Are you sure your innodb_file_per_table is enabled? check:
mysql> show variables like '%per_table%';
+-----------------------+-------+
| Variable_name | Value |
+-----------------------+-------+
| innodb_file_per_table | ON |
+-----------------------+-------+
I think this value is 'OFF', so global table space ib_data1 is used. then, huge amount of disk space is pre-allocated. you can find initial size like this:
mysql> show variables like '%innodb%data%';
+--------------------------+------------------------+
| Variable_name | Value |
+--------------------------+------------------------+
| innodb_data_file_path | ibdata1:10M:autoextend |
UPDATED
Here is what i tried. I keep watching how file size glows. it grow up by 32kb at once. also I'm using barracuda format. I suggest that insert more more many many records.
mysql> create table db_size_test( a int, b int, c int);
Query OK, 0 rows affected (0.01 sec)
[XXXX]$ ls -lh db_size_test.ibd
-rw-rw---- 1 xxxx xxxx 96K 11월 21 21:26 db_size_test.ibd
mysql> select count(*) from db_size_test;
+----------+
| count(*) |
+----------+
| 1001 |
+----------+
1 row in set (0.00 sec)
[XXX]$ ls -lh db_size_test.ibd
-rw-rw---- 1 xxxx xxxxx 128K 11월 21 21:28 db_size_test.ibd