remap every 100000 values

src/obiavl.c

@@ -477,23 +477,25 @@ int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
 	size_t 	new_data_size;
 	size_t 	header_size;
 	int 	avl_file_descriptor;
-	char* 	avl_file_name;
+//	char* 	avl_file_name;
 
-	// Get the avl file name
-	avl_file_name = build_avl_file_name((avl->header)->avl_name);
-	if (avl_file_name == NULL)
-		return -1;
+//	// Get the avl file name
+//	avl_file_name = build_avl_file_name((avl->header)->avl_name);
+//	if (avl_file_name == NULL)
+//		return -1;
+//
+//	// Open the avl file
+//	avl_file_descriptor = openat(avl->dir_fd, avl_file_name, O_RDWR);
+//	if (avl_file_descriptor < 0)
+//	{
+//		obi_set_errno(OBI_AVL_ERROR);
+//		obidebug(1, "\nError opening an AVL tree file");
+//		free(avl_file_name);
+//		return -1;
+//	}
+//	free(avl_file_name);
 
-	// Open the avl file
-	avl_file_descriptor = openat(avl->dir_fd, avl_file_name, O_RDWR);
-	if (avl_file_descriptor < 0)
-	{
-		obi_set_errno(OBI_AVL_ERROR);
-		obidebug(1, "\nError opening an AVL tree file");
-		free(avl_file_name);
-		return -1;
-	}
-	free(avl_file_name);
+	avl_file_descriptor = avl->avl_fd;
 
 	// Calculate the new file size
 	old_data_size = (avl->header)->avl_size;
@@ -542,7 +544,7 @@ int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
 	// Set the new avl size
 	(avl->header)->avl_size = new_data_size;
 
-	close(avl_file_descriptor);
+	//close(avl_file_descriptor);
 
 	return 0;
 }
@@ -555,23 +557,25 @@ int grow_avl_data(OBIDMS_avl_p avl)		// TODO Lock when needed
 	index_t new_data_size;
 	size_t 	header_size;
 	int 	avl_data_file_descriptor;
-	char* 	avl_data_file_name;
+//	char* 	avl_data_file_name;
+//
+//	// Get the avl data file name
+//	avl_data_file_name = build_avl_data_file_name((avl->header)->avl_name);
+//	if (avl_data_file_name == NULL)
+//		return -1;
+//
+//	// Open the avl data file
+//	avl_data_file_descriptor = openat(avl->dir_fd, avl_data_file_name, O_RDWR);
+//	if (avl_data_file_descriptor < 0)
+//	{
+//		obi_set_errno(OBI_AVL_ERROR);
+//		obidebug(1, "\nError opening an AVL tree data file");
+//		free(avl_data_file_name);
+//		return -1;
+//	}
+//	free(avl_data_file_name);
 
-	// Get the avl data file name
-	avl_data_file_name = build_avl_data_file_name((avl->header)->avl_name);
-	if (avl_data_file_name == NULL)
-		return -1;
-
-	// Open the avl data file
-	avl_data_file_descriptor = openat(avl->dir_fd, avl_data_file_name, O_RDWR);
-	if (avl_data_file_descriptor < 0)
-	{
-		obi_set_errno(OBI_AVL_ERROR);
-		obidebug(1, "\nError opening an AVL tree data file");
-		free(avl_data_file_name);
-		return -1;
-	}
-	free(avl_data_file_name);
+	avl_data_file_descriptor = avl->data_fd;
 
 	// Calculate the new file size
 	old_data_size = ((avl->data)->header)->data_size_max;
@@ -620,7 +624,7 @@ int grow_avl_data(OBIDMS_avl_p avl)		// TODO Lock when needed
 	// Initialize new data to 0
 	memset(((avl->data)->data)+old_data_size, 0, new_data_size - old_data_size);
 
-	close(avl_data_file_descriptor);
+	//close(avl_data_file_descriptor);
 
 	return 0;
 }
@@ -1090,7 +1094,7 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name)
 	// Initialize all bits to 0
 	memset(avl_data->data, 0, (avl_data->header)->data_size_max);
 
-	close(avl_data_file_descriptor);
+	//close(avl_data_file_descriptor);
 
 
 	// Create the AVL tree file
@@ -1190,7 +1194,10 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name)
 	(avl->header)->creation_date = time(NULL);
 	strcpy((avl->header)->avl_name, avl_name);
 
-	close(avl_file_descriptor);
+	//close(avl_file_descriptor);
+
+	avl->avl_fd = avl_file_descriptor;
+	avl->data_fd = avl_data_file_descriptor;
 
 	// Add in the list of opened AVL trees
 	*(((dms->opened_avls)->avls)+((dms->opened_avls)->nb_opened_avls)) = avl;
@@ -1297,7 +1304,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name)
 		return NULL;
 	}
 
-	close(avl_data_file_descriptor);
+	//close(avl_data_file_descriptor);
 
 
 	// Open the AVL tree file
@@ -1383,7 +1390,9 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name)
 	avl->directory = dms->avl_directory;
 	avl->dir_fd = avl_dir_file_descriptor;
 
-	close(avl_file_descriptor);
+	//close(avl_file_descriptor);
+	avl->avl_fd = avl_file_descriptor;
+	avl->data_fd = avl_data_file_descriptor;
 
 	// Add in the list of opened AVL trees
 	*(((dms->opened_avls)->avls)+((dms->opened_avls)->nb_opened_avls)) = avl;
@@ -1435,6 +1444,9 @@ int obi_close_avl(OBIDMS_avl_p avl)
 			ret_val = -1;
 		}
 
+		close(avl->avl_fd);
+		close(avl->data_fd);
+
 		free(avl);
 	}
 

src/obiavl.h

@@ -130,6 +130,12 @@ typedef struct OBIDMS_avl {
 	int							dir_fd;				/**< The file descriptor of the directory entry
 													 *    usable to refer and scan the AVL tree directory.
 													 */
+	int							avl_fd;				/**< The file descriptor of the file
+													 *    to refer and scan the AVL tree.
+													 */
+	int							data_fd;				/**< The file descriptor of the file
+													 *    to refer and scan the data referred to by the AVL tree.
+													 */
 	size_t						counter;			/**< Indicates by how many threads/programs (TODO) the AVL tree is used.
 													 */
 } OBIDMS_avl_t, *OBIDMS_avl_p;

src/obidmscolumn_str.c

@@ -12,6 +12,7 @@
 
 #include <stdlib.h>
 #include <stdio.h>
+#include <sys/mman.h>
 
 #include "obidmscolumn.h"
 #include "obiview.h"
@@ -60,6 +61,30 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 	if (value_b == NULL)
 		return -1;
 
+	if (!(line_nb%100000))
+	{
+		//fprintf(stderr, "\nbleeeh");
+		// Unmap and remap the AVL
+		if (munmap((column->avl)->tree, ((((column->avl)->header)->nb_items_max) * sizeof(AVL_node_t))) < 0)
+			return -1;
+		if (munmap(((column->avl)->data)->data, (((column->avl)->data)->header)->data_size_max) < 0)
+			return -1;
+		(column->avl)->tree = mmap(NULL,
+							  (((column->avl)->header)->nb_items_max) * sizeof(AVL_node_t),	// TODO store avl_size_max
+							  PROT_READ | PROT_WRITE,
+							  MAP_SHARED,
+							  (column->avl)->avl_fd,
+							  ((column->avl)->header)->header_size
+							  );
+		((column->avl)->data)->data = mmap(NULL,
+									  (((column->avl)->data)->header)->data_size_max,
+									  PROT_READ | PROT_WRITE,
+									  MAP_SHARED,
+									  (column->avl)->data_fd,
+									  (((column->avl)->data)->header)->header_size
+									  );
+	}
+
 	// Add in the AVL tree
 	idx = obi_avl_add(column->avl, value_b);
 	if (idx == -1)