Convert some H5MM calls to standard C equivalents (HDFGroup#2382)

* H5MM_calloc and malloc are now mapped to stdlib C calls
* H5MM_memcpy now maps directly to memcpy in release builds
* H5MM_memcpy is still implemented as a separate function that
   checks for buffer overlap when H5MM_DEBUG is defined
   (default w/ debug builds)
* Switches many library memcpy calls to use H5MM_memcpy
* Fixes a possible zero allocation in H5Olayout.c

config/cmake/HDFCompilerFlags.cmake

@@ -310,6 +310,7 @@ if (HDF5_ENABLE_DEBUG_APIS)
       H5F_DEBUG
       H5HL_DEBUG
       H5I_DEBUG
+      H5MM_DEBUG
       H5O_DEBUG
       H5S_DEBUG
       H5T_DEBUG

configure.ac

@@ -2492,8 +2492,8 @@ AC_SUBST([INTERNAL_DEBUG_OUTPUT])
 ## too specialized or have huge performance hits. These
 ## are not listed in the "all" packages list.
 ##
-## all_packages="AC,B,B2,D,F,FA,FL,FS,HL,I,O,S,T,Z"
-all_packages="AC,B2,CX,D,F,HL,I,O,S,T,Z"
+## all_packages="AC,B,B2,D,F,FA,FL,FS,HL,I,MM,O,S,T,Z"
+all_packages="AC,B2,CX,D,F,HL,I,MM,O,S,T,Z"
 
 case "X-$INTERNAL_DEBUG_OUTPUT" in
   X-yes|X-all)

src/H5CS.c

@@ -248,7 +248,7 @@ H5CS_copy_stack(void)
 
     /* Copy pointers on old stack to new one */
     /* (Strings don't need to be duplicated, they are statically allocated) */
-    memcpy(new_stack->rec, old_stack->rec, sizeof(char *) * old_stack->nused);
+    H5MM_memcpy(new_stack->rec, old_stack->rec, sizeof(char *) * old_stack->nused);
     new_stack->nused = new_stack->nalloc = old_stack->nused;
 
     /* Set the return value */

src/H5Dchunk.c

@@ -2790,7 +2790,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
 
         /* Set up contiguous I/O info object */
         H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
-        memcpy(&ctg_dset_info, dset_info, sizeof(ctg_dset_info));
+        H5MM_memcpy(&ctg_dset_info, dset_info, sizeof(ctg_dset_info));
         ctg_dset_info.store      = &ctg_store;
         ctg_dset_info.layout_ops = *H5D_LOPS_CONTIG;
         ctg_io_info.dsets_info   = &ctg_dset_info;
@@ -2802,7 +2802,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
 
         /* Set up compact I/O info object */
         H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
-        memcpy(&cpt_dset_info, dset_info, sizeof(cpt_dset_info));
+        H5MM_memcpy(&cpt_dset_info, dset_info, sizeof(cpt_dset_info));
         cpt_dset_info.store      = &cpt_store;
         cpt_dset_info.layout_ops = *H5D_LOPS_COMPACT;
         cpt_io_info.dsets_info   = &cpt_dset_info;
@@ -2950,7 +2950,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
 
     /* Set up contiguous I/O info object */
     H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
-    memcpy(&ctg_dset_info, dset_info, sizeof(ctg_dset_info));
+    H5MM_memcpy(&ctg_dset_info, dset_info, sizeof(ctg_dset_info));
     ctg_dset_info.store      = &ctg_store;
     ctg_dset_info.layout_ops = *H5D_LOPS_CONTIG;
     ctg_io_info.dsets_info   = &ctg_dset_info;
@@ -2962,7 +2962,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info)
 
     /* Set up compact I/O info object */
     H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
-    memcpy(&cpt_dset_info, dset_info, sizeof(cpt_dset_info));
+    H5MM_memcpy(&cpt_dset_info, dset_info, sizeof(cpt_dset_info));
     cpt_dset_info.store      = &cpt_store;
     cpt_dset_info.layout_ops = *H5D_LOPS_COMPACT;
     cpt_io_info.dsets_info   = &cpt_dset_info;

src/H5Dmpio.c

@@ -3772,7 +3772,7 @@ H5D__mpio_share_chunk_modification_data(H5D_filtered_collective_io_info_t *chunk
             mod_data_p = msg_send_bufs[num_send_requests];
 
             /* Store the chunk's index into the buffer */
-            memcpy(mod_data_p, &chunk_entry->index_info.chunk_idx, sizeof(hsize_t));
+            H5MM_memcpy(mod_data_p, &chunk_entry->index_info.chunk_idx, sizeof(hsize_t));
             mod_data_p += sizeof(hsize_t);
 
             /* Serialize the chunk's file dataspace into the buffer */
@@ -4491,7 +4491,7 @@ H5D__mpio_collective_filtered_chunk_update(H5D_filtered_collective_io_info_t *ch
 
         if (msg_ptr) {
             /* Retrieve the chunk's index value */
-            memcpy(&chunk_idx, msg_ptr, sizeof(hsize_t));
+            H5MM_memcpy(&chunk_idx, msg_ptr, sizeof(hsize_t));
             msg_ptr += sizeof(hsize_t);
 
             /* Find the chunk entry according to its chunk index */

src/H5Dscatgath.c

@@ -118,7 +118,7 @@ H5D__scatter_file(const H5D_io_info_t *_io_info, const H5D_dset_io_info_t *_dset
 
     /* Set up temporary I/O info object */
     H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
-    memcpy(&tmp_dset_info, _dset_info, sizeof(*_dset_info));
+    H5MM_memcpy(&tmp_dset_info, _dset_info, sizeof(*_dset_info));
     tmp_io_info.op_type    = H5D_IO_OP_WRITE;
     tmp_dset_info.buf.cvp  = _buf;
     tmp_io_info.dsets_info = &tmp_dset_info;
@@ -219,7 +219,7 @@ H5D__gather_file(const H5D_io_info_t *_io_info, const H5D_dset_io_info_t *_dset_
 
     /* Set up temporary I/O info object */
     H5MM_memcpy(&tmp_io_info, _io_info, sizeof(*_io_info));
-    memcpy(&tmp_dset_info, _dset_info, sizeof(*_dset_info));
+    H5MM_memcpy(&tmp_dset_info, _dset_info, sizeof(*_dset_info));
     tmp_io_info.op_type    = H5D_IO_OP_READ;
     tmp_dset_info.buf.vp   = _buf;
     tmp_io_info.dsets_info = &tmp_dset_info;

src/H5FDonion.c

@@ -295,7 +295,7 @@ H5Pget_fapl_onion(hid_t fapl_id, H5FD_onion_fapl_info_t *fa_out)
     if (NULL == (info_ptr = (const H5FD_onion_fapl_info_t *)H5P_peek_driver_info(plist)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "bad VFL driver info");
 
-    memcpy(fa_out, info_ptr, sizeof(H5FD_onion_fapl_info_t));
+    H5MM_memcpy(fa_out, info_ptr, sizeof(H5FD_onion_fapl_info_t));
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -514,7 +514,7 @@ H5FD__onion_commit_new_revision_record(H5FD_onion_t *file)
 
         if (NULL == (new_list = H5MM_calloc((history->n_revisions + 1) * sizeof(H5FD_onion_record_loc_t))))
             HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "unable to resize record pointer list");
-        memcpy(new_list, history->record_locs, sizeof(H5FD_onion_record_loc_t) * history->n_revisions);
+        H5MM_memcpy(new_list, history->record_locs, sizeof(H5FD_onion_record_loc_t) * history->n_revisions);
         H5MM_xfree(history->record_locs);
         history->record_locs                                   = new_list;
         new_list                                               = NULL;
@@ -980,7 +980,7 @@ H5FD__onion_open(const char *filename, unsigned flags, hid_t fapl_id, haddr_t ma
 
     /* Initialize file structure fields */
 
-    memcpy(&(file->fa), fa, sizeof(H5FD_onion_fapl_info_t));
+    H5MM_memcpy(&(file->fa), fa, sizeof(H5FD_onion_fapl_info_t));
 
     file->header.version   = H5FD_ONION_HEADER_VERSION_CURR;
     file->header.page_size = file->fa.page_size; /* guarded on FAPL-set */
@@ -1523,7 +1523,7 @@ H5FD__onion_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id,
                 if (H5FD_read(file->onion_file, H5FD_MEM_DRAW, entry_out->phys_addr, page_size, page_buf) < 0)
                     HGOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "can't get working file data");
                 /* Overlay delta from input buffer onto page buffer. */
-                memcpy(page_buf + page_gap_head, buf, page_n_used);
+                H5MM_memcpy(page_buf + page_gap_head, buf, page_n_used);
                 write_buf = page_buf;
             } /* end if partial page */
 
@@ -1571,7 +1571,7 @@ H5FD__onion_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id,
 
             /* Copy input buffer to temporary page buffer */
             assert((page_size - page_gap_head) >= page_n_used);
-            memcpy(page_buf + page_gap_head, buf, page_n_used);
+            H5MM_memcpy(page_buf + page_gap_head, buf, page_n_used);
             write_buf = page_buf;
 
         } /* end if data range does not span entire page */

src/H5FDonion_header.c

@@ -142,34 +142,34 @@ H5FD__onion_header_decode(unsigned char *buf, H5FD_onion_header_t *header)
 
     ptr  = buf + 5;
     ui32 = 0;
-    memcpy(&ui32, ptr, 3);
+    H5MM_memcpy(&ui32, ptr, 3);
     ui8p = (uint8_t *)&ui32;
     UINT32DECODE(ui8p, header->flags);
     ptr += 3;
 
-    memcpy(&ui32, ptr, 4);
+    H5MM_memcpy(&ui32, ptr, 4);
     ui8p = (uint8_t *)&ui32;
     UINT32DECODE(ui8p, header->page_size);
     ptr += 4;
 
-    memcpy(&ui64, ptr, 8);
+    H5MM_memcpy(&ui64, ptr, 8);
     ui8p = (uint8_t *)&ui64;
     UINT32DECODE(ui8p, header->origin_eof);
     ptr += 8;
 
-    memcpy(&ui64, ptr, 8);
+    H5MM_memcpy(&ui64, ptr, 8);
     ui8p = (uint8_t *)&ui64;
     UINT32DECODE(ui8p, header->history_addr);
     ptr += 8;
 
-    memcpy(&ui64, ptr, 8);
+    H5MM_memcpy(&ui64, ptr, 8);
     ui8p = (uint8_t *)&ui64;
     UINT32DECODE(ui8p, header->history_size);
     ptr += 8;
 
     sum = H5_checksum_fletcher32(buf, (size_t)(ptr - buf));
 
-    memcpy(&ui32, ptr, 4);
+    H5MM_memcpy(&ui32, ptr, 4);
     ui8p = (uint8_t *)&ui32;
     UINT32DECODE(ui8p, header->checksum);
     ptr += 4;
@@ -214,9 +214,9 @@ H5FD__onion_header_encode(H5FD_onion_header_t *header, unsigned char *buf, uint3
     assert(H5FD_ONION_HEADER_VERSION_CURR == header->version);
     assert(0 == (header->flags & 0xFF000000)); /* max three bits long */
 
-    memcpy(ptr, H5FD_ONION_HEADER_SIGNATURE, 4);
+    H5MM_memcpy(ptr, H5FD_ONION_HEADER_SIGNATURE, 4);
     ptr += 4;
-    memcpy(ptr, (unsigned char *)&header->version, 1);
+    H5MM_memcpy(ptr, (unsigned char *)&header->version, 1);
     ptr += 1;
     UINT32ENCODE(ptr, header->flags);
     ptr -= 1; /* truncate to three bytes */

src/H5FDonion_history.c

@@ -180,7 +180,7 @@ H5FD__onion_history_decode(unsigned char *buf, H5FD_onion_history_t *history)
 
     ptr = buf + 8;
 
-    memcpy(&ui64, ptr, 8);
+    H5MM_memcpy(&ui64, ptr, 8);
     ui8p = (uint8_t *)&ui64;
     UINT64DECODE(ui8p, n_revisions);
     ptr += 8;
@@ -207,19 +207,19 @@ H5FD__onion_history_decode(unsigned char *buf, H5FD_onion_history_t *history)
             uint64_t record_size;
             uint64_t phys_addr;
 
-            memcpy(&ui64, ptr, 8);
+            H5MM_memcpy(&ui64, ptr, 8);
             ui8p = (uint8_t *)&ui64;
             UINT64DECODE(ui8p, phys_addr);
             H5_CHECKED_ASSIGN(rloc->phys_addr, haddr_t, phys_addr, uint64_t);
             ptr += 8;
 
-            memcpy(&ui64, ptr, 8);
+            H5MM_memcpy(&ui64, ptr, 8);
             ui8p = (uint8_t *)&ui64;
             UINT64DECODE(ui8p, record_size);
             H5_CHECKED_ASSIGN(rloc->record_size, hsize_t, record_size, uint64_t);
             ptr += 8;
 
-            memcpy(&ui32, ptr, 4);
+            H5MM_memcpy(&ui32, ptr, 4);
             ui8p = (uint8_t *)&ui32;
             UINT32DECODE(ui8p, rloc->checksum);
             ptr += 4;
@@ -228,7 +228,7 @@ H5FD__onion_history_decode(unsigned char *buf, H5FD_onion_history_t *history)
 
     sum = H5_checksum_fletcher32(buf, (size_t)(ptr - buf));
 
-    memcpy(&ui32, ptr, 4);
+    H5MM_memcpy(&ui32, ptr, 4);
     ui8p = (uint8_t *)&ui32;
     UINT32DECODE(ui8p, history->checksum);
     ptr += 4;
@@ -275,7 +275,7 @@ H5FD__onion_history_encode(H5FD_onion_history_t *history, unsigned char *buf, ui
     assert(buf != NULL);
     assert(checksum != NULL);
 
-    memcpy(ptr, H5FD_ONION_HISTORY_SIGNATURE, 4);
+    H5MM_memcpy(ptr, H5FD_ONION_HISTORY_SIGNATURE, 4);
     ptr += 4;
     UINT32ENCODE(ptr, vers_u32);
     UINT64ENCODE(ptr, history->n_revisions);