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I am the senior developer on a Software-as-a-Service application used by many different customers. Our software runs on a cluster of Apache / PHP application servers, powered by a MySQL backend. On one particular instance of the software, the PHP code to query the list of category names is timing out when the customer has more than 29 categories. I know this makes no sense; there is nothing special about the number 30 that would break this and other customers have a lot more than 30 categories, however, the problem is 100% reproducible when this one installation has 30 or more categories and goes away when there's less than 30 categories.

The table in question is:

  `id` int(10) unsigned NOT NULL auto_increment,
  `name` varchar(64) NOT NULL,
  `title` varchar(128) NOT NULL,
  `parent` int(10) unsigned NOT NULL,
  `keywords` varchar(255) NOT NULL,
  `description` text NOT NULL,
  `status` enum('Active','Inactive','_Deleted','_New') NOT NULL default 'Active',
  `style` enum('_Unknown') default NULL COMMENT 'Autoenum;',
  `order` smallint(5) unsigned NOT NULL,
  `created_at` datetime NOT NULL,
  `modified_at` datetime default NULL,
  PRIMARY KEY  (`id`),
  KEY `name` (`name`),
  KEY `parent` (`parent`),
  KEY `created_at` (`created_at`),
  KEY `modified_at` (`modified_at`),
  KEY `status` (`status`)

The code in question recursively queries the table to fetch all the categories. It issues a

SELECT * FROM `categories` WHERE `parent`=0 ORDER BY `order`,`name`

And then repeats this query for each row returned, but using WHERE parent=$category_id each time. (I am sure this procedure could be improved, but that's probably another question)

As far as I can tell, the following query is hanging forever:

SELECT * FROM `categories` WHERE `parent`=22 ORDER BY `order`,`name`

I can execute this query in the mysql client on the server perfectly fine, and I can execute it in PHPMyAdmin without problems as well.

Note that it's not that specific query which is the problem. If I DELETE FROM categories WHERE id=22 then a different query similar to the one above will then hang. Also, the query above returns zero rows when I run it manually.

I suspected that the table may be corrupt, and I tried REPAIR TABLE and OPTIMIZE TABLE but nether of these reported problems nor solved the issue. I dropped the table and recreated, but the problem returned. This is exactly the same table structure and PHP code other customers are using with no issues for anyone else, including customers who have far more than 30 categories.

The PHP code is not recursing forever. (This is not and infinite loop)

MySQL server is running CentOS linux with mysqld Ver 5.0.92-community for pc-linux-gnu on i686 (MySQL Community Edition (GPL))

Load on the MySQL server is low: load average: 0.58, 0.75, 0.73, Cpu(s): 4.6%us, 2.9%sy, 0.0%ni, 92.2%id, 0.0%wa, 0.0%hi, 0.3%si, 0.0%st. Negligible swap being used (448k)

How can I troubleshoot this issue? Any suggestions as to what might be going on?

UPDATE: I TRUNCEed the table and inserted 30 rows of dummy data:

INSERT INTO `categories` (`id`, `name`, `title`, `parent`, `keywords`, `description`, `status`, `style`, `order`, `created_at`, `modified_at`) VALUES
(1, 'New Category', '', 0, '', '', 'Inactive', NULL, 1, '2011-10-25 12:06:30', '2011-10-25 12:06:34'),
(2, 'New Category', '', 0, '', '', 'Inactive', NULL, 2, '2011-10-25 12:06:39', '2011-10-25 12:06:40'),
(3, 'New Category', '', 0, '', '', 'Inactive', NULL, 3, '2011-10-25 12:06:41', '2011-10-25 12:06:42'),
(4, 'New Category', '', 0, '', '', 'Inactive', NULL, 4, '2011-10-25 12:06:46', '2011-10-25 12:06:47'),
(5, 'New Category', '', 0, '', '', 'Inactive', NULL, 5, '2011-10-25 12:06:49', NULL),
(6, 'New Category', '', 0, '', '', 'Inactive', NULL, 6, '2011-10-25 12:06:51', '2011-10-25 12:06:52'),
(7, 'New Category', '', 0, '', '', 'Inactive', NULL, 7, '2011-10-25 12:06:53', '2011-10-25 12:06:54'),
(8, 'New Category', '', 0, '', '', 'Inactive', NULL, 8, '2011-10-25 12:06:56', '2011-10-25 12:06:57'),
(9, 'New Category', '', 0, '', '', 'Inactive', NULL, 9, '2011-10-25 12:06:59', '2011-10-25 12:06:59'),
(10, 'New Category', '', 0, '', '', 'Inactive', NULL, 10, '2011-10-25 12:07:01', '2011-10-25 12:07:01'),
(11, 'New Category', '', 0, '', '', 'Inactive', NULL, 11, '2011-10-25 12:07:03', '2011-10-25 12:07:03'),
(12, 'New Category', '', 0, '', '', 'Inactive', NULL, 12, '2011-10-25 12:07:05', '2011-10-25 12:07:05'),
(13, 'New Category', '', 0, '', '', 'Inactive', NULL, 13, '2011-10-25 12:07:06', '2011-10-25 12:07:07'),
(14, 'New Category', '', 0, '', '', 'Inactive', NULL, 14, '2011-10-25 12:07:08', '2011-10-25 12:07:09'),
(15, 'New Category', '', 0, '', '', 'Inactive', NULL, 15, '2011-10-25 12:07:11', '2011-10-25 12:07:12'),
(16, 'New Category', '', 0, '', '', 'Inactive', NULL, 16, '2011-10-25 12:07:13', '2011-10-25 12:07:14'),
(17, 'New Category', '', 0, '', '', 'Inactive', NULL, 17, '2011-10-25 12:09:41', '2011-10-25 12:09:42'),
(18, 'New Category', '', 0, '', '', 'Inactive', NULL, 18, '2011-10-25 12:09:47', NULL),
(19, 'New Category', '', 0, '', '', 'Inactive', NULL, 19, '2011-10-25 12:09:48', NULL),
(20, 'New Category', '', 0, '', '', 'Inactive', NULL, 20, '2011-10-25 12:09:48', NULL),
(21, 'New Category', '', 0, '', '', 'Inactive', NULL, 21, '2011-10-25 12:09:49', NULL),
(22, 'New Category', '', 0, '', '', 'Inactive', NULL, 22, '2011-10-25 12:09:50', NULL),
(23, 'New Category', '', 0, '', '', 'Inactive', NULL, 23, '2011-10-25 12:09:51', NULL),
(24, 'New Category', '', 0, '', '', 'Inactive', NULL, 24, '2011-10-25 12:09:51', NULL),
(25, 'New Category', '', 0, '', '', 'Inactive', NULL, 25, '2011-10-25 12:09:52', NULL),
(26, 'New Category', '', 0, '', '', 'Inactive', NULL, 26, '2011-10-25 12:09:53', NULL),
(27, 'New Category', '', 0, '', '', 'Inactive', NULL, 27, '2011-10-25 12:09:54', NULL),
(28, 'New Category', '', 0, '', '', 'Inactive', NULL, 28, '2011-10-25 12:09:55', NULL),
(29, 'New Category', '', 0, '', '', 'Inactive', NULL, 29, '2011-10-25 12:09:56', NULL),
(30, 'New Category', '', 0, '', '', 'Inactive', NULL, 30, '2011-10-25 12:09:57', NULL);

No parents at all, all categories are on the top level. problem is still there. The following query, executed by PHP, fails:

SELECT * FROM `categories` WHERE `parent`=22 ORDER BY `order`,`name`

Here's the EXPLAIN:

mysql> EXPLAIN SELECT * FROM `categories` WHERE `parent`=22 ORDER BY `order`,`name`;
| id | select_type | table      | type | possible_keys | key    | key_len | ref   | rows | Extra                       |
|  1 | SIMPLE      | categories | ref  | parent        | parent | 4       | const |    1 | Using where; Using filesort | 
1 row in set (0.00 sec)

UPDATE #2: I have now tried all of the following:

  1. I copied this table and data to a different site with the same software. The problem did not follow the table. It seems to be confined to this one database.
  2. I changed the index as gbn's answer suggested. The problem remained.
  3. I dropped the table and recreated as an InnoDB table and inserted the same 30 test rows above. The problem remained.

I suspect it must be something with this database...

UPDATE #3: I completely dropped the database and recreated it under a new name, importing her data. The problem remains.

I have found that the actual PHP statement which hangs is a call to mysql_query(). Statements after this never get executed.

While that call hangs, MySQL lists the thread as sleeping!

mysql> show full processlist;
| Id    | User             | Host                        | db                   | Command | Time | State | Info                  |
|  5560 | root             | localhost                   | problem_db           | Query   |    0 | NULL  | show full processlist |  
                          ----- many rows which have no relevancy; only rows from this customer's app are shown ------
| 16341 | shared_db        | oak01.sitepalette.com:53237 | shared_db            | Sleep   |  308 |       | NULL                  | 
| 16342 | problem_db       | oak01.sitepalette.com:60716 | problem_db           | Sleep   |  307 |       | NULL                  | 
| 16344 | shared_db        | oak01.sitepalette.com:53241 | shared_db            | Sleep   |  308 |       | NULL                  | 
| 16346 | problem_db       | oak01.sitepalette.com:60720 | problem_db           | Sleep   |  308 |       | NULL                  |  

UPDATE #4: I have narrowed it down to the combination of two tables, the categories table detailed above and a media_images table with 556 rows. If the media_images table contains less than 556 rows, or the categories table contains less than 30 rows, the problem goes away. It's like it's some sort of MySQL limit I'm hitting here...

UPDATE #5: I just tried moving the database to a different MySQL server altogether and the problem went away... So it's related to my production database server...

UPDATE #6: Here's the relevant PHP code which hangs each time:

    public function find($type,$conditions='',$order='',$limit='')
            if($this->_link == self::AUTO_LINK)
                    $this->_link = DFStdLib::database_connect();

                    $q = "SELECT ".($type==_COUNT?'COUNT(*)':'*')." FROM `{$this->_table}`";
                            $q .= " WHERE $conditions";
                            $q .= " ORDER BY $order";
                            $q .= " LIMIT $limit";

                            case _ALL:
                                    $res = @mysql_query($q,$this->_link);
                                    DFSkel::log(DFSkel::LOG_DEBUG,"res = $res");

This code's in production and works fine on all other installs. Just on one install, it hangs at $res = @mysql_query($q,$this->_link);. I know because I see the mysql_query in the debug log, and not the res =, and when I strace the PHP process, it's hung at read(

UPDATE #whatever-it-is-I-hate-this-&(#^&-issue! This has now started happening to two customers of mine. I just fired up tcpdump and it looks like the response from MySQL is never sent completely. The TCP stream just seems to hang before the full MySQL response can be sent. (I am still investigating however)

UPDATE #I-have-gone-completly-crazy-but-it-works-now-kinda: Ok, this makes no sense, but I have found a solution. If I assign a second IP address to the MySQL server's eth2 interface, and use one IP for NFS traffic and the second IP for MySQL, then the problem goes away. It's like I'm somehow... overloading the Ip address if both NFS+MySQL traffic both go to that IP. But that makes zero sense because you can't "overload" an IP address. Saturating an interface sure, but it's the same interface.

Any idea what in the heck is going on here? This is probably a unix.SE or ServerFault question at this point... (At least it works now...)

UPDATE #why-oh-why: This issue is still occurring. It's started happening even using two different IPs. I can keep creating new private IPs, but clearly something's wrong.

share|improve this question
Well here's a link to the potential 'other question' on doing recursive hierarchical query all within mysql. –  Derek Downey Oct 25 '11 at 16:01
@DTest sure, I will add that in a moment. Thanks for the other link! –  Josh Oct 25 '11 at 16:08
We're actively trying to troubleshoot this in chat for anyone finding this question. –  Josh Oct 25 '11 at 19:11
Hi Josh. You said the queries run normally inside your MySQL client and in PHPMyAdmin? only the PHP application hangs out? –  marcioAlmada Oct 26 '11 at 9:48
@marcioAlmada yes, that's correct. I am extremely confused by this whole situation. –  Josh Oct 26 '11 at 12:57
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5 Answers

For general profiling of what exactly is going on in the query plan, you can try PROFILING

It will basically help you determine where the hangup is.

Of course, it only works if you've compiled MySQL with enable-profiling.

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Ideas (not sure if applies to MyISAM though, I work with InnoDB)

Change the index "parent" so it is on 3 columns: parent, order, name. This matches the WHERE .. ORDER BY

Remove SELECT *. Only take the columns you need. Add any other columns to the index "parent"

This will allow the optimiser to use only the index because it is now covering. As it stands, you have to read the whole table because the indexes aren't useful for that query

share|improve this answer
Problem persists after changing the parent index to (parent, order, name) –  Josh Oct 25 '11 at 16:29
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a) Hi Josh. You said the queries run normally inside your MySQL client and in PHPMyAdmin? only the PHP application hangs out?
b) @marcioAlmada yes, that's correct

I'd say you have hit schrödinbug. You might try to die() after or before your query and try to browse your code for if statements which happens very rarely. It's hard to say what hangs when we do not have your code.

EDIT: I'd currently say that it might be this line

$this->_link = DFStdLib::database_connect();

which (I assume) creates connection everytime function is called. That's might be the problem. What is your max_connections in my.cnf?

share|improve this answer
I know exactly where it hangs: it never gets past a call to mysql_query() –  Josh Oct 26 '11 at 18:50
Could you post +- 10 lines of your code? –  genesis Oct 26 '11 at 18:51
done. I am going to debug this with tcpdump in the next few days. If this really is a PHP issue, then I should post a new question on SO. –  Josh Oct 26 '11 at 19:40
@Josh: UPDATED my answer –  genesis Oct 26 '11 at 20:29
Thanks @genesis... but that's not it, for two reasons. 1. that code is only called if I am using my "Automatically establish a database link" feature, which is done by setting $this->_link to a constant: self::AUTO_LINK. 2. Even if I were, that code is in an if: if($this->_link == self::AUTO_LINK), and the next line $this->_link = DFStdLib::database_connect(); changes the value of $this->_link so the if would not be run again. I am sure there is only one connection to the database per thread. (See the processlist) –  Josh Oct 26 '11 at 20:35
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I would check out several things on the Production DB Server

  • Check #1 : Make sure the data volume where /var/lib/mysql is mounted does not have bad blocks. This may require downtime to perform fsck (file system check)
  • Check #2 : Make sure the table is not heavy with DML (INSERT/UPDATE/DELETE) or SELECTs
  • Check # 3 : Make sure PHP is issuing mysql_close() properly and the app is not relying on Apache to close the DB Connection for you. Otherwise, you may have some sort of race condition when PHP might attempt using DB Connection Resources that have been effectively closed by MySQL.
  • Check #4 : Make sure the DB Server's OS does not have a stockpilke of TIME_WAITs in the netstat listing of Connections that were closed in the eyes of PHP and MySQL but the OS is still hanging on to. You can see this with netstat | grep -i mysql | grep TIME_WAIT
  • Check #5 : Make sure you are not using mysql_pconnect. There is still an open bug report on persistent connections not closing properly. I hate to imagine trying to access those connections.
  • Check #6 : Make sure DB Traffic Throughput via Load Balancers, Switches, Firewalls, and DNS Servers are identical for Production DB Server and other outside servers. Personally, I hate using DNS names in the host column of mysql.user and mysql.db. I usually have clients strip them out and replaced with hard IPs. I also add skip-host-cache and skip-name-resolve to bypass mysqld's use of DNS. I could thus relate to @marcioAlmada's answer as a checkpoint to look over.

If you feel that none of these checks are useful, please comment ASAP and let me know so that I can remove my answer.

share|improve this answer
I definitely think this is a useful answer! I am not sure I am closing all connections, so I can try that. I don't think that /var has any bad blocks (it's on a RAID10) but I could easily be wrong. I'll check netstat, good idea there! I'm not using mysql_pconnect but will check network/dns/etc. –  Josh Oct 26 '11 at 22:23
@Josh: If you're seeing bad blocks, there will be a lot of messages about them in dmesg. Unless you have hardware RAID, in which case check your hardware raid monitor program. –  derobert Oct 31 '11 at 21:30
When this happens, I will sometimes (but not always) see a single TIME_WAIT MySQL connection. There are not a large number by any means... The table is not heavy with activity. –  Josh Nov 1 '11 at 21:37
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I am almost convinced this is a PHP issue rather than a MySQL issue, but yet why does it work when I switch MySQL servers?

Some attempts:

  • Firewalls?? Is there any firewall blocking your application and preventing it from making any request to your production database server or vice-versa?

  • Are you using a domain name in your connection configuration or an IP address? Using a domain name could slow down the database interaction a bit and this combined with a short PHP maximum script execution time would cause a forever hangout

This last suggestion seems to explain the strange variable behavior when switching database servers. One might be responding much faster than the other, and since for every found record you will have a secondary query, that hypotesis would explain why the application delays only with a certain amount of queried results (> 30).

At least we got to a primary conclusion. Definitely the problem is not with MySQL server istelf. Took a look at the documentation and there seems to be no feature limits that suits your specific situation, also I never had any problem with recursive tables and specific amount of entries.

Hope that helps.

share|improve this answer
There is a firewall on the MySQL server, but that shouldn't be an issue as it's the same MySQL server which so many other customers use without issue, and the issue goes away with <30 rows in categories. I was using a DNS name, I can switch to an IP and see if that changes anything... –  Josh Oct 26 '11 at 20:31
And what about the PHP maximun script execution time? Updated the anwser. –  marcioAlmada Oct 26 '11 at 20:35
Updated the anwser –  marcioAlmada Oct 26 '11 at 20:41
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