Mysql commit sometimes takes minutes to finish - mysql

Question

Ive been having this problem for over 1 week now. Ive allready gone though the similar problems other people had here on stackoverflow. Im running Mysql 5.6.10.
"query end" step very long at random times
UPDATE statements are in "query end state"
Lots of "Query End" states in MySQL, all connections used in a matter of minutes
It happends randomly. But every 5 minutes or so, the commit takes a very very long time. And the size of the transation insert is usually around 1-2000 rows.
Ive been changing settings so much, ive kind of lost it i decided to create a questions here.
My inserts/updates are sqlfiles that have been generated by my program. Then i have a windows service that runs every 1,5 minutes processing the files. I build up a string of many sql files in a transaction mode. It works 4 out of 5 time very smooth, but 1 out of 5 it jams.
It usually happends on the same table, and most of the times its regarding inserts but also happends on updates. So i doubt it has to do with the structure of my tables but you never know until its solved :)
This is the table structure
CREATE TABLE `int_links_root_1` (
`IntLinksRootId` bigint(20) NOT NULL AUTO_INCREMENT,
`UrlId` int(11) NOT NULL,
`Link` varchar(2000) NOT NULL,
`AnchorText` varchar(500) DEFAULT NULL,
`Title` varchar(2000) DEFAULT NULL,
`PageText` varchar(8000) DEFAULT NULL,
`Added` datetime DEFAULT NULL,
`LastModifiedDatetime` datetime DEFAULT NULL,
PRIMARY KEY (`IntLinksRootId`),
KEY `Int_Links_UrlId_idx_1` (`UrlId`),
FULLTEXT KEY `FullText` (`AnchorText`,`Title`,`PageText`),
CONSTRAINT `Int_Links_UrlId_idx_1` FOREIGN KEY (`UrlId`) REFERENCES `urls` (`UrlId`) ON DELETE CASCADE ON UPDATE NO ACTION
) ENGINE=InnoDB AUTO_INCREMENT=1708708 DEFAULT CHARSET=utf8$$
These are 'show variables'
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Ssl_finished_connects 0
Ssl_server_not_after
Ssl_server_not_before
Ssl_session_cache_hits 0
Ssl_session_cache_misses 0
Ssl_session_cache_mode NONE
Ssl_session_cache_overflows 0
Ssl_session_cache_size 0
Ssl_session_cache_timeouts 0
Ssl_sessions_reused 0
Ssl_used_session_cache_entries 0
Ssl_verify_depth 0
Ssl_verify_mode 0
Ssl_version
Table_locks_immediate 50440
Table_locks_waited 0
Table_open_cache_hits 4
Table_open_cache_misses 0
Table_open_cache_overflows 0
Tc_log_max_pages_used 0
Tc_log_page_size 0
Tc_log_page_waits 0
Threads_cached 3
Threads_connected 5
Threads_created 8
Threads_running 3
Uptime 3329
Uptime_since_flush_status 3329
I have tried all different innodb_flush_log_at_trx_commit settings. Im certain that my queries are optimal as they run very fast occasionaly, im almost certain that it has to do with my flushing. Ive also tried disabling autocommit but it still happends. Query cache is disabled. But any ideas are more than welcome. Maybe my disks are just to slow?
The system is not in production so i can restart it and test any suggestions.
Please let me know if i can provide any more details.

Answer 1

Are you sure that previous commits already finished ? I am not faniliar with inner structure of mysql but couldnt it rebuild indexing, which is really slow for large tables. Or you can run multiple queries at a time but fifth one is just out of rhreads count and is in queue waiting for rest to finish.