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In code, I drop a table and then create the table, and do the same in multi databases at one server, everything works ok. And then I query tables with the SQL " SHOW TABLES ", sometimes this sql throw exception: Fatal error encountered during command execution, sometimes it works ok. And I am sure this is not raised by COMMAND TIMEOUT. It should be other reasons.

here is the drop table and create table sql:

DROP TABLE IF EXISTS `a`;
CREATE TABLE IF NOT EXISTS `a`
SELECT 
  id,
  IF (mapping.name IS NULL, ne.autoname, mapping.name) AS autoname FROM b ne
LEFT JOIN test.a_mapping mapping ON ne.autoName = mapping.autoname;
ALTER TABLE `a` ADD INDEX `id_idx` (`id`); 
DELETE FROM `a` WHERE id = 1000000; 
INSERT INTO `a`(id, autoname) VALUES(1000000, @count);

here is the show tables codes:

  MySqlDataReader dataReader = null;
    try{            
        MySqlCommand cmd = new MySqlCommand(MySqlUtils.SQL_GET_TABLES, connection);
        cmd.CommandTimeout = BaseOptimonConfig.Instance.CommandTimeout;
        dataReader = MySqlUtils.ExecuteReader(cmd); // just add try catch in this method.
        while (dataReader.Read())
        {
            if (MySqlUtils.GetSqlString(dataReader, 0).ToLower().Equals(tableName))
            {
                return true;
            }
        }
    }
    finally
    {
        MySqlUtils.CloseSqlReader(dataReader);
    }
laalto
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