derived_type = TRUE; - HGOTO_DONE(SUCCEED); - -empty: - /* special case: empty hyperslab */ - *new_type = MPI_BYTE; - *count = 0; - *is_derived_type = FALSE; done: /* Release selection iterator */ @@ -972,21 +951,20 @@ done: HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") #ifdef H5S_DEBUG - if(H5DEBUG(S)) - HDfprintf(H5DEBUG(S), "Leave %s, count=%ld is_derived_type=%t\n", - FUNC, *count, *is_derived_type ); +if(H5DEBUG(S)) + HDfprintf(H5DEBUG(S), "Leave %s, count=%ld is_derived_type=%t\n", FUNC, *count, *is_derived_type); #endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_mpio_hyper_type() */ +} /* end H5S__mpio_reg_hyper_type() */ /*------------------------------------------------------------------------- - * Function: H5S_mpio_span_hyper_type + * Function: H5S__mpio_span_hyper_type * * Purpose: Translate an HDF5 irregular hyperslab selection into an MPI type. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection @@ -995,14 +973,10 @@ done: * * Programmer: kyang * - * Modifications: - * Mohamad Chaarawi - * Adding support for large datatypes (beyond the limit of a - * 32 bit integer. *------------------------------------------------------------------------- */ static herr_t -H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, +H5S__mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { MPI_Datatype elmt_type; /* MPI datatype for an element */ @@ -1012,7 +986,7 @@ H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, int mpi_code; /* MPI return code */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(space); @@ -1021,17 +995,13 @@ H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, HDassert(space->select.sel_info.hslab->span_lst->head); /* Create the base type for an element */ - if (bigio_count >= elmt_size) { - if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type))) { - HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - } - } - else { - if (H5S_mpio_create_large_type (elmt_size, 0, MPI_BYTE, &elmt_type) < 0) { - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, - "couldn't create a large element datatype in span_hyper selection") - } - } + if(bigio_count >= elmt_size) { + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) + } /* end if */ + else + if(H5S__mpio_create_large_type(elmt_size, 0, MPI_BYTE, &elmt_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large element datatype in span_hyper selection") elmt_type_is_derived = TRUE; /* Compute 'down' sizes for each dimension */ @@ -1039,8 +1009,8 @@ H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGETSIZE, FAIL, "couldn't compute 'down' dimension sizes") /* Obtain derived data type */ - if(H5S_obtain_datatype(down, space->select.sel_info.hslab->span_lst->head, &elmt_type, &span_type, elmt_size) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't obtain MPI derived data type") + if(H5S__obtain_datatype(down, space->select.sel_info.hslab->span_lst->head, &elmt_type, &span_type, elmt_size) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't obtain MPI derived data type") if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&span_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) *new_type = span_type; @@ -1056,16 +1026,15 @@ done: HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_mpio_span_hyper_type() */ +} /* end H5S__mpio_span_hyper_type() */ /*------------------------------------------------------------------------- - * Function: H5S_obtain_datatype + * Function: H5S__obtain_datatype * - * Purpose: Obtain an MPI derived datatype based on span-tree - * implementation + * Purpose: Obtain an MPI derived datatype for span-tree hyperslab selection * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *span_type the MPI type corresponding to the selection * @@ -1074,11 +1043,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5S_obtain_datatype(const hsize_t *down, H5S_hyper_span_t *span, +H5S__obtain_datatype(const hsize_t *down, H5S_hyper_span_t *span, const MPI_Datatype *elmt_type, MPI_Datatype *span_type, size_t elmt_size) { size_t alloc_count = 0; /* Number of span tree nodes allocated at this level */ - size_t outercount = 0; /* Number of span tree nodes at this level */ + size_t outercount; /* Number of span tree nodes at this level */ MPI_Datatype *inner_type = NULL; hbool_t inner_types_freed = FALSE; /* Whether the inner_type MPI datatypes have been freed */ hbool_t span_type_valid = FALSE; /* Whether the span_type MPI datatypes is valid */ @@ -1089,7 +1058,7 @@ H5S_obtain_datatype(const hsize_t *down, H5S_hyper_span_t *span, int mpi_code; /* MPI return status code */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Sanity check */ HDassert(span); @@ -1129,16 +1098,14 @@ H5S_obtain_datatype(const hsize_t *down, H5S_hyper_span_t *span, blocklen[outercount] = (int)tspan->nelem; tspan = tspan->next; - if (bigio_count < blocklen[outercount]) { + if(bigio_count < blocklen[outercount]) large_block = TRUE; /* at least one block type is large, so set this flag to true */ - } outercount++; } /* end while */ /* Everything fits into integers, so cast them and use hindexed */ - if (bigio_count >= outercount && large_block == FALSE) { - + if(bigio_count >= outercount && large_block == FALSE) { if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)outercount, blocklen, disp, *elmt_type, span_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) span_type_valid = TRUE; @@ -1150,7 +1117,7 @@ H5S_obtain_datatype(const hsize_t *down, H5S_hyper_span_t *span, MPI_Datatype temp_type = MPI_DATATYPE_NULL, outer_type = MPI_DATATYPE_NULL; /* create the block type from elmt_type while checking the 32 bit int limit */ if (blocklen[i] > bigio_count) { - if (H5S_mpio_create_large_type (blocklen[i], 0, *elmt_type, &temp_type) < 0) { + if (H5S__mpio_create_large_type (blocklen[i], 0, *elmt_type, &temp_type) < 0) { HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large element datatype in span_hyper selection") } @@ -1233,7 +1200,7 @@ H5S_obtain_datatype(const hsize_t *down, H5S_hyper_span_t *span, blocklen[outercount] = 1; /* Generate MPI datatype for next dimension down */ - if(H5S_obtain_datatype(down + 1, tspan->down->head, elmt_type, &down_type, elmt_size) < 0) + if(H5S__obtain_datatype(down + 1, tspan->down->head, elmt_type, &down_type, elmt_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't obtain MPI derived data type") /* Build the MPI datatype for this node */ @@ -1291,7 +1258,7 @@ done: } /* end if */ FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_obtain_datatype() */ +} /* end H5S__obtain_datatype() */ /*------------------------------------------------------------------------- @@ -1300,7 +1267,7 @@ done: * Purpose: Translate an HDF5 dataspace selection into an MPI type. * Currently handle only hyperslab and "all" selections. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection @@ -1312,7 +1279,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, +H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute_map, hbool_t *is_permuted) { @@ -1333,10 +1300,10 @@ H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type * out-of-order point selection, then permute this selection which * should be a memory selection to match the file space permutation. */ - if(TRUE == *is_permuted) { + if(TRUE == *is_permuted) { switch(H5S_GET_SELECT_TYPE(space)) { case H5S_SEL_NONE: - if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) + if(H5S__mpio_none_type(new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'none' selection to MPI type") break; @@ -1346,7 +1313,7 @@ H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type /* Sanity check */ HDassert(!do_permute); - if(H5S_mpio_permute_type(space, elmt_size, permute_map, new_type, count, is_derived_type) < 0) + if(H5S__mpio_permute_type(space, elmt_size, permute_map, new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'all' selection to MPI type") break; @@ -1361,29 +1328,28 @@ H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type else { switch(H5S_GET_SELECT_TYPE(space)) { case H5S_SEL_NONE: - if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) + if(H5S__mpio_none_type(new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'none' selection to MPI type") break; case H5S_SEL_ALL: - if(H5S_mpio_all_type(space, elmt_size, new_type, count, is_derived_type) < 0) + if(H5S__mpio_all_type(space, elmt_size, new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'all' selection to MPI type") break; case H5S_SEL_POINTS: - if(H5S_mpio_point_type(space, elmt_size, new_type, count, is_derived_type, do_permute, permute_map, is_permuted) < 0) + if(H5S__mpio_point_type(space, elmt_size, new_type, count, is_derived_type, do_permute, permute_map, is_permuted) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'point' selection to MPI type") break; case H5S_SEL_HYPERSLABS: if((H5S_SELECT_IS_REGULAR(space) == TRUE)) { - if(H5S_mpio_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) + if(H5S__mpio_reg_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert regular 'hyperslab' selection to MPI type") } /* end if */ - else { - if(H5S_mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) + else + if(H5S__mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert irregular 'hyperslab' selection to MPI type") - } /* end else */ break; case H5S_SEL_ERROR: @@ -1407,12 +1373,12 @@ done: /*------------------------------------------------------------------------- - * Function: H5S_mpio_create_large_type + * Function: H5S__mpio_create_large_type * - * Purpose: Create a large datatype of size larger than what a 32 bit integer + * Purpose: Create a large datatype of size larger than what a 32 bit integer * can hold. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * *new_type the new datatype created * @@ -1420,10 +1386,9 @@ done: * *------------------------------------------------------------------------- */ -static herr_t H5S_mpio_create_large_type (hsize_t num_elements, - MPI_Aint stride_bytes, - MPI_Datatype old_type, - MPI_Datatype *new_type) +static herr_t +H5S__mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, + MPI_Datatype old_type, MPI_Datatype *new_type) { int num_big_types; /* num times the 2G datatype will be repeated */ int remaining_bytes; /* the number of bytes left that can be held in an int value */ @@ -1434,7 +1399,7 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements, MPI_Aint disp[2], old_extent; herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Calculate how many Big MPI datatypes are needed to represent the buffer */ num_big_types = (int)(num_elements/bigio_count); @@ -1447,41 +1412,23 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements, * use type_hvector to create the type with the displacement provided */ if (0 == stride_bytes) { - if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(bigio_count, - old_type, - &inner_type))) { + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(bigio_count, old_type, &inner_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - } - } - else { - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector (bigio_count, - 1, - stride_bytes, - old_type, - &inner_type))) { + } /* end if */ + else + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector(bigio_count, 1, stride_bytes, old_type, &inner_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) - } - } /* Create a contiguous datatype of the buffer (minus the remaining < 2GB part) * If a stride is present, use hvector type */ - if (0 == stride_bytes) { - if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(num_big_types, - inner_type, - &outer_type))) { + if(0 == stride_bytes) { + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(num_big_types, inner_type, &outer_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - } - } - else { - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector (num_big_types, - 1, - stride_bytes, - inner_type, - &outer_type))) { + } /* end if */ + else + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector(num_big_types, 1, stride_bytes, inner_type, &outer_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) - } - } MPI_Type_free(&inner_type); @@ -1489,23 +1436,13 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements, * use a struct datatype to encapsulate everything. */ if(remaining_bytes) { - if (stride_bytes == 0) { - if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous (remaining_bytes, - old_type, - &leftover_type))) { + if(stride_bytes == 0) { + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(remaining_bytes, old_type, &leftover_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - } - } - else { - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector - ((int)(num_elements - (hsize_t)num_big_types*bigio_count), - 1, - stride_bytes, - old_type, - &leftover_type))) { + } /* end if */ + else + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector((int)(num_elements - (hsize_t)num_big_types * bigio_count), 1, stride_bytes, old_type, &leftover_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) - } - } /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default, * so we're using the MPI-2 version even though we don't need the lb @@ -1522,28 +1459,25 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements, block_len[0] = 1; block_len[1] = 1; disp[0] = 0; - disp[1] = (old_extent+stride_bytes)*num_big_types*(MPI_Aint)bigio_count; + disp[1] = (old_extent + stride_bytes) * num_big_types * (MPI_Aint)bigio_count; - if(MPI_SUCCESS != (mpi_code = - MPI_Type_create_struct(2, block_len, disp, type, new_type))) { + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(2, block_len, disp, type, new_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) - } MPI_Type_free(&outer_type); MPI_Type_free(&leftover_type); - } - else { + } /* end if */ + else /* There are no remaining bytes so just set the new type to * the outer type created */ *new_type = outer_type; - } if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_mpio_create_large_type */ +} /* end H5S__mpio_create_large_type() */ #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Snone.c b/src/H5Snone.c index a8aaf7e..86994dd 100644 --- a/src/H5Snone.c +++ b/src/H5Snone.c @@ -18,166 +18,197 @@ * Purpose: "None" selection dataspace I/O functions. */ +/****************/ +/* Module Setup */ +/****************/ + #include "H5Smodule.h" /* This source code file is part of the H5S module */ -#include "H5private.h" -#include "H5Eprivate.h" -#include "H5Iprivate.h" -#include "H5Spkg.h" -#include "H5VMprivate.h" -#include "H5Dprivate.h" +/***********/ +/* Headers */ +/***********/ +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Iprivate.h" /* ID Functions */ +#include "H5Spkg.h" /* Dataspace functions */ +#include "H5VMprivate.h" /* Vector functions */ + + +/****************/ +/* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ -/* Static function prototypes */ + +/********************/ +/* Local Prototypes */ +/********************/ /* Selection callbacks */ -static herr_t H5S_none_copy(H5S_t *dst, const H5S_t *src, hbool_t share_selection); -static herr_t H5S_none_get_seq_list(const H5S_t *space, unsigned flags, +static herr_t H5S__none_copy(H5S_t *dst, const H5S_t *src, hbool_t share_selection); +static herr_t H5S__none_get_seq_list(const H5S_t *space, unsigned flags, H5S_sel_iter_t *iter, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len); -static herr_t H5S_none_release(H5S_t *space); -static htri_t H5S_none_is_valid(const H5S_t *space); -static hssize_t H5S_none_serial_size(const H5S_t *space); -static herr_t H5S_none_serialize(const H5S_t *space, uint8_t **p); -static herr_t H5S_none_deserialize(H5S_t *space, uint32_t version, uint8_t flags, +static herr_t H5S__none_release(H5S_t *space); +static htri_t H5S__none_is_valid(const H5S_t *space); +static hssize_t H5S__none_serial_size(const H5S_t *space); +static herr_t H5S__none_serialize(const H5S_t *space, uint8_t **p); +static herr_t H5S__none_deserialize(H5S_t *space, uint32_t version, uint8_t flags, const uint8_t **p); -static herr_t H5S_none_bounds(const H5S_t *space, hsize_t *start, hsize_t *end); -static herr_t H5S_none_offset(const H5S_t *space, hsize_t *off); +static herr_t H5S__none_bounds(const H5S_t *space, hsize_t *start, hsize_t *end); +static herr_t H5S__none_offset(const H5S_t *space, hsize_t *off); static int H5S__none_unlim_dim(const H5S_t *space); -static htri_t H5S_none_is_contiguous(const H5S_t *space); -static htri_t H5S_none_is_single(const H5S_t *space); -static htri_t H5S_none_is_regular(const H5S_t *space); -static herr_t H5S_none_adjust_u(H5S_t *space, const hsize_t *offset); -static herr_t H5S_none_project_scalar(const H5S_t *space, hsize_t *offset); -static herr_t H5S_none_project_simple(const H5S_t *space, H5S_t *new_space, hsize_t *offset); -static herr_t H5S_none_iter_init(H5S_sel_iter_t *iter, const H5S_t *space); +static htri_t H5S__none_is_contiguous(const H5S_t *space); +static htri_t H5S__none_is_single(const H5S_t *space); +static htri_t H5S__none_is_regular(const H5S_t *space); +static herr_t H5S__none_adjust_u(H5S_t *space, const hsize_t *offset); +static herr_t H5S__none_project_scalar(const H5S_t *space, hsize_t *offset); +static herr_t H5S__none_project_simple(const H5S_t *space, H5S_t *new_space, hsize_t *offset); +static herr_t H5S__none_iter_init(H5S_sel_iter_t *iter, const H5S_t *space); /* Selection iteration callbacks */ -static herr_t H5S_none_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords); -static herr_t H5S_none_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); -static hsize_t H5S_none_iter_nelmts(const H5S_sel_iter_t *iter); -static htri_t H5S_none_iter_has_next_block(const H5S_sel_iter_t *iter); -static herr_t H5S_none_iter_next(H5S_sel_iter_t *sel_iter, size_t nelem); -static herr_t H5S_none_iter_next_block(H5S_sel_iter_t *sel_iter); -static herr_t H5S_none_iter_release(H5S_sel_iter_t *sel_iter); +static herr_t H5S__none_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords); +static herr_t H5S__none_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); +static hsize_t H5S__none_iter_nelmts(const H5S_sel_iter_t *iter); +static htri_t H5S__none_iter_has_next_block(const H5S_sel_iter_t *iter); +static herr_t H5S__none_iter_next(H5S_sel_iter_t *sel_iter, size_t nelem); +static herr_t H5S__none_iter_next_block(H5S_sel_iter_t *sel_iter); +static herr_t H5S__none_iter_release(H5S_sel_iter_t *sel_iter); + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*********************/ +/* Package Variables */ +/*********************/ /* Selection properties for "none" selections */ const H5S_select_class_t H5S_sel_none[1] = {{ H5S_SEL_NONE, /* Methods on selection */ - H5S_none_copy, - H5S_none_get_seq_list, - H5S_none_release, - H5S_none_is_valid, - H5S_none_serial_size, - H5S_none_serialize, - H5S_none_deserialize, - H5S_none_bounds, - H5S_none_offset, + H5S__none_copy, + H5S__none_get_seq_list, + H5S__none_release, + H5S__none_is_valid, + H5S__none_serial_size, + H5S__none_serialize, + H5S__none_deserialize, + H5S__none_bounds, + H5S__none_offset, H5S__none_unlim_dim, NULL, - H5S_none_is_contiguous, - H5S_none_is_single, - H5S_none_is_regular, - H5S_none_adjust_u, - H5S_none_project_scalar, - H5S_none_project_simple, - H5S_none_iter_init, + H5S__none_is_contiguous, + H5S__none_is_single, + H5S__none_is_regular, + H5S__none_adjust_u, + H5S__none_project_scalar, + H5S__none_project_simple, + H5S__none_iter_init, }}; + +/*******************/ +/* Local Variables */ +/*******************/ + /* Iteration properties for "none" selections */ static const H5S_sel_iter_class_t H5S_sel_iter_none[1] = {{ H5S_SEL_NONE, /* Methods on selection iterator */ - H5S_none_iter_coords, - H5S_none_iter_block, - H5S_none_iter_nelmts, - H5S_none_iter_has_next_block, - H5S_none_iter_next, - H5S_none_iter_next_block, - H5S_none_iter_release, + H5S__none_iter_coords, + H5S__none_iter_block, + H5S__none_iter_nelmts, + H5S__none_iter_has_next_block, + H5S__none_iter_next, + H5S__none_iter_next_block, + H5S__none_iter_release, }}; + /*------------------------------------------------------------------------- - * Function: H5S_none_iter_init + * Function: H5S__none_iter_init * * Purpose: Initializes iteration information for "none" selection. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Tuesday, June 16, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ static herr_t -H5S_none_iter_init(H5S_sel_iter_t *iter, const H5S_t H5_ATTR_UNUSED *space) +H5S__none_iter_init(H5S_sel_iter_t *iter, const H5S_t H5_ATTR_UNUSED *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ - HDassert(space && H5S_SEL_NONE==H5S_GET_SELECT_TYPE(space)); + HDassert(space && H5S_SEL_NONE == H5S_GET_SELECT_TYPE(space)); HDassert(iter); /* Initialize type of selection iterator */ iter->type = H5S_sel_iter_none; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_none_iter_init() */ +} /* end H5S__none_iter_init() */ /*------------------------------------------------------------------------- - * Function: H5S_none_iter_coords + * Function: H5S__none_iter_coords * * Purpose: Retrieve the current coordinates of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, April 22, 2003 * - * Modifications: - * *------------------------------------------------------------------------- */ static herr_t -H5S_none_iter_coords(const H5S_sel_iter_t H5_ATTR_UNUSED *iter, hsize_t H5_ATTR_UNUSED *coords) +H5S__none_iter_coords(const H5S_sel_iter_t H5_ATTR_UNUSED *iter, + hsize_t H5_ATTR_UNUSED *coords) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); HDassert(coords); FUNC_LEAVE_NOAPI(FAIL) -} /* H5S_none_iter_coords() */ +} /* end H5S__none_iter_coords() */ /*------------------------------------------------------------------------- - * Function: H5S_none_iter_block + * Function: H5S__none_iter_block * * Purpose: Retrieve the current block of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Monday, June 2, 2003 * - * Modifications: - * *------------------------------------------------------------------------- */ static herr_t -H5S_none_iter_block(const H5S_sel_iter_t H5_ATTR_UNUSED *iter, hsize_t H5_ATTR_UNUSED *start, hsize_t H5_ATTR_UNUSED *end) +H5S__none_iter_block(const H5S_sel_iter_t H5_ATTR_UNUSED *iter, + hsize_t H5_ATTR_UNUSED *start, hsize_t H5_ATTR_UNUSED *end) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); @@ -185,42 +216,40 @@ H5S_none_iter_block(const H5S_sel_iter_t H5_ATTR_UNUSED *iter, hsize_t H5_ATTR_U HDassert(end); FUNC_LEAVE_NOAPI(FAIL) -} /* H5S_none_iter_block() */ +} /* end H5S__none_iter_block() */ /*------------------------------------------------------------------------- - * Function: H5S_none_iter_nelmts + * Function: H5S__none_iter_nelmts * * Purpose: Return number of elements left to process in iterator * - * Return: non-negative number of elements on success, zero on failure + * Return: Non-negative number of elements on success, zero on failure * * Programmer: Quincey Koziol * Tuesday, June 16, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ static hsize_t -H5S_none_iter_nelmts(const H5S_sel_iter_t H5_ATTR_UNUSED *iter) +H5S__none_iter_nelmts(const H5S_sel_iter_t H5_ATTR_UNUSED *iter) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); FUNC_LEAVE_NOAPI(0) -} /* H5S_none_iter_nelmts() */ +} /* end H5S__none_iter_nelmts() */ /*-------------------------------------------------------------------------- NAME - H5S_none_iter_has_next_block + H5S__none_iter_has_next_block PURPOSE Check if there is another block left in the current iterator USAGE - htri_t H5S_none_iter_has_next_block(iter) + htri_t H5S__none_iter_has_next_block(iter) const H5S_sel_iter_t *iter; IN: Pointer to selection iterator RETURNS Non-negative (TRUE/FALSE) on success/Negative on failure @@ -232,24 +261,24 @@ H5S_none_iter_nelmts(const H5S_sel_iter_t H5_ATTR_UNUSED *iter) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_none_iter_has_next_block(const H5S_sel_iter_t H5_ATTR_UNUSED *iter) +H5S__none_iter_has_next_block(const H5S_sel_iter_t H5_ATTR_UNUSED *iter) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); FUNC_LEAVE_NOAPI(FAIL) -} /* H5S_none_iter_has_next_block() */ +} /* end H5S__none_iter_has_next_block() */ /*-------------------------------------------------------------------------- NAME - H5S_none_iter_next + H5S__none_iter_next PURPOSE Increment selection iterator USAGE - herr_t H5S_none_iter_next(iter, nelem) + herr_t H5S__none_iter_next(iter, nelem) H5S_sel_iter_t *iter; IN: Pointer to selection iterator size_t nelem; IN: Number of elements to advance by RETURNS @@ -262,25 +291,25 @@ H5S_none_iter_has_next_block(const H5S_sel_iter_t H5_ATTR_UNUSED *iter) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_iter_next(H5S_sel_iter_t H5_ATTR_UNUSED *iter, size_t H5_ATTR_UNUSED nelem) +H5S__none_iter_next(H5S_sel_iter_t H5_ATTR_UNUSED *iter, size_t H5_ATTR_UNUSED nelem) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); - HDassert(nelem>0); + HDassert(nelem > 0); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_none_iter_next() */ +} /* end H5S__none_iter_next() */ /*-------------------------------------------------------------------------- NAME - H5S_none_iter_next_block + H5S__none_iter_next_block PURPOSE Increment selection iterator to next block USAGE - herr_t H5S_none_iter_next(iter) + herr_t H5S__none_iter_next(iter) H5S_sel_iter_t *iter; IN: Pointer to selection iterator RETURNS Non-negative on success/Negative on failure @@ -292,24 +321,82 @@ H5S_none_iter_next(H5S_sel_iter_t H5_ATTR_UNUSED *iter, size_t H5_ATTR_UNUSED ne REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_iter_next_block(H5S_sel_iter_t H5_ATTR_UNUSED *iter) +H5S__none_iter_next_block(H5S_sel_iter_t H5_ATTR_UNUSED *iter) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); FUNC_LEAVE_NOAPI(FAIL) -} /* H5S_none_iter_next_block() */ +} /* end H5S__none_iter_next_block() */ /*-------------------------------------------------------------------------- NAME - H5S_none_iter_release + H5S__none_get_seq_list + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S__none_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + unsigned flags; IN: Flags for extra information about operation + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxelem; IN: Maximum number of elements to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nelem; OUT: Actual number of elements in sequences generated + hsize_t *off; OUT: Array of offsets + size_t *len; OUT: Array of lengths + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S__none_get_seq_list(const H5S_t H5_ATTR_UNUSED *space, unsigned H5_ATTR_UNUSED flags, H5S_sel_iter_t H5_ATTR_UNUSED *iter, + size_t H5_ATTR_UNUSED maxseq, size_t H5_ATTR_UNUSED maxelem, size_t *nseq, size_t *nelem, + hsize_t H5_ATTR_UNUSED *off, size_t H5_ATTR_UNUSED *len) +{ + FUNC_ENTER_STATIC_NOERR + + /* Check args */ + HDassert(space); + HDassert(iter); + HDassert(maxseq > 0); + HDassert(maxelem > 0); + HDassert(nseq); + HDassert(nelem); + HDassert(off); + HDassert(len); + + /* "none" selections don't generate sequences of bytes */ + *nseq = 0; + + /* They don't use any elements, either */ + *nelem = 0; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5S__none_get_seq_list() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S__none_iter_release PURPOSE Release "none" selection iterator information for a dataspace USAGE - herr_t H5S_none_iter_release(iter) + herr_t H5S__none_iter_release(iter) H5S_sel_iter_t *iter; IN: Pointer to selection iterator RETURNS Non-negative on success/Negative on failure @@ -321,24 +408,24 @@ H5S_none_iter_next_block(H5S_sel_iter_t H5_ATTR_UNUSED *iter) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_iter_release(H5S_sel_iter_t H5_ATTR_UNUSED * iter) +H5S__none_iter_release(H5S_sel_iter_t H5_ATTR_UNUSED *iter) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_none_iter_release() */ +} /* end H5S__none_iter_release() */ /*-------------------------------------------------------------------------- NAME - H5S_none_release + H5S__none_release PURPOSE Release none selection information for a dataspace USAGE - herr_t H5S_none_release(space) + herr_t H5S__none_release(space) H5S_t *space; IN: Pointer to dataspace RETURNS Non-negative on success/Negative on failure @@ -350,26 +437,27 @@ H5S_none_iter_release(H5S_sel_iter_t H5_ATTR_UNUSED * iter) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_release(H5S_t H5_ATTR_UNUSED * space) +H5S__none_release(H5S_t H5_ATTR_UNUSED *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_none_release() */ +} /* end H5S__none_release() */ /*-------------------------------------------------------------------------- NAME - H5S_none_copy + H5S__none_copy PURPOSE Copy a selection from one dataspace to another USAGE - herr_t H5S_none_copy(dst, src) + herr_t H5S__none_copy(dst, src, share_selection) H5S_t *dst; OUT: Pointer to the destination dataspace H5S_t *src; IN: Pointer to the source dataspace + hbool_t; IN: Whether to share the selection between the dataspaces RETURNS Non-negative on success/Negative on failure DESCRIPTION @@ -381,9 +469,10 @@ H5S_none_release(H5S_t H5_ATTR_UNUSED * space) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_copy(H5S_t *dst, const H5S_t H5_ATTR_UNUSED *src, hbool_t H5_ATTR_UNUSED share_selection) +H5S__none_copy(H5S_t *dst, const H5S_t H5_ATTR_UNUSED *src, + hbool_t H5_ATTR_UNUSED share_selection) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(src); HDassert(dst); @@ -392,17 +481,17 @@ H5S_none_copy(H5S_t *dst, const H5S_t H5_ATTR_UNUSED *src, hbool_t H5_ATTR_UNUSE dst->select.num_elem = 0; FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5S_none_copy() */ +} /* end H5S__none_copy() */ /*-------------------------------------------------------------------------- NAME - H5S_none_is_valid + H5S__none_is_valid PURPOSE Check whether the selection fits within the extent, with the current offset defined. USAGE - htri_t H5S_none_is_valid(space); + htri_t H5S__none_is_valid(space); H5S_t *space; IN: Dataspace pointer to query RETURNS TRUE if the selection fits within the extent, FALSE if it does not and @@ -416,24 +505,24 @@ H5S_none_copy(H5S_t *dst, const H5S_t H5_ATTR_UNUSED *src, hbool_t H5_ATTR_UNUSE REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_none_is_valid(const H5S_t H5_ATTR_UNUSED *space) +H5S__none_is_valid(const H5S_t H5_ATTR_UNUSED *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); FUNC_LEAVE_NOAPI(TRUE) -} /* end H5S_none_is_valid() */ +} /* end H5S__none_is_valid() */ /*-------------------------------------------------------------------------- NAME - H5S_none_serial_size + H5S__none_serial_size PURPOSE Determine the number of bytes needed to store the serialized "none" selection information. USAGE - hssize_t H5S_none_serial_size(space) + hssize_t H5S__none_serial_size(space) H5S_t *space; IN: Dataspace pointer to query RETURNS The number of bytes required on success, negative on an error. @@ -446,9 +535,9 @@ H5S_none_is_valid(const H5S_t H5_ATTR_UNUSED *space) REVISION LOG --------------------------------------------------------------------------*/ static hssize_t -H5S_none_serial_size(const H5S_t H5_ATTR_UNUSED *space) +H5S__none_serial_size(const H5S_t H5_ATTR_UNUSED *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); @@ -457,16 +546,16 @@ H5S_none_serial_size(const H5S_t H5_ATTR_UNUSED *space) * <length (4 bytes)> = 16 bytes */ FUNC_LEAVE_NOAPI(16) -} /* end H5S_none_serial_size() */ +} /* end H5S__none_serial_size() */ /*-------------------------------------------------------------------------- NAME - H5S_none_serialize + H5S__none_serialize PURPOSE Serialize the current selection into a user-provided buffer. USAGE - herr_t H5S_none_serialize(space, p) + herr_t H5S__none_serialize(space, p) const H5S_t *space; IN: Dataspace with selection to serialize uint8_t **p; OUT: Pointer to buffer to put serialized selection. Will be advanced to end of @@ -482,11 +571,11 @@ H5S_none_serial_size(const H5S_t H5_ATTR_UNUSED *space) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_serialize(const H5S_t *space, uint8_t **p) +H5S__none_serialize(const H5S_t *space, uint8_t **p) { uint8_t *pp = (*p); /* Local pointer for decoding */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space); @@ -503,16 +592,16 @@ H5S_none_serialize(const H5S_t *space, uint8_t **p) *p = pp; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_none_serialize() */ +} /* end H5S__none_serialize() */ /*-------------------------------------------------------------------------- NAME - H5S_none_deserialize + H5S__none_deserialize PURPOSE Deserialize the current selection from a user-provided buffer. USAGE - herr_t H5S_none_deserialize(space, version, flags, p) + herr_t H5S__none_deserialize(space, version, flags, p) H5S_t *space; IN/OUT: Dataspace pointer to place selection into uint32_t version IN: Selection version @@ -531,12 +620,12 @@ H5S_none_serialize(const H5S_t *space, uint8_t **p) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t H5_ATTR_UNUSED flags, - const uint8_t H5_ATTR_UNUSED **p) +H5S__none_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, + uint8_t H5_ATTR_UNUSED flags, const uint8_t H5_ATTR_UNUSED **p) { herr_t ret_value = SUCCEED; /* return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC HDassert(space); HDassert(p); @@ -548,16 +637,16 @@ H5S_none_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t H5_A done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_none_deserialize() */ +} /* end H5S__none_deserialize() */ /*-------------------------------------------------------------------------- NAME - H5S_none_bounds + H5S__none_bounds PURPOSE Gets the bounding box containing the selection. USAGE - herr_t H5S_none_bounds(space, start, end) + herr_t H5S__none_bounds(space, start, end) H5S_t *space; IN: Dataspace pointer of selection to query hsize_t *start; OUT: Starting coordinate of bounding box hsize_t *end; OUT: Opposite coordinate of bounding box @@ -577,25 +666,26 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_bounds(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSED *start, hsize_t H5_ATTR_UNUSED *end) +H5S__none_bounds(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSED *start, + hsize_t H5_ATTR_UNUSED *end) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); HDassert(start); HDassert(end); FUNC_LEAVE_NOAPI(FAIL) -} /* H5Sget_none_bounds() */ +} /* end H5Sget_none_bounds() */ /*-------------------------------------------------------------------------- NAME - H5S_none_offset + H5S__none_offset PURPOSE Gets the linear offset of the first element for the selection. USAGE - herr_t H5S_none_offset(space, offset) + herr_t H5S__none_offset(space, offset) const H5S_t *space; IN: Dataspace pointer of selection to query hsize_t *offset; OUT: Linear offset of first element in selection RETURNS @@ -610,15 +700,15 @@ H5S_none_bounds(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSED *start REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_offset(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSED *offset) +H5S__none_offset(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSED *offset) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); HDassert(offset); FUNC_LEAVE_NOAPI(FAIL) -} /* H5S_none_offset() */ +} /* end H5S__none_offset() */ /*-------------------------------------------------------------------------- @@ -651,11 +741,11 @@ H5S__none_unlim_dim(const H5S_t H5_ATTR_UNUSED *space) /*-------------------------------------------------------------------------- NAME - H5S_none_is_contiguous + H5S__none_is_contiguous PURPOSE Check if a "none" selection is contiguous within the dataspace extent. USAGE - htri_t H5S_none_is_contiguous(space) + htri_t H5S__none_is_contiguous(space) H5S_t *space; IN: Dataspace pointer to check RETURNS TRUE/FALSE/FAIL @@ -668,23 +758,23 @@ H5S__none_unlim_dim(const H5S_t H5_ATTR_UNUSED *space) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_none_is_contiguous(const H5S_t H5_ATTR_UNUSED *space) +H5S__none_is_contiguous(const H5S_t H5_ATTR_UNUSED *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); FUNC_LEAVE_NOAPI(FALSE) -} /* H5S_none_is_contiguous() */ +} /* end H5S__none_is_contiguous() */ /*-------------------------------------------------------------------------- NAME - H5S_none_is_single + H5S__none_is_single PURPOSE Check if a "none" selection is a single block within the dataspace extent. USAGE - htri_t H5S_none_is_single(space) + htri_t H5S__none_is_single(space) H5S_t *space; IN: Dataspace pointer to check RETURNS TRUE/FALSE/FAIL @@ -697,23 +787,23 @@ H5S_none_is_contiguous(const H5S_t H5_ATTR_UNUSED *space) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_none_is_single(const H5S_t H5_ATTR_UNUSED *space) +H5S__none_is_single(const H5S_t H5_ATTR_UNUSED *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); FUNC_LEAVE_NOAPI(FALSE) -} /* H5S_none_is_single() */ +} /* end H5S__none_is_single() */ /*-------------------------------------------------------------------------- NAME - H5S_none_is_regular + H5S__none_is_regular PURPOSE Check if a "none" selection is "regular" USAGE - htri_t H5S_none_is_regular(space) + htri_t H5S__none_is_regular(space) const H5S_t *space; IN: Dataspace pointer to check RETURNS TRUE/FALSE/FAIL @@ -727,15 +817,15 @@ H5S_none_is_single(const H5S_t H5_ATTR_UNUSED *space) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_none_is_regular(const H5S_t H5_ATTR_UNUSED *space) +H5S__none_is_regular(const H5S_t H5_ATTR_UNUSED *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space); FUNC_LEAVE_NOAPI(TRUE) -} /* H5S_none_is_regular() */ +} /* end H5S__none_is_regular() */ /*-------------------------------------------------------------------------- @@ -744,7 +834,7 @@ H5S_none_is_regular(const H5S_t H5_ATTR_UNUSED *space) PURPOSE Adjust an "none" selection by subtracting an offset USAGE - herr_t H5S_none_adjust_u(space, offset) + herr_t H5S__none_adjust_u(space, offset) H5S_t *space; IN/OUT: Pointer to dataspace to adjust const hsize_t *offset; IN: Offset to subtract RETURNS @@ -757,24 +847,24 @@ H5S_none_is_regular(const H5S_t H5_ATTR_UNUSED *space) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_none_adjust_u(H5S_t H5_ATTR_UNUSED *space, const hsize_t H5_ATTR_UNUSED *offset) +H5S__none_adjust_u(H5S_t H5_ATTR_UNUSED *space, const hsize_t H5_ATTR_UNUSED *offset) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space); HDassert(offset); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_none_adjust_u() */ +} /* end H5S__none_adjust_u() */ /*------------------------------------------------------------------------- - * Function: H5S_none_project_scalar + * Function: H5S__none_project_scalar * * Purpose: Projects a 'none' selection into a scalar dataspace * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -782,25 +872,25 @@ H5S_none_adjust_u(H5S_t H5_ATTR_UNUSED *space, const hsize_t H5_ATTR_UNUSED *off *------------------------------------------------------------------------- */ static herr_t -H5S_none_project_scalar(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSED *offset) +H5S__none_project_scalar(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSED *offset) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space && H5S_SEL_NONE == H5S_GET_SELECT_TYPE(space)); HDassert(offset); FUNC_LEAVE_NOAPI(FAIL) -} /* H5S_none_project_scalar() */ +} /* end H5S__none_project_scalar() */ /*------------------------------------------------------------------------- - * Function: H5S_none_project_simple + * Function: H5S__none_project_simple * * Purpose: Projects an 'none' selection onto/into a simple dataspace * of a different rank * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -808,11 +898,12 @@ H5S_none_project_scalar(const H5S_t H5_ATTR_UNUSED *space, hsize_t H5_ATTR_UNUSE *------------------------------------------------------------------------- */ static herr_t -H5S_none_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *offset) +H5S__none_project_simple(const H5S_t H5_ATTR_UNUSED *base_space, + H5S_t *new_space, hsize_t H5_ATTR_UNUSED *offset) { herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(base_space && H5S_SEL_NONE == H5S_GET_SELECT_TYPE(base_space)); @@ -825,7 +916,7 @@ H5S_none_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *offs done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_none_project_simple() */ +} /* end H5S__none_project_simple() */ /*-------------------------------------------------------------------------- @@ -867,7 +958,7 @@ H5S_select_none(H5S_t *space) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_none() */ +} /* end H5S_select_none() */ /*-------------------------------------------------------------------------- @@ -906,63 +997,5 @@ H5Sselect_none(hid_t spaceid) done: FUNC_LEAVE_API(ret_value) -} /* H5Sselect_none() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_none_get_seq_list - PURPOSE - Create a list of offsets & lengths for a selection - USAGE - herr_t H5S_none_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) - H5S_t *space; IN: Dataspace containing selection to use. - unsigned flags; IN: Flags for extra information about operation - H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last - position of interest in selection. - size_t maxseq; IN: Maximum number of sequences to generate - size_t maxelem; IN: Maximum number of elements to include in the - generated sequences - size_t *nseq; OUT: Actual number of sequences generated - size_t *nelem; OUT: Actual number of elements in sequences generated - hsize_t *off; OUT: Array of offsets - size_t *len; OUT: Array of lengths - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to generate a list of byte offsets and - lengths for the region(s) selected. Start/Restart from the position in the - ITER parameter. The number of sequences generated is limited by the MAXSEQ - parameter and the number of sequences actually generated is stored in the - NSEQ parameter. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S_none_get_seq_list(const H5S_t H5_ATTR_UNUSED *space, unsigned H5_ATTR_UNUSED flags, H5S_sel_iter_t H5_ATTR_UNUSED *iter, - size_t H5_ATTR_UNUSED maxseq, size_t H5_ATTR_UNUSED maxelem, size_t *nseq, size_t *nelem, - hsize_t H5_ATTR_UNUSED *off, size_t H5_ATTR_UNUSED *len) -{ - FUNC_ENTER_NOAPI_NOINIT_NOERR - - /* Check args */ - HDassert(space); - HDassert(iter); - HDassert(maxseq > 0); - HDassert(maxelem > 0); - HDassert(nseq); - HDassert(nelem); - HDassert(off); - HDassert(len); - - /* "none" selections don't generate sequences of bytes */ - *nseq = 0; - - /* They don't use any elements, either */ - *nelem = 0; - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5S_none_get_seq_list() */ +} /* end H5Sselect_none() */ diff --git a/src/H5Spkg.h b/src/H5Spkg.h index 9ad97dc..0575f03 100644 --- a/src/H5Spkg.h +++ b/src/H5Spkg.h @@ -26,8 +26,12 @@ #ifndef _H5Spkg_H #define _H5Spkg_H +/* Get package's private header */ #include "H5Sprivate.h" +/* Other private headers needed by this file */ +#include "H5Oprivate.h" /* Object headers */ + /* Flags to indicate special dataspace features are active */ #define H5S_VALID_MAX 0x01 #define H5S_VALID_PERM 0x02 @@ -77,6 +81,7 @@ struct H5S_extent_t { /* * Dataspace selection information */ + /* Node in point selection list (typedef'd in H5Sprivate.h) */ struct H5S_pnt_node_t { hsize_t *pnt; /* Pointer to a selected point */ @@ -88,9 +93,9 @@ typedef struct { H5S_pnt_node_t *head; /* Pointer to head of point list */ } H5S_pnt_list_t; -/* Information about new-style hyperslab spans */ +/* Information about hyperslab spans */ -/* Information a particular hyperslab span */ +/* Information a particular hyperslab span (typedef'd in H5Sprivate.h) */ struct H5S_hyper_span_t { hsize_t low, high; /* Low & high bounds of span */ hsize_t nelem; /* Number of elements in span (only needed during I/O) */ @@ -111,7 +116,7 @@ struct H5S_hyper_span_info_t { struct H5S_hyper_span_t *head; /* Pointer to list of spans in next dimension down */ }; -/* Information about new-style hyperslab selection */ +/* Information about 'diminfo' form of hyperslab selection */ typedef struct { hbool_t diminfo_valid; /* Whether the dataset has valid diminfo */ H5S_hyper_dim_t opt_diminfo[H5S_MAX_RANK]; /* per-dim selection info */ @@ -217,9 +222,11 @@ struct H5S_t { /* Selection iteration methods */ /* Method to retrieve the current coordinates of iterator for current selection */ -typedef herr_t (*H5S_sel_iter_coords_func_t)(const H5S_sel_iter_t *iter, hsize_t *coords); +typedef herr_t (*H5S_sel_iter_coords_func_t)(const H5S_sel_iter_t *iter, + hsize_t *coords); /* Method to retrieve the current block of iterator for current selection */ -typedef herr_t (*H5S_sel_iter_block_func_t)(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); +typedef herr_t (*H5S_sel_iter_block_func_t)(const H5S_sel_iter_t *iter, + hsize_t *start, hsize_t *end); /* Method to determine number of elements left in iterator for current selection */ typedef hsize_t (*H5S_sel_iter_nelmts_func_t)(const H5S_sel_iter_t *iter); /* Method to determine if there are more blocks left in the current selection */ @@ -269,19 +276,19 @@ H5_DLLVAR const H5S_select_class_t H5S_sel_point[1]; H5_DLLVAR const unsigned H5O_sdspace_ver_bounds[H5F_LIBVER_NBOUNDS]; /* Extent functions */ -H5_DLL herr_t H5S_extent_release(H5S_extent_t *extent); -H5_DLL herr_t H5S_extent_copy_real(H5S_extent_t *dst, const H5S_extent_t *src, +H5_DLL herr_t H5S__extent_release(H5S_extent_t *extent); +H5_DLL herr_t H5S__extent_copy_real(H5S_extent_t *dst, const H5S_extent_t *src, hbool_t copy_max); -/* Operations on selections */ +/* Operations on hyperslab selections */ H5_DLL herr_t H5S__hyper_project_intersection(const H5S_t *src_space, const H5S_t *dst_space, const H5S_t *src_intersect_space, H5S_t *proj_space); H5_DLL herr_t H5S__hyper_subtract(H5S_t *space, H5S_t *subtract_space); /* Testing functions */ #ifdef H5S_TESTING -H5_DLL htri_t H5S_select_shape_same_test(hid_t sid1, hid_t sid2); -H5_DLL htri_t H5S_get_rebuild_status_test(hid_t space_id); +H5_DLL htri_t H5S__select_shape_same_test(hid_t sid1, hid_t sid2); +H5_DLL htri_t H5S__get_rebuild_status_test(hid_t space_id); #endif /* H5S_TESTING */ #endif /*_H5Spkg_H*/ diff --git a/src/H5Spoint.c b/src/H5Spoint.c index aea7d5c..e62b48d 100644 --- a/src/H5Spoint.c +++ b/src/H5Spoint.c @@ -18,87 +18,124 @@ * Purpose: Point selection dataspace I/O functions. */ +/****************/ +/* Module Setup */ +/****************/ + #include "H5Smodule.h" /* This source code file is part of the H5S module */ -#include "H5private.h" /* Generic Functions */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5FLprivate.h" /* Free Lists */ -#include "H5Iprivate.h" /* ID Functions */ -#include "H5MMprivate.h" /* Memory Management functions */ -#include "H5Spkg.h" /* Dataspace functions */ -#include "H5VMprivate.h" /* Vector functions */ +/***********/ +/* Headers */ +/***********/ +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5Iprivate.h" /* ID Functions */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5Spkg.h" /* Dataspace functions */ +#include "H5VMprivate.h" /* Vector functions */ + + +/****************/ +/* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ -/* Static function prototypes */ + +/********************/ +/* Local Prototypes */ +/********************/ /* Selection callbacks */ -static herr_t H5S_point_copy(H5S_t *dst, const H5S_t *src, hbool_t share_selection); -static herr_t H5S_point_get_seq_list(const H5S_t *space, unsigned flags, +static herr_t H5S__point_copy(H5S_t *dst, const H5S_t *src, hbool_t share_selection); +static herr_t H5S__point_get_seq_list(const H5S_t *space, unsigned flags, H5S_sel_iter_t *iter, size_t maxseq, size_t maxbytes, size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len); -static herr_t H5S_point_release(H5S_t *space); -static htri_t H5S_point_is_valid(const H5S_t *space); -static hssize_t H5S_point_serial_size(const H5S_t *space); -static herr_t H5S_point_serialize(const H5S_t *space, uint8_t **p); -static herr_t H5S_point_deserialize(H5S_t *space, uint32_t version, uint8_t flags, +static herr_t H5S__point_release(H5S_t *space); +static htri_t H5S__point_is_valid(const H5S_t *space); +static hssize_t H5S__point_serial_size(const H5S_t *space); +static herr_t H5S__point_serialize(const H5S_t *space, uint8_t **p); +static herr_t H5S__point_deserialize(H5S_t *space, uint32_t version, uint8_t flags, const uint8_t **p); -static herr_t H5S_point_bounds(const H5S_t *space, hsize_t *start, hsize_t *end); -static herr_t H5S_point_offset(const H5S_t *space, hsize_t *off); +static herr_t H5S__point_bounds(const H5S_t *space, hsize_t *start, hsize_t *end); +static herr_t H5S__point_offset(const H5S_t *space, hsize_t *off); static int H5S__point_unlim_dim(const H5S_t *space); -static htri_t H5S_point_is_contiguous(const H5S_t *space); -static htri_t H5S_point_is_single(const H5S_t *space); -static htri_t H5S_point_is_regular(const H5S_t *space); -static herr_t H5S_point_adjust_u(H5S_t *space, const hsize_t *offset); -static herr_t H5S_point_project_scalar(const H5S_t *space, hsize_t *offset); -static herr_t H5S_point_project_simple(const H5S_t *space, H5S_t *new_space, hsize_t *offset); -static herr_t H5S_point_iter_init(H5S_sel_iter_t *iter, const H5S_t *space); +static htri_t H5S__point_is_contiguous(const H5S_t *space); +static htri_t H5S__point_is_single(const H5S_t *space); +static htri_t H5S__point_is_regular(const H5S_t *space); +static herr_t H5S__point_adjust_u(H5S_t *space, const hsize_t *offset); +static herr_t H5S__point_project_scalar(const H5S_t *space, hsize_t *offset); +static herr_t H5S__point_project_simple(const H5S_t *space, H5S_t *new_space, + hsize_t *offset); +static herr_t H5S__point_iter_init(H5S_sel_iter_t *iter, const H5S_t *space); /* Selection iteration callbacks */ -static herr_t H5S_point_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords); -static herr_t H5S_point_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); -static hsize_t H5S_point_iter_nelmts(const H5S_sel_iter_t *iter); -static htri_t H5S_point_iter_has_next_block(const H5S_sel_iter_t *iter); -static herr_t H5S_point_iter_next(H5S_sel_iter_t *sel_iter, size_t nelem); -static herr_t H5S_point_iter_next_block(H5S_sel_iter_t *sel_iter); -static herr_t H5S_point_iter_release(H5S_sel_iter_t *sel_iter); +static herr_t H5S__point_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords); +static herr_t H5S__point_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, + hsize_t *end); +static hsize_t H5S__point_iter_nelmts(const H5S_sel_iter_t *iter); +static htri_t H5S__point_iter_has_next_block(const H5S_sel_iter_t *iter); +static herr_t H5S__point_iter_next(H5S_sel_iter_t *sel_iter, size_t nelem); +static herr_t H5S__point_iter_next_block(H5S_sel_iter_t *sel_iter); +static herr_t H5S__point_iter_release(H5S_sel_iter_t *sel_iter); + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*********************/ +/* Package Variables */ +/*********************/ /* Selection properties for point selections */ const H5S_select_class_t H5S_sel_point[1] = {{ H5S_SEL_POINTS, /* Methods on selection */ - H5S_point_copy, - H5S_point_get_seq_list, - H5S_point_release, - H5S_point_is_valid, - H5S_point_serial_size, - H5S_point_serialize, - H5S_point_deserialize, - H5S_point_bounds, - H5S_point_offset, + H5S__point_copy, + H5S__point_get_seq_list, + H5S__point_release, + H5S__point_is_valid, + H5S__point_serial_size, + H5S__point_serialize, + H5S__point_deserialize, + H5S__point_bounds, + H5S__point_offset, H5S__point_unlim_dim, NULL, - H5S_point_is_contiguous, - H5S_point_is_single, - H5S_point_is_regular, - H5S_point_adjust_u, - H5S_point_project_scalar, - H5S_point_project_simple, - H5S_point_iter_init, + H5S__point_is_contiguous, + H5S__point_is_single, + H5S__point_is_regular, + H5S__point_adjust_u, + H5S__point_project_scalar, + H5S__point_project_simple, + H5S__point_iter_init, }}; + +/*******************/ +/* Local Variables */ +/*******************/ + /* Iteration properties for point selections */ static const H5S_sel_iter_class_t H5S_sel_iter_point[1] = {{ H5S_SEL_POINTS, /* Methods on selection iterator */ - H5S_point_iter_coords, - H5S_point_iter_block, - H5S_point_iter_nelmts, - H5S_point_iter_has_next_block, - H5S_point_iter_next, - H5S_point_iter_next_block, - H5S_point_iter_release, + H5S__point_iter_coords, + H5S__point_iter_block, + H5S__point_iter_nelmts, + H5S__point_iter_has_next_block, + H5S__point_iter_next, + H5S__point_iter_next_block, + H5S__point_iter_release, }}; /* Declare a free list to manage the H5S_pnt_node_t struct */ @@ -107,93 +144,88 @@ H5FL_DEFINE_STATIC(H5S_pnt_node_t); /* Declare a free list to manage the H5S_pnt_list_t struct */ H5FL_DEFINE_STATIC(H5S_pnt_list_t); + /*------------------------------------------------------------------------- - * Function: H5S_point_iter_init + * Function: H5S__point_iter_init * * Purpose: Initializes iteration information for point selection. * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Tuesday, June 16, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ static herr_t -H5S_point_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) +H5S__point_iter_init(H5S_sel_iter_t *iter, const H5S_t *space) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ - HDassert(space && H5S_SEL_POINTS==H5S_GET_SELECT_TYPE(space)); + HDassert(space && H5S_SEL_POINTS == H5S_GET_SELECT_TYPE(space)); HDassert(iter); /* Initialize the number of points to iterate over */ - iter->elmt_left=space->select.num_elem; + iter->elmt_left = space->select.num_elem; /* Start at the head of the list of points */ iter->u.pnt.curr=space->select.sel_info.pnt_lst->head; /* Initialize type of selection iterator */ - iter->type=H5S_sel_iter_point; + iter->type = H5S_sel_iter_point; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_iter_init() */ +} /* end H5S__point_iter_init() */ /*------------------------------------------------------------------------- - * Function: H5S_point_iter_coords + * Function: H5S__point_iter_coords * * Purpose: Retrieve the current coordinates of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Tuesday, April 22, 2003 * - * Modifications: - * *------------------------------------------------------------------------- */ static herr_t -H5S_point_iter_coords (const H5S_sel_iter_t *iter, hsize_t *coords) +H5S__point_iter_coords(const H5S_sel_iter_t *iter, hsize_t *coords) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); HDassert(coords); /* Copy the offset of the current point */ - HDmemcpy(coords,iter->u.pnt.curr->pnt,sizeof(hsize_t)*iter->rank); + H5MM_memcpy(coords, iter->u.pnt.curr->pnt, sizeof(hsize_t) * iter->rank); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_iter_coords() */ +} /* end H5S__point_iter_coords() */ /*------------------------------------------------------------------------- - * Function: H5S_point_iter_block + * Function: H5S__point_iter_block * * Purpose: Retrieve the current block of iterator for current * selection * - * Return: non-negative on success, negative on failure + * Return: Non-negative on success, negative on failure * * Programmer: Quincey Koziol * Monday, June 2, 2003 * - * Modifications: - * *------------------------------------------------------------------------- */ static herr_t -H5S_point_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) +H5S__point_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); @@ -201,46 +233,44 @@ H5S_point_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) HDassert(end); /* Copy the current point as a block */ - HDmemcpy(start,iter->u.pnt.curr->pnt,sizeof(hsize_t)*iter->rank); - HDmemcpy(end,iter->u.pnt.curr->pnt,sizeof(hsize_t)*iter->rank); + H5MM_memcpy(start, iter->u.pnt.curr->pnt, sizeof(hsize_t) * iter->rank); + H5MM_memcpy(end, iter->u.pnt.curr->pnt, sizeof(hsize_t) * iter->rank); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_iter_block() */ +} /* end H5S__point_iter_block() */ /*------------------------------------------------------------------------- - * Function: H5S_point_iter_nelmts + * Function: H5S__point_iter_nelmts * * Purpose: Return number of elements left to process in iterator * - * Return: non-negative number of elements on success, zero on failure + * Return: Non-negative number of elements on success, zero on failure * * Programmer: Quincey Koziol * Tuesday, June 16, 1998 * - * Modifications: - * *------------------------------------------------------------------------- */ static hsize_t -H5S_point_iter_nelmts (const H5S_sel_iter_t *iter) +H5S__point_iter_nelmts(const H5S_sel_iter_t *iter) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); FUNC_LEAVE_NOAPI(iter->elmt_left) -} /* H5S_point_iter_nelmts() */ +} /* end H5S__point_iter_nelmts() */ /*-------------------------------------------------------------------------- NAME - H5S_point_iter_has_next_block + H5S__point_iter_has_next_block PURPOSE Check if there is another block left in the current iterator USAGE - htri_t H5S_point_iter_has_next_block(iter) + htri_t H5S__point_iter_has_next_block(iter) const H5S_sel_iter_t *iter; IN: Pointer to selection iterator RETURNS Non-negative (TRUE/FALSE) on success/Negative on failure @@ -252,31 +282,31 @@ H5S_point_iter_nelmts (const H5S_sel_iter_t *iter) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_point_iter_has_next_block(const H5S_sel_iter_t *iter) +H5S__point_iter_has_next_block(const H5S_sel_iter_t *iter) { - htri_t ret_value=TRUE; /* Return value */ + htri_t ret_value = TRUE; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); /* Check if there is another point in the list */ - if(iter->u.pnt.curr->next==NULL) + if(iter->u.pnt.curr->next == NULL) HGOTO_DONE(FALSE); done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_iter_has_next_block() */ +} /* end H5S__point_iter_has_next_block() */ /*-------------------------------------------------------------------------- NAME - H5S_point_iter_next + H5S__point_iter_next PURPOSE Increment selection iterator USAGE - herr_t H5S_point_iter_next(iter, nelem) + herr_t H5S__point_iter_next(iter, nelem) H5S_sel_iter_t *iter; IN: Pointer to selection iterator size_t nelem; IN: Number of elements to advance by RETURNS @@ -289,31 +319,31 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_iter_next(H5S_sel_iter_t *iter, size_t nelem) +H5S__point_iter_next(H5S_sel_iter_t *iter, size_t nelem) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); - HDassert(nelem>0); + HDassert(nelem > 0); /* Increment the iterator */ - while(nelem>0) { - iter->u.pnt.curr=iter->u.pnt.curr->next; + while(nelem > 0) { + iter->u.pnt.curr = iter->u.pnt.curr->next; nelem--; } /* end while */ FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_iter_next() */ +} /* end H5S__point_iter_next() */ /*-------------------------------------------------------------------------- NAME - H5S_point_iter_next_block + H5S__point_iter_next_block PURPOSE Increment selection iterator to next block USAGE - herr_t H5S_point_iter_next_block(iter) + herr_t H5S__point_iter_next_block(iter) H5S_sel_iter_t *iter; IN: Pointer to selection iterator RETURNS Non-negative on success/Negative on failure @@ -325,27 +355,165 @@ H5S_point_iter_next(H5S_sel_iter_t *iter, size_t nelem) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_iter_next_block(H5S_sel_iter_t *iter) +H5S__point_iter_next_block(H5S_sel_iter_t *iter) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); /* Increment the iterator */ - iter->u.pnt.curr=iter->u.pnt.curr->next; + iter->u.pnt.curr = iter->u.pnt.curr->next; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_iter_next_block() */ +} /* end H5S__point_iter_next_block() */ + + +/*-------------------------------------------------------------------------- + NAME + H5S__point_get_seq_list + PURPOSE + Create a list of offsets & lengths for a selection + USAGE + herr_t H5S__point_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) + H5S_t *space; IN: Dataspace containing selection to use. + unsigned flags; IN: Flags for extra information about operation + H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last + position of interest in selection. + size_t maxseq; IN: Maximum number of sequences to generate + size_t maxelem; IN: Maximum number of elements to include in the + generated sequences + size_t *nseq; OUT: Actual number of sequences generated + size_t *nelem; OUT: Actual number of elements in sequences generated + hsize_t *off; OUT: Array of offsets (in bytes) + size_t *len; OUT: Array of lengths (in bytes) + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to generate a list of byte offsets and + lengths for the region(s) selected. Start/Restart from the position in the + ITER parameter. The number of sequences generated is limited by the MAXSEQ + parameter and the number of sequences actually generated is stored in the + NSEQ parameter. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5S__point_get_seq_list(const H5S_t *space, unsigned flags, H5S_sel_iter_t *iter, + size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, + hsize_t *off, size_t *len) +{ + size_t io_left; /* The number of bytes left in the selection */ + size_t start_io_left; /* The initial number of bytes left in the selection */ + H5S_pnt_node_t *node; /* Point node */ + hsize_t dims[H5S_MAX_RANK]; /* Total size of memory buf */ + int ndims; /* Dimensionality of space*/ + hsize_t acc; /* Coordinate accumulator */ + hsize_t loc; /* Coordinate offset */ + size_t curr_seq; /* Current sequence being operated on */ + int i; /* Local index variable */ + herr_t ret_value = SUCCEED; /* return value */ + + FUNC_ENTER_STATIC + + /* Check args */ + HDassert(space); + HDassert(iter); + HDassert(maxseq > 0); + HDassert(maxelem > 0); + HDassert(nseq); + HDassert(nelem); + HDassert(off); + HDassert(len); + + /* Choose the minimum number of bytes to sequence through */ + H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); + start_io_left = io_left = (size_t)MIN(iter->elmt_left, maxelem); + + /* Get the dataspace dimensions */ + if((ndims = H5S_get_simple_extent_dims (space, dims, NULL)) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to retrieve dataspace dimensions") + + /* Walk through the points in the selection, starting at the current */ + /* location in the iterator */ + node = iter->u.pnt.curr; + curr_seq = 0; + while(NULL != node) { + /* Compute the offset of each selected point in the buffer */ + for(i = ndims - 1, acc = iter->elmt_size, loc = 0; i >= 0; i--) { + loc += (hsize_t)((hssize_t)node->pnt[i] + space->select.offset[i]) * acc; + acc *= dims[i]; + } /* end for */ + + /* Check if this is a later point in the selection */ + if(curr_seq > 0) { + /* If a sorted sequence is requested, make certain we don't go backwards in the offset */ + if((flags&H5S_GET_SEQ_LIST_SORTED) && loc<off[curr_seq-1]) + break; + + /* Check if this point extends the previous sequence */ + /* (Unlikely, but possible) */ + if(loc == (off[curr_seq - 1] + len[curr_seq - 1])) { + /* Extend the previous sequence */ + len[curr_seq - 1] += iter->elmt_size; + } /* end if */ + else { + /* Add a new sequence */ + off[curr_seq] = loc; + len[curr_seq] = iter->elmt_size; + + /* Increment sequence count */ + curr_seq++; + } /* end else */ + } /* end if */ + else { + /* Add a new sequence */ + off[curr_seq] = loc; + len[curr_seq] = iter->elmt_size; + + /* Increment sequence count */ + curr_seq++; + } /* end else */ + + /* Decrement number of elements left to process */ + io_left--; + + /* Move the iterator */ + iter->u.pnt.curr = node->next; + iter->elmt_left--; + + /* Check if we're finished with all sequences */ + if(curr_seq == maxseq) + break; + + /* Check if we're finished with all the elements available */ + if(io_left == 0) + break; + + /* Advance to the next point */ + node = node->next; + } /* end while */ + + /* Set the number of sequences generated */ + *nseq = curr_seq; + + /* Set the number of elements used */ + *nelem = start_io_left - io_left; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5S__point_get_seq_list() */ /*-------------------------------------------------------------------------- NAME - H5S_point_iter_release + H5S__point_iter_release PURPOSE Release point selection iterator information for a dataspace USAGE - herr_t H5S_point_iter_release(iter) + herr_t H5S__point_iter_release(iter) H5S_sel_iter_t *iter; IN: Pointer to selection iterator RETURNS Non-negative on success/Negative on failure @@ -357,24 +525,24 @@ H5S_point_iter_next_block(H5S_sel_iter_t *iter) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_iter_release (H5S_sel_iter_t H5_ATTR_UNUSED * iter) +H5S__point_iter_release(H5S_sel_iter_t H5_ATTR_UNUSED * iter) { - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(iter); FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_iter_release() */ +} /* end H5S__point_iter_release() */ /*-------------------------------------------------------------------------- NAME - H5S_point_add + H5S__point_add PURPOSE Add a series of elements to a point selection USAGE - herr_t H5S_point_add(space, num_elem, coord) + herr_t H5S__point_add(space, num_elem, coord) H5S_t *space; IN: Dataspace of selection to modify size_t num_elem; IN: Number of elements in COORD array. const hsize_t *coord[]; IN: The location of each element selected @@ -388,14 +556,15 @@ H5S_point_iter_release (H5S_sel_iter_t H5_ATTR_UNUSED * iter) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_add(H5S_t *space, H5S_seloper_t op, size_t num_elem, const hsize_t *coord) +H5S__point_add(H5S_t *space, H5S_seloper_t op, size_t num_elem, const hsize_t *coord) { H5S_pnt_node_t *top = NULL, *curr = NULL, *new_node = NULL; /* Point selection nodes */ unsigned u; /* Counter */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC + /* Sanity checks */ HDassert(space); HDassert(num_elem > 0); HDassert(coord); @@ -412,7 +581,7 @@ H5S_point_add(H5S_t *space, H5S_seloper_t op, size_t num_elem, const hsize_t *co HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate coordinate information") /* Copy over the coordinates */ - HDmemcpy(new_node->pnt, coord + (u * space->extent.rank), (space->extent.rank * sizeof(hsize_t))); + H5MM_memcpy(new_node->pnt, coord + (u * space->extent.rank), (space->extent.rank * sizeof(hsize_t))); /* Link into list */ if(top == NULL) @@ -469,16 +638,16 @@ done: } /* end if */ FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_add() */ +} /* end H5S__point_add() */ /*-------------------------------------------------------------------------- NAME - H5S_point_release + H5S__point_release PURPOSE Release point selection information for a dataspace USAGE - herr_t H5S_point_release(space) + herr_t H5S__point_release(space) H5S_t *space; IN: Pointer to dataspace RETURNS Non-negative on success/Negative on failure @@ -490,11 +659,11 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_release (H5S_t *space) +H5S__point_release(H5S_t *space) { H5S_pnt_node_t *curr, *next; /* Point selection nodes */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space); @@ -515,7 +684,7 @@ H5S_point_release (H5S_t *space) space->select.num_elem = 0; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_release() */ +} /* end H5S__point_release() */ /*-------------------------------------------------------------------------- @@ -539,10 +708,7 @@ H5S_point_release (H5S_t *space) array elements are iterated through when I/O is performed. Duplicate coordinates are not checked for. The selection operator, OP, determines how the new selection is to be combined with the existing selection for - the dataspace. Currently, only H5S_SELECT_SET is supported, which replaces - the existing selection with the one defined in this call. When operators - other than H5S_SELECT_SET are used to combine a new selection with an - existing selection, the selection ordering is reset to 'C' array ordering. + the dataspace. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES @@ -552,9 +718,9 @@ herr_t H5S_select_elements(H5S_t *space, H5S_seloper_t op, size_t num_elem, const hsize_t *coord) { - herr_t ret_value = SUCCEED; /* return value */ + herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_NOAPI(FAIL) /* Check args */ HDassert(space); @@ -573,7 +739,7 @@ H5S_select_elements(H5S_t *space, H5S_seloper_t op, size_t num_elem, HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate element information") /* Add points to selection */ - if(H5S_point_add(space, op, num_elem, coord) < 0) + if(H5S__point_add(space, op, num_elem, coord) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert elements") /* Set selection type */ @@ -581,18 +747,19 @@ H5S_select_elements(H5S_t *space, H5S_seloper_t op, size_t num_elem, done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_elements() */ +} /* end H5S_select_elements() */ /*-------------------------------------------------------------------------- NAME - H5S_point_copy + H5S__point_copy PURPOSE Copy a selection from one dataspace to another USAGE - herr_t H5S_point_copy(dst, src) + herr_t H5S__point_copy(dst, src, share_selection) H5S_t *dst; OUT: Pointer to the destination dataspace H5S_t *src; IN: Pointer to the source dataspace + hbool_t share_selection; IN: Whether to share the selection between the dataspaces RETURNS Non-negative on success/Negative on failure DESCRIPTION @@ -604,13 +771,14 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_copy(H5S_t *dst, const H5S_t *src, hbool_t H5_ATTR_UNUSED share_selection) +H5S__point_copy(H5S_t *dst, const H5S_t *src, hbool_t H5_ATTR_UNUSED share_selection) { H5S_pnt_node_t *curr, *new_node, *new_tail; /* Point information nodes */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC + /* Sanity checks */ HDassert(src); HDassert(dst); @@ -631,7 +799,7 @@ H5S_point_copy(H5S_t *dst, const H5S_t *src, hbool_t H5_ATTR_UNUSED share_select } /* end if */ /* Copy over the point's coordinates */ - HDmemcpy(new_node->pnt, curr->pnt, (src->extent.rank * sizeof(hsize_t))); + H5MM_memcpy(new_node->pnt, curr->pnt, (src->extent.rank * sizeof(hsize_t))); /* Keep the order the same when copying */ if(NULL == new_tail) @@ -660,18 +828,18 @@ done: } /* end if */ FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_point_copy() */ +} /* end H5S__point_copy() */ /*-------------------------------------------------------------------------- NAME - H5S_point_is_valid + H5S__point_is_valid PURPOSE Check whether the selection fits within the extent, with the current offset defined. USAGE - htri_t H5S_point_is_valid(space); - H5S_t *space; IN: Dataspace pointer to query + htri_t H5S__point_is_valid(space); + const H5S_t *space; IN: Dataspace pointer to query RETURNS TRUE if the selection fits within the extent, FALSE if it does not and Negative on an error. @@ -684,13 +852,13 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_point_is_valid (const H5S_t *space) +H5S__point_is_valid(const H5S_t *space) { H5S_pnt_node_t *curr; /* Point information nodes */ unsigned u; /* Counter */ htri_t ret_value = TRUE; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); @@ -711,7 +879,7 @@ H5S_point_is_valid (const H5S_t *space) done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_point_is_valid() */ +} /* end H5S__point_is_valid() */ /*-------------------------------------------------------------------------- @@ -750,18 +918,18 @@ H5Sget_select_elem_npoints(hid_t spaceid) done: FUNC_LEAVE_API(ret_value) -} /* H5Sget_select_elem_npoints() */ +} /* end H5Sget_select_elem_npoints() */ /*-------------------------------------------------------------------------- NAME - H5S_point_serial_size + H5S__point_serial_size PURPOSE Determine the number of bytes needed to store the serialized point selection information. USAGE - hssize_t H5S_point_serial_size(space) - H5S_t *space; IN: Dataspace pointer to query + hssize_t H5S__point_serial_size(space) + const H5S_t *space; IN: Dataspace pointer to query RETURNS The number of bytes required on success, negative on an error. DESCRIPTION @@ -773,11 +941,11 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static hssize_t -H5S_point_serial_size (const H5S_t *space) +H5S__point_serial_size(const H5S_t *space) { hssize_t ret_value = -1; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); @@ -792,16 +960,16 @@ H5S_point_serial_size (const H5S_t *space) ret_value += (4 * space->extent.rank) * (hssize_t)H5S_GET_SELECT_NPOINTS(space); FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_point_serial_size() */ +} /* end H5S__point_serial_size() */ /*-------------------------------------------------------------------------- NAME - H5S_point_serialize + H5S__point_serialize PURPOSE Serialize the current selection into a user-provided buffer. USAGE - herr_t H5S_point_serialize(space, p) + herr_t H5S__point_serialize(space, p) const H5S_t *space; IN: Dataspace with selection to serialize uint8_t **p; OUT: Pointer to buffer to put serialized selection. Will be advanced to end of @@ -817,15 +985,15 @@ H5S_point_serial_size (const H5S_t *space) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_serialize (const H5S_t *space, uint8_t **p) +H5S__point_serialize(const H5S_t *space, uint8_t **p) { H5S_pnt_node_t *curr; /* Point information nodes */ uint8_t *pp = (*p); /* Local pointer for decoding */ - uint8_t *lenp; /* pointer to length location for later storage */ - uint32_t len=0; /* number of bytes used */ - unsigned u; /* local counting variable */ + uint8_t *lenp; /* Pointer to length location for later storage */ + uint32_t len = 0; /* Number of bytes used */ + unsigned u; /* Local counting variable */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space); @@ -841,23 +1009,23 @@ H5S_point_serialize (const H5S_t *space, uint8_t **p) /* Encode number of dimensions */ UINT32ENCODE(pp, (uint32_t)space->extent.rank); - len+=4; + len += 4; /* Encode number of elements */ UINT32ENCODE(pp, (uint32_t)space->select.num_elem); - len+=4; + len += 4; /* Encode each point in selection */ - curr=space->select.sel_info.pnt_lst->head; - while(curr!=NULL) { + curr = space->select.sel_info.pnt_lst->head; + while(curr != NULL) { /* Add 4 bytes times the rank for each element selected */ - len+=4*space->extent.rank; + len += 4 * space->extent.rank; /* Encode each point */ - for(u=0; u<space->extent.rank; u++) + for(u = 0; u < space->extent.rank; u++) UINT32ENCODE(pp, (uint32_t)curr->pnt[u]); - curr=curr->next; + curr = curr->next; } /* end while */ /* Encode length */ @@ -867,16 +1035,16 @@ H5S_point_serialize (const H5S_t *space, uint8_t **p) *p = pp; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_serialize() */ +} /* end H5S__point_serialize() */ /*-------------------------------------------------------------------------- NAME - H5S_point_deserialize + H5S__point_deserialize PURPOSE Deserialize the current selection from a user-provided buffer. USAGE - herr_t H5S_point_deserialize(space, p) + herr_t H5S__point_deserialize(space, p) H5S_t *space; IN/OUT: Dataspace pointer to place selection into uint32_t version IN: Selection version @@ -895,10 +1063,9 @@ H5S_point_serialize (const H5S_t *space, uint8_t **p) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t H5_ATTR_UNUSED flags, +H5S__point_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t H5_ATTR_UNUSED flags, const uint8_t **p) { - H5S_seloper_t op = H5S_SELECT_SET; /* Selection operation */ hsize_t *coord = NULL, *tcoord; /* Pointer to array of elements */ const uint8_t *pp = (*p); /* Local pointer for decoding */ size_t num_elem = 0; /* Number of elements in selection */ @@ -906,7 +1073,7 @@ H5S_point_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t H5_ unsigned i, j; /* local counting variables */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(space); @@ -928,7 +1095,7 @@ H5S_point_deserialize(H5S_t *space, uint32_t H5_ATTR_UNUSED version, uint8_t H5_ UINT32DECODE(pp, *tcoord); /* Select points */ - if(H5S_select_elements(space, op, num_elem, (const hsize_t *)coord) < 0) + if(H5S_select_elements(space, H5S_SELECT_SET, num_elem, (const hsize_t *)coord) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't change selection") /* Update decoding pointer */ @@ -940,17 +1107,17 @@ done: H5MM_xfree(coord); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_deserialize() */ +} /* end H5S__point_deserialize() */ /*-------------------------------------------------------------------------- NAME - H5S_get_select_elem_pointlist + H5S__get_select_elem_pointlist PURPOSE Get the list of element points currently selected USAGE - herr_t H5S_get_select_elem_pointlist(space, hsize_t *buf) - H5S_t *space; IN: Dataspace pointer of selection to query + herr_t H5S__get_select_elem_pointlist(space, hsize_t *buf) + const H5S_t *space; IN: Dataspace pointer of selection to query hsize_t startpoint; IN: Element point to start with hsize_t numpoints; IN: Number of element points to get hsize_t *buf; OUT: List of element points selected @@ -973,12 +1140,13 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_get_select_elem_pointlist(H5S_t *space, hsize_t startpoint, hsize_t numpoints, hsize_t *buf) +H5S__get_select_elem_pointlist(const H5S_t *space, hsize_t startpoint, + hsize_t numpoints, hsize_t *buf) { H5S_pnt_node_t *node; /* Point node */ unsigned rank; /* Dataspace rank */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); HDassert(buf); @@ -997,14 +1165,14 @@ H5S_get_select_elem_pointlist(H5S_t *space, hsize_t startpoint, hsize_t numpoint /* Iterate through the node, copying each point's information */ while(node != NULL && numpoints > 0) { - HDmemcpy(buf, node->pnt, sizeof(hsize_t) * rank); + H5MM_memcpy(buf, node->pnt, sizeof(hsize_t) * rank); buf += rank; numpoints--; node = node->next; } /* end while */ FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_get_select_elem_pointlist() */ +} /* end H5S__get_select_elem_pointlist() */ /*-------------------------------------------------------------------------- @@ -1054,20 +1222,20 @@ H5Sget_select_elem_pointlist(hid_t spaceid, hsize_t startpoint, if(H5S_GET_SELECT_TYPE(space) != H5S_SEL_POINTS) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a point selection") - ret_value = H5S_get_select_elem_pointlist(space, startpoint, numpoints, buf); + ret_value = H5S__get_select_elem_pointlist(space, startpoint, numpoints, buf); done: FUNC_LEAVE_API(ret_value) -} /* H5Sget_select_elem_pointlist() */ +} /* end H5Sget_select_elem_pointlist() */ /*-------------------------------------------------------------------------- NAME - H5S_point_bounds + H5S__point_bounds PURPOSE Gets the bounding box containing the selection. USAGE - herr_t H5S_point_bounds(space, start, end) + herr_t H5S__point_bounds(space, start, end) H5S_t *space; IN: Dataspace pointer of selection to query hsize_t *start; OUT: Starting coordinate of bounding box hsize_t *end; OUT: Opposite coordinate of bounding box @@ -1088,14 +1256,14 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_bounds(const H5S_t *space, hsize_t *start, hsize_t *end) +H5S__point_bounds(const H5S_t *space, hsize_t *start, hsize_t *end) { H5S_pnt_node_t *node; /* Point node */ unsigned rank; /* Dataspace rank */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Sanity check */ HDassert(space); @@ -1129,16 +1297,16 @@ H5S_point_bounds(const H5S_t *space, hsize_t *start, hsize_t *end) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_bounds() */ +} /* end H5S__point_bounds() */ /*-------------------------------------------------------------------------- NAME - H5S_point_offset + H5S__point_offset PURPOSE Gets the linear offset of the first element for the selection. USAGE - herr_t H5S_point_offset(space, offset) + herr_t H5S__point_offset(space, offset) const H5S_t *space; IN: Dataspace pointer of selection to query hsize_t *offset; OUT: Linear offset of first element in selection RETURNS @@ -1153,7 +1321,7 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_offset(const H5S_t *space, hsize_t *offset) +H5S__point_offset(const H5S_t *space, hsize_t *offset) { const hsize_t *pnt; /* Pointer to a selected point's coordinates */ const hssize_t *sel_offset; /* Pointer to the selection's offset */ @@ -1162,7 +1330,7 @@ H5S_point_offset(const H5S_t *space, hsize_t *offset) int i; /* index variable */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_STATIC HDassert(space); HDassert(offset); @@ -1193,7 +1361,7 @@ H5S_point_offset(const H5S_t *space, hsize_t *offset) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_offset() */ +} /* end H5S__point_offset() */ /*-------------------------------------------------------------------------- @@ -1227,11 +1395,11 @@ H5S__point_unlim_dim(const H5S_t H5_ATTR_UNUSED *space) /*-------------------------------------------------------------------------- NAME - H5S_point_is_contiguous + H5S__point_is_contiguous PURPOSE Check if a point selection is contiguous within the dataspace extent. USAGE - htri_t H5S_point_is_contiguous(space) + htri_t H5S__point_is_contiguous(space) H5S_t *space; IN: Dataspace pointer to check RETURNS TRUE/FALSE/FAIL @@ -1247,31 +1415,31 @@ H5S__point_unlim_dim(const H5S_t H5_ATTR_UNUSED *space) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_point_is_contiguous(const H5S_t *space) +H5S__point_is_contiguous(const H5S_t *space) { htri_t ret_value = FAIL; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); /* One point is definitely contiguous */ - if(space->select.num_elem==1) - ret_value=TRUE; + if(space->select.num_elem == 1) + ret_value = TRUE; else /* More than one point might be contiguous, but it's complex to check and we don't need it right now */ - ret_value=FALSE; + ret_value = FALSE; FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_is_contiguous() */ +} /* end H5S__point_is_contiguous() */ /*-------------------------------------------------------------------------- NAME - H5S_point_is_single + H5S__point_is_single PURPOSE Check if a point selection is single within the dataspace extent. USAGE - htri_t H5S_point_is_single(space) + htri_t H5S__point_is_single(space) H5S_t *space; IN: Dataspace pointer to check RETURNS TRUE/FALSE/FAIL @@ -1284,31 +1452,31 @@ H5S_point_is_contiguous(const H5S_t *space) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_point_is_single(const H5S_t *space) +H5S__point_is_single(const H5S_t *space) { htri_t ret_value = FAIL; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); /* One point is definitely 'single' :-) */ - if(space->select.num_elem==1) - ret_value=TRUE; + if(space->select.num_elem == 1) + ret_value = TRUE; else - ret_value=FALSE; + ret_value = FALSE; FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_is_single() */ +} /* end H5S__point_is_single() */ /*-------------------------------------------------------------------------- NAME - H5S_point_is_regular + H5S__point_is_regular PURPOSE Check if a point selection is "regular" USAGE - htri_t H5S_point_is_regular(space) + htri_t H5S__point_is_regular(space) const H5S_t *space; IN: Dataspace pointer to check RETURNS TRUE/FALSE/FAIL @@ -1324,32 +1492,32 @@ H5S_point_is_single(const H5S_t *space) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_point_is_regular(const H5S_t *space) +H5S__point_is_regular(const H5S_t *space) { htri_t ret_value = FAIL; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check args */ HDassert(space); /* Only simple check for regular points for now... */ - if(space->select.num_elem==1) - ret_value=TRUE; + if(space->select.num_elem == 1) + ret_value = TRUE; else - ret_value=FALSE; + ret_value = FALSE; FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_is_regular() */ +} /* end H5S__point_is_regular() */ /*-------------------------------------------------------------------------- NAME - H5S_point_adjust_u + H5S__point_adjust_u PURPOSE Adjust a "point" selection by subtracting an offset USAGE - herr_t H5S_point_adjust_u(space, offset) + herr_t H5S__point_adjust_u(space, offset) H5S_t *space; IN/OUT: Pointer to dataspace to adjust const hsize_t *offset; IN: Offset to subtract RETURNS @@ -1362,12 +1530,12 @@ H5S_point_is_regular(const H5S_t *space) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_point_adjust_u(H5S_t *space, const hsize_t *offset) +H5S__point_adjust_u(H5S_t *space, const hsize_t *offset) { H5S_pnt_node_t *node; /* Point node */ unsigned rank; /* Dataspace rank */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR HDassert(space); HDassert(offset); @@ -1392,16 +1560,16 @@ H5S_point_adjust_u(H5S_t *space, const hsize_t *offset) } /* end while */ FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_point_adjust_u() */ +} /* end H5S__point_adjust_u() */ /*------------------------------------------------------------------------- - * Function: H5S_point_project_scalar + * Function: H5S__point_project_scalar * * Purpose: Projects a single element point selection into a scalar * dataspace * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -1409,12 +1577,12 @@ H5S_point_adjust_u(H5S_t *space, const hsize_t *offset) *------------------------------------------------------------------------- */ static herr_t -H5S_point_project_scalar(const H5S_t *space, hsize_t *offset) +H5S__point_project_scalar(const H5S_t *space, hsize_t *offset) { const H5S_pnt_node_t *node; /* Point node */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(space && H5S_SEL_POINTS == H5S_GET_SELECT_TYPE(space)); @@ -1428,20 +1596,20 @@ H5S_point_project_scalar(const H5S_t *space, hsize_t *offset) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "point selection of one element has more than one node!") /* Calculate offset of selection in projected buffer */ - *offset = H5VM_array_offset(space->extent.rank, space->extent.size, node->pnt); + *offset = H5VM_array_offset(space->extent.rank, space->extent.size, node->pnt); done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_project_scalar() */ +} /* end H5S__point_project_scalar() */ /*------------------------------------------------------------------------- - * Function: H5S_point_project_simple + * Function: H5S__point_project_simple * * Purpose: Projects a point selection onto/into a simple dataspace * of a different rank * - * Return: non-negative on success, negative on failure. + * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Sunday, July 18, 2010 @@ -1449,7 +1617,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5S_point_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *offset) +H5S__point_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *offset) { const H5S_pnt_node_t *base_node; /* Point node in base space */ H5S_pnt_node_t *new_node; /* Point node in new space */ @@ -1457,7 +1625,7 @@ H5S_point_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *off unsigned rank_diff; /* Difference in ranks between spaces */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC /* Check args */ HDassert(base_space && H5S_SEL_POINTS == H5S_GET_SELECT_TYPE(base_space)); @@ -1481,8 +1649,8 @@ H5S_point_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *off /* Calculate offset of selection in projected buffer */ HDmemset(block, 0, sizeof(block)); - HDmemcpy(block, base_space->select.sel_info.pnt_lst->head->pnt, sizeof(hsize_t) * rank_diff); - *offset = H5VM_array_offset(base_space->extent.rank, base_space->extent.size, block); + H5MM_memcpy(block, base_space->select.sel_info.pnt_lst->head->pnt, sizeof(hsize_t) * rank_diff); + *offset = H5VM_array_offset(base_space->extent.rank, base_space->extent.size, block); /* Iterate through base space's point nodes, copying the point information */ base_node = base_space->select.sel_info.pnt_lst->head; @@ -1498,7 +1666,7 @@ H5S_point_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *off } /* end if */ /* Copy over the point's coordinates */ - HDmemcpy(new_node->pnt, &base_node->pnt[rank_diff], (new_space->extent.rank * sizeof(hsize_t))); + H5MM_memcpy(new_node->pnt, &base_node->pnt[rank_diff], (new_space->extent.rank * sizeof(hsize_t))); /* Keep the order the same when copying */ if(NULL == prev_node) @@ -1536,7 +1704,7 @@ H5S_point_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *off /* Copy over the point's coordinates */ HDmemset(new_node->pnt, 0, sizeof(hsize_t) * rank_diff); - HDmemcpy(&new_node->pnt[rank_diff], base_node->pnt, (new_space->extent.rank * sizeof(hsize_t))); + H5MM_memcpy(&new_node->pnt[rank_diff], base_node->pnt, (new_space->extent.rank * sizeof(hsize_t))); /* Keep the order the same when copying */ if(NULL == prev_node) @@ -1559,7 +1727,7 @@ H5S_point_project_simple(const H5S_t *base_space, H5S_t *new_space, hsize_t *off done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_point_project_simple() */ +} /* end H5S__point_project_simple() */ /*-------------------------------------------------------------------------- @@ -1620,143 +1788,5 @@ H5Sselect_elements(hid_t spaceid, H5S_seloper_t op, size_t num_elem, done: FUNC_LEAVE_API(ret_value) -} /* H5Sselect_elements() */ - - -/*-------------------------------------------------------------------------- - NAME - H5S_point_get_seq_list - PURPOSE - Create a list of offsets & lengths for a selection - USAGE - herr_t H5S_point_get_seq_list(space,flags,iter,maxseq,maxelem,nseq,nelem,off,len) - H5S_t *space; IN: Dataspace containing selection to use. - unsigned flags; IN: Flags for extra information about operation - H5S_sel_iter_t *iter; IN/OUT: Selection iterator describing last - position of interest in selection. - size_t maxseq; IN: Maximum number of sequences to generate - size_t maxelem; IN: Maximum number of elements to include in the - generated sequences - size_t *nseq; OUT: Actual number of sequences generated - size_t *nelem; OUT: Actual number of elements in sequences generated - hsize_t *off; OUT: Array of offsets - size_t *len; OUT: Array of lengths - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to generate a list of byte offsets and - lengths for the region(s) selected. Start/Restart from the position in the - ITER parameter. The number of sequences generated is limited by the MAXSEQ - parameter and the number of sequences actually generated is stored in the - NSEQ parameter. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5S_point_get_seq_list(const H5S_t *space, unsigned flags, H5S_sel_iter_t *iter, - size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, - hsize_t *off, size_t *len) -{ - size_t io_left; /* The number of bytes left in the selection */ - size_t start_io_left; /* The initial number of bytes left in the selection */ - H5S_pnt_node_t *node; /* Point node */ - hsize_t dims[H5O_LAYOUT_NDIMS]; /* Total size of memory buf */ - int ndims; /* Dimensionality of space*/ - hsize_t acc; /* Coordinate accumulator */ - hsize_t loc; /* Coordinate offset */ - size_t curr_seq; /* Current sequence being operated on */ - int i; /* Local index variable */ - herr_t ret_value=SUCCEED; /* return value */ - - FUNC_ENTER_NOAPI_NOINIT - - /* Check args */ - HDassert(space); - HDassert(iter); - HDassert(maxseq > 0); - HDassert(maxelem > 0); - HDassert(nseq); - HDassert(nelem); - HDassert(off); - HDassert(len); - - /* Choose the minimum number of bytes to sequence through */ - H5_CHECK_OVERFLOW(iter->elmt_left, hsize_t, size_t); - start_io_left = io_left = (size_t)MIN(iter->elmt_left, maxelem); - - /* Get the dataspace dimensions */ - if((ndims = H5S_get_simple_extent_dims (space, dims, NULL)) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to retrieve dataspace dimensions") - - /* Walk through the points in the selection, starting at the current */ - /* location in the iterator */ - node = iter->u.pnt.curr; - curr_seq = 0; - while(NULL != node) { - /* Compute the offset of each selected point in the buffer */ - for(i = ndims - 1, acc = iter->elmt_size, loc = 0; i >= 0; i--) { - loc += (hsize_t)((hssize_t)node->pnt[i] + space->select.offset[i]) * acc; - acc *= dims[i]; - } /* end for */ - - /* Check if this is a later point in the selection */ - if(curr_seq>0) { - /* If a sorted sequence is requested, make certain we don't go backwards in the offset */ - if((flags&H5S_GET_SEQ_LIST_SORTED) && loc<off[curr_seq-1]) - break; - - /* Check if this point extends the previous sequence */ - /* (Unlikely, but possible) */ - if(loc==(off[curr_seq-1]+len[curr_seq-1])) { - /* Extend the previous sequence */ - len[curr_seq-1]+=iter->elmt_size; - } /* end if */ - else { - /* Add a new sequence */ - off[curr_seq]=loc; - len[curr_seq]=iter->elmt_size; - - /* Increment sequence count */ - curr_seq++; - } /* end else */ - } /* end if */ - else { - /* Add a new sequence */ - off[curr_seq]=loc; - len[curr_seq]=iter->elmt_size; - - /* Increment sequence count */ - curr_seq++; - } /* end else */ - - /* Decrement number of elements left to process */ - io_left--; - - /* Move the iterator */ - iter->u.pnt.curr=node->next; - iter->elmt_left--; - - /* Check if we're finished with all sequences */ - if(curr_seq==maxseq) - break; - - /* Check if we're finished with all the elements available */ - if(io_left==0) - break; - - /* Advance to the next point */ - node=node->next; - } /* end while */ - - /* Set the number of sequences generated */ - *nseq=curr_seq; - - /* Set the number of elements used */ - *nelem=start_io_left-io_left; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_point_get_seq_list() */ +} /* end H5Sselect_elements() */ diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 32ac51a..f4e0006 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -17,9 +17,6 @@ #ifndef _H5Sprivate_H #define _H5Sprivate_H -/* Early typedefs to avoid circular dependencies */ -typedef struct H5S_t H5S_t; - /* Include package's public header */ #include "H5Spublic.h" @@ -30,7 +27,6 @@ typedef struct H5S_t H5S_t; #include "H5private.h" /* Generic Functions */ #include "H5Fprivate.h" /* Files */ #include "H5Gprivate.h" /* Groups */ -#include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5Tprivate.h" /* Datatypes */ @@ -62,20 +58,20 @@ typedef struct H5S_hyper_dim_t { /* Point selection iteration container */ typedef struct { - H5S_pnt_node_t *curr; /* Pointer to next node to output */ + H5S_pnt_node_t *curr; /* Pointer to next node to output */ } H5S_point_iter_t; /* Hyperslab selection iteration container */ typedef struct { /* Common fields for all hyperslab selections */ - hsize_t off[H5S_MAX_RANK]; /* Offset in span node (used as position for regular hyperslabs) */ + hsize_t off[H5S_MAX_RANK]; /* Offset in span node (used as position for regular hyperslabs) */ unsigned iter_rank; /* Rank of iterator information */ /* (This should always be the same as the dataspace - * rank, except for regular hyperslab selections in - * which there are contiguous regions in the lower - * dimensions which have been "flattened" out + * rank, except for regular hyperslab selections in + * which there are contiguous regions in the lower + * dimensions that have been "flattened") */ - hbool_t diminfo_valid; /* Whether the dimension information is valid */ + hbool_t diminfo_valid; /* Whether the dimension information is valid */ /* "Flattened" regular hyperslab selection fields */ H5S_hyper_dim_t diminfo[H5S_MAX_RANK]; /* "Flattened" regular selection information */ @@ -196,6 +192,12 @@ typedef struct H5S_sel_iter_op_t { #define H5S_SELECT_RELEASE(S) (H5S_select_release(S)) #define H5S_SELECT_DESERIALIZE(S,BUF) (H5S_select_deserialize(S,BUF)) +/* Forward declaration of structs used below */ +struct H5O_t; +struct H5O_loc_t; + +/* Early typedef to avoid circular dependencies */ +typedef struct H5S_t H5S_t; /* Operations on dataspaces */ H5_DLL H5S_t *H5S_copy(const H5S_t *src, hbool_t share_selection, hbool_t copy_max); @@ -207,7 +209,7 @@ H5_DLL hbool_t H5S_has_extent(const H5S_t *ds); H5_DLL int H5S_get_simple_extent_ndims(const H5S_t *ds); H5_DLL int H5S_get_simple_extent_dims(const H5S_t *ds, hsize_t dims[]/*out*/, hsize_t max_dims[]/*out*/); -H5_DLL herr_t H5S_write(H5F_t *f, H5O_t *oh, unsigned update_flags, H5S_t *ds); +H5_DLL herr_t H5S_write(H5F_t *f, struct H5O_t *oh, unsigned update_flags, H5S_t *ds); H5_DLL herr_t H5S_append(H5F_t *f, struct H5O_t *oh, H5S_t *ds); H5_DLL H5S_t *H5S_read(const struct H5O_loc_t *loc); H5_DLL htri_t H5S_set_extent(H5S_t *space, const hsize_t *size); @@ -284,9 +286,6 @@ H5_DLL herr_t H5S_hyper_add_span_element(H5S_t *space, unsigned rank, const hsize_t *coords); H5_DLL herr_t H5S_hyper_reset_scratch(H5S_t *space); H5_DLL herr_t H5S_hyper_convert(H5S_t *space); -#ifdef LATER -H5_DLL htri_t H5S_hyper_intersect (H5S_t *space1, H5S_t *space2); -#endif /* LATER */ H5_DLL htri_t H5S_hyper_intersect_block(H5S_t *space, const hsize_t *start, const hsize_t *end); H5_DLL herr_t H5S_hyper_adjust_s(H5S_t *space, const hssize_t *offset); H5_DLL htri_t H5S_hyper_normalize_offset(H5S_t *space, hssize_t *old_offset); @@ -302,7 +301,8 @@ H5_DLL hsize_t H5S_hyper_get_first_inc_block(const H5S_t *space, hsize_t clip_size, hbool_t *partial); /* Operations on selection iterators */ -H5_DLL herr_t H5S_select_iter_init(H5S_sel_iter_t *iter, const H5S_t *space, size_t elmt_size); +H5_DLL herr_t H5S_select_iter_init(H5S_sel_iter_t *iter, const H5S_t *space, + size_t elmt_size); H5_DLL herr_t H5S_select_iter_coords(const H5S_sel_iter_t *sel_iter, hsize_t *coords); H5_DLL hsize_t H5S_select_iter_nelmts(const H5S_sel_iter_t *sel_iter); H5_DLL herr_t H5S_select_iter_next(H5S_sel_iter_t *sel_iter, size_t nelem); @@ -314,7 +314,7 @@ H5_DLL herr_t H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, /* out: */ MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, - hbool_t do_permute, + hbool_t do_permute, hsize_t **permute_map, hbool_t * is_permuted); #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Spublic.h b/src/H5Spublic.h index d7a5d29..561875a 100644 --- a/src/H5Spublic.h +++ b/src/H5Spublic.h @@ -79,23 +79,22 @@ typedef enum H5S_seloper_t { typedef enum { H5S_SEL_ERROR = -1, /* Error */ H5S_SEL_NONE = 0, /* Nothing selected */ - H5S_SEL_POINTS = 1, /* Sequence of points selected */ - H5S_SEL_HYPERSLABS = 2, /* "New-style" hyperslab selection defined */ + H5S_SEL_POINTS = 1, /* Points / elements selected */ + H5S_SEL_HYPERSLABS = 2, /* Hyperslab selected */ H5S_SEL_ALL = 3, /* Entire extent selected */ H5S_SEL_N /*THIS MUST BE LAST */ -}H5S_sel_type; +} H5S_sel_type; #ifdef __cplusplus extern "C" { #endif -/* Functions in H5S.c */ +/* Operations on dataspaces */ H5_DLL hid_t H5Screate(H5S_class_t type); H5_DLL hid_t H5Screate_simple(int rank, const hsize_t dims[], - const hsize_t maxdims[]); + const hsize_t maxdims[]); H5_DLL herr_t H5Sset_extent_simple(hid_t space_id, int rank, - const hsize_t dims[], - const hsize_t max[]); + const hsize_t dims[], const hsize_t max[]); H5_DLL hid_t H5Scopy(hid_t space_id); H5_DLL herr_t H5Sclose(hid_t space_id); H5_DLL herr_t H5Sencode(hid_t obj_id, void *buf, size_t *nalloc); @@ -103,51 +102,37 @@ H5_DLL hid_t H5Sdecode(const void *buf); H5_DLL hssize_t H5Sget_simple_extent_npoints(hid_t space_id); H5_DLL int H5Sget_simple_extent_ndims(hid_t space_id); H5_DLL int H5Sget_simple_extent_dims(hid_t space_id, hsize_t dims[], - hsize_t maxdims[]); + hsize_t maxdims[]); H5_DLL htri_t H5Sis_simple(hid_t space_id); -H5_DLL hssize_t H5Sget_select_npoints(hid_t spaceid); -H5_DLL herr_t H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, - const hsize_t start[], - const hsize_t _stride[], - const hsize_t count[], - const hsize_t _block[]); -/* #define NEW_HYPERSLAB_API */ -/* Note that these haven't been working for a while and were never - * publicly released - QAK */ -#ifdef NEW_HYPERSLAB_API -H5_DLL hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op, - const hsize_t start[], - const hsize_t _stride[], - const hsize_t count[], - const hsize_t _block[]); -H5_DLL herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op, - hid_t space2_id); -H5_DLL hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op, - hid_t space2_id); -#endif /* NEW_HYPERSLAB_API */ -H5_DLL herr_t H5Sselect_elements(hid_t space_id, H5S_seloper_t op, - size_t num_elem, const hsize_t *coord); H5_DLL H5S_class_t H5Sget_simple_extent_type(hid_t space_id); H5_DLL herr_t H5Sset_extent_none(hid_t space_id); H5_DLL herr_t H5Sextent_copy(hid_t dst_id,hid_t src_id); H5_DLL htri_t H5Sextent_equal(hid_t sid1, hid_t sid2); + +/* Operations on dataspace selections */ +H5_DLL H5S_sel_type H5Sget_select_type(hid_t spaceid); +H5_DLL hssize_t H5Sget_select_npoints(hid_t spaceid); H5_DLL herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id); +H5_DLL htri_t H5Sselect_valid(hid_t spaceid); +H5_DLL herr_t H5Sget_select_bounds(hid_t spaceid, hsize_t start[], + hsize_t end[]); +H5_DLL herr_t H5Soffset_simple(hid_t space_id, const hssize_t *offset); H5_DLL herr_t H5Sselect_all(hid_t spaceid); H5_DLL herr_t H5Sselect_none(hid_t spaceid); -H5_DLL herr_t H5Soffset_simple(hid_t space_id, const hssize_t *offset); -H5_DLL htri_t H5Sselect_valid(hid_t spaceid); +H5_DLL herr_t H5Sselect_elements(hid_t space_id, H5S_seloper_t op, + size_t num_elem, const hsize_t *coord); +H5_DLL hssize_t H5Sget_select_elem_npoints(hid_t spaceid); +H5_DLL herr_t H5Sget_select_elem_pointlist(hid_t spaceid, hsize_t startpoint, + hsize_t numpoints, hsize_t buf[/*numpoints*/]); +H5_DLL herr_t H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, + const hsize_t start[], const hsize_t _stride[], const hsize_t count[], + const hsize_t _block[]); H5_DLL htri_t H5Sis_regular_hyperslab(hid_t spaceid); H5_DLL htri_t H5Sget_regular_hyperslab(hid_t spaceid, hsize_t start[], hsize_t stride[], hsize_t count[], hsize_t block[]); H5_DLL hssize_t H5Sget_select_hyper_nblocks(hid_t spaceid); -H5_DLL hssize_t H5Sget_select_elem_npoints(hid_t spaceid); H5_DLL herr_t H5Sget_select_hyper_blocklist(hid_t spaceid, hsize_t startblock, hsize_t numblocks, hsize_t buf[/*numblocks*/]); -H5_DLL herr_t H5Sget_select_elem_pointlist(hid_t spaceid, hsize_t startpoint, - hsize_t numpoints, hsize_t buf[/*numpoints*/]); -H5_DLL herr_t H5Sget_select_bounds(hid_t spaceid, hsize_t start[], - hsize_t end[]); -H5_DLL H5S_sel_type H5Sget_select_type(hid_t spaceid); #ifdef __cplusplus } diff --git a/src/H5Sselect.c b/src/H5Sselect.c index dd656b1..ef38746 100644 --- a/src/H5Sselect.c +++ b/src/H5Sselect.c @@ -17,9 +17,16 @@ * Purpose: Dataspace selection functions. */ +/****************/ +/* Module Setup */ +/****************/ + #include "H5Smodule.h" /* This source code file is part of the H5S module */ +/***********/ +/* Headers */ +/***********/ #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ @@ -27,16 +34,40 @@ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Spkg.h" /* Dataspaces */ -#include "H5VMprivate.h" /* Vector and array functions */ -#include "H5WBprivate.h" /* Wrapped Buffers */ +#include "H5VMprivate.h" /* Vector and array functions */ + + +/****************/ +/* Local Macros */ +/****************/ + + + +/******************/ +/* Local Typedefs */ +/******************/ + + +/********************/ +/* Local Prototypes */ +/********************/ -/* Local functions */ #ifdef LATER static herr_t H5S_select_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); static htri_t H5S_select_iter_has_next_block(const H5S_sel_iter_t *iter); static herr_t H5S_select_iter_next_block(H5S_sel_iter_t *iter); #endif /* LATER */ + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*********************/ +/* Package Variables */ +/*********************/ + /* Declare a free list to manage the H5S_sel_iter_t struct */ H5FL_DEFINE(H5S_sel_iter_t); @@ -47,6 +78,11 @@ H5FL_SEQ_EXTERN(size_t); H5FL_SEQ_EXTERN(hsize_t); +/*******************/ +/* Local Variables */ +/*******************/ + + /*-------------------------------------------------------------------------- NAME @@ -78,13 +114,56 @@ H5S_select_offset(H5S_t *space, const hssize_t *offset) HDassert(offset); /* Copy the offset over */ - HDmemcpy(space->select.offset, offset, sizeof(hssize_t)*space->extent.rank); + H5MM_memcpy(space->select.offset, offset, sizeof(hssize_t) * space->extent.rank); /* Indicate that the offset was changed */ space->select.offset_changed = TRUE; FUNC_LEAVE_NOAPI(SUCCEED) -} /* H5S_select_offset() */ +} /* end H5S_select_offset() */ + + +/*-------------------------------------------------------------------------- + NAME + H5Soffset_simple + PURPOSE + Changes the offset of a selection within a simple dataspace extent + USAGE + herr_t H5Soffset_simple(space_id, offset) + hid_t space_id; IN: Dataspace object to reset + const hssize_t *offset; IN: Offset to position the selection at + RETURNS + Non-negative on success/Negative on failure + DESCRIPTION + This function creates an offset for the selection within an extent, allowing + the same shaped selection to be moved to different locations within a + dataspace without requiring it to be re-defined. +--------------------------------------------------------------------------*/ +herr_t +H5Soffset_simple(hid_t space_id, const hssize_t *offset) +{ + H5S_t *space; /* Dataspace to query */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE2("e", "i*Hs", space_id, offset); + + /* Check args */ + if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "not a dataspace") + if(space->extent.rank == 0 || (H5S_GET_EXTENT_TYPE(space) == H5S_SCALAR + || H5S_GET_EXTENT_TYPE(space) == H5S_NULL)) + HGOTO_ERROR(H5E_ATOM, H5E_UNSUPPORTED, FAIL, "can't set offset on scalar or null dataspace") + if(offset == NULL) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no offset specified") + + /* Set the selection offset */ + if(H5S_select_offset(space, offset) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "can't set offset") + +done: + FUNC_LEAVE_API(ret_value) +} /* end H5Soffset_simple() */ /*-------------------------------------------------------------------------- @@ -139,9 +218,10 @@ done: PURPOSE Copy a selection from one dataspace to another USAGE - herr_t H5S_select_copy(dst, src) + herr_t H5S_select_copy(dst, src, share_selection) H5S_t *dst; OUT: Pointer to the destination dataspace H5S_t *src; IN: Pointer to the source dataspace + hbool_t; IN: Whether to share the selection between the dataspaces RETURNS Non-negative on success/Negative on failure DESCRIPTION @@ -177,7 +257,7 @@ H5S_select_copy(H5S_t *dst, const H5S_t *src, hbool_t share_selection) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_copy() */ +} /* end H5S_select_copy() */ /*------------------------------------------------------------------------- @@ -211,44 +291,7 @@ H5S_select_release(H5S_t *ds) done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_select_release() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_select_get_seq_list - * - * Purpose: Retrieves the next sequence of offset/length pairs for an - * iterator on a dataspace - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, May 18, 2004 - * - * Note: This routine participates in the "Inlining C function pointers" - * pattern, don't call it directly, use the appropriate macro - * defined in H5Sprivate.h. - * - *------------------------------------------------------------------------- - */ -herr_t -H5S_select_get_seq_list(const H5S_t *space, unsigned flags, - H5S_sel_iter_t *iter, size_t maxseq, size_t maxbytes, - size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len) -{ - herr_t ret_value = FAIL; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - HDassert(space); - - /* Call the selection type's get_seq_list function */ - if((ret_value = (*space->select.type->get_seq_list)(space, flags, iter, maxseq, maxbytes, nseq, nbytes, off, len)) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get selection sequence list") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_select_get_seq_list() */ +} /* end H5S_select_release() */ /*------------------------------------------------------------------------- @@ -278,10 +321,10 @@ H5S_select_serial_size(const H5S_t *space) HDassert(space); /* Call the selection type's serial_size function */ - ret_value=(*space->select.type->serial_size)(space); + ret_value = (*space->select.type->serial_size)(space); FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_select_serial_size() */ +} /* end H5S_select_serial_size() */ /*-------------------------------------------------------------------------- @@ -311,7 +354,7 @@ H5S_select_serial_size(const H5S_t *space) herr_t H5S_select_serialize(const H5S_t *space, uint8_t **p) { - herr_t ret_value=SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOERR @@ -319,10 +362,10 @@ H5S_select_serialize(const H5S_t *space, uint8_t **p) HDassert(p); /* Call the selection type's serialize function */ - ret_value=(*space->select.type->serialize)(space,p); + ret_value = (*space->select.type->serialize)(space, p); FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_select_serialize() */ +} /* end H5S_select_serialize() */ /*-------------------------------------------------------------------------- @@ -359,7 +402,7 @@ H5Sget_select_npoints(hid_t spaceid) done: FUNC_LEAVE_API(ret_value) -} /* H5Sget_select_npoints() */ +} /* H5Sget_select_npoints() */ /*-------------------------------------------------------------------------- @@ -382,7 +425,7 @@ done: EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -hssize_t +H5_ATTR_PURE hssize_t H5S_get_select_npoints(const H5S_t *space) { FUNC_ENTER_NOAPI_NOINIT_NOERR @@ -391,7 +434,7 @@ H5S_get_select_npoints(const H5S_t *space) HDassert(space); FUNC_LEAVE_NOAPI((hssize_t)space->select.num_elem) -} /* H5S_get_select_npoints() */ +} /* end H5S_get_select_npoints() */ /*-------------------------------------------------------------------------- @@ -413,8 +456,6 @@ H5S_get_select_npoints(const H5S_t *space) COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG - Christian Chilan 01/17/2007 - Changed the error return value from 0 to FAIL. --------------------------------------------------------------------------*/ htri_t H5Sselect_valid(hid_t spaceid) @@ -433,7 +474,7 @@ H5Sselect_valid(hid_t spaceid) done: FUNC_LEAVE_API(ret_value) -} /* H5Sselect_valid() */ +} /* end H5Sselect_valid() */ /*-------------------------------------------------------------------------- @@ -471,7 +512,7 @@ H5S_select_valid(const H5S_t *space) ret_value = (*space->select.type->is_valid)(space); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_valid() */ +} /* end H5S_select_valid() */ /*-------------------------------------------------------------------------- @@ -584,7 +625,7 @@ H5S_select_deserialize(H5S_t **space, const uint8_t **p) default: break; - } + } /* end switch */ if(ret_value < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTLOAD, FAIL, "can't deserialize selection") @@ -599,7 +640,7 @@ done: HDONE_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace") FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_deserialize() */ +} /* end H5S_select_deserialize() */ /*-------------------------------------------------------------------------- @@ -651,7 +692,7 @@ H5Sget_select_bounds(hid_t spaceid, hsize_t start[], hsize_t end[]) done: FUNC_LEAVE_API(ret_value) -} /* H5Sget_select_bounds() */ +} /* end H5Sget_select_bounds() */ /*-------------------------------------------------------------------------- @@ -693,10 +734,10 @@ H5S_get_select_bounds(const H5S_t *space, hsize_t *start, hsize_t *end) HDassert(start); HDassert(end); - ret_value = (*space->select.type->bounds)(space,start,end); + ret_value = (*space->select.type->bounds)(space, start, end); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_get_select_bounds() */ +} /* end H5S_get_select_bounds() */ /*-------------------------------------------------------------------------- @@ -736,7 +777,7 @@ H5S_get_select_offset(const H5S_t *space, hsize_t *offset) ret_value = (*space->select.type->offset)(space, offset); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_get_select_offset() */ +} /* end H5S_get_select_offset() */ /*-------------------------------------------------------------------------- @@ -774,7 +815,7 @@ H5S_get_select_unlim_dim(const H5S_t *space) ret_value = (*space->select.type->unlim_dim)(space); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_get_select_unlim_dim() */ +} /* end H5S_get_select_unlim_dim() */ /*-------------------------------------------------------------------------- @@ -819,7 +860,7 @@ H5S_get_select_num_elem_non_unlim(const H5S_t *space, done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_get_select_unlim_dim() */ +} /* end H5S_get_select_unlim_dim() */ /*-------------------------------------------------------------------------- @@ -856,7 +897,7 @@ H5S_select_is_contiguous(const H5S_t *space) ret_value = (*space->select.type->is_contiguous)(space); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_is_contiguous() */ +} /* end H5S_select_is_contiguous() */ /*-------------------------------------------------------------------------- @@ -893,7 +934,7 @@ H5S_select_is_single(const H5S_t *space) ret_value = (*space->select.type->is_single)(space); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_is_single() */ +} /* end H5S_select_is_single() */ /*-------------------------------------------------------------------------- @@ -930,7 +971,7 @@ H5S_select_is_regular(const H5S_t *space) ret_value = (*space->select.type->is_regular)(space); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_is_regular() */ +} /* end H5S_select_is_regular() */ /*-------------------------------------------------------------------------- @@ -968,7 +1009,7 @@ H5S_select_adjust_u(H5S_t *space, const hsize_t *offset) ret_value = (*space->select.type->adjust_u)(space, offset); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_adjust_u() */ +} /* end H5S_select_adjust_u() */ /*-------------------------------------------------------------------------- @@ -1007,7 +1048,7 @@ H5S_select_project_scalar(const H5S_t *space, hsize_t *offset) ret_value = (*space->select.type->project_scalar)(space, offset); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_project_scalar() */ +} /* end H5S_select_project_scalar() */ /*-------------------------------------------------------------------------- @@ -1048,7 +1089,7 @@ H5S_select_project_simple(const H5S_t *space, H5S_t *new_space, hsize_t *offset) ret_value = (*space->select.type->project_simple)(space, new_space, offset); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_project_simple() */ +} /* end H5S_select_project_simple() */ /*-------------------------------------------------------------------------- @@ -1098,7 +1139,7 @@ H5S_select_iter_init(H5S_sel_iter_t *sel_iter, const H5S_t *space, size_t elmt_s HDassert(sel_iter->type); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_init() */ +} /* end H5S_select_iter_init() */ /*-------------------------------------------------------------------------- @@ -1135,10 +1176,10 @@ H5S_select_iter_coords(const H5S_sel_iter_t *sel_iter, hsize_t *coords) HDassert(coords); /* Call iter_coords routine for selection type */ - ret_value = (*sel_iter->type->iter_coords)(sel_iter,coords); + ret_value = (*sel_iter->type->iter_coords)(sel_iter, coords); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_coords() */ +} /* end H5S_select_iter_coords() */ #ifdef LATER @@ -1170,7 +1211,7 @@ H5S_select_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) { herr_t ret_value; /* return value */ - FUNC_ENTER_NOAPI_NOINIT_NOINIT_NOERR + FUNC_ENTER_NOAPI_NOINIT_NOERR /* Check args */ HDassert(iter); @@ -1178,10 +1219,10 @@ H5S_select_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) HDassert(end); /* Call iter_block routine for selection type */ - ret_value = (*iter->type->iter_block)(iter,start,end); + ret_value = (*iter->type->iter_block)(iter, start, end); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_block() */ +} /* end H5S_select_iter_block() */ #endif /* LATER */ @@ -1219,7 +1260,7 @@ H5S_select_iter_nelmts(const H5S_sel_iter_t *sel_iter) ret_value = (*sel_iter->type->iter_nelmts)(sel_iter); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_nelmts() */ +} /* end H5S_select_iter_nelmts() */ #ifdef LATER @@ -1249,7 +1290,7 @@ H5S_select_iter_has_next_block(const H5S_sel_iter_t *iter) { herr_t ret_value; /* return value */ - FUNC_ENTER_NOAPI_NOINIT_NOINIT_NOERR + FUNC_ENTER_NOAPI_NOINIT_NOERR /* Check args */ HDassert(iter); @@ -1258,7 +1299,7 @@ H5S_select_iter_has_next_block(const H5S_sel_iter_t *iter) ret_value = (*iter->type->iter_has_next_block)(iter); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_has_next_block() */ +} /* end H5S_select_iter_has_next_block() */ #endif /* LATER */ @@ -1296,13 +1337,13 @@ H5S_select_iter_next(H5S_sel_iter_t *iter, size_t nelem) HDassert(nelem>0); /* Call iter_next routine for selection type */ - ret_value = (*iter->type->iter_next)(iter,nelem); + ret_value = (*iter->type->iter_next)(iter, nelem); /* Decrement the number of elements left in selection */ iter->elmt_left-=nelem; FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_next() */ +} /* end H5S_select_iter_next() */ #ifdef LATER @@ -1343,10 +1384,48 @@ H5S_select_iter_next_block(H5S_sel_iter_t *iter) ret_value = (*iter->type->iter_next_block)(iter); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_next_block() */ +} /* end H5S_select_iter_next_block() */ #endif /* LATER */ +/*------------------------------------------------------------------------- + * Function: H5S_select_get_seq_list + * + * Purpose: Retrieves the next sequence of offset/length pairs for an + * iterator on a dataspace + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, May 18, 2004 + * + * Note: This routine participates in the "Inlining C function pointers" + * pattern, don't call it directly, use the appropriate macro + * defined in H5Sprivate.h. + * + *------------------------------------------------------------------------- + */ +herr_t +H5S_select_get_seq_list(const H5S_t *space, unsigned flags, + H5S_sel_iter_t *iter, size_t maxseq, size_t maxbytes, + size_t *nseq, size_t *nbytes, hsize_t *off, size_t *len) +{ + herr_t ret_value = FAIL; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Sanity check */ + HDassert(space); + + /* Call the selection type's get_seq_list function */ + if((ret_value = (*space->select.type->get_seq_list)(space, flags, iter, maxseq, maxbytes, nseq, nbytes, off, len)) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get selection sequence list") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5S_select_get_seq_list() */ + + /*-------------------------------------------------------------------------- NAME H5S_select_iter_release @@ -1381,7 +1460,7 @@ H5S_select_iter_release(H5S_sel_iter_t *sel_iter) ret_value = (*sel_iter->type->iter_release)(sel_iter); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_iter_release() */ +} /* end H5S_select_iter_release() */ /*-------------------------------------------------------------------------- @@ -1421,7 +1500,7 @@ H5S_select_iterate(void *buf, const H5T_t *type, const H5S_t *space, hsize_t *off = NULL; /* Array to store sequence offsets */ size_t *len = NULL; /* Array to store sequence lengths */ hssize_t nelmts; /* Number of elements in selection */ - hsize_t space_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */ + hsize_t space_size[H5S_MAX_RANK]; /* Dataspace size */ size_t max_elem; /* Maximum number of elements allowed in sequences */ size_t elmt_size; /* Datatype size */ unsigned ndims; /* Number of dimensions in dataspace */ @@ -1459,7 +1538,7 @@ H5S_select_iterate(void *buf, const H5T_t *type, const H5S_t *space, if(ndims > 0) { /* Copy the size of the space */ HDassert(space->extent.size); - HDmemcpy(space_size, space->extent.size, ndims * sizeof(hsize_t)); + H5MM_memcpy(space_size, space->extent.size, ndims * sizeof(hsize_t)); } /* end if */ space_size[ndims] = elmt_size; @@ -1495,7 +1574,7 @@ H5S_select_iterate(void *buf, const H5T_t *type, const H5S_t *space, /* Loop, while bytes left in sequence */ while(curr_len > 0 && user_ret == 0) { - hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of element in dataspace */ + hsize_t coords[H5S_MAX_RANK]; /* Coordinates of element in dataspace */ hsize_t tmp_off; /* Temporary offset within sequence */ uint8_t *loc; /* Current element location in buffer */ int i; /* Local Index variable */ @@ -1558,7 +1637,7 @@ done: iter = H5FL_FREE(H5S_sel_iter_t, iter); FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_select_iterate() */ +} /* end H5S_select_iterate() */ /*-------------------------------------------------------------------------- @@ -1594,7 +1673,7 @@ H5Sget_select_type(hid_t space_id) done: FUNC_LEAVE_API(ret_value) -} /* end H5Sget_select_type() */ +} /* end H5Sget_select_type() */ /*-------------------------------------------------------------------------- @@ -1616,7 +1695,7 @@ done: pattern, don't call it directly, use the appropriate macro defined in H5Sprivate.h. --------------------------------------------------------------------------*/ -H5S_sel_type +H5_ATTR_PURE H5S_sel_type H5S_get_select_type(const H5S_t *space) { H5S_sel_type ret_value = H5S_SEL_ERROR; /* Return value */ @@ -1627,10 +1706,10 @@ H5S_get_select_type(const H5S_t *space) HDassert(space); /* Set return value */ - ret_value=H5S_GET_SELECT_TYPE(space); + ret_value = H5S_GET_SELECT_TYPE(space); FUNC_LEAVE_NOAPI(ret_value) -} /* end H5S_get_select_type() */ +} /* end H5S_get_select_type() */ /*-------------------------------------------------------------------------- @@ -1653,17 +1732,15 @@ H5S_get_select_type(const H5S_t *space) Assumes that there is only a single "block" for hyperslab selections. EXAMPLES REVISION LOG - Modified function to view identical shapes with different dimensions - as being the same under some circumstances. --------------------------------------------------------------------------*/ htri_t H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2) { H5S_sel_iter_t *iter_a = NULL; /* Selection a iteration info */ H5S_sel_iter_t *iter_b = NULL; /* Selection b iteration info */ - hbool_t iter_a_init = FALSE; /* Selection a iteration info has been initialized */ - hbool_t iter_b_init = FALSE; /* Selection b iteration info has been initialized */ - htri_t ret_value = TRUE; /* Return value */ + hbool_t iter_a_init = FALSE; /* Selection a iteration info has been initialized */ + hbool_t iter_b_init = FALSE; /* Selection b iteration info has been initialized */ + htri_t ret_value = TRUE; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -1683,20 +1760,19 @@ H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2) unsigned space_a_rank; /* Number of dimensions of dataspace A */ unsigned space_b_rank; /* Number of dimensions of dataspace B */ - /* need to be able to handle spaces of different rank: + /* Need to be able to handle spaces of different rank: * * To simplify logic, let space_a point to the element of the set - * {space1, space2} with the largest rank or space1 if the ranks + * {space1, space2} with the largest rank or space1 if the ranks * are identical. * * Similarly, let space_b point to the element of {space1, space2} * with the smallest rank, or space2 if they are identical. * - * Let: space_a_rank be the rank of space_a, + * Let: space_a_rank be the rank of space_a, * space_b_rank be the rank of space_b, - * delta_rank = space_a_rank - space_b_rank. * - * Set all this up below. + * Set all this up here. */ if(space1->extent.rank >= space2->extent.rank) { space_a = space1; @@ -1835,11 +1911,11 @@ H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2) space_a_dim = (int)space_a_rank - 1; space_b_dim = (int)space_b_rank - 1; - /* The first block only compares the sizes and sets the - * relative offsets for later blocks + /* The first block only compares the sizes and sets the + * relative offsets for later blocks */ if(first_block) { - /* If the block sizes in the common dimensions from + /* If the block sizes in the common dimensions from * each selection don't match, get out */ while(space_b_dim >= 0) { @@ -1855,7 +1931,7 @@ H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2) space_b_dim--; } /* end while */ - /* similarly, if the block size in any dimension that appears only + /* Similarly, if the block size in any dimension that appears only * in space_a is not equal to 1, get out. */ while(space_a_dim >= 0) { @@ -1873,7 +1949,7 @@ H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2) } /* end if */ /* Check over the blocks for each selection */ else { - /* for dimensions that space_a and space_b have in common: */ + /* For dimensions that space_a and space_b have in common: */ while(space_b_dim >= 0) { /* Check if the blocks are in the same relative location */ if((start_a[space_a_dim] - off_a[space_a_dim]) != @@ -1934,7 +2010,7 @@ done: iter_b = H5FL_FREE(H5S_sel_iter_t, iter_b); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_shape_same() */ +} /* end H5S_select_shape_same() */ /*-------------------------------------------------------------------------- @@ -1943,24 +2019,24 @@ done: PURPOSE Given a dataspace a of rank n with some selection, construct a new - dataspace b of rank m (m != n), with the selection in a being - topologically identical to that in b (as verified by + dataspace b of rank m (m != n), with the selection in a being + topologically identical to that in b (as verified by H5S_select_shape_same(). - This function exists, as some I/O code chokes on topologically - identical selections with different ranks. At least to begin + This function exists, as some I/O code chokes on topologically + identical selections with different ranks. At least to begin with, we will deal with the issue by constructing projections - of the memory dataspace with ranks equaling those of the file + of the memory dataspace with ranks equaling those of the file dataspace. - Note that if m > n, it is possible that the starting point in the - buffer associated with the memory dataspace will have to be + Note that if m > n, it is possible that the starting point in the + buffer associated with the memory dataspace will have to be adjusted to match the projected dataspace. If the buf parameter is not NULL, the function must return an adjusted buffer base address in *adj_buf_ptr. USAGE - htri_t H5S_select_construct_projection(base_space, + htri_t H5S_select_construct_projection(base_space, new_space_ptr, new_space_rank, buf, @@ -1969,30 +2045,30 @@ done: H5S_t ** new_space_ptr; OUT: Ptr to location in which to return the address of the projected space int new_space_rank; IN: Rank of the projected space. - const void * buf; IN: Base address of the buffer + const void * buf; IN: Base address of the buffer associated with the base space. May be NULL. void ** adj_buf_ptr; OUT: If buf != NULL, store the base - address of the section of buf + address of the section of buf that is described by *new_space_ptr in *adj_buf_ptr. - + RETURNS Non-negative on success/Negative on failure. DESCRIPTION - Construct a new dataspace and associated selection which is a - projection of the supplied dataspace and associated selection into + Construct a new dataspace and associated selection which is a + projection of the supplied dataspace and associated selection into the specified rank. Return it in *new_space_ptr. - If buf is supplied, computes the base address of the projected + If buf is supplied, computes the base address of the projected selection in buf, and stores the base address in *adj_buf_ptr. - + GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS - The selection in the supplied base_space has thickness 1 in all + The selection in the supplied base_space has thickness 1 in all dimensions greater than new_space_rank. Note that here we count - dimensions from the fastest changing coordinate to the slowest + dimensions from the fastest changing coordinate to the slowest changing changing coordinate. EXAMPLES REVISION LOG @@ -2038,28 +2114,28 @@ H5S_select_construct_projection(const H5S_t *base_space, H5S_t **new_space_ptr, /* Create new scalar dataspace */ if(NULL == (new_space = H5S_create(H5S_SCALAR))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create scalar dataspace") - + /* No need to register the dataspace(i.e. get an ID) as * we will just be discarding it shortly. */ - /* Selection for the new space will be either all or + /* Selection for the new space will be either all or * none, depending on whether the base space has 0 or * 1 elements selected. * - * Observe that the base space can't have more than + * Observe that the base space can't have more than * one selected element, since its selection has the - * same shape as the file dataspace, and that data + * same shape as the file dataspace, and that data * space is scalar. */ if(1 == npoints) { /* Assuming that the selection in the base dataspace is not - * empty, we must compute the offset of the selected item in + * empty, we must compute the offset of the selected item in * the buffer associated with the base dataspace. * - * Since the new space rank is zero, we know that the - * the base space must have rank at least 1 -- and - * hence it is a simple dataspace. However, the + * Since the new space rank is zero, we know that the + * the base space must have rank at least 1 -- and + * hence it is a simple dataspace. However, the * selection, may be either point, hyperspace, or all. * */ @@ -2077,25 +2153,25 @@ H5S_select_construct_projection(const H5S_t *base_space, H5S_t **new_space_ptr, hsize_t new_space_dims[H5S_MAX_RANK]; /* Current dimensions for new dataspace */ hsize_t new_space_maxdims[H5S_MAX_RANK];/* Maximum dimensions for new dataspace */ unsigned rank_diff; /* Difference in ranks */ - + /* Set up the dimensions of the new, projected dataspace. * - * How we do this depends on whether we are projecting up into - * increased dimensions, or down into a reduced number of + * How we do this depends on whether we are projecting up into + * increased dimensions, or down into a reduced number of * dimensions. * - * If we are projecting up (the first half of the following - * if statement), we copy the dimensions of the base data - * space into the fastest changing dimensions of the new + * If we are projecting up (the first half of the following + * if statement), we copy the dimensions of the base data + * space into the fastest changing dimensions of the new * projected dataspace, and set the remaining dimensions to * one. * * If we are projecting down (the second half of the following - * if statement), we just copy the dimensions with the most + * if statement), we just copy the dimensions with the most * quickly changing dimensions into the dims for the projected * data set. * - * This works, because H5S_select_shape_same() will return + * This works, because H5S_select_shape_same() will return * true on selections of different rank iff: * * 1) the selection in the lower rank dataspace matches that @@ -2103,37 +2179,37 @@ H5S_select_construct_projection(const H5S_t *base_space, H5S_t **new_space_ptr, * the larger rank dataspace, and * * 2) the selection has thickness 1 in all ranks that appear - * only in the higher rank dataspace (i.e. those with + * only in the higher rank dataspace (i.e. those with * more slowly changing indicies). - */ + */ if(new_space_rank > base_space_rank) { hsize_t tmp_dim_size = 1; /* Temporary dimension value, for filling arrays */ - /* we must copy the dimensions of the base space into + /* we must copy the dimensions of the base space into * the fastest changing dimensions of the new space, * and set the remaining dimensions to 1 */ rank_diff = new_space_rank - base_space_rank; H5VM_array_fill(new_space_dims, &tmp_dim_size, sizeof(tmp_dim_size), rank_diff); H5VM_array_fill(new_space_maxdims, &tmp_dim_size, sizeof(tmp_dim_size), rank_diff); - HDmemcpy(&new_space_dims[rank_diff], base_space_dims, sizeof(new_space_dims[0]) * base_space_rank); - HDmemcpy(&new_space_maxdims[rank_diff], base_space_maxdims, sizeof(new_space_maxdims[0]) * base_space_rank); + H5MM_memcpy(&new_space_dims[rank_diff], base_space_dims, sizeof(new_space_dims[0]) * base_space_rank); + H5MM_memcpy(&new_space_maxdims[rank_diff], base_space_maxdims, sizeof(new_space_maxdims[0]) * base_space_rank); } /* end if */ else { /* new_space_rank < base_space_rank */ - /* we must copy the fastest changing dimension of the + /* we must copy the fastest changing dimension of the * base space into the dimensions of the new space. */ rank_diff = base_space_rank - new_space_rank; - HDmemcpy(new_space_dims, &base_space_dims[rank_diff], sizeof(new_space_dims[0]) * new_space_rank); - HDmemcpy(new_space_maxdims, &base_space_maxdims[rank_diff], sizeof(new_space_maxdims[0]) * new_space_rank); + H5MM_memcpy(new_space_dims, &base_space_dims[rank_diff], sizeof(new_space_dims[0]) * new_space_rank); + H5MM_memcpy(new_space_maxdims, &base_space_maxdims[rank_diff], sizeof(new_space_maxdims[0]) * new_space_rank); } /* end else */ - /* now have the new space rank and dimensions set up -- + /* now have the new space rank and dimensions set up -- * so we can create the new simple dataspace. */ if(NULL == (new_space = H5S_create_simple(new_space_rank, new_space_dims, new_space_maxdims))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") - + /* No need to register the dataspace(i.e. get an ID) as * we will just be discarding it shortly. */ @@ -2144,22 +2220,22 @@ H5S_select_construct_projection(const H5S_t *base_space, H5S_t **new_space_ptr, */ if(H5S_SELECT_PROJECT_SIMPLE(base_space, new_space, &projected_space_element_offset) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "unable to project simple selection") - + /* If we get this far, we have created the new dataspace, and projected * the selection in the base dataspace into the new dataspace. * - * If the base dataspace is simple, check to see if the - * offset_changed flag on the base selection has been set -- if so, - * project the offset into the new dataspace and set the + * If the base dataspace is simple, check to see if the + * offset_changed flag on the base selection has been set -- if so, + * project the offset into the new dataspace and set the * offset_changed flag. */ if(H5S_GET_EXTENT_TYPE(base_space) == H5S_SIMPLE && base_space->select.offset_changed) { if(new_space_rank > base_space_rank) { HDmemset(new_space->select.offset, 0, sizeof(new_space->select.offset[0]) * rank_diff); - HDmemcpy(&new_space->select.offset[rank_diff], base_space->select.offset, sizeof(new_space->select.offset[0]) * base_space_rank); + H5MM_memcpy(&new_space->select.offset[rank_diff], base_space->select.offset, sizeof(new_space->select.offset[0]) * base_space_rank); } /* end if */ else - HDmemcpy(new_space->select.offset, &base_space->select.offset[rank_diff], sizeof(new_space->select.offset[0]) * new_space_rank); + H5MM_memcpy(new_space->select.offset, &base_space->select.offset[rank_diff], sizeof(new_space->select.offset[0]) * new_space_rank); /* Propagate the offset changed flag into the new dataspace. */ new_space->select.offset_changed = TRUE; @@ -2182,12 +2258,12 @@ H5S_select_construct_projection(const H5S_t *base_space, H5S_t **new_space_ptr, * Since we can't do pointer arithmetic on void pointers, we first * cast buf to a pointer to byte -- i.e. uint8_t. * - * We then multiply the projected space element offset we - * calculated earlier by the supplied element size, add this - * value to the type cast buf pointer, cast the result back + * We then multiply the projected space element offset we + * calculated earlier by the supplied element size, add this + * value to the type cast buf pointer, cast the result back * to a pointer to void, and assign the result to *adj_buf_ptr. */ - *adj_buf_ptr = (const void *)(((const uint8_t *)buf) + + *adj_buf_ptr = (const void *)(((const uint8_t *)buf) + ((size_t)(projected_space_element_offset * element_size))); } /* end if */ else @@ -2202,7 +2278,7 @@ done: HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_construct_projection() */ +} /* end H5S_select_construct_projection() */ /*-------------------------------------------------------------------------- @@ -2233,7 +2309,7 @@ herr_t H5S_select_fill(const void *fill, size_t fill_size, const H5S_t *space, void *_buf) { H5S_sel_iter_t *iter = NULL; /* Selection iteration info */ - hbool_t iter_init = 0; /* Selection iteration info has been initialized */ + hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ hsize_t *off = NULL; /* Array to store sequence offsets */ size_t *len = NULL; /* Array to store sequence lengths */ hssize_t nelmts; /* Number of elements in selection */ @@ -2255,7 +2331,7 @@ H5S_select_fill(const void *fill, size_t fill_size, const H5S_t *space, void *_b /* Initialize iterator */ if(H5S_select_iter_init(iter, space, fill_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") - iter_init = 1; /* Selection iteration info has been initialized */ + iter_init = TRUE; /* Selection iteration info has been initialized */ /* Get the number of elements in selection */ if((nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0) @@ -2310,7 +2386,7 @@ done: iter = H5FL_FREE(H5S_sel_iter_t, iter); FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_fill() */ +} /* end H5S_select_fill() */ /*-------------------------------------------------------------------------- @@ -2337,7 +2413,7 @@ done: src_intersect_space within the selection of src_space as a selection within the selection of dst_space. The result is placed in the selection of new_space_ptr. - + GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES @@ -2361,7 +2437,7 @@ H5S_select_project_intersection(const H5S_t *src_space, const H5S_t *dst_space, /* Create new space, using dst extent. Start with "all" selection. */ if(NULL == (new_space = H5S_create(H5S_SIMPLE))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create output dataspace") - if(H5S_extent_copy_real(&new_space->extent, &dst_space->extent, TRUE) < 0) + if(H5S__extent_copy_real(&new_space->extent, &dst_space->extent, TRUE) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy destination space extent") /* If the intersecting space is "all", the intersection must be equal to the @@ -2379,14 +2455,14 @@ H5S_select_project_intersection(const H5S_t *src_space, const H5S_t *dst_space, if(H5S_select_none(new_space) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't change selection") } /* end if */ - /* If any of the spaces use point selection, fall back to general algorithm - */ + /* If any of the spaces use point selection, fall back to general algorithm */ else if((src_intersect_space->select.type->type == H5S_SEL_POINTS) || (src_space->select.type->type == H5S_SEL_POINTS) || (dst_space->select.type->type == H5S_SEL_POINTS)) HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "point selections not currently supported") else { HDassert(src_intersect_space->select.type->type == H5S_SEL_HYPERSLABS); + /* Intersecting space is hyperslab selection. Call the hyperslab * routine to project to another hyperslab selection. */ if(H5S__hyper_project_intersection(src_space, dst_space, src_intersect_space, new_space) < 0) @@ -2403,7 +2479,7 @@ done: HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_project_intersection() */ +} /* end H5S_select_project_intersection() */ /*-------------------------------------------------------------------------- @@ -2425,7 +2501,7 @@ done: Removes any and all portions of space that are also present in subtract_space. In essence, performs an A_NOT_B operation with the two selections. - + GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES @@ -2493,5 +2569,5 @@ H5S_select_subtract(H5S_t *space, H5S_t *subtract_space) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_subtract() */ +} /* end H5S_select_subtract() */ diff --git a/src/H5Stest.c b/src/H5Stest.c index a7bee2b..50f5fa9 100644 --- a/src/H5Stest.c +++ b/src/H5Stest.c @@ -17,23 +17,60 @@ * Purpose: Dataspace selection testing functions. */ +/****************/ +/* Module Setup */ +/****************/ + #include "H5Smodule.h" /* This source code file is part of the H5S module */ #define H5S_TESTING /*suppress warning about H5S testing funcs*/ +/***********/ +/* Headers */ +/***********/ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5Iprivate.h" /* IDs */ #include "H5Spkg.h" /* Dataspaces */ +/****************/ +/* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ + + +/********************/ +/* Local Prototypes */ +/********************/ + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*********************/ +/* Package Variables */ +/*********************/ + + +/*******************/ +/* Local Variables */ +/*******************/ + + /*-------------------------------------------------------------------------- NAME - H5S_select_shape_same_test + H5S__select_shape_same_test PURPOSE Determine if two dataspace selections are the same shape USAGE - htri_t H5S_select_shape_same_test(sid1, sid2) + htri_t H5S__select_shape_same_test(sid1, sid2) hid_t sid1; IN: 1st dataspace to compare hid_t sid2; IN: 2nd dataspace to compare RETURNS @@ -48,13 +85,13 @@ REVISION LOG --------------------------------------------------------------------------*/ htri_t -H5S_select_shape_same_test(hid_t sid1, hid_t sid2) +H5S__select_shape_same_test(hid_t sid1, hid_t sid2) { H5S_t *space1; /* Pointer to 1st dataspace */ H5S_t *space2; /* Pointer to 2nd dataspace */ htri_t ret_value = FAIL; /* Return value */ - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_PACKAGE /* Get dataspace structures */ if(NULL == (space1 = (H5S_t *)H5I_object_verify(sid1, H5I_DATASPACE))) @@ -68,16 +105,16 @@ H5S_select_shape_same_test(hid_t sid1, hid_t sid2) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_select_shape_same_test() */ +} /* H5S__select_shape_same_test() */ /*-------------------------------------------------------------------------- NAME - H5S_get_rebuild_status_test + H5S__get_rebuild_status_test PURPOSE Determine the status of hyperslab rebuild USAGE - htri_t H5S_inquiry_rebuild_status(hid_t space_id) + htri_t H5S__get_rebuild_status_test(hid_t space_id) hid_t space_id; IN: dataspace id RETURNS Non-negative TRUE/FALSE on success, negative on failure @@ -90,12 +127,12 @@ done: REVISION LOG --------------------------------------------------------------------------*/ htri_t -H5S_get_rebuild_status_test(hid_t space_id) +H5S__get_rebuild_status_test(hid_t space_id) { H5S_t *space; /* Pointer to 1st dataspace */ htri_t ret_value = FAIL; /* Return value */ - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_PACKAGE /* Get dataspace structures */ if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) @@ -105,5 +142,5 @@ H5S_get_rebuild_status_test(hid_t space_id) done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5S_get_rebuild_status_test() */ +} /* H5S__get_rebuild_status_test() */ @@ -1397,7 +1397,7 @@ H5T_top_term_package(void) if((path->conv.u.lib_func)((hid_t)FAIL, (hid_t)FAIL, &(path->cdata), (size_t)0, (size_t)0, (size_t)0, NULL, NULL) < 0) { #ifdef H5T_DEBUG if (H5DEBUG(T)) { - fprintf(H5DEBUG(T), "H5T: conversion function " + HDfprintf(H5DEBUG(T), "H5T: conversion function " "0x%08lx failed to free private data for " "%s (ignored)\n", (unsigned long)(path->conv.u.lib_func), path->name); @@ -3338,7 +3338,7 @@ H5T_copy(H5T_t *old_dt, H5T_copy_t method) if (NULL == new_dt->shared->u.compnd.memb) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(new_dt->shared->u.compnd.memb, old_dt->shared->u.compnd.memb, + H5MM_memcpy(new_dt->shared->u.compnd.memb, old_dt->shared->u.compnd.memb, new_dt->shared->u.compnd.nmembs * sizeof(H5T_cmemb_t)); } /* end if */ @@ -3404,7 +3404,7 @@ H5T_copy(H5T_t *old_dt, H5T_copy_t method) (uint8_t *)H5MM_malloc(new_dt->shared->u.enumer.nalloc * new_dt->shared->size); if(NULL == new_dt->shared->u.enumer.value) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - HDmemcpy(new_dt->shared->u.enumer.value, old_dt->shared->u.enumer.value, + H5MM_memcpy(new_dt->shared->u.enumer.value, old_dt->shared->u.enumer.value, new_dt->shared->u.enumer.nmembs * new_dt->shared->size); for(i = 0; i < new_dt->shared->u.enumer.nmembs; i++) { s = old_dt->shared->u.enumer.name[i]; diff --git a/src/H5Tcommit.c b/src/H5Tcommit.c index 712b264..c6b85a5 100644 --- a/src/H5Tcommit.c +++ b/src/H5Tcommit.c @@ -1211,7 +1211,7 @@ H5T_save_refresh_state(hid_t tid, H5O_shared_t *cached_H5O_shared) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINC, FAIL, "can't increment object count") /* Cache the H5O_shared_t data */ - HDmemcpy(cached_H5O_shared, &(vol_dt->sh_loc), sizeof(H5O_shared_t)); + H5MM_memcpy(cached_H5O_shared, &(vol_dt->sh_loc), sizeof(H5O_shared_t)); done: FUNC_LEAVE_NOAPI(ret_value) @@ -1245,7 +1245,7 @@ H5T_restore_refresh_state(hid_t tid, H5O_shared_t *cached_H5O_shared) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "tid is not not a named datatype ID") /* Restore the H5O_shared_t data */ - HDmemcpy(&(vol_dt->sh_loc), cached_H5O_shared, sizeof(H5O_shared_t)); + H5MM_memcpy(&(vol_dt->sh_loc), cached_H5O_shared, sizeof(H5O_shared_t)); /* Decrement the ref. count for this object in the top file */ if(H5FO_top_decr(vol_dt->sh_loc.file, vol_dt->sh_loc.u.loc.oh_addr) < 0) diff --git a/src/H5Tconv.c b/src/H5Tconv.c index e6d83bb..7d47483 100644 --- a/src/H5Tconv.c +++ b/src/H5Tconv.c @@ -828,7 +828,7 @@ done: \ /* Macro defining action on source data which needs to be aligned (before main action) */ #define H5T_CONV_LOOP_PRE_SALIGN(ST) { \ - HDmemcpy(&src_aligned, src, sizeof(ST)); \ + H5MM_memcpy(&src_aligned, src, sizeof(ST)); \ } /* Macro defining action on source data which doesn't need to be aligned (before main action) */ @@ -854,7 +854,7 @@ done: \ /* Macro defining action on destination data which needs to be aligned (after main action) */ #define H5T_CONV_LOOP_POST_DALIGN(DT) { \ - HDmemcpy(dst, &dst_aligned, sizeof(DT)); \ + H5MM_memcpy(dst, &dst_aligned, sizeof(DT)); \ } /* Macro defining action on destination data which doesn't need to be aligned (after main action) */ @@ -1797,7 +1797,7 @@ H5T__conv_b_b(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, * should copy the value to the true destination buffer. */ if(d == dbuf) - HDmemcpy(dp, d, dst->shared->size); + H5MM_memcpy(dp, d, dst->shared->size); if(buf_stride) { sp += direction * (ssize_t)buf_stride; /* Note that cast is checked with H5_CHECK_OVERFLOW, above */ dp += direction * (ssize_t)buf_stride; /* Note that cast is checked with H5_CHECK_OVERFLOW, above */ @@ -2771,7 +2771,7 @@ H5T__conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, case H5T_CONV_FREE: #ifdef H5T_DEBUG if (H5DEBUG(T)) { - fprintf(H5DEBUG(T), " Using %s mapping function%s\n", + HDfprintf(H5DEBUG(T), " Using %s mapping function%s\n", priv->length?"O(1)":"O(log N)", priv->length?"":", where N is the number of enum members"); } @@ -2852,7 +2852,7 @@ H5T__conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, else if(except_ret == H5T_CONV_ABORT) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCONVERT, FAIL, "can't handle conversion exception") } else - HDmemcpy(d, + H5MM_memcpy(d, dst->shared->u.enumer.value + (unsigned)priv->src2dst[n] * dst->shared->size, dst->shared->size); } /* end if */ @@ -2888,7 +2888,7 @@ H5T__conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, } /* end if */ else { HDassert(priv->src2dst[md] >= 0); - HDmemcpy(d, + H5MM_memcpy(d, dst->shared->u.enumer.value + (unsigned)priv->src2dst[md] * dst->shared->size, dst->shared->size); } /* end else */ @@ -3846,7 +3846,7 @@ H5T__conv_i_i(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, * should copy the value to the true destination buffer. */ if(d==dbuf) - HDmemcpy(dp, d, dst->shared->size); + H5MM_memcpy(dp, d, dst->shared->size); /* Advance source & destination pointers by delta amounts */ sp += src_delta; @@ -4432,7 +4432,7 @@ H5T__conv_f_f(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, */ next: if(d == dbuf) - HDmemcpy(dp, d, dst_p->shared->size); + H5MM_memcpy(dp, d, dst_p->shared->size); /* Advance source & destination pointers by delta amounts */ sp += src_delta; @@ -4604,7 +4604,7 @@ H5T__conv_s_s(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, --nchars; nchars = MIN(dst->shared->size, nchars); if(d != s) - HDmemcpy(d, s, nchars); + H5MM_memcpy(d, s, nchars); break; case H5T_STR_RESERVED_3: @@ -4666,7 +4666,7 @@ H5T__conv_s_s(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, * should copy the value to the true destination buffer. */ if(d == dbuf) - HDmemcpy(dp, d, dst->shared->size); + H5MM_memcpy(dp, d, dst->shared->size); /* Advance source & destination pointers by delta amounts */ sp += src_delta; @@ -8825,7 +8825,7 @@ H5T__conv_f_i(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, * should copy the value to the true destination buffer. */ if (d==dbuf) - HDmemcpy (dp, d, dst_p->shared->size); + H5MM_memcpy (dp, d, dst_p->shared->size); if (buf_stride) { sp += direction * (ssize_t) buf_stride; dp += direction * (ssize_t) buf_stride; @@ -9235,7 +9235,7 @@ H5T__conv_i_f(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, * should copy the value to the true destination buffer. */ if (d==dbuf) - HDmemcpy (dp, d, dst_p->shared->size); + H5MM_memcpy (dp, d, dst_p->shared->size); if (buf_stride) { sp += direction * (ssize_t) buf_stride; dp += direction * (ssize_t) buf_stride; diff --git a/src/H5Tenum.c b/src/H5Tenum.c index 0ed1775..ff88fab 100644 --- a/src/H5Tenum.c +++ b/src/H5Tenum.c @@ -223,7 +223,7 @@ H5T__enum_insert(const H5T_t *dt, const char *name, const void *value) dt->shared->u.enumer.sorted = H5T_SORT_NONE; i = dt->shared->u.enumer.nmembs++; dt->shared->u.enumer.name[i] = H5MM_xstrdup(name); - HDmemcpy(dt->shared->u.enumer.value+i*dt->shared->size, value, dt->shared->size); + H5MM_memcpy(dt->shared->u.enumer.value+i*dt->shared->size, value, dt->shared->size); done: FUNC_LEAVE_NOAPI(ret_value) @@ -298,7 +298,7 @@ H5T__get_member_value(const H5T_t *dt, unsigned membno, void *value/*out*/) HDassert(dt); HDassert(value); - HDmemcpy(value, dt->shared->u.enumer.value + membno*dt->shared->size, dt->shared->size); + H5MM_memcpy(value, dt->shared->u.enumer.value + membno*dt->shared->size, dt->shared->size); FUNC_LEAVE_NOAPI(SUCCEED) } @@ -569,7 +569,7 @@ H5T_enum_valueof(const H5T_t *dt, const char *name, void *value/*out*/) if (cmp!=0) HGOTO_ERROR(H5E_DATATYPE, H5E_NOTFOUND, FAIL, "string doesn't exist in the enumeration type") - HDmemcpy(value, copied_dt->shared->u.enumer.value+md*copied_dt->shared->size, copied_dt->shared->size); + H5MM_memcpy(value, copied_dt->shared->u.enumer.value+md*copied_dt->shared->size, copied_dt->shared->size); done: if(copied_dt) diff --git a/src/H5Tfields.c b/src/H5Tfields.c index be62d85..8202c2c 100644 --- a/src/H5Tfields.c +++ b/src/H5Tfields.c @@ -351,10 +351,10 @@ H5T__sort_value(const H5T_t *dt, int *map) dt->shared->u.enumer.name[j + 1] = tmp; /* Swap values */ - HDmemcpy(tbuf, dt->shared->u.enumer.value + (j * size), size); - HDmemcpy(dt->shared->u.enumer.value + (j * size), + H5MM_memcpy(tbuf, dt->shared->u.enumer.value + (j * size), size); + H5MM_memcpy(dt->shared->u.enumer.value + (j * size), dt->shared->u.enumer.value + ((j + 1) * size), size); - HDmemcpy(dt->shared->u.enumer.value + ((j + 1) * size), tbuf, size); + H5MM_memcpy(dt->shared->u.enumer.value + ((j + 1) * size), tbuf, size); /* Swap map */ if(map) { @@ -457,10 +457,10 @@ H5T__sort_name(const H5T_t *dt, int *map) dt->shared->u.enumer.name[j+1] = tmp; /* Swap values */ - HDmemcpy(tbuf, dt->shared->u.enumer.value+j*size, size); - HDmemcpy(dt->shared->u.enumer.value+j*size, + H5MM_memcpy(tbuf, dt->shared->u.enumer.value+j*size, size); + H5MM_memcpy(dt->shared->u.enumer.value+j*size, dt->shared->u.enumer.value+(j+1)*size, size); - HDmemcpy(dt->shared->u.enumer.value+(j+1)*size, tbuf, size); + H5MM_memcpy(dt->shared->u.enumer.value+(j+1)*size, tbuf, size); /* Swap map */ if (map) { diff --git a/src/H5Tnative.c b/src/H5Tnative.c index c9ad01a..3554f75 100644 --- a/src/H5Tnative.c +++ b/src/H5Tnative.c @@ -369,7 +369,7 @@ H5T__get_native_type(H5T_t *dtype, H5T_direction_t direction, size_t *struct_ali HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "cannot get member name") if(H5T__get_member_value(dtype, u, tmp_memb_value) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "cannot get member value") - HDmemcpy(memb_value, tmp_memb_value, H5T_get_size(super_type)); + H5MM_memcpy(memb_value, tmp_memb_value, H5T_get_size(super_type)); if(H5T_convert(tpath, super_type_id, nat_super_type_id, (size_t)1, (size_t)0, (size_t)0, memb_value, NULL) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "cannot get member value") diff --git a/src/H5Torder.c b/src/H5Torder.c index d687d03..62662d6 100644 --- a/src/H5Torder.c +++ b/src/H5Torder.c @@ -100,11 +100,11 @@ H5Tget_order(hid_t type_id) /* Check args */ if(NULL == (dt = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) - HGOTO_ERROR(H5E_DATATYPE, H5E_BADTYPE, H5T_ORDER_ERROR, "not a datatype") + HGOTO_ERROR(H5E_DATATYPE, H5E_BADTYPE, H5T_ORDER_ERROR, "not a datatype") /* Get order */ if(H5T_ORDER_ERROR == (ret_value = H5T_get_order(dt))) - HGOTO_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, H5T_ORDER_ERROR, "cant't get order for specified datatype") + HGOTO_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, H5T_ORDER_ERROR, "can't get order for specified datatype") done: FUNC_LEAVE_API(ret_value) diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c index 841637d..bafb47f 100644 --- a/src/H5Tvlen.c +++ b/src/H5Tvlen.c @@ -302,7 +302,7 @@ H5T_vlen_seq_mem_getlen(const void *_vl) FUNC_LEAVE_NOAPI((ssize_t)vl->len) #else HDassert(_vl); - HDmemcpy(&vl, _vl, sizeof(hvl_t)); + H5MM_memcpy(&vl, _vl, sizeof(hvl_t)); FUNC_LEAVE_NOAPI((ssize_t)vl.len) #endif @@ -339,7 +339,7 @@ H5T_vlen_seq_mem_getptr(void *_vl) FUNC_LEAVE_NOAPI(vl->p) #else HDassert(_vl); - HDmemcpy(&vl, _vl, sizeof(hvl_t)); + H5MM_memcpy(&vl, _vl, sizeof(hvl_t)); FUNC_LEAVE_NOAPI(vl.p) #endif @@ -376,7 +376,7 @@ H5T_vlen_seq_mem_isnull(const H5F_t H5_ATTR_UNUSED *f, void *_vl) FUNC_LEAVE_NOAPI((vl->len==0 || vl->p==NULL) ? TRUE : FALSE) #else HDassert(_vl); - HDmemcpy(&vl, _vl, sizeof(hvl_t)); + H5MM_memcpy(&vl, _vl, sizeof(hvl_t)); FUNC_LEAVE_NOAPI((vl.len==0 || vl.p==NULL) ? TRUE : FALSE) #endif @@ -411,13 +411,13 @@ H5T_vlen_seq_mem_read(H5F_t H5_ATTR_UNUSED *f, void *_vl, void *buf, size_t len) #ifdef H5_NO_ALIGNMENT_RESTRICTIONS HDassert(vl && vl->p); - HDmemcpy(buf,vl->p,len); + H5MM_memcpy(buf,vl->p,len); #else HDassert(_vl); - HDmemcpy(&vl, _vl, sizeof(hvl_t)); + H5MM_memcpy(&vl, _vl, sizeof(hvl_t)); HDassert(vl.p); - HDmemcpy(buf,vl.p,len); + H5MM_memcpy(buf,vl.p,len); #endif FUNC_LEAVE_NOAPI(SUCCEED) @@ -463,7 +463,7 @@ H5T_vlen_seq_mem_write(H5F_t H5_ATTR_UNUSED *f, const H5T_vlen_alloc_info_t *vl_ } /* end else */ /* Copy the data into the newly allocated buffer */ - HDmemcpy(vl.p,buf,len); + H5MM_memcpy(vl.p,buf,len); } /* end if */ else @@ -473,7 +473,7 @@ H5T_vlen_seq_mem_write(H5F_t H5_ATTR_UNUSED *f, const H5T_vlen_alloc_info_t *vl_ vl.len=seq_len; /* Set pointer in user's buffer with memcpy, to avoid alignment issues */ - HDmemcpy(_vl,&vl,sizeof(hvl_t)); + H5MM_memcpy(_vl,&vl,sizeof(hvl_t)); done: FUNC_LEAVE_NOAPI(ret_value) @@ -507,7 +507,7 @@ H5T_vlen_seq_mem_setnull(H5F_t H5_ATTR_UNUSED *f, void *_vl, void H5_ATTR_UNUSED vl.p=NULL; /* Set pointer in user's buffer with memcpy, to avoid alignment issues */ - HDmemcpy(_vl,&vl,sizeof(hvl_t)); + H5MM_memcpy(_vl,&vl,sizeof(hvl_t)); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5T_vlen_seq_mem_setnull() */ @@ -541,7 +541,7 @@ H5T_vlen_str_mem_getlen(const void *_vl) HDassert(s); #else HDassert(_vl); - HDmemcpy(&s, _vl, sizeof(char *)); + H5MM_memcpy(&s, _vl, sizeof(char *)); #endif FUNC_LEAVE_NOAPI((ssize_t)HDstrlen(s)) @@ -576,7 +576,7 @@ H5T_vlen_str_mem_getptr(void *_vl) HDassert(s); #else HDassert(_vl); - HDmemcpy(&s, _vl, sizeof(char *)); + H5MM_memcpy(&s, _vl, sizeof(char *)); #endif FUNC_LEAVE_NOAPI(s) @@ -607,7 +607,7 @@ H5T_vlen_str_mem_isnull(const H5F_t H5_ATTR_UNUSED *f, void *_vl) FUNC_ENTER_NOAPI_NOINIT_NOERR #ifndef H5_NO_ALIGNMENT_RESTRICTIONS - HDmemcpy(&s, _vl, sizeof(char *)); + H5MM_memcpy(&s, _vl, sizeof(char *)); #endif FUNC_LEAVE_NOAPI(s==NULL ? TRUE : FALSE) @@ -644,10 +644,10 @@ H5T_vlen_str_mem_read(H5F_t H5_ATTR_UNUSED *f, void *_vl, void *buf, size_t len) HDassert(s); #else HDassert(_vl); - HDmemcpy(&s, _vl, sizeof(char *)); + H5MM_memcpy(&s, _vl, sizeof(char *)); #endif - HDmemcpy(buf,s,len); + H5MM_memcpy(buf,s,len); } /* end if */ FUNC_LEAVE_NOAPI(SUCCEED) @@ -690,11 +690,11 @@ H5T_vlen_str_mem_write(H5F_t H5_ATTR_UNUSED *f, const H5T_vlen_alloc_info_t *vl_ } /* end else */ len=(seq_len*base_size); - HDmemcpy(t,buf,len); + H5MM_memcpy(t,buf,len); t[len]='\0'; /* Set pointer in user's buffer with memcpy, to avoid alignment issues */ - HDmemcpy(_vl,&t,sizeof(char *)); + H5MM_memcpy(_vl,&t,sizeof(char *)); done: FUNC_LEAVE_NOAPI(ret_value) /*lint !e429 The pointer in 't' has been copied */ @@ -721,7 +721,7 @@ H5T_vlen_str_mem_setnull(H5F_t H5_ATTR_UNUSED *f, void *_vl, void H5_ATTR_UNUSED FUNC_ENTER_NOAPI_NOINIT_NOERR /* Set pointer in user's buffer with memcpy, to avoid alignment issues */ - HDmemcpy(_vl,&t,sizeof(char *)); + H5MM_memcpy(_vl,&t,sizeof(char *)); FUNC_LEAVE_NOAPI(SUCCEED) /*lint !e429 The pointer in 't' has been copied */ } /* end H5T_vlen_str_mem_setnull() */ @@ -156,9 +156,9 @@ H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id) HGOTO_ERROR(H5E_VOL, H5E_CANTREGISTER, H5I_INVALID_HID, "VOL connector class name cannot be the NULL pointer") if (0 == HDstrlen(cls->name)) HGOTO_ERROR(H5E_VOL, H5E_CANTREGISTER, H5I_INVALID_HID, "VOL connector class name cannot be the empty string") - if (cls->info_copy && !cls->info_free) + if (cls->info_cls.copy && !cls->info_cls.free) HGOTO_ERROR(H5E_VOL, H5E_CANTREGISTER, H5I_INVALID_HID, "VOL connector must provide free callback for VOL info objects when a copy callback is provided") - if (cls->get_wrap_ctx && !cls->free_wrap_ctx) + if (cls->wrap_cls.get_wrap_ctx && !cls->wrap_cls.free_wrap_ctx) HGOTO_ERROR(H5E_VOL, H5E_CANTREGISTER, H5I_INVALID_HID, "VOL connector must provide free callback for object wrapping contexts when a get callback is provided") op_data.kind = H5VL_GET_CONNECTOR_BY_NAME; @@ -488,6 +488,9 @@ done: * * Purpose: Compares two connector classes (based on their value field) * + * Note: This routine is _only_ for HDF5 VOL connector authors! It is + * _not_ part of the public API for HDF5 application developers. + * * Return: Success: Non-negative, *cmp set to a value like strcmp * * Failure: Negative, *cmp unset @@ -587,3 +590,159 @@ done: FUNC_LEAVE_API(ret_value) } /* H5VLobject() */ + +/*--------------------------------------------------------------------------- + * Function: H5VLretrieve_lib_state + * + * Purpose: Retrieves a copy of the internal state of the HDF5 library, + * so that it can be restored later. + * + * Note: This routine is _only_ for HDF5 VOL connector authors! It is + * _not_ part of the public API for HDF5 application developers. + * + * Return: Success: Non-negative, *state set + * Failure: Negative, *state unset + * + * Programmer: Quincey Koziol + * Thursday, January 10, 2019 + * + *--------------------------------------------------------------------------- + */ +herr_t +H5VLretrieve_lib_state(void **state) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + /* Must use this, to avoid modifying the API context stack in FUNC_ENTER */ + FUNC_ENTER_API_NOINIT + H5TRACE1("e", "**x", state); + + /* Check args */ + if(NULL == state) + HGOTO_ERROR(H5E_VOL, H5E_BADVALUE, FAIL, "invalid state pointer") + + /* Retrieve the library state */ + if(H5VL_retrieve_lib_state(state) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTGET, FAIL, "can't retrieve library state") + +done: + FUNC_LEAVE_API_NOINIT(ret_value) +} /* H5VLretrieve_lib_state() */ + + +/*--------------------------------------------------------------------------- + * Function: H5VLrestore_lib_state + * + * Purpose: Restores the internal state of the HDF5 library. + * + * Note: This routine is _only_ for HDF5 VOL connector authors! It is + * _not_ part of the public API for HDF5 application developers. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Quincey Koziol + * Thursday, January 10, 2019 + * + *--------------------------------------------------------------------------- + */ +herr_t +H5VLrestore_lib_state(const void *state) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + /* Must use this, to avoid modifying the API context stack in FUNC_ENTER */ + FUNC_ENTER_API_NOINIT + H5TRACE1("e", "*x", state); + + /* Check args */ + if(NULL == state) + HGOTO_ERROR(H5E_VOL, H5E_BADVALUE, FAIL, "invalid state pointer") + + /* Restore the library state */ + if(H5VL_restore_lib_state(state) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTSET, FAIL, "can't restore library state") + +done: + FUNC_LEAVE_API_NOINIT(ret_value) +} /* H5VLrestore_lib_state() */ + + +/*--------------------------------------------------------------------------- + * Function: H5VLreset_lib_state + * + * Purpose: Resets the internal state of the HDF5 library, undoing the + * affects of H5VLrestore_lib_state. + * + * Note: This routine is _only_ for HDF5 VOL connector authors! It is + * _not_ part of the public API for HDF5 application developers. + * + * Note: This routine must be called as a "pair" with + * H5VLrestore_lib_state. It can be called before / after / + * independently of H5VLfree_lib_state. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Quincey Koziol + * Saturday, February 23, 2019 + * + *--------------------------------------------------------------------------- + */ +herr_t +H5VLreset_lib_state(void) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + /* Must use this, to avoid modifying the API context stack in FUNC_ENTER */ + FUNC_ENTER_API_NOINIT + H5TRACE0("e",""); + + /* Reset the library state */ + if(H5VL_reset_lib_state() < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTRESET, FAIL, "can't reset library state") + +done: + FUNC_LEAVE_API_NOINIT(ret_value) +} /* H5VLreset_lib_state() */ + + +/*--------------------------------------------------------------------------- + * Function: H5VLfree_lib_state + * + * Purpose: Free a retrieved library state. + * + * Note: This routine is _only_ for HDF5 VOL connector authors! It is + * _not_ part of the public API for HDF5 application developers. + * + * Note: This routine must be called as a "pair" with + * H5VLretrieve_lib_state. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Quincey Koziol + * Thursday, January 10, 2019 + * + *--------------------------------------------------------------------------- + */ +herr_t +H5VLfree_lib_state(void *state) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE1("e", "*x", state); + + /* Check args */ + if(NULL == state) + HGOTO_ERROR(H5E_VOL, H5E_BADVALUE, FAIL, "invalid state pointer") + + /* Free the library state */ + if(H5VL_free_lib_state(state) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "can't free library state") + +done: + FUNC_LEAVE_API(ret_value) +} /* H5VLfree_lib_state() */ + diff --git a/src/H5VLcallback.c b/src/H5VLcallback.c index 811162d..2d5b7d8 100644 --- a/src/H5VLcallback.c +++ b/src/H5VLcallback.c @@ -348,14 +348,14 @@ H5VL_copy_connector_info(const H5VL_class_t *connector, void **dst_info, /* Check for actual source info */ if(src_info) { /* Allow the connector to copy or do it ourselves */ - if(connector->info_copy) { - if(NULL == (new_connector_info = (connector->info_copy)(src_info))) + if(connector->info_cls.copy) { + if(NULL == (new_connector_info = (connector->info_cls.copy)(src_info))) HGOTO_ERROR(H5E_VOL, H5E_CANTCOPY, FAIL, "connector info copy callback failed") } /* end if */ - else if(connector->info_size > 0) { - if(NULL == (new_connector_info = H5MM_malloc(connector->info_size))) + else if(connector->info_cls.size > 0) { + if(NULL == (new_connector_info = H5MM_malloc(connector->info_cls.size))) HGOTO_ERROR(H5E_VOL, H5E_CANTALLOC, FAIL, "connector info allocation failed") - HDmemcpy(new_connector_info, src_info, connector->info_size); + H5MM_memcpy(new_connector_info, src_info, connector->info_cls.size); } /* end else-if */ else HGOTO_ERROR(H5E_VOL, H5E_UNSUPPORTED, FAIL, "no way to copy connector info") @@ -444,13 +444,13 @@ H5VL_cmp_connector_info(const H5VL_class_t *connector, int *cmp_value, * if there is a a callback, otherwise just compare the info objects as * memory buffers */ - if(connector->info_cmp) { - if((connector->info_cmp)(cmp_value, info1, info2) < 0) + if(connector->info_cls.cmp) { + if((connector->info_cls.cmp)(cmp_value, info1, info2) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTCOMPARE, FAIL, "can't compare connector info") } /* end if */ else { - HDassert(connector->info_size > 0); - *cmp_value = HDmemcmp(info1, info2, connector->info_size); + HDassert(connector->info_cls.size > 0); + *cmp_value = HDmemcmp(info1, info2, connector->info_cls.size); } /* end else */ done: @@ -518,8 +518,8 @@ H5VL_free_connector_info(const H5VL_class_t *connector, void *info) /* Only free info object, if it's non-NULL */ if(info) { /* Allow the connector to free info or do it ourselves */ - if(connector->info_free) { - if((connector->info_free)(info) < 0) + if(connector->info_cls.free) { + if((connector->info_cls.free)(info) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "connector info free request failed") } /* end if */ else @@ -590,8 +590,8 @@ H5VLconnector_info_to_str(const void *info, hid_t connector_id, char **str) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a VOL connector ID") /* Allow the connector to serialize info */ - if(cls->info_to_str) { - if((cls->info_to_str)(info, str) < 0) + if(cls->info_cls.to_str) { + if((cls->info_cls.to_str)(info, str) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTSERIALIZE, FAIL, "can't serialize connector info") } /* end if */ else @@ -632,8 +632,8 @@ H5VLconnector_str_to_info(const char *str, hid_t connector_id, void **info) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a VOL connector ID") /* Allow the connector to deserialize info */ - if(cls->str_to_info) { - if((cls->str_to_info)(str, info) < 0) + if(cls->info_cls.from_str) { + if((cls->info_cls.from_str)(str, info) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTUNSERIALIZE, FAIL, "can't deserialize connector info") } /* end if */ else @@ -673,8 +673,8 @@ H5VLget_object(void *obj, hid_t connector_id) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a VOL connector ID") /* Check for 'get_object' callback in connector */ - if(cls->get_object) - ret_value = (cls->get_object)(obj); + if(cls->wrap_cls.get_object) + ret_value = (cls->wrap_cls.get_object)(obj); else ret_value = obj; @@ -706,12 +706,12 @@ H5VL_get_wrap_ctx(const H5VL_class_t *connector, void *obj, void **wrap_ctx) HDassert(wrap_ctx); /* Allow the connector to copy or do it ourselves */ - if(connector->get_wrap_ctx) { + if(connector->wrap_cls.get_wrap_ctx) { /* Sanity check */ - HDassert(connector->free_wrap_ctx); + HDassert(connector->wrap_cls.free_wrap_ctx); /* Invoke connector's callback */ - if((connector->get_wrap_ctx)(obj, wrap_ctx) < 0) + if((connector->wrap_cls.get_wrap_ctx)(obj, wrap_ctx) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, FAIL, "connector wrap context callback failed") } /* end if */ else @@ -777,7 +777,7 @@ H5VL_free_wrap_ctx(const H5VL_class_t *connector, void *wrap_ctx) /* Only free wrap context, if it's non-NULL */ if(wrap_ctx) { /* Free the connector's object wrapping context */ - if((connector->free_wrap_ctx)(wrap_ctx) < 0) + if((connector->wrap_cls.free_wrap_ctx)(wrap_ctx) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "connector wrap context free request failed") } /* end if */ @@ -829,7 +829,8 @@ done: *------------------------------------------------------------------------- */ void * -H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, void *obj) +H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, void *obj, + H5I_type_t obj_type) { void *ret_value = SUCCEED; /* Return value */ @@ -842,7 +843,7 @@ H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, void *obj) /* Only wrap object if there's a wrap context */ if(wrap_ctx) { /* Ask the connector to wrap the object */ - if(NULL == (ret_value = (connector->wrap_object)(obj, wrap_ctx))) + if(NULL == (ret_value = (connector->wrap_cls.wrap_object)(obj, obj_type, wrap_ctx))) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, NULL, "can't wrap object") } /* end if */ else @@ -864,13 +865,13 @@ done: *--------------------------------------------------------------------------- */ void * -H5VLwrap_object(void *obj, hid_t connector_id, void *wrap_ctx) +H5VLwrap_object(void *obj, H5I_type_t obj_type, hid_t connector_id, void *wrap_ctx) { H5VL_class_t *cls; /* VOL connector's class struct */ void *ret_value = NULL; /* Return value */ FUNC_ENTER_API_NOINIT - H5TRACE3("*x", "*xi*x", obj, connector_id, wrap_ctx); + H5TRACE4("*x", "*xIti*x", obj, obj_type, connector_id, wrap_ctx); /* Check args and get class pointer */ if(NULL == obj) @@ -879,7 +880,7 @@ H5VLwrap_object(void *obj, hid_t connector_id, void *wrap_ctx) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a VOL connector ID") /* Wrap the object */ - if(NULL == (ret_value = H5VL_wrap_object(cls, wrap_ctx, obj))) + if(NULL == (ret_value = H5VL_wrap_object(cls, wrap_ctx, obj, obj_type))) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, NULL, "unable to wrap object") done: @@ -2988,7 +2989,7 @@ H5VL_file_specific(const H5VL_object_t *vol_obj, H5VL_file_specific_t specific_t /* Get the file access property list to access the file */ HDva_copy(tmp_args, arguments); - fapl_id = va_arg(tmp_args, hid_t); + fapl_id = HDva_arg(tmp_args, hid_t); HDva_end(tmp_args); /* Get the VOL info from the FAPL */ diff --git a/src/H5VLint.c b/src/H5VLint.c index bdb2908..9d9dc94 100644 --- a/src/H5VLint.c +++ b/src/H5VLint.c @@ -51,7 +51,7 @@ /* Object wrapping context info */ typedef struct H5VL_wrap_ctx_t { unsigned rc; /* Ref. count for the # of times the context was set / reset */ - const H5VL_t *connector; /* VOL connector for "outermost" class to start wrap */ + H5VL_t *connector; /* VOL connector for "outermost" class to start wrap */ void *obj_wrap_ctx; /* "wrap context" for outermost connector */ } H5VL_wrap_ctx_t; @@ -65,10 +65,13 @@ typedef struct H5VL_wrap_ctx_t { /* Local Prototypes */ /********************/ static herr_t H5VL__free_cls(H5VL_class_t *cls); -static void *H5VL__wrap_obj(void *obj); +static void *H5VL__wrap_obj(void *obj, H5I_type_t obj_type); static H5VL_object_t *H5VL__new_vol_obj(H5I_type_t type, void *object, H5VL_t *vol_connector, hbool_t wrap_obj); +static int64_t H5VL__conn_inc_rc(H5VL_t *connector); +static int64_t H5VL__conn_dec_rc(H5VL_t *connector); static void *H5VL__object(hid_t id, H5I_type_t obj_type); +static herr_t H5VL__free_vol_wrapper(H5VL_wrap_ctx_t *vol_wrap_ctx); /*********************/ @@ -248,7 +251,7 @@ done: *------------------------------------------------------------------------- */ static void * -H5VL__wrap_obj(void *obj) +H5VL__wrap_obj(void *obj, H5I_type_t obj_type) { H5VL_wrap_ctx_t *vol_wrap_ctx = NULL; /* Object wrapping context */ void *ret_value = NULL; /* Return value */ @@ -265,7 +268,7 @@ H5VL__wrap_obj(void *obj) /* If there is a VOL object wrapping context, wrap the object */ if(vol_wrap_ctx) { /* Wrap object, using the VOL callback */ - if(NULL == (ret_value = H5VL_wrap_object(vol_wrap_ctx->connector->cls, vol_wrap_ctx->obj_wrap_ctx, obj))) + if(NULL == (ret_value = H5VL_wrap_object(vol_wrap_ctx->connector->cls, vol_wrap_ctx->obj_wrap_ctx, obj, obj_type))) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, NULL, "can't wrap object") } /* end if */ else @@ -310,14 +313,14 @@ H5VL__new_vol_obj(H5I_type_t type, void *object, H5VL_t *vol_connector, hbool_t HGOTO_ERROR(H5E_VOL, H5E_CANTALLOC, NULL, "can't allocate memory for VOL object") new_vol_obj->connector = vol_connector; if(wrap_obj) { - if(NULL == (new_vol_obj->data = H5VL__wrap_obj(object))) + if(NULL == (new_vol_obj->data = H5VL__wrap_obj(object, type))) HGOTO_ERROR(H5E_VOL, H5E_CANTCREATE, NULL, "can't wrap library object") } /* end if */ else new_vol_obj->data = object; /* Bump the reference count on the VOL connector */ - vol_connector->nrefs++; + H5VL__conn_inc_rc(vol_connector); /* If this is a datatype, we have to hide the VOL object under the H5T_t pointer */ if(H5I_DATATYPE == type) { @@ -550,6 +553,76 @@ done: /*------------------------------------------------------------------------- + * Function: H5VL__conn_inc_rc + * + * Purpose: Wrapper to increment the ref. count on a connector. + * + * Return: Current ref. count (can't fail) + * + * Programmer: Quincey Koziol + * February 23, 2019 + * + *------------------------------------------------------------------------- + */ +static int64_t +H5VL__conn_inc_rc(H5VL_t *connector) +{ + FUNC_ENTER_STATIC_NOERR + + /* Check arguments */ + HDassert(connector); + + /* Increment refcount for connector */ + connector->nrefs++; + + FUNC_LEAVE_NOAPI(connector->nrefs) +} /* end H5VL__conn_inc_rc() */ + + +/*------------------------------------------------------------------------- + * Function: H5VL__conn_dec_rc + * + * Purpose: Wrapper to decrement the ref. count on a connector. + * + * Return: Current ref. count (>=0) on success, <0 on failure + * + * Programmer: Quincey Koziol + * February 23, 2019 + * + *------------------------------------------------------------------------- + */ +static int64_t +H5VL__conn_dec_rc(H5VL_t *connector) +{ + int64_t ret_value = -1; /* Return value */ + + FUNC_ENTER_STATIC + + /* Check arguments */ + HDassert(connector); + + /* Decrement refcount for connector */ + connector->nrefs--; + + /* Check for last reference */ + if(0 == connector->nrefs) { + if(H5I_dec_ref(connector->id) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTDEC, FAIL, "unable to decrement ref count on VOL connector") + H5FL_FREE(H5VL_t, connector); + + /* Set return value */ + ret_value = 0; + } /* end if */ + else + /* Set return value */ + ret_value = connector->nrefs; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL__conn_dec_rc() */ + + +/*------------------------------------------------------------------------- * Function: H5VL_free_object * * Purpose: Wrapper to unregister an object ID with a VOL aux struct @@ -562,20 +635,16 @@ done: herr_t H5VL_free_object(H5VL_object_t *vol_obj) { - herr_t ret_value = SUCCEED; + herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI(SUCCEED) + FUNC_ENTER_NOAPI(FAIL) /* Check arguments */ HDassert(vol_obj); - vol_obj->connector->nrefs --; - - if(0 == vol_obj->connector->nrefs) { - if(H5I_dec_ref(vol_obj->connector->id) < 0) - HGOTO_ERROR(H5E_VOL, H5E_CANTDEC, FAIL, "unable to decrement ref count on VOL connector") - vol_obj->connector = H5FL_FREE(H5VL_t, vol_obj->connector); - } /* end if */ + /* Decrement refcount on connector */ + if(H5VL__conn_dec_rc(vol_obj->connector) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTDEC, FAIL, "unable to decrement ref count on VOL connector") vol_obj = H5FL_FREE(H5VL_object_t, vol_obj); @@ -612,7 +681,7 @@ H5VL_register_connector(const void *_cls, hbool_t app_ref, hid_t vipl_id) /* Copy the class structure so the caller can reuse or free it */ if (NULL == (saved = H5FL_CALLOC(H5VL_class_t))) HGOTO_ERROR(H5E_VOL, H5E_CANTALLOC, H5I_INVALID_HID, "memory allocation failed for VOL connector class struct") - HDmemcpy(saved, cls, sizeof(H5VL_class_t)); + H5MM_memcpy(saved, cls, sizeof(H5VL_class_t)); if(NULL == (saved->name = H5MM_strdup(cls->name))) HGOTO_ERROR(H5E_VOL, H5E_CANTALLOC, H5I_INVALID_HID, "memory allocation failed for VOL connector name") @@ -740,8 +809,8 @@ H5VL_object_data(const H5VL_object_t *vol_obj) FUNC_ENTER_NOAPI_NOINIT_NOERR /* Check for 'get_object' callback in connector */ - if(vol_obj->connector->cls->get_object) - ret_value = (vol_obj->connector->cls->get_object)(vol_obj->data); + if(vol_obj->connector->cls->wrap_cls.get_object) + ret_value = (vol_obj->connector->cls->wrap_cls.get_object)(vol_obj->data); else ret_value = vol_obj->data; @@ -933,15 +1002,15 @@ H5VL_cmp_connector_cls(int *cmp_value, const H5VL_class_t *cls1, const H5VL_clas HDassert(cls1->version == cls2->version); /* Compare connector info */ - if(cls1->info_size < cls2->info_size) { + if(cls1->info_cls.size < cls2->info_cls.size) { *cmp_value = -1; HGOTO_DONE(SUCCEED) } /* end if */ - if(cls1->info_size > cls2->info_size) { + if(cls1->info_cls.size > cls2->info_cls.size) { *cmp_value = 1; HGOTO_DONE(SUCCEED) } /* end if */ - HDassert(cls1->info_size == cls2->info_size); + HDassert(cls1->info_cls.size == cls2->info_cls.size); /* Set comparison value to 'equal' */ *cmp_value = 0; @@ -952,6 +1021,189 @@ done: /*------------------------------------------------------------------------- + * Function: H5VL_retrieve_lib_state + * + * Purpose: Retrieve the state of the library. + * + * Note: Currently just retrieves the API context state, but could be + * expanded in the future. + * + * Return: Success: Non-negative, *state set + * Failure: Negative, *state unset + * + *------------------------------------------------------------------------- + */ +herr_t +H5VL_retrieve_lib_state(void **state) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Sanity checks */ + HDassert(state); + + /* Retrieve the API context state */ + if(H5CX_retrieve_state((H5CX_state_t **)state) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTGET, FAIL, "can't get API context state") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL_retrieve_lib_state() */ + + +/*------------------------------------------------------------------------- + * Function: H5VL_restore_lib_state + * + * Purpose: Restore the state of the library. + * + * Note: Currently just restores the API context state, but could be + * expanded in the future. + * + * Return: SUCCEED / FAIL + * + * Programmer: Quincey Koziol + * Thursday, January 10, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5VL_restore_lib_state(const void *state) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Sanity checks */ + HDassert(state); + + /* Push a new API context on the stack */ + if(H5CX_push() < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTSET, FAIL, "can't push API context") + + /* Restore the API context state */ + if(H5CX_restore_state((const H5CX_state_t *)state) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTSET, FAIL, "can't set API context state") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL_restore_lib_state() */ + + +/*------------------------------------------------------------------------- + * Function: H5VL_reset_lib_state + * + * Purpose: Reset the state of the library, undoing affects of + * H5VL_restore_lib_state. + * + * Note: Currently just resets the API context state, but could be + * expanded in the future. + * + * Note: This routine must be called as a "pair" with + * H5VL_restore_lib_state. It can be called before / after / + * independently of H5VL_free_lib_state. + * + * Return: SUCCEED / FAIL + * + * Programmer: Quincey Koziol + * Saturday, February 23, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5VL_reset_lib_state(void) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Pop the API context off the stack */ + if(H5CX_pop() < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTRESET, FAIL, "can't pop API context") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL_reset_lib_state() */ + + +/*------------------------------------------------------------------------- + * Function: H5VL_free_lib_state + * + * Purpose: Free a library state. + * + * Note: This routine must be called as a "pair" with + * H5VL_retrieve_lib_state. + * + * Return: SUCCEED / FAIL + * + * Programmer: Quincey Koziol + * Thursday, January 10, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5VL_free_lib_state(void *state) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Sanity checks */ + HDassert(state); + + /* Free the API context state */ + if(H5CX_free_state((H5CX_state_t *)state) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "can't free API context state") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL_free_lib_state() */ + + +/*------------------------------------------------------------------------- + * Function: H5VL__free_vol_wrapper + * + * Purpose: Free object wrapping context for VOL connector + * + * Return: SUCCEED / FAIL + * + * Programmer: Quincey Koziol + * Wednesday, January 9, 2019 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5VL__free_vol_wrapper(H5VL_wrap_ctx_t *vol_wrap_ctx) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity check */ + HDassert(vol_wrap_ctx); + HDassert(0 == vol_wrap_ctx->rc); + HDassert(vol_wrap_ctx->connector); + HDassert(vol_wrap_ctx->connector->cls); + + /* If there is a VOL connector object wrapping context, release it */ + if(vol_wrap_ctx->obj_wrap_ctx) + /* Release the VOL connector's object wrapping context */ + if((*vol_wrap_ctx->connector->cls->wrap_cls.free_wrap_ctx)(vol_wrap_ctx->obj_wrap_ctx) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "unable to release connector's object wrapping context") + + /* Decrement refcount on connector */ + if(H5VL__conn_dec_rc(vol_wrap_ctx->connector) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTDEC, FAIL, "unable to decrement ref count on VOL connector") + + /* Release object wrapping context */ + H5FL_FREE(H5VL_wrap_ctx_t, vol_wrap_ctx); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL__free_vol_wrapper() */ + + +/*------------------------------------------------------------------------- * Function: H5VL_set_vol_wrapper * * Purpose: Set up object wrapping context for current VOL connector @@ -961,7 +1213,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5VL_set_vol_wrapper(void *obj, const H5VL_t *connector) +H5VL_set_vol_wrapper(void *obj, H5VL_t *connector) { H5VL_wrap_ctx_t *vol_wrap_ctx = NULL; /* Object wrapping context */ void *obj_wrap_ctx = NULL; /* VOL connector's wrapping context */ @@ -980,12 +1232,12 @@ H5VL_set_vol_wrapper(void *obj, const H5VL_t *connector) /* Check for existing wrapping context */ if(NULL == vol_wrap_ctx) { /* Check if the connector can create a wrap context */ - if(connector->cls->get_wrap_ctx) { + if(connector->cls->wrap_cls.get_wrap_ctx) { /* Sanity check */ - HDassert(connector->cls->free_wrap_ctx); + HDassert(connector->cls->wrap_cls.free_wrap_ctx); /* Get the wrap context from the connector */ - if((connector->cls->get_wrap_ctx)(obj, &obj_wrap_ctx) < 0) + if((connector->cls->wrap_cls.get_wrap_ctx)(obj, &obj_wrap_ctx) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTGET, FAIL, "can't retrieve VOL connector's object wrap context") } /* end if */ @@ -993,8 +1245,11 @@ H5VL_set_vol_wrapper(void *obj, const H5VL_t *connector) if(NULL == (vol_wrap_ctx = H5FL_MALLOC(H5VL_wrap_ctx_t))) HGOTO_ERROR(H5E_VOL, H5E_CANTALLOC, FAIL, "can't allocate VOL wrap context") + /* Increment the outstanding objects that are using the connector */ + H5VL__conn_inc_rc(connector); + /* Set up VOL object wrapper context */ - vol_wrap_ctx->rc = 1;; + vol_wrap_ctx->rc = 1; vol_wrap_ctx->connector = connector; vol_wrap_ctx->obj_wrap_ctx = obj_wrap_ctx; } /* end if */ @@ -1016,6 +1271,80 @@ done: /*------------------------------------------------------------------------- + * Function: H5VL_inc_vol_wrapper + * + * Purpose: Increment refcount on object wrapping context + * + * Return: SUCCEED / FAIL + * + * Programmer: Quincey Koziol + * Wednesday, January 9, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5VL_inc_vol_wrapper(void *_vol_wrap_ctx) +{ + H5VL_wrap_ctx_t *vol_wrap_ctx = (H5VL_wrap_ctx_t *)_vol_wrap_ctx; /* VOL object wrapping context */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Check for valid, active VOL object wrap context */ + if(NULL == vol_wrap_ctx) + HGOTO_ERROR(H5E_VOL, H5E_BADVALUE, FAIL, "no VOL object wrap context?") + if(0 == vol_wrap_ctx->rc) + HGOTO_ERROR(H5E_VOL, H5E_BADVALUE, FAIL, "bad VOL object wrap context refcount?") + + /* Increment ref count on wrapping context */ + vol_wrap_ctx->rc++; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL_inc_vol_wrapper() */ + + +/*------------------------------------------------------------------------- + * Function: H5VL_dec_vol_wrapper + * + * Purpose: Decrement refcount on object wrapping context, releasing it + * if the refcount drops to zero. + * + * Return: SUCCEED / FAIL + * + * Programmer: Quincey Koziol + * Wednesday, January 9, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5VL_dec_vol_wrapper(void *_vol_wrap_ctx) +{ + H5VL_wrap_ctx_t *vol_wrap_ctx = (H5VL_wrap_ctx_t *)_vol_wrap_ctx; /* VOL object wrapping context */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Check for valid, active VOL object wrap context */ + if(NULL == vol_wrap_ctx) + HGOTO_ERROR(H5E_VOL, H5E_BADVALUE, FAIL, "no VOL object wrap context?") + if(0 == vol_wrap_ctx->rc) + HGOTO_ERROR(H5E_VOL, H5E_BADVALUE, FAIL, "bad VOL object wrap context refcount?") + + /* Decrement ref count on wrapping context */ + vol_wrap_ctx->rc--; + + /* Release context if the ref count drops to zero */ + if(0 == vol_wrap_ctx->rc) + if(H5VL__free_vol_wrapper(vol_wrap_ctx) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "unable to release VOL object wrapping context") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5VL_dec_vol_wrapper() */ + + +/*------------------------------------------------------------------------- * Function: H5VL_reset_vol_wrapper * * Purpose: Reset object wrapping context for current VOL connector @@ -1045,25 +1374,18 @@ H5VL_reset_vol_wrapper(void) /* Release context if the ref count drops to zero */ if(0 == vol_wrap_ctx->rc) { - /* If there is a VOL connector object wrapping context, release it */ - if(vol_wrap_ctx->obj_wrap_ctx) { - /* Release the VOL connector's object wrapping context */ - if((*vol_wrap_ctx->connector->cls->free_wrap_ctx)(vol_wrap_ctx->obj_wrap_ctx) < 0) - HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "unable to release connector's object wrapping context") - } /* end if */ - /* Release object wrapping context */ - H5FL_FREE(H5VL_wrap_ctx_t, vol_wrap_ctx); + if(H5VL__free_vol_wrapper(vol_wrap_ctx) < 0) + HGOTO_ERROR(H5E_VOL, H5E_CANTRELEASE, FAIL, "unable to release VOL object wrapping context") /* Reset the wrapper context */ if(H5CX_set_vol_wrap_ctx(NULL) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTSET, FAIL, "can't set VOL object wrap context") } /* end if */ - else { + else /* Save the updated wrapper context */ if(H5CX_set_vol_wrap_ctx(vol_wrap_ctx) < 0) HGOTO_ERROR(H5E_VOL, H5E_CANTSET, FAIL, "can't set VOL object wrap context") - } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) @@ -1099,7 +1421,7 @@ H5VL_wrap_register(H5I_type_t type, void *obj, hbool_t app_ref) HGOTO_ERROR(H5E_VOL, H5E_BADTYPE, H5I_INVALID_HID, "can't wrap an uncommitted datatype") /* Wrap the object with VOL connector info */ - if(NULL == (new_obj = H5VL__wrap_obj(obj))) + if(NULL == (new_obj = H5VL__wrap_obj(obj, type))) HGOTO_ERROR(H5E_VOL, H5E_CANTCREATE, H5I_INVALID_HID, "can't wrap library object") /* Retrieve the VOL object wrapping context */ diff --git a/src/H5VLnative.c b/src/H5VLnative.c index fe0fd4e..f4f3b5f 100644 --- a/src/H5VLnative.c +++ b/src/H5VLnative.c @@ -38,16 +38,20 @@ static H5VL_class_t H5VL_native_cls_g = { 0, /* capability flags */ NULL, /* initialize */ H5VL__native_term, /* terminate */ - (size_t)0, /* info size */ - NULL, /* info copy */ - NULL, /* info compare */ - NULL, /* info free */ - NULL, /* info to str */ - NULL, /* str to info */ - NULL, /* get_object */ - NULL, /* get_wrap_ctx */ - NULL, /* wrap_object */ - NULL, /* free_wrap_ctx */ + { /* info_cls */ + (size_t)0, /* info size */ + NULL, /* info copy */ + NULL, /* info compare */ + NULL, /* info free */ + NULL, /* info to str */ + NULL /* str to info */ + }, + { /* wrap_cls */ + NULL, /* get_object */ + NULL, /* get_wrap_ctx */ + NULL, /* wrap_object */ + NULL /* free_wrap_ctx */ + }, { /* attribute_cls */ H5VL__native_attr_create, /* create */ H5VL__native_attr_open, /* open */ diff --git a/src/H5VLnative_file.c b/src/H5VLnative_file.c index e7f27e1..624cd30 100644 --- a/src/H5VLnative_file.c +++ b/src/H5VLnative_file.c @@ -755,7 +755,7 @@ H5VL__native_file_optional(void *obj, hid_t H5_ATTR_UNUSED dxpl_id, void H5_ATTR /* H5Fget_dset_no_attrs_hint */ case H5VL_NATIVE_FILE_GET_MIN_DSET_OHDR_FLAG: { - hbool_t *minimize = va_arg(arguments, hbool_t *); + hbool_t *minimize = HDva_arg(arguments, hbool_t *); *minimize = H5F_GET_MIN_DSET_OHDR(f); break; } @@ -763,7 +763,7 @@ H5VL__native_file_optional(void *obj, hid_t H5_ATTR_UNUSED dxpl_id, void H5_ATTR /* H5Fset_dset_no_attrs_hint */ case H5VL_NATIVE_FILE_SET_MIN_DSET_OHDR_FLAG: { - int minimize = va_arg(arguments, int); + int minimize = HDva_arg(arguments, int); if(H5F_set_min_dset_ohdr(f, (hbool_t)minimize) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "cannot set file's dataset object header minimization flag") break; diff --git a/src/H5VLpassthru.c b/src/H5VLpassthru.c index 13d8d8e..fe72000 100644 --- a/src/H5VLpassthru.c +++ b/src/H5VLpassthru.c @@ -82,15 +82,20 @@ static herr_t H5VL_pass_through_free_obj(H5VL_pass_through_t *obj); /* "Management" callbacks */ static herr_t H5VL_pass_through_init(hid_t vipl_id); static herr_t H5VL_pass_through_term(void); + +/* VOL info callbacks */ static void *H5VL_pass_through_info_copy(const void *info); static herr_t H5VL_pass_through_info_cmp(int *cmp_value, const void *info1, const void *info2); static herr_t H5VL_pass_through_info_free(void *info); static herr_t H5VL_pass_through_info_to_str(const void *info, char **str); static herr_t H5VL_pass_through_str_to_info(const char *str, void **info); + +/* VOL object wrap / retrieval callbacks */ static void *H5VL_pass_through_get_object(const void *obj); static herr_t H5VL_pass_through_get_wrap_ctx(const void *obj, void **wrap_ctx); static herr_t H5VL_pass_through_free_wrap_ctx(void *obj); -static void *H5VL_pass_through_wrap_object(void *obj, void *wrap_ctx); +static void *H5VL_pass_through_wrap_object(void *obj, H5I_type_t obj_type, + void *wrap_ctx); /* Attribute callbacks */ static void *H5VL_pass_through_attr_create(void *obj, const H5VL_loc_params_t *loc_params, const char *name, hid_t acpl_id, hid_t aapl_id, hid_t dxpl_id, void **req); @@ -172,82 +177,86 @@ static const H5VL_class_t H5VL_pass_through_g = { 0, /* capability flags */ H5VL_pass_through_init, /* initialize */ H5VL_pass_through_term, /* terminate */ - sizeof(H5VL_pass_through_info_t), /* info size */ - H5VL_pass_through_info_copy, /* info copy */ - H5VL_pass_through_info_cmp, /* info compare */ - H5VL_pass_through_info_free, /* info free */ - H5VL_pass_through_info_to_str, /* info to str */ - H5VL_pass_through_str_to_info, /* str to info */ - H5VL_pass_through_get_object, /* get_object */ - H5VL_pass_through_get_wrap_ctx, /* get_wrap_ctx */ - H5VL_pass_through_wrap_object, /* wrap_object */ - H5VL_pass_through_free_wrap_ctx, /* free_wrap_ctx */ + { /* info_cls */ + sizeof(H5VL_pass_through_info_t), /* size */ + H5VL_pass_through_info_copy, /* copy */ + H5VL_pass_through_info_cmp, /* compare */ + H5VL_pass_through_info_free, /* free */ + H5VL_pass_through_info_to_str, /* to_str */ + H5VL_pass_through_str_to_info, /* from_str */ + }, + { /* wrap_cls */ + H5VL_pass_through_get_object, /* get_object */ + H5VL_pass_through_get_wrap_ctx, /* get_wrap_ctx */ + H5VL_pass_through_wrap_object, /* wrap_object */ + H5VL_pass_through_free_wrap_ctx, /* free_wrap_ctx */ + }, { /* attribute_cls */ - H5VL_pass_through_attr_create, /* create */ - H5VL_pass_through_attr_open, /* open */ - H5VL_pass_through_attr_read, /* read */ - H5VL_pass_through_attr_write, /* write */ - H5VL_pass_through_attr_get, /* get */ - H5VL_pass_through_attr_specific, /* specific */ - H5VL_pass_through_attr_optional, /* optional */ - H5VL_pass_through_attr_close /* close */ + H5VL_pass_through_attr_create, /* create */ + H5VL_pass_through_attr_open, /* open */ + H5VL_pass_through_attr_read, /* read */ + H5VL_pass_through_attr_write, /* write */ + H5VL_pass_through_attr_get, /* get */ + H5VL_pass_through_attr_specific, /* specific */ + H5VL_pass_through_attr_optional, /* optional */ + H5VL_pass_through_attr_close /* close */ }, { /* dataset_cls */ - H5VL_pass_through_dataset_create, /* create */ - H5VL_pass_through_dataset_open, /* open */ - H5VL_pass_through_dataset_read, /* read */ - H5VL_pass_through_dataset_write, /* write */ - H5VL_pass_through_dataset_get, /* get */ - H5VL_pass_through_dataset_specific, /* specific */ - H5VL_pass_through_dataset_optional, /* optional */ - H5VL_pass_through_dataset_close /* close */ + H5VL_pass_through_dataset_create, /* create */ + H5VL_pass_through_dataset_open, /* open */ + H5VL_pass_through_dataset_read, /* read */ + H5VL_pass_through_dataset_write, /* write */ + H5VL_pass_through_dataset_get, /* get */ + H5VL_pass_through_dataset_specific, /* specific */ + H5VL_pass_through_dataset_optional, /* optional */ + H5VL_pass_through_dataset_close /* close */ }, - { /* datatype_cls */ - H5VL_pass_through_datatype_commit, /* commit */ - H5VL_pass_through_datatype_open, /* open */ - H5VL_pass_through_datatype_get, /* get_size */ - H5VL_pass_through_datatype_specific, /* specific */ - H5VL_pass_through_datatype_optional, /* optional */ - H5VL_pass_through_datatype_close /* close */ + { /* datatype_cls */ + H5VL_pass_through_datatype_commit, /* commit */ + H5VL_pass_through_datatype_open, /* open */ + H5VL_pass_through_datatype_get, /* get_size */ + H5VL_pass_through_datatype_specific, /* specific */ + H5VL_pass_through_datatype_optional, /* optional */ + H5VL_pass_through_datatype_close /* close */ }, { /* file_cls */ - H5VL_pass_through_file_create, /* create */ - H5VL_pass_through_file_open, /* open */ - H5VL_pass_through_file_get, /* get */ - H5VL_pass_through_file_specific, /* specific */ - H5VL_pass_through_file_optional, /* optional */ - H5VL_pass_through_file_close /* close */ + H5VL_pass_through_file_create, /* create */ + H5VL_pass_through_file_open, /* open */ + H5VL_pass_through_file_get, /* get */ + H5VL_pass_through_file_specific, /* specific */ + H5VL_pass_through_file_optional, /* optional */ + H5VL_pass_through_file_close /* close */ }, { /* group_cls */ - H5VL_pass_through_group_create, /* create */ - H5VL_pass_through_group_open, /* open */ - H5VL_pass_through_group_get, /* get */ - H5VL_pass_through_group_specific, /* specific */ - H5VL_pass_through_group_optional, /* optional */ - H5VL_pass_through_group_close /* close */ + H5VL_pass_through_group_create, /* create */ + H5VL_pass_through_group_open, /* open */ + H5VL_pass_through_group_get, /* get */ + H5VL_pass_through_group_specific, /* specific */ + H5VL_pass_through_group_optional, /* optional */ + H5VL_pass_through_group_close /* close */ }, { /* link_cls */ - H5VL_pass_through_link_create, /* create */ - H5VL_pass_through_link_copy, /* copy */ - H5VL_pass_through_link_move, /* move */ - H5VL_pass_through_link_get, /* get */ - H5VL_pass_through_link_specific, /* specific */ - H5VL_pass_through_link_optional, /* optional */ + H5VL_pass_through_link_create, /* create */ + H5VL_pass_through_link_copy, /* copy */ + H5VL_pass_through_link_move, /* move */ + H5VL_pass_through_link_get, /* get */ + H5VL_pass_through_link_specific, /* specific */ + H5VL_pass_through_link_optional, /* optional */ }, { /* object_cls */ - H5VL_pass_through_object_open, /* open */ - H5VL_pass_through_object_copy, /* copy */ - H5VL_pass_through_object_get, /* get */ - H5VL_pass_through_object_specific, /* specific */ - H5VL_pass_through_object_optional, /* optional */ + H5VL_pass_through_object_open, /* open */ + H5VL_pass_through_object_copy, /* copy */ + H5VL_pass_through_object_get, /* get */ + H5VL_pass_through_object_specific, /* specific */ + H5VL_pass_through_object_optional, /* optional */ }, { /* request_cls */ - H5VL_pass_through_request_wait, /* wait */ - H5VL_pass_through_request_notify, /* notify */ - H5VL_pass_through_request_cancel, /* cancel */ - H5VL_pass_through_request_specific, /* specific */ - H5VL_pass_through_request_optional, /* optional */ - H5VL_pass_through_request_free /* free */ + H5VL_pass_through_request_wait, /* wait */ + H5VL_pass_through_request_notify, /* notify */ + H5VL_pass_through_request_cancel, /* cancel */ + H5VL_pass_through_request_specific, /* specific */ + H5VL_pass_through_request_optional, /* optional */ + H5VL_pass_through_request_free /* free */ }, NULL /* optional */ }; @@ -660,7 +669,7 @@ H5VL_pass_through_get_wrap_ctx(const void *obj, void **wrap_ctx) *--------------------------------------------------------------------------- */ static void * -H5VL_pass_through_wrap_object(void *obj, void *_wrap_ctx) +H5VL_pass_through_wrap_object(void *obj, H5I_type_t obj_type, void *_wrap_ctx) { H5VL_pass_through_wrap_ctx_t *wrap_ctx = (H5VL_pass_through_wrap_ctx_t *)_wrap_ctx; H5VL_pass_through_t *new_obj; @@ -671,7 +680,7 @@ H5VL_pass_through_wrap_object(void *obj, void *_wrap_ctx) #endif /* Wrap the object with the underlying VOL */ - under = H5VLwrap_object(obj, wrap_ctx->under_vol_id, wrap_ctx->under_wrap_ctx); + under = H5VLwrap_object(obj, obj_type, wrap_ctx->under_vol_id, wrap_ctx->under_wrap_ctx); if(under) new_obj = H5VL_pass_through_new_obj(under, wrap_ctx->under_vol_id); else diff --git a/src/H5VLprivate.h b/src/H5VLprivate.h index ef5a81e..ac77ee0 100644 --- a/src/H5VLprivate.h +++ b/src/H5VLprivate.h @@ -41,8 +41,8 @@ typedef struct H5VL_object_t { /* Internal structure to hold the connector ID & info for FAPLs */ typedef struct H5VL_connector_prop_t { - hid_t connector_id; /* VOL connector's ID */ - const void *connector_info; /* VOL connector info, for open callbacks */ + hid_t connector_id; /* VOL connector's ID */ + void *connector_info; /* VOL connector info, for open callbacks */ } H5VL_connector_prop_t; /* Which kind of VOL connector field to use for searching */ @@ -92,10 +92,18 @@ H5_DLL herr_t H5VL_free_object(H5VL_object_t *obj); H5_DLL herr_t H5VL_get_wrap_ctx(const H5VL_class_t *connector, void *obj, void **wrap_ctx); H5_DLL herr_t H5VL_free_wrap_ctx(const H5VL_class_t *connector, void *wrap_ctx); -H5_DLL herr_t H5VL_set_vol_wrapper(void *obj, const H5VL_t *vol_connector); +H5_DLL herr_t H5VL_set_vol_wrapper(void *obj, H5VL_t *vol_connector); +H5_DLL herr_t H5VL_inc_vol_wrapper(void *vol_wrap_ctx); +H5_DLL herr_t H5VL_dec_vol_wrapper(void *vol_wrap_ctx); H5_DLL herr_t H5VL_reset_vol_wrapper(void); H5_DLL void * H5VL_wrap_object(const H5VL_class_t *connector, void *wrap_ctx, - void *obj); + void *obj, H5I_type_t obj_type); + +/* Library state functions */ +H5_DLL herr_t H5VL_retrieve_lib_state(void **state); +H5_DLL herr_t H5VL_restore_lib_state(const void *state); +H5_DLL herr_t H5VL_reset_lib_state(void); +H5_DLL herr_t H5VL_free_lib_state(void *state); /* ID registration functions */ H5_DLL hid_t H5VL_register(H5I_type_t type, void *object, H5VL_t *vol_connector, hbool_t app_ref); diff --git a/src/H5VLpublic.h b/src/H5VLpublic.h index dd1ed54..cf6246b 100644 --- a/src/H5VLpublic.h +++ b/src/H5VLpublic.h @@ -22,6 +22,7 @@ #include "H5Apublic.h" /* Attributes */ #include "H5ESpublic.h" /* Event Stack */ #include "H5Fpublic.h" /* Files */ +#include "H5Ipublic.h" /* IDs */ #include "H5Lpublic.h" /* Links */ #include "H5Opublic.h" /* Objects */ #include "H5Rpublic.h" /* References */ @@ -235,6 +236,25 @@ typedef struct H5VL_loc_params_t { } loc_data; } H5VL_loc_params_t; +/* VOL connector info fields & callbacks */ +typedef struct H5VL_info_class_t { + size_t size; /* Size of the VOL info */ + void * (*copy)(const void *info); /* Callback to create a copy of the VOL info */ + herr_t (*cmp)(int *cmp_value, const void *info1, const void *info2); /* Callback to compare VOL info */ + herr_t (*free)(void *info); /* Callback to release a VOL info */ + herr_t (*to_str)(const void *info, char **str); /* Callback to serialize connector's info into a string */ + herr_t (*from_str)(const char *str, void **info); /* Callback to deserialize a string into connector's info */ +} H5VL_info_class_t; + +/* VOL object wrap / retrieval callbacks */ +/* (These only need to be implemented by "pass through" VOL connectors) */ +typedef struct H5VL_wrap_class_t { + void * (*get_object)(const void *obj); /* Callback to retrieve underlying object */ + herr_t (*get_wrap_ctx)(const void *obj, void **wrap_ctx); /* Callback to retrieve the object wrapping context for the connector */ + void * (*wrap_object)(void *obj, H5I_type_t obj_type, void *wrap_ctx); /* Callback to wrap a library object */ + herr_t (*free_wrap_ctx)(void *wrap_ctx); /* Callback to release the object wrapping context for the connector */ +} H5VL_wrap_class_t; + /* H5A routines */ typedef struct H5VL_attr_class_t { void *(*create)(void *obj, const H5VL_loc_params_t *loc_params, const char *attr_name, @@ -369,34 +389,29 @@ typedef int H5VL_class_value_t; /* Class information for each VOL connector */ typedef struct H5VL_class_t { - unsigned int version; /* VOL connector class struct version # */ - H5VL_class_value_t value; /* Value to identify connector */ - const char *name; /* Connector name (MUST be unique!) */ - unsigned cap_flags; /* Capability flags for connector */ - herr_t (*initialize)(hid_t vipl_id); /* Connector initialization callback */ - herr_t (*terminate)(void); /* Connector termination callback */ - size_t info_size; /* Size of the VOL info */ - void * (*info_copy)(const void *info); /* Callback to create a copy of the VOL info */ - herr_t (*info_cmp)(int *cmp_value, const void *info1, const void *info2); /* Callback to compare VOL info */ - herr_t (*info_free)(void *info); /* Callback to release the VOL info copy */ - herr_t (*info_to_str)(const void *info, char **str); /* Callback to serialize connector's info into a string */ - herr_t (*str_to_info)(const char *str, void **info); /* Callback to deserialize a string into connector's info */ - void * (*get_object)(const void *obj); /* Callback to retrieve underlying object */ - herr_t (*get_wrap_ctx)(const void *obj, void **wrap_ctx); /* Callback to retrieve the object wrapping context for the connector */ - void* (*wrap_object)(void *obj, void *wrap_ctx); /* Callback to wrap a library object */ - herr_t (*free_wrap_ctx)(void *wrap_ctx); /* Callback to release the object wrapping context for the connector */ + /* Overall connector fields & callbacks */ + unsigned int version; /* VOL connector class struct version # */ + H5VL_class_value_t value; /* Value to identify connector */ + const char *name; /* Connector name (MUST be unique!) */ + unsigned cap_flags; /* Capability flags for connector */ + herr_t (*initialize)(hid_t vipl_id); /* Connector initialization callback */ + herr_t (*terminate)(void); /* Connector termination callback */ + + /* VOL framework */ + H5VL_info_class_t info_cls; /* VOL info fields & callbacks */ + H5VL_wrap_class_t wrap_cls; /* VOL object wrap / retrieval callbacks */ /* Data Model */ - H5VL_attr_class_t attr_cls; /* attribute class callbacks */ - H5VL_dataset_class_t dataset_cls; /* dataset class callbacks */ - H5VL_datatype_class_t datatype_cls; /* datatype class callbacks */ - H5VL_file_class_t file_cls; /* file class callbacks */ - H5VL_group_class_t group_cls; /* group class callbacks */ - H5VL_link_class_t link_cls; /* link class callbacks */ - H5VL_object_class_t object_cls; /* object class callbacks */ + H5VL_attr_class_t attr_cls; /* Attribute (H5A*) class callbacks */ + H5VL_dataset_class_t dataset_cls; /* Dataset (H5D*) class callbacks */ + H5VL_datatype_class_t datatype_cls; /* Datatype (H5T*) class callbacks */ + H5VL_file_class_t file_cls; /* File (H5F*) class callbacks */ + H5VL_group_class_t group_cls; /* Group (H5G*) class callbacks */ + H5VL_link_class_t link_cls; /* Link (H5L*) class callbacks */ + H5VL_object_class_t object_cls; /* Object (H5O*) class callbacks */ /* Services */ - H5VL_request_class_t request_cls; /* asynchronous request class callbacks */ + H5VL_request_class_t request_cls; /* Asynchronous request class callbacks */ /* Catch-all */ herr_t (*optional)(void *obj, hid_t dxpl_id, void **req, va_list arguments); /* Optional callback */ @@ -435,6 +450,10 @@ H5_DLL herr_t H5VLunregister_connector(hid_t connector_id); H5_DLL herr_t H5VLcmp_connector_cls(int *cmp, hid_t connector_id1, hid_t connector_id2); H5_DLL hid_t H5VLwrap_register(void *obj, H5I_type_t type); H5_DLL void *H5VLobject(hid_t obj_id); +H5_DLL herr_t H5VLretrieve_lib_state(void **state); +H5_DLL herr_t H5VLrestore_lib_state(const void *state); +H5_DLL herr_t H5VLreset_lib_state(void); +H5_DLL herr_t H5VLfree_lib_state(void *state); /* Public wrappers for generic callbacks */ @@ -450,7 +469,8 @@ H5_DLL herr_t H5VLconnector_info_to_str(const void *info, hid_t connector_id, ch H5_DLL herr_t H5VLconnector_str_to_info(const char *str, hid_t connector_id, void **info); H5_DLL void *H5VLget_object(void *obj, hid_t connector_id); H5_DLL herr_t H5VLget_wrap_ctx(void *obj, hid_t connector_id, void **wrap_ctx); -H5_DLL void *H5VLwrap_object(void *obj, hid_t connector_id, void *wrap_ctx); +H5_DLL void *H5VLwrap_object(void *obj, H5I_type_t obj_type, hid_t connector_id, + void *wrap_ctx); H5_DLL herr_t H5VLfree_wrap_ctx(void *wrap_ctx, hid_t connector_id); /* Public wrappers for attribute callbacks */ @@ -19,6 +19,7 @@ #include "H5private.h" #include "H5Eprivate.h" +#include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" #include "H5VMprivate.h" @@ -732,7 +733,7 @@ H5VM_stride_copy(unsigned n, hsize_t elmt_size, const hsize_t *size, /* Copy an element */ H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - HDmemcpy(dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ + H5MM_memcpy(dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ /* Decrement indices and advance pointers */ for (j=(int)(n-1), carry=TRUE; j>=0 && carry; --j) { @@ -749,7 +750,7 @@ H5VM_stride_copy(unsigned n, hsize_t elmt_size, const hsize_t *size, } } else { H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - HDmemcpy (dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ + H5MM_memcpy (dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ } FUNC_LEAVE_NOAPI(SUCCEED) @@ -801,7 +802,7 @@ H5VM_stride_copy_s(unsigned n, hsize_t elmt_size, const hsize_t *size, /* Copy an element */ H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - HDmemcpy(dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ + H5MM_memcpy(dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ /* Decrement indices and advance pointers */ for (j=(int)(n-1), carry=TRUE; j>=0 && carry; --j) { @@ -818,7 +819,7 @@ H5VM_stride_copy_s(unsigned n, hsize_t elmt_size, const hsize_t *size, } } else { H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - HDmemcpy (dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ + H5MM_memcpy (dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ } FUNC_LEAVE_NOAPI(SUCCEED) @@ -877,7 +878,7 @@ H5VM_stride_copy2(hsize_t nelmts, hsize_t elmt_size, /* Copy an element */ H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - HDmemcpy(dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ + H5MM_memcpy(dst, src, (size_t)elmt_size); /*lint !e671 The elmt_size will be OK */ /* Decrement indices and advance pointers */ for (j=(int)(dst_n-1), carry=TRUE; j>=0 && carry; --j) { @@ -936,7 +937,7 @@ H5VM_array_fill(void *_dst, const void *src, size_t size, size_t count) HDassert(size < SIZET_MAX && size > 0); HDassert(count < SIZET_MAX && count > 0); - HDmemcpy(dst, src, size); /* copy first item */ + H5MM_memcpy(dst, src, size); /* copy first item */ /* Initialize counters, etc. while compensating for first element copied */ copy_size = size; @@ -947,7 +948,7 @@ H5VM_array_fill(void *_dst, const void *src, size_t size, size_t count) /* copy until we've copied at least half of the items */ while (items_left >= copy_items) { - HDmemcpy(dst, _dst, copy_size); /* copy the current chunk */ + H5MM_memcpy(dst, _dst, copy_size); /* copy the current chunk */ dst += copy_size; /* move the offset for the next chunk */ items_left -= copy_items; /* decrement the number of items left */ @@ -955,7 +956,7 @@ H5VM_array_fill(void *_dst, const void *src, size_t size, size_t count) copy_items *= 2; /* increase the count of items we are copying */ } /* end while */ if (items_left > 0) /* if there are any items left to copy */ - HDmemcpy(dst, _dst, items_left * size); + H5MM_memcpy(dst, _dst, items_left * size); FUNC_LEAVE_NOAPI(SUCCEED) } /* H5VM_array_fill() */ @@ -1623,7 +1624,7 @@ src_smaller: acc_len = 0; do { /* Copy data */ - HDmemcpy(dst, src, tmp_src_len); + H5MM_memcpy(dst, src, tmp_src_len); /* Accumulate number of bytes copied */ acc_len += tmp_src_len; @@ -1666,7 +1667,7 @@ dst_smaller: acc_len = 0; do { /* Copy data */ - HDmemcpy(dst, src, tmp_dst_len); + H5MM_memcpy(dst, src, tmp_dst_len); /* Accumulate number of bytes copied */ acc_len += tmp_dst_len; @@ -1709,7 +1710,7 @@ equal: acc_len = 0; do { /* Copy data */ - HDmemcpy(dst, src, tmp_dst_len); + H5MM_memcpy(dst, src, tmp_dst_len); /* Accumulate number of bytes copied */ acc_len += tmp_dst_len; diff --git a/src/H5VMprivate.h b/src/H5VMprivate.h index decac7e..26f59e2 100644 --- a/src/H5VMprivate.h +++ b/src/H5VMprivate.h @@ -21,6 +21,7 @@ /* Private headers needed by this file */ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ /* Vector-Vector sequence operation callback */ typedef herr_t (*H5VM_opvv_func_t)(hsize_t dst_off, hsize_t src_off, @@ -41,7 +42,7 @@ typedef herr_t (*H5VM_opvv_func_t)(hsize_t dst_off, hsize_t src_off, /* Other functions */ #define H5VM_vector_cpy(N,DST,SRC) { \ HDassert(sizeof(*(DST))==sizeof(*(SRC))); \ - if (SRC) HDmemcpy (DST, SRC, (N)*sizeof(*(DST))); \ + if (SRC) H5MM_memcpy (DST, SRC, (N)*sizeof(*(DST))); \ else HDmemset (DST, 0, (N)*sizeof(*(DST))); \ } @@ -322,7 +322,7 @@ H5Z_register (const H5Z_class2_t *cls) /* Initialize */ i = H5Z_table_used_g++; - HDmemcpy(H5Z_table_g+i, cls, sizeof(H5Z_class2_t)); + H5MM_memcpy(H5Z_table_g+i, cls, sizeof(H5Z_class2_t)); #ifdef H5Z_DEBUG HDmemset(H5Z_stat_table_g+i, 0, sizeof(H5Z_stats_t)); #endif /* H5Z_DEBUG */ @@ -330,7 +330,7 @@ H5Z_register (const H5Z_class2_t *cls) /* Filter already registered */ else { /* Replace old contents */ - HDmemcpy(H5Z_table_g+i, cls, sizeof(H5Z_class2_t)); + H5MM_memcpy(H5Z_table_g+i, cls, sizeof(H5Z_class2_t)); } /* end else */ done: @@ -611,7 +611,7 @@ H5Z__flush_file_cb(void *obj_ptr, hid_t H5_ATTR_UNUSED obj_id, void *key) /* Sanity check for collectively calling H5Zunregister, if requested */ /* (Sanity check assumes that a barrier on one file's comm * is sufficient (i.e. that there aren't different comms for - * different files). -QAK, 2018/02/14 + * different files). -QAK, 2018/02/14) */ if(H5_coll_api_sanity_check_g && !object->sanity_checked) { MPI_Comm mpi_comm; /* File's communicator */ diff --git a/src/H5Zfletcher32.c b/src/H5Zfletcher32.c index 4cd77ef..4d75d14 100644 --- a/src/H5Zfletcher32.c +++ b/src/H5Zfletcher32.c @@ -108,7 +108,7 @@ H5Z_filter_fletcher32 (unsigned flags, size_t H5_ATTR_UNUSED cd_nelmts, const un * system. We'll check both the correct checksum and the wrong * checksum to be consistent with Release 1.6.2 and before. */ - HDmemcpy(c, &fletcher, (size_t)4); + H5MM_memcpy(c, &fletcher, (size_t)4); tmp = c[1]; c[1] = c[0]; @@ -118,7 +118,7 @@ H5Z_filter_fletcher32 (unsigned flags, size_t H5_ATTR_UNUSED cd_nelmts, const un c[3] = c[2]; c[2] = tmp; - HDmemcpy(&reversed_fletcher, c, (size_t)4); + H5MM_memcpy(&reversed_fletcher, c, (size_t)4); /* Verify computed checksum matches stored checksum */ if(stored_fletcher != fletcher && stored_fletcher != reversed_fletcher) @@ -140,7 +140,7 @@ H5Z_filter_fletcher32 (unsigned flags, size_t H5_ATTR_UNUSED cd_nelmts, const un dst = (unsigned char *) outbuf; /* Copy raw data */ - HDmemcpy((void*)dst, (void*)(*buf), nbytes); + H5MM_memcpy((void*)dst, (void*)(*buf), nbytes); /* Append checksum to raw data for storage */ dst += nbytes; diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c index cdf31a4..d3e8fc0 100644 --- a/src/H5Zscaleoffset.c +++ b/src/H5Zscaleoffset.c @@ -141,7 +141,7 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ } /* end if */ \ \ /* Copy the value */ \ - HDmemcpy(&_cd_value, _fv_p, _copy_size); \ + H5MM_memcpy(&_cd_value, _fv_p, _copy_size); \ (cd_values)[_i] = (unsigned)_cd_value; \ \ /* Next field */ \ @@ -158,7 +158,7 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ _fv_p = ((char *)&(fill_val)) + sizeof(type) - MIN(4, _size_rem); \ while(_size_rem >= 4) { \ /* Copy the value */ \ - HDmemcpy(&_cd_value, _fv_p, _copy_size); \ + H5MM_memcpy(&_cd_value, _fv_p, _copy_size); \ (cd_values)[_i] = (unsigned)_cd_value; \ \ /* Next field */ \ @@ -176,7 +176,7 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ * _cd_value as it will not be fully overwritten and copy to the end \ * of _cd value as it is BE. */ \ _cd_value = (uint32_t)0; \ - HDmemcpy((char *)&_cd_value + 4 - _size_rem, _fv_p, _size_rem); \ + H5MM_memcpy((char *)&_cd_value + 4 - _size_rem, _fv_p, _size_rem); \ (cd_values)[_i] = (unsigned)_cd_value; \ } /* end if */ \ } /* end else */ \ @@ -269,7 +269,7 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ \ /* Copy the value */ \ _cd_value = (uint32_t)(cd_values)[_i]; \ - HDmemcpy(_fv_p, &_cd_value, _copy_size); \ + H5MM_memcpy(_fv_p, &_cd_value, _copy_size); \ \ /* Next field */ \ _i++; \ @@ -286,7 +286,7 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ while(_size_rem >= 4) { \ /* Copy the value */ \ _cd_value = (uint32_t)(cd_values)[_i]; \ - HDmemcpy(_fv_p, &_cd_value, _copy_size); \ + H5MM_memcpy(_fv_p, &_cd_value, _copy_size); \ \ /* Next field */ \ _i++; \ @@ -303,7 +303,7 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ * _cd_value as it will not be fully overwritten and copy to the end \ * of _cd value as it is BE. */ \ _cd_value = (uint32_t)(cd_values)[_i]; \ - HDmemcpy(_fv_p, (char *)&_cd_value + 4 - _size_rem, _size_rem); \ + H5MM_memcpy(_fv_p, (char *)&_cd_value + 4 - _size_rem, _size_rem); \ } /* end if */ \ } /* end else */ \ } @@ -529,10 +529,10 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ * account for offset in BE if sizes differ \ */ \ if(H5T_native_order_g == H5T_ORDER_LE) \ - HDmemcpy(minval, &min, sizeof(type)); \ + H5MM_memcpy(minval, &min, sizeof(type)); \ else { \ HDassert(H5T_native_order_g == H5T_ORDER_BE); \ - HDmemcpy(((char *)minval) + (sizeof(long long) - sizeof(type)), \ + H5MM_memcpy(((char *)minval) + (sizeof(long long) - sizeof(type)), \ &min, sizeof(type)); \ } /* end else */ \ else \ @@ -604,10 +604,10 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{ * account for offset in BE if sizes differ \ */ \ if(H5T_native_order_g == H5T_ORDER_LE) \ - HDmemcpy(&min, &minval, sizeof(type)); \ + H5MM_memcpy(&min, &minval, sizeof(type)); \ else { \ HDassert(H5T_native_order_g == H5T_ORDER_BE); \ - HDmemcpy(&min, ((char *)&minval) + (sizeof(long long) \ + H5MM_memcpy(&min, ((char *)&minval) + (sizeof(long long) \ - sizeof(type)), sizeof(type)); \ } /* end else */ \ else \ @@ -1173,7 +1173,9 @@ H5Z_filter_scaleoffset(unsigned flags, size_t cd_nelmts, const unsigned cd_value /* special case: minbits equal to full precision */ if(minbits == p.size * 8) { - HDmemcpy(outbuf, (unsigned char*)(*buf)+buf_offset, size_out); + H5MM_memcpy(outbuf, (unsigned char*)(*buf)+buf_offset, size_out); + /* free the original buffer */ + H5MM_xfree(*buf); /* convert to dataset datatype endianness order if needed */ if(need_convert) @@ -1271,7 +1273,10 @@ H5Z_filter_scaleoffset(unsigned flags, size_t cd_nelmts, const unsigned cd_value /* special case: minbits equal to full precision */ if(minbits == p.size * 8) { - HDmemcpy(outbuf + buf_offset, *buf, nbytes); + H5MM_memcpy(outbuf + buf_offset, *buf, nbytes); + /* free the original buffer */ + H5MM_xfree(*buf); + *buf = outbuf; outbuf = NULL; *buf_size = size_out; diff --git a/src/H5Zshuffle.c b/src/H5Zshuffle.c index 1fef1c1..e70ef33 100644 --- a/src/H5Zshuffle.c +++ b/src/H5Zshuffle.c @@ -210,7 +210,7 @@ H5Z_filter_shuffle(unsigned flags, size_t cd_nelmts, const unsigned cd_values[], if(leftover>0) { /* Adjust back to end of shuffled bytes */ _dest -= (bytesoftype - 1); /*lint !e794 _dest is initialized */ - HDmemcpy((void*)_dest, (void*)_src, leftover); + H5MM_memcpy((void*)_dest, (void*)_src, leftover); } } /* end if */ else { @@ -268,7 +268,7 @@ H5Z_filter_shuffle(unsigned flags, size_t cd_nelmts, const unsigned cd_values[], if(leftover>0) { /* Adjust back to end of shuffled bytes */ _src -= (bytesoftype - 1); /*lint !e794 _src is initialized */ - HDmemcpy((void*)_dest, (void*)_src, leftover); + H5MM_memcpy((void*)_dest, (void*)_src, leftover); } } /* end else */ diff --git a/src/H5Ztrans.c b/src/H5Ztrans.c index 67646a0..6d07513 100644 --- a/src/H5Ztrans.c +++ b/src/H5Ztrans.c @@ -850,7 +850,7 @@ H5Z_parse_factor(H5Z_token *current, H5Z_datval_ptrs* dat_val_pointers) if (!factor) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "Unable to allocate new node") - sscanf(current->tok_begin, "%ld", &factor->value.int_val); + HDsscanf(current->tok_begin, "%ld", &factor->value.int_val); break; case H5Z_XFORM_FLOAT: @@ -858,7 +858,7 @@ H5Z_parse_factor(H5Z_token *current, H5Z_datval_ptrs* dat_val_pointers) if (!factor) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "Unable to allocate new node") - sscanf(current->tok_begin, "%lf", &factor->value.float_val); + HDsscanf(current->tok_begin, "%lf", &factor->value.float_val); break; case H5Z_XFORM_SYMBOL: @@ -1078,7 +1078,7 @@ H5Z_xform_eval(H5Z_data_xform_t *data_xform_prop, void* array, size_t array_size if(NULL == (data_xform_prop->dat_val_pointers->ptr_dat_val[i] = (void*)H5MM_malloc(array_size * H5T_get_size((H5T_t *)H5I_object(array_type))))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "Ran out of memory trying to allocate space for data in data transform") - HDmemcpy(data_xform_prop->dat_val_pointers->ptr_dat_val[i], array, array_size * H5T_get_size((H5T_t *)H5I_object(array_type))); + H5MM_memcpy(data_xform_prop->dat_val_pointers->ptr_dat_val[i], array, array_size * H5T_get_size((H5T_t *)H5I_object(array_type))); } /* end for */ } /* end else */ @@ -1086,7 +1086,7 @@ H5Z_xform_eval(H5Z_data_xform_t *data_xform_prop, void* array, size_t array_size HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "error while performing data transform") if(data_xform_prop->dat_val_pointers->num_ptrs > 1) - HDmemcpy(array, res.value.dat_val, array_size * H5T_get_size((H5T_t *)H5I_object(array_type))); + H5MM_memcpy(array, res.value.dat_val, array_size * H5T_get_size((H5T_t *)H5I_object(array_type))); /* Free the temporary arrays we used */ if(data_xform_prop->dat_val_pointers->num_ptrs > 1) diff --git a/src/H5dbg.c b/src/H5dbg.c index dd50034..4939bca 100644 --- a/src/H5dbg.c +++ b/src/H5dbg.c @@ -113,7 +113,7 @@ H5_buffer_dump(FILE *stream, int indent, const uint8_t *buf, } /* end else */ } /* end if */ else - fprintf(stream, " "); + HDfprintf(stream, " "); if(7 == v) HDfputc(' ', stream); } /* end for */ diff --git a/src/H5private.h b/src/H5private.h index f58faec..dad2d94 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -1104,12 +1104,8 @@ typedef off_t h5_stat_size_t; #ifndef HDmemcmp #define HDmemcmp(X,Y,Z) memcmp(X,Y,Z) #endif /* HDmemcmp */ -/* - * The (char*) casts are required for the DEC when optimizations are turned - * on and the source and/or destination are not aligned. - */ #ifndef HDmemcpy - #define HDmemcpy(X,Y,Z) memcpy((char*)(X),(const char*)(Y),Z) + #define HDmemcpy(X,Y,Z) memcpy(X,Y,Z) #endif /* HDmemcpy */ #ifndef HDmemmove #define HDmemmove(X,Y,Z) memmove((char*)(X),(const char*)(Y),Z) @@ -1156,6 +1152,9 @@ typedef off_t h5_stat_size_t; #ifndef HDpowf #define HDpowf(X,Y) powf(X,Y) #endif /* HDpowf */ +#ifndef HDpread + #define HDpread(F,B,C,O) pread(F,B,C,O) +#endif /* HDpread */ #ifndef HDprintf #define HDprintf(...) HDfprintf(stdout, __VA_ARGS__) #endif /* HDprintf */ @@ -1168,6 +1167,9 @@ typedef off_t h5_stat_size_t; #ifndef HDputs #define HDputs(S) puts(S) #endif /* HDputs */ +#ifndef HDpwrite + #define HDpwrite(F,B,C,O) pwrite(F,B,C,O) +#endif /* HDpwrite */ #ifndef HDqsort #define HDqsort(M,N,Z,F) qsort(M,N,Z,F) #endif /* HDqsort*/ @@ -1334,8 +1336,9 @@ typedef off_t h5_stat_size_t; #define HDsrandom(S) srand(S) #endif /* HDsrandom */ #endif /* H5_HAVE_RAND_R */ -/* sscanf() variable arguments */ - +#ifndef HDsscanf + #define HDsscanf(S,FMT,...) sscanf(S,FMT,__VA_ARGS__) +#endif /* HDsscanf */ #ifndef HDstrcat #define HDstrcat(X,Y) strcat(X,Y) #endif /* HDstrcat */ diff --git a/src/H5system.c b/src/H5system.c index f47d057..2ddc29a 100644 --- a/src/H5system.c +++ b/src/H5system.c @@ -985,6 +985,132 @@ Wroundf(float arg) return (float)(arg < 0.0F ? HDceil(arg - 0.5F) : HDfloor(arg + 0.5F)); } +/*------------------------------------------------------------------------- +* Function: H5_get_utf16_str +* +* Purpose: Gets a UTF-16 string from an UTF-8 (or ASCII) string. +* +* Return: Success: A pointer to a UTF-16 string +* This must be freed by the caller using H5MM_xfree() +* Failure: NULL +* +* Programmer: Dana Robinson +* Spring 2019 +* +*------------------------------------------------------------------------- +*/ +const wchar_t * +H5_get_utf16_str(const char *s) +{ + int nwchars = -1; /* Length of the UTF-16 buffer */ + wchar_t *ret_s = NULL; /* UTF-16 version of the string */ + + /* Get the number of UTF-16 characters needed */ + if(0 == (nwchars = MultiByteToWideChar(CP_UTF8, 0, s, -1, NULL, 0))) + goto error; + + /* Allocate a buffer for the UTF-16 string */ + if(NULL == (ret_s = (wchar_t *)H5MM_calloc(sizeof(wchar_t) * (size_t)nwchars))) + goto error; + + /* Convert the input UTF-8 string to UTF-16 */ + if(0 == MultiByteToWideChar(CP_UTF8, 0, s, -1, ret_s, nwchars)) + goto error; + + return ret_s; + +error: + if(ret_s) + H5MM_xfree((void *)ret_s); + return NULL; +} /* end H5_get_utf16_str() */ + +/*------------------------------------------------------------------------- + * Function: Wopen_utf8 + * + * Purpose: UTF-8 equivalent of open(2) for use on Windows. + * Converts a UTF-8 input path to UTF-16 and then opens the + * file via _wopen() under the hood + * + * Return: Success: A POSIX file descriptor + * Failure: -1 + * + * Programmer: Dana Robinson + * Spring 2019 + * + *------------------------------------------------------------------------- + */ +int +Wopen_utf8(const char *path, int oflag, ...) +{ + int fd = -1; /* POSIX file descriptor to be returned */ + wchar_t *wpath = NULL; /* UTF-16 version of the path */ + int pmode = 0; /* mode (optionally set via variable args) */ + + /* Convert the input UTF-8 path to UTF-16 */ + if(NULL == (wpath = H5_get_utf16_str(path))) + goto done; + + /* _O_BINARY must be set in Windows to avoid CR-LF <-> LF EOL + * transformations when performing I/O. Note that this will + * produce Unix-style text files, though. + */ + oflag |= _O_BINARY; + + /* Get the mode, if O_CREAT was specified */ + if(oflag & O_CREAT) { + va_list vl; + + HDva_start(vl, oflag); + pmode = HDva_arg(vl, int); + HDva_end(vl); + } + + /* Open the file */ + fd = _wopen(wpath, oflag, pmode); + +done: + if(wpath) + H5MM_xfree((void *)wpath); + + return fd; +} /* end Wopen_utf8() */ + +/*------------------------------------------------------------------------- + * Function: Wremove_utf8 + * + * Purpose: UTF-8 equivalent of remove(3) for use on Windows. + * Converts a UTF-8 input path to UTF-16 and then opens the + * file via _wremove() under the hood + * + * Return: Success: 0 + * Failure: -1 + * + * Programmer: Dana Robinson + * Spring 2019 + * + *------------------------------------------------------------------------- + */ +int +Wremove_utf8(const char *path) +{ + wchar_t *wpath = NULL; /* UTF-16 version of the path */ + int ret; + + /* Convert the input UTF-8 path to UTF-16 */ + if(NULL == (wpath = H5_get_utf16_str(path))) + goto done; + + /* Open the file */ + ret = _wremove(wpath); + +done: + if(wpath) + H5MM_xfree((void *)wpath); + + return ret; +} /* end Wremove_utf8() */ + #endif /* H5_HAVE_WIN32_API */ diff --git a/src/H5timer.c b/src/H5timer.c index 0ba8bd1..4b1ec06 100644 --- a/src/H5timer.c +++ b/src/H5timer.c @@ -213,26 +213,26 @@ H5_bandwidth(char *buf/*out*/, double nbytes, double nseconds) if(H5_DBL_ABS_EQUAL(bw, (double)0.0F)) HDstrcpy(buf, "0.000 B/s"); else if(bw < (double)1.0F) - sprintf(buf, "%10.4e", bw); + HDsprintf(buf, "%10.4e", bw); else if(bw < (double)H5_KB) { - sprintf(buf, "%05.4f", bw); + HDsprintf(buf, "%05.4f", bw); HDstrcpy(buf+5, " B/s"); } else if(bw < (double)H5_MB) { - sprintf(buf, "%05.4f", bw / (double)H5_KB); + HDsprintf(buf, "%05.4f", bw / (double)H5_KB); HDstrcpy(buf+5, " kB/s"); } else if(bw < (double)H5_GB) { - sprintf(buf, "%05.4f", bw / (double)H5_MB); + HDsprintf(buf, "%05.4f", bw / (double)H5_MB); HDstrcpy(buf+5, " MB/s"); } else if(bw < (double)H5_TB) { - sprintf(buf, "%05.4f", bw / (double)H5_GB); + HDsprintf(buf, "%05.4f", bw / (double)H5_GB); HDstrcpy(buf+5, " GB/s"); } else if(bw < (double)H5_PB) { - sprintf(buf, "%05.4f", bw / (double)H5_TB); + HDsprintf(buf, "%05.4f", bw / (double)H5_TB); HDstrcpy(buf+5, " TB/s"); } else { - sprintf(buf, "%10.4e", bw); + HDsprintf(buf, "%10.4e", bw); if(HDstrlen(buf) > 10) - sprintf(buf, "%10.3e", bw); + HDsprintf(buf, "%10.3e", bw); } } } /* end H5_bandwidth() */ diff --git a/src/H5win32defs.h b/src/H5win32defs.h index 140afc3..2ae2575 100644 --- a/src/H5win32defs.h +++ b/src/H5win32defs.h @@ -34,6 +34,7 @@ typedef __int64 h5_stat_size_t; #define HDaccess(F,M) _access(F,M) #define HDchdir(S) _chdir(S) #define HDclose(F) _close(F) +#define HDcreat(S,M) Wopen_utf8(S,O_CREAT|O_TRUNC|O_RDWR,M) #define HDdup(F) _dup(F) #define HDfdopen(N,S) _fdopen(N,S) #define HDfileno(F) _fileno(F) @@ -47,15 +48,13 @@ typedef __int64 h5_stat_size_t; #define HDmkdir(S,M) _mkdir(S) #define HDnanosleep(N, O) Wnanosleep(N, O) #define HDoff_t __int64 -/* _O_BINARY must be set in Windows to avoid CR-LF <-> LF EOL - * transformations when performing I/O. Note that this will - * produce Unix-style text files, though. - * - * Also note that the variadic macro is using a VC++ extension + +/* Note that the variadic HDopen macro is using a VC++ extension * where the comma is dropped if nothing is passed to the ellipsis. */ -#define HDopen(S,F,...) _open(S, F | _O_BINARY, __VA_ARGS__) +#define HDopen(S,F,...) Wopen_utf8(S,F,__VA_ARGS__) #define HDread(F,M,Z) _read(F,M,Z) +#define HDremove(S) Wremove_utf8(S) #define HDrmdir(S) _rmdir(S) #define HDsetvbuf(F,S,M,Z) setvbuf(F,S,M,(Z>1?Z:2)) #define HDsleep(S) Sleep(S*1000) @@ -128,6 +127,9 @@ extern "C" { H5_DLL int c99_vsnprintf(char* str, size_t size, const char* format, va_list ap); H5_DLL int Wnanosleep(const struct timespec *req, struct timespec *rem); H5_DLL herr_t H5_expand_windows_env_vars(char **env_var); + H5_DLL const wchar_t *H5_get_utf16_str(const char *s); + H5_DLL int Wopen_utf8(const char *path, int oflag, ...); + H5_DLL int Wremove_utf8(const char *path); /* Round functions only needed for VS2012 and earlier. * They are always built to ensure they don't go stale and |