Mysql – Database for efficient retrieval of data from large data set

The basic problem you have is that everything is recursive and you are attempting to lock pages of data in InnoDB, creating lots of MVCC info. In some case, you may have attempted to lock the same InnoDB page repeatedly. That explains the deadlocks. I have commented on this situation deeply with someone in three separate posts on this same issue:

• Trouble deciphering a deadlock in an innodb status log
• Will these two queries result in a deadlock if executed in sequence?
• Reasons for occasionally slow queries?

You need a workaround. You may want to try the following algorithm:

For this example

• id = 12
• amount = 22.75

Step 01) Make a table to collect all father_ids to be updated

DROP TABLE IF EXISTS fathers_to_update;
CREATE TABLE fathers_to_update
(
    father_id INT NOT NULL,
    PRIMARY KEY (father_id)
);

Step 02) Making a table that will be a FIFO queue. Put the value of 12 into the queue:

DROP TABLE IF EXISTS fathers_to_queue;
CREATE TABLE fathers_to_queue
(
    father_id INT,
    id INT NOT NULL AUTO_INCREMENT,
    PRIMARY KEY (id)
);
INSERT INTO fathers_to_queue (father_id) VALUES (12);

Step 03) Get the Count of fathers_to_queue

SELECT COUNT(1) FROM fathers_to_queue;

If the count is 0, goto Step 07)

Step 04) Remove the front number in fathers_to_queue

SELECT MIN(id),father_id INTO @frontndx,@dad FROM fathers_to_queue;
DELETE FROM fathers_to_queue WHERE id = @frontndx;

Step 05) Collect all father_ids from 161_ft_individual whose id is @dad into the queue

INSERT INTO fathers_to_update SELECT father_id FROM 161_ft_individual WHERE id = @dad;
INSERT INTO fathers_to_queue (father_id) SELECT father_id FROM 161_ft_individual WHERE id = @dad;

Step 06) Go back to Step 03

Step 07) Perform a single UPDATE of all records in 161_ft_individual you collected in fathers_to_update

UPDATE fathers_to_update A
LEFT JOIN 161_ft_individual B
USING (father_id)
SET B.total_leg=B.total_leg+@amount;

That's it. I basically performed a preoder tree traversal back up the hierarchy to all records until father_id was NULL, which makes Step 03 stop collecting father_ids.

Give it a Try !!!

UPDATE 2011-12-16 12:18 EDT

Back on October 24, 2011, I actually wrote an algorithm in the MySQL Stored Procedure language to perform preorder tree traversal: Find highest level of a hierarchical field: with vs without CTEs . Hope it helps !!!

MySQL should include a number of starting point configuration files for my.cnf that can adjust the memory usage. The files are named my-small.cnf, my-medium.cnf, my-large.cnf, and my-huge.cnf.

There is an online MySQL memory usage calculator at http://www.mysqlcalculator.com/. By comparing the starting point files and using the memory usage calculator you should be able to adjust your my.cnf configuration file to accomodate your server's memory constraints.

For more information about what each parameter does, you can reference the MySQL documentation available online. Here is a link to the MySQL documentation for MySQL server 5.1: http://dev.mysql.com/doc/refman/5.1/en/server-system-variables.html