The following are known problems with MERGE
tables:
If you use ALTER TABLE to change a
MERGE table to another storage engine, the
mapping to the underlying tables is lost. Instead, the rows
from the underlying MyISAM tables are
copied into the altered table, which then uses the specified
storage engine.
REPLACE does not work as expected because
the MERGE engine cannot enforce uniqueness
over the set of underlying tables. The two key facts are:
REPLACE can detect unique key
violations only in the underlying table to which it is
going to write (which is determined by
INSERT_METHOD). This differs from
violations in the MERGE table itself.
If REPLACE detects such a violation, it
will only change the corresponding row in the first
underlying table in which the row is present, whereas a
row with the same unique key value may be present in all
underlying tables.
Similar considerations apply for INSERT ... ON
DUPLICATE KEY UPDATE.
You cannot use REPAIR TABLE,
OPTIMIZE TABLE, DROP
TABLE, ALTER TABLE,
DELETE without a WHERE
clause, TRUNCATE TABLE, or ANALYZE
TABLE on any of the tables that are mapped into an
open MERGE table. If you do so, the
MERGE table may still refer to the original
table, which yields unexpected results. The easiest way to
work around this deficiency is to ensure that no
MERGE tables remain open by issuing a
FLUSH TABLES statement prior to performing
any of those operations.
The unexpected results include the possibility that the
operation on the MERGE table will report
table corruption. However, if this occurs after operations on
the underlying MyISAM tables such as those
listed in the previous paragraph (REPAIR
TABLE, OPTIMIZE TABLE, and so
forth), the corruption message is spurious. To deal with this,
issue a FLUSH TABLES statement after
modifying the MyISAM tables.
DROP TABLE on a table that is in use by a
MERGE table does not work on Windows
because the MERGE storage engine's table
mapping is hidden from the upper layer of MySQL. Windows does
not allow open files to be deleted, so you first must flush
all MERGE tables (with FLUSH
TABLES) or drop the MERGE table
before dropping the table.
A MERGE table cannot maintain uniqueness
constraints over the entire table. When you perform an
INSERT, the data goes into the first or
last MyISAM table (depending on the value
of the INSERT_METHOD option). MySQL ensures
that unique key values remain unique within that
MyISAM table, but not across all the tables
in the collection.
The INSERT_METHOD table option for a
MERGE table indicates which underlying
MyISAM table to use for inserts into the
MERGE table. However, use of the
AUTO_INCREMENT table option for that
MyISAM table has no effect for inserts into
the MERGE table until at least one row has
been inserted directly into the MyISAM
table.
In MySQL 5.0.36 and later, the definition of the
MyISAM tables and the
MERGE table are checked when the tables are
accessed (for example, as part of a SELECT
or INSERT statement). The checks ensure
that the definitions of the tables and the parent
MERGE table definition match by comparing
column order, types, sizes and associated indexes. If there is
a difference between the tables then an error will be returned
and the statement will fail.
Because these checks take place when the tables are opened, any changes to the definition of a single table, including column changes, column ordering and engine alterations will cause the statement to fail.
In MySQL 5.0.35 and earlier:
When you create or alter MERGE table,
there is no check to ensure that the underlying tables are
existing MyISAM tables and have
identical structures. When the MERGE
table is used, MySQL checks that the row length for all
mapped tables is equal, but this is not foolproof. If you
create a MERGE table from dissimilar
MyISAM tables, you are very likely to
run into strange problems.
Similarly, if you create a MERGE table
from non-MyISAM tables, or if you drop
an underlying table or alter it to be a
non-MyISAM table, no error for the
MERGE table occurs until later when you
attempt to use it.
Because the underlying MyISAM tables
need not exist when the MERGE table is
created, you can create the tables in any order, as long
as you do not use the MERGE table until
all of its underlying tables are in place. Also, if you
can ensure that a MERGE table will not
be used during a given period, you can perform maintenance
operations on the underlying tables, such as backing up or
restoring them, altering them, or dropping and recreating
them. It is not necessary to redefine the
MERGE table temporarily to exclude the
underlying tables while you are operating on them.
The order of indexes in the MERGE table and
its underlying tables should be the same. If you use
ALTER TABLE to add a
UNIQUE index to a table used in a
MERGE table, and then use ALTER
TABLE to add a non-unique index on the
MERGE table, the index ordering is
different for the tables if there was already a non-unique
index in the underlying table. (This happens because
ALTER TABLE puts UNIQUE
indexes before non-unique indexes to facilitate rapid
detection of duplicate keys.) Consequently, queries on tables
with such indexes may return unexpected results.
If you encounter an error message similar to ERROR
1017 (HY000): Can't find file:
'mm.MRG' (errno: 2) it
generally indicates that some of the base tables are not using
the MyISAM storage engine. Confirm that all
of these tables are MyISAM.
The maximum number of rows in a MERGE table
is 232 (~4.295E+09; the same as for
a MyISAM table). It is not possible to
merge multiple MyISAM tables into a single
MERGE table that would have more than this
number of rows. However, if you build MySQL using the
--with-big-tables option, then the maximum
number of rows is increased to 264
(1.844E+19); for more information, see
Section 2.4.15.2, “Typical configure Options”.
Beginning with MySQL 5.0.4, all standard binaries are built with this option.
The MERGE storage engine does not support
INSERT DELAYED statements.
Using MERGE on underlying
MyISAM tables that have different row
formats is possible.
As of MySQL 5.0.44, if a MERGE table cannot be
opened or used because of a problem with an underlying table,
CHECK TABLE displays information about which
table caused the problem.

User Comments
One thing to add: you can not create fulltext indexes on merge table.
If a MyISAM table is part of a MERGE table, you can not just copy the table files as you upgrade from MySQL 4.1 to 5.0. Instead, you HAVE TO dump the table and read it back in.
If you don't: you will get errors indicating that the tables are not defined identically.
Actually, you don't have to drop and repopulate your MyISAM tables; running an ALTER TABLE statement (for instance, using CHANGE COLUMN to transform the primary key into its current definition) will upgrade the MyISAM table to the current version and the MERGE table will continue to function.
You can see the MyISAM version in SHOW TABLE STATUS; notice that MyISAM tables created by MySQL 4.1 are version 9 and MyISAM tables created by MySQL 5.0 are version 10.
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