Bug #68722 Got error -1 from storage engine
Submitted: 19 Mar 2013 21:39 Modified: 16 Jul 2013 13:17
Reporter: Karel Dytrych Email Updates:
Status: Closed Impact on me:
None 
Category:MySQL Server: Errors Severity:S3 (Non-critical)
Version:5.6.10 OS:Linux (Debian)
Assigned to: CPU Architecture:Any
Tags: error -1, innodb, mysql 5.6

[19 Mar 2013 21:39] Karel Dytrych
Description:
Hi,
I moved my aplication from old server with MySQL 5.1 to new much more powerfull server where i run new MySQL 5.6.

Now I'm getting couple of time per day strange error:

"Got error -1 from storage engine"

It happen only couple of times per day with simple queries like:

UPDATE innoDbTable SET int_column = 1 WHERE primarykey = 96

or

INSERT INTO differentInnoTable (10cols) VALUES (10values)...

When i see this error in my log i use exactly the same query from mysql console and it always work...

Do you have any hints?

Btw server is not overloaded.

How to repeat:
It happen only time to time
[19 Mar 2013 21:45] Karel Dytrych
Variables from my server:

autocommit  ON
automatic_sp_privileges ON
back_log    350
basedir /opt/mysql/server-5.6
big_tables  OFF
bind_address    *
binlog_cache_size   32768
binlog_checksum CRC32
binlog_direct_non_transactional_updates OFF
binlog_format   STATEMENT
binlog_max_flush_queue_time 0
binlog_order_commits    ON
binlog_row_image    FULL
binlog_rows_query_log_events    OFF
binlog_stmt_cache_size  32768
bulk_insert_buffer_size 8388608
completion_type NO_CHAIN
concurrent_insert   AUTO
connect_timeout 10
core_file   OFF
datadir /var/lib/mysql/
delay_key_write ON
delayed_insert_limit    100
delayed_insert_timeout  300
delayed_queue_size  1000
disconnect_on_expired_password  ON
div_precision_increment 4
end_markers_in_json OFF
enforce_gtid_consistency    OFF
eq_range_index_dive_limit   10
error_count 0
event_scheduler OFF
expire_logs_days    10
explicit_defaults_for_timestamp OFF
external_user   
flush   OFF
flush_time  0
foreign_key_checks  ON
group_concat_max_len    1024
have_compress   YES
have_crypt  YES
have_dynamic_loading    YES
have_geometry   YES
have_openssl    DISABLED
have_profiling  YES
have_query_cache    YES
have_rtree_keys YES
have_ssl    DISABLED
have_symlink    YES
host_cache_size 678
hostname    tik02
identity    0
ignore_builtin_innodb   OFF
ignore_db_dirs  
init_connect    
init_file   
init_slave  
innodb_adaptive_flushing    ON
innodb_adaptive_flushing_lwm    10
innodb_adaptive_hash_index  ON
innodb_adaptive_max_sleep_delay 150000
innodb_additional_mem_pool_size 8388608
innodb_api_bk_commit_interval   5
innodb_api_disable_rowlock  OFF
innodb_api_enable_binlog    OFF
innodb_api_enable_mdl   OFF
innodb_api_trx_level    0
innodb_autoextend_increment 64
innodb_autoinc_lock_mode    1
innodb_buffer_pool_dump_at_shutdown OFF
innodb_buffer_pool_dump_now OFF
innodb_buffer_pool_filename ib_buffer_pool
innodb_buffer_pool_instances    8
innodb_buffer_pool_load_abort   OFF
innodb_buffer_pool_load_at_startup  OFF
innodb_buffer_pool_load_now OFF
innodb_buffer_pool_size 33554432
innodb_change_buffer_max_size   25
innodb_change_buffering all
innodb_checksum_algorithm   innodb
innodb_checksums    ON
innodb_cmp_per_index_enabled    OFF
innodb_commit_concurrency   0
innodb_compression_failure_threshold_pct    5
innodb_compression_level    6
innodb_compression_pad_pct_max  50
innodb_concurrency_tickets  5000
innodb_data_file_path   ibdata1:12M:autoextend
innodb_data_home_dir    
innodb_disable_sort_file_cache  OFF
innodb_doublewrite  ON
innodb_fast_shutdown    1
innodb_file_format  Antelope
innodb_file_format_check    ON
innodb_file_format_max  Antelope
innodb_file_per_table   ON
innodb_flush_log_at_timeout 1
innodb_flush_log_at_trx_commit  1
innodb_flush_method 
innodb_flush_neighbors  1
innodb_flushing_avg_loops   30
innodb_force_load_corrupted OFF
innodb_force_recovery   0
innodb_ft_aux_table 
innodb_ft_cache_size    8000000
innodb_ft_enable_diag_print OFF
innodb_ft_enable_stopword   ON
innodb_ft_max_token_size    84
innodb_ft_min_token_size    3
innodb_ft_num_word_optimize 2000
innodb_ft_server_stopword_table 
innodb_ft_sort_pll_degree   2
innodb_ft_user_stopword_table   
innodb_io_capacity  200
innodb_io_capacity_max  2000
innodb_large_prefix OFF
innodb_lock_wait_timeout    50
innodb_locks_unsafe_for_binlog  OFF
innodb_log_buffer_size  8388608
innodb_log_file_size    50331648
innodb_log_files_in_group   2
innodb_log_group_home_dir   ./
innodb_lru_scan_depth   1024
innodb_max_dirty_pages_pct  75
innodb_max_dirty_pages_pct_lwm  0
innodb_max_purge_lag    0
innodb_max_purge_lag_delay  0
innodb_mirrored_log_groups  1
innodb_monitor_disable  
innodb_monitor_enable   
innodb_monitor_reset    
innodb_monitor_reset_all    
innodb_old_blocks_pct   37
innodb_old_blocks_time  1000
innodb_online_alter_log_max_size    134217728
innodb_open_files   2000
innodb_optimize_fulltext_only   OFF
innodb_page_size    16384
innodb_print_all_deadlocks  OFF
innodb_purge_batch_size 300
innodb_purge_threads    1
innodb_random_read_ahead    OFF
innodb_read_ahead_threshold 56
innodb_read_io_threads  4
innodb_read_only    OFF
innodb_replication_delay    0
innodb_rollback_on_timeout  OFF
innodb_rollback_segments    128
innodb_sort_buffer_size 1048576
innodb_spin_wait_delay  6
innodb_stats_auto_recalc    ON
innodb_stats_method nulls_equal
innodb_stats_on_metadata    OFF
innodb_stats_persistent ON
innodb_stats_persistent_sample_pages    20
innodb_stats_sample_pages   8
innodb_stats_transient_sample_pages 8
innodb_strict_mode  OFF
innodb_support_xa   ON
innodb_sync_array_size  1
innodb_sync_spin_loops  30
innodb_table_locks  ON
innodb_thread_concurrency   0
innodb_thread_sleep_delay   10000
innodb_undo_directory   .
innodb_undo_logs    128
innodb_undo_tablespaces 0
innodb_use_native_aio   ON
innodb_use_sys_malloc   ON
innodb_version  1.2.10
innodb_write_io_threads 4
insert_id   0
interactive_timeout 28800
join_buffer_size    262144
keep_files_on_create    OFF
key_buffer_size 16777216
key_cache_age_threshold 300
key_cache_block_size    1024
key_cache_division_limit    100
lock_wait_timeout   31536000
locked_in_memory    OFF
long_query_time 2.000000
low_priority_updates    OFF
lower_case_file_system  OFF
lower_case_table_names  0
master_info_repository  FILE
master_verify_checksum  OFF
max_allowed_packet  33554432
max_binlog_cache_size   18446744073709547520
max_binlog_size 104857600
max_binlog_stmt_cache_size  18446744073709547520
max_connect_errors  100
max_connections 1500
max_delayed_threads 20
max_error_count 64
max_heap_table_size 16777216
max_insert_delayed_threads  20
max_join_size   18446744073709551615
max_length_for_sort_data    1024
max_prepared_stmt_count 16382
max_relay_log_size  0
max_seeks_for_key   18446744073709551615
max_sort_length 1024
max_sp_recursion_depth  0
max_tmp_tables  32
max_user_connections    0
max_write_lock_count    18446744073709551615
metadata_locks_cache_size   1024
metadata_locks_hash_instances   8
min_examined_row_limit  0
multi_range_count   256
net_buffer_length   16384
net_read_timeout    30
net_retry_count 10
net_write_timeout   60
preload_buffer_size 32768
profiling   OFF
profiling_history_size  15
protocol_version    10
proxy_user  
pseudo_slave_mode   OFF
pseudo_thread_id    43865
query_alloc_block_size  8192
query_cache_limit   1048576
query_cache_min_res_unit    4096
query_cache_size    16777216
query_cache_type    OFF
query_cache_wlock_invalidate    OFF
query_prealloc_size 8192
rand_seed1  0
rand_seed2  0
range_alloc_block_size  4096
read_buffer_size    131072
read_only   OFF
read_rnd_buffer_size    262144
skip_external_locking   ON
skip_name_resolve   ON
skip_networking OFF
skip_show_database  OFF
slow_launch_time    2
slow_query_log  ON
slow_query_log_file /var/log/mysql/mysql-slow.log
socket  /var/run/mysqld/mysqld.sock
sort_buffer_size    262144
storage_engine  InnoDB
stored_program_cache    256
sync_binlog 0
sync_frm    ON
sync_master_info    10000
sync_relay_log  10000
sync_relay_log_info 10000
system_time_zone    CET
table_definition_cache  1400
table_open_cache    2000
table_open_cache_instances  1
thread_cache_size   8
thread_concurrency  10
thread_handling one-thread-per-connection
thread_stack    262144
time_format %H:%i:%s
time_zone   SYSTEM
timed_mutexes   OFF
timestamp   1363551365.087333
tmp_table_size  16777216
tmpdir  /tmp
transaction_alloc_block_size    8192
transaction_allow_batching  OFF
transaction_prealloc_size   4096
tx_isolation    REPEATABLE-READ
tx_read_only    OFF
unique_checks   ON
wait_timeout    28800
warning_count   0
[20 Mar 2013 3:25] MySQL Verification Team
do you ever kill queries?  check if the errors happen when : show global status like '%kill%';  values increase ?
[20 Mar 2013 9:15] MySQL Verification Team
Is there anything of note in the error log?
[22 Mar 2013 13:37] Karel Dytrych
SHOW GLOBAL STATUS LIKE '%kill%';

It always return Com_kill 0

I see no error in mysql.log or anything in mysql-slow.log

I'm totally lost with this issue. At old server everything works fine, at this newer server is this... Both servers are Debian, new server has 3x more RAM etc. At this server there is no other application which could affect this one..

df says:
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/xvda2           309637120   3667968 290240512   2% /
tmpfs                  4189100         0   4189100   0% /lib/init/rw
udev                   4069824        32   4069792   1% /dev
tmpfs                  4189100         4   4189096   1% /dev/shm

Btw old server has MySQL Server: 5.1.66-0+squeeze1

I dumped all information about server to this file
http://k.webovy-servis.com/mysql.html

Does anyone see anything wrong?
[25 Mar 2013 9:29] Michail Epikhin
I get the same error on Windows Server:

on table
CREATE TABLE  `logs`.`DocumentSendLogs` (
  `Id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `UserId` int(10) unsigned NOT NULL,
  `DocumentId` int(10) unsigned NOT NULL,
  `UpdateId` int(10) unsigned DEFAULT NULL,
  `Committed` tinyint(1) unsigned NOT NULL DEFAULT '0',
  `FileDelivered` tinyint(1) unsigned NOT NULL DEFAULT '0' ,
  `DocumentDelivered` tinyint(1) unsigned NOT NULL DEFAULT '0' ,
  PRIMARY KEY (`Id`),
  KEY `FK_DocumentSendLogs_UserId` (`UserId`),
  KEY `FK_DocumentSendLogs_DocumentId` (`DocumentId`),
  KEY `FK_DocumentSendLogs_UpdateId` (`UpdateId`),
  CONSTRAINT `FK_DocumentSendLogs_DocumentId` FOREIGN KEY (`DocumentId`) REFERENCES `document_logs` (`RowId`) ON DELETE CASCADE,
  CONSTRAINT `FK_DocumentSendLogs_UpdateId` FOREIGN KEY (`UpdateId`) REFERENCES `analitfupdates` (`UpdateId`) ON DELETE CASCADE,
  CONSTRAINT `FK_DocumentSendLogs_UserId` FOREIGN KEY (`UserId`) REFERENCES `customers`.`users` (`Id`) ON DELETE CASCADE
) ENGINE=InnoDB AUTO_INCREMENT=27657887 DEFAULT CHARSET=cp1251 ROW_FORMAT=COMPACT;

query:

INSERT INTO Logs.DocumentSendLogs (UserId, DocumentId) VALUES (?, ?);SELECT LAST_INSERT_ID()

periodically returns:
Got error -1 from storage engine

SHOW GLOBAL STATUS LIKE '%kill%':2(static)

On 5.6.8-rc this error does not occur.
[25 Mar 2013 9:46] Karel Dytrych
Btw my table is:

CREATE TABLE `u_checks` 
(
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `u_monitor_id` int(11) DEFAULT NULL,
  `timestamp` timestamp NULL DEFAULT NULL,
  `timestamp_zone` timestamp NULL DEFAULT NULL,
  `code` varchar(45) DEFAULT NULL,
  `request` text ,
  `response` text,
  `response_time_ms` decimal(12,5) DEFAULT NULL,
  `main_time` datetime DEFAULT NULL,
  `freq` int(11) DEFAULT NULL,
  `dtime` tinyint(1) NOT NULL DEFAULT '0',
  `u_robot_id` int(11) DEFAULT NULL,
  PRIMARY KEY (`id`),
  KEY `fk_u_checks_u_monitoring1` (`u_monitoring_id`),
  KEY `monidTime` (`u_monitoring_id`,`timestamp`),
  KEY `u_robot_id` (`u_robot_id`),
  CONSTRAINT `fk_u_checks_u_monitoring1` FOREIGN KEY (`u_monitoring_id`) REFERENCES `u_monitoring` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `u_checks_ibfk_1` FOREIGN KEY (`u_robot_id`) REFERENCES `u_robot` (`id`) ON DELETE SET NULL ON UPDATE CASCADE

) ENGINE=InnoDB AUTO_INCREMENT=2633518 DEFAULT CHARSET=utf8;
[25 Mar 2013 11:21] MySQL Verification Team
http://bugs.mysql.com/bug.php?id=68762 marked as duplicate of this one.
[26 Mar 2013 6:44] MySQL Verification Team
Mark Leith asked me about this, and I could confirm the error -1 problem. It happens in case of deadlocks/lock wait timeouts.  was repeatable on 5.6.10, but not repeatable on the latest source code 5.6.12.  I don't know what bugfix fixed it, still looking.
[1 Apr 2013 16:57] MySQL Verification Team
cause by one of FK violations, lock waits, deadlock...
[13 Apr 2013 15:55] Andre Evertz
I´ve the same problem. The error appears two or three times a day but ist not repeatable.

I´m using MySQL 5.6.10

My log looks like this:

130331 00:01:30 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
2013-03-31 00:01:32 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2013-03-31 00:01:33 2055 [Note] Plugin 'FEDERATED' is disabled.
2013-03-31 00:01:33 7f1c826d5720 InnoDB: Warning: Using innodb_additional_mem_pool_size is DEPRECATED. This option may be removed in future releases, together with the option innodb_use_sys_malloc and with the InnoDB's internal memory allocator.
2013-03-31 00:01:33 2055 [Note] InnoDB: The InnoDB memory heap is disabled
2013-03-31 00:01:33 2055 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2013-03-31 00:01:33 2055 [Note] InnoDB: Compressed tables use zlib 1.2.3
2013-03-31 00:01:33 2055 [Note] InnoDB: CPU does not support crc32 instructions
2013-03-31 00:01:33 2055 [Note] InnoDB: Using Linux native AIO
2013-03-31 00:01:33 2055 [Note] InnoDB: Initializing buffer pool, size = 6.0G
2013-03-31 00:01:33 2055 [Note] InnoDB: Completed initialization of buffer pool
2013-03-31 00:01:33 2055 [Note] InnoDB: Highest supported file format is Barracuda.
2013-03-31 00:01:35 2055 [Note] InnoDB: 128 rollback segment(s) are active.
2013-03-31 00:01:35 2055 [Note] InnoDB: Waiting for purge to start
2013-03-31 00:01:35 2055 [Note] InnoDB: 1.2.10 started; log sequence number 31050205481
2013-03-31 00:01:36 2055 [Note] Server hostname (bind-address): '*'; port: 3306
2013-03-31 00:01:36 2055 [Note] IPv6 is available.
2013-03-31 00:01:36 2055 [Note]   - '::' resolves to '::';
2013-03-31 00:01:36 2055 [Note] Server socket created on IP: '::'.
2013-03-31 00:01:36 2055 [Note] Event Scheduler: Loaded 0 events
2013-03-31 00:01:36 2055 [Note] /usr/local/mysql/bin/mysqld: ready for connections.
Version: '5.6.10-log'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)
[17 Apr 2013 9:17] ymhr ymhr
With this kind of problems, the version should be neither GA nor release candidate!!!!!
[20 Apr 2013 19:09] Andre Evertz
Release 5.6.11 solved the problem for me. I´m running 5.6.11 for 2 days without the above error for now. Before I got one or two of these errors per day.
[22 Apr 2013 7:37] ymhr ymhr
There is no trace for this bug to be solved in the changelog for server version 5.6.11
[22 Apr 2013 12:19] Glaucio Scheibel
Version 5.6.11 solved this problem. I have a process with a big transaction that almost always this bug showed up and now looks all ok.
[23 Apr 2013 23:43] MySQL Verification Team
Please check with 5.6.11. Thanks.
[24 Apr 2013 19:27] Andre Evertz
Yes, after a week running 5.6.11 I´ve never seen this error again. I think 5.6.11 fixed the bug.
[26 Apr 2013 0:50] MySQL Verification Team
According last comments, please test 5.6.11. Thanks,
[26 Apr 2013 6:23] Karel Dytrych
I will check it as soon as possible, but my admin have some issues with upgrade..
[2 May 2013 9:49] Norman Rennhack
I was suffering from the same problem.
After updating to mysql server 5.6.11 I get another error:

2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Because of an error, this step can't continue: 
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : org.pentaho.di.core.exception.KettleException: 
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error inserting row into table [fact_table] with values: [1], [0], [0], [1331], [732], [12]
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error inserting/updating row
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Lock wait timeout exceeded; try restarting transaction
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at org.pentaho.di.trans.steps.tableoutput.TableOutput.writeToTable(TableOutput.java:445)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at org.pentaho.di.trans.steps.tableoutput.TableOutput.processRow(TableOutput.java:128)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at org.pentaho.di.trans.step.RunThread.run(RunThread.java:50)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at java.lang.Thread.run(Thread.java:722)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Caused by: org.pentaho.di.core.exception.KettleDatabaseException: 
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error inserting/updating row
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Lock wait timeout exceeded; try restarting transaction
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at org.pentaho.di.core.database.Database.insertRow(Database.java:1411)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at org.pentaho.di.trans.steps.tableoutput.TableOutput.writeToTable(TableOutput.java:284)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	... 3 more
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1074)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4120)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4052)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2503)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1399)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:857)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2458)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2375)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2359)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	at org.pentaho.di.core.database.Database.insertRow(Database.java:1360)
2013/05/02 11:43:48 - Write Fact table.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : 	... 4 more
[16 Jul 2013 13:17] Andrii Nikitin
The problem is fixed in 5.6.11 with following change note :

InnoDB: In the case of LOCK WAIT for an insert in a foreign key table, InnoDB could report a false dictionary-changed error and cause the insert to fail rather than being retried. (Bug #16174255)

Thus I close this bug.
Workaround = upgrade to 5.6.11 or later.

If somebody sees similar error in 5.6.11 or later and no explanation in error log - create new bug report .