diff options
| author | Mohamad Chaarawi <chaarawi@hdfgroup.org> | 2016-01-11 15:55:55 (GMT) |
|---|---|---|
| committer | Mohamad Chaarawi <chaarawi@hdfgroup.org> | 2016-01-11 15:55:55 (GMT) |
| commit | 5dbc03ac86cb05730467eb0cad4bf3fb51a74ae4 (patch) | |
| tree | 85afdc8134a6e0b512c8ffeb3a63b6af4eb5409e /src | |
| parent | 2824e6bef0f9ea6550845f75ad4580349eafb822 (diff) | |
| parent | 887cf130ff773568f90ec8bae66dafa761a77712 (diff) | |
| download | hdf5-5dbc03ac86cb05730467eb0cad4bf3fb51a74ae4.zip hdf5-5dbc03ac86cb05730467eb0cad4bf3fb51a74ae4.tar.gz hdf5-5dbc03ac86cb05730467eb0cad4bf3fb51a74ae4.tar.bz2 | |
[svn-r28851] merge from trunk.
Diffstat (limited to 'src')
58 files changed, 1708 insertions, 657 deletions
@@ -396,6 +396,11 @@ H5_term_library(void) (void)H5MM_free(tmp_open_stream); } /* end while */ +#if defined H5_MEMORY_ALLOC_SANITY_CHECK + /* Sanity check memory allocations */ + H5MM_final_sanity_check(); +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + /* Reset flag indicating that the library is being shut down */ H5_TERM_GLOBAL = FALSE; @@ -942,7 +947,6 @@ H5allocate_memory(size_t size, hbool_t clear) ret_value = H5MM_malloc(size); FUNC_LEAVE_API(ret_value) - } /* end H5allocate_memory() */ @@ -981,7 +985,6 @@ H5resize_memory(void *mem, size_t size) ret_value = H5MM_realloc(mem, size); FUNC_LEAVE_API(ret_value) - } /* end H5resize_memory() */ @@ -1004,10 +1007,9 @@ H5free_memory(void *mem) H5TRACE1("e", "*x", mem); /* At this time, it is impossible for this to fail. */ - HDfree(mem); + H5MM_xfree(mem); FUNC_LEAVE_API(SUCCEED) - } /* end H5free_memory() */ @@ -244,7 +244,6 @@ H5A_term_package(void) develop. --------------------------------------------------------------------------*/ -/* ARGSUSED */ hid_t H5Acreate2(hid_t loc_id, const char *attr_name, hid_t type_id, hid_t space_id, hid_t acpl_id, hid_t aapl_id) @@ -325,7 +324,6 @@ done: develop. --------------------------------------------------------------------------*/ -/* ARGSUSED */ hid_t H5Acreate_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id, hid_t space_id, hid_t acpl_id, hid_t aapl_id, @@ -46,6 +46,7 @@ #include "H5FDprivate.h" /* File drivers */ #include "H5Iprivate.h" /* IDs */ #include "H5Pprivate.h" /* Property lists */ +#include "H5SLprivate.h" /* Skip Lists */ /****************/ diff --git a/src/H5Abtree2.c b/src/H5Abtree2.c index 972fb0b..716ad4a 100644 --- a/src/H5Abtree2.c +++ b/src/H5Abtree2.c @@ -116,9 +116,7 @@ const H5B2_class_t H5A_BT2_NAME[1]={{ /* B-tree class information */ H5A__dense_btree2_name_compare, /* Record comparison callback */ H5A__dense_btree2_name_encode, /* Record encoding callback */ H5A__dense_btree2_name_decode, /* Record decoding callback */ - H5A__dense_btree2_name_debug, /* Record debugging callback */ - NULL, /* Create debugging context */ - NULL /* Destroy debugging context */ + H5A__dense_btree2_name_debug /* Record debugging callback */ }}; /* v2 B-tree class for indexing 'creation order' field of attributes */ @@ -132,9 +130,7 @@ const H5B2_class_t H5A_BT2_CORDER[1]={{ /* B-tree class information */ H5A__dense_btree2_corder_compare, /* Record comparison callback */ H5A__dense_btree2_corder_encode, /* Record encoding callback */ H5A__dense_btree2_corder_decode, /* Record decoding callback */ - H5A__dense_btree2_corder_debug, /* Record debugging callback */ - NULL, /* Create debugging context */ - NULL /* Destroy debugging context */ + H5A__dense_btree2_corder_debug /* Record debugging callback */ }}; diff --git a/src/H5Aint.c b/src/H5Aint.c index baa352c..12ffb7d 100644 --- a/src/H5Aint.c +++ b/src/H5Aint.c @@ -1878,7 +1878,7 @@ H5A_set_version(const H5F_t *f, H5A_t *attr) /* Check which version to encode attribute with */ if(use_latest_format) - attr->shared->version = H5O_ATTR_VERSION_LATEST; /* Write out latest version of format */ + attr->shared->version = H5O_ATTR_VERSION_LATEST; /* Write out latest attribute version */ else if(attr->shared->encoding != H5T_CSET_ASCII) attr->shared->version = H5O_ATTR_VERSION_3; /* Write version which includes the character encoding */ else if(type_shared || space_shared) @@ -612,6 +612,7 @@ H5B_insert(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr, void /* Check if the root node split */ if(H5B_INS_NOOP == my_ins) { + /* The root node did not split - just return */ HDassert(!split_bt_ud.bt); HGOTO_DONE(SUCCEED) } /* end if */ @@ -2035,7 +2036,7 @@ htri_t H5B_valid(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, haddr_t addr) { H5B_t *bt = NULL; /* The B-tree */ - H5UC_t *rc_shared; /* Ref-counted shared info */ + H5UC_t *rc_shared; /* Ref-counted shared info */ H5B_shared_t *shared; /* Pointer to shared B-tree info */ H5B_cache_ud_t cache_udata; /* User-data for metadata cache callback */ htri_t ret_value = SUCCEED; /* Return value */ @@ -42,6 +42,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5B2pkg.h" /* v2 B-trees */ #include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ /****************/ @@ -86,6 +87,7 @@ extern const H5B2_class_t H5G_BT2_CORDER[1]; extern const H5B2_class_t H5SM_INDEX[1]; extern const H5B2_class_t H5A_BT2_NAME[1]; extern const H5B2_class_t H5A_BT2_CORDER[1]; +extern const H5B2_class_t H5B2_TEST2[1]; const H5B2_class_t *const H5B2_client_class_g[] = { H5B2_TEST, /* 0 - H5B2_TEST_ID */ @@ -98,6 +100,7 @@ const H5B2_class_t *const H5B2_client_class_g[] = { H5SM_INDEX, /* 7 - H5B2_SOHM_INDEX_ID */ H5A_BT2_NAME, /* 8 - H5B2_ATTR_DENSE_NAME_ID */ H5A_BT2_CORDER, /* 9 - H5B2_ATTR_DENSE_CORDER_ID */ + H5B2_TEST2, /* 10 - H5B2_TEST_ID */ }; @@ -134,7 +137,6 @@ H5B2_create(H5F_t *f, hid_t dxpl_id, const H5B2_create_t *cparam, void *ctx_udat { H5B2_t *bt2 = NULL; /* Pointer to the B-tree */ H5B2_hdr_t *hdr = NULL; /* Pointer to the B-tree header */ - H5B2_hdr_cache_ud_t cache_udata; /* User-data for callback */ haddr_t hdr_addr; /* B-tree header address */ H5B2_t *ret_value = NULL; /* Return value */ @@ -158,11 +160,8 @@ H5B2_create(H5F_t *f, hid_t dxpl_id, const H5B2_create_t *cparam, void *ctx_udat HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for v2 B-tree info") /* Look up the B-tree header */ - cache_udata.f = f; - cache_udata.addr = hdr_addr; - cache_udata.ctx_udata = ctx_udata; - if(NULL == (hdr = (H5B2_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_BT2_HDR, hdr_addr, &cache_udata, H5AC__NO_FLAGS_SET))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, NULL, "unable to load B-tree header") + if(NULL == (hdr = H5B2__hdr_protect(f, dxpl_id, hdr_addr, ctx_udata, H5AC__NO_FLAGS_SET))) + HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, NULL, "unable to protect v2 B-tree header") /* Point v2 B-tree wrapper at header and bump it's ref count */ bt2->hdr = hdr; @@ -180,7 +179,7 @@ H5B2_create(H5F_t *f, hid_t dxpl_id, const H5B2_create_t *cparam, void *ctx_udat ret_value = bt2; done: - if(hdr && H5AC_unprotect(f, dxpl_id, H5AC_BT2_HDR, hdr_addr, hdr, H5AC__NO_FLAGS_SET) < 0) + if(hdr && H5B2__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0) HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, NULL, "unable to release v2 B-tree header") if(!ret_value && bt2) if(H5B2_close(bt2, dxpl_id) < 0) @@ -209,7 +208,6 @@ H5B2_open(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *ctx_udata) { H5B2_t *bt2 = NULL; /* Pointer to the B-tree */ H5B2_hdr_t *hdr = NULL; /* Pointer to the B-tree header */ - H5B2_hdr_cache_ud_t cache_udata; /* User-data for callback */ H5B2_t *ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI_NOINIT @@ -219,11 +217,8 @@ H5B2_open(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *ctx_udata) HDassert(H5F_addr_defined(addr)); /* Look up the B-tree header */ - cache_udata.f = f; - cache_udata.addr = addr; - cache_udata.ctx_udata = ctx_udata; - if(NULL == (hdr = (H5B2_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_BT2_HDR, addr, &cache_udata, H5AC__READ_ONLY_FLAG))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, NULL, "unable to load B-tree header") + if(NULL == (hdr = H5B2__hdr_protect(f, dxpl_id, addr, ctx_udata, H5AC__READ_ONLY_FLAG))) + HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, NULL, "unable to protect v2 B-tree header") /* Check for pending heap deletion */ if(hdr->pending_delete) @@ -249,7 +244,7 @@ H5B2_open(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *ctx_udata) ret_value = bt2; done: - if(hdr && H5AC_unprotect(f, dxpl_id, H5AC_BT2_HDR, addr, hdr, H5AC__NO_FLAGS_SET) < 0) + if(hdr && H5B2__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0) HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, NULL, "unable to release v2 B-tree header") if(!ret_value && bt2) if(H5B2_close(bt2, dxpl_id) < 0) @@ -290,36 +285,78 @@ H5B2_insert(H5B2_t *bt2, hid_t dxpl_id, void *udata) /* Get the v2 B-tree header */ hdr = bt2->hdr; + /* Insert the record */ + if(H5B2__insert_hdr(hdr, dxpl_id, udata) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B-tree") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5B2_insert() */ + + +/*------------------------------------------------------------------------- + * Function: H5B2_update + * + * Purpose: Insert or modify a record to the B-tree. + * If the record exists already, it is modified as if H5B2_modify + * was called). If it doesn't exist, it is inserted as if + * H5B2_insert was called. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * koziol@hdfgroup.org + * Dec 23 2015 + * + *------------------------------------------------------------------------- + */ +herr_t +H5B2_update(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_modify_t op, void *op_data) +{ + H5B2_hdr_t *hdr; /* Pointer to the B-tree header */ + H5B2_update_status_t status = H5B2_UPDATE_UNKNOWN; /* Whether the record was inserted/modified */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Check arguments. */ + HDassert(bt2); + HDassert(udata); + + /* Set the shared v2 B-tree header's file context for this operation */ + bt2->hdr->f = bt2->f; + + /* Get the v2 B-tree header */ + hdr = bt2->hdr; + /* Check if the root node is allocated yet */ if(!H5F_addr_defined(hdr->root.addr)) { /* Create root node as leaf node in B-tree */ if(H5B2__create_leaf(hdr, dxpl_id, &(hdr->root)) < 0) HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "unable to create root node") } /* end if */ - /* Check if we need to split the root node (equiv. to a 1->2 node split) */ - else if(hdr->root.node_nrec == hdr->node_info[hdr->depth].split_nrec) { - /* Split root node */ - if(H5B2__split_root(hdr, dxpl_id) < 0) - HGOTO_ERROR(H5E_BTREE, H5E_CANTSPLIT, FAIL, "unable to split root node") - } /* end if */ /* Attempt to insert record into B-tree */ if(hdr->depth > 0) { - if(H5B2__insert_internal(hdr, dxpl_id, hdr->depth, NULL, &hdr->root, H5B2_POS_ROOT, udata) < 0) - HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B-tree internal node") + if(H5B2__update_internal(hdr, dxpl_id, hdr->depth, NULL, &hdr->root, &status, H5B2_POS_ROOT, udata, op, op_data) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to update record in B-tree internal node") } /* end if */ else { - if(H5B2__insert_leaf(hdr, dxpl_id, &hdr->root, H5B2_POS_ROOT, udata) < 0) - HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B-tree leaf node") + if(H5B2__update_leaf(hdr, dxpl_id, &hdr->root, &status, H5B2_POS_ROOT, udata, op, op_data) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to update record in B-tree leaf node") } /* end else */ - /* Mark B-tree header as dirty */ - if(H5B2__hdr_dirty(hdr) < 0) - HGOTO_ERROR(H5E_BTREE, H5E_CANTMARKDIRTY, FAIL, "unable to mark B-tree header dirty") + /* Sanity check */ + HDassert(H5B2_UPDATE_UNKNOWN != status); + + /* Use insert algorithm if nodes to leaf full */ + if(H5B2_UPDATE_INSERT_CHILD_FULL == status) + if(H5B2__insert_hdr(hdr, dxpl_id, udata) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B-tree") done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5B2_insert() */ +} /* H5B2_update() */ /*------------------------------------------------------------------------- @@ -578,7 +615,7 @@ H5B2_find(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_found_t op, if(idx == 0) { if(H5B2_POS_LEFT == curr_pos || H5B2_POS_ROOT == curr_pos) { if(hdr->min_native_rec == NULL) - if(NULL == (hdr->min_native_rec = (uint8_t *)HDmalloc(hdr->cls->nrec_size))) + 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); } /* end if */ @@ -586,7 +623,7 @@ H5B2_find(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_found_t op, if(idx == (unsigned)(leaf->nrec - 1)) { if(H5B2_POS_RIGHT == curr_pos || H5B2_POS_ROOT == curr_pos) { if(hdr->max_native_rec == NULL) - if(NULL == (hdr->max_native_rec = (uint8_t *)HDmalloc(hdr->cls->nrec_size))) + 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); } /* end if */ @@ -1188,7 +1225,7 @@ H5B2_modify(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_modify_t op, if(idx == 0) { if(H5B2_POS_LEFT == curr_pos || H5B2_POS_ROOT == curr_pos) { if(hdr->min_native_rec == NULL) - if(NULL == (hdr->min_native_rec = (uint8_t *)HDmalloc(hdr->cls->nrec_size))) + 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); } /* end if */ @@ -1196,7 +1233,7 @@ H5B2_modify(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_modify_t op, if(idx == (unsigned)(leaf->nrec - 1)) { if(H5B2_POS_RIGHT == curr_pos || H5B2_POS_ROOT == curr_pos) { if(hdr->max_native_rec == NULL) - if(NULL == (hdr->max_native_rec = (uint8_t *)HDmalloc(hdr->cls->nrec_size))) + 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); } /* end if */ @@ -1210,7 +1247,7 @@ H5B2_modify(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_modify_t op, /* Unlock current node */ if(H5AC_unprotect(hdr->f, dxpl_id, H5AC_BT2_LEAF, curr_node_ptr.addr, leaf, leaf_flags) < 0) HGOTO_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release B-tree node") - } + } /* end block */ done: FUNC_LEAVE_NOAPI(ret_value) @@ -1282,7 +1319,7 @@ H5B2_close(H5B2_t *bt2, hid_t dxpl_id) /* Lock the v2 B-tree header into memory */ /* (OK to pass in NULL for callback context, since we know the header must be in the cache) */ - if(NULL == (hdr = (H5B2_hdr_t *)H5AC_protect(bt2->f, dxpl_id, H5AC_BT2_HDR, bt2_addr, NULL, H5AC__NO_FLAGS_SET))) + if(NULL == (hdr = H5B2__hdr_protect(bt2->f, dxpl_id, bt2_addr, NULL, H5AC__NO_FLAGS_SET))) HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect v2 B-tree header") /* Set the shared v2 B-tree header's file context for this operation */ @@ -1344,7 +1381,6 @@ H5B2_delete(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *ctx_udata, H5B2_remove_t op, void *op_data) { H5B2_hdr_t *hdr = NULL; /* Pointer to the B-tree header */ - H5B2_hdr_cache_ud_t cache_udata; /* User-data for callback */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -1357,10 +1393,7 @@ H5B2_delete(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *ctx_udata, #ifdef QAK HDfprintf(stderr, "%s: addr = %a\n", FUNC, addr); #endif /* QAK */ - cache_udata.f = f; - cache_udata.addr = addr; - cache_udata.ctx_udata = ctx_udata; - if(NULL == (hdr = (H5B2_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_BT2_HDR, addr, &cache_udata, H5AC__NO_FLAGS_SET))) + if(NULL == (hdr = H5B2__hdr_protect(f, dxpl_id, addr, ctx_udata, H5AC__NO_FLAGS_SET))) HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect v2 B-tree header") /* Remember the callback & context for later */ @@ -1382,7 +1415,7 @@ HDfprintf(stderr, "%s: addr = %a\n", FUNC, addr); done: /* Unprotect the header, if an error occurred */ - if(hdr && H5AC_unprotect(f, dxpl_id, H5AC_BT2_HDR, addr, hdr, H5AC__NO_FLAGS_SET) < 0) + if(hdr && H5B2__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0) HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release v2 B-tree header") FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5B2dbg.c b/src/H5B2dbg.c index ad9f970..ddff9e9 100644 --- a/src/H5B2dbg.c +++ b/src/H5B2dbg.c @@ -92,10 +92,8 @@ H5B2__hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, const H5B2_class_t *type, haddr_t obj_addr) { H5B2_hdr_t *hdr = NULL; /* B-tree header info */ - void *dbg_ctx = NULL; /* v2 B-tree debugging context */ unsigned u; /* Local index variable */ char temp_str[128]; /* Temporary string, for formatting */ - H5B2_hdr_cache_ud_t cache_udata; /* User-data for callback */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -110,23 +108,9 @@ H5B2__hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, HDassert(indent >= 0); HDassert(fwidth >= 0); HDassert(type); - HDassert((type->crt_dbg_ctx && type->dst_dbg_ctx) || - (NULL == type->crt_dbg_ctx && NULL == type->dst_dbg_ctx)); - /* Check for debugging context callback available */ - if(type->crt_dbg_ctx) { - /* Create debugging context */ - if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, obj_addr))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "unable to create v2 B-tree debugging context") - } /* end if */ - - /* - * Load the B-tree header. - */ - cache_udata.f = f; - cache_udata.addr = addr; - cache_udata.ctx_udata = dbg_ctx; - if(NULL == (hdr = (H5B2_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_BT2_HDR, addr, &cache_udata, H5AC__READ_ONLY_FLAG))) + /* Load the B-tree header */ + if(NULL == (hdr = H5B2__hdr_protect(f, dxpl_id, addr, f, H5AC__READ_ONLY_FLAG))) HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "unable to load B-tree header") /* Set file pointer for this B-tree operation */ @@ -178,13 +162,8 @@ H5B2__hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, } /* end for */ done: - if(dbg_ctx && (type->dst_dbg_ctx)(dbg_ctx) < 0) - HDONE_ERROR(H5E_BTREE, H5E_CANTRELEASE, FAIL, "unable to release v2 B-tree debugging context") - if(hdr) { - hdr->f = NULL; - if(H5AC_unprotect(f, dxpl_id, H5AC_BT2_HDR, addr, hdr, H5AC__NO_FLAGS_SET) < 0) - HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree header") - } /* end if */ + if(hdr && H5B2__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0) + HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release v2 B-tree header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5B2__hdr_debug() */ @@ -209,10 +188,8 @@ H5B2__int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, { H5B2_hdr_t *hdr = NULL; /* B-tree header */ H5B2_internal_t *internal = NULL; /* B-tree internal node */ - void *dbg_ctx = NULL; /* v2 B-tree debugging context */ unsigned u; /* Local index variable */ char temp_str[128]; /* Temporary string, for formatting */ - H5B2_hdr_cache_ud_t cache_udata; /* User-data for callback */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -226,27 +203,13 @@ H5B2__int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, HDassert(indent >= 0); HDassert(fwidth >= 0); HDassert(type); - HDassert((type->crt_dbg_ctx && type->dst_dbg_ctx) || - (NULL == type->crt_dbg_ctx && NULL == type->dst_dbg_ctx)); HDassert(H5F_addr_defined(hdr_addr)); HDassert(H5F_addr_defined(obj_addr)); HDassert(nrec > 0); - /* Check for debugging context callback available */ - if(type->crt_dbg_ctx) { - /* Create debugging context */ - if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, obj_addr))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "unable to create v2 B-tree debugging context") - } /* end if */ - - /* - * Load the B-tree header. - */ - cache_udata.f = f; - cache_udata.addr = hdr_addr; - cache_udata.ctx_udata = dbg_ctx; - if(NULL == (hdr = (H5B2_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_BT2_HDR, hdr_addr, &cache_udata, H5AC__READ_ONLY_FLAG))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "unable to load B-tree header") + /* Load the B-tree header */ + if(NULL == (hdr = H5B2__hdr_protect(f, dxpl_id, hdr_addr, f, H5AC__READ_ONLY_FLAG))) + HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL, "unable to load v2 B-tree header") /* Set file pointer for this B-tree operation */ hdr->f = f; @@ -295,7 +258,7 @@ H5B2__int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, HDfprintf(stream, "%*s%-*s\n", indent + 3, "", MAX(0, fwidth - 3), temp_str); HDassert(H5B2_INT_NREC(internal, hdr, u)); - (void)(type->debug)(stream, indent + 6, MAX (0, fwidth-6), H5B2_INT_NREC(internal, hdr, u), dbg_ctx); + (void)(type->debug)(stream, indent + 6, MAX (0, fwidth-6), H5B2_INT_NREC(internal, hdr, u), hdr->cb_ctx); } /* end for */ /* Print final node pointer */ @@ -307,13 +270,8 @@ H5B2__int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, internal->node_ptrs[u].addr); done: - if(dbg_ctx && (type->dst_dbg_ctx)(dbg_ctx) < 0) - HDONE_ERROR(H5E_BTREE, H5E_CANTRELEASE, FAIL, "unable to release v2 B-tree debugging context") - if(hdr) { - hdr->f = NULL; - if(H5AC_unprotect(f, dxpl_id, H5AC_BT2_HDR, hdr_addr, hdr, H5AC__NO_FLAGS_SET) < 0) - HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree header") - } /* end if */ + if(hdr && H5B2__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0) + HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release v2 B-tree header") if(internal && H5AC_unprotect(f, dxpl_id, H5AC_BT2_INT, addr, internal, H5AC__NO_FLAGS_SET) < 0) HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree internal node") @@ -340,8 +298,6 @@ H5B2__leaf_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent { H5B2_hdr_t *hdr = NULL; /* B-tree header */ H5B2_leaf_t *leaf = NULL; /* B-tree leaf node */ - H5B2_hdr_cache_ud_t cache_udata; /* User-data for callback */ - void *dbg_ctx = NULL; /* v2 B-tree debugging context */ unsigned u; /* Local index variable */ char temp_str[128]; /* Temporary string, for formatting */ herr_t ret_value = SUCCEED; /* Return value */ @@ -357,27 +313,13 @@ H5B2__leaf_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent HDassert(indent >= 0); HDassert(fwidth >= 0); HDassert(type); - HDassert((type->crt_dbg_ctx && type->dst_dbg_ctx) || - (NULL == type->crt_dbg_ctx && NULL == type->dst_dbg_ctx)); HDassert(H5F_addr_defined(hdr_addr)); HDassert(H5F_addr_defined(obj_addr)); HDassert(nrec > 0); - /* Check for debugging context callback available */ - if(type->crt_dbg_ctx) { - /* Create debugging context */ - if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, obj_addr))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "unable to create v2 B-tree debugging context") - } /* end if */ - - /* - * Load the B-tree header. - */ - cache_udata.f = f; - cache_udata.addr = hdr_addr; - cache_udata.ctx_udata = dbg_ctx; - if(NULL == (hdr = (H5B2_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_BT2_HDR, hdr_addr, &cache_udata, H5AC__READ_ONLY_FLAG))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree header") + /* Load the B-tree header */ + if(NULL == (hdr = H5B2__hdr_protect(f, dxpl_id, hdr_addr, f, H5AC__READ_ONLY_FLAG))) + HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect v2 B-tree header") /* Set file pointer for this B-tree operation */ hdr->f = f; @@ -417,17 +359,12 @@ H5B2__leaf_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent HDfprintf(stream, "%*s%-*s\n", indent + 3, "", MAX(0, fwidth - 3), temp_str); HDassert(H5B2_LEAF_NREC(leaf, hdr, u)); - (void)(type->debug)(stream, indent + 6, MAX (0, fwidth-6), H5B2_LEAF_NREC(leaf, hdr, u), dbg_ctx); + (void)(type->debug)(stream, indent + 6, MAX (0, fwidth-6), H5B2_LEAF_NREC(leaf, hdr, u), hdr->cb_ctx); } /* end for */ done: - if(dbg_ctx && (type->dst_dbg_ctx)(dbg_ctx) < 0) - HDONE_ERROR(H5E_BTREE, H5E_CANTRELEASE, FAIL, "unable to release v2 B-tree debugging context") - if(hdr) { - hdr->f = NULL; - if(H5AC_unprotect(f, dxpl_id, H5AC_BT2_HDR, hdr_addr, hdr, H5AC__NO_FLAGS_SET) < 0) - HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree header") - } /* end if */ + if(hdr && H5B2__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0) + HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree header") if(leaf && H5AC_unprotect(f, dxpl_id, H5AC_BT2_LEAF, addr, leaf, H5AC__NO_FLAGS_SET) < 0) HDONE_ERROR(H5E_BTREE, H5E_PROTECT, FAIL, "unable to release B-tree leaf node") diff --git a/src/H5B2hdr.c b/src/H5B2hdr.c index 16d8467..ab424b7 100644 --- a/src/H5B2hdr.c +++ b/src/H5B2hdr.c @@ -38,7 +38,8 @@ #include "H5B2pkg.h" /* v2 B-trees */ #include "H5Eprivate.h" /* Error handling */ #include "H5MFprivate.h" /* File memory management */ -#include "H5VMprivate.h" /* Vectors and arrays */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5VMprivate.h" /* Vectors and arrays */ /****************/ /* Local Macros */ @@ -209,10 +210,9 @@ HDmemset(hdr->page, 0, hdr->node_size); } /* end if */ /* Create the callback context, if the callback exists */ - if(hdr->cls->crt_context) { + if(hdr->cls->crt_context) if(NULL == (hdr->cb_ctx = (*hdr->cls->crt_context)(ctx_udata))) HGOTO_ERROR(H5E_BTREE, H5E_CANTCREATE, FAIL, "unable to create v2 B-tree client callback context") - } /* end if */ done: if(ret_value < 0) @@ -488,6 +488,82 @@ done: /*------------------------------------------------------------------------- + * Function: H5B2__hdr_protect + * + * Purpose: Convenience wrapper around protecting v2 B-tree header + * + * Return: Non-NULL pointer to header on success/NULL on failure + * + * Programmer: Quincey Koziol + * koziol@hdfgroup.org + * Dec 18 2015 + * + *------------------------------------------------------------------------- + */ +H5B2_hdr_t * +H5B2__hdr_protect(H5F_t *f, hid_t dxpl_id, haddr_t hdr_addr, void *ctx_udata, + unsigned flags) +{ + H5B2_hdr_cache_ud_t udata; /* User data for cache callbacks */ + H5B2_hdr_t *ret_value = NULL; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Sanity check */ + HDassert(f); + HDassert(H5F_addr_defined(hdr_addr)); + + /* only the H5AC__READ_ONLY_FLAG may appear in flags */ + HDassert((flags & (unsigned)(~H5AC__READ_ONLY_FLAG)) == 0); + + /* Set up user data for cache callbacks */ + udata.f = f; + udata.addr = hdr_addr; + udata.ctx_udata = ctx_udata; + + /* Protect the header */ + if(NULL == (ret_value = (H5B2_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_BT2_HDR, hdr_addr, &udata, flags))) + HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, NULL, "unable to load v2 B-tree header, address = %llu", (unsigned long long)hdr_addr) + ret_value->f = f; /* (Must be set again here, in case the header was already in the cache -QAK) */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5B2__hdr_protect() */ + + +/*------------------------------------------------------------------------- + * Function: H5B2__hdr_unprotect + * + * Purpose: Convenience wrapper around unprotecting v2 B-tree header + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * koziol@hdfgroup.org + * Dec 18 2015 + * + *------------------------------------------------------------------------- + */ +herr_t +H5B2__hdr_unprotect(H5B2_hdr_t *hdr, hid_t dxpl_id, unsigned cache_flags) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Sanity check */ + HDassert(hdr); + + /* Unprotect the header */ + if(H5AC_unprotect(hdr->f, dxpl_id, H5AC_BT2_HDR, hdr->addr, hdr, cache_flags) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to unprotect v2 B-tree header, address = %llu", (unsigned long long)hdr->addr) + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5B2__hdr_unprotect() */ + + +/*------------------------------------------------------------------------- * Function: H5B2__hdr_free * * Purpose: Free B-tree header info @@ -544,14 +620,10 @@ H5B2__hdr_free(H5B2_hdr_t *hdr) } /* end if */ /* Release the min & max record info, if set */ - if(hdr->min_native_rec) { - HDfree(hdr->min_native_rec); - hdr->min_native_rec = NULL; - } /* end if */ - if(hdr->max_native_rec) { - HDfree(hdr->max_native_rec); - hdr->max_native_rec = NULL; - } /* end if */ + if(hdr->min_native_rec) + hdr->min_native_rec = H5MM_xfree(hdr->min_native_rec); + if(hdr->max_native_rec) + hdr->max_native_rec = H5MM_xfree(hdr->max_native_rec); /* Free B-tree header info */ hdr = H5FL_FREE(H5B2_hdr_t, hdr); @@ -609,8 +681,8 @@ H5B2__hdr_delete(H5B2_hdr_t *hdr, hid_t dxpl_id) done: /* Unprotect the header with appropriate flags */ - if(H5AC_unprotect(hdr->f, dxpl_id, H5AC_BT2_HDR, hdr->addr, hdr, cache_flags) < 0) - HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release B-tree header") + if(H5B2__hdr_unprotect(hdr, dxpl_id, cache_flags) < 0) + HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release v2 B-tree header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5B2__hdr_delete() */ diff --git a/src/H5B2int.c b/src/H5B2int.c index b8c9634..a69774a 100644 --- a/src/H5B2int.c +++ b/src/H5B2int.c @@ -38,7 +38,8 @@ #include "H5B2pkg.h" /* v2 B-trees */ #include "H5Eprivate.h" /* Error handling */ #include "H5MFprivate.h" /* File memory management */ -#include "H5VMprivate.h" /* Vectors and arrays */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5VMprivate.h" /* Vectors and arrays */ /****************/ /* Local Macros */ @@ -1513,6 +1514,62 @@ done: /*------------------------------------------------------------------------- + * Function: H5B2__insert_hdr + * + * Purpose: Adds a new record to the B-tree. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * koziol@hdfgroup.org + * Dec 23 2015 + * + *------------------------------------------------------------------------- + */ +herr_t +H5B2__insert_hdr(H5B2_hdr_t *hdr, hid_t dxpl_id, void *udata) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check arguments. */ + HDassert(hdr); + HDassert(udata); + + /* Check if the root node is allocated yet */ + if(!H5F_addr_defined(hdr->root.addr)) { + /* Create root node as leaf node in B-tree */ + if(H5B2__create_leaf(hdr, dxpl_id, &(hdr->root)) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "unable to create root node") + } /* end if */ + /* Check if we need to split the root node (equiv. to a 1->2 node split) */ + else if(hdr->root.node_nrec == hdr->node_info[hdr->depth].split_nrec) { + /* Split root node */ + if(H5B2__split_root(hdr, dxpl_id) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTSPLIT, FAIL, "unable to split root node") + } /* end if */ + + /* Attempt to insert record into B-tree */ + if(hdr->depth > 0) { + if(H5B2__insert_internal(hdr, dxpl_id, hdr->depth, NULL, &hdr->root, H5B2_POS_ROOT, udata) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B-tree internal node") + } /* end if */ + else { + if(H5B2__insert_leaf(hdr, dxpl_id, &hdr->root, H5B2_POS_ROOT, udata) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into B-tree leaf node") + } /* end else */ + + /* Mark B-tree header as dirty */ + if(H5B2__hdr_dirty(hdr) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTMARKDIRTY, FAIL, "unable to mark B-tree header dirty") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5B2__insert_hdr() */ + + +/*------------------------------------------------------------------------- * Function: H5B2__insert_leaf * * Purpose: Adds a new record to a B-tree leaf node. @@ -1584,7 +1641,7 @@ H5B2__insert_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, H5B2_node_ptr_t *curr_node_ptr if(idx == 0) { if(H5B2_POS_LEFT == curr_pos || H5B2_POS_ROOT == curr_pos) { if(hdr->min_native_rec == NULL) - if(NULL == (hdr->min_native_rec = (uint8_t *)HDmalloc(hdr->cls->nrec_size))) + 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); } /* end if */ @@ -1592,7 +1649,7 @@ H5B2__insert_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, H5B2_node_ptr_t *curr_node_ptr if(idx == (unsigned)(leaf->nrec - 1)) { if(H5B2_POS_RIGHT == curr_pos || H5B2_POS_ROOT == curr_pos) { if(hdr->max_native_rec == NULL) - if(NULL == (hdr->max_native_rec = (uint8_t *)HDmalloc(hdr->cls->nrec_size))) + 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); } /* end if */ @@ -1644,6 +1701,9 @@ H5B2__insert_internal(H5B2_hdr_t *hdr, hid_t dxpl_id, uint16_t depth, if(NULL == (internal = H5B2__protect_internal(hdr, dxpl_id, curr_node_ptr->addr, curr_node_ptr->node_nrec, depth, H5AC__NO_FLAGS_SET))) HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree internal node") + /* Sanity check number of records */ + HDassert(internal->nrec == curr_node_ptr->node_nrec); + /* Split or redistribute child node pointers, if necessary */ { int cmp; /* Comparison value of records */ @@ -1755,6 +1815,348 @@ done: /*------------------------------------------------------------------------- + * Function: H5B2__update_leaf + * + * Purpose: Insert or modify a record in a B-tree leaf node. + * If the record exists already, it is modified as if H5B2_modify + * was called). If it doesn't exist, it is inserted as if + * H5B2_insert was called. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * koziol@hdfgroup.org + * Dec 23 2015 + * + *------------------------------------------------------------------------- + */ +herr_t +H5B2__update_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, H5B2_node_ptr_t *curr_node_ptr, + H5B2_update_status_t *status, H5B2_nodepos_t curr_pos, void *udata, + H5B2_modify_t op, void *op_data) +{ + H5B2_leaf_t *leaf; /* Pointer to leaf node */ + unsigned leaf_flags = H5AC__NO_FLAGS_SET; /* Flags for unprotecting the leaf node */ + int cmp = -1; /* Comparison value of records */ + unsigned idx; /* Location of record which matches key */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check arguments. */ + HDassert(hdr); + HDassert(curr_node_ptr); + HDassert(H5F_addr_defined(curr_node_ptr->addr)); + + /* Lock current B-tree node */ + if(NULL == (leaf = H5B2__protect_leaf(hdr, dxpl_id, curr_node_ptr->addr, curr_node_ptr->node_nrec, H5AC__NO_FLAGS_SET))) + HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree leaf node") + + /* Sanity check number of records */ + HDassert(curr_node_ptr->all_nrec == curr_node_ptr->node_nrec); + HDassert(leaf->nrec == curr_node_ptr->node_nrec); + + /* Check for inserting into empty leaf */ + if(leaf->nrec == 0) + idx = 0; + else { + /* Find correct location to insert this record */ + cmp = H5B2__locate_record(hdr->cls, leaf->nrec, hdr->nat_off, leaf->leaf_native, udata, &idx); + + /* Check for inserting a record */ + if(0 != cmp) { + /* Check if the leaf node is full */ + if(curr_node_ptr->node_nrec == hdr->node_info[0].split_nrec) { + /* Indicate that the leaf is full, but we need to insert */ + *status = H5B2_UPDATE_INSERT_CHILD_FULL; + + /* Let calling routine handle insertion */ + HGOTO_DONE(SUCCEED) + } /* end if */ + + /* Adjust index to leave room for record to insert */ + if(cmp > 0) + idx++; + + /* Make room for new record */ + if(idx < leaf->nrec) + HDmemmove(H5B2_LEAF_NREC(leaf, hdr, idx + 1), H5B2_LEAF_NREC(leaf, hdr, idx), hdr->cls->nrec_size * (leaf->nrec - idx)); + } /* end if */ + } /* end else */ + + /* Check for modifying existing record */ + if(0 == cmp) { + hbool_t changed = FALSE; /* Whether the 'modify' callback changed the record */ + + /* Make callback for current record */ + if((op)(H5B2_LEAF_NREC(leaf, hdr, idx), op_data, &changed) < 0) { + /* Make certain that the callback didn't modify the value if it failed */ + HDassert(changed == FALSE); + + HGOTO_ERROR(H5E_BTREE, H5E_CANTMODIFY, FAIL, "'modify' callback failed for B-tree update operation") + } /* end if */ + + /* Mark the node as dirty if it changed */ + leaf_flags |= (changed ? H5AC__DIRTIED_FLAG : 0); + + /* Indicate that the record was modified */ + *status = H5B2_UPDATE_MODIFY_DONE; + } /* end if */ + else { + /* Must have a leaf node with enough space to insert a record now */ + HDassert(curr_node_ptr->node_nrec < hdr->node_info[0].max_nrec); + + /* Make callback to store record in native form */ + if((hdr->cls->store)(H5B2_LEAF_NREC(leaf, hdr, idx), udata) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into leaf node") + + /* Mark the node as dirty if it changed */ + leaf_flags |= H5AC__DIRTIED_FLAG; + + /* Indicate that the record was inserted */ + *status = H5B2_UPDATE_INSERT_DONE; + + /* Update record count for node pointer to current node */ + curr_node_ptr->all_nrec++; + curr_node_ptr->node_nrec++; + + /* Update record count for current node */ + leaf->nrec++; + } /* end else */ + + /* Check for new record being the min or max for the tree */ + /* (Don't use 'else' for the idx check, to allow for root leaf node) */ + if(H5B2_POS_MIDDLE != curr_pos) { + if(idx == 0) { + if(H5B2_POS_LEFT == curr_pos || H5B2_POS_ROOT == curr_pos) { + 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); + } /* end if */ + } /* end if */ + if(idx == (unsigned)(leaf->nrec - 1)) { + if(H5B2_POS_RIGHT == curr_pos || H5B2_POS_ROOT == curr_pos) { + 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); + } /* end if */ + } /* end if */ + } /* end if */ + +done: + /* Release the B-tree leaf node */ + if(leaf && H5AC_unprotect(hdr->f, dxpl_id, H5AC_BT2_LEAF, curr_node_ptr->addr, leaf, leaf_flags) < 0) + HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release leaf B-tree node") + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5B2__update_leaf() */ + + +/*------------------------------------------------------------------------- + * Function: H5B2__update_internal + * + * Purpose: Insert or modify a record in a B-tree leaf node. + * If the record exists already, it is modified as if H5B2_modify + * was called). If it doesn't exist, it is inserted as if + * H5B2_insert was called. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * koziol@hdfgroup.org + * Dec 24 2015 + * + *------------------------------------------------------------------------- + */ +herr_t +H5B2__update_internal(H5B2_hdr_t *hdr, hid_t dxpl_id, uint16_t depth, + unsigned *parent_cache_info_flags_ptr, H5B2_node_ptr_t *curr_node_ptr, + H5B2_update_status_t *status, H5B2_nodepos_t curr_pos, void *udata, + H5B2_modify_t op, void *op_data) +{ + H5B2_internal_t *internal = NULL; /* Pointer to internal node */ + unsigned internal_flags = H5AC__NO_FLAGS_SET; + int cmp; /* Comparison value of records */ + unsigned idx; /* Location of record which matches key */ + H5B2_nodepos_t next_pos = H5B2_POS_MIDDLE; /* Position of node */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check arguments. */ + HDassert(hdr); + HDassert(depth > 0); + HDassert(curr_node_ptr); + HDassert(H5F_addr_defined(curr_node_ptr->addr)); + + /* Lock current B-tree node */ + if(NULL == (internal = H5B2__protect_internal(hdr, dxpl_id, curr_node_ptr->addr, curr_node_ptr->node_nrec, depth, H5AC__NO_FLAGS_SET))) + HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree internal node") + + /* Sanity check number of records */ + HDassert(internal->nrec == curr_node_ptr->node_nrec); + + /* Locate node pointer for child */ + cmp = H5B2__locate_record(hdr->cls, internal->nrec, hdr->nat_off, internal->int_native, udata, &idx); + + /* Check for modifying existing record */ + if(0 == cmp) { + hbool_t changed = FALSE; /* Whether the 'modify' callback changed the record */ + + /* Make callback for current record */ + if((op)(H5B2_INT_NREC(internal, hdr, idx), op_data, &changed) < 0) { + /* Make certain that the callback didn't modify the value if it failed */ + HDassert(changed == FALSE); + + HGOTO_ERROR(H5E_BTREE, H5E_CANTMODIFY, FAIL, "'modify' callback failed for B-tree update operation") + } /* end if */ + + /* Mark the node as dirty if it changed */ + internal_flags |= (changed ? H5AC__DIRTIED_FLAG : 0); + + /* Indicate that the record was modified */ + *status = H5B2_UPDATE_MODIFY_DONE; + } /* end if */ + else { + /* Adjust index to leave room for node to insert */ + if(cmp > 0) + idx++; + + /* Check if this node is left/right-most */ + if(H5B2_POS_MIDDLE != curr_pos) { + if(idx == 0) { + if(H5B2_POS_LEFT == curr_pos || H5B2_POS_ROOT == curr_pos) + next_pos = H5B2_POS_LEFT; + } /* end if */ + else if(idx == internal->nrec) { + if(H5B2_POS_RIGHT == curr_pos || H5B2_POS_ROOT == curr_pos) + next_pos = H5B2_POS_RIGHT; + } /* end else */ + } /* end if */ + + /* Attempt to update record in child */ + if(depth > 1) { + if(H5B2__update_internal(hdr, dxpl_id, (uint16_t)(depth - 1), &internal_flags, &internal->node_ptrs[idx], status, next_pos, udata, op, op_data) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTUPDATE, FAIL, "unable to update record in internal B-tree node") + } /* end if */ + else { + if(H5B2__update_leaf(hdr, dxpl_id, &internal->node_ptrs[idx], status, next_pos, udata, op, op_data) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTUPDATE, FAIL, "unable to update record in leaf B-tree node") + } /* end else */ + + /* Take actions based on child's status report */ + switch(*status) { + case H5B2_UPDATE_MODIFY_DONE: + /* No action */ + break; + + case H5B2_UPDATE_INSERT_DONE: + /* Mark node as dirty */ + internal_flags |= H5AC__DIRTIED_FLAG; + + /* Update total record count for node pointer to current node */ + curr_node_ptr->all_nrec++; + break; + + case H5B2_UPDATE_INSERT_CHILD_FULL: + /* Split/redistribute this node */ + if(internal->nrec == hdr->node_info[depth].split_nrec) { + hbool_t could_split = FALSE; /* Whether the child node could split */ + +#ifdef QAK +HDfprintf(stderr, "%s: idx = %u, internal->nrec = %u\n", FUNC, idx, internal->nrec); +HDfprintf(stderr, "%s: hdr->node_info[%u].split_nrec = %u\n", FUNC, (unsigned)depth, (unsigned)hdr->node_info[depth].split_nrec); +HDfprintf(stderr, "%s: hdr->node_info[%u].split_nrec = %u\n", FUNC, (unsigned)(depth - 1), (unsigned)hdr->node_info[depth - 1].split_nrec); +#endif /* QAK */ + if(idx == 0) { /* Left-most child */ +#ifdef QAK +HDfprintf(stderr, "%s: Left-most child\n", FUNC); +HDfprintf(stderr, "%s: internal->node_ptrs[%u].node_nrec = %u\n", FUNC, (unsigned)idx, (unsigned)internal->node_ptrs[idx].node_nrec); +HDfprintf(stderr, "%s: internal->node_ptrs[%u].node_nrec = %u\n", FUNC, (unsigned)(idx + 1), (unsigned)internal->node_ptrs[idx + 1].node_nrec); +#endif /* QAK */ + /* Check for left-most child and its neighbor being close to full */ + if((internal->node_ptrs[idx].node_nrec + internal->node_ptrs[idx + 1].node_nrec) + >= ((hdr->node_info[depth - 1].split_nrec * 2) - 1)) + could_split = TRUE; + } /* end if */ + else if(idx == internal->nrec) { /* Right-most child */ +#ifdef QAK +HDfprintf(stderr, "%s: Right-most child\n", FUNC); +HDfprintf(stderr, "%s: internal->node_ptrs[%u].node_nrec = %u\n", FUNC, (unsigned)(idx - 1), (unsigned)internal->node_ptrs[idx - 1].node_nrec); +HDfprintf(stderr, "%s: internal->node_ptrs[%u].node_nrec = %u\n", FUNC, (unsigned)idx, (unsigned)internal->node_ptrs[idx].node_nrec); +#endif /* QAK */ + /* Check for right-most child and its neighbor being close to full */ + if((internal->node_ptrs[idx - 1].node_nrec + internal->node_ptrs[idx].node_nrec) + >= ((hdr->node_info[depth - 1].split_nrec * 2) - 1)) + could_split = TRUE; + } /* end else-if */ + else { /* Middle child */ +#ifdef QAK +HDfprintf(stderr, "%s: Middle child\n", FUNC); +HDfprintf(stderr, "%s: internal->node_ptrs[%u].node_nrec = %u\n", FUNC, (unsigned)(idx - 1), (unsigned)internal->node_ptrs[idx - 1].node_nrec); +HDfprintf(stderr, "%s: internal->node_ptrs[%u].node_nrec = %u\n", FUNC, (unsigned)idx, (unsigned)internal->node_ptrs[idx].node_nrec); +HDfprintf(stderr, "%s: internal->node_ptrs[%u].node_nrec = %u\n", FUNC, (unsigned)(idx + 1), (unsigned)internal->node_ptrs[idx + 1].node_nrec); +#endif /* QAK */ + /* Check for middle child and its left neighbor being close to full */ + if((internal->node_ptrs[idx - 1].node_nrec + internal->node_ptrs[idx].node_nrec) + >= ((hdr->node_info[depth - 1].split_nrec * 2) - 1)) + could_split = TRUE; + /* Check for middle child and its right neighbor being close to full */ + else if((internal->node_ptrs[idx].node_nrec + internal->node_ptrs[idx + 1].node_nrec) + >= ((hdr->node_info[depth - 1].split_nrec * 2) - 1)) + could_split = TRUE; + } /* end if */ + + /* If this node is full and the child node insertion could + * cause a split, punt back up to caller, leaving the + * "insert child full" status. + */ + if(could_split) { + /* Release the internal B-tree node */ + if(H5AC_unprotect(hdr->f, dxpl_id, H5AC_BT2_INT, curr_node_ptr->addr, internal, internal_flags) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release internal B-tree node") + internal = NULL; + +#ifdef QAK +HDfprintf(stderr, "%s: Punting back to caller\n", FUNC); +#endif /* QAK */ + /* Punt back to caller */ + HGOTO_DONE(SUCCEED); + } /* end if */ + } /* end if */ + + /* Release the internal B-tree node */ + if(H5AC_unprotect(hdr->f, dxpl_id, H5AC_BT2_INT, curr_node_ptr->addr, internal, internal_flags) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release internal B-tree node") + internal = NULL; + + /* Indicate that the record was inserted */ + *status = H5B2_UPDATE_INSERT_DONE; + + /* Dodge sideways into inserting a record into this node */ + if(H5B2__insert_internal(hdr, dxpl_id, depth, parent_cache_info_flags_ptr, curr_node_ptr, curr_pos, udata) < 0) + HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into internal B-tree node") + break; + + case H5B2_UPDATE_UNKNOWN: + default: + HDassert(0 && "Invalid update status"); + HGOTO_ERROR(H5E_BTREE, H5E_CANTUPDATE, FAIL, "invalid update status") + } /* end switch */ + } /* end else */ + +done: + /* Release the internal B-tree node */ + if(internal && H5AC_unprotect(hdr->f, dxpl_id, H5AC_BT2_INT, curr_node_ptr->addr, internal, internal_flags) < 0) + HDONE_ERROR(H5E_BTREE, H5E_CANTUNPROTECT, FAIL, "unable to release internal B-tree node") + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5B2__update_internal() */ + + +/*------------------------------------------------------------------------- * Function: H5B2__create_leaf * * Purpose: Creates empty leaf node of a B-tree and update node pointer @@ -2151,18 +2553,14 @@ H5B2__remove_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, H5B2_node_ptr_t *curr_node_ptr /* (Don't use 'else' for the idx check, to allow for root leaf node) */ if(idx == 0) { if(H5B2_POS_LEFT == curr_pos || H5B2_POS_ROOT == curr_pos) { - if(hdr->min_native_rec) { - HDfree(hdr->min_native_rec); - hdr->min_native_rec = NULL; - } /* end if */ + if(hdr->min_native_rec) + hdr->min_native_rec = H5MM_xfree(hdr->min_native_rec); } /* end if */ } /* end if */ if(idx == (unsigned)(leaf->nrec - 1)) { if(H5B2_POS_RIGHT == curr_pos || H5B2_POS_ROOT == curr_pos) { - if(hdr->max_native_rec) { - HDfree(hdr->max_native_rec); - hdr->max_native_rec = NULL; - } /* end if */ + if(hdr->max_native_rec) + hdr->max_native_rec = H5MM_xfree(hdr->max_native_rec); } /* end if */ } /* end if */ } /* end if */ @@ -2466,18 +2864,14 @@ H5B2__remove_leaf_by_idx(H5B2_hdr_t *hdr, hid_t dxpl_id, /* (Don't use 'else' for the idx check, to allow for root leaf node) */ if(idx == 0) { if(H5B2_POS_LEFT == curr_pos || H5B2_POS_ROOT == curr_pos) { - if(hdr->min_native_rec) { - HDfree(hdr->min_native_rec); - hdr->min_native_rec = NULL; - } /* end if */ + if(hdr->min_native_rec) + hdr->min_native_rec = H5MM_xfree(hdr->min_native_rec); } /* end if */ } /* end if */ if(idx == (unsigned)(leaf->nrec - 1)) { if(H5B2_POS_RIGHT == curr_pos || H5B2_POS_ROOT == curr_pos) { - if(hdr->max_native_rec) { - HDfree(hdr->max_native_rec); - hdr->max_native_rec = NULL; - } /* end if */ + if(hdr->max_native_rec) + hdr->max_native_rec = H5MM_xfree(hdr->max_native_rec); } /* end if */ } /* end if */ } /* end if */ diff --git a/src/H5B2pkg.h b/src/H5B2pkg.h index d661efa..2b2c145 100644 --- a/src/H5B2pkg.h +++ b/src/H5B2pkg.h @@ -182,8 +182,8 @@ typedef struct H5B2_hdr_t { uint8_t *page; /* Common disk page for I/O */ size_t *nat_off; /* Array of offsets of native records */ H5B2_node_info_t *node_info; /* Table of node info structs for current depth of B-tree */ - uint8_t *min_native_rec; /* Pointer to minimum native record */ - uint8_t *max_native_rec; /* Pointer to maximum native record */ + void *min_native_rec; /* Pointer to minimum native record */ + void *max_native_rec; /* Pointer to maximum native record */ /* Client information (not stored) */ const H5B2_class_t *cls; /* Class of B-tree client */ @@ -228,6 +228,14 @@ typedef enum H5B2_nodepos_t { H5B2_POS_MIDDLE /* Node is neither right or left-most in tree */ } H5B2_nodepos_t; +/* Update status */ +typedef enum H5B2_update_status_t { + H5B2_UPDATE_UNKNOWN, /* Unknown update status (initial state) */ + H5B2_UPDATE_MODIFY_DONE, /* Update successfully modified existing record */ + H5B2_UPDATE_INSERT_DONE, /* Update inserted record successfully */ + H5B2_UPDATE_INSERT_CHILD_FULL /* Update will insert record, but child is full */ +} H5B2_update_status_t; + /* Callback info for loading a free space header into the cache */ typedef struct H5B2_hdr_cache_ud_t { H5F_t *f; /* File that v2 b-tree header is within */ @@ -252,7 +260,7 @@ typedef struct H5B2_leaf_cache_ud_t { #ifdef H5B2_TESTING /* Node information for testing */ -typedef struct { +typedef struct H5B2_node_info_test_t { unsigned depth; /* Depth of node */ unsigned nrec; /* Number of records in node */ } H5B2_node_info_test_t; @@ -281,6 +289,13 @@ H5FL_EXTERN(H5B2_leaf_t); /* Internal v2 B-tree testing class */ #ifdef H5B2_TESTING H5_DLLVAR const H5B2_class_t H5B2_TEST[1]; +H5_DLLVAR const H5B2_class_t H5B2_TEST2[1]; + +/* B-tree record for testing H5B2_TEST2 class */ +typedef struct H5B2_test_rec_t { + hsize_t key; /* Key for record */ + hsize_t val; /* Value for record */ +} H5B2_test_rec_t; #endif /* H5B2_TESTING */ /* Array of v2 B-tree client ID -> client class mappings */ @@ -302,6 +317,10 @@ H5_DLL herr_t H5B2__hdr_decr(H5B2_hdr_t *hdr); H5_DLL herr_t H5B2__hdr_fuse_incr(H5B2_hdr_t *hdr); H5_DLL size_t H5B2__hdr_fuse_decr(H5B2_hdr_t *hdr); H5_DLL herr_t H5B2__hdr_dirty(H5B2_hdr_t *hdr); +H5_DLL H5B2_hdr_t *H5B2__hdr_protect(H5F_t *f, hid_t dxpl_id, haddr_t hdr_addr, + void *ctx_udata, unsigned flags); +H5_DLL herr_t H5B2__hdr_unprotect(H5B2_hdr_t *hdr, hid_t dxpl_id, + unsigned cache_flags); H5_DLL herr_t H5B2__hdr_delete(H5B2_hdr_t *hdr, hid_t dxpl_id); /* Routines for operating on leaf nodes */ @@ -323,12 +342,22 @@ H5_DLL herr_t H5B2__leaf_free(H5B2_leaf_t *l); H5_DLL herr_t H5B2__internal_free(H5B2_internal_t *i); /* Routines for inserting records */ +H5_DLL herr_t H5B2__insert_hdr(H5B2_hdr_t *hdr, hid_t dxpl_id, void *udata); H5_DLL herr_t H5B2__insert_internal(H5B2_hdr_t *hdr, hid_t dxpl_id, uint16_t depth, unsigned *parent_cache_info_flags_ptr, H5B2_node_ptr_t *curr_node_ptr, H5B2_nodepos_t curr_pos, void *udata); H5_DLL herr_t H5B2__insert_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, H5B2_node_ptr_t *curr_node_ptr, H5B2_nodepos_t curr_pos, void *udata); +/* Routines for update records */ +H5_DLL herr_t H5B2__update_internal(H5B2_hdr_t *hdr, hid_t dxpl_id, + uint16_t depth, unsigned *parent_cache_info_flags_ptr, + H5B2_node_ptr_t *curr_node_ptr, H5B2_update_status_t *status, + H5B2_nodepos_t curr_pos, void *udata, H5B2_modify_t op, void *op_data); +H5_DLL herr_t H5B2__update_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, + H5B2_node_ptr_t *curr_node_ptr, H5B2_update_status_t *status, + H5B2_nodepos_t curr_pos, void *udata, H5B2_modify_t op, void *op_data); + /* Routines for iterating over nodes/records */ H5_DLL herr_t H5B2__iterate_node(H5B2_hdr_t *hdr, hid_t dxpl_id, uint16_t depth, const H5B2_node_ptr_t *curr_node, H5B2_operator_t op, void *op_data); diff --git a/src/H5B2private.h b/src/H5B2private.h index 9e3c2d7..ff94680 100644 --- a/src/H5B2private.h +++ b/src/H5B2private.h @@ -54,6 +54,7 @@ typedef enum H5B2_subid_t { H5B2_SOHM_INDEX_ID, /* B-tree is an index for shared object header messages */ H5B2_ATTR_DENSE_NAME_ID, /* B-tree is for indexing 'name' field for "dense" attribute storage on objects */ H5B2_ATTR_DENSE_CORDER_ID, /* B-tree is for indexing 'creation order' field for "dense" attribute storage on objects */ + H5B2_TEST2_ID, /* Another B-tree is for testing (do not use for actual data) */ H5B2_NUM_BTREE_ID /* Number of B-tree IDs (must be last) */ } H5B2_subid_t; @@ -94,8 +95,6 @@ struct H5B2_class_t { herr_t (*decode)(const uint8_t *raw, void *record, void *ctx); /* Decode record from disk storage form to native form */ herr_t (*debug)(FILE *stream, int indent, int fwidth, /* Print a record for debugging */ const void *record, const void *ctx); - void *(*crt_dbg_ctx)(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr); /* Create debugging context */ - herr_t (*dst_dbg_ctx)(void *dbg_ctx); /* Destroy debugging context */ }; /* v2 B-tree creation parameters */ @@ -140,6 +139,8 @@ H5_DLL herr_t H5B2_neighbor(H5B2_t *bt2, hid_t dxpl_id, H5B2_compare_t range, void *udata, H5B2_found_t op, void *op_data); H5_DLL herr_t H5B2_modify(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_modify_t op, void *op_data); +H5_DLL herr_t H5B2_update(H5B2_t *bt2, hid_t dxpl_id, void *udata, + H5B2_modify_t op, void *op_data); H5_DLL herr_t H5B2_remove(H5B2_t *b2, hid_t dxpl_id, void *udata, H5B2_remove_t op, void *op_data); H5_DLL herr_t H5B2_remove_by_idx(H5B2_t *bt2, hid_t dxpl_id, diff --git a/src/H5B2test.c b/src/H5B2test.c index 87fddf7..e0c96fb 100644 --- a/src/H5B2test.c +++ b/src/H5B2test.c @@ -61,6 +61,7 @@ typedef struct H5B2_test_ctx_t { /* Local Prototypes */ /********************/ +/* v2 B-tree driver callbacks for 'test' B-trees */ static void *H5B2__test_crt_context(void *udata); static herr_t H5B2__test_dst_context(void *ctx); static herr_t H5B2__test_store(void *nrecord, const void *udata); @@ -69,13 +70,21 @@ static herr_t H5B2__test_encode(uint8_t *raw, const void *nrecord, void *ctx); static herr_t H5B2__test_decode(const uint8_t *raw, void *nrecord, void *ctx); static herr_t H5B2__test_debug(FILE *stream, int indent, int fwidth, const void *record, const void *_udata); -static void *H5B2__test_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t addr); + +/* v2 B-tree driver callbacks for 'test2' B-trees */ +static herr_t H5B2__test2_store(void *nrecord, const void *udata); +static herr_t H5B2__test2_compare(const void *rec1, const void *rec2); +static herr_t H5B2__test2_encode(uint8_t *raw, const void *nrecord, void *ctx); +static herr_t H5B2__test2_decode(const uint8_t *raw, void *nrecord, void *ctx); +static herr_t H5B2__test2_debug(FILE *stream, int indent, int fwidth, + const void *record, const void *_udata); /*********************/ /* Package Variables */ /*********************/ +/* Class structure for testing simple B-tree records */ const H5B2_class_t H5B2_TEST[1]={{ /* B-tree class information */ H5B2_TEST_ID, /* Type of B-tree */ "H5B2_TEST_ID", /* Name of B-tree class */ @@ -86,9 +95,21 @@ const H5B2_class_t H5B2_TEST[1]={{ /* B-tree class information */ H5B2__test_compare, /* Record comparison callback */ H5B2__test_encode, /* Record encoding callback */ H5B2__test_decode, /* Record decoding callback */ - H5B2__test_debug, /* Record debugging callback */ - H5B2__test_crt_dbg_context, /* Create debugging context */ - H5B2__test_dst_context /* Destroy debugging context */ + H5B2__test_debug /* Record debugging callback */ +}}; + +/* Class structure for testing key/value B-tree records */ +const H5B2_class_t H5B2_TEST2[1]={{ /* B-tree class information */ + H5B2_TEST2_ID, /* Type of B-tree */ + "H5B2_TEST2_ID", /* Name of B-tree class */ + sizeof(H5B2_test_rec_t), /* Size of native record */ + H5B2__test_crt_context, /* Create client callback context */ + H5B2__test_dst_context, /* Destroy client callback context */ + H5B2__test2_store, /* Record storage callback */ + H5B2__test2_compare, /* Record comparison callback */ + H5B2__test2_encode, /* Record encoding callback */ + H5B2__test2_decode, /* Record decoding callback */ + H5B2__test2_debug /* Record debugging callback */ }}; @@ -310,42 +331,139 @@ H5B2__test_debug(FILE *stream, int indent, int fwidth, const void *record, /*------------------------------------------------------------------------- - * Function: H5B2__test_crt_dbg_context + * Function: H5B2__test2_store * - * Purpose: Create context for debugging callback + * Purpose: Store native information into record for B-tree * - * Return: Success: non-NULL - * Failure: NULL + * Return: Success: non-negative + * Failure: negative * * Programmer: Quincey Koziol - * Tuesday, December 1, 2009 + * Friday, December 25, 2015 * *------------------------------------------------------------------------- */ -static void * -H5B2__test_crt_dbg_context(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t H5_ATTR_UNUSED addr) +static herr_t +H5B2__test2_store(void *nrecord, const void *udata) { - H5B2_test_ctx_t *ctx; /* Callback context structure */ - void *ret_value = NULL; /* Return value */ + FUNC_ENTER_STATIC_NOERR - FUNC_ENTER_STATIC + *(H5B2_test_rec_t *)nrecord = *(const H5B2_test_rec_t *)udata; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5B2__test2_store() */ + + +/*------------------------------------------------------------------------- + * Function: H5B2__test2_compare + * + * Purpose: Compare two native information records, according to some key + * + * Return: <0 if rec1 < rec2 + * =0 if rec1 == rec2 + * >0 if rec1 > rec2 + * + * Programmer: Quincey Koziol + * Friday, December 25, 2015 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5B2__test2_compare(const void *rec1, const void *rec2) +{ + FUNC_ENTER_STATIC_NOERR + + FUNC_LEAVE_NOAPI((herr_t)(((const H5B2_test_rec_t *)rec1)->key - ((const H5B2_test_rec_t *)rec2)->key)) +} /* H5B2__test2_compare() */ + + +/*------------------------------------------------------------------------- + * Function: H5B2__test2_encode + * + * Purpose: Encode native information into raw form for storing on disk + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Quincey Koziol + * Friday, December 25, 2015 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5B2__test2_encode(uint8_t *raw, const void *nrecord, void *_ctx) +{ + H5B2_test_ctx_t *ctx = (H5B2_test_ctx_t *)_ctx; /* Callback context structure */ + + FUNC_ENTER_STATIC_NOERR /* Sanity check */ - HDassert(f); + HDassert(ctx); - /* Allocate callback context */ - if(NULL == (ctx = H5FL_MALLOC(H5B2_test_ctx_t))) - HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "can't allocate callback context") + H5F_ENCODE_LENGTH_LEN(raw, ((const H5B2_test_rec_t *)nrecord)->key, ctx->sizeof_size); + H5F_ENCODE_LENGTH_LEN(raw, ((const H5B2_test_rec_t *)nrecord)->val, ctx->sizeof_size); - /* Determine the size of addresses & lengths in the file */ - ctx->sizeof_size = H5F_SIZEOF_SIZE(f); + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5B2__test2_encode() */ - /* Set return value */ - ret_value = ctx; + +/*------------------------------------------------------------------------- + * Function: H5B2__test2_decode + * + * Purpose: Decode raw disk form of record into native form + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Quincey Koziol + * Friday, December 25, 2015 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5B2__test2_decode(const uint8_t *raw, void *nrecord, void *_ctx) +{ + H5B2_test_ctx_t *ctx = (H5B2_test_ctx_t *)_ctx; /* Callback context structure */ -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5B2__test_crt_dbg_context() */ + FUNC_ENTER_STATIC_NOERR + + /* Sanity check */ + HDassert(ctx); + + H5F_DECODE_LENGTH_LEN(raw, ((H5B2_test_rec_t *)nrecord)->key, ctx->sizeof_size); + H5F_DECODE_LENGTH_LEN(raw, ((H5B2_test_rec_t *)nrecord)->val, ctx->sizeof_size); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5B2__test2_decode() */ + + +/*------------------------------------------------------------------------- + * Function: H5B2__test2_debug + * + * Purpose: Debug native form of record + * + * Return: Success: non-negative + * Failure: negative + * + * Programmer: Quincey Koziol + * Friday, December 25, 2015 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5B2__test2_debug(FILE *stream, int indent, int fwidth, const void *record, + const void H5_ATTR_UNUSED *_udata) +{ + FUNC_ENTER_STATIC_NOERR + + HDassert(record); + + HDfprintf(stream, "%*s%-*s (%Hu, %Hu)\n", indent, "", fwidth, "Record:", + ((const H5B2_test_rec_t *)record)->key, + ((const H5B2_test_rec_t *)record)->val); + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* H5B2__test2_debug() */ /*------------------------------------------------------------------------- @@ -6992,7 +6992,7 @@ H5C_flush_invalidate_ring(const H5F_t * f, hid_t dxpl_id, H5C_ring_t ring, /* Get cache entry for this node */ next_entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr); - if ( NULL == next_entry_ptr ) + if(NULL == next_entry_ptr) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "next_entry_ptr == NULL ?!?!") HDassert(next_entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC); @@ -7430,8 +7430,8 @@ H5C_flush_ring(H5F_t *f, hid_t dxpl_id, H5C_ring_t ring, unsigned flags) #if H5C_DO_EXTREME_SANITY_CHECKS if((H5C_validate_protected_entry_list(cache_ptr) < 0) || - (H5C_validate_pinned_entry_list(cache_ptr) < 0 || - (H5C_validate_lru_list(cache_ptr) < 0)) { + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || + (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry.\n"); #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -7794,7 +7794,7 @@ done: * * Refactored function to delay all modifications of the * metadata cache data structures until after any calls - * to the pre-serialize or serialize callbacks. + * to the pre-serialize or serialize callbacks. * * Need to do this, as some pre-serialize or serialize * calls result in calls to the metadata cache and @@ -7862,7 +7862,7 @@ H5C__flush_single_entry(const H5F_t *f, hid_t dxpl_id, H5C_cache_entry_t *entry_ HDassert(FALSE == entry_ptr->coll_access); #endif - /* we will write the entry to disk if it exists, is dirty, and if the + /* we will write the entry to disk if it exists, is dirty, and if the * clear only flag is not set. */ if(entry_ptr->is_dirty && !clear_only) @@ -8270,7 +8270,7 @@ H5C__flush_single_entry(const H5F_t *f, hid_t dxpl_id, H5C_cache_entry_t *entry_ /* only log a flush if we actually wrote to disk */ H5C__UPDATE_STATS_FOR_FLUSH(cache_ptr, entry_ptr) - } + } /* end else if */ if(destroy) { if(take_ownership) @@ -8279,7 +8279,7 @@ H5C__flush_single_entry(const H5F_t *f, hid_t dxpl_id, H5C_cache_entry_t *entry_ HDassert(destroy_entry); H5C__UPDATE_STATS_FOR_EVICTION(cache_ptr, entry_ptr, take_ownership) - } + } /* end if */ /* If the entry's type has a 'notify' callback and the entry is about * to be removed from the cache, send a 'before eviction' notice while @@ -8527,12 +8527,12 @@ H5C_load_entry(H5F_t * f, /* verify absence of prohibited or unsupported type flag combinations */ HDassert(!(type->flags & H5C__CLASS_NO_IO_FLAG)); - + /* for now, we do not combine the speculative load and compressed flags */ HDassert(!((type->flags & H5C__CLASS_SPECULATIVE_LOAD_FLAG) && (type->flags & H5C__CLASS_COMPRESSED_FLAG))); - /* Can't see how skip reads could be usefully combined with + /* Can't see how skip reads could be usefully combined with * either the speculative read or compressed flags. Hence disallow. */ HDassert(!((type->flags & H5C__CLASS_SKIP_READS) && @@ -8654,12 +8654,10 @@ H5C_load_entry(H5F_t * f, } /* Allocate the buffer for reading the on-disk entry image */ if(NULL == (image = H5MM_malloc(len + H5C_IMAGE_EXTRA_SPACE))) - - HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, \ - "memory allocation failed for on disk image buffer.") + HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "memory allocation failed for on disk image buffer.") #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)image) + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + HDmemcpy(image + len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ #ifdef H5_HAVE_PARALLEL @@ -8721,12 +8719,9 @@ H5C_load_entry(H5F_t * f, /* Get the actual image size for the thing */ if(type->image_len(thing, &new_len, &compressed, &compressed_size) < 0) - - HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, NULL, \ - "can't retrieve image length") + HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, NULL, "can't retrieve image length") if(new_len == 0) - HGOTO_ERROR(H5E_CACHE, H5E_BADVALUE, NULL, "image length is 0") HDassert(((type->flags & H5C__CLASS_COMPRESSED_FLAG) != 0) || @@ -8770,15 +8765,13 @@ H5C_load_entry(H5F_t * f, if(NULL == (new_image = H5MM_realloc(image, new_len + H5C_IMAGE_EXTRA_SPACE))) - HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, \ - "image null after H5MM_realloc()") + HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, NULL, "image null after H5MM_realloc()") image = new_image; #if H5C_DO_MEMORY_SANITY_CHECKS - HDmemcpy(((uint8_t *)image) + new_len, - H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); + HDmemcpy(((uint8_t *)image) + new_len, H5C_IMAGE_SANITY_VALUE, H5C_IMAGE_EXTRA_SPACE); #endif /* H5C_DO_MEMORY_SANITY_CHECKS */ @@ -8799,8 +8792,7 @@ H5C_load_entry(H5F_t * f, if ( type->free_icr(thing) < 0 ) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, \ - "free_icr callback failed") + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "free_icr callback failed") #ifdef H5_HAVE_PARALLEL if(!coll_access || 0 == mpi_rank) { @@ -8881,7 +8873,7 @@ H5C_load_entry(H5F_t * f, * * HDassert( ( dirty == FALSE ) || ( type->id == 5 || type->id == 6 ) ); * - * note that type ids 5 & 6 are associated with object headers in the + * note that type ids 5 & 6 are associated with object headers in the * metadata cache. * * When we get to using H5C for other purposes, we may wish to @@ -9089,8 +9081,8 @@ H5C_make_space_in_cache(H5F_t * f, ( entry_ptr != NULL ) ) { - HDassert(entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC); - HDassert( ! (entry_ptr->is_protected) ); + HDassert(entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC); + HDassert( !(entry_ptr->is_protected) ); HDassert( ! (entry_ptr->is_read_only) ); HDassert( (entry_ptr->ro_ref_count) == 0 ); @@ -9122,8 +9114,8 @@ H5C_make_space_in_cache(H5F_t * f, * last_entry_removed_ptr prior to the call to * H5C__flush_single_entry() so that we can spot * unexpected removals of entries from the cache, - * and set the restart_scan flag if proceeding - * would be likely to cause us to scan an entry + * and set the restart_scan flag if proceeding + * would be likely to cause us to scan an entry * that is no longer in the cache. */ cache_ptr->entries_removed_counter = 0; @@ -9186,15 +9178,15 @@ H5C_make_space_in_cache(H5F_t * f, if ( didnt_flush_entry ) { - /* epoch markers don't get flushed, and we don't touch + /* epoch markers don't get flushed, and we don't touch * entries that are in the process of being flushed. - * Hence no need for sanity checks, as we haven't - * flushed anything. Thus just set entry_ptr to prev_ptr + * Hence no need for sanity checks, as we haven't + * flushed anything. Thus just set entry_ptr to prev_ptr * and go on. */ entry_ptr = prev_ptr; - } else if ( ( restart_scan ) + } else if ( ( restart_scan ) || ( prev_ptr->is_dirty != prev_is_dirty ) || @@ -9370,10 +9362,8 @@ H5C_validate_lru_list(H5C_t * cache_ptr) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 1 failed") } - if ( ( cache_ptr->LRU_list_len < 0 ) || ( cache_ptr->LRU_list_size < 0 ) ) { - + if(cache_ptr->LRU_list_len < 0) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") - } if ( ( cache_ptr->LRU_list_len == 1 ) && @@ -9500,10 +9490,8 @@ H5C_validate_pinned_entry_list(H5C_t * cache_ptr) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 1 failed") } - if ( ( cache_ptr->pel_len < 0 ) || ( cache_ptr->pel_size < 0 ) ) { - + if(cache_ptr->pel_len < 0) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") - } if ( ( cache_ptr->pel_len == 1 ) && @@ -9623,21 +9611,12 @@ H5C_validate_protected_entry_list(H5C_t * cache_ptr) HDassert( cache_ptr ); HDassert( cache_ptr->magic == H5C__H5C_T_MAGIC ); - if ( ( ( cache_ptr->pl_head_ptr == NULL ) - || - ( cache_ptr->pl_tail_ptr == NULL ) - ) - && - ( cache_ptr->pl_head_ptr != cache_ptr->pl_tail_ptr ) - ) { - + if(((cache_ptr->pl_head_ptr == NULL) || (cache_ptr->pl_tail_ptr == NULL)) + && (cache_ptr->pl_head_ptr != cache_ptr->pl_tail_ptr)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 1 failed") - } - - if ( ( cache_ptr->pl_len < 0 ) || ( cache_ptr->pl_size < 0 ) ) { + if(cache_ptr->pl_len < 0) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") - } if ( ( cache_ptr->pl_len == 1 ) && @@ -9968,7 +9947,7 @@ done: * Function: H5C_ignore_tags * * Purpose: Override all assertion frameworks associated with making - * sure proper tags are applied to metadata. + * sure proper tags are applied to cache entries. * * NOTE: This should really only be used in tests that need * to access internal functions without going through @@ -10080,7 +10059,7 @@ done: * Return: FAIL if error is detected, SUCCEED otherwise. * * Programmer: Mike McGreevy - * November 3, 2009 + * August 19, 2010 * *------------------------------------------------------------------------- */ @@ -10123,7 +10102,7 @@ done: * Return: FAIL if error is detected, SUCCEED otherwise. * * Programmer: Mike McGreevy - * November 3, 2009 + * September 9, 2010 * *------------------------------------------------------------------------- */ @@ -10169,7 +10148,7 @@ H5C_mark_tagged_entries(H5C_t * cache_ptr, haddr_t tag) * Return: FAIL if error is detected, SUCCEED otherwise. * * Programmer: Mike McGreevy - * November 3, 2009 + * November 3, 2010 * *------------------------------------------------------------------------- */ diff --git a/src/H5Dbtree.c b/src/H5Dbtree.c index 30c3a28..85238da 100644 --- a/src/H5Dbtree.c +++ b/src/H5Dbtree.c @@ -127,7 +127,7 @@ static herr_t H5D__btree_idx_init(const H5D_chk_idx_info_t *idx_info, static herr_t H5D__btree_idx_create(const H5D_chk_idx_info_t *idx_info); static hbool_t H5D__btree_idx_is_space_alloc(const H5O_storage_chunk_t *storage); static herr_t H5D__btree_idx_insert(const H5D_chk_idx_info_t *idx_info, - H5D_chunk_ud_t *udata); + H5D_chunk_ud_t *udata, const H5D_t *dset); static herr_t H5D__btree_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata); static int H5D__btree_idx_iterate(const H5D_chk_idx_info_t *idx_info, @@ -218,7 +218,6 @@ H5FL_DEFINE_STATIC(H5O_layout_chunk_t); * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static H5UC_t * H5D__btree_get_shared(const H5F_t H5_ATTR_UNUSED *f, const void *_udata) { @@ -439,7 +438,6 @@ H5D__btree_cmp3(void *_lt_key, void *_udata, void *_rt_key) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static htri_t H5D__btree_found(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, const void *_lt_key, void *_udata) @@ -539,7 +537,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static H5B_ins_t H5D__btree_insert(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, void *_lt_key, hbool_t *lt_key_changed, @@ -633,7 +630,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static H5B_ins_t H5D__btree_remove(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key /*in,out */ , hbool_t *lt_key_changed /*out */ , @@ -761,7 +757,6 @@ H5D__btree_encode_key(const H5B_shared_t *shared, uint8_t *raw, const void *_key * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5D__btree_debug_key(FILE *stream, int indent, int fwidth, const void *_key, const void *_udata) @@ -991,7 +986,8 @@ H5D__btree_idx_is_space_alloc(const H5O_storage_chunk_t *storage) *------------------------------------------------------------------------- */ static herr_t -H5D__btree_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata) +H5D__btree_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata, + const H5D_t H5_ATTR_UNUSED *dset) { herr_t ret_value = SUCCEED; /* Return value */ @@ -1071,7 +1067,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static int H5D__btree_idx_iterate_cb(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, const void *_lt_key, haddr_t addr, const void H5_ATTR_UNUSED *_rt_key, diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index e935f93..8194cf4 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -73,6 +73,10 @@ #define H5D_CHUNK_GET_NODE_INFO(map, node) (map->use_single ? map->single_chunk_info : (H5D_chunk_info_t *)H5SL_item(node)) #define H5D_CHUNK_GET_NEXT_NODE(map, node) (map->use_single ? (H5SL_node_t *)NULL : H5SL_next(node)) +/* Sanity check on chunk index types: commonly used by a lot of routines in this file */ +#define H5D_CHUNK_STORAGE_INDEX_CHK(storage) \ + HDassert((H5D_CHUNK_IDX_BTREE == storage->idx_type && H5D_COPS_BTREE == storage->ops)); + /* * Feature: If this constant is defined then every cache preemption and load * causes a character to be printed on the standard error stream: @@ -104,6 +108,25 @@ /* Local Typedefs */ /******************/ +/* Raw data chunks are cached. Each entry in the cache is: */ +typedef struct H5D_rdcc_ent_t { + hbool_t locked; /*entry is locked in cache */ + hbool_t dirty; /*needs to be written to disk? */ + hbool_t deleted; /*chunk about to be deleted */ + hsize_t scaled[H5O_LAYOUT_NDIMS]; /*scaled chunk 'name' (coordinates) */ + uint32_t rd_count; /*bytes remaining to be read */ + uint32_t wr_count; /*bytes remaining to be written */ + H5F_block_t chunk_block; /*offset/length of chunk in file */ + hsize_t chunk_idx; /*index of chunk in dataset */ + uint8_t *chunk; /*the unfiltered chunk data */ + unsigned idx; /*index in hash table */ + struct H5D_rdcc_ent_t *next;/*next item in doubly-linked list */ + struct H5D_rdcc_ent_t *prev;/*previous item in doubly-linked list */ + struct H5D_rdcc_ent_t *tmp_next;/*next item in temporary doubly-linked list */ + struct H5D_rdcc_ent_t *tmp_prev;/*previous item in temporary doubly-linked list */ +} H5D_rdcc_ent_t; +typedef H5D_rdcc_ent_t *H5D_rdcc_ent_ptr_t; /* For free lists */ + /* Callback info for iteration to prune chunks */ typedef struct H5D_chunk_it_ud1_t { H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ @@ -216,7 +239,7 @@ H5D__nonexistent_readvv(const H5D_io_info_t *io_info, /* Helper routines */ static herr_t H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims, - const hsize_t *curr_dims); + const hsize_t *curr_dims, const hsize_t *max_dims); static void *H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline); static void *H5D__chunk_mem_xfree(void *chk, const H5O_pline_t *pline); static void *H5D__chunk_mem_realloc(void *chk, size_t size, @@ -241,11 +264,17 @@ static herr_t H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache, H5D_rdcc_ent_t *ent, hbool_t reset); static herr_t H5D__chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache, H5D_rdcc_ent_t *ent, hbool_t flush); +static void *H5D__chunk_lock(const H5D_io_info_t *io_info, + H5D_chunk_ud_t *udata, hbool_t relax); +static herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, + const H5D_chunk_ud_t *udata, hbool_t dirty, void *chunk, + uint32_t naccessed); static herr_t H5D__chunk_cache_prune(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache, size_t size); static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata); static herr_t H5D__chunk_file_alloc(const H5D_chk_idx_info_t *idx_info, - const H5F_block_t *old_chunk, H5F_block_t *new_chunk, hbool_t *need_insert); + const H5F_block_t *old_chunk, H5F_block_t *new_chunk, hbool_t *need_insert, + hsize_t scaled[]); #ifdef H5_HAVE_PARALLEL static herr_t H5D__chunk_collective_fill(const H5D_t *dset, hid_t dxpl_id, H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, const void *fill_buf); @@ -378,7 +407,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, /* Create the chunk it if it doesn't exist, or reallocate the chunk * if its size changed. */ - if(H5D__chunk_file_alloc(&idx_info, &old_chunk, &udata.chunk_block, &need_insert) < 0) + 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") /* Make sure the address of the chunk is returned. */ @@ -409,7 +438,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, /* Set the chunk's filter mask to the new settings */ udata.filter_mask = filters; - if((layout->storage.u.chunk.ops->insert)(&idx_info, &udata) < 0) + if((layout->storage.u.chunk.ops->insert)(&idx_info, &udata, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") } /* end if */ @@ -431,7 +460,8 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims, const hsize_t *curr_dims) +H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims, + const hsize_t *curr_dims, const hsize_t *max_dims) { unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ @@ -444,17 +474,21 @@ H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims, const hsize HDassert(curr_dims); /* Compute the # of chunks in dataset dimensions */ - for(u = 0, layout->nchunks = 1; u < ndims; u++) { + for(u = 0, layout->nchunks = 1, layout->max_nchunks = 1; u < ndims; u++) { /* Round up to the next integer # of chunks, to accomodate partial chunks */ layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u]; + layout->max_chunks[u] = ((max_dims[u] + layout->dim[u]) - 1) / layout->dim[u]; /* Accumulate the # of chunks */ layout->nchunks *= layout->chunks[u]; + layout->max_nchunks *= layout->max_chunks[u]; } /* end for */ /* Get the "down" sizes for each dimension */ if(H5VM_array_down(ndims, layout->chunks, layout->down_chunks) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value") + if(H5VM_array_down(ndims, layout->max_chunks, layout->max_down_chunks) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value") done: FUNC_LEAVE_NOAPI(ret_value) @@ -484,7 +518,7 @@ H5D__chunk_set_info(const H5D_t *dset) HDassert(dset); /* Set the base layout information */ - if(H5D__chunk_set_info_real(&dset->shared->layout.u.chunk, dset->shared->ndims, dset->shared->curr_dims) < 0) + if(H5D__chunk_set_info_real(&dset->shared->layout.u.chunk, dset->shared->ndims, dset->shared->curr_dims, dset->shared->max_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout's chunk info") /* Call the index's "resize" callback */ @@ -597,6 +631,7 @@ H5D__chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id) H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Convenience pointer to dataset's chunk cache */ H5P_genplist_t *dapl; /* Data access property list object pointer */ + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -604,6 +639,7 @@ H5D__chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id) /* Sanity check */ HDassert(f); HDassert(dset); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); if(NULL == (dapl = (H5P_genplist_t *)H5I_object(dapl_id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for fapl ID") @@ -687,12 +723,14 @@ done: hbool_t H5D__chunk_is_space_alloc(const H5O_storage_t *storage) { + const H5O_storage_chunk_t *sc = &(storage->u.chunk); hbool_t ret_value = FALSE; /* Return value */ FUNC_ENTER_PACKAGE_NOERR /* Sanity checks */ HDassert(storage); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Query index layer */ ret_value = (storage->u.chunk.ops->is_space_alloc)(&storage->u.chunk); @@ -1021,9 +1059,8 @@ H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline) FUNC_ENTER_STATIC_NOERR HDassert(size); - HDassert(pline); - if(pline->nused > 0) + if(pline && pline->nused) ret_value = H5MM_malloc(size); else ret_value = H5FL_BLK_MALLOC(chunk, size); @@ -1051,10 +1088,8 @@ H5D__chunk_mem_xfree(void *chk, const H5O_pline_t *pline) { FUNC_ENTER_STATIC_NOERR - HDassert(pline); - if(chk) { - if(pline->nused > 0) + if(pline && pline->nused) H5MM_xfree(chk); else chk = H5FL_BLK_FREE(chunk, chk); @@ -1344,6 +1379,9 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t HDmemcpy(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); @@ -1601,6 +1639,7 @@ H5D__chunk_file_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, /* Set the chunk's scaled coordinates */ HDmemcpy(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); /* Insert the new chunk into the skip list */ if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) { @@ -1649,7 +1688,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, unsigned ndims, const hsize_t *coords, void *_fm) { @@ -1735,6 +1773,7 @@ H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_ FUNC_ENTER_PACKAGE + /* Sanity check */ HDassert(io_info); HDassert(dataset); @@ -1887,6 +1926,9 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, void *chunk = NULL; /* Pointer to locked chunk buffer */ htri_t cacheable; /* Whether the chunk is cacheable */ + /* Set chunk's [scaled] coordinates */ + io_info->store->chunk.scaled = chunk_info->scaled; + /* Determine if we should use the chunk cache */ if((cacheable = H5D__chunk_cacheable(io_info, udata.chunk_block.offset, FALSE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") @@ -1897,9 +1939,6 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5_CHECK_OVERFLOW(type_info->src_type_size, /*From:*/ size_t, /*To:*/ uint32_t); src_accessed_bytes = chunk_info->chunk_points * (uint32_t)type_info->src_type_size; - /* Set chunk's [scaled] coordinates */ - io_info->store->chunk.scaled = chunk_info->scaled; - /* Lock the chunk into the cache */ if(NULL == (chunk = H5D__chunk_lock(io_info, &udata, FALSE))) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") @@ -2013,6 +2052,9 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) || (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0)); + /* Set chunk's [scaled] coordinates */ + io_info->store->chunk.scaled = chunk_info->scaled; + /* Determine if we should use the chunk cache */ if((cacheable = H5D__chunk_cacheable(io_info, udata.chunk_block.offset, TRUE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") @@ -2031,9 +2073,6 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, fm->fsel_type == H5S_SEL_POINTS) entire_chunk = FALSE; - /* Set chunk's [scaled] coordinates */ - io_info->store->chunk.scaled = chunk_info->scaled; - /* Lock the chunk into the cache */ if(NULL == (chunk = H5D__chunk_lock(io_info, &udata, entire_chunk))) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") @@ -2058,7 +2097,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, udata.chunk_block.length = io_info->dset->shared->layout.u.chunk.size; /* Allocate the chunk */ - if(H5D__chunk_file_alloc(&idx_info, NULL, &udata.chunk_block, &need_insert) < 0) + if(H5D__chunk_file_alloc(&idx_info, NULL, &udata.chunk_block, &need_insert, chunk_info->scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") /* Make sure the address of the chunk is returned. */ @@ -2091,7 +2130,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, } /* end if */ else { if(need_insert && io_info->dset->shared->layout.storage.u.chunk.ops->insert) - if((io_info->dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata) < 0) + if((io_info->dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") } /* end else */ @@ -2223,12 +2262,14 @@ H5D__chunk_dest(H5D_t *dset, hid_t dxpl_id) H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Dataset's chunk cache */ H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Pointer to current & next cache entries */ int nerrors = 0; /* Accumulated count of errors */ + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL) /* Sanity checks */ HDassert(dset); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Fill the DXPL cache values for later use */ if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) @@ -2289,6 +2330,7 @@ H5D_chunk_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr) /* Sanity checks */ HDassert(storage); HDassert(storage->ops); + H5D_CHUNK_STORAGE_INDEX_CHK(storage); /* Reset index structures */ if((storage->ops->reset)(storage, reset_addr) < 0) @@ -2353,6 +2395,7 @@ H5D__chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *ud HDmemcpy(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; last->filter_mask = udata->filter_mask; /* Indicate that the cached info is valid */ @@ -2399,6 +2442,7 @@ H5D__chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *uda /* Retrieve the information from the cache */ udata->chunk_block.offset = last->addr; udata->chunk_block.length = last->nbytes; + udata->chunk_idx = last->chunk_idx; udata->filter_mask = last->filter_mask; /* Indicate that the data was found */ @@ -2429,6 +2473,7 @@ herr_t H5D__chunk_create(const H5D_t *dset /*in,out*/, hid_t dxpl_id) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -2437,6 +2482,8 @@ H5D__chunk_create(const H5D_t *dset /*in,out*/, hid_t dxpl_id) HDassert(dset); HDassert(H5D_CHUNKED == dset->shared->layout.type); HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); + #ifndef NDEBUG { unsigned u; /* Local index variable */ @@ -2527,21 +2574,24 @@ H5D__chunk_lookup(const H5D_t *dset, hid_t dxpl_id, const hsize_t *scaled, H5D_chunk_ud_t *udata) { H5D_rdcc_ent_t *ent = NULL; /* Cache entry */ - hbool_t found = FALSE; /* In cache? */ - unsigned u; /* Counter */ - herr_t ret_value = SUCCEED; /* Return value */ + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); + unsigned idx; /* Index of chunk in cache, if present */ + hbool_t found = FALSE; /* In cache? */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE + /* Sanity checks */ HDassert(dset); HDassert(dset->shared->layout.u.chunk.ndims > 0); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(scaled); HDassert(udata); /* Initialize the query information about the chunk we are looking for */ udata->common.layout = &(dset->shared->layout.u.chunk); udata->common.storage = &(dset->shared->layout.storage.u.chunk); - udata->common.scaled = scaled; + udata->common.scaled = scaled; /* Reset information about the chunk we are looking for */ udata->chunk_block.offset = HADDR_UNDEF; @@ -2550,21 +2600,32 @@ H5D__chunk_lookup(const H5D_t *dset, hid_t dxpl_id, const hsize_t *scaled, /* Check for chunk in cache */ if(dset->shared->cache.chunk.nslots > 0) { - udata->idx_hint = H5D__chunk_hash_val(dset->shared, scaled); - ent = dset->shared->cache.chunk.slot[udata->idx_hint]; + /* Determine the chunk's location in the hash table */ + idx = H5D__chunk_hash_val(dset->shared, scaled); - if(ent) - for(u = 0, found = TRUE; u < dset->shared->ndims; u++) + /* Get the chunk cache entry for that location */ + ent = dset->shared->cache.chunk.slot[idx]; + if(ent) { + unsigned u; /* Counter */ + + /* Speculatively set the 'found' flag */ + found = TRUE; + + /* Verify that the cache entry is the correct chunk */ + for(u = 0; u < dset->shared->ndims; u++) if(scaled[u] != ent->scaled[u]) { found = FALSE; break; } /* end if */ + } /* end if */ } /* end if */ - /* Find chunk addr */ + /* Retrieve chunk addr */ if(found) { + udata->idx_hint = idx; udata->chunk_block.offset = ent->chunk_block.offset; udata->chunk_block.length = ent->chunk_block.length;; + udata->chunk_idx = ent->chunk_idx; } /* end if */ else { /* Invalidate idx_hint, to signal that the chunk is not in cache */ @@ -2636,12 +2697,14 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t { void *buf = NULL; /* Temporary buffer */ hbool_t point_of_no_return = FALSE; + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL) HDassert(dset); HDassert(dset->shared); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(dxpl_cache); HDassert(ent); HDassert(!ent->locked); @@ -2660,6 +2723,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t udata.chunk_block.offset = ent->chunk_block.offset; udata.chunk_block.length = dset->shared->layout.u.chunk.size; udata.filter_mask = 0; + udata.chunk_idx = ent->chunk_idx; /* Should the chunk be filtered before writing it to disk? */ if(dset->shared->dcpl_cache.pline.nused) { @@ -2719,7 +2783,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t /* Create the chunk it if it doesn't exist, or reallocate the chunk * if its size changed. */ - if(H5D__chunk_file_alloc(&idx_info, &(ent->chunk_block), &udata.chunk_block, &need_insert) < 0) + if(H5D__chunk_file_alloc(&idx_info, &(ent->chunk_block), &udata.chunk_block, &need_insert, ent->scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") /* Update the chunk entry's info, in case it was allocated or relocated */ @@ -2735,7 +2799,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t /* Insert the chunk record into the index */ if(need_insert && dset->shared->layout.storage.u.chunk.ops->insert) - if((dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata) < 0) + if((dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata, dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") /* Cache the chunk's info, in case it's accessed again shortly */ @@ -2826,8 +2890,19 @@ H5D__chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t rdcc->tail = ent->prev; ent->prev = ent->next = NULL; - /* Only clear hash table slot if chunk was not marked as deleted already */ - if(!ent->deleted) + /* Unlink from temporary list */ + if(ent->tmp_prev) { + HDassert(rdcc->tmp_head->tmp_next); + ent->tmp_prev->tmp_next = ent->tmp_next; + if(ent->tmp_next) { + ent->tmp_next->tmp_prev = ent->tmp_prev; + ent->tmp_next = NULL; + } /* end if */ + ent->tmp_prev = NULL; + } /* end if */ + else + /* Only clear hash table slot if the chunk was not on the temporary list + */ rdcc->slot[ent->idx] = NULL; /* Remove from cache */ @@ -2978,7 +3053,7 @@ done: * *------------------------------------------------------------------------- */ -void * +static void * H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax) { @@ -2994,7 +3069,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, void *chunk = NULL; /*the file chunk */ void *ret_value = NULL; /* Return value */ - FUNC_ENTER_PACKAGE + FUNC_ENTER_STATIC HDassert(io_info); HDassert(io_info->dxpl_cache); @@ -3002,6 +3077,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, HDassert(udata); HDassert(dset); HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER)); + HDassert(!rdcc->tmp_head); /* Get the chunk's size */ HDassert(layout->u.chunk.size > 0); @@ -3021,7 +3097,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, unsigned u; /*counters */ /* Make sure this is the right chunk */ - for(u = 0; u < layout->u.chunk.ndims; u++) + for(u = 0; u < layout->u.chunk.ndims - 1; u++) HDassert(io_info->store->chunk.scaled[u] == ent->scaled[u]); } #endif /* NDEBUG */ @@ -3169,6 +3245,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, /* Initialize the new entry */ 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); H5_CHECKED_ASSIGN(ent->rd_count, uint32_t, chunk_size, size_t); H5_CHECKED_ASSIGN(ent->wr_count, uint32_t, chunk_size, size_t); @@ -3189,6 +3266,9 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, } /* end if */ else rdcc->head = rdcc->tail = ent; + ent->tmp_next = NULL; + ent->tmp_prev = NULL; + } /* end if */ else /* We did not add the chunk to cache */ @@ -3251,7 +3331,7 @@ done: * *------------------------------------------------------------------------- */ -herr_t +static herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty, void *chunk, uint32_t naccessed) { @@ -3259,8 +3339,9 @@ H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk); herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE + FUNC_ENTER_STATIC + /* Sanity check */ HDassert(io_info); HDassert(udata); @@ -3268,8 +3349,6 @@ H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, /* * It's not in the cache, probably because it's too big. If it's * dirty then flush it to disk. In any case, free the chunk. - * Note: we have to copy the layout and filter messages so we - * don't discard the `const' qualifier. */ if(dirty) { H5D_rdcc_ent_t fake_ent; /* "fake" chunk cache entry */ @@ -3277,7 +3356,9 @@ H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, HDmemset(&fake_ent, 0, sizeof(fake_ent)); fake_ent.dirty = TRUE; HDmemcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); + HDmemcpy(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; fake_ent.chunk_block.length = udata->chunk_block.length; fake_ent.chunk = (uint8_t *)chunk; @@ -3330,7 +3411,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static int H5D__chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { @@ -3367,12 +3447,14 @@ H5D__chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes) H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ hsize_t chunk_bytes = 0; /* Number of bytes allocated for chunks */ + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE HDassert(dset); HDassert(dset->shared); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Fill the DXPL cache values for later use */ if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) @@ -3449,6 +3531,7 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, unsigned op_dim; /* Current operating dimension */ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ + const H5O_storage_chunk_t *sc = &(layout->storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dxpl_id, dset->oloc.addr, FAIL) @@ -3456,6 +3539,7 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER)); /* Retrieve the dataset dimensions */ @@ -3575,6 +3659,7 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, * Note that min_unalloc & max_unalloc are in scaled coordinates. * */ + chunk_size = orig_chunk_size; for(op_dim = 0; op_dim < space_ndims; op_dim++) { H5D_chunk_ud_t udata; /* User data for querying chunk info */ int i; /* Local index variable */ @@ -3593,18 +3678,11 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, while(!carry) { hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */ - /* Reset size of chunk in bytes, in case filtered size changes */ - chunk_size = orig_chunk_size; - + /* Look up this chunk */ + if(H5D__chunk_lookup(dset, dxpl_id, scaled, &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") #ifndef NDEBUG /* None of the chunks should be allocated */ - { - /* Look up this chunk */ - if(H5D__chunk_lookup(dset, dxpl_id, scaled, &udata) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") - - HDassert(!H5F_addr_defined(udata.chunk_block.offset)); - } /* end block */ /* Make sure the chunk is really in the dataset and outside the * original dimensions */ @@ -3659,6 +3737,8 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, /* Keep the number of bytes the chunk turned in to */ chunk_size = nbytes; } /* end if */ + else + chunk_size = layout->u.chunk.size; } /* end if */ /* Initialize the chunk information */ @@ -3670,7 +3750,7 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, udata.filter_mask = filter_mask; /* Allocate the chunk (with all processes) */ - if(H5D__chunk_file_alloc(&idx_info, NULL, &udata.chunk_block, &need_insert) < 0) + if(H5D__chunk_file_alloc(&idx_info, NULL, &udata.chunk_block, &need_insert, scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") HDassert(H5F_addr_defined(udata.chunk_block.offset)); @@ -3687,7 +3767,7 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, write collectively at the end */ /* allocate/resize address array if no more space left */ if(0 == chunk_info.num_io % 1024) - if(NULL == (chunk_info.addr = (haddr_t *)HDrealloc(chunk_info.addr, (chunk_info.num_io + 1024) * sizeof(haddr_t)))) + if(NULL == (chunk_info.addr = (haddr_t *)H5MM_realloc(chunk_info.addr, (chunk_info.num_io + 1024) * sizeof(haddr_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed for chunk addresses") /* Store the chunk's address for later */ @@ -3707,11 +3787,8 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, } /* end if */ /* Insert the chunk record into the index */ - /* (Note that this isn't safe, from a SWMR perspective, unlike - * serial operation. -QAK - */ if(need_insert && ops->insert) - if((ops->insert)(&idx_info, &udata) < 0) + if((ops->insert)(&idx_info, &udata, dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") /* Increment indices and adjust the edge chunk state */ @@ -3757,7 +3834,7 @@ done: #ifdef H5_HAVE_PARALLEL if(using_mpi && chunk_info.addr) - HDfree(chunk_info.addr); + H5MM_free(chunk_info.addr); #endif FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) @@ -4165,6 +4242,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */ uint32_t elmts_per_chunk; /* Elements in chunk */ unsigned u; /* Local index variable */ + const H5O_storage_chunk_t *sc = &(layout->storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -4172,6 +4250,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) /* Check args */ HDassert(dset && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(dxpl_cache); /* Fill the DXPL cache values for later use */ @@ -4310,6 +4389,8 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) while(!carry) { int i; /* Local index variable */ + udata.common.scaled = scaled; + if(0 == ndims_outside_fill) { HDassert(fill_dim[op_dim]); HDassert(scaled[op_dim] == min_mod_chunk_sc[op_dim]); @@ -4348,7 +4429,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) /* Remove the chunk from disk, if present */ if(H5F_addr_defined(chk_udata.chunk_block.offset)) { /* Update the offset in idx_udata */ - idx_udata.scaled = scaled; + idx_udata.scaled = udata.common.scaled; /* Remove the chunk from disk */ if((layout->storage.u.chunk.ops->remove)(&idx_info, &idx_udata) < 0) @@ -4470,12 +4551,14 @@ H5D__chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[]) H5D_chk_idx_info_t idx_info; /* Chunked index info */ const H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ H5D_chunk_it_ud2_t udata; /* User data for iteration callback */ + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE HDassert(dset); HDassert(dset->shared); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(chunk_addr); /* Set up user data for B-tree callback */ @@ -4523,6 +4606,7 @@ H5D__chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh, H5O_storage_t *storage) H5O_pline_t pline; /* I/O pipeline message */ hbool_t pline_read = FALSE; /* Whether the I/O pipeline message was read from the file */ htri_t exists; /* Flag if header message of interest exists */ + H5O_storage_chunk_t *sc = &(storage->u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -4531,6 +4615,7 @@ H5D__chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh, H5O_storage_t *storage) HDassert(f); HDassert(oh); HDassert(storage); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Check for I/O pipeline message */ if((exists = H5O_msg_exists_oh(oh, H5O_PLINE_ID)) < 0) @@ -4597,6 +4682,8 @@ H5D__chunk_update_cache(H5D_t *dset, hid_t dxpl_id) { H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent, *next; /*cache entry */ + H5D_rdcc_ent_t tmp_head; /* Sentinel entry for temporary entry list */ + H5D_rdcc_ent_t *tmp_tail; /* Tail pointer for temporary entry list */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ herr_t ret_value = SUCCEED; /* Return value */ @@ -4614,6 +4701,11 @@ H5D__chunk_update_cache(H5D_t *dset, hid_t dxpl_id) if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") + /* Add temporary entry list to rdcc */ + (void)HDmemset(&tmp_head, 0, sizeof(tmp_head)); + rdcc->tmp_head = &tmp_head; + tmp_tail = &tmp_head; + /* Recompute the index for each cached chunk that is in a dataset */ for(ent = rdcc->head; ent; ent = next) { unsigned old_idx; /* Previous index number */ @@ -4634,37 +4726,58 @@ H5D__chunk_update_cache(H5D_t *dset, hid_t dxpl_id) HDassert(old_ent->locked == FALSE); HDassert(old_ent->deleted == FALSE); - /* Mark the old entry as deleted, but do not evict (yet). - * Make sure we do not make any calls to the index + /* Insert the old entry into the temporary list, but do not + * evict (yet). Make sure we do not make any calls to the index * until all chunks have updated indices! */ - old_ent->deleted = TRUE; + HDassert(!old_ent->tmp_next); + HDassert(!old_ent->tmp_prev); + tmp_tail->tmp_next = old_ent; + old_ent->tmp_prev = tmp_tail; + tmp_tail = old_ent; } /* end if */ /* Insert this chunk into correct location in hash table */ rdcc->slot[ent->idx] = ent; - /* If this chunk was previously marked as deleted and therefore - * not in the hash table, reset the deleted flag. + /* If this chunk was previously on the temporary list and therefore + * not in the hash table, remove it from the temporary list. * Otherwise clear the old hash table slot. */ - if(ent->deleted) - ent->deleted = FALSE; + if(ent->tmp_prev) { + HDassert(tmp_head.tmp_next); + HDassert(tmp_tail != &tmp_head); + ent->tmp_prev->tmp_next = ent->tmp_next; + if(ent->tmp_next) { + ent->tmp_next->tmp_prev = ent->tmp_prev; + ent->tmp_next = NULL; + } /* end if */ + else { + HDassert(tmp_tail == ent); + tmp_tail = ent->tmp_prev; + } /* end else */ + ent->tmp_prev = NULL; + } /* end if */ else rdcc->slot[old_idx] = NULL; } /* end if */ } /* end for */ - /* Evict chunks that are still marked as deleted */ - for(ent = rdcc->head; ent; ent = next) { - /* Get the pointer to the next cache entry */ - next = ent->next; + /* tmp_tail is no longer needed, and will be invalidated by + * H5D_chunk_cache_evict anyways. */ + tmp_tail = NULL; + + /* Evict chunks that are still on the temporary list */ + while(tmp_head.tmp_next) { + ent = tmp_head.tmp_next; /* Remove the old entry from the cache */ - if(ent->deleted) - if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") - } /* end for */ + if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") + } /* end while */ done: + /* Remove temporary list from rdcc */ + rdcc->tmp_head = NULL; + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_update_cache() */ @@ -4829,8 +4942,11 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) udata->buf_size = buf_size; } /* end if */ + udata_dst.chunk_idx = H5VM_array_offset_pre(udata_dst.common.layout->ndims - 1, + udata_dst.common.layout->down_chunks, udata_dst.common.scaled); + /* Allocate chunk in the file */ - if(H5D__chunk_file_alloc(udata->idx_info_dst, NULL, &udata_dst.chunk_block, &need_insert) < 0) + if(H5D__chunk_file_alloc(udata->idx_info_dst, NULL, &udata_dst.chunk_block, &need_insert, udata_dst.common.scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level") /* Write chunk data to destination file */ @@ -4843,7 +4959,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) /* Insert chunk record into index */ if(need_insert && udata->idx_info_dst->storage->ops->insert) - if((udata->idx_info_dst->storage->ops->insert)(udata->idx_info_dst, &udata_dst) < 0) + if((udata->idx_info_dst->storage->ops->insert)(udata->idx_info_dst, &udata_dst, NULL) < 0) HGOTO_ERROR_TAG(H5E_DATASET, H5E_CANTINSERT, H5_ITER_ERROR, "unable to insert chunk addr into index") /* Reset metadata tag in dxpl_id */ @@ -4876,6 +4992,9 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src, H5D_chunk_it_ud3_t udata; /* User data for iteration callback */ H5D_chk_idx_info_t idx_info_dst; /* Dest. chunked index info */ H5D_chk_idx_info_t idx_info_src; /* Source chunked index info */ + int sndims; /* Rank of dataspace */ + hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Curr. size of dataset dimensions */ + hsize_t max_dims[H5O_LAYOUT_NDIMS]; /* Curr. size of dataset dimensions */ H5O_pline_t _pline; /* Temporary pipeline info */ const H5O_pline_t *pline; /* Pointer to pipeline info to use */ H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ @@ -4899,9 +5018,11 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src, /* Check args */ HDassert(f_src); HDassert(storage_src); + H5D_CHUNK_STORAGE_INDEX_CHK(storage_src); HDassert(layout_src); HDassert(f_dst); HDassert(storage_dst); + H5D_CHUNK_STORAGE_INDEX_CHK(storage_dst); HDassert(ds_extent_src); HDassert(dt_src); @@ -4919,17 +5040,15 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src, /* Initialize layout information */ { - hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Curr. size of dataset dimensions */ - int sndims; /* Rank of dataspace */ unsigned ndims; /* Rank of dataspace */ /* Get the dim info for dataset */ - if((sndims = H5S_extent_get_dims(ds_extent_src, curr_dims, NULL)) < 0) + if((sndims = H5S_extent_get_dims(ds_extent_src, curr_dims, max_dims)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace dimensions") H5_CHECKED_ASSIGN(ndims, unsigned, sndims, int); /* Set the source layout chunk information */ - if(H5D__chunk_set_info_real(layout_src, ndims, curr_dims) < 0) + if(H5D__chunk_set_info_real(layout_src, ndims, curr_dims, max_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout's chunk info") } /* end block */ @@ -5131,6 +5250,7 @@ H5D__chunk_bh_info(const H5O_loc_t *loc, hid_t dxpl_id, H5O_t *oh, H5O_layout_t H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5S_t *space = NULL; /* Dataset's dataspace */ H5O_pline_t pline; /* I/O pipeline message */ + H5O_storage_chunk_t *sc = &(layout->storage.u.chunk); htri_t exists; /* Flag if header message of interest exists */ hbool_t idx_info_init = FALSE; /* Whether the chunk index info has been initialized */ hbool_t pline_read = FALSE; /* Whether the I/O pipeline message was read */ @@ -5143,6 +5263,7 @@ H5D__chunk_bh_info(const H5O_loc_t *loc, hid_t dxpl_id, H5O_t *oh, H5O_layout_t HDassert(loc->file); HDassert(H5F_addr_defined(loc->addr)); HDassert(layout); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); HDassert(index_size); /* Check for I/O pipeline message */ @@ -5205,7 +5326,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static int H5D__chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { @@ -5253,12 +5373,14 @@ H5D__chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) herr_t H5D__chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream) { + H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk); herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(dset); + H5D_CHUNK_STORAGE_INDEX_CHK(sc); /* Only display info if stream is defined */ if(stream) { @@ -5476,7 +5598,7 @@ done: */ static herr_t H5D__chunk_file_alloc(const H5D_chk_idx_info_t *idx_info, const H5F_block_t *old_chunk, - H5F_block_t *new_chunk, hbool_t *need_insert) + H5F_block_t *new_chunk, hbool_t *need_insert, hsize_t scaled[]) { hbool_t alloc_chunk = FALSE; /* Whether to allocate chunk */ herr_t ret_value = SUCCEED; /* Return value */ diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index ebe75bd..df2a740 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -440,12 +440,9 @@ H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src, H5F_t *f_dst HDassert(storage_src); HDassert(f_dst); HDassert(storage_dst); + HDassert(storage_dst->buf); HDassert(dt_src); - /* Allocate space for destination data */ - if(NULL == (storage_dst->buf = H5MM_malloc(storage_src->size))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate memory for compact dataset") - /* Create datatype ID for src datatype, so it gets freed */ if((tid_src = H5I_register(H5I_DATATYPE, dt_src, FALSE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register source file datatype") diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 988bb61..b5b9b0d 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -390,7 +390,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5D__contig_construct(H5F_t *f, H5D_t *dset) { diff --git a/src/H5Dint.c b/src/H5Dint.c index b9899c8..ab2f8d0 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -718,6 +718,7 @@ static herr_t H5D__cache_dataspace_info(const H5D_t *dset) { int sndims; /* Signed number of dimensions of dataspace rank */ + unsigned u; /* Local index value */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -730,6 +731,10 @@ H5D__cache_dataspace_info(const H5D_t *dset) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't cache dataspace dimensions") dset->shared->ndims = (unsigned)sndims; + /* Compute the inital 'power2up' values */ + for(u = 0; u < dset->shared->ndims; u++) + dset->shared->curr_power2up[u] = H5VM_power2up(dset->shared->curr_dims[u]); + done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__cache_dataspace_info() */ @@ -1847,7 +1852,7 @@ H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc case H5D_CHUNKED: if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { - /* Create the root of the B-tree that describes chunked storage */ + /* Create the root of the index that manages chunked storage */ if(H5D__chunk_create(dset /*in,out*/, dxpl_id) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") @@ -1860,7 +1865,7 @@ H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc /* If space allocation is set to 'early' and we are extending * the dataset, indicate that space should be allocated, so the - * B-tree gets expanded. -QAK + * index gets expanded. -QAK */ if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY && time_alloc == H5D_ALLOC_EXTEND) @@ -1911,7 +1916,7 @@ H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc /* Check if we need to initialize the space */ if(must_init_space) { if(layout->type == H5D_CHUNKED) { - /* If we are doing incremental allocation and the B-tree got + /* If we are doing incremental allocation and the index got * created during a H5Dwrite call, don't initialize the storage * now, wait for the actual writes to each block and let the * low-level chunking routines handle initialize the fill-values. @@ -1934,10 +1939,9 @@ H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc /* If we are filling the dataset on allocation or "if set" and * the fill value _is_ set, do that now */ if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || - (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { + (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) if(H5D__init_storage(dset, full_overwrite, old_dim, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") - } /* end if */ } /* end else */ } /* end if */ @@ -2253,7 +2257,6 @@ H5D__vlen_get_buf_size_alloc(size_t size, void *info) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ herr_t H5D__vlen_get_buf_size(void H5_ATTR_UNUSED *elem, hid_t type_id, unsigned H5_ATTR_UNUSED ndim, const hsize_t *point, void *op_data) { @@ -2623,7 +2626,7 @@ H5D__mark(const H5D_t *dataset, hid_t H5_ATTR_UNUSED dxpl_id, unsigned flags) /* Update the layout on disk, if it's been changed */ if(flags & H5D_MARK_LAYOUT) { if(H5D__layout_oh_write(dataset, dxpl_id, oh, update_flags) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout/pline/efl info") + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout info") /* Reset the "update the modification time" flag, so we only do it once */ update_flags = 0; diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c index 8676d7c..16ff81b 100644 --- a/src/H5Dlayout.c +++ b/src/H5Dlayout.c @@ -150,6 +150,7 @@ H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t includ switch(layout->type) { case H5D_COMPACT: + /* This information only present in older versions of message */ /* Size of raw data */ ret_value += 2; if(include_compact_data) @@ -157,6 +158,7 @@ H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t includ break; case H5D_CONTIGUOUS: + /* This information only present in older versions of message */ ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */ ret_value += H5F_SIZEOF_SIZE(f); /* Length of data */ break; @@ -206,7 +208,7 @@ herr_t H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset, hid_t dapl_id) { - H5O_layout_t *layout; /* Dataset's layout information */ + H5O_layout_t *layout; /* Dataset's layout information */ const H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ herr_t ret_value = SUCCEED; /* Return value */ @@ -401,7 +403,7 @@ done: /*------------------------------------------------------------------------- * Function: H5D__layout_oh_write * - * Purpose: Write layout/pline/efl information for dataset + * Purpose: Write layout information for dataset * * Return: Success: SUCCEED * Failure: FAIL diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index a5f34d1..0ba340a 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -1680,7 +1680,6 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, MPI_Comm comm; int ic, root; int mpi_code; - hbool_t mem_cleanup = FALSE; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY int new_value; htri_t check_prop; @@ -1715,12 +1714,14 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, threshold_nproc_per_chunk = mpi_size * percent_nproc_per_chunk/100; /* Allocate memory */ - io_mode_info = (uint8_t *)H5MM_calloc(total_chunks); - mergebuf = H5MM_malloc((sizeof(haddr_t) + 1) * total_chunks); + if(NULL == (io_mode_info = (uint8_t *)H5MM_calloc(total_chunks))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate I/O mode info buffer") + if(NULL == (mergebuf = H5MM_malloc((sizeof(haddr_t) + 1) * total_chunks))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate mergebuf buffer") tempbuf = mergebuf + total_chunks; if(mpi_rank == root) - recv_io_mode_info = (uint8_t *)H5MM_malloc(total_chunks * mpi_size); - mem_cleanup = TRUE; + if(NULL == (recv_io_mode_info = (uint8_t *)H5MM_malloc(total_chunks * mpi_size))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate recv I/O mode info buffer") /* Obtain the regularity and selection information for all chunks in this process. */ chunk_node = H5SL_first(fm->sel_chunks); @@ -1742,11 +1743,12 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, /* pre-computing: calculate number of processes and regularity of the selection occupied in each chunk */ - nproc_per_chunk = (int*)H5MM_calloc(total_chunks * sizeof(int)); + if(NULL == (nproc_per_chunk = (int*)H5MM_calloc(total_chunks * sizeof(int)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate nproc_per_chunk buffer") /* calculating the chunk address */ if(H5D__chunk_addrmap(io_info, chunk_addr) < 0) { - HDfree(nproc_per_chunk); + H5MM_free(nproc_per_chunk); HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") } /* end if */ @@ -1774,7 +1776,7 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, HDmemcpy(mergebuf, assign_io_mode, total_chunks); HDmemcpy(tempbuf, chunk_addr, sizeof(haddr_t) * total_chunks); - HDfree(nproc_per_chunk); + H5MM_free(nproc_per_chunk); } /* end if */ /* Broadcasting the MPI_IO option info. and chunk address info. */ @@ -1824,11 +1826,13 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, #endif done: - if(mem_cleanup) { - HDfree(io_mode_info); - HDfree(mergebuf); - if(mpi_rank == root) - HDfree(recv_io_mode_info); + if(io_mode_info) + H5MM_free(io_mode_info); + if(mergebuf) + H5MM_free(mergebuf); + if(recv_io_mode_info) { + HDassert(mpi_rank == root); + H5MM_free(recv_io_mode_info); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index f391e8c..97fc442 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -240,7 +240,7 @@ typedef struct H5D_chk_idx_info_t { typedef struct H5D_chunk_rec_t { hsize_t scaled[H5O_LAYOUT_NDIMS]; /* Logical offset to start */ uint32_t nbytes; /* Size of stored data */ - unsigned filter_mask; /* Excluded filters */ + uint32_t filter_mask; /* Excluded filters */ haddr_t chunk_addr; /* Address of chunk in file */ } H5D_chunk_rec_t; @@ -250,7 +250,6 @@ typedef struct H5D_chunk_rec_t { * to which the index points. */ typedef struct H5D_chunk_common_ud_t { - /* downward */ const H5O_layout_chunk_t *layout; /* Chunk layout description */ const H5O_storage_chunk_t *storage; /* Chunk storage description */ const hsize_t *scaled; /* Scaled coordinates for a chunk */ @@ -258,12 +257,14 @@ typedef struct H5D_chunk_common_ud_t { /* B-tree callback info for various operations */ typedef struct H5D_chunk_ud_t { + /* Downward */ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ /* Upward */ - unsigned idx_hint; /*index of chunk in cache, if present */ - H5F_block_t chunk_block; /*offset/length of chunk in file */ - unsigned filter_mask; /*excluded filters */ + unsigned idx_hint; /* Index of chunk in cache, if present */ + H5F_block_t chunk_block; /* Offset/length of chunk in file */ + unsigned filter_mask; /* Excluded filters */ + hsize_t chunk_idx; /* Chunk index for EA, FA indexing */ } H5D_chunk_ud_t; /* Typedef for "generic" chunk callbacks */ @@ -276,7 +277,7 @@ typedef herr_t (*H5D_chunk_init_func_t)(const H5D_chk_idx_info_t *idx_info, typedef herr_t (*H5D_chunk_create_func_t)(const H5D_chk_idx_info_t *idx_info); typedef hbool_t (*H5D_chunk_is_space_alloc_func_t)(const H5O_storage_chunk_t *storage); typedef herr_t (*H5D_chunk_insert_func_t)(const H5D_chk_idx_info_t *idx_info, - H5D_chunk_ud_t *udata); + H5D_chunk_ud_t *udata, const H5D_t *dset); typedef herr_t (*H5D_chunk_get_addr_func_t)(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata); typedef herr_t (*H5D_chunk_resize_func_t)(H5O_layout_chunk_t *layout); @@ -363,10 +364,12 @@ typedef struct H5D_chunk_cached_t { hsize_t scaled[H5O_LAYOUT_NDIMS]; /*scaled offset of chunk*/ haddr_t addr; /*file address of chunk */ uint32_t nbytes; /*size of stored data */ + hsize_t chunk_idx; /*index of chunk in dataset */ unsigned filter_mask; /*excluded filters */ } H5D_chunk_cached_t; /* The raw data chunk cache */ +struct H5D_rdcc_ent_t; /* Forward declaration of struct used below */ typedef struct H5D_rdcc_t { struct { unsigned ninits; /* Number of chunk creations */ @@ -379,6 +382,7 @@ typedef struct H5D_rdcc_t { double w0; /* Chunk preemption policy */ struct H5D_rdcc_ent_t *head; /* Head of doubly linked list */ struct H5D_rdcc_ent_t *tail; /* Tail of doubly linked list */ + struct H5D_rdcc_ent_t *tmp_head; /* Head of temporary doubly linked list. Chunks on this list are not in the hash table (slot). The head entry is a sentinel (does not refer to an actual chunk). */ size_t nbytes_used; /* Current cached raw data in bytes */ int nused; /* Number of chunk slots in use */ H5D_chunk_cached_t last; /* Cached copy of last chunk information */ @@ -422,6 +426,7 @@ typedef struct H5D_shared_t { /* Cached dataspace info */ unsigned ndims; /* The dataset's dataspace rank */ hsize_t curr_dims[H5S_MAX_RANK]; /* The curr. size of dataset dimensions */ + hsize_t curr_power2up[H5S_MAX_RANK]; /* The curr. dim sizes, rounded up to next power of 2 */ hsize_t max_dims[H5S_MAX_RANK]; /* The max. size of dataset dimensions */ /* Buffered/cached information for types of raw data storage*/ @@ -493,22 +498,6 @@ typedef struct { hsize_t size; /* Accumulated number of bytes for the selection */ } H5D_vlen_bufsize_t; -/* Raw data chunks are cached. Each entry in the cache is: */ -typedef struct H5D_rdcc_ent_t { - hbool_t locked; /*entry is locked in cache */ - hbool_t dirty; /*needs to be written to disk? */ - hbool_t deleted; /*chunk about to be deleted */ - hsize_t scaled[H5O_LAYOUT_NDIMS]; /*scaled chunk 'name' (coordinates) */ - uint32_t rd_count; /*bytes remaining to be read */ - uint32_t wr_count; /*bytes remaining to be written */ - H5F_block_t chunk_block; /*offset/length of chunk in file */ - uint8_t *chunk; /*the unfiltered chunk data */ - unsigned idx; /*index in hash table */ - struct H5D_rdcc_ent_t *next;/*next item in doubly-linked list */ - struct H5D_rdcc_ent_t *prev;/*previous item in doubly-linked list */ -} H5D_rdcc_ent_t; -typedef H5D_rdcc_ent_t *H5D_rdcc_ent_ptr_t; /* For free lists */ - /*****************************/ /* Package Private Variables */ @@ -616,11 +605,6 @@ 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 herr_t H5D__chunk_lookup(const H5D_t *dset, hid_t dxpl_id, const hsize_t *scaled, H5D_chunk_ud_t *udata); -H5_DLL void *H5D__chunk_lock(const H5D_io_info_t *io_info, - H5D_chunk_ud_t *udata, hbool_t relax); -H5_DLL herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, - const H5D_chunk_ud_t *udata, hbool_t dirty, void *chunk, - uint32_t naccessed); H5_DLL herr_t H5D__chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes); H5_DLL herr_t H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, hsize_t old_dim[]); diff --git a/src/H5Dvirtual.c b/src/H5Dvirtual.c index 7c5186d..bf754cb 100644 --- a/src/H5Dvirtual.c +++ b/src/H5Dvirtual.c @@ -446,10 +446,10 @@ H5D__virtual_copy_layout(H5O_layout_t *layout) /* Copy original source names */ if(NULL == (layout->storage.u.virt.list[i].source_file_name - = HDstrdup(orig_list[i].source_file_name))) + = H5MM_strdup(orig_list[i].source_file_name))) HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source file name") if(NULL == (layout->storage.u.virt.list[i].source_dset_name - = HDstrdup(orig_list[i].source_dset_name))) + = H5MM_strdup(orig_list[i].source_dset_name))) HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source dataset name") /* Copy source selection */ @@ -488,7 +488,7 @@ H5D__virtual_copy_layout(H5O_layout_t *layout) } /* end if */ else if(NULL == (layout->storage.u.virt.list[i].source_dset.file_name - = HDstrdup(orig_list[i].source_dset.file_name))) + = H5MM_strdup(orig_list[i].source_dset.file_name))) HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source file name") } /* end if */ if(orig_list[i].source_dset.dset_name) { @@ -504,7 +504,7 @@ H5D__virtual_copy_layout(H5O_layout_t *layout) } /* end if */ else if(NULL == (layout->storage.u.virt.list[i].source_dset.dset_name - = HDstrdup(orig_list[i].source_dset.dset_name))) + = H5MM_strdup(orig_list[i].source_dset.dset_name))) HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source dataset name") } /* end if */ @@ -1124,7 +1124,7 @@ H5D__virtual_copy_parsed_name(H5O_storage_virtual_name_seg_t **dst, /* Duplicate name segment */ if(p_src->name_segment) { - if(NULL == ((*p_dst)->name_segment = HDstrdup(p_src->name_segment))) + if(NULL == ((*p_dst)->name_segment = H5MM_strdup(p_src->name_segment))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to duplicate name segment") } /* end if */ @@ -1417,8 +1417,13 @@ H5Epush2(hid_t err_stack, const char *file, const char *func, unsigned line, done: if(va_started) va_end(ap); +#ifdef H5_HAVE_VASPRINTF + if(tmp) + HDfree(tmp); +#else /* H5_HAVE_VASPRINTF */ if(tmp) H5MM_xfree(tmp); +#endif /* H5_HAVE_VASPRINTF */ FUNC_LEAVE_API(ret_value) } /* end H5Epush2() */ diff --git a/src/H5EAdblkpage.c b/src/H5EAdblkpage.c index 15bad43..9f3b39a 100644 --- a/src/H5EAdblkpage.c +++ b/src/H5EAdblkpage.c @@ -290,7 +290,6 @@ END_FUNC(PKG) /* end H5EA__dblk_page_unprotect() */ * *------------------------------------------------------------------------- */ -/* ARGSUSED */ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL, H5EA__dblk_page_dest(H5EA_dblk_page_t *dblk_page)) diff --git a/src/H5EAdblock.c b/src/H5EAdblock.c index cd20bba..3eaaf1c 100644 --- a/src/H5EAdblock.c +++ b/src/H5EAdblock.c @@ -457,7 +457,6 @@ END_FUNC(PKG) /* end H5EA__dblock_delete() */ * *------------------------------------------------------------------------- */ -/* ARGSUSED */ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL, H5EA__dblock_dest(H5EA_dblock_t *dblock)) diff --git a/src/H5EAhdr.c b/src/H5EAhdr.c index eff4b54..da15087 100644 --- a/src/H5EAhdr.c +++ b/src/H5EAhdr.c @@ -43,7 +43,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5EApkg.h" /* Extensible Arrays */ #include "H5MFprivate.h" /* File memory management */ -#include "H5VMprivate.h" /* Vectors and arrays */ +#include "H5VMprivate.h" /* Vectors and arrays */ /****************/ @@ -128,7 +128,7 @@ H5EA__hdr_alloc(H5F_t *f)) /* Allocate space for the shared information */ if(NULL == (hdr = H5FL_CALLOC(H5EA_hdr_t))) - H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array shared header") + H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array shared header") /* Set non-zero internal fields */ hdr->addr = HADDR_UNDEF; @@ -390,35 +390,35 @@ HDfprintf(stderr, "%s: Called\n", FUNC); /* Check for valid parameters */ if(cparam->raw_elmt_size == 0) - H5E_THROW(H5E_BADVALUE, "element size must be greater than zero") + H5E_THROW(H5E_BADVALUE, "element size must be greater than zero") if(cparam->max_nelmts_bits == 0) - H5E_THROW(H5E_BADVALUE, "max. # of elements bits must be greater than zero") + H5E_THROW(H5E_BADVALUE, "max. # of elements bits must be greater than zero") if(cparam->max_nelmts_bits > H5EA_MAX_NELMTS_IDX_MAX) - H5E_THROW(H5E_BADVALUE, "max. # of elements bits must be <= %u", (unsigned)H5EA_MAX_NELMTS_IDX_MAX) + H5E_THROW(H5E_BADVALUE, "max. # of elements bits must be <= %u", (unsigned)H5EA_MAX_NELMTS_IDX_MAX) if(cparam->sup_blk_min_data_ptrs < 2) - H5E_THROW(H5E_BADVALUE, "min # of data block pointers in super block must be >= two") + H5E_THROW(H5E_BADVALUE, "min # of data block pointers in super block must be >= two") if(!POWER_OF_TWO(cparam->sup_blk_min_data_ptrs)) - H5E_THROW(H5E_BADVALUE, "min # of data block pointers in super block must be power of two") + H5E_THROW(H5E_BADVALUE, "min # of data block pointers in super block must be power of two") if(!POWER_OF_TWO(cparam->data_blk_min_elmts)) - H5E_THROW(H5E_BADVALUE, "min # of elements per data block must be power of two") + H5E_THROW(H5E_BADVALUE, "min # of elements per data block must be power of two") dblk_page_nelmts = (size_t)1 << cparam->max_dblk_page_nelmts_bits; if(dblk_page_nelmts < cparam->idx_blk_elmts) - H5E_THROW(H5E_BADVALUE, "# of elements per data block page must be greater than # of elements in index block") + H5E_THROW(H5E_BADVALUE, "# of elements per data block page must be greater than # of elements in index block") /* Compute the number of elements in data blocks for first actual super block */ sblk_idx = H5EA_SBLK_FIRST_IDX(cparam->sup_blk_min_data_ptrs); dblk_nelmts = H5EA_SBLK_DBLK_NELMTS(sblk_idx, cparam->data_blk_min_elmts); if(dblk_page_nelmts < dblk_nelmts) - H5E_THROW(H5E_BADVALUE, "max. # of elements per data block page bits must be > # of elements in first data block from super block") + H5E_THROW(H5E_BADVALUE, "max. # of elements per data block page bits must be > # of elements in first data block from super block") if(cparam->max_dblk_page_nelmts_bits > cparam->max_nelmts_bits) - H5E_THROW(H5E_BADVALUE, "max. # of elements per data block page bits must be <= max. # of elements bits") + H5E_THROW(H5E_BADVALUE, "max. # of elements per data block page bits must be <= max. # of elements bits") } #endif /* NDEBUG */ /* Allocate space for the shared information */ if(NULL == (hdr = H5EA__hdr_alloc(f))) - H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array shared header") + H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array shared header") /* Set the internal parameters for the array */ hdr->idx_blk_addr = HADDR_UNDEF; @@ -428,15 +428,15 @@ HDfprintf(stderr, "%s: Called\n", FUNC); /* Finish initializing extensible array header */ if(H5EA__hdr_init(hdr, ctx_udata) < 0) - H5E_THROW(H5E_CANTINIT, "initialization failed for extensible array header") + H5E_THROW(H5E_CANTINIT, "initialization failed for extensible array header") /* Allocate space for the header on disk */ if(HADDR_UNDEF == (hdr->addr = H5MF_alloc(f, H5FD_MEM_EARRAY_HDR, dxpl_id, (hsize_t)hdr->size))) - H5E_THROW(H5E_CANTALLOC, "file allocation failed for extensible array header") + H5E_THROW(H5E_CANTALLOC, "file allocation failed for extensible array header") /* Cache the new extensible array header */ if(H5AC_insert_entry(f, dxpl_id, H5AC_EARRAY_HDR, hdr->addr, hdr, H5AC__NO_FLAGS_SET) < 0) - H5E_THROW(H5E_CANTINSERT, "can't add extensible array header to cache") + H5E_THROW(H5E_CANTINSERT, "can't add extensible array header to cache") /* Set address of array header to return */ ret_value = hdr->addr; @@ -616,7 +616,7 @@ END_FUNC(PKG) /* end H5EA__hdr_modified() */ * * Purpose: Convenience wrapper around protecting extensible array header * - * Return: Non-NULL pointer to index block on success/NULL on failure + * Return: Non-NULL pointer to header on success/NULL on failure * * Programmer: Quincey Koziol * koziol@hdfgroup.org @@ -647,6 +647,7 @@ H5EA__hdr_protect(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr, void *ctx_udata, /* Protect the header */ if(NULL == (ret_value = (H5EA_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_EARRAY_HDR, ea_addr, &udata, flags))) H5E_THROW(H5E_CANTPROTECT, "unable to protect extensible array header, address = %llu", (unsigned long long)ea_addr) + ret_value->f = f; /* (Must be set again here, in case the header was already in the cache -QAK) */ CATCH diff --git a/src/H5EAiblock.c b/src/H5EAiblock.c index 3f49d0d..623ae30 100644 --- a/src/H5EAiblock.c +++ b/src/H5EAiblock.c @@ -432,7 +432,6 @@ END_FUNC(PKG) /* end H5EA__iblock_delete() */ * *------------------------------------------------------------------------- */ -/* ARGSUSED */ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL, H5EA__iblock_dest(H5EA_iblock_t *iblock)) diff --git a/src/H5EAsblock.c b/src/H5EAsblock.c index 7753f0e..f775484 100644 --- a/src/H5EAsblock.c +++ b/src/H5EAsblock.c @@ -409,7 +409,6 @@ END_FUNC(PKG) /* end H5EA__sblock_delete() */ * *------------------------------------------------------------------------- */ -/* ARGSUSED */ BEGIN_FUNC(PKG, ERR, herr_t, SUCCEED, FAIL, H5EA__sblock_dest(H5EA_sblock_t *sblock)) diff --git a/src/H5Eint.c b/src/H5Eint.c index 6e84a09..6ed405f 100644 --- a/src/H5Eint.c +++ b/src/H5Eint.c @@ -743,8 +743,13 @@ H5E_printf_stack(H5E_t *estack, const char *file, const char *func, unsigned lin done: if(va_started) va_end(ap); +#ifdef H5_HAVE_VASPRINTF + if(tmp) + HDfree(tmp); +#else /* H5_HAVE_VASPRINTF */ if(tmp) H5MM_xfree(tmp); +#endif /* H5_HAVE_VASPRINTF */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5E_printf_stack() */ diff --git a/src/H5FAhdr.c b/src/H5FAhdr.c index 62b1837..ac9a103 100644 --- a/src/H5FAhdr.c +++ b/src/H5FAhdr.c @@ -397,7 +397,7 @@ END_FUNC(PKG) /* end H5FA__hdr_modified() */ * * Purpose: Convenience wrapper around protecting fixed array header * - * Return: Non-NULL pointer to index block on success/NULL on failure + * Return: Non-NULL pointer to header on success/NULL on failure * * Programmer: Quincey Koziol * koziol@hdfgroup.org @@ -428,6 +428,7 @@ H5FA__hdr_protect(H5F_t *f, hid_t dxpl_id, haddr_t fa_addr, void *ctx_udata, /* Protect the header */ if(NULL == (ret_value = (H5FA_hdr_t *)H5AC_protect(f, dxpl_id, H5AC_FARRAY_HDR, fa_addr, &udata, flags))) H5E_THROW(H5E_CANTPROTECT, "unable to protect fixed array header, address = %llu", (unsigned long long)fa_addr) + ret_value->f = f; /* (Must be set again here, in case the header was already in the cache -QAK) */ CATCH diff --git a/src/H5FDfamily.c b/src/H5FDfamily.c index 310b72f..b92a685 100644 --- a/src/H5FDfamily.c +++ b/src/H5FDfamily.c @@ -861,7 +861,6 @@ H5FD_family_cmp(const H5FD_t *_f1, const H5FD_t *_f2) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5FD_family_query(const H5FD_t * _file, unsigned long *flags /* out */) { diff --git a/src/H5FDlog.c b/src/H5FDlog.c index a8228e0..4bb72ce 100644 --- a/src/H5FDlog.c +++ b/src/H5FDlog.c @@ -406,7 +406,7 @@ H5FD_log_fapl_copy(const void *_old_fa) /* Deep copy the log file name */ if(old_fa->logfile != NULL) - if(NULL == (new_fa->logfile = H5MM_xstrdup(old_fa->logfile))) + if(NULL == (new_fa->logfile = H5MM_strdup(old_fa->logfile))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate log file name") /* Set return value */ @@ -416,7 +416,7 @@ done: if(NULL == ret_value) if(new_fa) { if(new_fa->logfile) - H5MM_free(new_fa->logfile); + new_fa->logfile = H5MM_xfree(new_fa->logfile); H5MM_free(new_fa); } /* end if */ @@ -445,7 +445,7 @@ H5FD_log_fapl_free(void *_fa) /* Free the fapl information */ if(fa->logfile) - H5MM_xfree(fa->logfile); + fa->logfile = H5MM_xfree(fa->logfile); H5MM_xfree(fa); FUNC_LEAVE_NOAPI(SUCCEED) @@ -594,7 +594,7 @@ H5FD_log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr) /* Get the flags for logging */ file->fa.flags = fa->flags; if(fa->logfile) - file->fa.logfile = HDstrdup(fa->logfile); + file->fa.logfile = H5MM_strdup(fa->logfile); else file->fa.logfile = NULL; file->fa.buf_size = fa->buf_size; @@ -798,10 +798,8 @@ H5FD_log_close(H5FD_t *_file) HDfclose(file->logfp); } /* end if */ - if(file->fa.logfile) { - HDfree(file->fa.logfile); - file->fa.logfile = NULL; - } + if(file->fa.logfile) + file->fa.logfile = H5MM_xfree(file->fa.logfile); /* Release the file info */ file = H5FL_FREE(H5FD_log_t, file); diff --git a/src/H5Fint.c b/src/H5Fint.c index 4e44bcb..0c4ffb9 100644 --- a/src/H5Fint.c +++ b/src/H5Fint.c @@ -130,7 +130,7 @@ H5F_get_access_plist(H5F_t *f, hbool_t app_ref) H5FD_driver_prop_t driver_prop; /* Property for driver ID & info */ hbool_t driver_prop_copied = FALSE; /* Whether the driver property has been set up */ unsigned efc_size = 0; - hid_t ret_value = SUCCEED; + hid_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -1062,6 +1062,7 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id, if(H5G_mkroot(file, dxpl_id, TRUE) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "unable to create/open root group") } else if (1 == shared->nrefs) { + /* Read the superblock if it hasn't been read before. */ if(H5F__super_read(file, dxpl_id) < 0) HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock") @@ -1109,8 +1110,8 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id, done: if(!ret_value && file) - if(H5F_dest(file, dxpl_id, FALSE) < 0) - HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, NULL, "problems closing file") + if(H5F_dest(file, dxpl_id, FALSE) < 0) + HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, NULL, "problems closing file") FUNC_LEAVE_NOAPI(ret_value) } /* end H5F_open() */ diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 2d61a4c..be4acb7 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -646,8 +646,7 @@ H5_DLL hid_t H5F_get_driver_id(const H5F_t *f); H5_DLL herr_t H5F_get_fileno(const H5F_t *f, unsigned long *filenum); H5_DLL hbool_t H5F_has_feature(const H5F_t *f, unsigned feature); H5_DLL haddr_t H5F_get_eoa(const H5F_t *f, H5FD_mem_t type); -H5_DLL herr_t H5F_get_vfd_handle(const H5F_t *file, hid_t fapl, - void **file_handle); +H5_DLL herr_t H5F_get_vfd_handle(const H5F_t *file, hid_t fapl, void **file_handle); /* Functions that check file mounting information */ H5_DLL hbool_t H5F_is_mount(const H5F_t *file); diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c index c6b1c83..332dfa6 100644 --- a/src/H5Fsuper.c +++ b/src/H5Fsuper.c @@ -296,7 +296,7 @@ H5F__super_read(H5F_t *f, hid_t dxpl_id) /* Make certain we can read the fixed-size portion of the superblock */ if(H5F__set_eoa(f, H5FD_MEM_SUPER, - H5F_SUPERBLOCK_FIXED_SIZE + H5F_SUPERBLOCK_MINIMAL_VARLEN_SIZE) < 0) + (haddr_t)(H5F_SUPERBLOCK_FIXED_SIZE + H5F_SUPERBLOCK_MINIMAL_VARLEN_SIZE)) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "set end of space allocation request failed") /* Set up the user data for cache callbacks */ @@ -510,8 +510,10 @@ H5F__super_read(H5F_t *f, hid_t dxpl_id) HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "driver info message not present") /* Validate and decode driver information */ - if(H5FD_sb_load(f->shared->lf, drvinfo.name, drvinfo.buf) < 0) + if(H5FD_sb_load(f->shared->lf, drvinfo.name, drvinfo.buf) < 0) { + H5O_msg_reset(H5O_DRVINFO_ID, &drvinfo); HGOTO_ERROR(H5E_FILE, H5E_CANTDECODE, FAIL, "unable to decode driver information") + } /* end if */ /* Reset driver info message */ H5O_msg_reset(H5O_DRVINFO_ID, &drvinfo); diff --git a/src/H5Gbtree2.c b/src/H5Gbtree2.c index b464930..1a99b12 100644 --- a/src/H5Gbtree2.c +++ b/src/H5Gbtree2.c @@ -114,9 +114,7 @@ const H5B2_class_t H5G_BT2_NAME[1]={{ /* B-tree class information */ H5G_dense_btree2_name_compare, /* Record comparison callback */ H5G_dense_btree2_name_encode, /* Record encoding callback */ H5G_dense_btree2_name_decode, /* Record decoding callback */ - H5G_dense_btree2_name_debug, /* Record debugging callback */ - NULL, /* Create debugging context */ - NULL /* Destroy debugging context */ + H5G_dense_btree2_name_debug /* Record debugging callback */ }}; /* v2 B-tree class for indexing 'creation order' field of links */ @@ -130,9 +128,7 @@ const H5B2_class_t H5G_BT2_CORDER[1]={{ /* B-tree class information */ H5G_dense_btree2_corder_compare, /* Record comparison callback */ H5G_dense_btree2_corder_encode, /* Record encoding callback */ H5G_dense_btree2_corder_decode, /* Record decoding callback */ - H5G_dense_btree2_corder_debug, /* Record debugging callback */ - NULL, /* Create debugging context */ - NULL /* Destroy debugging context */ + H5G_dense_btree2_corder_debug /* Record debugging callback */ }}; /*****************************/ diff --git a/src/H5HFbtree2.c b/src/H5HFbtree2.c index d82de93..a79bf58 100644 --- a/src/H5HFbtree2.c +++ b/src/H5HFbtree2.c @@ -71,7 +71,6 @@ typedef struct H5HF_huge_bt2_ctx_t { /* Common callbacks */ static void *H5HF__huge_bt2_crt_context(void *udata); static herr_t H5HF__huge_bt2_dst_context(void *ctx); -static void *H5HF__huge_bt2_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t addr); /* Callbacks for indirect objects */ static herr_t H5HF__huge_bt2_indir_store(void *native, const void *udata); @@ -127,9 +126,7 @@ const H5B2_class_t H5HF_HUGE_BT2_INDIR[1]={{ /* B-tree class information */ H5HF__huge_bt2_indir_compare, /* Record comparison callback */ H5HF__huge_bt2_indir_encode, /* Record encoding callback */ H5HF__huge_bt2_indir_decode, /* Record decoding callback */ - H5HF__huge_bt2_indir_debug, /* Record debugging callback */ - H5HF__huge_bt2_crt_dbg_context, /* Create debugging context */ - H5HF__huge_bt2_dst_context /* Destroy debugging context */ + H5HF__huge_bt2_indir_debug /* Record debugging callback */ }}; /* v2 B-tree class for indirectly accessed, filtered 'huge' objects */ @@ -143,9 +140,7 @@ const H5B2_class_t H5HF_HUGE_BT2_FILT_INDIR[1]={{ /* B-tree class information */ H5HF__huge_bt2_filt_indir_compare, /* Record comparison callback */ H5HF__huge_bt2_filt_indir_encode, /* Record encoding callback */ H5HF__huge_bt2_filt_indir_decode, /* Record decoding callback */ - H5HF__huge_bt2_filt_indir_debug, /* Record debugging callback */ - H5HF__huge_bt2_crt_dbg_context, /* Create debugging context */ - H5HF__huge_bt2_dst_context /* Destroy debugging context */ + H5HF__huge_bt2_filt_indir_debug /* Record debugging callback */ }}; /* v2 B-tree class for directly accessed 'huge' objects */ @@ -159,9 +154,7 @@ const H5B2_class_t H5HF_HUGE_BT2_DIR[1]={{ /* B-tree class information */ H5HF__huge_bt2_dir_compare, /* Record comparison callback */ H5HF__huge_bt2_dir_encode, /* Record encoding callback */ H5HF__huge_bt2_dir_decode, /* Record decoding callback */ - H5HF__huge_bt2_dir_debug, /* Record debugging callback */ - H5HF__huge_bt2_crt_dbg_context, /* Create debugging context */ - H5HF__huge_bt2_dst_context /* Destroy debugging context */ + H5HF__huge_bt2_dir_debug /* Record debugging callback */ }}; /* v2 B-tree class for directly accessed, filtered 'huge' objects */ @@ -175,9 +168,7 @@ const H5B2_class_t H5HF_HUGE_BT2_FILT_DIR[1]={{ /* B-tree class information */ H5HF__huge_bt2_filt_dir_compare, /* Record comparison callback */ H5HF__huge_bt2_filt_dir_encode, /* Record encoding callback */ H5HF__huge_bt2_filt_dir_decode, /* Record decoding callback */ - H5HF__huge_bt2_filt_dir_debug, /* Record debugging callback */ - H5HF__huge_bt2_crt_dbg_context, /* Create debugging context */ - H5HF__huge_bt2_dst_context /* Destroy debugging context */ + H5HF__huge_bt2_filt_dir_debug /* Record debugging callback */ }}; /*****************************/ @@ -270,46 +261,6 @@ H5HF__huge_bt2_dst_context(void *_ctx) /*------------------------------------------------------------------------- - * Function: H5HF__huge_bt2_crt_dbg_context - * - * Purpose: Create context for debugging callback - * - * Return: Success: non-NULL - * Failure: NULL - * - * Programmer: Quincey Koziol - * Tuesday, December 1, 2009 - * - *------------------------------------------------------------------------- - */ -static void * -H5HF__huge_bt2_crt_dbg_context(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t H5_ATTR_UNUSED addr) -{ - H5HF_huge_bt2_ctx_t *ctx; /* Callback context structure */ - void *ret_value = NULL; /* Return value */ - - FUNC_ENTER_STATIC - - /* Sanity check */ - HDassert(f); - - /* Allocate callback context */ - if(NULL == (ctx = H5FL_MALLOC(H5HF_huge_bt2_ctx_t))) - HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, NULL, "can't allocate callback context") - - /* Determine the size of addresses & lengths in the file */ - ctx->sizeof_addr = H5F_SIZEOF_ADDR(f); - ctx->sizeof_size = H5F_SIZEOF_SIZE(f); - - /* Set return value */ - ret_value = ctx; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5HF__huge_bt2_crt_dbg_context() */ - - -/*------------------------------------------------------------------------- * Function: H5HF__huge_bt2_indir_found * * Purpose: Retrieve record for indirectly accessed 'huge' object, when @@ -93,6 +93,17 @@ typedef struct { hid_t dxpl_id; /* Dataset transfer property list */ } H5L_trav_mv2_t; +/* User data for path traversal routine for checking if a link exists */ +typedef struct { + /* Down */ + char *sep; /* Pointer to next separator in the string */ + hid_t lapl_id; /* Link access property list */ + hid_t dxpl_id; /* Dataset transfer property list */ + + /* Up */ + hbool_t exists; /* Whether the link exists or not */ +} H5L_trav_le_t; + /* User data for path traversal routine for getting link value */ typedef struct { size_t size; /* Size of user buffer */ @@ -170,10 +181,13 @@ static herr_t H5L_move_cb(H5G_loc_t *grp_loc/*in*/, const char *name, static herr_t H5L_move_dest_cb(H5G_loc_t *grp_loc/*in*/, const char *name, const H5O_link_t *lnk, H5G_loc_t *obj_loc, void *_udata/*in,out*/, H5G_own_loc_t *own_loc/*out*/); -static herr_t H5L_exists_cb(H5G_loc_t *grp_loc/*in*/, const char *name, +static herr_t H5L__exists_final_cb(H5G_loc_t *grp_loc/*in*/, const char *name, + const H5O_link_t *lnk, H5G_loc_t *obj_loc, void *_udata/*in,out*/, + H5G_own_loc_t *own_loc/*out*/); +static herr_t H5L__exists_inter_cb(H5G_loc_t *grp_loc/*in*/, const char *name, const H5O_link_t *lnk, H5G_loc_t *obj_loc, void *_udata/*in,out*/, H5G_own_loc_t *own_loc/*out*/); -static htri_t H5L_exists(const H5G_loc_t *loc, const char *name, hid_t lapl_id, +static htri_t H5L__exists(const H5G_loc_t *loc, const char *name, hid_t lapl_id, hid_t dxpl_id); static herr_t H5L_get_info_cb(H5G_loc_t *grp_loc/*in*/, const char *name, const H5O_link_t *lnk, H5G_loc_t *obj_loc, void *_udata/*in,out*/, @@ -859,7 +873,7 @@ H5Lexists(hid_t loc_id, const char *name, hid_t lapl_id) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set access and transfer property lists") /* Check for the existence of the link */ - if((ret_value = H5L_exists(&loc, name, lapl_id, dxpl_id)) < 0) + if((ret_value = H5L__exists(&loc, name, lapl_id, dxpl_id)) < 0) HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, FAIL, "unable to get link info") done: @@ -2752,9 +2766,10 @@ done: /*------------------------------------------------------------------------- - * Function: H5L_exists_cb + * Function: H5L__exists_final_cb * - * Purpose: Callback for checking whether a link exists + * Purpose: Callback for checking whether a link exists, as the final + * component of a path * * Return: Non-negative on success/Negative on failure * @@ -2764,30 +2779,162 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5L_exists_cb(H5G_loc_t H5_ATTR_UNUSED *grp_loc/*in*/, const char H5_ATTR_UNUSED *name, +H5L__exists_final_cb(H5G_loc_t H5_ATTR_UNUSED *grp_loc/*in*/, const char H5_ATTR_UNUSED *name, const H5O_link_t *lnk, H5G_loc_t H5_ATTR_UNUSED *obj_loc, void *_udata/*in,out*/, H5G_own_loc_t *own_loc/*out*/) { - hbool_t *udata = (hbool_t *)_udata; /* User data passed in */ + H5L_trav_le_t *udata = (H5L_trav_le_t *)_udata; /* User data passed in */ - FUNC_ENTER_NOAPI_NOINIT_NOERR + FUNC_ENTER_STATIC_NOERR /* Check if the name in this group resolved to a valid link */ - *udata = (hbool_t)(lnk != NULL); + udata->exists = (hbool_t)(lnk != NULL); /* Indicate that this callback didn't take ownership of the group * * location for the object */ *own_loc = H5G_OWN_NONE; FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5L_exists_cb() */ +} /* end H5L__exists_final_cb() */ /*------------------------------------------------------------------------- - * Function: H5L_exists + * Function: H5L__exists_inter_cb + * + * Purpose: Callback for checking whether a link exists, as an intermediate + * component of a path + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, December 31 2015 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5L__exists_inter_cb(H5G_loc_t H5_ATTR_UNUSED *grp_loc/*in*/, const char H5_ATTR_UNUSED *name, + const H5O_link_t *lnk, H5G_loc_t *obj_loc, void *_udata/*in,out*/, + H5G_own_loc_t *own_loc/*out*/) +{ + H5L_trav_le_t *udata = (H5L_trav_le_t *)_udata; /* User data passed in */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Check if the name in this group resolved to a valid link */ + if(lnk != NULL) { + /* Check for more components to the path */ + if(udata->sep) { + H5G_traverse_t cb_func; /* Callback function for tranversal */ + char *next; /* Pointer to next component name */ + + /* Look for another separator */ + next = udata->sep; + if(NULL == (udata->sep = HDstrchr(udata->sep, '/'))) + cb_func = H5L__exists_final_cb; + else { + /* Chew through adjacent separators, if present */ + do { + *udata->sep = '\0'; + udata->sep++; + } while('/' == *udata->sep); + cb_func = H5L__exists_inter_cb; + } /* end else */ + if(H5G_traverse(obj_loc, next, H5G_TARGET_SLINK | H5G_TARGET_UDLINK, cb_func, udata, udata->lapl_id, udata->dxpl_id) < 0) + HGOTO_ERROR(H5E_SYM, H5E_CANTGET, FAIL, "can't determine if link exists") + } /* end if */ + else + udata->exists = TRUE; + } /* end if */ + else + udata->exists = FALSE; + + /* Indicate that this callback didn't take ownership of the group * + * location for the object */ + *own_loc = H5G_OWN_NONE; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5L__exists_inter_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5L_exists_tolerant * * Purpose: Returns whether a link exists in a group * + * Note: Same as H5L_exists, except that missing links are reported + * as 'FALSE' instead of causing failures + * + * Return: Non-negative (TRUE/FALSE) on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, December 31 2015 + * + *------------------------------------------------------------------------- + */ +htri_t +H5L_exists_tolerant(const H5G_loc_t *loc, const char *name, hid_t lapl_id, hid_t dxpl_id) +{ + H5L_trav_le_t udata; /* User data for traversal */ + H5G_traverse_t cb_func; /* Callback function for tranversal */ + char *name_copy = NULL; /* Duplicate of name */ + char *name_trav; /* Name to traverse */ + htri_t ret_value = FAIL; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Sanity checks */ + HDassert(loc); + HDassert(name); + + /* Copy the name and skip leading '/'s */ + name_trav = name_copy = H5MM_strdup(name); + while('/' == *name_trav) + name_trav++; + + /* A path of "/" will always exist in a file */ + if('\0' == *name_trav) + HGOTO_DONE(TRUE) + + /* Set up user data & correct callback */ + udata.lapl_id = lapl_id; + udata.dxpl_id = dxpl_id; + udata.exists = FALSE; + if(NULL == (udata.sep = HDstrchr(name_trav, '/'))) + cb_func = H5L__exists_final_cb; + else { + /* Chew through adjacent separators, if present */ + do { + *udata.sep = '\0'; + udata.sep++; + } while('/' == *udata.sep); + cb_func = H5L__exists_inter_cb; + } /* end else */ + + /* Traverse the group hierarchy to locate the link to check */ + if(H5G_traverse(loc, name_trav, H5G_TARGET_SLINK | H5G_TARGET_UDLINK, cb_func, &udata, lapl_id, dxpl_id) < 0) + HGOTO_ERROR(H5E_SYM, H5E_CANTGET, FAIL, "can't determine if link exists") + + /* Set return value */ + ret_value = (htri_t)udata.exists; + +done: + /* Release duplicated string */ + H5MM_xfree(name_copy); + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5L_exists_tolerant() */ + + +/*------------------------------------------------------------------------- + * Function: H5L__exists + * + * Purpose: Returns whether a link exists in a group + * + * Note: Same as H5L_exists_tolerant, except that missing links are reported + * as failures + * * Return: Non-negative (TRUE/FALSE) on success/Negative on failure * * Programmer: Quincey Koziol @@ -2796,23 +2943,28 @@ H5L_exists_cb(H5G_loc_t H5_ATTR_UNUSED *grp_loc/*in*/, const char H5_ATTR_UNUSED *------------------------------------------------------------------------- */ static htri_t -H5L_exists(const H5G_loc_t *loc, const char *name, hid_t lapl_id, hid_t dxpl_id) +H5L__exists(const H5G_loc_t *loc, const char *name, hid_t lapl_id, hid_t dxpl_id) { - hbool_t exists = FALSE; /* Whether the link exists in the group */ + H5L_trav_le_t udata; /* User data for traversal */ htri_t ret_value = FAIL; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC + + /* A path of "/" will always exist in a file */ + if(0 == HDstrcmp(name, "/")) + HGOTO_DONE(TRUE) /* Traverse the group hierarchy to locate the object to get info about */ - if(H5G_traverse(loc, name, H5G_TARGET_SLINK|H5G_TARGET_UDLINK, H5L_exists_cb, &exists, lapl_id, dxpl_id) < 0) + udata.exists = FALSE; + if(H5G_traverse(loc, name, H5G_TARGET_SLINK | H5G_TARGET_UDLINK, H5L__exists_final_cb, &udata, lapl_id, dxpl_id) < 0) HGOTO_ERROR(H5E_SYM, H5E_EXISTS, FAIL, "path doesn't exist") /* Set return value */ - ret_value = (htri_t)exists; + ret_value = (htri_t)udata.exists; done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5L_exists() */ +} /* H5L__exists() */ /*------------------------------------------------------------------------- diff --git a/src/H5Lprivate.h b/src/H5Lprivate.h index f3079bc..1c8690b 100644 --- a/src/H5Lprivate.h +++ b/src/H5Lprivate.h @@ -81,6 +81,8 @@ H5_DLL hid_t H5L_get_default_lcpl(void); H5_DLL herr_t H5L_move(H5G_loc_t *src_loc, const char *src_name, H5G_loc_t *dst_loc, const char *dst_name, hbool_t copy_flag, hid_t lcpl_id, hid_t lapl_id, hid_t dxpl_id); +H5_DLL htri_t H5L_exists_tolerant(const H5G_loc_t *loc, const char *name, hid_t lapl_id, + hid_t dxpl_id); H5_DLL herr_t H5L_get_info(const H5G_loc_t *loc, const char *name, H5L_info_t *linkbuf/*out*/, hid_t lapl_id, hid_t dxpl_id); H5_DLL herr_t H5L_delete(H5G_loc_t *loc, const char *name, hid_t lapl_id, @@ -25,9 +25,225 @@ */ -#include "H5private.h" -#include "H5Eprivate.h" -#include "H5MMprivate.h" +/****************/ +/* Module Setup */ +/****************/ + + +/***********/ +/* Headers */ +/***********/ +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5MMprivate.h" /* Memory management */ + + +/****************/ +/* Local Macros */ +/****************/ +#if defined H5_MEMORY_ALLOC_SANITY_CHECK +#define H5MM_SIG_SIZE 4 +#define H5MM_HEAD_GUARD_SIZE 8 +#define H5MM_TAIL_GUARD_SIZE 8 +#define H5MM_BLOCK_FROM_BUF(mem) ((H5MM_block_t *)((unsigned char *)mem - (offsetof(H5MM_block_t, b) + H5MM_HEAD_GUARD_SIZE))) +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + + +/******************/ +/* Local Typedefs */ +/******************/ + +#if defined H5_MEMORY_ALLOC_SANITY_CHECK +/* Memory allocation "block", wrapped around each allocation */ +struct H5MM_block_t; /* Forward declaration for typedef */ +typedef struct H5MM_block_t { + unsigned char sig[H5MM_SIG_SIZE]; /* Signature for the block, to indicate it was allocated with H5MM* interface */ + struct H5MM_block_t *next; /* Pointer to next block in the list of allocated blocks */ + struct H5MM_block_t *prev; /* Pointer to previous block in the list of allocated blocks */ + union { + struct { + size_t size; /* Size of allocated block */ + hbool_t in_use; /* Whether the block is in use or is free */ + } info; + double _align; /* Align following buffer (b) to double boundary (unused) */ + } u; + unsigned char b[]; /* Buffer for caller (includes header and footer) */ +} H5MM_block_t; +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + + +/********************/ +/* Local Prototypes */ +/********************/ +#if defined H5_MEMORY_ALLOC_SANITY_CHECK +static hbool_t H5MM__is_our_block(void *mem); +static void H5MM__sanity_check_block(const H5MM_block_t *block); +static void H5MM__sanity_check(void *mem); +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + + +/*********************/ +/* Package Variables */ +/*********************/ + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*******************/ +/* Local Variables */ +/*******************/ + +#if defined H5_MEMORY_ALLOC_SANITY_CHECK +/* Constant strings for block signature, head & tail guards */ +static const char H5MM_block_signature_s[H5MM_SIG_SIZE] = {'H', '5', 'M', 'M'}; +static const char H5MM_block_head_guard_s[H5MM_HEAD_GUARD_SIZE] = {'D', 'E', 'A', 'D', 'B', 'E', 'E', 'F'}; +static const char H5MM_block_tail_guard_s[H5MM_TAIL_GUARD_SIZE] = {'B', 'E', 'E', 'F', 'D', 'E', 'A', 'D'}; + +/* Flag to indicate the the interface has been initialized */ +static hbool_t H5MM_init_s = FALSE; + +/* Head of the list of allocated blocks */ +static H5MM_block_t H5MM_block_head_s; + +/* Statistics about block allocations */ +static unsigned long long H5MM_total_alloc_bytes_s = 0; +static unsigned long long H5MM_curr_alloc_bytes_s = 0; +static unsigned long long H5MM_peak_alloc_bytes_s = 0; +static size_t H5MM_max_block_size_s = 0; +static size_t H5MM_total_alloc_blocks_count_s = 0; +static size_t H5MM_curr_alloc_blocks_count_s = 0; +static size_t H5MM_peak_alloc_blocks_count_s = 0; +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + + +#if defined H5_MEMORY_ALLOC_SANITY_CHECK + +/*------------------------------------------------------------------------- + * Function: H5MM__is_our_block + * + * Purpose: Try to determine if a memory buffer has been allocated through + * the H5MM* interface, instead of the system's malloc() routines. + * + * Return: Success: TRUE/FALSE + * Failure: (Can't fail) + * + * Programmer: Quincey Koziol + * Dec 30 2015 + * + *------------------------------------------------------------------------- + */ +static hbool_t +H5MM__is_our_block(void *mem) +{ + H5MM_block_t *block = H5MM_BLOCK_FROM_BUF(mem); + + return(0 == HDmemcmp(block->sig, H5MM_block_signature_s, H5MM_SIG_SIZE)); +} + + +/*------------------------------------------------------------------------- + * Function: H5MM__sanity_check_block + * + * Purpose: Check a block wrapper around a buffer to validate it. + * + * Return: N/A (void) + * + * Programmer: Quincey Koziol + * Dec 30 2015 + * + *------------------------------------------------------------------------- + */ +static void +H5MM__sanity_check_block(const H5MM_block_t *block) +{ + HDassert(block->u.info.size > 0); + HDassert(block->u.info.in_use); + /* Check for head & tail guards, if not head of linked list */ + if(block->u.info.size != SIZET_MAX) { + HDassert(0 == HDmemcmp(block->b, H5MM_block_head_guard_s, H5MM_HEAD_GUARD_SIZE)); + HDassert(0 == HDmemcmp(block->b + H5MM_HEAD_GUARD_SIZE + block->u.info.size, H5MM_block_tail_guard_s, H5MM_TAIL_GUARD_SIZE)); + } +} + + +/*------------------------------------------------------------------------- + * Function: H5MM__sanity_check + * + * Purpose: Check a buffer to validate it (just calls + * H5MM__sanity_check_block after finding block for buffer) + * + * Return: N/A (void) + * + * Programmer: Quincey Koziol + * Dec 30 2015 + * + *------------------------------------------------------------------------- + */ +static void +H5MM__sanity_check(void *mem) +{ + H5MM_block_t *block = H5MM_BLOCK_FROM_BUF(mem); + + H5MM__sanity_check_block(block); +} + + +/*------------------------------------------------------------------------- + * Function: H5MM_sanity_check_all + * + * Purpose: Sanity check all current memory allocations. + * + * Return: N/A (void) + * + * Programmer: Quincey Koziol + * Jan 5 2016 + * + *------------------------------------------------------------------------- + */ +void +H5MM_sanity_check_all(void) +{ + H5MM_block_t *curr; + + curr = H5MM_block_head_s.next; + while(curr != &H5MM_block_head_s) { + H5MM__sanity_check_block(curr); + curr = curr->next; + } /* end while */ +} /* end H5MM_sanity_check_all() */ + + +/*------------------------------------------------------------------------- + * Function: H5MM_final_sanity_check + * + * Purpose: Final sanity checks on memory allocation. + * + * Return: N/A (void) + * + * Programmer: Quincey Koziol + * Jan 1 2016 + * + *------------------------------------------------------------------------- + */ +void +H5MM_final_sanity_check(void) +{ + HDassert(0 == H5MM_curr_alloc_bytes_s); + HDassert(0 == H5MM_curr_alloc_blocks_count_s); + HDassert(H5MM_block_head_s.next == &H5MM_block_head_s); + HDassert(H5MM_block_head_s.prev == &H5MM_block_head_s); +#ifdef H5MM_PRINT_MEMORY_STATS + HDfprintf(stderr, "%s: H5MM_total_alloc_bytes_s = %llu\n", __func__, H5MM_total_alloc_bytes_s); + HDfprintf(stderr, "%s: H5MM_peak_alloc_bytes_s = %llu\n", __func__, H5MM_peak_alloc_bytes_s); + HDfprintf(stderr, "%s: H5MM_max_block_size_s = %zu\n", __func__, H5MM_max_block_size_s); + HDfprintf(stderr, "%s: H5MM_total_alloc_blocks_count_s = %zu\n", __func__, H5MM_total_alloc_blocks_count_s); + HDfprintf(stderr, "%s: H5MM_peak_alloc_blocks_count_s = %zu\n", __func__, H5MM_peak_alloc_blocks_count_s); +#endif /* H5MM_PRINT_MEMORY_STATS */ +} +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ /*------------------------------------------------------------------------- @@ -42,7 +258,6 @@ * bytes usually indicate problems. * * Return: Success: Pointer new memory - * * Failure: NULL * * Programmer: Quincey Koziol @@ -60,12 +275,61 @@ H5MM_malloc(size_t size) /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOERR - if(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_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; + H5MM_block_head_s.u.info.in_use = TRUE; + + H5MM_init_s = TRUE; + } /* end if */ +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + + if(size) { +#if defined H5_MEMORY_ALLOC_SANITY_CHECK + H5MM_block_t *block; + size_t alloc_size = sizeof(H5MM_block_t) + size + H5MM_HEAD_GUARD_SIZE + H5MM_TAIL_GUARD_SIZE; + + if(NULL != (block = (H5MM_block_t *)HDmalloc(alloc_size))) { + /* Set up block */ + HDmemcpy(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); + + /* Update statistics */ + H5MM_total_alloc_bytes_s += size; + H5MM_curr_alloc_bytes_s += size; + if(H5MM_curr_alloc_bytes_s > H5MM_peak_alloc_bytes_s) + H5MM_peak_alloc_bytes_s = H5MM_curr_alloc_bytes_s; + if(size > H5MM_max_block_size_s) + H5MM_max_block_size_s = size; + H5MM_total_alloc_blocks_count_s++; + H5MM_curr_alloc_blocks_count_s++; + if(H5MM_curr_alloc_blocks_count_s > H5MM_peak_alloc_blocks_count_s) + H5MM_peak_alloc_blocks_count_s = H5MM_curr_alloc_blocks_count_s; + + /* Set buffer to return */ + ret_value = block->b + H5MM_HEAD_GUARD_SIZE; + } /* end if */ + else + ret_value = NULL; +#else /* H5_MEMORY_ALLOC_SANITY_CHECK */ ret_value = HDmalloc(size); +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + } /* end if */ else ret_value = NULL; - FUNC_LEAVE_NOAPI(ret_value); + FUNC_LEAVE_NOAPI(ret_value) } /* end H5MM_malloc() */ @@ -83,7 +347,6 @@ H5MM_malloc(size_t size) * * * Return: Success: Pointer new memory - * * Failure: NULL * * Programmer: Quincey Koziol @@ -101,12 +364,18 @@ H5MM_calloc(size_t size) /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOERR - if(size) + if(size) { +#if defined H5_MEMORY_ALLOC_SANITY_CHECK + if(NULL != (ret_value = H5MM_malloc(size))) + HDmemset(ret_value, 0, size); +#else /* H5_MEMORY_ALLOC_SANITY_CHECK */ ret_value = HDcalloc((size_t)1, size); +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + } /* end if */ else ret_value = NULL; - FUNC_LEAVE_NOAPI(ret_value); + FUNC_LEAVE_NOAPI(ret_value) } /* end H5MM_calloc() */ @@ -123,9 +392,7 @@ H5MM_calloc(size_t size) * Note that the (NULL, 0) combination is undefined behavior * in the C standard. * - * Return: Success: Ptr to new memory if size > 0 - * NULL if size is zero - * + * Return: Success: Ptr to new memory if size > 0, NULL if size is zero * Failure: NULL (input buffer is unchanged on failure) * * Programmer: Robb Matzke @@ -143,17 +410,39 @@ H5MM_realloc(void *mem, size_t size) HDassert(mem || size); - if(NULL == mem && 0 == size) { + if(NULL == mem && 0 == size) /* Not defined in the standard, return NULL */ ret_value = NULL; - } else { +#if defined H5_MEMORY_ALLOC_SANITY_CHECK + if(size > 0) { + if(mem) { + if(H5MM__is_our_block(mem)) { + H5MM_block_t *block = H5MM_BLOCK_FROM_BUF(mem); + size_t old_size = block->u.info.size; + + H5MM__sanity_check(mem); + + ret_value = H5MM_malloc(size); + HDmemcpy(ret_value, mem, MIN(size, old_size)); + H5MM_xfree(mem); + } /* end if */ + else + ret_value = HDrealloc(mem, size); + } + else + ret_value = H5MM_malloc(size); + } + else + ret_value = H5MM_xfree(mem); +#else /* H5_MEMORY_ALLOC_SANITY_CHECK */ ret_value = HDrealloc(mem, size); /* Some platforms do not return NULL if size is zero. */ if(0 == size) ret_value = NULL; - } +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + } /* end else */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5MM_realloc() */ @@ -250,8 +539,38 @@ H5MM_xfree(void *mem) /* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */ FUNC_ENTER_NOAPI_NOINIT_NOERR - if(mem) + if(mem) { +#if defined H5_MEMORY_ALLOC_SANITY_CHECK + if(H5MM__is_our_block(mem)) { + H5MM_block_t *block = H5MM_BLOCK_FROM_BUF(mem); + + /* Run sanity checks on this block and its neighbors */ + H5MM__sanity_check(mem); + H5MM__sanity_check_block(block->next); + H5MM__sanity_check_block(block->prev); + + /* Update statistics */ + H5MM_curr_alloc_bytes_s -= block->u.info.size; + H5MM_curr_alloc_blocks_count_s--; + + /* Reset block info */ + HDmemset(block->sig, 0, H5MM_SIG_SIZE); + block->next->prev = block->prev; + block->prev->next = block->next; + block->next = NULL; + block->prev = NULL; + block->u.info.in_use = FALSE; + + /* Free the block (finally!) */ + HDfree(block); + } + else + HDfree(mem); +#else /* H5_MEMORY_ALLOC_SANITY_CHECK */ HDfree(mem); +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + } /* end if */ - FUNC_LEAVE_NOAPI(NULL); + FUNC_LEAVE_NOAPI(NULL) } /* end H5MM_xfree() */ + diff --git a/src/H5MMprivate.h b/src/H5MMprivate.h index 0d608b2..14bd28d 100644 --- a/src/H5MMprivate.h +++ b/src/H5MMprivate.h @@ -21,8 +21,6 @@ * * Purpose: Private header for memory management. * - * Modifications: - * *------------------------------------------------------------------------- */ #ifndef _H5MMprivate_H @@ -33,7 +31,12 @@ /* Private headers needed by this file */ #include "H5private.h" +#if defined H5_MEMORY_ALLOC_SANITY_CHECK +/*#define H5MM_PRINT_MEMORY_STATS */ +#define H5MM_free(Z) H5MM_xfree(Z) +#else /* H5_MEMORY_ALLOC_SANITY_CHECK */ #define H5MM_free(Z) HDfree(Z) +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ /* * Library prototypes... @@ -44,5 +47,10 @@ 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); +#if defined H5_MEMORY_ALLOC_SANITY_CHECK +H5_DLL void H5MM_sanity_check_all(void); +H5_DLL void H5MM_final_sanity_check(void); +#endif /* H5_MEMORY_ALLOC_SANITY_CHECK */ + +#endif /* _H5MMprivate_H */ -#endif diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c index 02c72e7..70dc560 100644 --- a/src/H5Ocopy.c +++ b/src/H5Ocopy.c @@ -213,10 +213,10 @@ H5Ocopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, /* for opening the destination object */ H5G_name_t src_path; /* Opened source object hier. path */ H5O_loc_t src_oloc; /* Opened source object object location */ + htri_t dst_exists; /* Does destination name exist already? */ hbool_t loc_found = FALSE; /* Location at 'name' found */ hbool_t obj_open = FALSE; /* Entry at 'name' found */ - - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE6("e", "i*si*sii", src_loc_id, src_name, dst_loc_id, dst_name, @@ -233,22 +233,10 @@ H5Ocopy(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id, HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no destination name specified") /* check if destination name already exists */ - { - H5G_name_t tmp_path; - H5O_loc_t tmp_oloc; - H5G_loc_t tmp_loc; - - /* Set up group location */ - tmp_loc.oloc = &tmp_oloc; - tmp_loc.path = &tmp_path; - H5G_loc_reset(&tmp_loc); - - /* Check if object already exists in destination */ - if(H5G_loc_find(&dst_loc, dst_name, &tmp_loc, H5P_DEFAULT, H5AC_ind_dxpl_id) >= 0) { - H5G_name_free(&tmp_path); - HGOTO_ERROR(H5E_SYM, H5E_EXISTS, FAIL, "destination object already exists") - } /* end if */ - } + if((dst_exists = H5L_exists_tolerant(&dst_loc, dst_name, H5P_DEFAULT, H5AC_ind_dxpl_id)) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to check if destination name exists") + if(TRUE == dst_exists) + HGOTO_ERROR(H5E_OHDR, H5E_EXISTS, FAIL, "destination object already exists") /* Set up opened group location to fill in */ src_loc.oloc = &src_oloc; @@ -475,7 +463,7 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out*/, /* Allocate memory for "deleted" array. This array marks the message in * the source that shouldn't be copied to the destination. */ - if(NULL == (deleted = (hbool_t *)HDmalloc(sizeof(hbool_t) * oh_src->nmesgs))) + if(NULL == (deleted = (hbool_t *)H5MM_malloc(sizeof(hbool_t) * oh_src->nmesgs))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") HDmemset(deleted, FALSE, sizeof(hbool_t) * oh_src->nmesgs); @@ -882,7 +870,7 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out*/, done: /* Free deleted array */ if(deleted) - HDfree(deleted); + H5MM_free(deleted); /* Release pointer to source object header and its derived objects */ if(oh_src && H5O_unprotect(oloc_src, dxpl_id, oh_src, H5AC__NO_FLAGS_SET) < 0) diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index 0d77a83..9235d6c 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -506,10 +506,14 @@ typedef struct H5O_storage_t { typedef struct H5O_layout_chunk_t { unsigned ndims; /* Num dimensions in chunk */ uint32_t dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in elements */ + unsigned enc_bytes_per_dim; /* Encoded # of bytes for storing each chunk dimension */ uint32_t size; /* Size of chunk in bytes */ hsize_t nchunks; /* Number of chunks in dataset */ + hsize_t max_nchunks; /* Max. number of chunks in dataset */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* # of chunks in each dataset dimension */ + hsize_t max_chunks[H5O_LAYOUT_NDIMS]; /* # of chunks in each dataset's max. dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ + hsize_t max_down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each max dim */ } H5O_layout_chunk_t; typedef struct H5O_layout_t { @@ -413,9 +413,9 @@ H5PL__init_path_table(void) */ origin_dl_path = HDgetenv("HDF5_PLUGIN_PATH"); if(NULL == origin_dl_path) - dl_path = HDstrdup(H5PL_DEFAULT_PATH); + dl_path = H5MM_strdup(H5PL_DEFAULT_PATH); else - dl_path = HDstrdup(origin_dl_path); + dl_path = H5MM_strdup(origin_dl_path); if(NULL == dl_path) HGOTO_ERROR(H5E_PLUGIN, H5E_CANTALLOC, FAIL, "can't allocate memory for path") @@ -425,7 +425,7 @@ H5PL__init_path_table(void) /* Check for too many directories in path */ if(H5PL_num_paths_g == H5PL_MAX_PATH_NUM) HGOTO_ERROR(H5E_PLUGIN, H5E_NOSPACE, FAIL, "too many directories in path for table") - if(NULL == (H5PL_path_table_g[H5PL_num_paths_g] = HDstrdup(dir))) + if(NULL == (H5PL_path_table_g[H5PL_num_paths_g] = H5MM_strdup(dir))) HGOTO_ERROR(H5E_PLUGIN, H5E_CANTALLOC, FAIL, "can't allocate memory for path") H5PL_num_paths_g++; dir = HDstrtok(NULL, H5PL_PATH_SEPARATOR); diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c index afef06b..971394c 100644 --- a/src/H5Pdcpl.c +++ b/src/H5Pdcpl.c @@ -29,14 +29,14 @@ /****************/ #include "H5Pmodule.h" /* This source code file is part of the H5P module */ +#define H5D_FRIEND /* Suppress error about including H5Dpkg */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ -#include "H5ACprivate.h" /* Metadata cache */ -#include "H5Dprivate.h" /* Datasets */ +#include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ @@ -45,6 +45,7 @@ #include "H5Ppkg.h" /* Property lists */ #include "H5Sprivate.h" /* Dataspaces */ #include "H5Tprivate.h" /* Datatypes */ +#include "H5VMprivate.h" /* Vectors and arrays */ #include "H5Zprivate.h" /* Data filters */ @@ -55,28 +56,28 @@ /* Define default layout information */ #define H5D_DEF_STORAGE_COMPACT_INIT {(hbool_t)FALSE, (size_t)0, NULL} #define H5D_DEF_STORAGE_CONTIG_INIT {HADDR_UNDEF, (hsize_t)0} -#define H5D_DEF_STORAGE_CHUNK_INIT {H5D_CHUNK_IDX_BTREE, HADDR_UNDEF, NULL, {{HADDR_UNDEF, NULL}}} -#define H5D_DEF_LAYOUT_CHUNK_INIT {(unsigned)0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, (uint32_t)0, (hsize_t)0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}} +#define H5D_DEF_STORAGE_CHUNK_INIT {H5D_CHUNK_IDX_BTREE, HADDR_UNDEF, H5D_COPS_BTREE, {{HADDR_UNDEF, NULL}}} +#define H5D_DEF_LAYOUT_CHUNK_INIT {(unsigned)0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, (unsigned)0, (uint32_t)0, (hsize_t)0, (hsize_t)0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}} #define H5D_DEF_STORAGE_VIRTUAL_INIT {{HADDR_UNDEF, 0}, 0, NULL, 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}, H5D_VDS_ERROR, HSIZE_UNDEF, -1, -1, FALSE} #ifdef H5_HAVE_C99_DESIGNATED_INITIALIZER #define H5D_DEF_STORAGE_COMPACT {H5D_COMPACT, { .compact = H5D_DEF_STORAGE_COMPACT_INIT }} #define H5D_DEF_STORAGE_CONTIG {H5D_CONTIGUOUS, { .contig = H5D_DEF_STORAGE_CONTIG_INIT }} #define H5D_DEF_STORAGE_CHUNK {H5D_CHUNKED, { .chunk = H5D_DEF_STORAGE_CHUNK_INIT }} #define H5D_DEF_STORAGE_VIRTUAL {H5D_VIRTUAL, { .virt = H5D_DEF_STORAGE_VIRTUAL_INIT }} -#define H5D_DEF_LAYOUT_COMPACT {H5D_COMPACT, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_COMPACT} -#define H5D_DEF_LAYOUT_CONTIG {H5D_CONTIGUOUS, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_CONTIG} -#define H5D_DEF_LAYOUT_CHUNK {H5D_CHUNKED, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_CHUNK} -#define H5D_DEF_LAYOUT_VIRTUAL {H5D_VIRTUAL, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_VIRTUAL} +#define H5D_DEF_LAYOUT_COMPACT {H5D_COMPACT, H5O_LAYOUT_VERSION_DEFAULT, H5D_LOPS_COMPACT, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_COMPACT} +#define H5D_DEF_LAYOUT_CONTIG {H5D_CONTIGUOUS, H5O_LAYOUT_VERSION_DEFAULT, H5D_LOPS_CONTIG, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_CONTIG} +#define H5D_DEF_LAYOUT_CHUNK {H5D_CHUNKED, H5O_LAYOUT_VERSION_DEFAULT, H5D_LOPS_CHUNK, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_CHUNK} +#define H5D_DEF_LAYOUT_VIRTUAL {H5D_VIRTUAL, H5O_LAYOUT_VERSION_4, H5D_LOPS_VIRTUAL, {H5D_DEF_LAYOUT_CHUNK_INIT}, H5D_DEF_STORAGE_VIRTUAL} #else /* H5_HAVE_C99_DESIGNATED_INITIALIZER */ /* Note that the compact & chunked layout initialization values are using the * contiguous layout initialization in the union, because the contiguous * layout is first in the union. These values are overridden in the * H5P__init_def_layout() routine. -QAK */ -#define H5D_DEF_LAYOUT_COMPACT {H5D_COMPACT, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} -#define H5D_DEF_LAYOUT_CONTIG {H5D_CONTIGUOUS, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} -#define H5D_DEF_LAYOUT_CHUNK {H5D_CHUNKED, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} -#define H5D_DEF_LAYOUT_VIRTUAL {H5D_VIRTUAL, H5O_LAYOUT_VERSION_3, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} +#define H5D_DEF_LAYOUT_COMPACT {H5D_COMPACT, H5O_LAYOUT_VERSION_DEFAULT, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} +#define H5D_DEF_LAYOUT_CONTIG {H5D_CONTIGUOUS, H5O_LAYOUT_VERSION_DEFAULT, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} +#define H5D_DEF_LAYOUT_CHUNK {H5D_CHUNKED, H5O_LAYOUT_VERSION_DEFAULT, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} +#define H5D_DEF_LAYOUT_VIRTUAL {H5D_VIRTUAL, H5O_LAYOUT_VERSION_4, NULL, {H5D_DEF_LAYOUT_CHUNK_INIT}, {H5D_CONTIGUOUS, H5D_DEF_STORAGE_CONTIG_INIT}} #endif /* H5_HAVE_C99_DESIGNATED_INITIALIZER */ /* ======== Dataset creation properties ======== */ @@ -288,7 +289,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__dcrt_layout_set(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) @@ -1998,6 +1998,7 @@ H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]) H5P_genplist_t *plist; /* Property list pointer */ H5O_layout_t chunk_layout; /* Layout information for setting chunk info */ uint64_t chunk_nelmts; /* Number of elements in chunk */ + unsigned max_enc_bytes_per_dim; /* Max. number of bytes required to encode this dimension */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2025,7 +2026,10 @@ H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]) HDmemcpy(&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; + max_enc_bytes_per_dim = 0; for(u = 0; u < (unsigned)ndims; u++) { + unsigned enc_bytes_per_dim; /* Number of bytes required to encode this dimension */ + if(dim[u] == 0) HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "all chunk dimensions must be positive") if(dim[u] != (dim[u] & 0xffffffff)) @@ -2034,7 +2038,16 @@ H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]) if(chunk_nelmts > (uint64_t)0xffffffff) HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "number of elements in chunk must be < 4GB") chunk_layout.u.chunk.dim[u] = (uint32_t)dim[u]; /* Store user's chunk dimensions */ + + /* Get encoded size of dim, in bytes */ + enc_bytes_per_dim = (H5VM_log2_gen(dim[u]) + 8) / 8; + + /* Check if this is the largest value so far */ + if(enc_bytes_per_dim > max_enc_bytes_per_dim) + max_enc_bytes_per_dim = enc_bytes_per_dim; } /* end for */ + HDassert(max_enc_bytes_per_dim > 0 && max_enc_bytes_per_dim <= 8); + chunk_layout.u.chunk.enc_bytes_per_dim = max_enc_bytes_per_dim; /* Get the plist structure */ if(NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_CREATE))) @@ -2214,9 +2227,9 @@ H5Pset_virtual(hid_t dcpl_id, hid_t vspace_id, const char *src_file_name, HDmemset(ent, 0, sizeof(H5O_storage_virtual_ent_t)); /* Clear before starting to set up */ if(NULL == (ent->source_dset.virtual_select = H5S_copy(vspace, FALSE, TRUE))) HGOTO_ERROR(H5E_PLIST, H5E_CANTCOPY, FAIL, "unable to copy virtual selection") - if(NULL == (ent->source_file_name = HDstrdup(src_file_name))) + if(NULL == (ent->source_file_name = H5MM_xstrdup(src_file_name))) HGOTO_ERROR(H5E_PLIST, H5E_RESOURCE, FAIL, "can't duplicate source file name") - if(NULL == (ent->source_dset_name = HDstrdup(src_dset_name))) + if(NULL == (ent->source_dset_name = H5MM_xstrdup(src_dset_name))) HGOTO_ERROR(H5E_PLIST, H5E_RESOURCE, FAIL, "can't duplicate source file name") if(NULL == (ent->source_select = H5S_copy(src_space, FALSE, TRUE))) HGOTO_ERROR(H5E_PLIST, H5E_CANTCOPY, FAIL, "unable to copy source selection") diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c index 59b3188..1181c16 100644 --- a/src/H5Pdxpl.c +++ b/src/H5Pdxpl.c @@ -872,7 +872,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__dxfr_xform_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -904,7 +903,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__dxfr_xform_copy(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -991,7 +989,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__dxfr_xform_close(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { diff --git a/src/H5Plapl.c b/src/H5Plapl.c index b311238..0d5507a 100644 --- a/src/H5Plapl.c +++ b/src/H5Plapl.c @@ -463,7 +463,6 @@ done: * *-------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__lacc_elink_fapl_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -500,7 +499,6 @@ done: * *-------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__lacc_elink_fapl_copy(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -590,7 +588,6 @@ done: * *--------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__lacc_elink_fapl_close(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -797,7 +794,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__lacc_elink_pref_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -823,7 +819,6 @@ H5P__lacc_elink_pref_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__lacc_elink_pref_copy(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -884,7 +879,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__lacc_elink_pref_close(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { diff --git a/src/H5Pocpypl.c b/src/H5Pocpypl.c index 7657d52..faa2a04 100644 --- a/src/H5Pocpypl.c +++ b/src/H5Pocpypl.c @@ -497,7 +497,6 @@ done: * *-------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__ocpy_merge_comm_dt_list_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) @@ -527,7 +526,6 @@ H5P__ocpy_merge_comm_dt_list_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATT * *-------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__ocpy_merge_comm_dt_list_copy(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) @@ -616,7 +614,6 @@ done: * *--------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5P__ocpy_merge_comm_dt_list_close(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value) { @@ -1375,11 +1375,23 @@ H5SM_write_mesg(H5F_t *f, hid_t dxpl_id, H5O_t *open_oh, } /* end else */ } /* end else */ - if(found) + if(found) { /* If the message was found, it's shared in the heap (now). Set up a * shared message so we can mark it as shared. */ shared.type = H5O_SHARE_TYPE_SOHM; + +#ifdef H5_USING_MEMCHECKER + /* Reset the shared message payload if deferring. This doesn't matter + * in the long run since the payload will get overwritten when the + * non-deferred call to this routine occurs, but it stops memory + * checkers like valgrind from whining when the partially initialized + * shared message is serialized. -QAK + */ + if(defer) + HDmemset(&shared.u, 0, sizeof(shared.u)); +#endif /* H5_USING_MEMCHECKER */ + } /* end if */ else { htri_t share_in_ohdr; /* Whether the new message can be shared in another object's header */ diff --git a/src/H5SMbtree2.c b/src/H5SMbtree2.c index e533ae8..0110c1e 100644 --- a/src/H5SMbtree2.c +++ b/src/H5SMbtree2.c @@ -50,7 +50,6 @@ static herr_t H5SM__bt2_dst_context(void *ctx); static herr_t H5SM__bt2_store(void *native, const void *udata); static herr_t H5SM__bt2_debug(FILE *stream, int indent, int fwidth, const void *record, const void *_udata); -static void *H5SM__bt2_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t addr); /*****************************/ @@ -67,9 +66,7 @@ const H5B2_class_t H5SM_INDEX[1]={{ /* B-tree class information */ H5SM__message_compare, /* Record comparison callback */ H5SM__message_encode, /* Record encoding callback */ H5SM__message_decode, /* Record decoding callback */ - H5SM__bt2_debug, /* Record debugging callback */ - H5SM__bt2_crt_dbg_context, /* Create debugging context */ - H5SM__bt2_dst_context /* Destroy debugging context */ + H5SM__bt2_debug /* Record debugging callback */ }}; @@ -218,45 +215,6 @@ H5SM__bt2_debug(FILE *stream, int indent, int fwidth, /*------------------------------------------------------------------------- - * Function: H5SM__bt2_crt_dbg_context - * - * Purpose: Create context for debugging callback - * - * Return: Success: non-NULL - * Failure: NULL - * - * Programmer: Quincey Koziol - * Tuesday, December 1, 2009 - * - *------------------------------------------------------------------------- - */ -static void * -H5SM__bt2_crt_dbg_context(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t H5_ATTR_UNUSED addr) -{ - H5SM_bt2_ctx_t *ctx; /* Callback context structure */ - void *ret_value = NULL; /* Return value */ - - FUNC_ENTER_STATIC - - /* Sanity check */ - HDassert(f); - - /* Allocate callback context */ - if(NULL == (ctx = H5FL_MALLOC(H5SM_bt2_ctx_t))) - HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, NULL, "can't allocate callback context") - - /* Determine the size of addresses & lengths in the file */ - ctx->sizeof_addr = H5F_SIZEOF_ADDR(f); - - /* Set return value */ - ret_value = ctx; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* H5SM__bt2_crt_dbg_context() */ - - -/*------------------------------------------------------------------------- * Function: H5SM_bt2_convert_to_list_op * * Purpose: An H5B2_remove_t callback function to convert a SOHM @@ -255,19 +255,18 @@ H5TS_cancel_count_inc(void) if (!cancel_counter) { /* - * First time thread calls library - create new counter and associate + * First time thread calls library - create new counter and associate * with key */ - cancel_counter = (H5TS_cancel_t *)H5MM_calloc(sizeof(H5TS_cancel_t)); + cancel_counter = (H5TS_cancel_t *)HDcalloc(1, sizeof(H5TS_cancel_t)); - if (!cancel_counter) { - H5E_push_stack(NULL, "H5TS_cancel_count_inc", - __FILE__, __LINE__, H5E_ERR_CLS_g, H5E_RESOURCE, H5E_NOSPACE, "memory allocation failed"); - return FAIL; - } + if (!cancel_counter) { + H5E_push_stack(NULL, "H5TS_cancel_count_inc", __FILE__, __LINE__, + H5E_ERR_CLS_g, H5E_RESOURCE, H5E_NOSPACE, "memory allocation failed"); + return FAIL; + } - ret_value = pthread_setspecific(H5TS_cancel_key_g, - (void *)cancel_counter); + ret_value = pthread_setspecific(H5TS_cancel_key_g, (void *)cancel_counter); } if (cancel_counter->cancel_count == 0) diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c index 26346d6..0ed8209 100644 --- a/src/H5Tvlen.c +++ b/src/H5Tvlen.c @@ -365,7 +365,6 @@ H5T_vlen_seq_mem_getptr(void *_vl) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static htri_t H5T_vlen_seq_mem_isnull(const H5F_t H5_ATTR_UNUSED *f, void *_vl) { @@ -403,7 +402,6 @@ H5T_vlen_seq_mem_isnull(const H5F_t H5_ATTR_UNUSED *f, void *_vl) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_seq_mem_read(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, void *_vl, void *buf, size_t len) { @@ -445,7 +443,6 @@ H5T_vlen_seq_mem_read(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, voi * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_seq_mem_write(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, const H5T_vlen_alloc_info_t *vl_alloc_info, void *_vl, void *buf, void H5_ATTR_UNUSED *_bg, size_t seq_len, size_t base_size) { @@ -468,7 +465,7 @@ H5T_vlen_seq_mem_write(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, co HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for VL data") } /* end if */ else { /* Default to system malloc */ - if(NULL==(vl.p=H5MM_malloc(len))) + if(NULL == (vl.p = HDmalloc(len))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for VL data") } /* end else */ @@ -502,7 +499,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_seq_mem_setnull(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, void *_vl, void H5_ATTR_UNUSED *_bg) { @@ -606,7 +602,6 @@ H5T_vlen_str_mem_getptr(void *_vl) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static htri_t H5T_vlen_str_mem_isnull(const H5F_t H5_ATTR_UNUSED *f, void *_vl) { @@ -638,7 +633,6 @@ H5T_vlen_str_mem_isnull(const H5F_t H5_ATTR_UNUSED *f, void *_vl) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_str_mem_read(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, void *_vl, void *buf, size_t len) { @@ -679,7 +673,6 @@ H5T_vlen_str_mem_read(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, voi * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_str_mem_write(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, const H5T_vlen_alloc_info_t *vl_alloc_info, void *_vl, void *buf, void H5_ATTR_UNUSED *_bg, size_t seq_len, size_t base_size) { @@ -698,7 +691,7 @@ H5T_vlen_str_mem_write(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, co HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for VL data") } /* end if */ else { /* Default to system malloc */ - if(NULL==(t = (char *)H5MM_malloc((seq_len+1)*base_size))) + if(NULL == (t = (char *)HDmalloc((seq_len + 1) * base_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for VL data") } /* end else */ @@ -726,7 +719,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_str_mem_setnull(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, void *_vl, void H5_ATTR_UNUSED *_bg) { @@ -782,7 +774,6 @@ H5T_vlen_disk_getlen(const void *_vl) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static void * H5T_vlen_disk_getptr(void H5_ATTR_UNUSED *vl) { @@ -840,7 +831,6 @@ H5T_vlen_disk_isnull(const H5F_t *f, void *_vl) * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_disk_read(H5F_t *f, hid_t dxpl_id, void *_vl, void *buf, size_t H5_ATTR_UNUSED len) { @@ -886,7 +876,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5T_vlen_disk_write(H5F_t *f, hid_t dxpl_id, const H5T_vlen_alloc_info_t H5_ATTR_UNUSED *vl_alloc_info, void *_vl, void *buf, void *_bg, size_t seq_len, size_t base_size) @@ -1084,14 +1073,14 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi if(free_func != NULL) (*free_func)(vl->p, free_info); else - H5MM_xfree(vl->p); + HDfree(vl->p); } /* end if */ } else if(dt->shared->u.vlen.type == H5T_VLEN_STRING) { /* Free the VL string */ if(free_func != NULL) (*free_func)(*(char **)elem, free_info); else - H5MM_xfree(*(char **)elem); + HDfree(*(char **)elem); } else { HDassert(0 && "Invalid VL type"); } /* end else */ @@ -1146,7 +1135,6 @@ done: EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -/* ARGSUSED */ herr_t H5T_vlen_reclaim(void *elem, hid_t type_id, unsigned H5_ATTR_UNUSED ndim, const hsize_t H5_ATTR_UNUSED *point, void *op_data) { diff --git a/src/H5Zfletcher32.c b/src/H5Zfletcher32.c index 690d7a2..9ff85cc 100644 --- a/src/H5Zfletcher32.c +++ b/src/H5Zfletcher32.c @@ -70,7 +70,6 @@ const H5Z_class2_t H5Z_FLETCHER32[1] = {{ * with Release 1.6.2 and before. *------------------------------------------------------------------------- */ -/* ARGSUSED */ static size_t H5Z_filter_fletcher32 (unsigned flags, size_t H5_ATTR_UNUSED cd_nelmts, const unsigned H5_ATTR_UNUSED cd_values[], size_t nbytes, size_t *buf_size, void **buf) diff --git a/src/H5Zshuffle.c b/src/H5Zshuffle.c index 3fa6c8d..4cf6adf 100644 --- a/src/H5Zshuffle.c +++ b/src/H5Zshuffle.c @@ -61,7 +61,6 @@ const H5Z_class2_t H5Z_SHUFFLE[1] = {{ * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5Z_set_local_shuffle(hid_t dcpl_id, hid_t type_id, hid_t H5_ATTR_UNUSED space_id) { diff --git a/src/H5Ztrans.c b/src/H5Ztrans.c index 0a9a4da..2627a29 100644 --- a/src/H5Ztrans.c +++ b/src/H5Ztrans.c @@ -1032,7 +1032,7 @@ H5Z_xform_eval(H5Z_data_xform_t *data_xform_prop, void* array, size_t array_size /* Free the temporary arrays we used */ if(data_xform_prop->dat_val_pointers->num_ptrs > 1) for(i=0; i<data_xform_prop->dat_val_pointers->num_ptrs; i++) - HDfree(data_xform_prop->dat_val_pointers->ptr_dat_val[i]); + H5MM_xfree(data_xform_prop->dat_val_pointers->ptr_dat_val[i]); } /* end else */ done: @@ -1042,7 +1042,7 @@ done: if(data_xform_prop->dat_val_pointers->num_ptrs > 1) for(i = 0; i < data_xform_prop->dat_val_pointers->num_ptrs; i++) if(data_xform_prop->dat_val_pointers->ptr_dat_val[i]) - HDfree(data_xform_prop->dat_val_pointers->ptr_dat_val[i]); + H5MM_xfree(data_xform_prop->dat_val_pointers->ptr_dat_val[i]); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5public.h b/src/H5public.h index 5b95fb7..554ad26 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -94,10 +94,10 @@ extern "C" { /* Version numbers */ #define H5_VERS_MAJOR 1 /* For major interface/format changes */ #define H5_VERS_MINOR 9 /* For minor interface/format changes */ -#define H5_VERS_RELEASE 233 /* For tweaks, bug-fixes, or development */ +#define H5_VERS_RELEASE 234 /* For tweaks, bug-fixes, or development */ #define H5_VERS_SUBRELEASE "" /* For pre-releases like snap0 */ /* Empty string for real releases. */ -#define H5_VERS_INFO "HDF5 library version: 1.9.233" /* Full version string */ +#define H5_VERS_INFO "HDF5 library version: 1.9.234" /* Full version string */ #define H5check() H5check_version(H5_VERS_MAJOR,H5_VERS_MINOR, \ H5_VERS_RELEASE) diff --git a/src/libhdf5.settings.in b/src/libhdf5.settings.in index 2355543..90224c1 100644 --- a/src/libhdf5.settings.in +++ b/src/libhdf5.settings.in @@ -66,6 +66,7 @@ Features: dmalloc: @HAVE_DMALLOC@ Clear file buffers before write: @CLEARFILEBUF@ Using memory checker: @USINGMEMCHECKER@ +Memory allocation sanity checks: @MEMORYALLOCSANITYCHECK@ Function Stack Tracing: @CODESTACK@ Strict File Format Checks: @STRICT_FORMAT_CHECKS@ Optimization Instrumentation: @INSTRUMENT@ |